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Dear GEOS-Chem Users,
=== Species added ===


Here is the June 2009 GEOS-Chem Newsletter.
Species added between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:
 
''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 [http://www.as.harvard.edu/ctm/geos/word_pdf_docs/steering_cmte/gc_sc_minutes_061109.pdf 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
{| border=1 cellspacing=0 cellpadding=5
|- bgcolor="#cccccc"
!width='100px' bgcolor='#CCCCCC'|Name
!Item
!width='100px' bgcolor='#CCCCCC'|Formula
!Author(s)
!width='200px' bgcolor='#CCCCCC'|Fullname
!Completion Date
!width='30px' bgcolor='#CCCCCC'|Advected
|-
!width='30px' bgcolor='#CCCCCC'|Dry deposited
|Improved BL mixing scheme
!width='30px' bgcolor='#CCCCCC'|Gas
|Jintai Lin
!width='30px' bgcolor='#CCCCCC'|Photolyzed
|Now included in [[GEOS-Chem v8-02-02]];<br>released 08 Jun 2009
!width='30px' bgcolor='#CCCCCC'|Wet deposited
|-
|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 remaining [[GEOS-Chem model development priorities|model development items]] as top priorities (listed in order):
|-valign='top'
 
|ACO3
{| border=1 cellspacing=0 cellpadding=5
|C3H3O3
|- bgcolor="#cccccc"
|Peroxyacetyl radical for APAN
!#
|
!Development priority
|
!Point person(s)
|X
!Status
|
|-
|
|1.
|GEOS-5 ozone columns
|-valign='top'
|GC support team
|ACR
|Validation is ongoing
|C3H4O
|-
|Acrolein
|2
|X
|KPP implementation
|X
|GC support team<br>Virginia Tech
|X
|In beta testing
|X
|-
|
|3.
|TOMAS implementation
|-valign='top'
|Win Trivitayanurak<br>GC Support Team
|ACRO2
|Telecon to discuss implementation<br>scheduled for June 16th
|C3H5O4
|-
|Peroxy radical from ACR
|4.
|
|Linoz
|
|Dylan Jones and<br>U. Toronto group
|X
|In beta testing
|
|-
|
|5.
|Updated methane simulation
|-valign='top'
|Christopher Pickett-Heaps<br>Kevin Wecht
|ALK7
|Debugging and code cleanup is ongoing
|C7H16
|-
|Lumped >= C6 Alkanes
|6.
|X
|Updated CO2 Simulation
|
|Ray Nassar
|X
|&nbsp;
|
|-
|
|7.
|Updated MEGAN emission from terpenes
|-valign='top'
|Dylan Millet
|APAN
|&nbsp;
|C3H3NO5
|-
|Peroxyacryloyl nitrate
|8.
|X
|COADS ship emissions
|X
|Chulkyu Lee
|X
|&nbsp;
|X
|-
|X
|9.
|Include updated aerosol optics  
|-valign='top'
|Colette Heald<br>Randall Martin<br>and aerosols Working Group
|APINN
|&nbsp;
|C10H17NO4
|-  
|1st gen organic nitrate from APIN
|10.
|X
|Include aromatic SOA
|X
|Daven Henze
|X
|&nbsp;
|X
|-
|X
|11.
|Archive OH fields from benchmark<br>for use in off-line simulations
|-valign='top'
|GC support team
|APINO2
|&nbsp}
|C10H17O3
|Peroxy radical from APIN
|
|
|X
|
|
|-valign='top'
|APINP
|C10H18O3
|Hydroperoxide from APIN
|X
|X
|X
|
|X
|-valign='top'
|AROMCHO
|C5H6O4
|ACCOMECHO from MCM
|X
|X
|X
|
|X
|-valign='top'
|AROMCO3
|C5H5O6
|Lumped aromatic peroxyacetyl radical
|
|
|X
|
|
|-valign='top'
|AROMPN
|C5H5NO8
