Difference between revisions of "Collections for History diagnostics"

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__FORCETOC__
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'''''[[Legend for History diagnostics|Previous]] | [[History collections for advection and mixing|Next]] | [[Guide to GEOS-Chem History diagnostics]]'''''
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#[[Overview of History diagnostics]]
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#[[Legend for History diagnostics]]
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#<span style="color:blue">'''Collections for History diagnostics'''</span>
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#[[History collections for advection and mixing]]
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#[[History collections for aerosols]]
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#[[History collections for budgets]]
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#[[History collections for chemistry and photolysis]]
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#[[History collections for convection and wet deposition]]
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#[[History collections for dry deposition]]
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#[[History collections for mercury and POPs]]
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#[[History collections for met fields and related quantities]]
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#[[History collections for methane]]
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#[[History collections for species concentrations]]
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#[[History collections for TransportTracers]]
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#[[History collections for CO2]]
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#[[Replicating the behavior of the prior timeseries diagnostics]]
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#[[Adding new History diagnostics]]
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== Overview ==
 
== Overview ==
  
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  ::
 
  ::
  
We have already discussed how <tt>EXPID</tt> works [[#netCDF filename convention|in a previous section]].
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We have already discussed how <tt>EXPID</tt> works [[Overview_of_History_diagnostics#netCDF_filename_convention|in a previous section]].
  
 
The <tt>COLLECTIONS:</tt> tag specifies all of the diagnostic '''collections''' that you wish to activate during a GEOS-Chem simulation.  Each collection represents a group of diagnostic quantities that will be written to disk in netCDF file format.  The collection name will be automatically added to the netCDF file name along with the date/or time, [[#netCDF filename convention|as we have seen above]].
 
The <tt>COLLECTIONS:</tt> tag specifies all of the diagnostic '''collections''' that you wish to activate during a GEOS-Chem simulation.  Each collection represents a group of diagnostic quantities that will be written to disk in netCDF file format.  The collection name will be automatically added to the netCDF file name along with the date/or time, [[#netCDF filename convention|as we have seen above]].
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GEOS-Chem will expect to find a collection definition section for each of the activated collections listed under the <tt>COLLECTIONS:</tt> section.  In other words, if you have <tt>SpeciesConc</tt> listed under <tt>COLLECTIONS:</tt>, but there is no further information provided about the <tt>SpeciesConc</tt> collection, then GEOS-Chem will halt with an error message.
 
GEOS-Chem will expect to find a collection definition section for each of the activated collections listed under the <tt>COLLECTIONS:</tt> section.  In other words, if you have <tt>SpeciesConc</tt> listed under <tt>COLLECTIONS:</tt>, but there is no further information provided about the <tt>SpeciesConc</tt> collection, then GEOS-Chem will halt with an error message.
  
