List of diagnostics archived to netCDF format

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On this page we list the information about the new netCDF diagnostics that will be introduced in GEOS-Chem v11-02.

NOTE: We will NOT retire the legacy bpch diagnostics in GEOS-Chem v11-02. We will preserve the bpch diagnostic output until we can find alternatives for specialty diagnostics, especially those which involve averaging in a local solar time window.

Overview

An introduction to netCDF diagnostics

GEOS-Chem v11-02 (aka 12.0.0) and later versions can save diagnostic output to netCDF format. There are two types of netCDF diagnostic output files:

  1. Emissions diagnostics archived directly by HEMCO
  2. Non-emissions diagnostics computed by GEOS-Chem

The GEOS-Chem Support Team has developed a new netCDF diagnostic capability for GEOS-Chem "Classic" (point #2 above) that replicates how the existing netCDF diagnostics work in GCHP (aka "History"). A common input file named HISTORY.rc can be used for both GEOS-Chem "Classic" and GCHP.

Bob Yantosca has created an overview presentation about the new netCDF diagnostics for v11-02.

--Bob Yantosca (talk) 13:20, 8 June 2018 (UTC)

Sample HISTORY.rc diagnostic input file

Here is a sample HISTORY.rc file that is used to request netCDF diagnostic output from a GEOS-Chem “Classic” simulation.

#============================================================================ 
# 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: 'SpeciesConc',
             'ConcAfterChem',
::
#==============================================================================
# %%%%% THE SpeciesConc COLLECTION %%%%%
#
# GEOS-Chem species concentrations (default = advected species)
#
# Available for all simulations
#==============================================================================
SpeciesConc.template:     '%y4%m2%d2_%h2%n2z.nc4',
SpeciesConc.frequency:    060000,
SpeciesConc.format:       'CFIO',
SpeciesConc.duration:     240000,
SpeciesConc.mode:         'instantaneous',
SpeciesConc.fields:       'SpeciesConc_?ADV?',  'GIGCchem',
::
#==============================================================================
# %%%%% THE ConcAfterChem COLLECTION %%%%%
#
# Concentrations of OH, HO2, O1D, O3P immediately after exiting the KPP solver
# or OH after the CH4 specialty-simulation chemistry routine.
#
# OH:       Available for all full-chemistry simulations and CH4 specialty sim
# HO2:      Available for all full-chemistry simulations
# O1D, O3P: Availalbe for full-chemistry simulations using UCX mechanism
#==============================================================================
ConcAfterChem.template:   '%y4%m2%d2_%h2%n2z.nc4',
ConcAfterChem.frequency:  00000100 000000,
ConcAfterChem.format:     'CFIO',
ConcAfterChem.duration:   00000100 000000,
ConcAfterChem.mode:       'time-averaged',
ConcAfterChem.fields:     'OHconcAfterChem',     'GIGCchem',
                          'HO2concAfterChem',    'GIGCchem',
                          'O1DconcAfterChem',    ‘GIGCchem’,
                          'O3PconcAfterChem',    ‘GIGCchem’,
::


In this HISTORY.rc file, we are requesting two collections, or types of netCDF file output. The table below explains in more detail parameters shown in the HISTORY.rc file above.

Attribute Explanation
SpeciesConc Name of the first collection in this HISTORY.rc file. A collection is a series of files containing the same GEOS-Chem diagnostic quantities.
SpeciesConc.template Determines the date and time format for each netCDF file name belonging to the SpeciesConc collection.
  • The string %y4%m2%d2_%h2%n2z.nc4 will print YYYYMMDD_hhmmz.nc4 to the end of each netCDF filename
    • YYYYMMDD is the date in year/month/day format
    • hhmm is the time in hour:minutes format.
    • z denotes "Zulu", which is an abbreviation for UTC time.
    • .nc4 denotes that the data file is in the netCDF-4 format.
SpeciesConc.frequency Determines how often the diagnostic quantities belonging to SpeciesConc collection will be saved to a netCDF file.
  • This can be specified as either "hhmmss" or "YYYYMMDD hhmmss".
  • In the above example, data belonging to the SpeciesConc collection will be written to the file every 6 hours. (Because SpeciesConc is an instantaneous collection, no time-averaging will be performed.)
SpeciesConc.format For GCHP simulations only: indicates the I/O library that will be used. This can be omitted for GEOS-Chem "Classic" simualations.
SpeciesConc.duration Determines how often a new SpeciesConc netCDF file will be created.
  • This can be specified as either hhmmss or YYYYMMDD hhmmss.
  • In the above example, a new SpeciesConc netCDF file will be created every 24 hours.
SpeciesConc.mode Determines the averaging method for the SpeciesConc collection
  • In this example, SpeciesConc is defined as an instantaneous (aka "time-series") collection.
  • Diagnostic quantities belonging to SpeciesConc will be written directly to disk without any temporal averaging, at the specified frequency.
SpeciesConc.fields Lists the diagnostic quantities to be included in the SpeciesConc collection.
  • In the above example, we are requesting to archive the concentrations of all advected species to the SpeciesConc collection.
  • The text 'GIGCchem' is only needed for GCHP simulations. It is ignored for GEOS-Chem "Classic" simulations. We keep the 'GIGCchem' in the file in order HISTORY.rc files to be interchanged between GEOS-Chem "Classic" and GCHP simulations.

See the sections below for in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format.

NOTE: You may use wildcards to request a subset of all possible chemical species. See the next section for more information about wildcards.

:: Signifies the end of the SpeciesConc definition section.
  • "::" may be placed at any column in the file.
ConcAfterChem Name of the second collection in this HISTORY.rc file.
ConcAfterChem.template Determines the date and time format for each netCDF file name belonging to the ConcAfterChem collection.
ConcAfterChem.frequency Determines the length of the period in which the diagnostic quantities belonging to ConcAfterChem collection will be temporally-averaged, before being saved to a netCDF file.
  • This can be can be specified as either "hhmmss" or "YYYYMMDD hhmmss".
  • In the above example, data belonging to the ConcAfterChem collection will be averaged into monthly mean output.
ConcAfterChem.format For GCHP simulations only: indicates the I/O library that will be used. This can be omitted for GEOS-Chem "Classic" simualations.
ConcAfterChem.duration Determines how often a new netCDF file belongng to the ConcAfterChem will be created.
  • The duration attribute can be specified as either hhmmss or YYYYMMDD hhmmss.
  • In the above example, a new ConcAfterChem netCDF file will be created at the start of each new month.
ConcAfterChem.mode Determines the averaging method for the ConcAfterChem collection
  • In the above example, ConcAfterChem is defined as an time-averaged collection.
  • Diagnostic quantities belonging to the ConcAfterChem collection will be temporally-averaged for a period whose length is specified by the frequency attribute before being written to a netCDF file.
ConcAfterChem.fields Lists the diagnostic quantities to be included in the ConcAfterChem collection.
  • In the above example, we are requesting to archive to the ConcAfterChem collection the concentrations of OH, HO2, O1D, and O3P upon exiting the FlexChem/KPP solver
  • The text 'GIGCchem' is only needed for GCHP simulations. It is ignored for GEOS-Chem "Classic" simulations. We keep the 'GIGCchem' in the file in order HISTORY.rc files to be interchanged between GEOS-Chem "Classic" and GCHP simulations.

See the sections below for in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format.

NOTE: You may use wildcards to request a subset of all possible species. See the next section for more information about wildcards.

:: Signifies the end of the ConcAfterChem definition section.
  • "::" may be placed at any column in the file.

For more examples, please see Bob Yantosca’s netCDF diagnostics overview presentation. We will also add more documentation to the GEOS-Chem wiki in the coming weeks.

--Bob Yantosca (talk) 22:12, 8 February 2018 (UTC)

netCDF filename convention

The names of the netCDF files corresponding to each collection will adhere to this convention:

 EXPID.CollectionName.Template

Where EXPID can be specified at the very top of the HISTORY.rc file. This parameter controls the filename prefix. In the example from the previous section, EXPID is set to ./GEOSChem. This means that all netCDF output files will be placed in the current run directory (specified by ./) and will begin with GeosChem.

If you wish to send the netCDF diagnostic output to a sub-folder of the run directory (say named OutputDir), then you can set e.g. EXPID: ./OutputDir/GeosChem. (NOTE: You can also omit the ./, but we have included it to make it clear that the files will be placed in the same directory where the GEOS-Chem executable resides.)

The CollectionName and Template settings are defined as shown in our example HISTORY.rc file from the previous section, namely:

 SpeciesConc.template:     '%y4%m2%d2_%h2%n2z.nc4',
 . . .
 ConcAfterChem.template:   '%y4%m2%d2_%h2%n2z.nc4',

In the template tags:

  • The notation %y4%m2%d5_%h2%n2 specifies a in the format YYYYMMDD_hhmm into the netCDF filename.
  • The lowercase zdenotes UTC time (aka "Zulu time").
  • The .nc4 extension denotes that the file will be in netCDF-4 format.

Also recall that the duration tag of HISTORY.rc controls how often a new file will be written to disk, as we saw in our example from the previous section:

 SpeciesConc.duration:     240000,              # Write a new file each day
 . . .
 ConcAfterChem.duration:   00000100 000000,     # Write a new file each month

Therefore, based on all of these settings in our example HISTORY.rc file, GEOS-Chem will write the following netCDF files to disk in the current run directory:

GEOSChem.SpeciesConc.20160101_0000z.nc4
GEOSChem.SpeciesConc.20160102_0000z.nc4
GEOSChem.SpeciesConc.20160103_0000z.nc4
GEOSChem.SpeciesConc.20160104_0000z.nc4
... etc one file per day...

and

GEOSChem.ConcAfterChem.20160101_0000z.nc4
GEOSChem.ConcAfterChem.20160201_0000z.nc4
GEOSChem.ConcAfterChem.20160301_0000z.nc4
GEOSChem.ConcAfterChem.20160401_0000z.nc4
... etc one file per month ...

--Bob Yantosca (talk) 18:45, 24 May 2018 (UTC)

Legend to sections below

This section contains a description of how the information about each diagnostic quantity is arranged in the sections below.

General information about each diagnostic

The tables below list the following parameters for each diagnostic that is archived to bpch format:

Diagnostic name The name of the given diagnostic quantity that will be archived to netCDF file format.
  • NOTE: Wildcards can be used with certain diagnostics. This will let you specify all possible species, wavelength bins, etc. for a given diagnostic instead of having to list them individually. See the next section for a list of all possible wildcards.
  • ALSO NOTE: At this time, wildcards are not allowed in GCHP simulations. We are working to resolve this.
Description A short overview of the given diagnostic.
Units The physical units of the given diagnostic quantity.
Wildcards A list of wildcards that can be used to specify all possible species, wavelength bins, etc. for the given diagnostic quantity. For a complete list of wildcards, please see the table below.
Simulations A list of simulations for which this particular diagnostic is valid.
Bpch equivalent The NDxx diagnostic number (and slot) under which the same diagnostic is available as bpch output. See the List of diagnostics archived to bpch format wiki page for more information.
Notes Lists supplemental information for the given diagnostic.

Wildcards and prefixes

The following terms are used in the tables below.

Term Explanation Example
<spcname> Short name of a GEOS-Chem species, used in several diagnostics listed below.

NOTES:

  1. The single-underscore (_) preceding the species name indicates that use of a species wildcard (e.g SpeciesConc_?ADV?, which only selects advected species) is possible.
  2. Allowable wild card values (case-insensitive) for species name are:
    • ?ADV?: Only the advected species
    • ?AER?: Only the aerosol species
    • ?ALL?: All GEOS-Chem species
    • ?DRY?: Only the dry-deposited species
    • ?FIX?: Only the inactive (aka "fixed") species in the KPP chemical mechanism
    • ?GAS?: Only the gas-phase species
    • ?HYG?: Only aerosols that undergo hygroscopic growth
      • (e.g. sulfate, BC, OC, SALA, SALC)
    • ?KPP?: Only the KPP species
    • ?PHO: Only the photolyzed species
    • ?VAR?: Only the active (aka "variable") species in the KPP chemical mechanism
    • ?WET?: Only the wet-deposited species
    • ?PRODLOSS?: Only prod/loss diagnostic species
    • ?DUSTBIN: Only the dust bin number
  3. <spcname> should be case-insensitive. In most places where species names are compared, species names are first converted to uppercase and then a string match test is done. But because most species names represent a chemical formula (e.g. NO, CO),they will be mostly all uppercase. Some species names would have mixed-case, e.g. BrCl, Rn, Pb, Be7, etc.
  • SpeciesConc_NO
  • SpeciesConc_CO
  • SpeciesConc_?ADV?
  • SpeciesConc_?AER?
  • SpeciesConc_?ALL?
  • SpeciesConc_?DRY?
  • SpeciesConc_?FIX?
  • SpeciesConc_?GAS?
  • SpeciesConc_?HYG
  • SpeciesConc_?KPP?
  • SpeciesConc_?PHO?
  • SpeciesConc_?VAR?
  • SpeciesConc_?WET?
<photobin> Number of a given wavelength bin for FAST-JX photolysis
  • 1-18 (with UCX on);
  • 1-12 (with UCX off)
Chem_ To request diagnostic output for fields of the State_Chm object (other than SpeciesConc), add this prefix in front of the field name. (Prefix is case-insensitive.)
  • Chem_phCloud
  • Chem_HplusSav
Met_ To request diagnostic output for fields of the State_Met object, add this prefix in front of the field name. (Prefix is case-insensitive.)
  • Met_T
  • Met_PS
  • Met_SPHU
  • Met_U10M

--Bob Yantosca (talk) 14:00, 8 June 2018 (UTC)

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: 'SpeciesConc',
             'AerosolMass',
             'Aerosols',
             'CloudConvFlux',
             'ConcAfterChem',
             'DryDep',
             'JValues',
             'JValuesLocalNoon',
             '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)

The SpeciesConc collection

The SpeciesConc diagnostic collection contains advected species concentrations. This type of diagnostic output is used in all GEOS-Chem simulations; therefore, we have listed SpeciesConc first in the HISTORY.rc files that ship with each GEOS-Chem run directory.

