Difference between revisions of "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]].
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#REDIRECT [[Guide to GEOS-Chem History diagnostics]]
 
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''NOTE: We will NOT retire the [[List of diagnostics archived to bpch format|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.''
+
 
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== Overview ==
+
 
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=== An introduction to netCDF diagnostics ===
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[[GEOS-Chem v11-02|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:
+
 
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#[[#Diagnostics_that_are_currently_archived_by_HEMCO|Emissions diagnostics archived directly by HEMCO]]
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#Non-emissions diagnostics computed by GEOS-Chem
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+
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 <tt>HISTORY.rc</tt> can be used for both GEOS-Chem "Classic" and GCHP.
+
 
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Bob Yantosca has created [[Media:Netcdf_Diagnostics.pdf|an overview presentation about the new netCDF diagnostics for v11-02]].
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 13:20, 8 June 2018 (UTC)
+
 
+
=== 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. 
+
 
+
#============================================================================
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# EXPID allows you to specify the beginning of the file path corresponding
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# to each diagnostic collection.  For example:
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#
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#  EXPID: ./GEOSChem
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#      Will create netCDF files whose names begin "GEOSChem",
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#      in this run directory.
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#
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#  EXPID: ./OutputDir/GEOSChem
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#      Will create netCDF files whose names begin with "GEOSChem"
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#      in the OutputDir sub-folder of this run directory.
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#
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#============================================================================
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EXPID:  ./GEOSChem
+
+
#==============================================================================
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# %%%%% COLLECTION NAME DECLARATIONS %%%%%
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#
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# To disable a collection, place a "#" character in front of its name
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#
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# NOTE: These are the "default" collections for GEOS-Chem. 
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# But you can create your own custom diagnostic collections as well.
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#==============================================================================
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COLLECTIONS: <span style="color:red">'SpeciesConc'</span>,
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              <span style="color:blue">'ConcAfterChem'</span>,
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::
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#==============================================================================
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# %%%%% THE SpeciesConc COLLECTION %%%%%
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#
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# GEOS-Chem species concentrations (default = advected species)
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#
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# Available for all simulations
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#==============================================================================
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<span style="color:red">SpeciesConc</span>.<span style="color:gray">template:    '%y4%m2%d2_%h2%n2z.nc4'</span>,
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<span style="color:red">SpeciesConc</span>.<span style="color:darkorange">frequency:    060000</span>,
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<span style="color:red">SpeciesConc</span>.format:      'CFIO',
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<span style="color:red">SpeciesConc</span>.<span style="color:purple">duration:    240000</span>,
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<span style="color:red">SpeciesConc</span>.<span style="color:brown">mode:        'instantaneous'</span>,
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<span style="color:red">SpeciesConc</span>.<span style="color:green">fields:      'SpeciesConc_?ADV?'</span>,  'GIGCchem',
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::
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#==============================================================================
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# %%%%% THE ConcAfterChem COLLECTION %%%%%
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#
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# Concentrations of OH, HO2, O1D, O3P immediately after exiting the KPP solver
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# or OH after the CH4 specialty-simulation chemistry routine.
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#
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# OH:      Available for all full-chemistry simulations and CH4 specialty sim
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# HO2:      Available for all full-chemistry simulations
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# O1D, O3P: Availalbe for full-chemistry simulations using UCX mechanism
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#==============================================================================
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<span style="color:blue">ConcAfterChem</span>.<span style="color:gray">template:  '%y4%m2%d2_%h2%n2z.nc4'</span>,
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<span style="color:blue">ConcAfterChem</span>.<span style="color:magenta">frequency:  00000100 000000</span>,
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<span style="color:blue">ConcAfterChem</span>.format:    'CFIO',
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<span style="color:blue">ConcAfterChem</span>.<span style="color:purple">duration:  00000100 000000</span>,
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<span style="color:blue">ConcAfterChem</span>.<span style="color:darkcyan">mode:      'time-averaged'</span>,
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<span style="color:blue">ConcAfterChem</span>.<span style="color:green">fields:    'OHconcAfterChem'</span>,    'GIGCchem',
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                          <span style="color:green">'HO2concAfterChem'</span>,    'GIGCchem',
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                          <span style="color:green">'O1DconcAfterChem'</span>,    ‘GIGCchem’,
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                          <span style="color:green">'O3PconcAfterChem'</span>,    ‘GIGCchem’,
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::
+
 
+
 
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In this <tt>HISTORY.rc</tt> file, we are requesting two collections, or types of netCDF file output.  The table below explains in more detail parameters shown in the <tt>HISTORY.rc</tt> file above.
+
 
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{| border=1 cellspacing=0 cellpadding=5
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|-valign="top" bgcolor="#CCCCCC"
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!width="200px"|Attribute
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!width="900px"|Explanation
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|-valign="top"
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|<tt><span style="color:red">SpeciesConc</span></tt>
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|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"
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|<tt><span style="color:red">SpeciesConc</span>.<span style="color:gray">template</span></tt>
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|Determines the date and time format for each netCDF file name belonging to the <tt><span style="color:red">SpeciesConc</span></tt> collection.
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*The string <tt>%y4%m2%d2_%h2%n2z.nc4</tt> will print <tt>YYYYMMDD_hhmmz.nc4</tt> to the end of each netCDF filename
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**<tt>YYYYMMDD</tt> is the date in year/month/day format
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**<tt>hhmm</tt> is the time in hour:minutes format.
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**<tt>z</tt> denotes "Zulu", which is an abbreviation for UTC time.
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**<tt>.nc4</tt> denotes that the data file is in the netCDF-4 format.
+
 
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|-valign="top"
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|<tt><span style="color:red">SpeciesConc</span>.<span style="color:darkorange">frequency</span></tt>
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|Determines how often the diagnostic quantities belonging to <tt><span style="color:red">SpeciesConc</span></tt> collection will be saved to a netCDF file.
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*This can be specified as either "<tt>hhmmss</tt>" or "<tt>YYYYMMDD hhmmss</tt>".
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*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"
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|<tt><span style="color:red">SpeciesConc</span>.format</tt>
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|For GCHP simulations only: indicates the I/O library that will be used.  This can be omitted for GEOS-Chem "Classic" simualations.
+
 
