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==feel free to experiment here ==
==feel free to experiment here ==
== Overview ==
=== An introduction to netCDF diagnostics ===
Bob Yantosca has created [[Media:Netcdf_Diagnostics.pdf|an overview presentation about the new netCDF diagnostics for v11-02]]. 
=== Sample HISTORY.rc diagnostic input file ===
Here is a sample <tt>HISTORY.rc</tt> file that is used to request netCDF diagnostic output from a GEOS-Chem “Classic” simulation. 
#===================================================================
# Declare collection names.  Disable collections by commenting
# each collection name out with a "#" character.
#===================================================================
COLLECTIONS: <span style="color:red">'SpeciesConc'</span>,
              <span style="color:blue">'ConcAfterChem'</span>,
::
#===================================================================
# Collection to save out GEOS-Chem species concentrations
#===================================================================
<span style="color:red">SpeciesConc</span>.<span style="color:gray">template:    '%y4%m2%d2_%h2%n2z.nc4'</span>,
<span style="color:red">SpeciesConc</span>.<span style="color:darkorange">frequency:    060000</span>,
<span style="color:red">SpeciesConc</span>.format:      'CFIO',
<span style="color:red">SpeciesConc</span>.<span style="color:purple">duration:    240000</span>,
<span style="color:red">SpeciesConc</span>.<span style="color:brown">mode:        'instantaneous'</span>,
<span style="color:red">SpeciesConc</span>.<span style="color:green">fields:      'SpeciesConc_?ADV?'</span>,  'GIGCchem',
::
#===================================================================
# Collection to save out concentrations after chemistry
# (from the FlexChem/KPP solver)
#===================================================================
<span style="color:blue">ConcAfterChem</span>.<span style="color:gray">template:  '%y4%m2%d2_%h2%n2z.nc4'</span>,
<span style="color:blue">ConcAfterChem</span>.<span style="color:magenta">frequency:  000100 000000</span>,
<span style="color:blue">ConcAfterChem</span>.format:    'CFIO',
<span style="color:blue">ConcAfterChem</span>.<span style="color:purple">duration:  000100 000000</span>,
<span style="color:blue">ConcAfterChem</span>.<span style="color:darkcyan">mode:      'time-averaged'</span>,
<span style="color:blue">ConcAfterChem</span>.<span style="color:green">fields:    'OHconcAfterChem'</span>,    'GIGCchem',
                          <span style="color:green">'HO2concAfterChem'</span>,    'GIGCchem',
                          <span style="color:green">'O1DconcAfterChem'</span>,    ‘GIGCchem’,
                          <span style="color:green">'O3PconcAfterChem'</span>,    ‘GIGCchem’,
::
In this <tt>HISTORY.rc</tt> file, we are requesting two collections, or types of netCDF file output.
{| border=1 cellspacing=0 cellpadding=5
|-valign="top" bgcolor="#CCCCCC"
!width="200px"|Attribute
!width="900px"|Explanation
|-valign="top"
|<tt><span style="color:red">SpeciesConc</span></tt>
|Name of the first collection in this <tt>HISTORY.rc</tt> file.  A collection is a series of files containing the same GEOS-Chem diagnostic quantities.
|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:gray">template</span></tt>
|Determines the date and time format for each netCDF file name belonging to the <tt><span style="color:red">SpeciesConc</span></tt> collection.
*The string <tt>%y4%m2%d2_%h2%n2z.nc4</tt> will print <tt>YYYYMMDD_hhmmz.nc4</tt> to the end of each netCDF filename
**<tt>YYYYMMDD</tt> is the date in year/month/day format
**<tt>hhmm</tt> is the time in hour:minutes format.
**<tt>z</tt> denotes "Zulu", which is an abbreviation for UTC time.
**<tt>.nc4</tt> denotes that the data file is in the netCDF-4 format.
|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:darkorange">frequency</span></tt>
|Determines how often the diagnostic quantities belonging to <tt><span style="color:red">SpeciesConc</span></tt> collection will be saved to a netCDF file.
*This can be specified as either "<tt>hhmmss</tt>" or "<tt>YYMMDD hhmmss</tt>".
*In the above example, data belonging to the <tt><span style="color:red">SpeciesConc</span></tt> collection will be written to the file <span style="color:darkorange">every 6 hours</span>.  (Because <tt><span style="color:red">SpeciesConc</span></tt> is an <span style="color:brown">instantaneous</span> collection, no time-averaging will be performed.)
|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.format</tt>
|Indicates the I/O library that will be used (for GCHP simulations only).
|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:purple">duration</span></tt>
|Determines how often a new <tt><span style="color:red">SpeciesConc</span></tt> netCDF file will be created. 
*This can be specified as either <tt>hhmmss</tt> or <tt>YYMMDD hhmmss</tt>.
