Difference between revisions of "Sandbox"

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Dear GEOS-Chem Users,
 +
 +
Here is the June 2009 GEOS-Chem Newsletter.
 +
 +
''Bob Yantosca, Philippe Le Sager, and Claire Carouge''<br>
 +
''geos-chem-support@as.harvard.edu''
 +
 +
== GEOS-Chem Update ==
 +
 +
=== GEOS-Chem v8-02-02 ===
 +
 +
[[GEOS-Chem v8-02-02]] "beta" has now been released.  This version includes the new boundary layer mixing scheme (developed by Jintai Lin) as well as updated Bond emission inventories for BC & OC (prepared by Eric Leibensperger).  The new version may be downloaded from:
 +
 +
  ftp ftp.as.harvard.edu
 +
  cd pub/geos-chem/beta_releases
 +
  get GEOS-Chem.v8-02-02-beta.stdrun.tar.gz
 +
 +
'''''NOTE: We currently working on enabling access to our CVS repository to outside users so that you will be able to obtain the GEOS-Chem source code without having to download a large TAR file.  Stay tuned...'''
 +
 +
=== GEOS-Chem Steering Committee ===
 +
 +
The [http://www.as.harvard.edu/ctm/geos/geos_steering_cmte.html GEOS-Chem Steering Committee] held a telecon on June 11, 2009.  Click [HERE] to view the meeting minutes.
 +
 +
Since the GEOS-Chem meeting, a number of [[GEOS-Chem model development priorities]] that were identified by the Steering Committee and Working Groups have now been implemented into GEOS-Chem:
 +
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|- bgcolor="#cccccc"
 +
!Item
 +
!Author(s)
 +
!Completion Date
 +
|-
 +
|Improved BL mixing scheme
 +
|Jintai Lin
 +
|Now included in [[GEOS-Chem v8-02-02]];<br>released 08 Jun 2009
 +
|-
 +
|BC/OC aerosol emissions from Bond inventory
 +
|Eric Leibensperger
 +
|Now included in [[GEOS-Chem v8-02-02]];<br>released 08 Jun 2009
 +
|-
 +
|Chemical updates
 +
|Mat Evans<br>Fabien Paulot<br>Jingqiu Mao<br>Paul Palmer
 +
|Updated chemical mechanism and photolysis files<br><tt>globchem.dat</tt>, <tt>jv_spec.dat</tt>, <tt>ratj.d</tt><br>(see [http://www.as.harvard.edu/ctm/geos/wiki_docs/chemistry/chemistry_updates_v4.pdf documentation])<br>Now included in [[GEOS-Chem v8-02-01]];<br>released 26 May 2009
 +
|}
 +
 +
At the June 10, 2009 telecon, the GEOS-Chem Steering Committee identified the following model development items as top priorities (listed in order):
 +
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|- bgcolor="#cccccc"
 +
!#
 +
!Development priority
 +
!Point person(s)
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!Status
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|-
 +
|1.
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|GEOS-5 ozone columns
 +
|GC support team
 +
|Validation is ongoing
 +
|-
 +
|2
 +
|KPP implementation
 +
|GC support team<br>Virginia Tech
 +
|In beta testing
 +
|-
 +
|3.
 +
|TOMAS implementation
 +
|Win Trivitayanurak<br>GC Support Team
 +
|Telecon to discuss implementation<br>scheduled for June 16th
 +
|-
 +
|4.
 +
|Linoz
 +
|Dylan Jones and<br>U. Toronto group
 +
|In beta testing
 +
|-
 +
|5.
 +
|Updated methane simulation
 +
|Christopher Pickett-Heaps<br>Kevin Wecht
 +
|Debugging and code cleanup is ongoing
 +
|-
 +
|6.
 +
|Updated CO2 Simulation
 +
|Ray Nassar
 +
|&nbsp;
 +
|-
 +
|7.
 +
|Updated MEGAN emission from terpenes
 +
|Dylan Millet
 +
|&nbsp;
 +
|-
 +
|8.
 +
|COADS ship emissions
 +
|Chulkyu Lee
 +
|&nbsp;
 +
|-
 +
|9.
 +
|Include updated aerosol optics 
 +
|Colette Heald<br>Randall Martin<br>and aerosols Working Group
 +
|&nbsp;
 +
|-
 +
|10.
 +
|Include aromatic SOA
 +
|Daven Henze
 +