Here is a sample definition section for the SpeciesConc collection. To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  SpeciesConc.template:       '%y4%m2%d2_%h2%n2z.nc4',
  SpeciesConc.format:         'CFIO',
  SpeciesConc.frequency:      00000100 000000
  SpeciesConc.duration:       00000100 000000
  SpeciesConc.mode:           'time-averaged'
  SpeciesConc.fields:         'SpeciesConc_?ADV?             ', 'GIGCchem',
::

This table describes the diagnostic quantities belonging to the SpeciesConc collection:

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
SpeciesConc_<spcname> Chemical species concentrations mol/mol dry air
  • ?ADV?
  • ?AER?
  • ?ALL?
  • ?DRY?
  • ?FIX?
  • ?GAS?
  • ?HYG?
  • ?KPP?
  • ?PHO?
  • ?VAR?
  • ?WET?
  • all simulations

--Bob Yantosca (talk) 19:43, 16 May 2018 (UTC)

The AerosolMass collection

The AerosolMass collection contains diagnostics for aerosol mass and particulate matter from full-chemistry simulations.

Here is a sample definition section for the AerosolMass collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  AerosolMass.template:       '%y4%m2%d2_%h2%n2z.nc4',
  AerosolMass.format:         'CFIO',
  AerosolMass.frequency:      00000100 000000
  AerosolMass.duration:       00000100 000000
  AerosolMass.mode:           'time-averaged'
  AerosolMass.fields:         'AerMassASOA                  ', 'GIGCchem',
                              'AerMassBC                    ', 'GIGCchem',
                              'AerMassINDIOL                ', 'GIGCchem',
                              'AerMassISN1OA                ', 'GIGCchem',
                              'AerMassISOA                  ', 'GIGCchem',
                              'AerMassLVOCOA                ', 'GIGCchem',
                              'AerMassNH4                   ', 'GIGCchem',
                              'AerMassNIT                   ', 'GIGCchem',
                              'AerMassOPOA                  ', 'GIGCchem',
                              'AerMassPOA                   ', 'GIGCchem',
                              'AerMassSAL                   ', 'GIGCchem',
                              'AerMassSO4                   ', 'GIGCchem',
                              'AerMassSOAGX                 ', 'GIGCchem',
                              'AerMassSOAIE                 ', 'GIGCchem',
                              'AerMassSOAME                 ', 'GIGCchem',
                              'AerMassSOAMG                 ', 'GIGCchem',
                              'AerMassTSOA                  ', 'GIGCchem',
                              'BetaNO                       ', 'GIGCchem',
                              'PM25                         ', 'GIGCchem',
                              'TotalBiogenicOA              ', 'GIGCchem',
                              'TotalOA                      ', 'GIGCchem',
                              'TotalOC                      ', 'GIGCchem',
::

This table describes the diagnostic quantities belonging to the AerosolMass collection:

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
AerMassTSOA Aerosol products of terpene oxidation ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
AerMassISOA Aerosol products of isoprene oxidation ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
AerMassTSOA Aerosol products of terpene oxidation ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
AerMassASOA Aerosol products of light aromatics + IVOC oxidation ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
AerMassPOA Aerosols from SVOCs ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
AerMassTSOA Aerosol products of terpene oxidation ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
AerMassOPOA Aerosol products of POG oxidation ug/m3
  • complexSOA_SVPOA
TotalOA Sum of all organic aerosol ug/m3
  • aerosol
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
  • Will probably be renamed to AerMassTotalOA for consistency with other diagnostics in this collection
TotalOC Sum of all organic carbon ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
  • Will probably be renamed to AerMassTotalOC for consistency with other diagnostics in this collection
BetaNO NO branching ratio ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • Will probably be renamed to AerMassBetaNO for consistency with other diagnostics in this collection
AerMassBC Black carbon (BCPI + BCPO) ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
AerMassSO4 Sulfate ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
AerMassNH4 Ammonium ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
AerMassNIT Nitrate ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
AerMassSAL Sea salt aerosol (SALA + SALC) ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
PM25 Particulate matter (r < 2.5 μm) ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
  • Will probably be renamed to AerMassBetaNO for consistency with other diagnostics in this collection
AerMassSOAGX Aerosol-phase glyoxal ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
AerMassSOAMG Aerosol-phase methylglyoxal ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
AerMassSOAIE Aerosol-phase IEPOX ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
AerMassSOAME Aerosol-phase IMAE ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • New in v11-02
AerMassINDIOL Generic aerosol-phase organonitrate hydrolysis product ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • New in v11-02
AerMassLVOCOA Aerosol-phase low-volatility non-IEPOX product of ISOPOOH (RIP) oxidation ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • New in v11-02
AerMassISN1OA Aerosol-phase 2nd generation hydroxynitrates formed from ISOP+NO3 reaction pathway ug/m3
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • New in v11-02

--Bob Yantosca (talk) 20:19, 16 May 2018 (UTC)

The Aerosols collection

The Aerosols collection contains diagnostics for aerosol optical depth and related quantities from full-chemistry simulations.

Here is a sample definition section for the Aerosols collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  Aerosols.template:          '%y4%m2%d2_%h2%n2z.nc4',
  Aerosols.format:            'CFIO',
  Aerosols.frequency:         00000100 000000
  Aerosols.duration:          00000100 000000
  Aerosols.mode:              'time-averaged'
  Aerosols.fields:            'AODDust                       ', 'GIGCchem',
                              'AODDustWL1_?DUSTBIN?          ', 'GIGCchem',
                              'AODHygWL1_?HYG?               ', 'GIGCchem',
                              'AODSOAfromAqIsopreneWL1       ', 'GIGCchem',
                              'AODStratLiquidAerWL1          ', 'GIGCchem',
                              'AODPolarStratCloudWL1         ', 'GIGCchem',
                              'AerHygroscopicGrowth_?HYG?    ', 'GIGCchem',
                              'AerNumDensityStratLiquid      ', 'GIGCchem',
                              'AerNumDensityStratParticulate ', 'GIGCchem',
                              'AerAqueousVolume              ', 'GIGCchem',
                              'AerSurfAreaDust               ', 'GIGCchem',
                              'AerSurfAreaHyg_?HYG?          ', 'GIGCchem',
                              'AerSurfAreaStratLiquid        ', 'GIGCchem',
                              'AerSurfAreaPolarStratCloud    ', 'GIGCchem',
                              'Chem_AeroAreaMDUST1           ', 'GIGCchem',
                              'Chem_AeroAreaMDUST2           ', 'GIGCchem',
                              'Chem_AeroAreaMDUST3'          ', 'GIGCchem',
                              'Chem_AeroAreaMDUST4           ', 'GIGCchem',
                              'Chem_AeroAreaMDUST5           ', 'GIGCchem',
                              'Chem_AeroAreaMDUST6           ', 'GIGCchem',
                              'Chem_AeroAreaMDUST7           ', 'GIGCchem',
                              'Chem_AeroAreaSULF             ', 'GIGCchem',
                              'Chem_AeroAreaBC               ', 'GIGCchem',
                              'Chem_AeroAreaOC               ', 'GIGCchem',
                              'Chem_AeroAreaSSA              ', 'GIGCchem',
                              'Chem_AeroAreaSSC              ', 'GIGCchem',
                              'Chem_AeroAreaBGSULF           ', 'GIGCchem',
                              'Chem_AeroAreaICEI             ', 'GIGCchem',
                              'Chem_AeroRadiMDUST1           ', 'GIGCchem',
                              'Chem_AeroRadiMDUST2           ', 'GIGCchem',
                              'Chem_AeroRadiMDUST3           ', 'GIGCchem',
                              'Chem_AeroRadiMDUST4           ', 'GIGCchem',
                              'Chem_AeroRadiMDUST5           ', 'GIGCchem',
                              'Chem_AeroRadiMDUST6           ', 'GIGCchem',
                              'Chem_AeroRadiMDUST7           ', 'GIGCchem',
                              'Chem_AeroRadiSULF             ', 'GIGCchem',
                              'Chem_AeroRadiBC               ', 'GIGCchem',
                              'Chem_AeroRadiOC               ', 'GIGCchem',
                              'Chem_AeroRadiSSA              ', 'GIGCchem',
                              'Chem_AeroRadiSSC              ', 'GIGCchem',
                              'Chem_AeroRadiBGSULF           ', 'GIGCchem',
                              'Chem_AeroRadiICEI             ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST1        ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST2        ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST3        ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST4        ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST5        ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST6        ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST7        ', 'GIGCchem',
                              'Chem_WetAeroAreaSULF          ', 'GIGCchem',
                              'Chem_WetAeroAreaBC            ', 'GIGCchem',
                              'Chem_WetAeroAreaOC            ', 'GIGCchem',
                              'Chem_WetAeroAreaSSA           ', 'GIGCchem',
                              'Chem_WetAeroAreaSSC           ', 'GIGCchem',
                              'Chem_WetAeroAreaBGSULF        ', 'GIGCchem',
                              'Chem_WetAeroAreaICEI          ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST1        ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST2        ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST3        ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST4        ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST5        ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST6        ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST7        ', 'GIGCchem',
                              'Chem_WetAeroRadiSULF          ', 'GIGCchem',
                              'Chem_WetAeroRadiBC            ', 'GIGCchem',
                              'Chem_WetAeroRadiOC            ', 'GIGCchem',
                              'Chem_WetAeroRadiSSA           ', 'GIGCchem',
                              'Chem_WetAeroRadiSSC           ', 'GIGCchem',
                              'Chem_WetAeroRadiBGSULF        ', 'GIGCchem',
                              'Chem_WetAeroRadiICEI          ', 'GIGCchem',
                              'Chem_StatePSC                 ', 'GIGCchem',
                              'Chem_KhetiSLAN2O5H2O          ', 'GIGCchem',
                              'Chem_KhetiSLAN2O5HCl          ', 'GIGCchem',
                              'Chem_KhetiSLAClNO3H2O         ', 'GIGCchem',
                              'Chem_KhetiSLAClNO3HCl         ', 'GIGCchem',
                              'Chem_KhetiSLAClNO3HBr         ', 'GIGCchem',
                              'Chem_KhetiSLABrNO3H2O         ', 'GIGCchem',
                              'Chem_KhetiSLABrNO3HCl         ', 'GIGCchem',
                              'Chem_KhetiSLAHOClHCl          ', 'GIGCchem',
                              'Chem_KhetiSLAHOClHBr          ', 'GIGCchem',
                              'Chem_KhetiSLAHOBrHCl          ', 'GIGCchem',
                              'Chem_KhetiSLAHOBrHBr          ', 'GIGCchem',
::

This table describes the diagnostic quantities belonging to the Aerosols collection:

NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).

NOTE: UCX fullchem refers to all full-chemistry simulations that use UCX (i.e. benchmark, standard, aciduptake, marinePOA).