The collections listed on this wiki page are the "default" diagnostic collections that we have created for GEOS-Chem.  You are certainly not limited to just using these collections.  We have created these default collections such that related quantities will be grouped together in the same netCDF files (to the greatest extent possible).  But you can create your own customized diagnostic collections by referring to our [[#Sample HISTORY.rc diagnostic input file|sample <tt>HISTORY.rc</tt> file shown above]].
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The collections listed on this wiki page are the "default" diagnostic collections that we have created for GEOS-Chem.  You are certainly not limited to just using these collections.  We have created these default collections such that related quantities will be grouped together in the same netCDF files (to the greatest extent possible).  But you can create your own customized diagnostic collections by referring to our [[Overview of History diagnostics#Sample HISTORY.rc diagnostic input file|sample <tt>HISTORY.rc</tt> file shown previously]].
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== Alphabetical list of diagnostic collections ==
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Here is a list of all GEOS-Chem History collections, sorted alphabetically:
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#[[History_collections_for_advection_and_mixing#The_AdvFluxVert_collection|The AdvFluxVert collection]]
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#[[History_collections_for_aerosols#The_AerosolMass_collection|The AerosolMass collection]]
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#[[History_collections_for_aerosols#The_Aerosols_collection|The Aerosols collection]]
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#[[History_collections_for_species_concentrations#The_BoundaryConditions_collection|The BoundaryConditions collection ]]
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#[[History_collections_for_budgets#The_Budget_collection|The Budget collection]]
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#[[History_collections_for_methane#The_CH4_collection|The CH4 collection]]
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#[[History_collections_for_convection_and_wet_deposition#The_CloudConvFlux_collection|The CloudConvFlux collection]]
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#[[History_collections_for_dry_deposition#The_ConcAboveSfc_collection|The ConcAboveSfc collection]]
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#[[History_collections_for_chemistry_and_photolysis#The_ConcAfterChem_collection|The ConcAfterChem collection]]
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#[[History_collections_for_dry_deposition#The_DryDep_collection|The DryDep collection]]
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#[[History_collections_for_chemistry_and_photolysis#The_JValues_collection|The Jvalues collection]]
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#[[History_collections_for_met_fields_and_related_quantities#The_LevelEdgeDiags_collection|The LevelEdgeDiags collection]]
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#[[History_collections_for_mercury_and_POPs#The_MercuryChem_collection|The MercuryChem collection]]
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#[[History_collections_for_mercury_and_POPs#The_MercuryEmis_collection|The MercuryEmis collection]]
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#[[History_collections_for_mercury_and_POPs#The_MercuryOcean_collection|The MercuryOcean collection]]
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#[[History_collections_for_mercury_and_POPs#The_POPs_collection|The POPs collection]]
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#[[History_collections_for_chemistry_and_photolysis#The_ProdLoss_Collection|The ProdLoss collection]]
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#[[History_collections_for_TransportTracers#The_RadioNuclide_Collection|The RadioNuclide collection]]
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#[[History_collections_for_species_concentrations#The_Restart_collection|The Restart collection]]
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#[[History_collections_for_species_concentrations#The_SpeciesConc_collection|The SpeciesConc collection]]
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#[[History_collections_for_chemistry_and_photolysis#The_StateChm_Collection|The StateChm collection]]
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#[[History_collections_for_met_fields_and_related_quantities#The_StateMet_collection|The StateMet collection ]]
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#[[History_collections_for_advection_and_mixing#The_Transport_collection|The Transport collection]]
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#[[History_collections_for_convection_and_wet_deposition#The_WetLossConv_collection|The WetLossConv collection]]
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#[[History_collections_for_convection_and_wet_deposition#The_WetLossLS_collection|The WetLossLS collection]]
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:51, 24 May 2018 (UTC)
 
  
== Links to diagnostic collections ==
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----
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'''''[[Legend for History diagnostics|Previous]] | [[History collections for advection and mixing|Next]] | [[Guide to GEOS-Chem History diagnostics]]'''''

Latest revision as of 16:43, 22 April 2021

Previous | Next | Guide to GEOS-Chem History diagnostics

  1. Overview of History diagnostics
  2. Legend for History diagnostics
  3. Collections for History diagnostics
  4. History collections for advection and mixing
  5. History collections for aerosols
  6. History collections for budgets
  7. History collections for chemistry and photolysis
  8. History collections for convection and wet deposition
  9. History collections for dry deposition
  10. History collections for mercury and POPs
  11. History collections for met fields and related quantities
  12. History collections for methane
  13. History collections for species concentrations
  14. History collections for TransportTracers
  15. History collections for CO2
  16. Replicating the behavior of the prior timeseries diagnostics
  17. Adding new History diagnostics


Overview

The diagnostic collections described in the sections below are used by default in GEOS-Chem simulations. You can create your own customized collections by modifying the HISTORY.rc file.

The only restriction is that you cannot mix data that is placed on grid box layer edges in the same collection as data placed on grid box layer centers. This violates the netCDF convention that all data variables have to be defined with the same vertical dimension.