+
|-valign="top"
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|<tt><span style="color:red">SpeciesConc</span>.<span style="color:purple">duration</span></tt>
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|Determines how often a new <tt><span style="color:red">SpeciesConc</span></tt> netCDF file will be created. 
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*This can be specified as either <tt>hhmmss</tt> or <tt>YYYYMMDD hhmmss</tt>.
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*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"
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|<tt><span style="color:red">SpeciesConc</span>.<span style="color:brown">mode</span></tt>
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|Determines the averaging method for the <tt><span style="color:red">SpeciesConc</span></tt> collection
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*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. 
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*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"
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|<tt><span style="color:red">SpeciesConc</span>.<span style="color:green">fields</span></tt>
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|Lists the diagnostic quantities to be included in the <tt><span style="color:red">SpeciesConc</span></tt> collection.
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*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.
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*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.
+
 
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See the sections below for in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format.
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NOTE: You may use wildcards to request a subset of all possible chemical species.  See the next section for more information about wildcards.
+
 
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|-valign="top"
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|<tt>::</tt>
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|Signifies the end of the <tt><span style="color:red">SpeciesConc</span></tt> definition section.
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*"<tt>::</tt>" may be placed at any column in the file.
+
 
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|-valign="top"
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|<tt><span style="color:blue">ConcAfterChem</span></tt>
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|Name of the second collection in this <tt>HISTORY.rc</tt> file.
+
 
+
|-valign="top"
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|<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"
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|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:magenta">frequency</span></tt>
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|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.
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*This can be can be specified as either "<tt>hhmmss</tt>" or "<tt>YYYYMMDD hhmmss</tt>".
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*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"
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|<tt><span style="color:blue">ConcAfterChem</span>.format</tt>
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|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.
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*The <tt><span style="color:purple">duration</span></tt> attribute can be specified as either <tt>hhmmss</tt> or <tt>YYYYMMDD 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>
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|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 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.
+
 
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|-valign="top"
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|<tt>::</tt>
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|Signifies the end of the <tt><span style="color:blue">ConcAfterChem</span></tt> definition section.
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*"<tt>::</tt>" may be placed at any column in the file.
+
 
+
|}
+
 
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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]]) 22:12, 8 February 2018 (UTC)
+
 
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=== netCDF filename convention ===
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The names of the netCDF files corresponding to each collection will adhere to this convention:
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  EXPID.CollectionName.Template
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+
Where <tt>EXPID</tt> can be specified at the very top of the <tt>HISTORY.rc</tt> file.  This parameter controls the filename prefix.  [[#Sample HISTORY.rc diagnostic input file|In the example from the previous section]], <tt>EXPID</tt> is set to <tt>./GEOSChem</tt>.  This means that all netCDF output files will be placed in the current run directory (specified by <tt>./</tt>) and will begin with <tt>GeosChem</tt>. 
+
 
+
If you wish to send the netCDF diagnostic output to a sub-folder of the run directory (say named <tt>OutputDir</tt>), then you can set e.g. <tt>EXPID: ./OutputDir/GeosChem</tt>.  (''NOTE: You can also omit the <tt>./</tt>, 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 <tt>CollectionName</tt> and <tt>Template</tt> settings are defined [[#Sample HISTORY.rc diagnostic input file|as shown in our example <tt>HISTORY.rc</tt> file from the previous section]], namely:
+
 
+
  <span style="color:red">SpeciesConc</span>.<span style="color:gray">template:    '%y4%m2%d2_%h2%n2z.nc4'</span>,
+
  . . .
+
  <span style="color:blue">ConcAfterChem</span>.<span style="color:gray">template:  '%y4%m2%d2_%h2%n2z.nc4'</span>,
+
 
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In the template tags:
+
 
+
* The notation <tt>%y4%m2%d5_%h2%n2</tt> specifies a in the format <tt>YYYYMMDD_hhmm</tt> into the netCDF filename.
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* The lowercase <tt>z</tt>denotes UTC time (aka "Zulu time").
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* The <tt>.nc4</tt> extension denotes that the file will be in netCDF-4 format.
+
 
+
Also recall that the <tt>duration</tt> tag of <tt>HISTORY.rc</tt> controls how often a new file will be written to disk, as we saw [[#Sample HISTORY.rc diagnostic input file|in our example from the previous section]]:
+
 
+
  <span style="color:red">SpeciesConc</span>.<span style="color:purple">duration:    240000</span>,              # Write a new file each day
+
  . . .
+
  <span style="color:blue">ConcAfterChem</span>.<span style="color:purple">duration:  00000100 000000</span>,    # Write a new file each month
+
 
+
Therefore, based on all of these settings in our example <tt>HISTORY.rc</tt> 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 ...
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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.
+
 
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=== General information about each diagnostic ===
+
 
+
The tables below list the following parameters for each diagnostic that is archived to bpch format:
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top"
+
!bgcolor="#CCCCCC" width="175px"|Diagnostic name
+
|width="835px"|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.  [[#Wildcards|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.
+
 
+
|-valign="top"
+
!bgcolor="#CCCCCC"|Description
+
|A short overview of the given diagnostic.
+
 
+
|-valign="top"
+
!bgcolor="#CCCCCC"|Units
+
|The physical units of the given diagnostic quantity.
+
 
+
|-valign="top"
+
!bgcolor="#CCCCCC"|Wildcards
+
|[[#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.
+
 
+
|-valign="top"
+
!bgcolor="#CCCCCC"|Simulations
+
|A list of simulations for which this particular diagnostic is valid.
+
 
+
|-valign="top"
+
!bgcolor="#CCCCCC"|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.
+
 
+
|-valign="top"
+
!bgcolor="#CCCCCC"|Notes
+
|Lists supplemental information for the given diagnostic.
+
 
+
|}
+
 
+
=== Wildcards and prefixes ===
+
 
+
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>?HYG?</tt>: Only aerosols that undergo hygroscopic growth
+
#**(e.g. sulfate, BC, OC, SALA, SALC)
+
#*<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>
+
*<tt>SpeciesConc_<span style="color:red">CO</span></tt>
+
*<tt>SpeciesConc_<span style="color:red">?ADV?</span></tt>
+
*<tt>SpeciesConc_<span style="color:red">?AER?</span></tt>
+
*<tt>SpeciesConc_<span style="color:red">?ALL?</span></tt>
+
*<tt>SpeciesConc_<span style="color:red">?DRY?</span></tt>
+
*<tt>SpeciesConc_<span style="color:red">?FIX?</span></tt>
+
*<tt>SpeciesConc_<span style="color:red">?GAS?</span></tt>
+
*<tt>SpeciesConc_<span style="color:red">?HYG</span></tt>
+
*<tt>SpeciesConc_<span style="color:red">?KPP?</span></tt>
+
*<tt>SpeciesConc_<span style="color:red">?PHO?</span></tt>
+
*<tt>SpeciesConc_<span style="color:red">?VAR?</span></tt>
+
*<tt>SpeciesConc_<span style="color:red">?WET?</span></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"
+
|<tt>Chem_</tt>
+
|To request diagnostic output for fields of the <tt>State_Chm</tt> object (other than <tt>SpeciesConc</tt>), add this prefix in front of the field name.  (Prefix is case-insensitive.)
+
|
+
*<tt><span style="color:red">Chem_</span>phCloud</tt>
+
*<tt><span style="color:red">Chem_</span>HplusSav</tt>
+
 