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
AODDust Mineral dust optical depth for 1st wavelength specified in Radiation Menu 1
  • all fullchem
  • aerosol
AODDust_WL1_?DUSTBIN? AOD for 1st wavelength specified in Radiation Menu, for each dust bin 1 ?DUSTBIN?
  • all fullchem
  • aerosol
AODHygWL1_<spcname> Optical depth for selected species (SO4, BC, OC, SALA, SALC) at the 1st wavelength specified in the Radiation Menu 1 ?HYG?
  • all fullchem
  • aerosol
AODSOAfromAqIsopreneWL1 Optical depth of SOA from aqueous isoprene optical depth 1
  • benchmark
  • complexSOA*
  • New in v11-02
AODStratLiquidAerWL1 Stratospheric liquid aerosol optical depth (600 nm)
  • UCX fullchem
  • New in v11-02
AODPolarStratCloudWL1 Polar stratospheric cloud type 1a/2 optical depth (600 nm) 1
  • UCX fullchem
AerHygroscopicGrowth_<spcname> Hygroscopic growth of selected species (SO4, BC, OC, SALA, SALC) 1 ?HYG?
  • all fullchem
  • aerosol
AerNumDensityStratLiquid Stratospheric liquid aerosol number density (UCX simulation only) 1/cm3
  • UCX fullchem
AerSurfAreaStratLiquid Stratospheric liquid aerosol surface area (UCX simulation only) cm2/cm3
  • UCX fullchem
AerSurfAreaPolarStratCloud Polar stratospheric cloud type 1a/2 surface area (UCX simulation only) cm2/cm3
  • UCX fullchem
Chem_AeroAreaMDUST1 Dry aerosol area for mineral dust (bin Reff = 0.15 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_AeroAreaMDUST2 Dry aerosol area for mineral dust (bin Reff = 0.25 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_AeroAreaMDUST3 Dry aerosol area for mineral dust (bin Reff = 0.4 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_AeroAreaMDUST4 Dry aerosol area for mineral dust (bin Reff = 0.8 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_AeroAreaMDUST5 Dry aerosol area for mineral dust (bin Reff = 1.5 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_AeroAreaMDUST6 Dry aerosol area for mineral dust (bin Reff = 2.5 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_AeroAreaMDUST7 Dry aerosol area for mineral dust (bin Reff = 4.0 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_AeroAreaSULF Dry aerosol area for sulfate cm2/cm3
  • all fullchem
  • aerosol
Chem_AeroAreaBC Dry aerosol area for black carbon cm2/cm3
  • all fullchem
  • aerosol
Chem_AeroAreaOC Dry aerosol area for organic carbon cm2/cm3
  • all fullchem
  • aerosol
Chem_AeroAreaSSA Dry aerosol area for sea salt, accumulation mode cm2/cm3
  • all fullchem
  • aerosol
Chem_AeroAreaSSA Dry aerosol area for sea salt, coarse mode cm2/cm3
  • all fullchem
  • aerosol
Chem_AeroAreaBGSULF Dry aerosol area for background stratospheric sulfate cm2/cm3
  • UCX fullchem
Chem_AeroAreaICEI Dry aerosol area for irregular ice cloud (Mischenko) cm2/cm3
  • UCX fullchem
Chem_AeroRadiMDUST1 Dry aerosol radius for mineral dust (bin Reff = 0.15 μm) cm
  • all fullchem
  • aerosol
Chem_AeroRadiMDUST2 Dry aerosol radius for mineral dust (bin Reff = 0.25 μm) cm
  • all fullchem
  • aerosol
Chem_AeroRadiMDUST3 Dry aerosol radius for mineral dust (bin Reff = 0.4 μm) cm
  • all fullchem
  • aerosol
Chem_AeroRadiMDUST4 Dry aerosol radius for mineral dust (bin Reff = 0.8 μm) cm
  • all fullchem
  • aerosol
Chem_AeroRadiMDUST5 Dry aerosol radius for mineral dust (bin Reff = 1.5 μm) cm
  • all fullchem
  • aerosol
Chem_AeroRadiMDUST6 Dry aerosol radius for mineral dust (bin Reff = 2.5 μm) cm
  • all fullchem
  • aerosol
Chem_AeroRadiMDUST7 Dry aerosol radius for mineral dust (bin Reff = 4.0 μm) cm
  • all fullchem
  • aerosol
Chem_AeroRadiSULF Dry aerosol radius for sulfate cm
  • all fullchem
  • aerosol
Chem_AeroRadiBC Dry aerosol radius for black carbon cm
  • all fullchem
  • aerosol
Chem_AeroRadiOC Dry aerosol radius for organic carbon cm
  • all fullchem
  • aerosol
Chem_AeroRadiSSA Dry aerosol radius for sea salt, accumulation mode cm
  • all fullchem
  • aerosol
Chem_AeroRadiusSSC Dry aerosol radius for sea salt, coarse mode cm
  • all fullchem
  • aerosol
Chem_AeroRadiBGSULF Dry aerosol radius for background stratospheric sulfate cm
  • UCX fullchem
Chem_AeroRadiusICEI Dry aerosol radius for irregular ice cloud (Mischenko) cm
  • UCX fullchem
Chem_WetAeroAreaMDUST1 Wet aerosol area for mineral dust (bin Reff = 0.15 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_WetAeroAreaMDUST2 Wet aerosol area for mineral dust (bin Reff = 0.25 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_WetAeroAreaMDUST3 Wet aerosol area for mineral dust (bin Reff = 0.4 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_WetAeroAreaMDUST4 Wet aerosol area for mineral dust (bin Reff = 0.8 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_WetAeroAreaMDUST5 Wet aerosol area for mineral dust (bin Reff = 1.5 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_WetAeroAreaMDUST6 Wet aerosol area for mineral dust (bin Reff = 2.5 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_WetAeroAreaMDUST7 Wet aerosol area for mineral dust (bin Reff = 4.0 μm) cm2/cm3
  • all fullchem
  • aerosol
Chem_WetAeroAreaSULF Wet aerosol area for sulfate cm2/cm3
  • all fullchem
  • aerosol
Chem_WetAeroAreaBC Wet aerosol area for black carbon cm2/cm3
  • all fullchem
  • aerosol
Chem_WetAeroAreaOC Wet aerosol area for organic carbon cm2/cm3
  • all fullchem
  • aerosol
Chem_WetAeroAreaSSA Wet aerosol area for sea salt, accumulation mode cm2/cm3
  • all fullchem
  • aerosol
Chem_WetAeroAreaSSA Wet aerosol area for sea salt, coarse mode cm2/cm3
  • all fullchem
  • aerosol
Chem_WetAeroAreaBGSULF Wet aerosol area for background stratospheric sulfate cm2/cm3
  • UCX fullchem
Chem_WetAeroAreaICEI Wet aerosol area for irregular ice cloud (Mischenko) cm2/cm3
  • UCX fullchem
Chem_WetAeroRadiMDUST1 Wet aerosol radius for mineral dust (bin Reff = 0.15 μm) cm
  • all fullchem
  • aerosol
Chem_WetAeroRadiMDUST2 Wet aerosol radius for mineral dust (bin Reff = 0.25 μm) cm
  • all fullchem
  • aerosol
Chem_WetAeroRadiMDUST3 Wet aerosol radius for mineral dust (bin Reff = 0.4 μm) cm
  • all fullchem
  • aerosol
Chem_WetAeroRadiMDUST4 Wet aerosol radius for mineral dust (bin Reff = 0.8 μm) cm
  • all fullchem
  • aerosol
Chem_WetAeroRadiMDUST5 Wet aerosol radius for mineral dust (bin Reff = 1.5 μm) cm
  • all fullchem
  • aerosol
Chem_WetAeroRadiMDUST6 Wet aerosol radius for mineral dust (bin Reff = 2.5 μm) cm
  • all fullchem
  • aerosol
Chem_WetAeroRadiMDUST7 Wet aerosol radius for mineral dust (bin Reff = 4.0 μm) cm
  • all fullchem
  • aerosol
Chem_WetAeroRadiSULF Wet aerosol radius for sulfate cm
  • all fullchem
  • aerosol
Chem_WetAeroRadiBC Wet aerosol radius for black carbon cm
  • all fullchem
  • aerosol
Chem_WetAeroRadiOC Wet aerosol radius for organic carbon cm
  • all fullchem
  • aerosol
WetChem_AeroRadiSSA Wet aerosol radius for sea salt, accumulation mode cm
  • all fullchem
  • aerosol
Chem_WetAeroRadiusSSC Wet aerosol radius for sea salt, coarse mode cm
  • all fullchem
  • aerosol
Chem_WetAeroRadiBGSULF Wet aerosol radius for background stratospheric sulfate cm
  • UCX fullchem
Chem_WetAeroRadiusICEI Wet aerosol radius for irregular ice cloud (Mischenko) cm
  • UCX fullchem
Chem_StatePSC Polar stratospheric cloud type (cf Kirner et al, 2011, GMD) count
  • UCX fullchem
Chem_KhetiSLAN2O5H2O Sticking coeff. for N2O5 + H2O rxn 1
  • UCX fullchem
Chem_KhetiSLAN2O5HCl Sticking coeff. for N2O5 + HCl rxn 1
  • UCX fullchem
Chem_KhetiSLAClNO3H2O Sticking coeff. for ClNO3 + H2O rxn 1
  • UCX fullchem
Chem_KhetiSLAClNO3HCl Sticking coeff. for ClNO3 + HCl rxn 1
  • UCX fullchem
Chem_KhetiSLAClNO3HBr Sticking coeff. for ClNO3 + HBr rxn 1
  • UCX fullchem
Chem_KhetiSLABrNO3H2O Sticking coeff. for BrNO3 + H2O rxn 1
  • UCX fullchem
Chem_KhetiSLABrNO3HCl Sticking coeff. for BrNO3 + HCl rxn 1
  • UCX fullchem
Chem_KhetiSLAHOClHCl Sticking coeff. for HOCl + HCl rxn 1
  • UCX fullchem
Chem_KhetiSLAHOClBr Sticking coeff. for HOCl + HBr rxn 1
  • UCX fullchem
Chem_KhetiSLAHOBrHCl Sticking coeff. for HOBr + HCl rxn 1
  • UCX fullchem
Chem_KhetiSLAHOBrHCl Sticking coeff. for HOBr + HBr rxn 1
  • UCX fullchem

--Bob Yantosca (talk) 19:07, 7 June 2018 (UTC)

The Budget collection

The Budget diagnostic collection was introduced in GEOS-Chem 12.1.0. It is a 2D diagnostic containing the mass tendencies per grid cell, in kg/s, for each species within a region of the column and across each GEOS-Chem component. The diagnostic is calculated by taking the difference in vertically summed column mass before and after major GEOS-Chem components.

There are three column regions defined for this diagnostic: troposphere-only, PBL-only, and full column. By post-processing this diagnostic you can calculate global mass change or mass change across regions by summing the diagnostic values for the relevant grid cells. You can also retrieve the mass change across a longer chunk of time by multiplying the time-averaged output by the number of seconds in the averaging period.

While there are seven major components in GEOS-Chem, there are only six implemented for the budget diagnostics. Emissions and dry deposition components are combined together for this diagnostic because of the way they are applied at the same time. Furthermore, if using non-local PBL mixing then the emissions and dry deposition budget diagnostic will not capture all fluxes from these sources and sinks. This is because emissions and dry deposition tendencies below the PBL are applied within mixing instead. When using full mixing, however, mixing and emissions/dry deposition budget diagnostics are fully separated.

Here is a sample definition section for the Budget collection such that 1-month averages are output per species. To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name. This will prevent the diagnostic arrays from being initialized and therefore reduce required memory. You may also replace the species wildcards with individual species names, e.g. BudgetChemistryFull_O3 for full column ozone.

# %%%%% THE Budget COLLECTION %%%%% 
#
GEOS-Chem budget diagnostics defined as species kg/s in the column 
# (full, troposphere, or PBL) due to a single component (e.g. chemistry)
# (default = advected species)
#
# Available for all simulations
#==============================================================================
 Budget.template:     '%y4%m2%d2_%h2%n2z.nc4',
 Budget.format:       'CFIO',
 Budget.frequency:    00000100 000000
 Budget.duration:     00000100 000000
 Budget.mode:         'time-averaged'
 Budget.fields:      'BudgetChemistryFull_?ADV?            ', 'GIGCchem',
                      'BudgetChemistryPBL_?ADV?             ', 'GIGCchem',
                      'BudgetChemistryTrop_?ADV?            ', 'GIGCchem',
                      'BudgetEmisDepFull_?ADV?              ', 'GIGCchem',
                      'BudgetEmisDepTrop_?ADV?              ', 'GIGCchem',
                      'BudgetEmisDepPBL_?ADV?               ', 'GIGCchem',
                      'BudgetTransportFull_?ADV?            ', 'GIGCchem',
                      'BudgetTransportTrop_?ADV?            ', 'GIGCchem',
                      'BudgetTransportPBL_?ADV?             ', 'GIGCchem',
                      'BudgetMixingFull_?ADV?               ', 'GIGCchem',
                      'BudgetMixingTrop_?ADV?               ', 'GIGCchem',
                      'BudgetMixingPBL_?ADV?                ', 'GIGCchem',
                      'BudgetConvectionFull_?ADV?           ', 'GIGCchem',
                      'BudgetConvectionTrop_?ADV?           ', 'GIGCchem',
                      'BudgetConvectionPBL_?ADV?            ', 'GIGCchem',
                      'BudgetWetDepFull_?WET?               ', 'GIGCchem',
                      'BudgetWetDepTrop_?WET?               ', 'GIGCchem',
                      'BudgetWetDepPBL_?WET?                ', 'GIGCchem',

This table describes the diagnostic quantities belonging to the Budget collection:

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
BudgetXY_<spcname> Mass tendency across component X in column region Y kg/s
  • ?ADV?
  • ?WET?

All simulations

None

Components X include:

  • Chemistry
  • Transport (GEOS-Chem Classic only)
  • Mixing1
  • Convection
  • Wet deposition
  • Emissions and dry deposition2

Column regions Y include:

  • Troposphere (Trop)
  • PBL-only (PBL)
  • Full column (Full)

1The mixing budget diagnostics includes the application of emissions and dry deposition below the PBL if using the non-local PBL mixing scheme (vdiff).
2The emissions and dry deposition budget diagnostics will not capture all fluxes if using the non-local PBL mixing scheme since these tendencies are applied within mixing in vdiff_mod below the PBL. When using full mixing, however, mixing and emissions/dry deposition are fully separated.

--Lizzie Lundgren (talk) 21:33, 9 October 2018 (UTC)

The CloudConvFlux collection

The CloudConvFlux collection contains diagnostics for mass fluxes in cloud convection.

