Difference between revisions of "Sandbox"

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== feel free to experiment here ==
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== Instructions for adding tracers to GEOS-Chem ==
  
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Dear GEOS-Chem Users,
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'''''By [mailto:mpayer@seas.harvard.edu Melissa Payer]'''''
  
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A belated Happy St. Patrick's Day to one and all!  Here is the March 2009 edition of the GEOS-Chem newsletter.   
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These instructions describe how to add advected tracers to GEOS-Chem.  Advected tracers are carried in the <tt>STT</tt> array (which is declared in <tt>GeosCore/tracer_mod.F</tt>), and are transported by the winds.   
  
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''Bob Yantosca, Philippe Le Sager, and Claire Carouge''<br>
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NOTE: Some advected tracers are also chemical species, which comprise GEOS-Chem's NOx-Ox-HC-aerosol chemistry mechanism.
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''geos-chem-support@as.harvard.edu''
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== Requests for help ==
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#<p>Add tracers to input.geos under Tracer Menu</p>
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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.
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##<p>Increase “Number of tracers” accordingly</p>
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##<p>Add tracer number, name, molecular weight, and emitted species to end of tracer list</p>
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#<p>Add tracer(s) to restart file – see separate instructions</p>
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#<p>Modify the following source code routines:</p>
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##<p><tt>Headers/CMN_SIZE_mod.F</tt></p>
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###<p>Increase <tt>NNPAR</tt> by number of tracers being added</p>
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###<p>If the species have anthropogenic emissions, increase NEMPARA accordingly</p>
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###<p>If the species have biogenic emissions, increase NEMPARB accordingly</p>
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###<p>If the species have biomass burning emissions, increase NBIOMAX accordingly</p>
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##<p><tt>GeosCore/tracerid_mod.F</tt></p>
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###<p>Increase <tt>NNNTRID</tt> by the number of tracers being added NOTE: <tt>NNNTRID</tt> must be equal to <tt>NNPAR</tt> in <tt>CMN_SIZE_mod.F</tt></p>
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###<p>Define tracer IDs as needed:</p>
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####<p>IDxxxx – ID for SMVGEAR species</p>
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####<p>IDTxxxx – GEOS-Chem tracer ID</p>
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####<p>IDExxxx – GEOS-Chem emission ID</p>
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####<p>IDBFxxxx – GEOS-Chem biofuel ID</p>
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####<p>IDBxxxx – GEOS-Chem biomass ID</p>
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###<p>In subroutine <tt>TRACERID</tt>,</p>
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####<p>Under “Assign tracer, biomass, biofuel, and anthro emission ID’s,” add case for added tracers to initialize IDTxxxx, IDBFxxxx, IDBxxxx</p>
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####<p>Under “Initialize the IDExxx flags,” add IF statement for added tracer IDs and initialize IDExxxx</p>
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####<p>Under “Fill IDEMS with appropriate tracer ID #’s,” add IF statement for added tracers</p>
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####<p>Under “Print additional information,” add WRITE statements for added tracers</p>
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###<p>In subroutine SETTRACE (NOTE: Only do the following if species is included in SMVGEAR chemical mechanism<p>
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####<p>Add IF statement, to initialize IDxxxx</p>
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####<p>In subroutine INIT_TRACERID,</p>
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####<p>Zero all IDs added (IDxxxx, IDTxxxx, IDExxxx, etc.)</p>
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##<p>Other modules that may need to be updated include:</p>
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###<p>wetscav_mod.F</p>
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###<p>drydep_mod.F</p>
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###<p>emissions_mod.F</p>
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###<p>biomass_mod.F</p>
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###<p>biofuel_mod.F</p> etc.
  
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== GEOS-Chem update ==
 
  
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=== Emissions release v8-01-04 "beta" ===
 
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[[GEOS-Chem versions under development|GEOS-Chem v8-01-04 "beta"]], our emissions release, is now released!  This version contains several updated emissions inventories.  For a full description, including information about the 1-year benchmark simulations that were performed, [[GEOS-Chem versions under development|please visit this link]].
 
  
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=== Chemistry release v8-02-01 ===
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Instructions for adding species to GEOS-Chem
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[[GEOS-Chem versions under development|GEOS-Chem v8-02-01]], our chemistry release, is undergoing final testing at this point.  A few technical problems with the GLYX chemistry mechanism (cf. May Fu) are being ironed out. 
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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.
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Modify run directory files
  
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GEOS-Chem v8-02-01 will be a "public" release. However, due to time concerns, it will probably not be ready before the GEOS-Chem meeting, but hopefully should be ready soon thereafter.
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1) Add tracers to input.geos under Tracer Menu
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c) Increase “Number of tracers” accordingly
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d) Add tracer number, name, molecular weight, and emitted species to end of tracer list
  
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=== GEOS-Chem email lists===
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2) Add tracer(s) to restart file – see separate instructions
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The following email lists:
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*GEOS-Chem users
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3) Modify globchem.dat to include additional species, kinetic reactions (including emissions and drydep), or photolysis reactions
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*GEOS-Chem aerosols
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NOTE: If you modify globchem.dat and plan to run GEOS-Chem using the KPP chemical solver, you will need to generate new gckpp*.F90 files. For more information see the following wiki pages:
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*GEOS-Chem adjoint
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http://wiki.seas.harvard.edu/geos-chem/index.php/KPP_solvers_FAQ#What_are_the_cons_of_using_KPP.3F
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http://wiki.seas.harvard.edu/geos-chem/index.php/Interfacing_GEOS-Chem_with_KPP#Generating_KPP_input_files_from_GEOS-Chem_globchem.dat
  
