Difference between revisions of "Sandbox"

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Dear GEOS-Chem Users,
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== Instructions for adding tracers to GEOS-Chem ==
  
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Here is the June 2009 GEOS-Chem Newsletter.
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'''''By [mailto:mpayer@seas.harvard.edu Melissa Payer]'''''
  
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''Bob Yantosca, Philippe Le Sager, and Claire Carouge''<br>
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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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''geos-chem-support@as.harvard.edu''
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== GEOS-Chem Update ==
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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 v8-02-02 ===
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#<p>Add tracers to input.geos under Tracer Menu</p>
 +
##<p>Increase “Number of tracers” accordingly</p>
 +
##<p>Add tracer number, name, molecular weight, and emitted species to end of tracer list</p>
 +
#<p>Add tracer(s) to restart file – see separate instructions</p>
 +
#<p>Modify the following source code routines:</p>
 +
##<p><tt>Headers/CMN_SIZE_mod.F</tt></p>
 +
###<p>Increase <tt>NNPAR</tt> by number of tracers being added</p>
 +
###<p>If the species have anthropogenic emissions, increase NEMPARA accordingly</p>
 +
###<p>If the species have biogenic emissions, increase NEMPARB accordingly</p>
 +
###<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>
 +
####<p>Under “Fill IDEMS with appropriate tracer ID #’s,” add IF statement for added tracers</p>
 +
####<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>
 +
##<p>Other modules that may need to be updated include:</p>
 +
###<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 v8-02-02]] "beta" has now been released.  This version includes:
 
  
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*new boundary layer mixing scheme (developed by Jintai Lin)
 
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*updated Bond emission inventories for BC & OC (prepared by Eric Leibensperger). 
 
  
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This version may be downloaded from:
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Instructions for adding species to GEOS-Chem
  
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  ftp ftp.as.harvard.edu
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Modify run directory files
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  cd pub/geos-chem/beta_releases
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  get GEOS-Chem.v8-02-02-beta.stdrun.tar.gz
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'''''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...'''
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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 Steering Committee ===
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2) Add tracer(s) to restart file – see separate instructions
  