Here is a sample definition section for the CloudConvFlux collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  CloudConvFlux.template:     '%y4%m2%d2_%h2%n2z.nc4',
  CloudConvFlux.format:       'CFIO',
  CloudConvFlux.frequency:    00000100 000000
  CloudConvFlux.duration:     00000100 000000
  CloudConvFlux.mode:         'time-averaged'
  CloudConvFlux.fields:       'CloudConvFlux_?ADV?           ', 'GIGCchem',
::

This table describes the diagnostic quantities belonging to the CloudConvFlux collection:

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
CloudConvFlux_<spcname> Mass change due to cloud convection kg/s
  • ?ADV?
  • ?GAS?
  • ?WET?
  • all simulations
  • Will soon be replaced by new flux diagnostics

--Bob Yantosca (talk) 19:18, 7 June 2018 (UTC)

The ConcAfterChem collection

The ConcAfterChem collection contains diagnostics for OH, HO2, etc. species immediately upon exiting the FlexChem solver.

Here is a sample definition section for the ConcAfterChem collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  ConcAfterChem.template:     '%y4%m2%d2_%h2%n2z.nc4',
  ConcAfterChem.format:       'CFIO',
  ConcAfterChem.frequency:    00000100 000000
  ConcAfterChem.duration:     00000100 000000
  ConcAfterChem.mode:         'time-averaged'
  ConcAfterChem.fields:       'OHconcAfterChem                ', 'GIGCchem',  
                              'HO2concAfterChem               ', 'GIGCchem',  
                              'O1DconcAfterChem               ', 'GIGCchem',  
                              'O3PconcAfterChem               ', 'GIGCchem',  
::

This table describes the diagnostic quantities belonging to the ConcAfterChem collection:

NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).

NOTE: UCX fullchem refers to all full-chemistry simulations that use UCX (i.e. benchmark, standard, aciduptake, marinePOA).

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
OHconcAfterChem OH concentration immediately after exiting the FlexChem solver molec/cm3
  • all fullchem
HO2concAfterChem HO2 concentration immediately after exiting the FlexChem solver molec/cm3
  • all fullchem
O1DconcAfterChem O1D concentration immediately after exiting the FlexChem solver molec/cm3
  • UCX fullchem
O3PconcAfterChem O3P concentration immediately after exiting the FlexChem solver molec/cm3
  • UCX fullchem

--Bob Yantosca (talk) 19:12, 7 June 2018 (UTC)

The DryDep collection

The DryDep collection contains diagnostics for the flux and velocity of each species lost to dry-deposition.

Here is a sample definition section for the DryDep collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  DryDep.template:            '%y4%m2%d2_%h2%n2z.nc4',
  DryDep.format:              'CFIO',
  DryDep.frequency:           00000100 000000
  DryDep.duration:            00000100 000000
  DryDep.mode:                'time-averaged'
  DryDep.fields:              'DryDepVel_?DRY?               ', 'GIGCchem',
                              'DryDepMix_?DRY?               ', 'GIGCchem',
                              'DryDepChm_?DRY?               ', 'GIGCchem',
                              'DryDep_?DRY?                  ', 'GIGCchem',
::

This table describes the diagnostic quantities belonging to the DryDep collection:

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
DryDepVel_<spcname> Dry deposition velocity cm/s
  • ?DRY?
  • all simulations with drydep species
DryDepMix_<spcname> Dry deposition flux
(computed in PBL mixing)
molec/cm2/s
  • ?DRY?
  • all simulations with drydep species
DryDepChm_<spcname> Dry deposition flux
(computed in chemistry)
molec/cm2/s
  • ?DRY?
  • all simulations with drydep species
DryDep_<spcname> Total dry deposition flux molec/cm2/s
  • ?DRY?
  • all simulations with drydep species
  • Sum of drydep flux in mixing and drydep flux in chemistry.

--Bob Yantosca (talk) 20:33, 16 May 2018 (UTC)

The JValues collection

The JValues collection contains diagnostics for photolysis rates for various chemical species, obtained from the FAST-JX photolysis mechanism.

Here is a sample definition section for the JValues collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  JValues.template:           '%y4%m2%d2_%h2%n2z.nc4',
  JValues.format:             'CFIO',
  JValues.frequency:          00000000 010000
  JValues.duration:           00000000 010000
  JValues.mode:               'instantaneous'
  JValues.fields:             'Jval_?PHO?                    ', 'GIGCchem',
::

This table describes the diagnostic quantities belonging to the JValues collection:

NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
Jval_<spcname> Photolysis rates 1/s
  • ?PHO?
  • all fullchem
  • We recommend using saving out instantaneous values with this collection.

--Bob Yantosca (talk) 20:38, 16 May 2018 (UTC)

The JValuesLocalNoon collection

NOTE: At present, we are debugging an issue in how the noontime J-values are archived for netCDF. Until further notice, we recommend that you use the ND22 bpch diagnostic to archive noontime J-values. (Bob Yantosca, 16 May 2018)

The JValuesLocalNoon collection contains diagnostics for photolysis rates for various chemical species, obtained from the FAST-JX photolysis mechanism, at the grid box where it is nearest to local solar noon.

Here is a sample definition section for the JValuesLocalNoon collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  JValuesLocalNoon.template:           '%y4%m2%d2_%h2%n2z.nc4',
  JValuesLocalNoon.format:             'CFIO',
  JValuesLocalNoon.frequency:          00000100 000000
  JValuesLocalNoon.duration:           00000100 000000
  JValuesLocalNoon.mode:               'time-averaged'
  JValuesLocalNoon.fields:             'JNoon_?PHO?                    ', 'GIGCchem',
::

This table describes the diagnostic quantities belonging to the JValuesLocalNoon collection:

NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
JNoon_<spcname> Photolysis rates (archived where it is local noon) 1/s
  • ?PHO?
  • all fullchem
  • Currently debgugging an issue with locating the nearest box to noontime.

--Bob Yantosca (talk) 21:07, 16 May 2018 (UTC)

The LevelEdgeDiags collection

The LevelEdgeDiags collection contains diagnostics for quantities (mostly met fields) that are defined on the vertical edges of each grid box. According to the COARDS convention, all of the data variables in a netCDF file must be defined with the same vertical dimension.

Here is a sample definition section for the LevelEdgeDiags collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  LevelEdgeDiags.template:    '%y4%m2%d2_%h2%n2z.nc4',
  LevelEdgeDiags.format:      'CFIO',
  LevelEdgeDiags.frequency:   00000100 000000
  LevelEdgeDiags.duration:    00000100 000000
  LevelEdgeDiags.mode:        'time-averaged'
  LevelEdgeDiags.fields:      'Met_CMFMC                     ', 'GIGCchem',
                              'Met_PEDGE                     ', 'GIGCchem',
                              'Met_PEDGEDRY                  ', 'GIGCchem',
                              'Met_PFICU                     ', 'GIGCchem',
                              'Met_PFILSAN                   ', 'GIGCchem',
                              'Met_PFLCU                     ', 'GIGCchem',
                              'Met_PFLLSAN                   ', 'GIGCchem',
::

This table describes the diagnostic quantities belonging to the JValuesLocalNoon collection:

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
Met_CMFMC Upward moist convective mass flux kg/m2/s
  • all simulations
Met_PEDGE Surface pressure at level edges (based on moist air) hP
  • all simulations
Met_PEDGEDRY Surface pressure at level edges (based on dry air) hP
  • all simulations
Met_PFICU 3d flux of ice convective precipitation kg/m2/s
  • all simulations
Met_PFILSAN 3d flux of ice non-convective precipitation kg/m2/s
  • all simulations
Met_PFLCU 3d flux of liquid convective precipitation kg/m2/s
  • all simulations
Met_PFLLSAN 3d flux of liquid non-convective precipitation kg/m2/s
  • all simulations

--Bob Yantosca (talk) 21:23, 16 May 2018 (UTC)

The POPS collection

NOTE: This collection is currently under development and is slated to be introduced into GEOS-Chem 12.1.0.

The POPS collection contains diagnostic quantities for the Persistent Organic Pollutants (aka POPs) specialty simulation.

Here is a sample definition section for the POPS collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  POPS.template:         '%y4%m2%d2_%h2%n2z.nc4',
  POPS.format:           'CFIO',
  POPS.frequency:        00000100 000000
  POPS.duration:         00000100 000000
  POPS.mode:             'time-averaged'
  POPS.fields:           'EmisPOPPOCPO                       ', 'GIGCchem',
                         'EmisPOPPBCPO                       ', 'GIGCchem',
                         'EmisPOPG                           ', 'GIGCchem',
                         'EmisPOPGfromSoil                   ', 'GIGCchem',
                         'EmisPOPGfromLake                   ', 'GIGCchem',
                         'EmisPOPGfromLeaf                   ', 'GIGCchem',
                         'FluxPOPGfromSoilToAir              ', 'GIGCchem',
                         'FluxPOPGfromAirToSoil              ', 'GIGCchem',
                         'FluxPOPGfromLakeToAir              ', 'GIGCchem',
                         'FluxPOPGfromAirtoLake              ', 'GIGCchem',
                         'FluxPOPGfromLeafToAir              ', 'GIGCchem',
                         'FluxPOPGfromAirToLeaf              ', 'GIGCchem',
                         'FugacitySoilToAir                  ', 'GIGCchem',
                         'FugacityLakeToAir                  ', 'GIGCchem',
                         'FugacityLeafToAir                  ', 'GIGCchem',
                         'LossPOPPOCPObyGasPhase             ', 'GIGCchem',
                         'ProdPOPPOCPOfromGasPhase           ', 'GIGCchem',
                         'LossPOPPBPOCbyGasPhase             ', 'GIGCchem',
                         'ProdPOPPBCPOfromGasPhase           ', 'GIGCchem',
                         'ProdPOPGfromOH                     ', 'GIGCchem',
                         'ProdPOPPOCPOfromO3                 ', 'GIGCchem',
                         'ProdPOPPOCPIfromO3                 ', 'GIGCchem',
                         'ProdPOPPBCPIfromO3                 ', 'GIGCchem',
                         'ProdPOPPBCPOfromO3                 ', 'GIGCchem',
                         'ProdPOPPOCPOfromNO3                ', 'GIGCchem',
                         'ProdPOPPOCPIfromNO3                ', 'GIGCchem',
                         'ProdPOPPBCPIfromNO3                ', 'GIGCchem',
                         'ProdPOPPBCPOfromNO3                ', 'GIGCchem',
  :: 
Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
EmisPOPPOCPO Particulate (hydrophobic organic carbon) POPS emissions kg/m2/s
  • POPs
  • TBA in 12.1.0
EmisPOPPBCPO Particulate (hydrophobic black carbon) POPS emissions kg/m2/s
  • POPs
  • TBA in 12.1.0
EmisPOPG POPG (gas-phase) POPS emissions kg/m2/s
  • POPs
  • TBA in 12.1.0
EmisPOPGfromSoil Secondary emission of POPG from soils kg/s
  • POPs
  • TBA in 12.1.0
EmisPOPGfromLake Secondary emission of POPG from lakes kg/s
  • POPs
  • TBA in 12.1.0
EmisPOPGfromLeaf Secondary emission of POPG from leaves kg/m2/s
  • POPs
  • TBA in 12.1.0
FluxPOPGfromSoilToAir Secondary (positive) flux of POPG from soils to air ng/m2/day
  • POPs
  • TBA in 12.1.0
FluxPOPGfromAirToSoil Secondary (negative) flux of POPG from air to soil ng/m2/day
  • POPs
  • TBA in 12.1.0
FluxPOPGfromLakeToAir Secondary (positive) flux of POPG from lakes to air ng/m2/day
  • POPs
  • TBA in 12.1.0
FluxPOPGfromAirToLake Secondary (negative) flux of POPG from air to lakes ng/m2/day
  • POPs
  • TBA in 12.1.0
FluxPOPGfromLeafToAir Secondary (positive) flux of POPG from leaves to air ng/m2/day
  • POPs
  • TBA in 12.1.0
FluxPOPGfromAirToLeaf Secondary (negative) flux of POPG from air to leaves ng/m2/day
  • POPs
  • TBA in 12.1.0
FugacitySoilToAir Fugacity ratio: soil/air 1
  • POPs
  • TBA in 12.1.0
FugacityLakeToAir Fugacity ratio: lake/air 1
  • POPs
  • TBA in 12.1.0
FugacityLeafToAir Fugacity ratio: leaf/air 1
  • POPs
  • TBA in 12.1.0
LossPOPPOCPObyGasPhase Gross POP OC lost to gas kg/s
  • POPs
  • TBA in 12.1.0
LossPOPPOCPObyGasPhase Gross POP OC produced from gas kg/s
  • POPs
  • TBA in 12.1.0
LossPOPPBCPObyGasPhase Gross POP BC lost to gas kg/s
  • POPs
  • TBA in 12.1.0
LossPOPPBCPObyGasPhase Gross POP BC produced from gas kg/s
  • POPs
  • TBA in 12.1.0
ProdPOPGfromOH Production of oxidized POPG from reaction with OH kg/s
  • POPs
  • TBA in 12.1.0
ProdPOPPOCPOfromO3 Production of oxidized POPPOCPO from reaction with O3 kg/s
  • POPs
  • TBA in 12.1.0
ProdPOPPOCPIfromO3 Production of oxidized POPPOCPI from reaction with O3 kg/s
  • POPs
  • TBA in 12.1.0
ProdPOPPBCPOfromO3 Production of oxidized POPPBCPO from reaction with O3 kg/s
  • POPs
  • TBA in 12.1.0
ProdPOPPBCPIfromO3 Production of oxidized POPPBCPI from reaction with O3 kg/s
  • POPs
  • TBA in 12.1.0
ProdPOPPOCPOfromNO3 Production of oxidized POPPOCPO from reaction with NO3 kg/s
  • POPs
  • TBA in 12.1.0
ProdPOPPOCPIfromNO3 Production of oxidized POPPOCPI from reaction with NO3 kg/s
  • POPs
  • TBA in 12.1.0
ProdPOPPBCPOfromNO3 Production of oxidized POPPBCPO from reaction with NO3 kg/s
  • POPs
  • TBA in 12.1.0
ProdPOPPBCPIfromNO3 Production of oxidized POPPBCPI from reaction with NO3 kg/s
  • POPs
  • TBA in 12.1.0

--Bob Yantosca (talk) 18:09, 17 October 2018 (UTC)

The ProdLoss Collection

The ProdLoss collection contains chemical production and loss rates.