+
|-valign="top"
+
|<tt>Met_</tt>
+
|To request diagnostic output for fields of the <tt>State_Met</tt> object, add this prefix in front of the field name.  (Prefix is case-insensitive.)
+
|
+
*<tt><span style="color:red">Met_</span>T</tt>
+
*<tt><span style="color:red">Met_</span>PS</tt>
+
*<tt><span style="color:red">Met_</span>SPHU</tt>
+
*<tt><span style="color:red">Met_</span>U10M</tt>
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>HISTORY.rc</tt> 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 <tt>HISTORY.rc</tt> 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 <tt>EXPID</tt> works [[#netCDF filename convention|in a previous section]].
+
 
+
The <tt>COLLECTIONS:</tt> tag specifies all of the diagnostic '''collections''' that you wish to activate during a GEOS-Chem simulation.  Each collection represents a group of diagnostic quantities that will be written to disk in netCDF file format.  The collection name will be automatically added to the netCDF file name along with the date/or time, [[#netCDF filename convention|as we have seen above]].
+
 
+
[[Creating GEOS-Chem run directories|Each of the run directories for the various GEOS-Chem simulations]] will have its own customized <tt>HISTORY.rc</tt> file.  Only the diagnostic collections pertaining to a particular GEOS-Chem simulation will be included in the corresponding <tt>HISTORY.rc</tt> file.  (In other words, you will not find diagnostic collections for full-chemistry simulations in the <tt>HISTORY.rc</tt> 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 <tt>COLLECTIONS:</tt> section.
+
 
+
GEOS-Chem will expect to find a collection definition section for each of the activated collections listed under the <tt>COLLECTIONS:</tt> section.  In other words, if you have <tt>SpeciesConc</tt> listed under <tt>COLLECTIONS:</tt>, but there is no further information provided about the <tt>SpeciesConc</tt> collection, then GEOS-Chem will halt with an error message.
+
 
+
The collections listed on this wiki page are the "default" diagnostic collections that we have created for GEOS-Chem.  You are certainly not limited to just using these collections.  We have created these default collections such that related quantities will be grouped together in the same netCDF files (to the greatest extent possible).  But you can create your own customized diagnostic collections by referring to our [[#Sample HISTORY.rc diagnostic input file|sample <tt>HISTORY.rc</tt> file shown above]].
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>HISTORY.rc</tt> files that ship with each [[Creating_GEOS-Chem_run_directories|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 <tt>#</tt> 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:
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|SpeciesConc_<spcname>
+
|Chemical species concentrations
+
|mol/mol dry air
+
|
+
*?ADV?
+
*?AER?
+
*?ALL?
+
*?DRY?
+
*?FIX?
+
*?GAS?
+
*?HYG?
+
*?KPP?
+
*?PHO?
+
*?VAR?
+
*?WET?
+
|
+
*all simulations
+
|
+
*[[List of diagnostics archived to bpch format|ND45]]
+
*[[List of diagnostics archived to bpch format|ND47]]
+
*[[List of diagnostics archived to bpch format|ND48]]
+
*[[List of diagnostics archived to bpch format|ND49]]
+
*[[List of diagnostics archived to bpch format|ND50]]
+
*[[List of diagnostics archived to bpch format|ND51]]
+
|
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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:
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|AerMassTSOA
+
|Aerosol products of terpene oxidation
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #1]]
+
|
+
 
+
|-valign="top"
+
|AerMassISOA
+
|Aerosol products of isoprene oxidation
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #2]]
+
|
+
 
+
|-valign="top"
+
|AerMassTSOA
+
|Aerosol products of terpene oxidation
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #1]]
+
|
+
 
+
|-valign="top"
+
|AerMassASOA
+
|Aerosol products of light aromatics + IVOC oxidation
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #3]]
+
|
+
 
+
|-valign="top"
+
|AerMassPOA
+
|Aerosols from SVOCs
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
*standard
+
*tropchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #4]]
+
|
+
 
+
|-valign="top"
+
|AerMassTSOA
+
|Aerosol products of terpene oxidation
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #1]]
+
|
+
 
+
|-valign="top"
+
|AerMassOPOA
+
|Aerosol products of POG oxidation
+
|ug/m3
+
|
+
|
+
*complexSOA_SVPOA
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #5]]
+
|
+
 
+
|-valign="top"
+
|TotalOA
+
|Sum of all organic aerosol
+
|ug/m3
+
|
+
|
+
*aerosol
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
*standard
+
*tropchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #6]]
+
|
+
*Will probably be renamed to AerMassTotalOA for consistency with other diagnostics in this collection
+
 
+
|-valign="top"
+
|TotalOC
+
|Sum of all organic carbon
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
*standard
+
*tropchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #7]]
+
|
+
*Will probably be renamed to AerMassTotalOC for consistency with other diagnostics in this collection
+
 
+
|-valign="top"
+
|BetaNO
+
|NO branching ratio
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #8]]
+
|
+
*Will probably be renamed to AerMassBetaNO for consistency with other diagnostics in this collection
+
 
+
|-valign="top"
+
|AerMassBC
+
|Black carbon (BCPI + BCPO)
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
*standard
+
*tropchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #13]]
+
|
+
 
+
|-valign="top"
+
|AerMassSO4
+
|Sulfate
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
*standard
+
*tropchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #14]]
+
|
+
 
+
|-valign="top"
+
|AerMassNH4
+
|Ammonium
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
*standard
+
*tropchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #15]]
+
|
+
 
+
|-valign="top"
+
|AerMassNIT
+
|Nitrate
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
*standard
+
*tropchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #16]]
+
|
+
 
+
|-valign="top"
+
|AerMassSAL
+
|Sea salt aerosol (SALA + SALC)
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
*standard
+
*tropchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #17]]
+
|
+
 
+
|-valign="top"
+
|PM25
+
|Particulate matter (r < 2.5 &mu;m)
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
*standard
+
*tropchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #18]]
+
|
+
*Will probably be renamed to AerMassBetaNO for consistency with other diagnostics in this collection
+
 
