Collections for History diagnostics

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Diagnostic collections

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)