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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.
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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
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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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Since last April's 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:
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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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{| border=1 cellspacing=0 cellpadding=5
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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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|- bgcolor="#cccccc"
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b) jv_spec.dat – contains cross-sections and quantum yields for FAST–JX photolysis species
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!Item
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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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!Author(s)
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!Completion Date
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|-
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|Improved BL mixing scheme
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|Jintai Lin
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|Now included in [[GEOS-Chem v8-02-02]];<br>released 08 Jun 2009
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|-
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|BC/OC aerosol emissions from Bond inventory
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|Eric Leibensperger
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|Now included in [[GEOS-Chem v8-02-02]];<br>released 08 Jun 2009
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|-
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|Chemical updates
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|Mat Evans<br>Fabien Paulot<br>Jingqiu Mao<br>Paul Palmer
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|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
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|}
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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 (here listed in order):
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{| border=1 cellspacing=0 cellpadding=5
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|- bgcolor="#cccccc"
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!#
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!Development priority
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!Point person(s)
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!Status
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|-
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|1.
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|GEOS-5 ozone columns
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|GC support team
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|Validation is ongoing
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|-
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|2
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|KPP implementation
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|GC support team<br>Virginia Tech
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|In beta testing
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|-
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|3.
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|TOMAS implementation
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|Win Trivitayanurak<br>GC Support Team
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|Telecon to discuss implementation<br>scheduled for June 16th
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|-
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|4.
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|Linoz
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|Dylan Jones and<br>U. Toronto group
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|In beta testing
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|-
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|5.
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|Updated methane simulation
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|Christopher Pickett-Heaps<br>Kevin Wecht
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|Debugging and code cleanup is ongoing
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|-
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|6.
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|Updated CO2 Simulation
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|Ray Nassar
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|&nbsp;
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|-
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|7.
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|Updated MEGAN emission from terpenes
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|Dylan Millet
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|&nbsp;
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|-
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|8.
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|COADS ship emissions
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|Chulkyu Lee
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|&nbsp;
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|-
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|9.
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|Include updated aerosol optics 
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|Colette Heald<br>Randall Martin<br>and Aerosols Working Group
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|Randall Martin will create "master list" of optical properties
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|-
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|10.
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|Include aromatic SOA
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|Daven Henze
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|&nbsp;
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|-
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|11.
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|Archive OH fields from benchmark<br>for use in off-line simulations
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|GC support team
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|&nbsp;
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|}
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=== GEOS-Chem Working Groups ===
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A couple of the [http://www.as.harvard.edu/ctm/geos/geos_steering_cmte.html GEOS-Chem Working Groups] have been renamed:
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* "Carbon Gases" and "Organics" has been merged into "Carbon Gases & Organics" (co-chairs Dylan Jones, Dylan Millet)
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* "Regional Modeling" is now "Regional Air Quality" (co-chairs Rokjin Park, Yuxuan Wang)
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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].
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For more information about a particular working group, please contact the appropriate Working Group Chairperson(s).
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=== Subscribing to the GEOS-Chem email lists ===
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There are now several GEOS-Chem email lists:
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{| border=1 cellspacing=0 cellpadding=5
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|- bgcolor="#cccccc"
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!Email list address
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!Intended audience
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|-
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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'''''
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|-
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|<tt>geos-chem-adjoint@seas.harvard.edu</tt>
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|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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|-
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|<tt>geos-chem-oxidants@seas.harvard.edu</tt>
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|Members of the [[Chemistry Issues|Oxidants and Chemistry Working Group]]
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|-
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|<tt>geos-chem-regional@seas.harvard.edu</tt>
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|Members of the [[Regional Air Quality Working Group]]
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|}
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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.
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'''''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.'''''
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=== Being a member of the GEOS-Chem community ===
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We would like to encourage all new GEOS-Chem users to take a moment to read our [[GEOS-Chem welcome letter for new users]].  (Also, veteran users may want to look at this too for a "refresher"...)
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We expect that each GEOS-Chem user will possess at least some familiarity with the following:
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* The Fortran programming language (F77 OK, F90 preferred)
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* IDL (preferred), or other graphics software (e.g. Splus, Matlab)
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* The Unix environment (i.e. commands, file paths, etc.)
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* Unix scripts (not strictly required but is very helpful to know!)
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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'''.]
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We invite you to read our document on 
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[http://www.as.harvard.edu/ctm/geos/word_pdf_docs/resources_guidelines_tips.pdf '''User Resources, Code Development Guidelines, and Debugging Tips'''].
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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'''].
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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.
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=== Adjoint Model Update ===
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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.
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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 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:
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* 2003: December only
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* 2004: entire year
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* 2005: entire year
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* 2006: entire year
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* 2007: thru 2007/06/29
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* 2008: entire year
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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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'''''Therefore, the only "missing" data as of June 15, 2009 is the remainder of 2007.'''''
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=== Notes ===
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(1) As of June 2009, Harvard's filesystem has been modified.  The directories on the FTP site
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  ftp ftp.as.harvard.edu
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  cd pub/geos-chem/data
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are now a straight mirror of the internal firewall-protected directories.  Any files that are added to the internal directories will be automatically mirrored to the FTP site during the nightly system reboots.  '''''This means that the *.tar.gz files are no longer stored on the FTP site.'''''
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(2) As of June 16, 2009, the following data is now available for download:
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  Nested China
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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/YYYY/MM/
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  2 x 2.5 Global (except 2006-2007)
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  ftp ftp.as.harvard.edu
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  cd pub/geos-chem/data/GEOS_2x2.5.d/GEOS_5/YYYY/MM/
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  2 x 2.5 Global (2006-2007 only)
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  ftp ftp.as.harvard.edu
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  cd pub/geos-chem/data/bmy_temp/GEOS_2x2.5.d/GEOS_5/YYYY/MM/
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  4 x 5 Global (except 2006-2007)
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  ftp ftp.as.harvard.edu
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  cd pub/geos-chem/data/GEOS_4x5.d/GEOS_5/YYYY/MM/
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  4 x 5 Global (2006-2007 only)
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  ftp ftp.as.harvard.edu
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  cd pub/geos-chem/data/bmy_temp/GEOS_2x2.5.d/GEOS_5/YYYY/MM/
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where <tt>YYYY/MM/</tt> are the year and month that you wish to download.
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As you may have noticed, the 2006 and 2007 reprocessed GEOS-5 met data is placed in a "temporary" directory <tt>bmy_temp</tt>.  These met data have also not been placed in a "temporary" folder in the internal firewall-protected directories (so as to avoid confusion w/ the existing met data). 
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As soon as all of the met fields for 2006-2007 have been reprocessed then we will move them from the "temporary" directory structure into the normal directory structure.  At that point, they will also be mirrored into the "normal" FTP directory structure.
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(3) '''''IMPORTANT!  At present the OTD/LIS lightning flash redistribution has not been done for years 2006-2007.  Therefore, if you run a full-chemistry simulation with 2006 or 2007 reprocessed met fields, the lightning NOx emissions will be incorrect.  We will recompute the OTD/LIS lightning flash redistribution at a later date.'''''
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== ESMF and Column Code Update ==
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We have created a [[GEOS-Chem column code]] wiki page.  At present the page is still under construction, but content will be added here on a regular basis.  Please check back often for the latest information!
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The GEOS-Chem column chemistry code has achieved a milestone: the SMVGEAR chemistry solver, as well as its various supporting routines, have been columnized and appear to work properly!  Also, the "driver" loop over longitude and latitude has now been parallelized with OpenMP.  This will allow us to do longer testing runs (i.e. 1 month instead of 1 day, etc.)
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Several of the chemistry routines for aerosol tracers, including sea salt, dust, and carbon/SOA tracers, have been columnized.  Work is still progressing to columnize the sulfate tracer chemistry routines.
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The challenging part of this work is that several of the "legacy" code routines need to be rewritten in order to separate any input/output from the places where we do computation.  Also, several references to some GEOS-Chem modules need to be removed in certain places in the code in order to make the column code more cleanly separatable from the rest of GEOS-Chem.  The work is ongoing.
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== Vacation Schedule ==
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Please note: Claire Carouge will be on vacation from June 17th thru July 5th.  Bob and Philippe will be available during this time period; however, we will be a little short-handed during this time so please plan accordingly.
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--[[User:Bmy|Bob Y.]] 11:33, 15 June 2009 (EDT)
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== feel free to experiment here ==
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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

Retrieved from "https://wiki.seas.harvard.edu/geos-chem/index.php?title=Sandbox&oldid=52410"