Here is a sample definition section for the ProdLoss collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

NOTE: This example is for the benchmark simulation. Some quantities in this collection are not applicable to certain simulations.

  ProdLoss.template:          '%y4%m2%d2_%h2%n2z.nc4',
  ProdLoss.format:            'CFIO',
  ProdLoss.frequency:         00000100 000000
  ProdLoss.duration:          00000100 000000
  ProdLoss.mode:              'time-averaged'
  ProdLoss.fields:            'Prod_?PRD?                    ', 'GIGCchem', 
                              'ProdBCPIfromBCPO              ', 'GIGCchem', 
                              'ProdOCPIfromOCPO              ', 'GIGCchem',
                              'ProdSO4fromH2O2inCloud        ', 'GIGCchem',
                              'ProdSO4fromO2inCloudMetal     ', 'GIGCchem',
                              'ProdSO4fromO3inCloud          ', 'GIGCchem',
                              'ProdSO4fromO3inSeaSalt        ', 'GIGCchem',
                              'ProdSO4fromHOBrInCloud        ', 'GIGCchem',
                              'ProdSO4fromSRO3               ', 'GIGCchem',
                              'ProdSO4fromSRHObr             ', 'GIGCchem',
                              'ProdSO4fromO3s                ', 'GIGCchem',
                              'Loss_?LOS?                    ', 'GIGCchem',
                              'LossHNO3onSeaSalt             ', 'GIGCchem',
::

The table below describes diagnostic quantities belonging to the ProdLoss collection.

NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
Diagnostics applicable only to the aciduptake simulation
ProdSO4fromOxidationOnDust Production of SO4 from oxidation on dust aerosols kg S/s
  • aciduptake
ProdNITfromHNO3uptakeOnDust Production of NIT from HNO3 uptake on dust aerosols kg N/s
  • aciduptake
ProdSO4fromUptakeOfH2SO4g Production of SO4 from uptake of H2SO4(g) kg S/s
  • aciduptake
Diagnostics applicable only to the aerosol-only simulation
ProdSO2fromDMSandOH Production of SO2 from DMS + OH (in sulfate_mod.F) kg S/s
  • aerosol
ProdSO2fromDMSandNO3 Production of SO2 from DMS + NO3R kg S/s
  • aerosol
ProdSO2fromDMS Total P(SO2) from DMS kg S/s
  • aerosol
ProdMSAfromDMS Production of MSA from DMS kg S/s
  • aerosol
ProdSO4fromGasPhase Production of SO4 in the gas phase kg S/s
  • aerosol
Diagnostics applicable only to the aerosol-only and all fullchem simulations
ProdBCPIfromBCPO Production of hydrophilic BC from hydrophobic BCs kg
  • aerosol
  • all fullchem
ProdOCPIfromOCPO Production of hydrophilic BC from hydrophobic BCs kg
  • aerosol
  • all fullchem
ProdSO4fromH2O2inCloud Production of SO4 from aqueous oxidation of H2O2 in clouds kg S/s
  • aerosol
  • all fullchem
ProdSO4fromO2inCloudMetal Production of SO4 from aqueous oxidation of O2 from metals in cloud kg S/s
  • aerosol
  • all fullchem
  • New in v11-02
ProdSO4fromO3inCloud Production of SO4 from aqueous oxidation of O3 in clouds kg S/s
  • aerosol
  • all fullchem
ProdSO4fromO3inSeaSalt Production of SO4 from O3 in sea salt kg S/s
  • aerosol
  • all fullchem
ProdSO4fromO3s Production of SO4 from aqueous phase SO3-- loss by OH kg S/s
  • aerosol
  • all fullchem
  • New in v11-02
ProdSO4fromSRO3 Production of SO4 from sulfur production rate of O3 kg S/s
  • aerosol
  • all fullchem
  • New in v11-02
LossHNO3onSeaSalt Loss of HNO3 on sea salt aerosols kg S/s
  • aerosol
  • all fullchem
Diagnostics applicable only to full-chemistry simulations
ProdSO4fromHOBrinCloud Production of SO4 from aqueous oxidation of HOBr in clouds kg S/s
  • all fullchem
  • New in v11-02
ProdSO4fromSRHOBr Production of SO4 from sulfur production rate of HOBr+O3 kg S/s
  • all fullchem
  • New in v11-02
Diagnostics for production and loss of species or chemical families (e.g. Ox)
Prod_<spcname> Chemical production for a given species or family molec/cm3/s
  • ?PRD?
  • all fullchem
  • tagCO
  • tagO3
Loss_<spcname> Chemical loss for a given species or family molec/cm3/s
  • ?LOS?
  • all fullchem
  • tagCO
  • tagO3

--Bob Yantosca (talk) 19:25, 17 May 2018 (UTC)

The RadioNuclide Collection

The RadioNuclide collection contains diagnostic outputs from the Radon-Lead-Beryllium specialty simulation.

NOTE: Emissions of Rn and Be7 are archived to diagnostic output by HEMCO, and are thus not contained in this collection. For more information, please see the HEMCO diagnostics for the Rn-Pb-Be simulation below.

Here is a sample definition section for the RadioNuclide collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  RadioNuclide.template:      '%y4%m2%d2_%h2%n2z.nc4',
  RadioNuclide.format:        'CFIO',
  RadioNuclide.frequency:     00000100 000000
  RadioNuclide.duration:      00000100 000000
  RadioNuclide.mode:          'time-averaged'
  RadioNuclide.fields:        'PbFromRnDecay                 ', 'GIGCchem',  
                              'RadDecay_Rn                   ', 'GIGCchem',  
                              'RadDecay_Pb                   ', 'GIGCchem',  
                              'RadDecay_Be7                  ', 'GIGCchem',  
::

The table below describes diagnostic quantities belonging to the RadioNuclide collection.

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
PbFromRnDecay Production of 210Pb from 222Rn radioactive decay kg/s
  • Rn-Pb-Be
RadDecay_Rn Loss of 222Rn due to radiactive decay kg/s
  • Rn-Pb-Be
RadDecay_Pb Loss of 210Pb due to radiaoactive decay kg/s
  • Rn-Pb-Be
RadDecay_Be7 Loss of 7Be due to radioactive decay kg/s
  • Rn-Pb-Be

--Bob Yantosca (talk) 20:56, 22 May 2018 (UTC)

The StateChm Collection

The StateChm collection contains quantities from State_Chm, the Chemistry state object (other than the species concentrations, which are stored in the SpeciesConc collection).

Here is a sample definition section for the StateChm collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

Other fields of the State_Chm object can be added to this collection by prefixing the field name with Chem_.

  StateChm.template:          '%y4%m2%d2_%h2%n2z.nc4',
  StateChm.format:            'CFIO',
  StateChm.frequency:         00000100 000000
  StateChm.duration:          00000100 000000
  StateChm.mode:              'time-averaged'
  StateChm.fields:            'Chem_phSav                    ', 'GIGCchem',  
                              'Chem_HplusSav                 ', 'GIGCchem',  
                              'Chem_WaterSav                 ', 'GIGCchem',  
                              'Chem_SulRatSav                ', 'GIGCchem',  
                              'Chem_NaRatSav                 ', 'GIGCchem',  
                              'Chem_AcidPurSav               ', 'GIGCchem',  
                              'Chem_BiSulSav                 ', 'GIGCchem',
                              'Chem_pHCloud                  ', 'GIGCchem',
                              'Chem_SSAlk',                  ', 'GIGCchem',
                              'Chem_HSO3AQ                   ', 'GIGCchem',
                              'Chem_SO3AQ                    ', 'GIGCchem',
                              'Chem_fupdateHOBr              ', 'GIGCchem',
::

The table below describes diagnostic quantities belonging to the StateChm collection.

NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
Chem_phSav ISORROPIA aerosol pH 1
  • all fullchem
Chem_HplusSav ISORROPIA H+ concentration M
  • all fullchem
Chem_WaterSav ISORROPIA aerosol water μg/m3
  • all fullchem
Chem_SulRatSav ISORROPIA sulfate concentration M
  • all fullchem
Chem_NaRatSav ISORROPIA Na+ concentration M
  • all fullchem
Chem_AcidPurSav ISORROPIA acidpur ?? concentration M
  • all fullchem
Chem_BiSulSav ISORROPIA bisulfate (general acid) concentration M
  • all fullchem
Chem_phCloud Cloud PH 1
  • all fullchem
  • New in v11-02
Chem_SSAlk Sea salt alkalinity 1
  • all fullchem
  • New in v11-02
Chem_HSO3AQ Cloud bisulfite concentration mol/L
  • all fullchem
  • New in v11-02
Chem_SO3AQ Cloud sulfite concentration mol/L
  • all fullchem
  • New in v11-02
Chem_fupdateHOBr Correction factor for HOBr removal by SO2 mol/L
  • all fullchem
  • New in v11-02

--Bob Yantosca (talk) 19:55, 17 May 2018 (UTC)

The StateMet collection

The StateMet collection contains met fields and other derived quantities that are carried in the State_Met object.

Here is a sample definition section for the StateMet collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

Other fields of the State_Met object can be added to this collection by prefixing the field name with Met_.

