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== Instructions for adding tracers to GEOS-Chem ==
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|<p><font color="#FFFFFF" size="+3">'''GEOS&#150;Chem Wiki'''</font></p>
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'''''By [mailto:mpayer@seas.harvard.edu Melissa Payer]'''''
  
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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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NOTE: Some advected tracers are also chemical species, which comprise GEOS-Chem's NOx-Ox-HC-aerosol chemistry mechanism.
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----
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#<p>Add tracers to input.geos under Tracer Menu</p>
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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.
  
<p align="center"><big>'''GEOS-Chem Community Mission: to advance understanding of human and natural influences on the environment<br>through a comprehensive, state-of-the-science, readily accessible global model of atmospheric composition.'''</big></p>
 
  
The [http://acmg.seas.harvard.edu/geos/ GEOS–Chem model] is a global 3-D model of atmospheric composition driven by assimilated meteorological observations from the Goddard Earth Observing System (GEOS) of the [http://gmao.gsfc.nasa.gov/ NASA Global Modeling and Assimilation Office]. It is applied by [http://acmg.seas.harvard.edu/geos/geos_people.html research groups around the world] to a wide range of atmospheric composition problems, Central management and support of the model is provided by the [http://acmg.seas.harvard.edu/index.html Atmospheric Chemistry Modeling Group at Harvard University.]
 
  
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Instructions for adding species to GEOS-Chem
  
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Modify run directory files
  
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1) Add tracers to input.geos under Tracer Menu
|width="225px" align="center"|<font size="+2">[[GEOS-Chem versions|Past releases]]</font>
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c) Increase “Number of tracers” accordingly
|width="450px" align="center" bgcolor="#CCFFFF"|<font size="+2">[[GEOS-Chem 12#12.3.2|'''Current release: GEOS-Chem 12.3.2''']]</font>
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d) Add tracer number, name, molecular weight, and emitted species to end of tracer list
|width="225px" align="center"|<font size="+2">[[GEOS-Chem model development_priorities|Future releases]]</font>
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|}
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2) Add tracer(s) to restart file – see separate instructions
  
== News ==
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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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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
  
*'''6-9 May 2019:''' The [http://acmg.seas.harvard.edu/geos/meetings/2019/index.html 9th International GEOS-Chem GEOS-Chem Meeting (IGC9)] was held at Harvard University.
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4) If necessary, modify:
*'''2 May 2019:''' [[GEOS-Chem_12#12.3.2|GEOS-Chem 12.3.2]] is now released.
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a) ratj.d – contains species names and branching ratios for FAST–JX photolysis species
*'''5 March 2019:''' * [[Media:GEOS-Chem_Newsletter_Spring_2019.pdf|GEOS-Chem Newsletter, Spring 2019 Edition]]
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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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b) jv_spec.dat – contains cross-sections and quantum yields for FAST–JX photolysis species
For access to all past GEOS-Chem newsletters, visit [[GEOS-Chem newsletters|this page]].
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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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== Documentation ==
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*[[GEOS-Chem overview]]
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*[[GEOS-Chem basics]]
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*[[Getting Started with GEOS-Chem]]
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*[[Getting Started With GCHP|Getting Started with GCHP]]
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*[http://cloud.geos-chem.org Running GEOS-Chem on the Amazon Web Services cloud computing platform]
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== Featured links ==
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*[[GEOS-Chem HP]]
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*[[GEOS-Chem Adjoint]]
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*[http://wrf.geos-chem.org GEOS-Chem coupled with WRF]
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*[[GEOS-Chem nested grid simulations]]
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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