|&nbsp;
 +
|-
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|11.
 +
|Archive OH fields from benchmark<br>for use in off-line simulations
 +
|GC support team
 +
|&nbsp}
 +
|}
 +
 +
=== GEOS-Chem Working Groups ===
 +
 +
A couple of the [http://www.as.harvard.edu/ctm/geos/geos_steering_cmte.html GEOS-Chem Working Groups] have been merged together:
 +
* "Carbon Gases" and "Organics" is now "Carbon Gases & Organics" (co-chairs Dylan Jones, Dylan Millet)
 +
* "Regional Air Quality"
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=== Subscribing to the GEOS-Chem email lists = ==
 +
 +
There are now several GEOS-Chem email lists:
 +
 +
{| border=1 cellspacing=0 cellpadding=5
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|- bgcolor="#cccccc"
 +
!Email list address
 +
!Intended audience
 +
|-
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|<tt>geos-chem@seas.harvard.edu</tt>
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|All GEOS-Chem users and developers<br>'''''NOTE: This is the email list to which information about <br>new model versions, bugs & fixes, etc. will be sent'''''
 +
|-
 +
|<tt>geos-chem-adjoint@seas.harvard.edu</tt>
 +
|Members of the [[GEOS-Chem Adjoint|Adjoint Model and Data Assimilation Working Group]]
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|-
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|<tt>geos-chem-aerosols@seas.harvard.edu</tt>
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|Members of the [[Aerosols_overview:_projects_and_developments|Aerosols Working Group]]
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|-
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||<tt>geos-chem-carbon@seas.harvard.edu</tt>
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|Members of the [[Carbon Gases and Organics Working Group]]
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|-
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|<tt>geos-chem-emissions@seas.harvard.edu</tt>
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|Members of the [[Emissions Working Group]]
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|-
 +
|<tt>geos-chem-oxidants@seas.harvard.edu</tt>
 +
|Members of the [[Chemistry Issues|Oxidants and Chemistry Working Group]]
 +
|-
 +
|<tt>geos-chem-regional@seas.harvard.edu</tt>
 +
|Members of the [[Regional Air Quality Working Group]]
 +
|}
 +
 +
To subscribe to any of these lists, please visit the page: https://lists.seas.harvard.edu/mailman/listinfo and then click on the name of the list to which you wish to subscribe.  You will be taken to a page where you can specify your email address and a password and then click SUBMIT.  You will then receive a confirmation email from the system.  Follow the directions in the confirmation email and then you will be added to the list.
 +
 +
'''''PLEASE NOTE: If you wish to send an email to any of the above GEOS-Chem mailing lists, then please be sure to send your email from the same address with which you subscribed to the list.  Otherwise your email may bounce back to you. The GEOS-Chem mailing lists are set up to reject emails from non-list members.  This is done in order to prevent spam.'''''
 +
 +
=== Being a member of the GEOS-Chem community ===
 +
 +
We ask that each GEOS-Chem user join the [http://www.as.harvard.edu/ctm/geos/geos_working_groups.html Working Group] that is most relevant to his/her area of research.  The Working Groups are meant to foster communication and information sharing between GEOS-Chem users, as well as to identify [[GEOS-Chem_model_development_priorities|priorities for model development]] to the [http://www.as.harvard.edu/ctm/geos/geos_steering_cmte.html GEOS-Chem Steering Committee].