+
|-valign="top"
+
|AerMassSOAGX
+
|Aerosol-phase glyoxal
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
*standard
+
*tropchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #19]]
+
|
+
*New in [[GEOS-Chem v11-02|v11-02]]
+
 
+
|-valign="top"
+
|AerMassSOAMG
+
|Aerosol-phase methylglyoxal
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
*standard
+
*tropchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #20]]
+
|
+
*New in [[GEOS-Chem v11-02|v11-02]]
+
 
+
|-valign="top"
+
|AerMassSOAIE
+
|Aerosol-phase IEPOX
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #21]]
+
|
+
*New in [[GEOS-Chem v11-02|v11-02]]
+
 
+
|-valign="top"
+
|AerMassSOAME
+
|Aerosol-phase IMAE
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #22]]
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|AerMassINDIOL
+
|Generic aerosol-phase organonitrate hydrolysis product
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #23]]
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|AerMassLVOCOA
+
|Aerosol-phase low-volatility non-IEPOX product of ISOPOOH (RIP) oxidation
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #24]]
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|AerMassISN1OA
+
| Aerosol-phase 2nd generation hydroxynitrates formed from ISOP+NO3 reaction pathway
+
|ug/m3
+
|
+
|
+
*benchmark
+
*complexSOA
+
*complexSOA_SVPOA
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND42:_Aerosol_mass_and_PM2.5_diagnostics|ND42 #25]]
+
|
+
*New in v11-02
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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 [[GEOS-Chem_chemistry_mechanisms#Mechanisms_for_GEOS-Chem_v11-02|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 chemistry mechanism|UCX]] (i.e. benchmark, standard, aciduptake, marinePOA).''
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|AODDust
+
|Mineral dust optical depth for 1st wavelength specified in Radiation Menu
+
|1
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND21:_Cloud_diagnostics|ND21 #4]]
+
|
+
 
+
|-valign="top"
+
|AODDust_WL1_?DUSTBIN?
+
|AOD for 1st wavelength specified in Radiation Menu, for each dust bin
+
|1
+
|?DUSTBIN?
+
|
+
*all fullchem
+
*aerosol
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND21:_Cloud_diagnostics|ND21<br>#21 - #27]]
+
|
+
 
+
|-valign="top"
+
|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
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND21:_Cloud_diagnostics|ND21 #6, #9, #12, #15, #18]]
+
|
+
 
+
|-valign="top"
+
|AODSOAfromAqIsopreneWL1
+
|Optical depth of SOA from aqueous isoprene optical depth
+
|1
+
|
+
|
+
*benchmark
+
*complexSOA*
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND21:_Cloud_diagnostics|ND21 #58]]
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|AODStratLiquidAerWL1
+
|Stratospheric liquid aerosol optical depth (600 nm)
+
|
+
|
+
|
+
*UCX fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND21:_Cloud_diagnostics|ND21 #52]]
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|AODPolarStratCloudWL1
+
|Polar stratospheric cloud type 1a/2 optical depth (600 nm)
+
|1
+
|
+
|
+
*UCX fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND21:_Cloud_diagnostics|ND21 #56]]
+
|
+
 
+
|-valign="top"
+
|AerHygroscopicGrowth_<spcname>
+
|Hygroscopic growth of selected species (SO4, BC, OC, SALA, SALC)
+
|1
+
|?HYG?
+
|
+
*all fullchem
+
*aerosol
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND21:_Cloud_diagnostics|ND21 #7, #10, #13, #16, #19]]
+
|
+
 
+
|-valign="top"
+
|AerNumDensityStratLiquid
+
|Stratospheric liquid aerosol number density (UCX simulation only)
+
|1/cm3
+
|
+
|
+
*UCX fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND21:_Cloud_diagnostics|ND21 #54]]
+
|
+
 
+
|-valign="top"
+
|AerSurfAreaStratLiquid
+
|Stratospheric liquid aerosol surface area (UCX simulation only) 
+
|cm2/cm3
+
|
+
|
+
*UCX fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND21:_Cloud_diagnostics|ND21 #53]]
+
|
+
 
