Difference between revisions of "Collections for History diagnostics"

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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:51, 24 May 2018 (UTC)
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:51, 24 May 2018 (UTC)
  
== Links to diagnostic collections ==
+
== Alphabetical list of diagnostic collections ==
 +
 
 +
#[[History_collections_for_advection_and_mixing#The_AdvFluxVert_collection|The AdvFluxVert collection]]
 +
#[[History_collections_for_aerosols#The_AerosolMass_collection|The AerosolMass collection]]
 +
#[[History_collections_for_aerosols#The_Aerosols_collection|The Aerosols collection]]
 +
#[[History_collections_for_budgets#The_Budget_collection|The Budget collection]]
 +
#[[History_collections_for_dry_deposition#The_ConcAboveSfc_collection|The ConcAboveSfc collection]]
 +
#[[History_collections_for_chemistry_and_photolysis#The_ConcAfterChem_collection|The ConcAfterChem collection]]
 +
 
 +
 
 +
 
 +
[[History_collections_for_advection_and_mixing#The_Transport_collection|The Transport collection]]
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
[[History_collections_for_chemistry_and_photolysis#The_JValues_collection]]
 +
[[History_collections_for_chemistry_and_photolysis#The_ProdLoss_Collection]]
 +
[[History_collections_for_chemistry_and_photolysis#The_StateChm_Collection]]
 +
 
 +
[[History_collections_for_convection_and_wet_deposition#The_CloudConvFlux_collection]]
 +
[[History_collections_for_convection_and_wet_deposition#The_WetLossConv_collection ]]
 +
[[History_collections_for_convection_and_wet_deposition#The_WetLossLS_collection ]]
 +
 
 +
 
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[[History_collections_for_dry_deposition#The_DryDep_collection]]
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[[History_collections_for_mercury_and_POPs#The_MercuryChem_collection]]
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[[History_collections_for_mercury_and_POPs#The_MercuryEmis_collection]]
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[[History_collections_for_mercury_and_POPs#The_MercuryOcean_collection]]
 +
[[History_collections_for_mercury_and_POPs#The_POPs_collection]]
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 +
 
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[[History_collections_for_met_fields_and_related_quantities#The_LevelEdgeDiags_collection ]]
 +
[[History_collections_for_met_fields_and_related_quantities#The_StateMet_collection ]]
 +
 
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[[History_collections_for_methane#The_CH4_collection]]
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[[History_collections_for_species_concentrations#The_BoundaryConditions_collection ]]
 +
[[History_collections_for_species_concentrations#The_Restart_collection ]]
 +
[[History_collections_for_species_concentrations#The_SpeciesConc_collection ]]
 +
 
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[[History_collections_for_species_concentrations#The_BoundaryConditions_collection ]]
 +
 
 +
 
 +
[[History_collections_for_TransportTracers#The_RadioNuclide_Collection ]]
 +
 
  
TBD
 
  
 
----
 
----
 
'''''[[Legend for History diagnostics|Previous]] | [[History collections for advection and mixing|Next]] | [[Guide to GEOS-Chem History diagnostics]] | [[Guide to GEOS-Chem diagnostics]] | [[Getting Started with GEOS-Chem]] | [[Main Page|GEOS-Chem Main Page]]'''''
 
'''''[[Legend for History diagnostics|Previous]] | [[History collections for advection and mixing|Next]] | [[Guide to GEOS-Chem History diagnostics]] | [[Guide to GEOS-Chem diagnostics]] | [[Getting Started with GEOS-Chem]] | [[Main Page|GEOS-Chem Main Page]]'''''

Revision as of 18:43, 19 July 2019

Previous | Next | Guide to GEOS-Chem History diagnostics | Guide to GEOS-Chem diagnostics | Getting Started with GEOS-Chem | GEOS-Chem Main Page

  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. Replicating the behavior of the prior timeseries diagnostics
  16. 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 above.

--Bob Yantosca (talk) 18:51, 24 May 2018 (UTC)

Alphabetical list of diagnostic collections

  1. The AdvFluxVert collection
  2. The AerosolMass collection
  3. The Aerosols collection
  4. The Budget collection
  5. The ConcAboveSfc collection
  6. The ConcAfterChem collection


The Transport collection




History_collections_for_chemistry_and_photolysis#The_JValues_collection History_collections_for_chemistry_and_photolysis#The_ProdLoss_Collection History_collections_for_chemistry_and_photolysis#The_StateChm_Collection

History_collections_for_convection_and_wet_deposition#The_CloudConvFlux_collection History_collections_for_convection_and_wet_deposition#The_WetLossConv_collection History_collections_for_convection_and_wet_deposition#The_WetLossLS_collection


History_collections_for_dry_deposition#The_DryDep_collection

History_collections_for_mercury_and_POPs#The_MercuryChem_collection History_collections_for_mercury_and_POPs#The_MercuryEmis_collection History_collections_for_mercury_and_POPs#The_MercuryOcean_collection History_collections_for_mercury_and_POPs#The_POPs_collection


History_collections_for_met_fields_and_related_quantities#The_LevelEdgeDiags_collection History_collections_for_met_fields_and_related_quantities#The_StateMet_collection

History_collections_for_methane#The_CH4_collection

History_collections_for_species_concentrations#The_BoundaryConditions_collection History_collections_for_species_concentrations#The_Restart_collection History_collections_for_species_concentrations#The_SpeciesConc_collection

History_collections_for_species_concentrations#The_BoundaryConditions_collection


History_collections_for_TransportTracers#The_RadioNuclide_Collection



Previous | Next | Guide to GEOS-Chem History diagnostics | Guide to GEOS-Chem diagnostics | Getting Started with GEOS-Chem | GEOS-Chem Main Page