*In the above example, a new <tt><span style="color:red">SpeciesConc</span></tt> netCDF file will be created <span style="color:purple">every 24 hours</span>.
|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:brown">mode</span></tt>
|Determines the averaging method for the <tt><span style="color:red">SpeciesConc</span></tt> collection
*In this example, <tt><span style="color:red">SpeciesConc</span></tt> is defined as an <tt><span style="color:brown">instantaneous</span></tt> (aka "time-series") collection. 
*Diagnostic quantities belonging to <tt><span style="color:red">SpeciesConc</span></tt> will be written directly to disk without any temporal averaging, at the specified <tt><span style="color:darkorange">frequency</span></tt>.
|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:green">fields</span></tt>
|Lists the diagnostic quantities to be included in the <tt><span style="color:red">SpeciesConc</span></tt> collection.
*In the above example, we are requesting to archive the <span style="color:green">concentrations of all advected species</span> to the <tt><span style="color:red">SpeciesConc</span></tt> collection.
*The text <tt>'GIGCchem'</tt> is only needed for GCHP simulations.  It is ignored for GEOS-Chem "Classic" simulations.  We keep the <tt>'GIGCchem'</tt> in the file in order <tt>HISTORY.rc</tt> files to be interchanged between GEOS-Chem "Classic" and GCHP simulations.
See the sections below contain 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.
|-valign="top"
|<tt>::</tt>
|Signifies the end of the <tt><span style="color:red">SpeciesConc</span></tt> definition section.
*"<tt>::</tt>" may be placed at any column in the file.
|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span></tt>
|Name of the second collection in this <tt>HISTORY.rc</tt> file.
|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:gray">template</span></tt>
|Determines the date and time format for each netCDF file name belonging to the <tt><span style="color:blue">ConcAfterChem</span></tt> collection.
|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:magenta">frequency</span></tt>
|Determines the length of the period in which the diagnostic quantities belonging to <tt><span style="color:blue">ConcAfterChem</span></tt> collection will be temporally-averaged, before being saved to a netCDF file.
*This can be can be specified as either "<tt>hhmmss</tt>" or "<tt>YYMMDD hhmmss</tt>".
*In the above example, data belonging to the <tt><span style="color:blue">ConcAfterChem</span></tt> collection will be <span style="color:magenta">averaged into monthly mean output</span>.
|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.format</tt>
|For GCHP simulations only: indicates the I/O library that will be used.  This can be omitted for GEOS-Chem "Classic" simualations.
|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:purple">duration</span></tt>
|Determines how often a new netCDF file belongng to the <tt><span style="color:blue">ConcAfterChem</span></tt> will be created.
*The <tt><span style="color:purple">duration</span></tt> attribute can be specified as either <tt>hhmmss</tt> or <tt>YYMMDD hhmmss</tt>.
*In the above example, a new <tt><span style="color:blue">ConcAfterChem</span></tt> netCDF file will be created <span style="color:purple">at the start of each new month</span>.
|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:darkcyan">mode</span></tt>
|Determines the averaging method for the <tt><span style="color:blue">ConcAfterChem</span></tt> collection
*In the above example, <tt><span style="color:blue">ConcAfterChem</span></tt> is defined as an <tt><span style="color:darkcyan">time-averaged</span></tt> collection. 
*Diagnostic quantities belonging to the <tt><span style="color:blue">ConcAfterChem</span></tt> collection will be temporally-averaged for a period whose length is specified by the <tt><span style="color:magenta">frequency</span></tt> attribute before being written to a netCDF file.
|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:green">fields</span></tt>
|Lists the diagnostic quantities to be included in the <tt><span style="color:blue">ConcAfterChem</span></tt> collection.
*In the above example, we are requesting to archive to the <tt><span style="color:blue">ConcAfterChem</span></tt> collection the <span style="color:green">concentrations of OH, HO2, O1D, and O3P upon exiting the FlexChem/KPP solver</span>
*The text <tt>'GIGCchem'</tt> is only needed for GCHP simulations.  It is ignored for GEOS-Chem "Classic" simulations.  We keep the <tt>'GIGCchem'</tt> in the file in order <tt>HISTORY.rc</tt> files to be interchanged between GEOS-Chem "Classic" and GCHP simulations.
See the sections below contain 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.
|-valign="top"
|<tt>::</tt>
|Signifies the end of the <tt><span style="color:blue">ConcAfterChem</span></tt> definition section.