+
|-valign="top"
+
|AerSurfAreaPolarStratCloud
+
|Polar stratospheric cloud type 1a/2 surface area (UCX simulation only)
+
|cm2/cm3
+
|
+
|
+
*UCX fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND21:_Cloud_diagnostics|ND21 #56]]
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaMDUST1
+
|Dry aerosol area for mineral dust (bin R<sub>eff</sub> = 0.15 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaMDUST2
+
|Dry aerosol area for mineral dust (bin R<sub>eff</sub> = 0.25 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaMDUST3
+
|Dry aerosol area for mineral dust (bin R<sub>eff</sub> = 0.4 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaMDUST4
+
|Dry aerosol area for mineral dust (bin R<sub>eff</sub> = 0.8 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaMDUST5
+
|Dry aerosol area for mineral dust (bin R<sub>eff</sub> = 1.5 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaMDUST6
+
|Dry aerosol area for mineral dust (bin R<sub>eff</sub> = 2.5 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaMDUST7
+
|Dry aerosol area for mineral dust (bin R<sub>eff</sub> = 4.0 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaSULF
+
|Dry aerosol area for sulfate
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaBC
+
|Dry aerosol area for black carbon
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaOC
+
|Dry aerosol area for organic carbon
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaSSA
+
|Dry aerosol area for sea salt, accumulation mode
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaSSA
+
|Dry aerosol area for sea salt, coarse mode
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaBGSULF
+
|Dry aerosol area for background stratospheric sulfate
+
|cm2/cm3
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroAreaICEI
+
|Dry aerosol area for irregular ice cloud (Mischenko)
+
|cm2/cm3
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiMDUST1
+
|Dry aerosol radius for mineral dust (bin R<sub>eff</sub> = 0.15 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiMDUST2
+
|Dry aerosol radius for mineral dust (bin R<sub>eff</sub> = 0.25 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiMDUST3
+
|Dry aerosol radius for mineral dust (bin R<sub>eff</sub> = 0.4 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiMDUST4
+
|Dry aerosol radius for mineral dust (bin R<sub>eff</sub> = 0.8 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiMDUST5
+
|Dry aerosol radius for mineral dust (bin R<sub>eff</sub> = 1.5 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiMDUST6
+
|Dry aerosol radius for mineral dust (bin R<sub>eff</sub> = 2.5 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiMDUST7
+
|Dry aerosol radius for mineral dust (bin R<sub>eff</sub> = 4.0 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiSULF
+
|Dry aerosol radius for sulfate
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiBC
+
|Dry aerosol radius for black carbon
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiOC
+
|Dry aerosol radius for organic carbon
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiSSA
+
|Dry aerosol radius for sea salt, accumulation mode
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiusSSC
+
|Dry aerosol radius for sea salt, coarse mode
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiBGSULF
+
|Dry aerosol radius for background stratospheric sulfate
+
|cm
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AeroRadiusICEI
+
|Dry aerosol radius for irregular ice cloud (Mischenko)
+
|cm
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaMDUST1
+
|Wet aerosol area for mineral dust (bin R<sub>eff</sub> = 0.15 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaMDUST2
+
|Wet aerosol area for mineral dust (bin R<sub>eff</sub> = 0.25 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaMDUST3
+
|Wet aerosol area for mineral dust (bin R<sub>eff</sub> = 0.4 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaMDUST4
+
|Wet aerosol area for mineral dust (bin R<sub>eff</sub> = 0.8 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaMDUST5
+
|Wet aerosol area for mineral dust (bin R<sub>eff</sub> = 1.5 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaMDUST6
+
|Wet aerosol area for mineral dust (bin R<sub>eff</sub> = 2.5 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaMDUST7
+
|Wet aerosol area for mineral dust (bin R<sub>eff</sub> = 4.0 &mu;m)
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaSULF
+
|Wet aerosol area for sulfate
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaBC
+
|Wet aerosol area for black carbon
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaOC
+
|Wet aerosol area for organic carbon
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaSSA
+
|Wet aerosol area for sea salt, accumulation mode
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaSSA
+
|Wet aerosol area for sea salt, coarse mode
+
|cm2/cm3
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaBGSULF
+
|Wet aerosol area for background stratospheric sulfate
+
|cm2/cm3
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroAreaICEI
+
|Wet aerosol area for irregular ice cloud (Mischenko)
+
|cm2/cm3
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiMDUST1
+
|Wet aerosol radius for mineral dust (bin R<sub>eff</sub> = 0.15 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiMDUST2
+
|Wet aerosol radius for mineral dust (bin R<sub>eff</sub> = 0.25 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiMDUST3
+
|Wet aerosol radius for mineral dust (bin R<sub>eff</sub> = 0.4 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiMDUST4
+
|Wet aerosol radius for mineral dust (bin R<sub>eff</sub> = 0.8 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiMDUST5
+
|Wet aerosol radius for mineral dust (bin R<sub>eff</sub> = 1.5 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiMDUST6
+
|Wet aerosol radius for mineral dust (bin R<sub>eff</sub> = 2.5 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiMDUST7
+
|Wet aerosol radius for mineral dust (bin R<sub>eff</sub> = 4.0 &mu;m)
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiSULF
+
|Wet aerosol radius for sulfate
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiBC
+
|Wet aerosol radius for black carbon
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiOC
+
|Wet aerosol radius for organic carbon
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|WetChem_AeroRadiSSA
+
|Wet aerosol radius for sea salt, accumulation mode
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiusSSC
+
|Wet aerosol radius for sea salt, coarse mode
+
|cm
+
|
+
|
+
*all fullchem
+
*aerosol
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiBGSULF
+
|Wet aerosol radius for background stratospheric sulfate
+
|cm
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_WetAeroRadiusICEI
+
|Wet aerosol radius for irregular ice cloud (Mischenko)
+
|cm
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_StatePSC
+
|Polar stratospheric cloud type (cf Kirner et al, 2011, GMD)
+
|count
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_KhetiSLAN2O5H2O
+
|Sticking coeff. for N2O5 + H2O rxn
+
|1
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_KhetiSLAN2O5HCl
+
|Sticking coeff. for N2O5 + HCl rxn
+
|1
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_KhetiSLAClNO3H2O
+
|Sticking coeff. for ClNO3 + H2O rxn
+
|1
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_KhetiSLAClNO3HCl
+
|Sticking coeff. for ClNO3 + HCl rxn
+
|1
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_KhetiSLAClNO3HBr
+
|Sticking coeff. for ClNO3 + HBr rxn
+
|1
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_KhetiSLABrNO3H2O
+
|Sticking coeff. for BrNO3 + H2O rxn
+
|1
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_KhetiSLABrNO3HCl
+
|Sticking coeff. for BrNO3 + HCl rxn
+
|1
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_KhetiSLAHOClHCl
+
|Sticking coeff. for HOCl + HCl rxn
+
|1
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_KhetiSLAHOClBr
+
|Sticking coeff. for HOCl + HBr rxn
+
|1
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_KhetiSLAHOBrHCl
+
|Sticking coeff. for HOBr + HCl rxn
+
|1
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_KhetiSLAHOBrHCl
+
|Sticking coeff. for HOBr + HBr rxn
+
|1
+
|
+
|
+
*UCX fullchem
+
|
+
|
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:07, 7 June 2018 (UTC)
+
 
+
=== The Budget collection ===
+
 
+
The '''Budget''' diagnostic collection was introduced in [[GEOS-Chem 12#12.1.0|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 <tt>#</tt> 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:
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="125px"|Diagnostic name
+
!width="175px"|Description
+
!width="80px"|Units
+
!width="80px"|Wildcards
+
!width="80px"|Simulations
+
!width="80px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="250px"|Notes
+
 
+
|-valign="top"
+
|Budget'''XY'''_<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)
+
*Mixing<sup>1</sup>
+
*Convection
+
*Wet deposition
+
*Emissions and dry deposition<sup>2</sup>
+
Column regions '''Y''' include:
+
*Troposphere (Trop)
+
*PBL-only (PBL)
+
*Full column (Full)
+
|}
+
<sup>1</sup>The mixing budget diagnostics includes the application of emissions and dry deposition below the PBL if using the non-local PBL mixing scheme (vdiff).<br>
+
<sup>2</sup>The 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.
+
 
+
--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 21:33, 9 October 2018 (UTC)
+
 
+
=== The CH4 collection ===
+
 
+
The '''CH4''' collection contains diagnostics for loss of CH4 and OH concentration for the [[CH4 simulation|CH4 specialty simulation]].
+
 
+
Here is a sample definition section for the CH4 collection.  If this collection is not already present in the <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name.
+
 
+
  CH4.template:              '%y4%m2%d2_%h2%n2z.nc4',
+
  CH4.format:                'CFIO',
+
  CH4.frequency:              00000100 000000
+
  CH4.duration:              00000100 000000
+
  CH4.mode:                  'time-averaged'
+
  CH4.fields:                'OHconcAfterChem              ', 'GIGCchem',
+
                              'LossCH4byClinTrop            ', 'GIGCchem',
+
                              'LossCH4byOHinTrop            ', 'GIGCchem',
+
                              'LossCH4inStrat                ', 'GIGCchem',
+
::
+
 