 +
 +
Each GEOS-Chem user is also expected to adhere to our list of [http://www.as.harvard.edu/ctm/geos/geos_best_practices.html best practices].
 +
 +
We also would like to invite all GEOS-Chem users outside Harvard who have run the 1-month benchmark simulation on their own systems to take a moment and to update the table of [[GEOS-Chem supported platforms and compilers]] with your timing information.
 +
 +
 +
 +
An additional 1-year benchmark ([[GEOS-Chem v8-01-04#Run2|v8-01-04 Run2]]) was performed so that we could have a clean comparison between the "reprocessed" GEOS-5.1.0 met fields and the older GEOS-5.0.1 met fields.  For more information about the different GEOS-5 versions, see [http://gmao.gsfc.nasa.gov/pubs/docs/GEOS5_104606-Vol27.pdf this document from GMAO].
 +
 +
=== Adjoint Model Update ===
 +
 +
A successful meeting was held at Virginia Tech to develop a standard version of the GC adjoint merging the capabilities developed by individual groups: participants were Kumaresh Singh, Adrian Sandu, Monika Kopacz, Changshub Shim, and Daven Henze. The result was an integrated adjoint code based on v8-02-01 with GEOS-5 and including updates from the different groups, improved file formats and input files, etc.
 +
 +
== GEOS-5 met field reprocessing ==
 +
 +
=== Status ===
 +
As described in the [[GEOS-Chem Newsletter March 2009|March 2009 newsletter]], we are reprocessing the entire archive of GEOS-5 met field data.  As of May 6, 2009 the following fields have been completed:
 +
 +
* 2003: December only
 +
* 2004: entire year
 +
* 2005: entire year
 +
* 2008: entire year
 +
 +
for each of the following geographic domains:
 +
 +
* China nested 0.5 x 0.667
 +
* Global 2 x 2.5
 +
* Global 4 x 5
 +
 +
The files have been TAR'd and Gzip'd for your convienience (as this dramatically reduces the size of the data).  In each directory there are files <tt>01.tar.gz</tt>, <tt>02.tar.gz</tt> .. <tt>12.tar.gz</tt>, each of which contains a single month of met field data.  GEOS-Chem users outside Harvard may obtain these data files via anonymous FTP:
 +
 +
  ftp ftp.as.harvard.edu
 +
  cd pub/geos-chem/data/GEOS_0.5x0.666_CH.d/GEOS_5/2008
 +
  mget *.tar.gz
 +
  cd pub/geos-chem/data/GEOS_2x2.5.d/GEOS_5/2008
 +
  mget *.tar.gz
 +
  cd pub/geos-chem/data/GEOS_4x5.d/GEOS_5/2008
 +
  mget *.tar.gz
 +
  cd pub/geos-chem/data/GEOS_0.5x0.666_CH.d/GEOS_5/2004
 +
  mget *.tar.gz
 +
  cd pub/geos-chem/data/GEOS_2x2.5.d/GEOS_5/2004
 +
  mget *.tar.gz
 +
  cd pub/geos-chem/data/GEOS_4x5.d/GEOS_5/2004
 +
  mget *.tar.gz
 +
 +
However, to simplify the FTP process you might want to use a 3rd party FTP software program with a GUI interface, such as [http://fireftp.mozdev.org/ Mozilla FireFTP].
 +
 +
We are currently working on reprocessing GEOS-5 met data for 2006; however, this effort has been slowed down by some filesystem problems at Harvard.
 +
 +
== ESMF update ==
 +
 +
Development of the GEOS-Chem column chemistry module continues to proceed swiftly.  The SMVGEAR solver has been columnized and is now in testing to ensure that it gives similar results to the existing GEOS-Chem.  Also, the dust, sea salt, and carbon aerosol chemistry routines have been columnized and are working correctly. 
 +
 +
--[[User:Bmy|Bob Y.]] 16:31, 7 May 2009 (EDT)
 +
 +
 +
 