  StateMet.template:          '%y4%m2%d2_%h2%n2z.nc4',
  StateMet.format:            'CFIO',
  StateMet.frequency:         00000100 000000
  StateMet.duration:          00000100 000000
  StateMet.mode:              'time-averaged'
  StateMet.fields:            'Met_AD                        ', 'GIGCchem',
                              'Met_AIRDEN                    ', 'GIGCchem',
                              'Met_AIRVOL                    ', 'GIGCchem',
                              'Met_ALBD                      ', 'GIGCchem',
                              'Met_AREAM2                    ', 'GIGCchem',
                              'Met_AVGW                      ', 'GIGCchem',
                              'Met_BXHEIGHT                  ', 'GIGCchem',
                              'Met_ChemGridLev               ', 'GIGCchem',
                              'Met_CLDF                      ', 'GIGCchem',
                              'Met_CLDFRC                    ', 'GIGCchem',
                              'Met_CLDTOPS                   ', 'GIGCchem',
                              'Met_DELP                      ', 'GIGCchem',
                              'Met_DQRCU                     ', 'GIGCchem',
                              'Met_DQRLSAN                   ', 'GIGCchem',
                              'Met_DTRAIN                    ', 'GIGCchem',
                              'Met_EFLUX                     ', 'GIGCchem',
                              'Met_FRCLND                    ', 'GIGCchem',
                              'Met_FRLAKE                    ', 'GIGCchem',
                              'Met_FRLAND                    ', 'GIGCchem',
                              'Met_FRLANDIC                  ', 'GIGCchem',
                              'Met_FROCEAN                   ', 'GIGCchem',
                              'Met_FRSEAICE                  ', 'GIGCchem',
                              'Met_FRSNO                     ', 'GIGCchem',
                              'Met_GWETROOT                  ', 'GIGCchem',
                              'Met_GWETTOP                   ', 'GIGCchem',
                              'Met_HFLUX                     ', 'GIGCchem',
                              'Met_LAI                       ', 'GIGCchem',
                              'Met_LWI                       ', 'GIGCchem',
                              'Met_PARDR                     ', 'GIGCchem',
                              'Met_PARDF                     ', 'GIGCchem',
                              'Met_PBLTOPL                   ', 'GIGCchem',
                              'Met_PBLH                      ', 'GIGCchem',
                              'Met_PHIS                      ', 'GIGCchem',
                              'Met_PMID                      ', 'GIGCchem',
                              'Met_PMIDDRY                   ', 'GIGCchem',
                              'Met_PRECANV                   ', 'GIGCchem',
                              'Met_PRECCON                   ', 'GIGCchem',
                              'Met_PRECLSC                   ', 'GIGCchem',
                              'Met_PRECTOT                   ', 'GIGCchem',
                              'Met_PS1DRY                    ', 'GIGCchem',
                              'Met_PS1WET                    ', 'GIGCchem',
                              'Met_PS2DRY                    ', 'GIGCchem',
                              'Met_PS2WET                    ', 'GIGCchem',
                              'Met_PSC2WET                   ', 'GIGCchem',
                              'Met_PSC2DRY                   ', 'GIGCchem',
                              'Met_QI                        ', 'GIGCchem',
                              'Met_QL                        ', 'GIGCchem',
                              'Met_OMEGA                     ', 'GIGCchem',
                              'Met_OPTD                      ', 'GIGCchem',
                              'Met_REEVAPCN                  ', 'GIGCchem',
                              'Met_REEVAPLS                  ', 'GIGCchem',
                              'Met_SLP                       ', 'GIGCchem',
                              'Met_SNODP                     ', 'GIGCchem',
                              'Met_SNOMAS                    ', 'GIGCchem',
                              'Met_SPHU                      ', 'GIGCchem',
                              'Met_SPHU1                     ', 'GIGCchem',
                              'Met_SPHU2                     ', 'GIGCchem',
                              'Met_SUNCOS                    ', 'GIGCchem',
                              'Met_SUNCOSmid                 ', 'GIGCchem',
                              'Met_SWGDN                     ', 'GIGCchem',
                              'Met_T                         ', 'GIGCchem',
                              'Met_TAUCLI                    ', 'GIGCchem',
                              'Met_TAUCLW                    ', 'GIGCchem',
                              'Met_THETA                     ', 'GIGCchem',
                              'Met_TMPU1                     ', 'GIGCchem',
                              'Met_TMPU2                     ', 'GIGCchem',
                              'Met_TO3                       ', 'GIGCchem',
                              'Met_TropHt                    ', 'GIGCchem',
                              'Met_TropLev                   ', 'GIGCchem',
                              'Met_TropP                     ', 'GIGCchem',
                              'Met_TS                        ', 'GIGCchem',
                              'Met_TSKIN                     ', 'GIGCchem',
                              'Met_TV                        ', 'GIGCchem',
                              'Met_U                         ', 'GIGCchem',
                              'Met_U10M                      ', 'GIGCchem',
                              'Met_USTAR                     ', 'GIGCchem',
                              'Met_UVALBEDO                  ', 'GIGCchem',
                              'Met_V                         ', 'GIGCchem',
                              'Met_V10M                      ', 'GIGCchem',
                              'Met_Z0                        ', 'GIGCchem',
::
Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
Met_AD Visible surface albedo 1
  • all simulations
Met_AIRDEN Dry air density kg/m3
  • all simulations
Met_AIRVOL Grid box volume, dry air m3
  • all simulations
Met_ALBD Surface albedo 1
  • all simulations
Met_AREAM2 Grid box area m2
  • all simulations
  • AREA is written to each netCDF file
Met_AVGW Water vapor volume mixing ratio vol H2O/vol dry air
  • all simulations
Met_BXHEIGHT Grid box height m
  • all simulations
Met_ChemGridLev Chemistry grid level 1
  • all simulations
  • Equivalent to ITS_IN_THE_CHEMGRID
Met_CLDF 3-D cloud fraction 1
  • all simulations
Met_CLDFRC Column cloud fraction 1
  • all simulations
Met_CLDTOPS Maximum cloud top height 1
  • all simulations
Met_DELP Delta-pressure between top and bottom edges of grid box (wet air) hPa
  • all simulations
Met_DQRCU Convective precipitation production rate (dry air) kg/kg/s
  • all simulations
Met_DTRAIN Detrainment flux kg/m2/s
  • all simulations
Met_EFLUX Latent heat flux W/m2
  • all simulations
Met_FRCLND Olson land fraction 1
  • all simulations
Met_FRLAKE Fraction of grid box covered by lakes 1
  • all simulations
Met_FRLAND Fraction of grid box covered by land 1
  • all simulations
Met_FRLANDIC Fraction of grid box covered by land ice 1
  • all simulations
Met_FROCEAN Fraction of grid box covered by ocean 1
  • all simulations
Met_FRSEAICE Fraction of grid box covered by sea ice 1
  • all simulations
Met_FRSNO Fraction of grid box covered by snow 1
  • all simulations
Met_GWETROOT Root soil moisture 1
  • all simulations
Met_GWETTOP Topsoil moisture 1
  • all simulations
Met_HFLUX Sensible heat flux W/m2
  • all simulations
Met_LAI Leaf area index from met field archive m2/m2
  • all simulations
  • Lacks interannual variability; use MODIS LAI instead
Met_LWI Land-water-ice indices 1
  • all simulations
Met_PARDF Diffuse photosynthetically active radiation W/m2
  • all simulations
Met_PARDR Diffuse photosynthetically active radiation W/m2
  • all simulations
Met_PBLTOPL PBL top layer 1
  • all simulations
Met_PBLH PBL height m
  • all simulations
Met_PHIS Surface geopotential height m2/s2
  • all simulations

= Height * g

Met_PMID Pressure at midpoint of model layers, defined as arithmetic average of edge pressures (wet air) hPa
  • all simulations
Met_PMIDDRY Pressure at midpoint of model layers, defined as arithmetic average of edge pressures (dry air) hPa
  • all simulations
Met_PRECANV Anvil precipitation (at surface) kg/m2/s
  • all simulations
Met_PRECCON Convective precipitation (at surface) kg/m2/s
  • all simulations
Met_PRECLSC Large-scale precipitation (at surface) kg/m2/s
  • all simulations
Met_PRECTOT Total precipitation (at surface) kg/m2/s
  • all simulations
Met_PS1DRY Instantaneous surface pressure at start of 3-hr met field interval (dry air) hPa
  • all simulations
Met_PS2DRY Instantaneous surface pressure at end of 3-hr met field interval (dry air) hPa
  • all simulations
Met_PSC2DRY Surface pressure interpolated to current time (dry air) hPa
  • all simulations
  • Linearly interpolated from PS1DRY and PD2DRY
Met_PS1WET Instantaneous surface pressure at start of 3-hr met field interval (wet air) hPa
  • all simulations
Met_PS2WET Instantaneous surface pressure at end of 3-hr met field interval (wet air) hPa
  • all simulations
Met_PSC2WET Surface pressure interpolated to current time (wet air) hPa
  • all simulations
  • Linearly interpolated from PS1WET and PS2WET
Met_QI Ice mixing ratio (dry air) kg/kg dry air
  • all simulations
Met_QL Liquid water mixing ratio (dry air) kg/kg dry air
  • all simulations
Met_OMEGA Updraft velocity Pa/s
  • all simulations
Met_OPTD Visible optical depth 1i
  • all simulations
Met_REEVAPCN Evaporation of convective precipitation (dry air) kg/kg/s
  • all simulations
Met_REEVAPLS Evaporation of large-scale + anvil precipitation (dry air) kg/kg/s
  • all simulations
Met_SLP Sea level pressure hPa
  • all simulations
Met_SNODP Snow depth m
  • all simulations
Met_SNOMAS Snow mass kg/m2
  • all simulations
Met_SPHU1 Instantaneous specific humidity at start of 3 hr met field interval (wet air) kg/kg
  • all simulations
Met_SPHU2 Instantaneous specific humidity at end of 3-hr met field interval (wet air) kg/kg
  • all simulations
Met_SPHU Specific humidity interpolated to current time (wet air) g H2O/kg air
  • all simulations
  • Linearly interpolated from SPHU1 and SPHU2
Met_SUNCOS Cosine of solar zenith angle at current time 1
  • all simulations
Met_SUNCOSMID Cosine of solar zenith angle at midpoint of chemistry timestep 1
  • all simulations
Met_SWGDN Incident shortwave radiation at ground W/m2
  • all simulations
Met_TAUCLI Visible optical depth of ice clouds 1
  • all simulations
Met_TAUCLW Visible optical depth of water clouds 1
  • all simulations
Met_THETA Potential temperature K
  • all simulations
Met_TMPU1 Instantaneous temperature at start of 3-hr met field interval K
  • all simulations
Met_TMPU2 Instantaneous temperature at end of 3-hr met field interval K
  • all simulations
Met_T Temperature interpolated to current time K
  • all simulations
  • Linearly interpoalted from TMPU1 and TMPU2
Met_TO3 Total overhead ozone column Dobsons
  • all simulations
Met_TropHt Tropopause height u
  • all simulations
Met_TropLev Tropopause height km
  • all simulations
Met_TROPP Tropopause pressure hPa
  • all simulations
Met_TS Surface temperature K
  • all simulations
Met_TSKIN Surface skin temperature K
  • all simulations
Met_U East-west ccomponent of wind m/s
  • all simulations
Met_U10M East-west component of wind at 10 m height above surface m/s
  • all simulations
Met_USTAR Friction velocity m/s
  • all simulations
Met_UVALBEDO Ultraviolet surface albedo 1
  • all simulations
Met_V North-south ccomponent of wind m/s
  • all simulations
Met_V10M North-south component of wind at 10 m height above surface m/s
  • all simulations
Met_Z0 Surface roughness height m
  • all simulations

--Bob Yantosca (talk) 20:40, 22 May 2018 (UTC)

The WetLossConv collection

The WetLossConv collection contains diagnostics fluxes of soluble species lost to wet scaveinging in convective updrafts.

Here is a sample definition section for the WetLossConv collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  WetLossConv.template:       '%y4%m2%d2_%h2%n2z.nc4',
  WetLossConv.format:         'CFIO',
  WetLossConv.frequency:      00000100 000000
  WetLossConv.duration:       00000100 000000
  WetLossConv.mode:           'time-averaged'
  WetLossConv.fields:         'WetLossConv_?WET?             ', 'GIGCchem',
                              'WetLossConvFrac_?WET?         ', 'GIGCchem',
::

The table below describes diagnostic quantities belonging to the WetLossConv collection.

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
WetLossConv_<spcname> Loss of soluble species scavenged by cloud updrafts in moist convection kg/s
  • ?WET?
  • all simulations
WetLossConvFrac_<spcname> Fraction of species scavenged by cloud updrafts in moist convection 1
  • ?WET?
  • all simulations

--Bob Yantosca (talk) 20:23, 17 May 2018 (UTC)

The WetLossLS collection

The WetLossLS collection contains diagnostics fluxes of soluble species lost to rainout and washout in large-scale wet deposition.

Here is a sample definition section for the WetLossConv collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.

To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.

  WetLossLS.template:         '%y4%m2%d2_%h2%n2z.nc4',
  WetLossLS.format:           'CFIO',
  WetLossLS.frequency:        010000
  WetLossLS.duration:         010000
  WetLossLS.mode:             'time-averaged'
  WetLossLS.fields:           'WetLossLS_?WET?               ', 'GIGCchem',
::

The table below describes diagnostic quantities belonging to the WetLossLS collection.

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
WetLossLS_<spcname> Loss of soluble species in large-scale precipitation kg/s
  • ?WET?
  • all simulations
WetLossConvFrac_<spcname> Fraction of species scavenged by cloud updrafts in moist convection 1
  • ?WET?
  • all simulations

--Bob Yantosca (talk) 20:23, 17 May 2018 (UTC)

Replicating the existing specialty diagnostics

Here we discuss our plans to replicate specialty diagnostic outputs (timeseries, local-time diagnostics, etc.) in the new GEOS-Chem netCDF diagnostic package.

NOTE: We will NOT retire the legacy bpch diagnostics in GEOS-Chem v11-02. We will preserve the bpch diagnostic output until we can find alternatives for specialty diagnostics, especially those which involve averaging in a local solar time window.

ND40 planeflight diagnostic

Bob Yansotca wrote:

For the “planeflight” diagnostic, we will investigate using a separate package (such as NOAA ObsPack, as recommended by Andy Jacobsen at IGC8) that can more efficiently store point data. Then new diagnostic package we are developing works well for array data but not as well for point data.

Mat Evans replied:

I’ve had a quick look at obspack. I’m not sure its well suited to our needs.
I personally don’t see much need to update the plane flight files. They are easy to understand at the moment and easy to manipulate being in ascii. The biggest problem at the moment is that the rate constants have fallen out of them because of the move to FlexChem. If we can get that sorted I don’t think there is a pressing need to update the format.

--Bob Yantosca (talk) 16:20, 15 November 2017 (UTC)

ND48 station diagnostics

We will keep the current ND48 station diagnostics (bpch format) in GEOS-Chem v11-02 until we can find a suitable replacement.

Jenny Fisher wrote:

It seems we are losing compatibility for both ND48 (station) and ND51 (satellite) diagnostics. These are probably the two my group uses most frequently (and replacing with e.g. hourly output everywhere will require a lot of extra disk space). If we are going to have regional subsetting of diagnostics available, then ND48 can probably be dealt with by subsetting down to the level of a single box – but ND51 is harder.

ND49 instantaneous timeseries diagnostic

You can replicate the ND49 bpch diagnostic (instantaneous timeseries) as follows:

  1. Define a diagnostic collection in HISTORY.rc:
    • Specify instantaneous output:
      • Set mode: instantaneous
    • Specify the desired output frequency:
      • Set frequency: 010000 for hourly output
      • Set frequency: 030000 for 3-hourly output
      • Set frequency: 120000 for 12-hourly output, etc.
        • You can also use the full date/time descriptor (00000000 010000, etc.)
    • Specify that a new netCDF file should be created every 24 hours:
      • Set duration: 240000
        • You can also use the full date/time descriptor (00000001 000000)
  2. Within this diagnostic collection, you can add archive any available quantity from the State_Met, State_Chm, or State_Diag objects.