+
This table describes the diagnostic quantities belonging to the CH4 collection:
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|LossCH4byClinTrop
+
|Loss of CH4 by reaction with Cl in the troposphere
+
|kg/s
+
|
+
|
+
*[[CH4 simulation|CH4]]
+
|
+
*[[List of diagnostics archived to bpch format#ND19: CH4 loss|ND19 #3]]
+
|
+
*New in [[GEOS-Chem 12#12.1.0|12.1.0]]
+
 
+
|-valign="top"
+
|LossCH4byOHinTrop
+
|Loss of CH4 by reaction with OH in the troposphere
+
|kg/s
+
|
+
|
+
*[[CH4 simulation|CH4]]
+
|
+
*[[List of diagnostics archived to bpch format#ND19: CH4 loss|ND19 #1]]
+
|
+
*New in [[GEOS-Chem 12#12.1.0|12.1.0]]
+
 
+
|-valign="top"
+
|LossCH4inStrat
+
|Loss of CH4 in the stratosphere
+
|kg/s
+
|
+
|
+
*[[CH4 simulation|CH4]]
+
|
+
*[[List of diagnostics archived to bpch format#ND19: CH4 loss|ND19 #2]]
+
|
+
*New in [[GEOS-Chem 12#12.1.0|12.1.0]]
+
 
+
|-valign="top"
+
|OHconcAfterChem
+
|OH concentration after chemistry
+
|kg/s
+
|
+
|
+
*[[CH4 simulation|CH4]]
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND43:_Chemical_production_of_OH_and_HO2|ND43 #1]]
+
|
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:20, 19 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 CH4 collection.  If this collection is not already present in the <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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:
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|CloudConvFlux_<spcname>
+
|Mass change due to cloud convection
+
|kg/s
+
|
+
*?ADV?
+
*?GAS?
+
*?WET?
+
|
+
*all simulations
+
|
+
*[[List of diagnostics archived to bpch format|ND14]]
+
|
+
*Will soon be replaced by new flux diagnostics
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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 [[GEOS-Chem_chemistry_mechanisms#Mechanisms_for_GEOS-Chem_v11-02|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 chemistry mechanism|UCX]] (i.e. benchmark, standard, aciduptake, marinePOA).''
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|OHconcAfterChem
+
|OH concentration immediately after exiting the FlexChem solver
+
|molec/cm3
+
|
+
|
+
*all fullchem
+
|
+
*[[List of diagnostics archived to bpch format|ND43]], #1
+
|
+
 
+
|-valign="top"
+
|HO2concAfterChem
+
|HO2 concentration immediately after exiting the FlexChem solver
+
|molec/cm3
+
|
+
|
+
*all fullchem
+
|
+
*[[List of diagnostics archived to bpch format|ND43]], #3
+
|
+
+
|-valign="top"
+
|O1DconcAfterChem
+
|O1D concentration immediately after exiting the FlexChem solver
+
|molec/cm3
+
|
+
|
+
*UCX fullchem
+
|
+
*[[List of diagnostics archived to bpch format|ND43]], #4
+
|
+
 
+
|-valign="top"
+
|O3PconcAfterChem
+
|O3P concentration immediately after exiting the FlexChem solver
+
|molec/cm3
+
|
+
|
+
*UCX fullchem
+
|
+
*[[List of diagnostics archived to bpch format|ND43]], #5
+
|
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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:
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|DryDepVel_<spcname>
+
|Dry deposition velocity
+
|cm/s
+
|
+
*?DRY?
+
|
+
*all simulations with drydep species
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND44:_Dry_deposition_diagnostics|ND44]]
+
|
+
 
+
|-valign="top"
+
|DryDepMix_<spcname>
+
|Dry deposition flux<br>(computed in PBL mixing)
+
|molec/cm2/s
+
|
+
*?DRY?
+
|
+
*all simulations with drydep species
+
|
+
|
+
 
+
|-valign="top"
+
|DryDepChm_<spcname>
+
|Dry deposition flux<br>(computed in chemistry)
+
|molec/cm2/s
+
|
+
*?DRY?
+
|
+
*all simulations with drydep species
+
|
+
|
+
 
+
|-valign="top"
+
|DryDep_<spcname>
+
|Total dry deposition flux
+
|molec/cm2/s
+
|
+
*?DRY?
+
|
+
*all simulations with drydep species
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND44:_Dry_deposition_diagnostics|ND44]]
+
|
+
*Sum of drydep flux in mixing and drydep flux in chemistry.
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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 [[GEOS-Chem_chemistry_mechanisms#Mechanisms_for_GEOS-Chem_v11-02|a full-chemistry mechanism]] (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).''
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|Jval_<spcname>
+
|Photolysis rates
+
|1/s
+
|
+
*?PHO?
+
|
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND22:_Photolysis_diagnostics|ND22]]
+
|
+
*We recommend using saving out instantaneous values with this collection.
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:38, 16 May 2018 (UTC)
+
 
+
=== The JValuesLocalNoon collection ===
+
 
+
<span style="color:red">'''''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)'''''</span>
+
 
+
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 <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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 [[GEOS-Chem_chemistry_mechanisms#Mechanisms_for_GEOS-Chem_v11-02|a full-chemistry mechanism]] (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).''
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|JNoon_<spcname>
+
|Photolysis rates (archived where it is local noon)
+
|1/s
+
|
+
*?PHO?
+
|
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND22:_Photolysis_diagnostics|ND22]]
+
|
+
*Currently debgugging an issue with locating the nearest box to noontime.
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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:
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|Met_CMFMC
+
|Upward moist convective mass flux
+
|kg/m2/s
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND66: GMAO 3-D met fields|ND66 #5]]
+
|
+
 
+
|-valign="top"
+
|Met_PEDGE
+
|Surface pressure at level edges (based on moist air)
+
|hP
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND31:_Pressure_at_model_edges|ND31 #1]]
+
|
+
 
+
|-valign="top"
+
|Met_PEDGEDRY
+
|Surface pressure at level edges (based on dry air)
+
|hP
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_PFICU
+
|3d flux of ice convective precipitation
+
|kg/m2/s
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_PFILSAN
+
|3d flux of ice non-convective precipitation
+
|kg/m2/s
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_PFLCU
+
|3d flux of liquid convective precipitation
+
|kg/m2/s
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_PFLLSAN
+
|3d flux of liquid non-convective precipitation
+
|kg/m2/s
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:23, 16 May 2018 (UTC)
+
 