== feel free to experiment here ==
 
== feel free to experiment here ==

Revision as of 15:21, 15 June 2009

Dear GEOS-Chem Users,

Here is the June 2009 GEOS-Chem Newsletter.

Bob Yantosca, Philippe Le Sager, and Claire Carouge
geos-chem-support@as.harvard.edu

GEOS-Chem Update

GEOS-Chem v8-02-02

GEOS-Chem v8-02-02 "beta" has now been released. This version includes the new boundary layer mixing scheme (developed by Jintai Lin) as well as updated Bond emission inventories for BC & OC (prepared by Eric Leibensperger). The new version may be downloaded from: 

 ftp ftp.as.harvard.edu
 cd pub/geos-chem/beta_releases
 get GEOS-Chem.v8-02-02-beta.stdrun.tar.gz

NOTE: We currently working on enabling access to our CVS repository to outside users so that you will be able to obtain the GEOS-Chem source code without having to download a large TAR file. Stay tuned...

GEOS-Chem Steering Committee

The GEOS-Chem Steering Committee held a telecon on June 11, 2009. Click [HERE] to view the meeting minutes.

Since the GEOS-Chem meeting, a number of GEOS-Chem model development priorities that were identified by the Steering Committee and Working Groups have now been implemented into GEOS-Chem:

Item Author(s) Completion Date
Improved BL mixing scheme Jintai Lin Now included in GEOS-Chem v8-02-02;
released 08 Jun 2009
BC/OC aerosol emissions from Bond inventory Eric Leibensperger Now included in GEOS-Chem v8-02-02;
released 08 Jun 2009
Chemical updates Mat Evans
Fabien Paulot
Jingqiu Mao
Paul Palmer 		Updated chemical mechanism and photolysis files
globchem.dat, jv_spec.dat, ratj.d
(see documentation)
Now included in GEOS-Chem v8-02-01;
released 26 May 2009

At the June 10, 2009 telecon, the GEOS-Chem Steering Committee identified the following model development items as top priorities (listed in order):

# Development priority Point person(s) Status
1. GEOS-5 ozone columns GC support team Validation is ongoing
2 KPP implementation GC support team
Virginia Tech 		In beta testing
3. TOMAS implementation Win Trivitayanurak
GC Support Team 		Telecon to discuss implementation
scheduled for June 16th
4. Linoz Dylan Jones and
U. Toronto group 		In beta testing
5. Updated methane simulation Christopher Pickett-Heaps
Kevin Wecht 		Debugging and code cleanup is ongoing
6. Updated CO2 Simulation Ray Nassar  
7. Updated MEGAN emission from terpenes Dylan Millet  
8. COADS ship emissions Chulkyu Lee  
9. Include updated aerosol optics Colette Heald
Randall Martin
and aerosols Working Group 		 
10. Include aromatic SOA Daven Henze  
11. Archive OH fields from benchmark
for use in off-line simulations 		GC support team &nbsp}

GEOS-Chem Working Groups

A couple of the GEOS-Chem Working Groups have been merged together:

  • "Carbon Gases" and "Organics" is now "Carbon Gases & Organics" (co-chairs Dylan Jones, Dylan Millet)
  • "Regional Air Quality"

= Subscribing to the GEOS-Chem email lists =

There are now several GEOS-Chem email lists:

Email list address Intended audience
geos-chem@seas.harvard.edu All GEOS-Chem users and developers
NOTE: This is the email list to which information about
new model versions, bugs & fixes, etc. will be sent
geos-chem-adjoint@seas.harvard.edu Members of the Adjoint Model and Data Assimilation Working Group
geos-chem-aerosols@seas.harvard.edu Members of the Aerosols Working Group
geos-chem-carbon@seas.harvard.edu Members of the Carbon Gases and Organics Working Group
geos-chem-emissions@seas.harvard.edu Members of the Emissions Working Group
geos-chem-oxidants@seas.harvard.edu Members of the Oxidants and Chemistry Working Group
geos-chem-regional@seas.harvard.edu Members of the Regional Air Quality Working Group

To subscribe to any of these lists, please visit the page: https://lists.seas.harvard.edu/mailman/listinfo and then click on the name of the list to which you wish to subscribe. You will be taken to a page where you can specify your email address and a password and then click SUBMIT. You will then receive a confirmation email from the system. Follow the directions in the confirmation email and then you will be added to the list.

