Difference between revisions of "GEOS-Chem Newsletter Winter 2013"

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:Dear colleagues and GEOS-Chem users:  
 
: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 [http://meeting.geos-chem.org '''''meeting.geos-chem.org'''''] to register.  We expect the meeting to be oversubscribed.  You will hear of acceptance in mid-February.
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: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 [http://meeting.geos-chem.org '''''meeting.geos-chem.org'''''] to register.  We expect the meeting to be oversubscribed.  You will hear of acceptance in mid-February.
  
 
:Daniel Jacob<br>
 
:Daniel Jacob<br>
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The [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html GEOS-Chem Steering Committee] (GCSC) last met on '''Tuesday January 8th, 2013'''.  We invite you to read [http://acmg.seas.harvard.edu/geos/word_pdf_docs/steering_cmte/gc_sc_minutes_08Jan2013.pdf the meeting minutes].
 
The [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html GEOS-Chem Steering Committee] (GCSC) last met on '''Tuesday January 8th, 2013'''.  We invite you to read [http://acmg.seas.harvard.edu/geos/word_pdf_docs/steering_cmte/gc_sc_minutes_08Jan2013.pdf the meeting minutes].
  
The next GCSC telecon will take place in April 2013, date TBD.
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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 [http://acmg.seas.harvard.edu/geos/geos_working_group Working Group chairpersons].
  
 
=== GCSC Elections ===
 
=== GCSC Elections ===
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:Daniel Jacob<br>GEOS-Chem Model Scientist<br>for the GCSC
 
:Daniel Jacob<br>GEOS-Chem Model Scientist<br>for the GCSC
 
== GEOS-Chem Support Team ==
 
 
Here is a summary of [[GEOS-Chem Support Team]] activities:
 
 
#Bob Yantosca has been working on the code to process GEOS-5.7.2 data (see below). He also oversees general GC development and the development of the Grid-Independent model.
 
#Michael Long is primarily working on the Grid-Independent GEOS-Chem project (see below).
 
#Melissa Payer has been working on general GC development tasks (i.e. code merging, generating 1-month benchmark simulations, user support, documentation, etc.).
 
#Matt Cooper (Dalhousie) has been working on regridding the MERRA met data to 2&deg; x 2.5&deg; degree resolution (see below).  He has also begun replacing the existing regridding routines in GEOS-Chem with the MAP_A2A regridding package (which is what is currently use for regridding the GMAO met fields).
 
  
 
== GEOS-Chem v9-01-03 was released in September 2012 ==
 
== GEOS-Chem v9-01-03 was released in September 2012 ==
  
The current public release of GEOS-Chem is [[GEOS-Chem 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.
+
The current released version of GEOS-Chem is [[GEOS-Chem v9-01-03|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, [[GEOS-Chem_v9-01-03#What.27s_new_in_this_version|please see this table]].  We also invite you to view the [http://acmg.seas.harvard.edu/geos/doc/man/ Online GEOS-Chem User's Manual] for more information.
+
For a complete list of all new features and fixes in GEOS-Chem v9-01-03, [[GEOS-Chem_v9-01-03#What.27s_new_in_this_version|please see this table]].  We also invite you to view the [http://acmg.seas.harvard.edu/geos/doc/archive/man.v9-01-03/index.html Online GEOS-Chem User's Manual] for more information.
  
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, we have 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.
+
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 <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.
  
 
== GEOS-Chem v9-02 news ==
 
== GEOS-Chem v9-02 news ==
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#[[GEOS-Chem_v9-02_benchmark_history#v9-02b|v9-02b]]: New soil NOx emissions module + minor bug fixes
 
#[[GEOS-Chem_v9-02_benchmark_history#v9-02b|v9-02b]]: New soil NOx emissions module + minor bug fixes
 
#[[GEOS-Chem_v9-02_benchmark_history#v9-02c|v9-02c]]: Updates for the Hg simulaton: emissions + kinetics
 
#[[GEOS-Chem_v9-02_benchmark_history#v9-02c|v9-02c]]: Updates for the Hg simulaton: emissions + kinetics
#[[GEOS-Chem_v9-02_benchmark_history#v9-02d|v9-02d]]: Structural updates for the Grid-Independnent GEOS-Chem
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#[[GEOS-Chem_v9-02_benchmark_history#v9-02d|v9-02d]]: Structural updates for the Grid-Independent GEOS-Chem
 