+
=== The MercuryChem collection ===
+
 
+
<span style="color:darkorange">'''''NOTE: This collection is currently under development and is slated to be introduced into [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]].'''''</span>
+
 
+
The '''MercuryChem'' collection contains concentrations and prod/loss diagnostic outputs for the [[Mercury|Hg specialty simulationl]]
+
 
+
Here is a sample definition section for the MercuryEmis collection.  If this collection is not already present in the <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name.
+
 
+
  MercuryChem.template:      '%y4%m2%d2_%h2%n2z.nc4',
+
  MercuryChem.format:        'CFIO',
+
  MercuryChem.frequency:      00000000 040000
+
  MercuryChem.duration:      00000000 040000
+
  MercuryChem.mode:          'time-averaged'
+
  MercuryChem.fields:        'ConcBr                        ', 'GIGCchem',
+
                              'ConcBrO                      ', 'GIGCchem',
+
                              'LossHg2bySeaSalt              ', 'GIGCchem',
+
                              'LossRateHg2bySeaSalt          ', 'GIGCchem',
+
                              'PolarConcBr                  ', 'GIGCchem',
+
                              'PolarConcBrO                  ', 'GIGCchem',
+
                              'PolarConcO3                  ', 'GIGCchem',
+
                              'ProdHg2fromBr                ', 'GIGCchem',
+
                              'ProdHg2fromBrY                ', 'GIGCchem',
+
                              'ProdHg2fromClY                ', 'GIGCchem',
+
                              'ProdHg2fromHg0                ', 'GIGCchem',
+
                              'ProdHg2fromHgBrPlusBr2        ', 'GIGCchem',
+
                              'ProdHg2fromHgBrPlusBrBrO      ', 'GIGCchem',
+
                              'ProdHg2fromHgBrPlusBrClO      ', 'GIGCchem',
+
                              'ProdHg2fromHgBrPlusBrHO2      ', 'GIGCchem',
+
                              'ProdHg2fromHgBrPlusBrNO2      ', 'GIGCchem',
+
                              'ProdHg2fromHgBrPlusBrOH      ', 'GIGCchem',
+
                              'ProdHg2fromO3                ', 'GIGCchem',
+
                              'ProdHg2fromOH                ', 'GIGCchem',
+
                              'ParticulateBoundHg            ', 'GIGCchem',
+
                              'ReactiveGaseousHg            ', 'GIGCchem',
+
::
+
 
+
The table below describes the diagnostic quantities belonging to the MercuryEmis collection:
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|ConcBr
+
|Br concentration
+
|molec/cm3
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #9<br>(PL-HG2-$)]]
+
|
+
 
+
|-valign="top"
+
|ConcBrO
+
|BrO concentration
+
|molec/cm3
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #10<br>(PL-HG2-$)]]
+
|
+
 
+
|-valign="top"
+
|LossHg2bySeaSalt
+
|Loss of Hg2 by reaction with sea salt aerosols
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #4<br>(PL-HG2-$)]]
+
|
+
 
+
|-valign="top"
+
|LossRateHg2bySeaSalt
+
|Rate of loss of Hg2 by reaction with sea salt aerosols
+
|1/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #5<br>(PL-HG2-$)]]
+
|
+
 
+
|-valign="top"
+
|PolarConcBr
+
|Br concentration in polar regions
+
|pptv
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #13<br>(PL-HG2-$)]]
+
|
+
 
+
|-valign="top"
+
|PolarConcBrO
+
|BrO concentration in polar regions
+
|molec/cm3
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #14<br>(PL-HG2-$)]]
+
|
+
 
+
|-valign="top"
+
|PolarConcO3
+
|O3 concentration in polar regions
+
|molec/cm3
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #15<br>(PL-HG2-$)]]
+
|
+
 
+
|}
+
 
+
=== The MercuryEmis Collection ===
+
 
+
<span style="color:darkorange">'''''NOTE: This collection is currently under development and is slated to be introduced into [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]].'''''</span>
+
 
+
The '''MercuryEmis''' collection contains emission diagnostics for the [[Mercury|Hg specialty simulation]].
+
 
+
Here is a sample definition section for the MercuryEmis collection.  If this collection is not already present in the <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name.
+
 
+
  MercuryEmis.template:      '%y4%m2%d2_%h2%n2z.nc4',
+
  MercuryEmis.format:        'CFIO',
+
  MercuryEmis.frequency:      00000000 040000
+
  MercuryEmis.duration:      00000000 040000
+
  MercuryEmis.mode:          'time-averaged'
+
  MercuryEmis.fields:        'EmisHg0anthro                ', 'GIGCchem',
+
                              'EmisHg0biomass                ', 'GIGCchem',
+
                              'EmisHg0geogenic              ', 'GIGCchem',
+
                              'EmisHg0land                  ', 'GIGCchem',
+
                              'EmisHg0ocean                  ', 'GIGCchem',
+
                              'EmisHg0soil                  ', 'GIGCchem',
+
                              'EmisHg0snow                  ', 'GIGCchem',
+
                              'EmisHg0vegetation            ', 'GIGCchem',
+
                              'EmisHg2HgPanthro              ', 'GIGCchem',
+
                              'EmisHg2snowToOcean            ', 'GIGCchem',
+
                              'EmisHg2rivers                ', 'GIGCchem',
+
                              'FluxHg2HgPfromAirToSnow      ', 'GIGCchem',
+
::
+
 
+
The table below describes the diagnostic quantities belonging to the MercuryEmis collection:
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|EmisHg0anthro
+
|Emission of Hg0 from anthropogenic sources
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #1<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|EmisHg0biomass
+
|Emissions of Hg0 from biomass burning
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #17<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|EmisHg0geogenic
+
|Emissions of Hg0 from geogenic sources
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #5<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|EmisHg0land
+
|Re-emission of Hg0 from land
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #4<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|EmisHg0ocean
+
|Emissions of Hg0 from oceans
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #3<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|EmisHg0snow
+
|Emission of Hg0 from snowpack
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #18<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|EmisHg0soil
+
|Emissions of Hg0 from soils
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #15<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|EmisHg0vegetation
+
|Emission of Hg0 from vegetation
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #14<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|EmisHg2HgPanthro
+
|Emission of Hg2 + HgP from anthropogenic sources
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #9<br>(HG-SRCE)]]
+
|
+
*NOTE: HgP is emitted as Hg2 in HEMCO_Config.rc.
+
 
+
|-valign="top"
+
|EmisHg2snowToOcean
+
|Hg2 delivered to oceans from melting snow
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #19<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|EmisHg2rivers
+
|Emissions of Hg2 from delivered to oceans from melting snow
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #22<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|FluxHg2HgPfromAirToSnow
+
|Deposition flux of Hg2 + HgP from the atmosphere onto snow
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #21<br>(HG-SRCE)]]
+
|
+
 