*"<tt>::</tt>" may be placed at any column in the file.
|}
For more examples, please see [[Media:Netcdf_Diagnostics.pdf|Bob Yantosca’s netCDF diagnostics overview presentation]]. We will also add more documentation to the GEOS-Chem wiki in the coming weeks.
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:14, 8 February 2018 (UTC)
=== Legend ===
The following terms are used in the tables below.
{| border=1 cellspacing=0 cellpadding=5
|-valign="top" bgcolor="#CCCCCC"
!width="175px"|Term
!width="600px"|Explanation
!width="225px"|Example
|-valign="top"
|<tt><spcname></tt>
|Short name of a GEOS-Chem species, used in several diagnostics listed below. 
NOTES:
#The single-underscore (<tt>_</tt>) preceding the species name indicates that use of a species wildcard (e.g <tt>SpeciesConc_<span style="color:red">?ADV?</span></tt>, which only selects advected species) is possible.
#Allowable wild card values (case-insensitive) for species name are:
#*<tt>?ADV?</tt>: Only the advected species
#*<tt>?AER?</tt>: Only the aerosol species
#*<tt>?ALL?</tt>: All GEOS-Chem species
#*<tt>?DRY?</tt>: Only the dry-deposited species
#*<tt>?FIX?</tt>: Only the inactive (aka "fixed") species in the KPP chemical mechanism
#*<tt>?GAS?</tt>: Only the gas-phase species
#*<tt>?KPP?</tt>: Only the KPP species
#*<tt>?PHO</tt>: Only the photolyzed species
#*<tt>?VAR?</tt>: Only the active (aka "variable") species in the KPP chemical mechanism
#*<tt>?WET?</tt>: Only the wet-deposited species
#*<tt>?PRODLOSS?</tt>: Only prod/loss diagnostic species
#*<tt>?DUSTBIN</tt>: Only the dust bin number
#<tt><spcname></tt> 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.
|<tt>SpeciesConc_<span style="color:red">NO</span></tt><br><tt>SpeciesConc_<span style="color:red">CO</span></tt><br><tt>SpeciesConc_<span style="color:red">?ADV?</span></tt><br><tt>SpeciesConc_<span style="color:red">?AER?</span></tt><br><tt>SpeciesConc_<span style="color:red">?ALL?</span></tt><br><tt>SpeciesConc_<span style="color:red">?DRY?</span></tt><br><tt>SpeciesConc_<span style="color:red">?FIX?</span></tt><br><tt>SpeciesConc_<span style="color:red">?GAS?</span></tt><br><tt>SpeciesConc_<span style="color:red">?KPP?</span></tt><br><tt>SpeciesConc_<span style="color:red">?PHO?</span></tt><br><tt>SpeciesConc_<span style="color:red">?VAR?</span></tt><br><tt>SpeciesConc_<span style="color:red">?WET?</span></tt><br><tt>...etc...</tt>
|-valign="top" bgcolor="#CCFFFF"
|<tt><metname></tt>
|Denotes a met field (or derived quantity such as total optical depth).
NOTES:
#<tt>MET_</tt>, <tt>Met_</tt> or <tt>met_</tt> (case-insensitive) must precede <tt><metname></tt>.  This tells the diagnostic code to look for the corresponding field of the <tt>State_Met</tt> object.
|<tt>MET_<span style="color:red">U10M</span></tt><br><tt>MET_<span style="color:red">PS</span></tt><br><tt>MET_<span style="color:red">HFLUX</span></tt><br><tt>MET_<span style="color:red">T</span></tt><br><tt>...etc...</tt>
|-valign="top"
|<tt><photobin></tt>
|Number of a given wavelength bin for FAST-JX photolysis
|<tt>1-18</tt> (with UCX on);<br><tt>1-12</tt> (with UCX off)
|-valign="top" bgcolor="#CCFFFF"
|<tt><aername></tt>
|Aerosol quanatities included in the following array fields:
#<tt>State_Chm%AeroArea</tt>
#<tt>State_Chm%AeroRadi</tt>
#<tt>State_Chm%WetAeroArea</tt>
#<tt>State_Chm%WetAeroRadi</tt>
These do not always conform to GEOS-Chem species (for example, the mineral dust bins are the bins that are used as input for photolysis).
#<tt>MDUST1</tt>: Mineral dust (0.15&mu;m)
#<tt>MDUST2</tt>: Mineral dust (0.25&mu;m)
#<tt>MDUST3</tt>: Mineral dust (0.40&mu;m)
#<tt>MDUST4</tt>: Mineral dust (0.80&mu;m)
#<tt>MDUST5</tt>: Mineral dust (1.50&mu;m)
#<tt>MDUST6</tt>: Mineral dust (2.50&mu;m)
#<tt>MDUST7</tt>: Mineral dust (4.00&mu;m)
#<tt>SULF</tt>: Sulfate
#<tt>BC</tt>: Black Carbon
#<tt>OC</tt>: Organic Carbon
#<tt>SSA</tt>: Sea salt aerosol, accumulation mode
#<tt>SSC</tt>: Sea salt aerosol, coarse mode
#<tt>BGSULF</tt>: Background stratospheric sulfate
#<tt>ICEI</tt>: Irregular ice cloud (Mischenko)
|<tt>CHEM_AeroArea<span style="color:red">MDUST1</span></tt><br><tt>CHEM_WetAeroRadi<span style="color:red">SSA</span></tt><br><tt>...etc...</tt>
|-valign="top"
|<tt>nAdvect</tt>
|Number of advected GEOS-Chem species
|
|-valign="top" bgcolor="#CCFFFF"
|<tt>nDryDep</tt>
|Number of dry-depositing GEOS-Chem species
|
|-valign="top"
|<tt>nKppSpc</tt>
|Number of species in the KPP chemistry mechanism
|
|-valign="top" bgcolor="#CCFFFF"
|<tt>nPhoto</tt>
|Number of photolyzing GEOS-Chem species
|
|-valign="top"
|<tt>nTomas</tt>
|Number of size-resolved TOMAS species
|<tt>IBINS*(ICOMP-IDIAG+1)</tt>
|-valign="top" bgcolor="#CCFFFF"
|<tt>nWetDep</tt>
|Number of soluble, wet-depositing GEOS-Chem species
|
|}
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:10, 8 February 2018 (UTC)