#[[GEOS-Chem_v9-02_benchmark_history#v9-02e|v9-02e]]: Bug fix for regridding of anthro emissions (Streets, NEI2005)
 
#[[GEOS-Chem_v9-02_benchmark_history#v9-02e|v9-02e]]: Bug fix for regridding of anthro emissions (Streets, NEI2005)
  
 
We are still working on the following benchmarks:
 
We are still working on the following benchmarks:
  
#The [[Hg and POPs Working Group]] is working on a 1-yr Hg benchmark simulation, based on v9-02c.
+
#The [[Hg and POPs Working Group]] is working on a 1-yr [[Mercury|Hg simulation]], based on v9-02c.
#The [[Nested Model Working Group]] is performing a 1-yr simulation for the North American Nested Grid with GEOS-5 met (0.5&deg x 0.666&deg;).  They have completed 6 months of the benchmark.
+
#The [[Nested Model Working Group]] is performing a 1-yr [[NOx-Ox-HC-aerosol|full-chemistry simulation]] for the North American Nested Grid with GEOS-5 met (0.5&deg; x 0.666&deg;).  They have completed 6 months of the benchmark.
  
 
The next set of updates to [[GEOS-Chem v9-02]] shall be chemistry updates, including:
 
The next set of updates to [[GEOS-Chem v9-02]] shall be chemistry updates, including:
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Please see [[GEOS-Chem v9-02#What's new in this version|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 [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html Steering Committee], with input from the [http://acmg.seas.harvard.edu/geos/geos_working_groups.html Working Groups].
 
Please see [[GEOS-Chem v9-02#What's new in this version|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 [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html Steering Committee], with input from the [http://acmg.seas.harvard.edu/geos/geos_working_groups.html Working Groups].
  
== Grid-Independent GEOS-Chem ==
+
== 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 std GEOS-Chem code.
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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 [http://www.earthsystemmodeling Earth System Model Framework (ESMF)] interface that connects GEOS-Chem to the GEOS-5 GCM.  GEOS-Chem now can obtain the following information from the GEOS-5 GCM, via ESMF:
+
We’ve also streamlined the [http://www.earthsystemmodeling 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:
  
#Size of data arrays on each CPU: (IIPAR, JJPAR, LLPAR)
+
#Size of data arrays on each CPU: (<tt>IIPAR</tt>, <tt>JJPAR</tt>, <tt>LLPAR</tt>)
#Size of the entire global grid: (IM_WORLD, JM_WORLD, LM_WORLD)
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#Size of the entire global grid: (<tt>IM_WORLD</tt>, <tt>JM_WORLD</tt>, <tt>LM_WORLD</tt>)
#Corner grid box indices on each CPU (I_LO, I_HI, J_LO, J_HI)
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#Corner grid box indices on each CPU (<tt>I_LO</tt>, <tt>I_HI</tt>, <tt>J_LO</tt>, <tt>J_HI</tt>)
 
#Date and time from the GCM
 
#Date and time from the GCM
 
#Level edge pressures from the GCM
 
#Level edge pressures from the GCM
  
We’ve also updated the ESMF interface to be consistent with the tracers and species introduced by the latest [[Bromine chemistry mechanism|bromine chemistry updates]].  (Every time new tracers are added we have to also update the various input files etc. that are used by the ESMF interface.)
+
We also made sure to bring the ESMF interface up-to-date with the tracers and species introduced by the latest [[Bromine chemistry mechanism|bromine chemistry mechanism]].   
  
We've also updated the various GIGC wiki pages to reflect these recent updates.  Please see these pages for details:
+
All of these updates are now reflected on the GIGC wiki pages.  Please see:
  
 
#[[Grid-Independent GEOS-Chem]]
 
#[[Grid-Independent GEOS-Chem]]
 
#[[Grid-Independent GEOS-Chem: Chemistry Component]]
 
#[[Grid-Independent GEOS-Chem: Chemistry Component]]
#[[Grid-Independent GEOS-Chem: Emissions Component]]
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#[[HEMCO|Grid-Independent GEOS-Chem: Emissions Component]]
#[[Derived type objects used by the Grid-Independent GEOS-Chem]]
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#[[Derived type objects used by GEOS-Chem|Derived type objects used by the Grid-Independent GEOS-Chem]]
#[[Programming techniques used for the Grid-Independent GEOS-Chem]]
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#[[Programming techniques for HPC environments|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 with MPI parallelization.   
+
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 [[Grid-Independent GEOS-Chem: Emissions Component|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 necessary in order to be run in the ESMF environment.  Please see [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/ckeller_emissions_group_mtg_20121218_web.pdf this presentation] for further details.
+
Christoph Keller is working on the [[HEMCO|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 [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/ckeller_emissions_group_mtg_20121218_web.pdf this presentation] for further details.
  
