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== feel free to experiment here ==
=== Species added ===


Dear GEOS-Chem Users,
Species added between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:


A belated Happy St. Patrick's Day to one and all! Here is the March 2009 edition of the GEOS-Chem newsletter. 
{| 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


''Bob Yantosca, Philippe Le Sager, and Claire Carouge''<br>
|-valign='top'
''geos-chem-support@as.harvard.edu''
|ACO3
|C3H3O3
|Peroxyacetyl radical for APAN
|
|
|X
|
|
|-valign='top'
|ACR
|C3H4O
|Acrolein
|X
|X
|X
|X
|
|-valign='top'
|ACRO2
|C3H5O4
|Peroxy radical from ACR
|
|
|X
|
|
|-valign='top'
|ALK7
|C7H16
|Lumped >= C6 Alkanes
|X
|
|X
|
|
|-valign='top'
|APAN
|C3H3NO5
|Peroxyacryloyl nitrate
|X
|X
|X
|X
|X
|-valign='top'
|APINN
|C10H17NO4
|1st gen organic nitrate from APIN
|X
|X
|X
|X
|X
|-valign='top'
|APINO2
|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
|
|
|}


== Requests for help ==
Just a reminder: all GEOS-Chem questions should be sent to the email address '''''geos-chem-support@as.harvard.edu'''''.  This will ensure that Bob, Philippe, and Claire will all receive your email question at the same time.  This will allow us to serve you better.  If one of us is unavailable then the others will be able to respond to you. 
=== Species removed===


== GEOS-Chem update ==
Species removed between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:


=== Reporting Bugs ===
{| border=1 cellspacing=0 cellpadding=5
A friendly reminder: if you should find and fix a bug in GEOS-Chem, please report it to Bob, Philippe, and Claire at <tt>geos-chem-support@as.harvard.edu</tt> as soon as possible.  This will make sure that the bug fix gets included in the mainline GEOS-Chem code.  Also, other GEOS-Chem users will surely benefit from your discovery!
!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


=== Emissions release v8-01-04 "beta" ===
|}
[[GEOS-Chem versions under development|GEOS-Chem v8-01-04 "beta"]], our emissions release, is now ready for public use.  This version contains several updated emissions inventories.  You may obtain the code from:
 
ftp ftp.as.harvard.edu
cd pub/geos-chem/beta_releases
get GEOS-Chem.v8-01-04-beta.stdrun.tar.gz
 
Please see the following resources for more information about this version:
 
* [http://www.as.harvard.edu/ctm/geos/doc/man/appendix_8.html#A8.4 The "Addenda" section of the GEOS-Chem User's Manual]
* [[GEOS-Chem versions under development#v8-01-04|The wiki page (including 1-yr benchmark information) for v8-01-04]]
* Philippe Le Sager has prepared [http://wiki.seas.harvard.edu/geos-chem/images/Anth_emiss_gc_v8-01-04.pdf a document (PDF format)] which describes the anthropogenic emissions sources in more detail.
 
=== Chemistry release v8-02-01 ===
[[GEOS-Chem versions under development#v8-02-01|GEOS-Chem v8-02-01]], our chemistry release, is undergoing final testing at this point.  A few technical problems with the GLYX chemistry mechanism are being ironed out by May Fu and Claire Carouge.
 
Also, we would like to acknowledge the Palmer group (U. Edinburgh), Dylan Millet (UMN), and Jingqiu Mao (Harvard), who have been reviewing the GEOS-Chem chemistry mechanism file to make sure that we have the most up-to-date list of reactions.  The updated mechanism will be included in v8-02-01.
 
GEOS-Chem v8-02-01 will be a "public" release (i.e. the manual page and other documentation will be rewritten).  However, due to time concerns, it will probably not be ready before the GEOS-Chem meeting.  We hope to have this version ready soon thereafter.
 