== Collection list ==
== Collection list ==

Revision as of 22:21, 8 February 2018

feel free to experiment here

Collection list

EXPID:  OutputDir/GCHP
EXPDSC: GEOS-Chem_devel
CoresPerNode: 6

#===================================================================
# Declare collection names and toggle on/off
# by commenting out with a #
#===================================================================
COLLECTIONS: 'SpeciesConc',
             'Aerosols',
             'CloudConvFlux',
             'ConcAfterChem',
             'DryDep',
             'JValues',
             'JValuesLocalNoon',
             'LevelEdgeDiags',      
             'ProdLoss',
             'StateChm',     
             'StateMet',      
             'WetLossConv',
             'WetLossLS',

Species concentrations

  1. Species concentrations (per advected species)
 SpeciesConc.template:       '%y4%m2%d2_%h2%n2z.nc4',
 SpeciesConc.format:         'CFIO',
 SpeciesConc.frequency:      010000
 SpeciesConc.duration:       010000
 SpeciesConc.mode:           'time-averaged'
 SpeciesConc.fields:         'SpeciesConc_?ADV?             ', 'GIGCchem',

Aerosol diagnostics

#===================================================================
# Aerosol optical depth, surface area, number density, and hygroscopic growth
 Aerosols.template:          '%y4%m2%d2_%h2%n2z.nc4',
 Aerosols.format:            'CFIO',
 Aerosols.frequency:         010000
 Aerosols.duration:          010000
 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',
                             ::

Cloud convective flux

  1. Cloud convective flux (per advected species)
 CloudConvFlux.template:     '%y4%m2%d2_%h2%n2z.nc4',
 CloudConvFlux.format:       'CFIO',
 CloudConvFlux.frequency:    010000
 CloudConvFlux.duration:     010000
 CloudConvFlux.mode:         'time-averaged'
 CloudConvFlux.fields:       'CloudConvFlux_?ADV?           ', 'GIGCchem',

Concentrations after chemistry

 # Concentrations after chemistry
 ConcAfterChem.template:     '%y4%m2%d2_%h2%n2z.nc4',
 ConcAfterChem.format:       'CFIO',
 ConcAfterChem.frequency:    010000
 ConcAfterChem.duration:     010000
 ConcAfterChem.mode:         'time-averaged'
 ConcAfterChem.fields:       'OHconcAfterChem               ', 'GIGCchem',  
                             'HO2concAfterChem              ', 'GIGCchem',  
                             'O1DconcAfterChem              ', 'GIGCchem',  
                             'O3PconcAfterChem              ', 'GIGCchem',