 
Still to do:
 
Still to do:
  
#Modify the GIGC code to read data from ASCII input files (i.e. input.geos, globchem.dat, ratj.d) 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.
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#Modify the GIGC code to read data from ASCII input files (i.e. <tt>input.geos</tt>, <tt>globchem.dat</tt>, <tt>ratj.d</tt>, 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.
#Bring dry depositions into the ESMF interface.  Mike Long has been working on this.
+
#Bring [[Dry deposition|dry deposition]] into the ESMF interface.  Mike Long has been working on this.
 
#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.
 
#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 [http://meeting.geos-chem.org IGC6 meeting in May]].
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We anticipate to be able to run a GEOS-5 GCM/GEOS-Chem simulation before the [http://meeting.geos-chem.org IGC6 meeting in May].  Stay tuned for results!
 
+
== GEOS-5.7.2 met field update ==
+
 
+
This past summer, NASA/GMAO 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:
+
 
+
#Horizontal resolution: 0.25&deg; lat x 0.3125&deg; lon (i.e. 1/4&deg; x 5/16&deg;)
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#Vertical resolution: 72 hybrid layers (identical to the vertical grids used by the GEOS-5.2.0 and MERRA met data products)
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#[[GEOS-5.7.2#GEOS-5.7.2_time_archiving|Time resolution]]: Hourly and 3-hourly data (timestamps very similar to MERRA)
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#Input data format: netCDF-4 (as opposed to HDF4-EOS, used for past GMAO data products)
+
 
+
Bob Yantosca has been preparing GEOS-Chem to run with the new GEOS-5.7.2 met data.  He has completed the following tasks:
+
 
+
#Added documentation to the GC wiki with information about the GEOS-5.7.2 data.
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#Activated a “data subscription” for the GEOS-5.7.2 data.
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#Written scripts to transfer GEOS-5.7.2 data from NASA to Harvard and to automate the data download process.
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#Finalized the GEOS-5.7.2 data processing/regridding software.
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#Created a new Git repository for GEOS-5.7.2 data processing code and scripts.
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#Completed initial modifications in GEOS-Chem to read the GEOS-5.7.2 data.
+
 
+
For more information about the implementation of GEOS-5.7.2 into GEOS-Chem (including a detailed list of all modifications made to individual GEOS-Chem routines), please see the following wiki pages:
+
 
+
#[[GEOS-5.7.2]]
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#[[List of GEOS-5.7.2 met fields]]
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#[[GEOS-5.7.2 implementation details]]
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+
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:
+
 
+
#Global 2&deg; x 2.5&deg;
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#Global 4&deg; x 5&deg;
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#SEA4CRS Nested grid 0.25&deg; x 0.3125&deg;: 20S-50N; 60E-150E
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Consistent with our [http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf established nested grid protocol], we will distribute the GEOS-5.7.2 data processing code & scripts to any user groups who wish to pull the nested data themselves.
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One important new feature is that the GEOS-Chem Support Team shall be archiving the processed GEOS-5.7.2 data in [[#Transition to netCDF file format| netCDF format]] instead of the traditional binary format (see below for more information).
+
 
+
At present, GEOS-Chem can read the GEOS-5.7.2 met data from within the timestepping loop in the main program for 2&deg; x 2.5&deg;, 4&deg; x 5&deg; global grids and the 0.25&deg; x 0.3125&deg; SEA4CRS nested China grid.  Further testing is required to make sure that the individual operations (i.e. convection, deposition, chemistry) will work properly with the GEOS-5.7.2 data.
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Bob Yantosca and the SEA4CRS team (Jenny Fisher, Patrick Kim, Lin Zhang, Yuxuan Wang) are coordinating several of the remaining tasks (e.g. regridding emissions data files, debugging, etc.) among themselves.
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== De-supporting of GEOS-3 meteorology ==
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The [[Overview_of_GMAO_met_data_products#GEOS-3|GMAO GEOS-3 met data product]] is now several versions behind the current GMAO operational product ([[GEOS-5.7.2]]).  The GEOS-3 data period only covered the years 2000-2002 (with some data in 1998). 
+
 