=== GEOS-Chem email lists===
The following email lists:
 
*GEOS-Chem users
*GEOS-Chem aerosols
*GEOS-Chem adjoint
 
were recently switched over from the <tt>geos.as.harvard.edu</tt> server to the <tt>seas.harvard.edu</tt> server.  Therefore, to send email to the entire list, you must now use the following addresses:
 
*<tt>geos-chem@seas.harvard.edu</tt>
*<tt>geos-chem-aerosols@seas.harvard.edu</tt>
*<tt>geos-chem-adjoint@seas.harvard.edu</tt>
 
Also note, during the transition, some email addresses may have not been copied over correctly.  If you feel that you have been deleted from the list, you can resubscribe via [https://lists.seas.harvard.edu/mailman/listinfo/ this web interface].
 
=== FLAMBE data has been reprocessed ===
This will be of interest to those of you who are doing ARCTAS-related work.  The FLAMBE hourly biomass product has been reprocessed by Ed Hyer after several problems were discovered with the data. 
 
Data files (binary punch format) have been created for GEOS-Chem, and may be downloaded from the following site:
 
ftp ftp.as.harvard.edu
cd pub/geos-chem/NRT-ARCTAS/flambe/2008/
 
there are subdirectories <tt>01, 02 .. 12</tt> which contain the data from Jan thru Dec 2008.  Please discard the old data for 2008 and re-download the new data.
 
'''''PLEASE NOTE!'''''  According to Ed Hyer, there are a few days which have one or more hours of missing data.  Therefore, it is recommended to check in <tt>flambe_arctas_mod.f</tt> if each file exists before it is read.
 
Also note: FLAMBE is not an option in the standard mainline GEOS-Chem code; at present it is only used in certain ARCTAS-related research versions of GEOS-Chem.
 
=== GEOS-Chem advection running slower than before? ===
A couple of users have pointed out that the new TPCORE advection code implemented into [[GEOS-Chem versions under development#v8-01-03|GEOS-Chem v8-01-03]] seems to run slower than in previous versions.  We are investigating, but cannot say if there is a definite "fix" for this at this point.
 
== ESMF update ==
Development of the GEOS-Chem column chemistry module  is proceeding swiftly.  Several of the sub-processes in the chemistry (e.g. inputs, photolysis, carbon & sea salt aerosol chemistry, aerosol thermodynamical equilibrium) have been columnized.  Much of the remaining code lends itself to columnization; however, in many cases legacy code must be removed or updated.
 
Bob and Philippe have provided GSFC with a list of input and output arguments that the GEOS-Chem column chemistry module will use.  This list is being refined with the assistance of Max Suarez and Arlindo da Silva from GSFC.  Once the list is finalized, GSFC will create an interface to the GEOS-5 GCM to which the GEOS-Chem column chemistry module will be attached.
 
Development of the ESMF component for the GEOS-Chem emissions has been temporarily suspended, as the priority now is to prepare the GEOS-Chem column chemistry component for inclusion into the GEOS-5 GCM.  However, the emissions component will more than likely be adapted to become the GEOS-Chem "emissions" driver within the GEOS-5 GCM.  Also, the emmissions component will be an important part of an eventual standalone ESMF GEOS-Chem model.
 
== GEOS-5 met field reprocessing ==
 
=== Status ===
As described in the [[GEOS-Chem Newsletter February 2009|February 2009 newsletter]], we are reprocessing the entire archive of GEOS-5 met field data.  As of March 18th, 2009 the following fields have been completed:
 
* 2008: entire year
* 2004: July - December
* 2005: January - March (NOTE: these have not yet been TAR'ed yet)
 
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].
 
At present, the throughput rate is approximately 28 days of model data per day.  Therefore it will still be a couple of months before the entire GEOS-5 dataset has been reprocessed.
 
 
 
== GEOS-Chem Meeting: April 7-10, 2009 ==
 
The 4th Annual GEOS-Chem Scientific & Users' Meeting is rapidly approaching.  Daniel has provided a first draft of the meeting agenda [http://www.as.harvard.edu/ctm/geos/meetings/2009/agenda_gc4_v3_031109.pdf (click here for PDF format)]. Please direct your questions about the agenda to Daniel Jacob ('''''djacob@fas.harvard.edu''''').
 
Registration for the meeting is now closed.
 
--[[User:Bmy|Bob Y.]] 11:00, 18 March 2009 (EDT)

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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