Example:

#===================================================================
# Add an instantaneous timeseries collection to the master list
#===================================================================
COLLECTIONS: inst3hr',
::
#====================================================================
# Define the properties of the instantaneous timeseries collection 
#====================================================================
  inst3hr.template:      '%y4%m2%d2_%h2%n2z.nc4',
  inst3hr.frequency:      030000,
  inst3hr.duration:       240000,
  inst3hr.mode:          'instantaneous',
  inst3hr.fields:        'SpeciesConc_?ADV?', 'GIGCchem',
                         'Met_T',             'GIGCchem',
                         'DryDepVel_?DRY?',   'GIGCchem',
::

--Bob Yantosca (talk) 21:55, 7 June 2018 (UTC)

ND50 24-hr average timeseries diagnostic

You can replicate the ND50 bpch diagnostic (24-hr average timeseries) as follows:

  1. Define a diagnostic collection in HISTORY.rc:
    • Specify time-averaged output:
      • Set mode: time-averaged
    • Specify daily output frequency. This will also set the averaging interval to be daily.
      • Set frequency: 240000
        • You can also use the full date/time descriptor: 00000001 000000
    • Specify that a new netCDF file should be created every 24 hours:
      • Set duration: 240000
        • You can also use the full date/time descriptor: 00000001 000000
  2. Within this diagnostic collection, you can add archive any available quantity from the State_Met, State_Chm, or State_Diag objects.

Example:

#===================================================================
# Add an 24-hr average timeseries collection to the master list
#===================================================================
COLLECTIONS: avg24hr',
::
#===================================================================
# Define the properties of the 24-hr average timeseries collection
#===================================================================
  avg24hr.template:      '%y4%m2%d2_%h2%n2z.nc4',
  avg24hr.frequency:      240000,
  avg24hr.duration:       240000,
  avg24hr.mode:          'time-averaged',
  avg24hr.fields:        'SpeciesConc_?ADV?', 'GIGCchem',
                         'Met_T',             'GIGCchem',
                         'DryDepVel_?DRY?',   'GIGCchem',
::

--Bob Yantosca (talk) 21:58, 7 June 2018 (UTC)

ND51 satellite diagnostic

Aaron van Donkelaar wrote:

I wanted to double check about how the satellite-overpass diagnostic (ND51) was being included. There was some mention of it within the (netCDF diagnostic) presentation, but I wasn’t clear to me how the time-averaged netcdf collection could be made to output something similar to the current ND51.

My main concern was that ND51 samples between two defined local times once each day. From what I understood of the time-averaged collection via netcdf, it could be set to regularly sample between a defined interval of time (e.g. every six hours), but I didn’t understand how this could be set to sample between, say, 10am-12pm local time each day. Neither local time, nor once per day seemed an option.

Apologies if I’ve just misunderstood, but I thought I should check that an ND51-type output would still be possible.

Bob Yantosca replied:

At this time we don't yet have a good substitute for the ND51 satellite timeseries diagnostics. We may be able to replicate this with some type of satellite simulator package, but that remains to be seen as of yet. Right now we are focusing our efforts on implementing the netCDF diagnostics that are required for benchmarking. (Specialty diagnostics will be added later.)

We have designed the netCDF diagnostics for GC-Classic to replicate the behavior of the diagnostics in GCHP. Having the diagnostics work the same way in both configurations of GC facilitates benchmarking and comparing GC-Classic to GCHP. It also makes it easier for users to switch between GC-Classic to GCHP. But GCHP does not allow for local-time diagnostics. GCHP relies on the MAPL library, and its diagnostic package (aka "History") only allows for instantaneous or time-averaged output.

One could save e.g hourly timeseries, along with a local time field, to netCDF, and apply the local time comparison in post-processing. This would be doable but it would also end up generating a ton of output.

The good news is that we will preserve the bpch diagnostics in v11-02 (I need to update the wiki better to reflect that). We will not remove the bpch diagnostics until we have found a suitable replacement for the local-time diagnostics. So for the time being you can still rely on ND51.

--Bob Yantosca (talk) 15:33, 15 November 2017 (UTC)

netCDF diagnostics for GEOS-Chem specialty simulations

In order to prioritize the GEOS-Chem v11-02 (aka 12.0.0) release, we focused on creating netCDF diagnostics that correspond to the bpch diagnostics used for benchmarking GEOS-Chem. Following v11-02 we will start to add the netCDF diagnostics for the following specialty simulations.

NOTE: Emissions for any specialty simulation can be archived as diagnostic output directly by HEMCO. See the following section for more information.

--Bob Yantosca (talk) 13:50, 8 June 2018 (UTC)

Diagnostics that are currently archived by HEMCO

The diagnostic collections described above do not contain any emissions diagnostics. These are archived by the HEMCO emissions component.

Brief overview of HEMCO diagnostics

A file named HEMCO_Diagn.rc will be included in each GEOS-Chem run directory that you create. This file lists the quantities that you want to archive as diagnostic output. You can archive any quantity computed by HEMCO (i.e. the container names listed in the HEMCO.log file) to diagnostic output. Typically you will want to save the following types of diagnostic quantities:

  • Emissions for a given species, summed over all inventories and sectors (e.g. EmisCO_Total)
  • Emissions for a given species, for a single emissions sector (e.g. EmisCO_Bioburn)
  • Emissions for a given species, from a single inventory (e.g. EmisCO_EMEP)

The HEMCO diagnostic file name and archival frequency can be specified at the top of your HEMCO_Config.rc file, as shown here:

DiagnPrefix:                 HEMCO_diagnostics 
DiagnFreq:                   End

This will send HEMCO diagnostic output to netCDF files named HEMCO_diagnostics.YYYYMMDDhhmm.nc. You can also change the archival frequency to e.g. monthly with

DiagnFreq:                   00000100 000000

or to any other interval.

For more information about HEMCO diagnostics, please see The HEMCO User's Guide: Diagnostics section.

--Bob Yantosca (talk) 20:10, 7 June 2018 (UTC)

HEMCO diagnostics for full-chemistry simulations

The HEMCO_Diagn.rc file corresponding to most GEOS-Chem full-chemistry simulations is shown below. To disable a particular diagnostic quantity, simply place a # comment character in front of its name. You can of course add more diagnostics to this list.

For more information how to add new diagnostic fields to the HEMCO_Diagn.rc file, please see The HEMCO User's Guide: Diagnostics section.

#------------------------------------------------------------------------------
#                  GEOS-Chem Global Chemical Transport Model                  !
#------------------------------------------------------------------------------
#BOP
#
# !MODULE: HEMCO_Diagn.rc 
#
# !DESCRIPTION: Configuration file for netCDF diagnostic output from HEMCO.
#\\
#\\
# !REMARKS:
#  Customized for the benchmark simulation.
#  TO DO: Add long names, which are used for netCDF variable attributes.
#
# !REVISION HISTORY:
#  13 Feb 2018 - E. Lundgren - Initial version
#EOP
#------------------------------------------------------------------------------
#BOC
# Name             Spec  ExtNr  Cat Hier Dim OutUnit       LongName

###############################################################################
#####   ACET emissions (in bpch ND11, ND28, ND34, ND36, ND46)             #####
###############################################################################
EmisACET_Total     ACET   -1     -1  -1   3   molec/cm2/s  
EmisACET_Anthro    ACET   0      1   -1   3   atomsC/cm2/s
EmisACET_BioBurn   ACET   111    -1  -1   2   atomsC/cm2/s
EmisACET_Biofuel   ACET   0      2   -1   2   atomsC/cm2/s
EmisACET_Biogenic  ACET   108    -1  -1   2   atomsC/cm2/s
EmisACET_DirectBio ACET   108    -1  -1   2   atomsC/cm2/s ACET_from_direct_emissions
EmisACET_MethylBut ACET   108    -1  -1   2   atomsC/cm2/s ACET_from_methyl_butenol
EmisACET_Monoterp  ACET   108    -1  -1   2   atomsC/cm2/s ACET_from_monoterpenes
EmisACET_Ocean     ACET   101    -1  -1   2   atomsC/cm2/s ACET_from_ocean_source

###############################################################################
#####  ALD2 emissions (in bpch ND28, ND34, ND36, ND46. ALD2_Ocean         #####
#####  and is new)                                                        #####
###############################################################################
EmisALD2_Total     ALD2   -1     -1  -1   3   molec/cm2/s
EmisALD2_Anthro    ALD2   0      1   -1   3   atomsC/cm2/s
EmisALD2_BioBurn   ALD2   111    -1  -1   2   atomsC/cm2/s
EmisALD2_Biofuel   ALD2   0      2   -1   2   atomsC/cm2/s
EmisALD2_Biogenic  ALD2   108    -1  -1   2   atomsC/cm2/s
EmisALD2_Ocean     ALD2   101    -1  -1   2   atomsC/cm2/s
EmisALD2_Senesc    ALD2   0      4   -1   2   atomsC/cm2/s

###############################################################################
#####  ALK4 emissions (in bpch ND28, ND34, ND36)                          ##### 
###############################################################################
EmisALK4_Total     ALK4   -1     -1  -1   3   molec/cm2/s
EmisALK4_Anthro    ALK4   0      1   -1   3   atomsC/cm2/s
EmisALK4_BioBurn   ALK4   111    -1  -1   2   atomsC/cm2/s
EmisALK4_Biofuel   ALK4   0      2   -1   2   atomsC/cm2/s

###############################################################################
#####  C2H6 emissions (in bpch ND28, ND34, ND36 )                        ######
###############################################################################
EmisC2H6_Total     C2H6   -1     -1  -1   3   molec/cm2/s
EmisC2H6_Anthro    C2H6   0      1   -1   3   atomsC/cm2/s
EmisC2H6_BioBurn   C2H6   111    -1  -1   2   atomsC/cm2/s
EmisC2H6_Biofuel   C2H6   0      2   -1   2   atomsC/cm2/s

###############################################################################
#####   C3H8 emissions (in bpch ND28, ND34, ND36)                         ##### 
###############################################################################
EmisC3H8_Total     C3H8   -1     -1  -1   3   molec/cm2/s
EmisC3H8_Anthro    C3H8   0      1   -1   3   atomsC/cm2/s
EmisC3H8_BioBurn   C3H8   111    -1  -1   2   atomsC/cm2/s
EmisC3H8_Biofuel   C3H8   0      2   -1   2   atomsC/cm2/s

###############################################################################
#####  CH2O emissions (in bpch ND28, ND34, ND36 )                         ##### 
###############################################################################
EmisCH2O_Total     CH2O   -1     -1  -1   3   molec/cm2/s
EmisCH2O_Anthro    CH2O   0      1   -1   3   atomsC/cm2/s
EmisCH2O_BioBurn   CH2O   111    -1  -1   2   atomsC/cm2/s
EmisCH2O_Biofuel   CH2O   0      2   -1   2   atomsC/cm2/s

###############################################################################
#####  CO sources (in bpch ND29)                                          ##### 
###############################################################################
EmisCO_Total       CO     -1     -1  -1   3   molec/cm2/s
EmisCO_Anthro      CO     0      1   -1   3   molec/cm2/s
EmisCO_BioBurn     CO     111    -1  -1   2   molec/cm2/s
EmisCO_Biofuel     CO     0      2   -1   2   molec/cm2/s
EmisCO_Monoterp    CO     109    -1  -1   2   molec/cm2/s
EmisCO_Ship        CO     0      10  -1   2   molec/cm2/s

###############################################################################
#####  DMS emissions (in bpch ND13)                                       ##### 
###############################################################################
EmisDMS_Ocean      DMS    101    -1  -1   2   kg

###############################################################################
#####  Dust emissions (in bpch ND06)                                      ##### 
###############################################################################
EmisDST1_Natural   DST1   105    -1  -1   2   kg 
EmisDST2_Natural   DST2   105    -1  -1   2   kg
EmisDST3_Natural   DST3   105    -1  -1   2   kg
EmisDST4_Natural   DST4   105    -1  -1   2   kg

###############################################################################
#####  OCPI emissions (in bpch ND07 combined with OCPO)                   ##### 
###############################################################################
EmisOCPI_Total     OCPI   -1     -1  -1   3   kgC
EmisOCPI_Anthro    OCPI   0      1   -1   3   kgC
EmisOCPI_BioBurn   OCPI   111    -1  -1   2   kgC
EmisOCPI_Biofuel   OCPI   0      2   -1   2   kgC
EmisOCPI_Biogenic  OCPI   109    -1  -1   2   kgC

###############################################################################
#####  OCPO emissions (in bpch ND07 combined with OCPI)                   ##### 
###############################################################################
EmisOCPO_Total     OCPO   -1     -1  -1   3   kgC
EmisOCPO_Anthro    OCPO   0      1   -1   3   kgC
EmisOCPO_BioBurn   OCPO   111    -1  -1   2   kgC
EmisOCPO_Biofuel   OCPO   0      2   -1   2   kgC