+
Bob Yantosca queried the GEOS-Chem user community to see if there were any users who still relied on the GEOS-3 met data for their research.  He found that none of the GEOS-Chem users still rely on GEOS-3 meteorology.
+
 
+
Therefore, the GEOS-Chem Support Team recommends that we remove support for GEOS-3 met data from within GEOS-Chem.  This will help to clean up the GEOS-Chem source code and remove unnecessary routines and coding constructs which may impede development of the [[Grid-independent GEOS-Chem]].
+
 
+
  
 +
== GEOS-Chem Adjoint News ==
  
== Downtime at Harvard: Feb 19-23, 2012 ==
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[[GEOS-Chem Adjoint v34]] is now the standard version of the GEOS-Chem adjoint model.  Please see [[GEOS-Chem_Adjoint_v34#What.27s_new_in_this_version|this table]] for a list of new features in v34.
  
The Harvard Atmospheric Chemistry Modeling Group will be moving its computational resources from its existing location into a more modern server room.  The transition will take place starting on Sunday Feb 19, 2012 and will take at 3-4 days to complete.
+
Some key improvements:
  
Our sysadmin Jack Yatteau writes:
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#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:
 +
#Makefiles were updated to better follow the makefile structure used by the forward model.  For more information please see [http://adjoint.colorado.edu/~yanko/gcadj_std/GC_adj_man.pdf this link].
 +
#Implemented GFED3 emissions.
  
Downtime:
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Most of the additions to v34 were technical software updatesThe next version of the GEOS-Chem adjoint will have more scientific updates.
        1) Sunday, February 19, 16:00. Most services will go down.
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        Running jobs on the computational cluster will be rescheduled.
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        Minimal services will remain up overnight and go down early Monday
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        morningSome services might be available Tuesday.  Interactive
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        and batch systems should be available by EOB Wednesday 2/22.
+
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        2) Thursday, February 23.  Backup power for our equipment
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        will be unavailable for a few hours due to UPS maintenance.
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        No downtime is anticipated, but we will not be protected against
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        power failure while the work is being performed.
+
  
The following services will be unavailable during the transition:
+
Please contact GEOS-Chem Support Team Adjoint Specialist [mailto:mailto:boun0479@gmail.com Nicolas Bousserez] for specific support requests regarding the GEOS-Chem Adjoint code.
  
#<tt>ftp.as.harvard.edu</tt>: main FTP site for data downloads
+
== In other news ==
#<tt>git.as.harvard.edu</tt>: Git server for GEOS-Chem source code & run directory downloads
+
#[http://acmg.seas.harvard.edu/ GEOS-Chem web site]
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#[http://acmg.seas.harvard.edu/ GAMAP web site]
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#[http://acmg.seas.harvard.edu/ Jacob Group web site]
+
  
The GEOS-Chem wiki is hosted on a different server and should not be affected.  However, some links to documents on the GEOS-Chem web server will not function during the downtime.
+
Here are some other noteworthy news items ...
  
Please plan accordinglyMet data may also be obtained from the Dalhousie server (<tt>rain.ucis.dal.ca</tt>)
+
#<p>The [[GEOS-Chem Support Team|GEOS-Chem Support Team (GCST)]] is currently investigating why [[NOx-Ox-HC-aerosol|full-chemistry simulations]] done with [[GEOS-Chem v9-01-03]] and [[GEOS-Chem v9-02]] take longer to run than older model versionsMelissa Payer is taking the lead on this effort.</p>
 +
#<p>We are continuing to work on the 0.25&deg; x 0.3125&deg; 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.</p>
 +
#<p>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.</p>
 +
#<p>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.</p>
 +
#<p>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]].</p>
 +
#<p>Debra Weisenstein (Harvard) and Steven Barrett (MIT) are working on a state-of-the-art OCS simulation for GEOS-Chem.</p>
 +
#<p>Colette Heald (MIT) is working with AER Corp. to install the RRTMG radiative transfer model into GEOS-Chem.</p>
 +
#<p>We invite you to view the [https://trello.com/board/geos-chem-support-team/4fe36668fc79a1d3540ba80b GEOS-Chem board on Trello.com] 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).</p>
  
--[[User:Bmy|Bob Y.]] 11:21, 14 February 2012 (EST)
+
--[[User:Bmy|Bob Y.]] 14:57, 9 January 2013 (EST)

Latest revision as of 14:08, 19 June 2019

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.

Sincerely,

The GEOS-Chem Support Team
geos-chem-support@as.harvard.edu

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 meeting.geos-chem.org 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

Development

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 Trello.com 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)