|Lumped PN from aromatics
|X
|X
|X
|X
|X
|-valign='top'
|BPINN
|C10H17NO4
|Saturated 1st gen BPIN organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|BPINO
|C9H14O
|Ketone from BPIN
|X
|X
|X
|
|X
|-valign='top'
|BPINO2
|C10H17O3
|Peroxy radical from BPIN
|
|
|X
|
|
|-valign='top'
|BPINON
|C9H13NO4
|Saturated 2nd gen BPIN organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|BPINOO2
|C10H17O3
|2nd-gen peroxy radical from BPIN
|
|
|X
|
|
|-valign='top'
|BPINOOH
|C9H14O3
|2nd-gen peroxide from BPIN
|X
|X
|X
|
|X
|-valign='top'
|BPINP
|C10H18O3
|Peroxide from BPIN
|X
|X
|X
|
|X
|-valign='top'
|BUTN
|C4H7NO4
|C4H6 alkyl nitrate
|X
|X
|X
|
|X
|-valign='top'
|BUTO2
|C4H7O3
|peroxy radical from C4H6
|
|
|X
|
|
|-valign='top'
|C4H6
|C4H6
|1,3-butadiene
|X
|
|X
|
|
|-valign='top'
|C96N
|C9H15NO4
|Saturated 2nd gen monoterpene organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|C96O2
|C10H17O3
|2nd-gen peroxy radical from APIN
|
|
|X
|
|
|-valign='top'
|C96O2H
|C9H16O3
|Peroxide from APIN 2nd gen
|X
|X
|X
|
|X
|-valign='top'
|EBZ
|C8H10
|Ethylbenzene
|X
|
|X
|
|
|-valign='top'
|GCO3
|HOCH2CO3
|Peroxyacetyl radical for PHAN
|
|
|X
|
|
|-valign='top'
|HACTA
|HOCH2CO2H
|Hydroxyacetic/glycolic acid
|X
|X
|X
|
|X
|-valign='top'
|LIMAL
|C10H16O2
|Aldehyde from limonene
|X
|X
|X
|
|X
|-valign='top'
|LIMKB
|C10H16O3
|2nd gen ketone from limonene
|X
|X
|X
|
|X
|-valign='top'
|LIMKET
|C10H16O2
|Ketone from limonene
|X
|X
|X
|
|X
|-valign='top'
|LIMKO2
|C10H17O3
|2nd-gen peroxy radical from LIMO
|
|
|X
|
|
|-valign='top'
|LIMN
|C10H17NO4
|Saturated 1st gen limonene organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|LIMNB
|C10H15NO4
|Saturated 1st gen LIMO organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|LIMO2H
|C10H18O3
|Acid from LIMO
|X
|X
|X
|
|X
|-valign='top'
|LIMO3
|C10H17O3
|Acylperoxy radical from LIMO
|
|
|X
|
|
|-valign='top'
|LIMO3H
|C10H18O4
|Peracid from LIMO
|X
|X
|X
|
|X
|-valign='top'
|LIMPAN
|C10H17NO4
|PAN from LIMO
|X
|X
|X
|X
|X
|-valign='top'
|MEKCO3
|C3H5O4
|False
|
|
|X
|
|
|-valign='top'
|MEKPN
|C3H5NO6
|MEK peroxyacetyl nitrate
|X
|X
|X
|X
|X
|-valign='top'
|MYRCO
|C10H18O3
|Aldehyde or ketone from myrcene
|X
|X
|X
|
|X
|-valign='top'
|PHAN
|C2H3NO6
|Peroxyhydroxyacetic nitric anhydride
|X
|X
|X
|X
|X
|-valign='top'
|PIN
|C10H17NO4
|Saturated 1st gen monoterpene organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|PINAL
|C10H16O2
|Pinonaldehyde
|X
|X
|X
|
|X
|-valign='top'
|PINO3
|C10H17O3
|Acylperoxy radical from APIN
|
|
|X
|
|
|-valign='top'
|PINO3H
|C10H18O4
|Pinonic peracid
|X
|X
|X
|
|X
|-valign='top'
|PINONIC
|C10H18O3
|Pinonic acid
|X
|X
|X
|
|X
|-valign='top'
|PINPAN
|C10H17NO4
|PAN from pinonaldehyde
|X
|X
|X
|X
|X
|-valign='top'
|R7N1
|C7H15NO5
|Peroxy radical from R7N2
|
|
|X
|
|
|-valign='top'
|R7N2
|RO2NO
|C7 Lumped alkyl nitrate
|X
|X
|X
|X
|X
   