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were recently switched over from the "geos.as.harvard.edu" server to the "seas.harvard.edu" server.  Therefore, to send email to the entire list, you must now use the following addresses:
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4) If necessary, modify:
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a) ratj.d – contains species names and branching ratios for FAST–JX photolysis species
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*geos-chem@seas.harvard.edu
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For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.1
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*geos-chem-aerosols@seas.harvard.edu
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b) jv_spec.dat – contains cross-sections and quantum yields for FAST–JX photolysis species
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*geos-chem-adjoint@seas.harvard.edu
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For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.3
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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].
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== ESMF update ==
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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.
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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
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== GEOS-5 met field reprocessing ==
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=== Status ===
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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:
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* 2008: entire year
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* 2004: July - December
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* 2005: January - March
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for each of the following geographic domains:
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* China nested 0.5 x 0.667
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* Global 2 x 2.5
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* Global 4 x 5
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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:
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  ftp ftp.as.harvard.edu
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  cd pub/geos-chem/data/GEOS_0.5x0.666_CH.d/GEOS_5/2008
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  mget *.tar.gz
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  cd pub/geos-chem/data/GEOS_2x2.5.d/GEOS_5/2008
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  mget *.tar.gz
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  cd pub/geos-chem/data/GEOS_4x5.d/GEOS_5/2008
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  mget *.tar.gz
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  cd pub/geos-chem/data/GEOS_0.5x0.666_CH.d/GEOS_5/2004
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  mget *.tar.gz
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  cd pub/geos-chem/data/GEOS_2x2.5.d/GEOS_5/2004
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  mget *.tar.gz
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  cd pub/geos-chem/data/GEOS_4x5.d/GEOS_5/2004
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  mget *.tar.gz
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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].
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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.
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=== Required code modifications  ===
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== GEOS-Chem Meeting: April 7-10, 2009 ==
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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''''').
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Registration for the meeting is now closed.
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--[[User:Bmy|Bob Y.]] 11:00, 18 March 2009 (EDT)
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Latest revision as of 21:25, 10 May 2023

Instructions for adding tracers to GEOS-Chem

By Melissa Payer

These instructions describe how to add advected tracers to GEOS-Chem. Advected tracers are carried in the STT array (which is declared in GeosCore/tracer_mod.F), and are transported by the winds.

NOTE: Some advected tracers are also chemical species, which comprise GEOS-Chem's NOx-Ox-HC-aerosol chemistry mechanism.

  1. Add tracers to input.geos under Tracer Menu

    1. Increase “Number of tracers” accordingly

    2. Add tracer number, name, molecular weight, and emitted species to end of tracer list

  2. Add tracer(s) to restart file – see separate instructions

  3. Modify the following source code routines:

    1. Headers/CMN_SIZE_mod.F

      1. Increase NNPAR by number of tracers being added

      2. If the species have anthropogenic emissions, increase NEMPARA accordingly

      3. If the species have biogenic emissions, increase NEMPARB accordingly

      4. If the species have biomass burning emissions, increase NBIOMAX accordingly

    2. GeosCore/tracerid_mod.F

      1. Increase NNNTRID by the number of tracers being added NOTE: NNNTRID must be equal to NNPAR in CMN_SIZE_mod.F

      2. Define tracer IDs as needed:

        1. IDxxxx – ID for SMVGEAR species

        2. IDTxxxx – GEOS-Chem tracer ID

        3. IDExxxx – GEOS-Chem emission ID

        4. IDBFxxxx – GEOS-Chem biofuel ID

        5. IDBxxxx – GEOS-Chem biomass ID

      3. In subroutine TRACERID,

        1. Under “Assign tracer, biomass, biofuel, and anthro emission ID’s,” add case for added tracers to initialize IDTxxxx, IDBFxxxx, IDBxxxx

        2. Under “Initialize the IDExxx flags,” add IF statement for added tracer IDs and initialize IDExxxx

        3. Under “Fill IDEMS with appropriate tracer ID #’s,” add IF statement for added tracers

        4. Under “Print additional information,” add WRITE statements for added tracers

      4. In subroutine SETTRACE (NOTE: Only do the following if species is included in SMVGEAR chemical mechanism<p>

        1. <p>Add IF statement, to initialize IDxxxx

        2. In subroutine INIT_TRACERID,

        3. Zero all IDs added (IDxxxx, IDTxxxx, IDExxxx, etc.)

    3. Other modules that may need to be updated include:

      1. wetscav_mod.F

      2. drydep_mod.F

      3. emissions_mod.F

      4. biomass_mod.F

      5. biofuel_mod.F

        etc.


Instructions for adding species to GEOS-Chem

Modify run directory files

1) Add tracers to input.geos under Tracer Menu c) Increase “Number of tracers” accordingly d) Add tracer number, name, molecular weight, and emitted species to end of tracer list

2) Add tracer(s) to restart file – see separate instructions

3) Modify globchem.dat to include additional species, kinetic reactions (including emissions and drydep), or photolysis reactions NOTE: If you modify globchem.dat and plan to run GEOS-Chem using the KPP chemical solver, you will need to generate new gckpp*.F90 files. For more information see the following wiki pages: http://wiki.seas.harvard.edu/geos-chem/index.php/KPP_solvers_FAQ#What_are_the_cons_of_using_KPP.3F http://wiki.seas.harvard.edu/geos-chem/index.php/Interfacing_GEOS-Chem_with_KPP#Generating_KPP_input_files_from_GEOS-Chem_globchem.dat

4) If necessary, modify: a) ratj.d – contains species names and branching ratios for FAST–JX photolysis species For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.1 b) jv_spec.dat – contains cross-sections and quantum yields for FAST–JX photolysis species For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.3

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