The master collection list

The top of each HISTORY.rc file will look similar to this:

###############################################################################
###  HISTORY.rc file for GEOS-Chem                                          ###
###  Contact: GEOS-Chem Support Team (geos-chem-support@as.harvard.edu)     ###
###############################################################################

#============================================================================
# EXPID allows you to specify the beginning of the file path corresponding
# to each diagnostic collection.  For example:
#
#   EXPID: ./GEOSChem 
#      Will create netCDF files whose names begin "GEOSChem",
#      in this run directory.
#
#   EXPID: ./OutputDir/GEOSChem
#      Will create netCDF files whose names begin with "GEOSChem"
#      in the OutputDir sub-folder of this run directory.
#
#============================================================================
EXPID:  ./GEOSChem

#==============================================================================
# %%%%% COLLECTION NAME DECLARATIONS %%%%%
#
# To disable a collection, place a "#" character in front of its name
#
# NOTE: These are the "default" collections for GEOS-Chem.  
# But you can create your own custom diagnostic collections as well.
#==============================================================================
COLLECTIONS: 'Restart',
             'SpeciesConc',
             'AerosolMass',
             'Aerosols',
             'CloudConvFlux',
             'ConcAfterChem',
             'DryDep',
             'JValues',
             'LevelEdgeDiags',      
             'ProdLoss',
             'StateChm',     
             'StateMet',      
             'WetLossConv',
             'WetLossLS',
::

We have already discussed how EXPID works in a previous section.

The COLLECTIONS: tag specifies all of the diagnostic collections that you wish to activate during a GEOS-Chem simulation. Each collection represents a group of diagnostic quantities that will be written to disk in netCDF file format. The collection name will be automatically added to the netCDF file name along with the date/or time, as we have seen above.

Each of the run directories for the various GEOS-Chem simulations will have its own customized HISTORY.rc file. Only the diagnostic collections pertaining to a particular GEOS-Chem simulation will be included in the corresponding HISTORY.rc file. (In other words, you will not find diagnostic collections for full-chemistry simulations in the HISTORY.rc file for the Rn-Pb-Be simulation.)

Each collection name must be bracketed by single quotes, and be followed by a comma.

To disable an entire diagnostic collection, simply put a # comment character in front of the collection name in the COLLECTIONS: section.

GEOS-Chem will expect to find a collection definition section for each of the activated collections listed under the COLLECTIONS: section. In other words, if you have SpeciesConc listed under COLLECTIONS:, but there is no further information provided about the SpeciesConc collection, then GEOS-Chem will halt with an error message.

The collections listed on this wiki page are the "default" diagnostic collections that we have created for GEOS-Chem. You are certainly not limited to just using these collections. We have created these default collections such that related quantities will be grouped together in the same netCDF files (to the greatest extent possible). But you can create your own customized diagnostic collections by referring to our sample HISTORY.rc file shown previously.

Alphabetical list of diagnostic collections

Here is a list of all GEOS-Chem History collections, sorted alphabetically:

  1. The AdvFluxVert collection
  2. The AerosolMass collection
  3. The Aerosols collection
  4. The BoundaryConditions collection
  5. The Budget collection
  6. The CH4 collection
  7. The CloudConvFlux collection
  8. The ConcAboveSfc collection
  9. The ConcAfterChem collection
  10. The DryDep collection
  11. The Jvalues collection
  12. The LevelEdgeDiags collection
  13. The MercuryChem collection
  14. The MercuryEmis collection
  15. The MercuryOcean collection
  16. The POPs collection
  17. The ProdLoss collection
  18. The RadioNuclide collection
  19. The Restart collection
  20. The SpeciesConc collection
  21. The StateChm collection
  22. The StateMet collection
  23. The Transport collection
  24. The WetLossConv collection
  25. The WetLossLS collection



Previous | Next | Guide to GEOS-Chem History diagnostics