|-valign='top'
|R7O2
|C7H15O2
|Peroxy radical from ALK7
|
|
|X
|
|
|-valign='top'
|R7P
|C7H16O2
|Peroxide from R7O2
|X
|X
|X
|X
|X
|-valign='top'
|RNO3
|RO2NO
|Lumped aromatic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|STYR
|C8H8
|Styrene
|X
|
|X
|
|
|-valign='top'
|TLFUO2
|C5H7O5
|False
|
|
|X
|
|
|-valign='top'
|TLFUONE
|C5H6O2
|Aromatic furanones
|X
|X
|X
|
|X
|-valign='top'
|TMB
|C8H10
|Trimethylbenzenes
|
|
|X
|
|
|-valign='top'
|ZRO2
|C7H9O5
|RO2 for making lumped aromatic nitrate
|
|
|X
|
|
|}
|}


=== GEOS-Chem Working Groups ===
=== Species removed===


A couple of the [http://www.as.harvard.edu/ctm/geos/geos_steering_cmte.html GEOS-Chem Working Groups] have been merged together:
Species removed between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:
* "Carbon Gases" and "Organics" is now "Carbon Gases & Organics" (co-chairs Dylan Jones, Dylan Millet)
* "Regional Modeling" is now "Regional Air Quality" (co-chairs Rokjin Park, Yuxuan Wang)


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].
{| border=1 cellspacing=0 cellpadding=5
!width='100px' bgcolor='#CCCCCC'|Name
!width='100px' bgcolor='#CCCCCC'|Formula
!width='200px' bgcolor='#CCCCCC'|Fullname
!width='30px' bgcolor='#CCCCCC'|Advected
!width='30px' bgcolor='#CCCCCC'|Dry deposited
!width='30px' bgcolor='#CCCCCC'|Gas
!width='30px' bgcolor='#CCCCCC'|Photolyzed
!width='30px' bgcolor='#CCCCCC'|Wet deposited


For more information about a particular working group, please contact the Working Group Chairperson(s).
=== Subscribing to the GEOS-Chem email lists ===
There are now several GEOS-Chem email lists:
{| border=1 cellspacing=0 cellpadding=5
|- bgcolor="#cccccc"
!Email list address
!Intended audience
|-
|<tt>geos-chem@seas.harvard.edu</tt>
|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]]
|-
|<tt>geos-chem-aerosols@seas.harvard.edu</tt>
|Members of the [[Aerosols_overview:_projects_and_developments|Aerosols Working Group]]
|-
||<tt>geos-chem-carbon@seas.harvard.edu</tt>
|Members of the [[Carbon Gases and Organics Working Group]]
|-
|<tt>geos-chem-emissions@seas.harvard.edu</tt>
|Members of the [[Emissions Working Group]]
|-
|<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 would like to encourage all new GEOS-Chem users to take a moment to read our [[GEOS-Chem welcome letter for new users]]. 
We expect that each GEOS-Chem user will possess at least some familiarity with the following:
* The Fortran programming language (F77 OK, F90 preferred)
* IDL (preferred), or other graphics software (e.g. Splus, Matlab)
* The Unix environment (i.e. commands, file paths, etc.)
* Unix scripts (not strictly required but is very helpful to know!)
The GEOS-Chem support team cannot provide you with general instruction in programming languages or answer general programming questions.  We would like to invite you to view to view the list of tutorials and other relevant resources that are listed on the GEOS-Chem web page at [http://www.as.harvard.edu/ctm/geos/geos_resources.html '''GEOS-Chem Resources Page'''.]
We invite you to read our document on 
[http://www.as.harvard.edu/ctm/geos/word_pdf_docs/resources_guidelines_tips.pdf User Resources, Code Development Guidelines, and Debugging Tips].
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 update the table of [[GEOS-Chem supported platforms and compilers]] with your timing information.
=== 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 April-May 2009|April-May 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
* 2006: entire year
* 2007: thru May 2007
* 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
MOTE:
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/YYYY/MM/
  mget *
  cd pub/geos-chem/data/GEOS_2x2.5.d/GEOS_5/YYYY/MM/
  mget *
  cd pub/geos-chem/data/GEOS_4x5.d/GEOS_5/YYYY/MM/
  mget *
where <tt>YYYY</tt> and <tt>MM</tt> are the year and month that you wish to download.
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.]] 11:33, 15 June 2009 (EDT)
== feel free to experiment here ==

Latest revision as of 19:10, 3 October 2024

Species added

Species added between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:

Name Formula Fullname Advected Dry deposited Gas Photolyzed Wet deposited
ACO3 C3H3O3 Peroxyacetyl radical for APAN X
ACR C3H4O Acrolein X X X X
ACRO2 C3H5O4 Peroxy radical from ACR X
ALK7 C7H16 Lumped >= C6 Alkanes X X
APAN C3H3NO5 Peroxyacryloyl nitrate X X X X X
APINN C10H17NO4 1st gen organic nitrate from APIN X X X X X
APINO2 C10H17O3 Peroxy radical from APIN X
APINP C10H18O3 Hydroperoxide from APIN X X X X
AROMCHO C5H6O4 ACCOMECHO from MCM X X X X
AROMCO3 C5H5O6 Lumped aromatic peroxyacetyl radical X
AROMPN C5H5NO8 Lumped PN from aromatics X X X X X
BPINN C10H17NO4 Saturated 1st gen BPIN organic nitrate X X X X X
BPINO C9H14O Ketone from BPIN X X X X
BPINO2 C10H17O3 Peroxy radical from BPIN X
BPINON C9H13NO4 Saturated 2nd gen BPIN organic nitrate X X X X X
BPINOO2 C10H17O3 2nd-gen peroxy radical from BPIN X
BPINOOH C9H14O3 2nd-gen peroxide from BPIN X X X X
BPINP C10H18O3 Peroxide from BPIN X X X X
BUTN C4H7NO4 C4H6 alkyl nitrate X X X X
BUTO2 C4H7O3 peroxy radical from C4H6 X
C4H6 C4H6 1,3-butadiene X X
C96N C9H15NO4 Saturated 2nd gen monoterpene organic nitrate X X X X X
C96O2 C10H17O3 2nd-gen peroxy radical from APIN X
C96O2H C9H16O3 Peroxide from APIN 2nd gen X X X X
EBZ C8H10 Ethylbenzene X X
GCO3 HOCH2CO3 Peroxyacetyl radical for PHAN X
HACTA HOCH2CO2H Hydroxyacetic/glycolic acid X X X X
LIMAL C10H16O2 Aldehyde from limonene X X X X
LIMKB C10H16O3 2nd gen ketone from limonene X X X X
LIMKET C10H16O2 Ketone from limonene X X X X
LIMKO2 C10H17O3 2nd-gen peroxy radical from LIMO X
LIMN C10H17NO4 Saturated 1st gen limonene organic nitrate X X X X X
LIMNB C10H15NO4 Saturated 1st gen LIMO organic nitrate X X X X X
LIMO2H C10H18O3 Acid from LIMO X X X X
LIMO3 C10H17O3 Acylperoxy radical from LIMO X
LIMO3H C10H18O4 Peracid from LIMO X X X X
LIMPAN C10H17NO4 PAN from LIMO X X X X X
MEKCO3 C3H5O4 False X
MEKPN C3H5NO6 MEK peroxyacetyl nitrate X X X X X
MYRCO C10H18O3 Aldehyde or ketone from myrcene X X X X
PHAN C2H3NO6 Peroxyhydroxyacetic nitric anhydride X X X X X
PIN C10H17NO4 Saturated 1st gen monoterpene organic nitrate X X X X X
PINAL C10H16O2 Pinonaldehyde X X X X
PINO3 C10H17O3 Acylperoxy radical from APIN X
PINO3H C10H18O4 Pinonic peracid X X X X
PINONIC C10H18O3 Pinonic acid X X X X
PINPAN C10H17NO4 PAN from pinonaldehyde X X X X X
R7N1 C7H15NO5 Peroxy radical from R7N2 X
R7N2 RO2NO C7 Lumped alkyl nitrate X X X X X
R7O2 C7H15O2 Peroxy radical from ALK7 X
R7P C7H16O2 Peroxide from R7O2 X X X X X
RNO3 RO2NO Lumped aromatic nitrate X X X X X
STYR C8H8 Styrene X X
TLFUO2 C5H7O5 False X
TLFUONE C5H6O2 Aromatic furanones X X X X
TMB C8H10 Trimethylbenzenes X
ZRO2 C7H9O5 RO2 for making lumped aromatic nitrate X


Species removed

Species removed between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:

Name Formula Fullname Advected Dry deposited Gas Photolyzed Wet deposited
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