Dry deposition diagnostics

  1. Dry deposition flux velocity (per dry deposited species)
 DryDep.template:            '%y4%m2%d2_%h2%n2z.nc4',
 DryDep.format:              'CFIO',
 DryDep.frequency:           010000
 DryDep.duration:            010000
 DryDep.mode:                'time-averaged'
 DryDep.fields:              'DryDepVel_?DRY?               ', 'GIGCchem',
                             'DryDepMix_?DRY?               ', 'GIGCchem',
                             'DryDepChm_?DRY?               ', 'GIGCchem',
                             'DryDep_?DRY?                  ', 'GIGCchem',

Photolysis diagnostics

  1. Photolysis rates (J-values)
 JValues.template:           '%y4%m2%d2_%h2%n2z.nc4',
 JValues.format:             'CFIO',
 JValues.frequency:          010000
 JValues.duration:           010000
 JValues.mode:               'time-averaged'
 JValues.fields:             'Jval_?PHO?                    ', 'GIGCchem',
  1. Photolysis rates at local noon (J-values)
 JValuesLocalNoon.template:  '%y4%m2%d2_%h2%n2z.nc4',
 JValuesLocalNoon.format:    'CFIO',
 JValuesLocalNoon.frequency: 010000
 JValuesLocalNoon.duration:  010000
 JValuesLocalNoon.mode:      'instantaneous'
 JValuesLocalNoon.fields:    'JNoon_?PHO?                   ', 'GIGCchem',

Diagnostics on level edges

  1. Level edge diagnostics (73-level only)
 LevelEdgeDiags.template:    '%y4%m2%d2_%h2%n2z.nc4',
 LevelEdgeDiags.format:      'CFIO',
 LevelEdgeDiags.frequency:   010000
 LevelEdgeDiags.duration:    010000
 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',

Production and loss rates

 # Prod/loss rates
 ProdLoss.template:          '%y4%m2%d2_%h2%n2z.nc4',
 ProdLoss.format:            'CFIO',
 ProdLoss.frequency:         010000
 ProdLoss.duration:          010000
 ProdLoss.mode:              'time-averaged'
 ProdLoss.fields:            'PROD_?PRD?                    ', 'GIGCchem', 
                             'ProdBCPIfromBCPO              ', 'GIGCchem', 
                             'ProdOCPIfromOCPO              ', 'GIGCchem',
                             'ProdSO4fromH2O2inCloud        ', 'GIGCchem',
                             'ProdSO4fromO3inCloud          ', 'GIGCchem',
                             'ProdSO4fromO3inSeaSalt        ', 'GIGCchem',
                             'ProdSO4fromHOBrInCloud        ', 'GIGCchem',
                             'ProdSO4fromSRO3               ', 'GIGCchem',
                             'ProdSO4fromSRHObr             ', 'GIGCchem',
                             'ProdSO4fromO3s                ', 'GIGCchem',
                             'LOSS_?LOS?                    ', 'GIGCchem',
                             'LossHNO3onSeaSalt             ', 'GIGCchem',

Fields of the State_Chm object

  1. State_Chm array diagnostics (see also Aerosols collection
 StateChm.template:          '%y4%m2%d2_%h2%n2z.nc4',
 StateChm.format:            'CFIO',
 StateChm.frequency:         010000
 StateChm.duration:          010000
 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',

Fields of the State_Met object

# State_Met array diagnostics
 StateMet.template:          '%y4%m2%d2_%h2%n2z.nc4',
 StateMet.format:            'CFIO',
 StateMet.frequency:         010000
 StateMet.duration:          010000
 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',

Loss of soluble species in cloud updrafts

  1. Loss due to convection (per wet deposited species)
 WetLossConv.template:       '%y4%m2%d2_%h2%n2z.nc4',
 WetLossConv.format:         'CFIO',
 WetLossConv.frequency:      010000
 WetLossConv.duration:       010000
 WetLossConv.mode:           'time-averaged'
 WetLossConv.fields:         'WetLossConv_?WET?             ', 'GIGCchem',

Loss of soluble species in large-scale wet deposition

  1. Loss due to rainout and washout (per deposited species)
 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',
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