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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:


Here is the February 2009 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


== Requests for help ==
|-valign='top'
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.
|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
|
|
   
|}


== GEOS-Chem update ==
=== Species removed===


=== Emissions release v8-01-04 ===
Species removed between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:
Our emissions release, [[GEOS-Chem versions under development#v8-01-04|GEOS-Chem v8-01-04]] is in the final testing phase. We are running a couple of 1-year benchmarks in order to assess how the most up-to-date emissions inventories impact the full-chemistry simulation.


Because the menu of emissions options is more complex than in prior versions, we are also in the process of documenting everything up in a clear and consistent manner.
{| 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


=== Bug with Intel Fortran Compiler ("IFORT") 11 ===
|}
A couple of users have reported problems when migrating GEOS-Chem from the Intel "IFORT" compiler version 10 to version 11.  [[Machine issues & portability#Problems_with_IFORT_11|Please visit this page to view the complete discussion thread]].
 
In the interim, our recommendation is for GEOS-Chem users to stay with IFORT 10, as we know that this compiler produces code that optimizes well on multi-core chipsets.  We have not yet had chance to examine this problem more thoroughly.
 
== ESMF update ==
Max Suarez from GSFC visited us in mid February.  While Max was present, we held a telecon with some other members of the GSFC team to discuss the best way in which GEOS-Chem could be incorporated into the GEOS-5 GCM at NASA.  Based on their recommendations, we are moving forward to provide them with a column-ized version of the chemistry solver of GEOS-Chem.
 
Bob and Philippe also have recently created an ESMF-ized version of the GEOS-Chem emissions module.  This module will also be an important part of the future GEOS-Chem model.
 
== GEOS-5 met field reprocessing ==
 
=== Status ===
As described in the [[GEOS-Chem Newsletter January 2009|January 2009 newsletter]], we are reprocessing the entire archive of GEOS-5 met field data.  As of February 17, 2009 the following fields have been completed:
 
* 2008: entire year
* 2004: July - December
 
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 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.
 
=== Required code modifications  ===
To use the new, reprocessed GEOS-5 met data in GEOS-Chem, you must first install [[GEOS-Chem versions under development#v8-01-02|GEOS-Chem v8-01-02]] (or higher) and make sure the following switch in "define.h" is uncommented.
 
    !----- FOR GEOS-5 MET FIELDS ONLY -----
    ! NOTE: If you are using GEOS-5 met fields that were reprocessed to
    ! correctly regrid the in-cloud optical depth and cloud fraction fields,
    ! then be sure to uncomment the following line of code.  This will cause
    ! FAST-J to interpret the optical depth correctly.  Leaving this option
    ! commented will cause a "quick fix" (i.e. multiplying the optical depth
    ! by the cloud fracton) to be applied, which should be a good enough fix
    ! in the meantime. (bmy, hyl, 10/24/08)
    #define IN_CLOUD_OD  'IN_CLOUD_OD'
 
Also, if you are using [[GEOS-Chem versions under development#v8-01-02|v8-01-02]] or [[GEOS-Chem versions under development#v8-01-03|v8-01-03]], you must also insert a minor bug fix to manually set the variable <tt>N_A6_FIELDS</tt> to 21.  Otherwise the fields will not be read in correctly.  This has to be done in routine <tt>OPEN_A6_FIELDS</tt> (located in source code file <tt>a6_read_mod.f</tt>, directly after the variable <tt>N_A6_FIELDS</tt> is read in:
 
        ! The last 2 digits of the ident string
        ! is the # of fields contained in the file
        READ( IDENT(7:8), '(i2.2)' ) N_A6_FIELDS
 
#if  defined( GEOS_5 ) && defined( IN_CLOUD_OD )
        !%%% KLUDGE: set N_A6_FIELDS=21 when using the reprocessed
        !%%% GEOS-5 met.  This accounts for CMFMC (which doesn't seem
        !%%% to get counted) as well as for MOISTQ, which is an extra
        !%%% derived field.  (jmao, bmy, 2/12/09)
        N_A6_FIELDS = 21
#endif
 
However, it is probably just easier to install [[GEOS-Chem versions under development#v8-01-04|v8-01-04]] GEOS-Chem v8-01-04, which is slated for release shortly.  The above bug for <tt>N_A6_FIELDS</tt> is fixed in v8-01-04.
 
== 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_v1.pdf (click here for PDF format)]. Please direct your questions about the agenda to Daniel Jacob ('''''djacob@fas.harvard.edu''''').
 
If you have not registered for the meeting but would like to attend, then please contact Brenda Mathieu ('''''blm@as.harvard.edu''''') with your name and affiliation as you would like it to appear on your badge. There is no registration fee.
 
 
Thanks for your continued support of GEOS-Chem!
 
Bob Yantosca, Philippe Le Sager, and Claire Carouge
geos-chem-support@as.harvard.edu
 
--[[User:Bmy|Bob Y.]] 12:09, 17 February 2009 (EST)

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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