PLEASE NOTE: If you wish to send an email to any of the above GEOS-Chem mailing lists, then please be sure to send your email from the same address with which you subscribed to the list. Otherwise your email may bounce back to you. The GEOS-Chem mailing lists are set up to reject emails from non-list members. This is done in order to prevent spam.

Being a member of the GEOS-Chem community

We ask that each GEOS-Chem user join the Working Group that is most relevant to his/her area of research. The Working Groups are meant to foster communication and information sharing between GEOS-Chem users, as well as to identify priorities for model development to the GEOS-Chem Steering Committee.

Each GEOS-Chem user is also expected to adhere to our list of best practices.

We also would like to invite all GEOS-Chem users outside Harvard who have run the 1-month benchmark simulation on their own systems to take a moment and to update the table of GEOS-Chem supported platforms and compilers with your timing information.


An additional 1-year benchmark (v8-01-04 Run2) was performed so that we could have a clean comparison between the "reprocessed" GEOS-5.1.0 met fields and the older GEOS-5.0.1 met fields. For more information about the different GEOS-5 versions, see this document from GMAO.

Adjoint Model Update

A successful meeting was held at Virginia Tech to develop a standard version of the GC adjoint merging the capabilities developed by individual groups: participants were Kumaresh Singh, Adrian Sandu, Monika Kopacz, Changshub Shim, and Daven Henze. The result was an integrated adjoint code based on v8-02-01 with GEOS-5 and including updates from the different groups, improved file formats and input files, etc.

GEOS-5 met field reprocessing

Status

As described in the March 2009 newsletter, we are reprocessing the entire archive of GEOS-5 met field data. As of May 6, 2009 the following fields have been completed:

  • 2003: December only
  • 2004: entire year
  • 2005: entire year
  • 2008: entire year

for each of the following geographic domains:

  • China nested 0.5 x 0.667
  • Global 2 x 2.5
  • Global 4 x 5

The files have been TAR'd and Gzip'd for your convienience (as this dramatically reduces the size of the data). In each directory there are files 01.tar.gz, 02.tar.gz .. 12.tar.gz, each of which contains a single month of met field data. GEOS-Chem users outside Harvard may obtain these data files via anonymous FTP: 

 ftp ftp.as.harvard.edu
 cd pub/geos-chem/data/GEOS_0.5x0.666_CH.d/GEOS_5/2008
 mget *.tar.gz
 cd pub/geos-chem/data/GEOS_2x2.5.d/GEOS_5/2008
 mget *.tar.gz
 cd pub/geos-chem/data/GEOS_4x5.d/GEOS_5/2008
 mget *.tar.gz
 cd pub/geos-chem/data/GEOS_0.5x0.666_CH.d/GEOS_5/2004
 mget *.tar.gz
 cd pub/geos-chem/data/GEOS_2x2.5.d/GEOS_5/2004
 mget *.tar.gz
 cd pub/geos-chem/data/GEOS_4x5.d/GEOS_5/2004
 mget *.tar.gz

However, to simplify the FTP process you might want to use a 3rd party FTP software program with a GUI interface, such as Mozilla FireFTP.

We are currently working on reprocessing GEOS-5 met data for 2006; however, this effort has been slowed down by some filesystem problems at Harvard.

ESMF update

Development of the GEOS-Chem column chemistry module continues to proceed swiftly. The SMVGEAR solver has been columnized and is now in testing to ensure that it gives similar results to the existing GEOS-Chem. Also, the dust, sea salt, and carbon aerosol chemistry routines have been columnized and are working correctly.

--Bob Y. 16:31, 7 May 2009 (EDT)


feel free to experiment here

Retrieved from "https://wiki.seas.harvard.edu/geos-chem/index.php?title=Sandbox&oldid=2272"