###############################################################################
#####  Sea salt emissions (in bpch ND08)                                  ##### 
###############################################################################
EmisSALA_Natural   SALA   107    -1  -1   2   kg
EmisSALC_Natural   SALC   107    -1  -1   2   kg

###############################################################################
#####  SO2 emissions (in bpch ND13, ND28)                                 ##### 
###############################################################################
EmisSO2_Total      SO2    -1     -1  -1   3   kg
EmisSO2_Aircraft   SO2    0      20  -1   3   kg
EmisSO2_Anthro     SO2    0      1   -1   3   kg
EmisSO2_BioBurn    SO2    111    -1  -1   2   kg
EmisSO2_Biofuel    SO2    0      2   -1   2   kg
EmisSO2_EVOL       SO2    0      51  -1   2   kg
EmisSO2_NVOL       SO2    0      52  -1   2   kg
EmisSO2_Ship       SO2    0      10  -1   2   kg

###############################################################################
#####  SO4 emissions (in bpch ND13)                                       ##### 
###############################################################################
EmisSO4_Total      SO4    -1     -1  -1   3   kg
EmisSO4_Anthro     SO4    0      1   -1   3   kg
EmisSO4_Biofuel    SO4    0      2   -1   2   kg

###############################################################################
#####  NH3 emissions (in bpch ND13, ND28 )                                #####
###############################################################################
EmisNH3_Total      NH3    -1     -1  -1   3   kg
EmisNH3_Anthro     NH3    0      1   -1   3   kg
EmisNH3_BioBurn    NH3    111    -1  -1   2   kg
EmisNH3_Biofuel    NH3    0      2   -1   2   kg
EmisNH3_Natural    NH3    0      3   -1   2   kg

###############################################################################
#####  NOx emissions (in bpch ND28, ND32, ND36)                           #####
###############################################################################
EmisNO_Total       NO     -1     -1  -1   3   molec/cm2/s
EmisNO_Aircraft    NO     0      20  -1   3   molec/cm2/s
EmisNO_Anthro      NO     0      1   -1   3   molec/cm2/s
EmisNO_BioBurn     NO     111    -1  -1   2   molec/cm2/s
EmisNO_Biofuel     NO     0      2   -1   2   molec/cm2/s
EmisNO_Fert        NO     104    -1  -1   2   molec/cm2/s
EmisNO_Lightning   NO     103    -1  -1   2   molec/cm2/s
EmisNO_Ship        NO     102    -1  -1   2   molec/cm2/s
EmisNO_Soil        NO     104    -1  -1   2   molec/cm2/s

###############################################################################
#####  MEK emissions (in bpch ND28, ND34, ND36)                           #####
###############################################################################
EmisMEK_Total      MEK    -1     -1  -1   3   molec/cm2/s
EmisMEK_Anthro     MEK    0      1   -1   3   atomsC/cm2/s
EmisMEK_BioBurn    MEK    111    -1  -1   2   atomsC/cm2/s
EmisMEK_Biofuel    MEK    0      2   -1   2   atomsC/cm2/s

###############################################################################
#####  RCHO emissions (in bpch ND34?, ND36?)                              ##### 
###############################################################################
EmisRCHO_Total     RCHO   -1     -1  -1   3   molec/cm2/s
EmisRCHO_Anthro    RCHO   0      1   -1   3   atomsC/cm2/s
EmisRCHO_Biofuel   RCHO   0      2   -1   2   atomsC/cm2/s

###############################################################################
#####  MACR emissions (in bpch ND34?, ND36?)                              ##### 
###############################################################################
EmisMACR_Total     MACR   -1     -1  -1   3   molec/cm2/s
EmisMACR_Anthro    MACR   0      1   -1   3   atomsC/cm2/s
EmisMACR_Biofuel   MACR   0      2   -1   2   atomsC/cm2/s

###############################################################################
#####  PRPE emissions (in bpch ND28, ND34, ND36, ND46)                    ##### 
###############################################################################
EmisPRPE_Total     PRPE   -1     -1  -1   3   molec/cm2/s
EmisPRPE_Anthro    PRPE   0      1   -1   3   atomsC/cm2/s
EmisPRPE_BioBurn   PRPE   111    -1  -1   2   atomsC/cm2/s
EmisPRPE_Biofuel   PRPE   0      2   -1   2   atomsC/cm2/s
EmisPRPE_Biogenic  PRPE   108    -1  -1   2   atomsC/cm2/s

###############################################################################
#####  ISOP emissions (in bpch ND46)                                      #####
###############################################################################
EmisISOP_Biogenic  ISOP   108    -1  -1   2   atomsC/cm2/s

###############################################################################
#####  BC emissions (combined with BCPO in bpch ND07, ND28)               ##### 
###############################################################################
EmisBCPI_Total     BCPI   -1     -1  -1   3   kgC
EmisBCPI_Anthro    BCPI   0      1   -1   3   kgC
EmisBCPI_BioBurn   BCPI   111    -1  -1   2   kgC
EmisBCPI_Biofuel   BCPI   0      2   -1   2   kgC

###############################################################################
##### BC emissions (combined with BCPI in bpch ND07, ND28)               ######
###############################################################################
EmisBCPO_Total     BCPO   -1     -1  -1   3   kgC
EmisBCPO_Anthro    BCPO   0      1   -1   3   kgC
EmisBCPO_BioBurn   BCPO   111    -1  -1   2   kgC
EmisBCPO_Biofuel   BCPO   0      2   -1   2   kgC

###############################################################################
##### CHBr3 emissions (in bpch ND46)                                      ##### 
###############################################################################
EmisCHBr3_Ocean    CHBr3  0      1   -1   2   kg/m2/s

###############################################################################
#####  CH2Br2 emissions (in bpch ND46)                                    ##### 
###############################################################################
EmisCH2Br2_Ocean   CH2Br2 0      1   -1   2   kg/m2/s

###############################################################################
#####  Br2 emissions (in bpch ND46)                                       ##### 
###############################################################################
EmisBr2_Ocean      Br2    107    -1  -1   2   kg/m2/s

###############################################################################
#####  NO2 emissions (in bpch ND36?)                                      ##### 
###############################################################################
EmisNO2_Anthro     NO2    0      1   -1   3   molec/cm2/s

###############################################################################
#####  HNO2 emissions (in bpch ND36?)                                     #####
###############################################################################
EmisHNO2_Anthro    HNO2   0      1   -1   3   molec/cm2/s

###############################################################################
#####  BENZ emissions (in bpch ND34?, ND36?)                              ##### 
###############################################################################
EmisBENZ_Total     BENZ   -1     -1  -1   3   atomsC/cm2/s
EmisBENZ_Anthro    BENZ   0      1   -1   3   atomsC/cm2/s
EmisBENZ_BioBurn   BENZ   111    -1  -1   2   atomsC/cm2/s
EmisBENZ_Biofuel   BENZ   0      2   -1   2   atomsC/cm2/s

###############################################################################
#####  TOLU emissions (in bpch ND34?, ND36?)                              #####
###############################################################################
EmisTOLU_Total     TOLU   -1     -1  -1   3   atomsC/cm2/s
EmisTOLU_Anthro    TOLU   0      1   -1   3   atomsC/cm2/s
EmisTOLU_BioBurn   TOLU   111    -1  -1   2   atomsC/cm2/s
EmisTOLU_Biofuel   TOLU   0      2   -1   2   atomsC/cm2/s

###############################################################################
#####  XYLE emissions (in bpch ND34?, ND36?)                              ##### 
###############################################################################
EmisXYLE_Total     XYLE   -1     -1  -1   3   atomsC/cm2/s
EmisXYLE_Anthro    XYLE   0      1   -1   3   atomsC/cm2/s
EmisXYLE_BioBurn   XYLE   111    -1  -1   2   atomsC/cm2/s
EmisXYLE_Biofuel   XYLE   0      2   -1   2   atomsC/cm2/s

###############################################################################
#####   EOH emissions (in bpch ND34?, ND36?, ND46?)                       ##### 
###############################################################################
EmisEOH_Total      EOH    -1     -1  -1   3   atomsC/cm2/s
EmisEOH_Anthro     EOH    0      1   -1   3   atomsC/cm2/s
EmisEOH_BioBurn    EOH    111    -1  -1   2   atomsC/cm2/s
EmisEOH_Biofuel    EOH    0      2   -1   2   atomsC/cm2/s
EmisEOH_Biogenic   EOH    108    -1  -1   2   atomsC/cm2/s
EmisEOH_Senesc     EOH    0      4   -1   2   atomsC/cm2/s

###############################################################################
#####  MGLY emissions (new?)                                              ##### 
###############################################################################
EmisMGLY_BioBurn   MGLY   111    -1  -1   2   atomsC/cm2/s

#EOC

HEMCO diagnostics for the Rn-Pb-Be simulation

The HEMCO_Diagn.rc file corresponding to the Rn-Pb-Be specialty simulation is shown below. To disable a particular diagnostic quantity, simply place a # comment character in front of its name.

#------------------------------------------------------------------------------
#                  GEOS-Chem Global Chemical Transport Model                  !
#------------------------------------------------------------------------------
#BOP
#
# !MODULE: HEMCO_Diagn.rc 
#
# !DESCRIPTION: Configuration file for netCDF diagnostic output from HEMCO.
#\\
#\\
# !REMARKS:
#  Customized for the RnPbBe simulation.
#  TO DO: Add long names, which are used for netCDF variable attributes.
#
# !REVISION HISTORY:
#  13 Feb 2018 - E. Lundgren - Initial version
#EOP
#------------------------------------------------------------------------------
#BOC
# Name             Spec  ExtNr  Cat Hier Dim OutUnit       LongName  

###############################################################################
#####  Rn emissions (in bpch ND01)                                        #####
###############################################################################
EmisRn_Total       Rn    -1     -1  -1   3   kg/m2/s  
EmisRn_Soil        Rn     1001   1  -1   3   kg/m2/s 

###############################################################################
#####  Rn emissions (in bpch ND01)                                        #####
###############################################################################
EmisBe7_Total      Be7   -1     -1  -1   3   kg/m2/s
EmisBe7_Cosmic     Be7    1001   1  -1   3   kg/m2/s 

#EOC

--Bob Yantosca (talk) 20:00, 7 June 2018 (UTC)

Validating the netCDF diagnostics

In GEOS-Chem Classic

We invite you to view the the presentation NetCDF diagnostic validation in GEOS-Chem "Classic" by Bob Yantosca and the GCST which summarizes the initial validation process. A more robust validation will take place shortly.

One of the take-aways of the validation is that the timestep at which diagnostics are update could cause non-negligble differences. For example, several GEOS-Chem time-averaged diagnostics are updated on each chemistry timestep, which is 20 minutes for most GEOS-Chem simulations. But the default behavior of the new netCDF diagnostics in GEOS-Chem updates time-averaged diagnostic quantities every "heartbeat" timestep, which is 10 minutes for most simulations. Therefore, the netCDF diagnostics will capture the state of the atmopshere on those timesteps where chemistry does not happen. As shown in the presentation, this could cause non-negligible differences when comparing to the legacy diagnostics.

The GCST recommends that time-averaged diagnostic quantities in GEOS-Chem "Classic" be updated on each "heartbeat" timestep, as this mimics the behavior the diagnostics in GCHP.

--Bob Yantosca (talk) 20:14, 27 November 2017 (UTC)

Adding New Diagnostics

To add your own diagnostics we recommend that you find a similar existing diagnostic and use its implementation as a template. Most of the work is done in Headers/state_diag_mod.F90. Briefly, the following updates to that file are essential for adding in your own netcdf diagnostics:

  1. Declare diagnostic array at top of module
  2. Set diagnostic array pointer to null in Init_State_Diag subroutine
  3. Create a section in Init_State_Diag subroutine to allocate and register the array
  4. Deallocate the diagnostic array in subroutine Cleanup_State_Diag
  5. Add an if block for the diagnostic within subroutine Get_Metadata_State_Diag to define its metadata

Good diagnostics to use as templates are SpeciesConc for 3-dimensional arrays that are for all species and DryDepVel for 2-dimensional arrays that are for a subset of species. If your diagnostic is not per species then AODDust is a good diagnostic to look at. Search the file Headers/state_diag_mod.F90 for any of these strings to find all instances of code related to their implementation.

Note that information about the dimensions and species collection the diagnostic will include must be specified when allocating the array in Init_State_Diag and in Get_Metadata_State_Diag. In the latter subroutine the Rank is the integer number of dimensions of the diagnostic (not including species) and the TagID string, if any, specifies the species collection to output the diagnostic per. TagIDs are defined in subroutine Get_TagInfo. Each TagID string can also be used as a wildcard within HISTORY.rc to simplify diagnostic name specification (for GEOS-Chem classic only).

Once you have implemented your diagnostic in Headers/state_diag_mod.F90 and checked that it compiles using NC_DIAG=y, try adding it to HISTORY.rc and running. You should get your diagnostic output in the netcdf output file as all zeros. The next step is to populate the array with whatever value you want to output. You should do this by passing the State_Diag array to the location where you want to set the values. Then write code to fill the array being sure to wrap it in #if defined( NC_DIAG ) and #endif C-preprocessor code (no indent). A simple test of your understanding is to initially set values to a constant other than zero and see if that works.

--Lizzie Lundgren (talk) 17:45, 24 August 2018 (UTC)