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:42, 26 October 2018 (UTC)
+
 
+
=== The MercuryOcean collection ===
+
 
+
<span style="color:darkorange">'''''NOTE: This collection is currently under development and is slated to be introduced into [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]].'''''</span>
+
 
+
The '''MercuryOcean''' collection contains diagnostics from the mercury ocean model, used in the [[Mercury|Hg specialty simulaton]].
+
 
+
Here is a sample definition section for the MercuryOcean collection.  If this collection is not already present in the <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name.
+
 
+
  MercuryOcean.template:      '%y4%m2%d2_%h2%n2z.nc4',
+
  MercuryOcean.format:        'CFIO',
+
  MercuryOcean.frequency:    00000000 040000
+
  MercuryOcean.duration:      00000000 040000
+
  MercuryOcean.mode:          'time-averaged'
+
  MercuryOcean.fields:        'FluxHg0fromAirToOcean        ', 'GIGCchem',
+
                              'FluxHg0fromOceanToAir        ', 'GIGCchem',
+
                              'FluxHg2HgPfromAirToOcean      ', 'GIGCchem',
+
                              'FluxHg2toDeepOcean            ', 'GIGCchem',
+
                              'FluxOCtoDeepOcean            ', 'GIGCchem',
+
                              'MassHg0inOcean                ', 'GIGCchem',
+
                              'MassHg2inOcean                ', 'GIGCchem',
+
                              'MassHgPinOcean                ', 'GIGCchem',
+
                              'MassHgTotalInOcean            ', 'GIGCchem',
+
::
+
 
+
The table below describes diagnostic quantities belonging to the MercuryOcean collection
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|FluxHg0fromAirToOcean
+
|Deposition flux of Hg0 from the atmosphere to the ocean
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #16<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|FluxHg0fromOceanToAir
+
|Volatilizatoin flux of Hg0 from the ocean to the atmosphere
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #17<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|FluxHg2HgPfromAirToOcean
+
|Deposition flux of Hg2 + HgP from the atmosphere to the ocean
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #20<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|FluxHg2toDeepOcean
+
|Flux of Hg2 sunk to the deep ocean
+
|kg/s
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #8<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|MassHg0inOcean
+
|Total mass of oceanic Hg0
+
|kg
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #2<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|MassHg2inOcean
+
|Total mass of oceanic Hg2
+
|kg
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #7<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|MassHgPinOcean
+
|Total mass of oceanic Hg2
+
|kg
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #11<br>(HG-SRCE)]]
+
|
+
 
+
|-valign="top"
+
|MassHgTotalInOcean
+
|Total mass of all organic mercury
+
|kg
+
|
+
|
+
*Hg
+
*tagHg
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND03: Mercury emissions and P/L|ND03 #10<br>(HG-SRCE)]]
+
|
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:56, 26 October 2018 (UTC)
+
 
+
=== The POPS collection ===
+
 
+
<span style="color:darkorange">'''''NOTE: This collection is currently under development and is slated to be introduced into [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]].'''''</span>
+
 
+
The '''POPS''' collection contains diagnostic quantities for the [[POPs simulation|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 <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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',
+
  ::
+
 
+
The table below describes diagnostic quantities belonging to the POPS collection.
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|EmisPOPPOCPO
+
|Particulate (hydrophobic organic carbon) POPS emissions
+
|kg/m2/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #2]]
+
|
+
 
+
|-valign="top"
+
|EmisPOPPBCPO
+
|Particulate (hydrophobic black carbon) POPS emissions
+
|kg/m2/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #3]]
+
|
+
 
+
 
+
|-valign="top"
+
|EmisPOPG
+
|POPG (gas-phase) POPS emissions
+
|kg/m2/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #4]]
+
|
+
 
+
|-valign="top"
+
|EmisPOPGfromSoil
+
|Secondary emission of POPG from soils
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #5]]
+
|
+
 
+
|-valign="top"
+
|EmisPOPGfromLake
+
|Secondary emission of POPG from lakes
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #6]]
+
|
+
 
+
|-valign="top"
+
|EmisPOPGfromLeaf
+
|Secondary emission of POPG from leaves
+
|kg/m2/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #7]]
+
|
+
 
+
|-valign="top"
+
|FluxPOPGfromSoilToAir
+
|Secondary (positive) flux of POPG from soils to air
+
|ng/m2/day
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #8]]
+
|
+
 
+
|-valign="top"
+
|FluxPOPGfromAirToSoil
+
|Secondary (negative) flux of POPG from air to soil
+
|ng/m2/day
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #9]]
+
|
+
 
+
|-valign="top"
+
|FluxPOPGfromLakeToAir
+
|Secondary (positive) flux of POPG from lakes to air
+
|ng/m2/day
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #10]]
+
|
+
 
+
|-valign="top"
+
|FluxPOPGfromAirToLake
+
|Secondary (negative) flux of POPG from air to lakes
+
|ng/m2/day
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #11]]
+
|
+
 
+
|-valign="top"
+
|FluxPOPGfromLeafToAir
+
|Secondary (positive) flux of POPG from leaves to air
+
|ng/m2/day
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #12]]
+
|
+
 
+
|-valign="top"
+
|FluxPOPGfromAirToLeaf
+
|Secondary (negative) flux of POPG from air to leaves
+
|ng/m2/day
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #13]]
+
|
+
 
+
|-valign="top"
+
|FugacitySoilToAir
+
|Fugacity ratio: soil/air
+
|1
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #14]]
+
|
+
 
+
|-valign="top"
+
|FugacityLakeToAir
+
|Fugacity ratio: lake/air
+
|1
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #15]]
+
|
+
 
+
|-valign="top"
+
|FugacityLeafToAir
+
|Fugacity ratio: leaf/air
+
|1
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #16]]
+
|
+
 
+
|-valign="top"
+
|LossPOPPOCPObyGasPhase
+
|Gross POP OC lost to gas
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #17]]
+
|
+
 
+
|-valign="top"
+
|LossPOPPOCPObyGasPhase
+
|Gross POP OC produced from gas
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #18]]
+
|
+
 
+
|-valign="top"
+
|LossPOPPBCPObyGasPhase
+
|Gross POP BC lost to gas
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #19]]
+
|
+
 
+
|-valign="top"
+
|LossPOPPBCPObyGasPhase
+
|Gross POP BC produced from gas
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #20]]
+
|
+
 
+
|-valign="top"
+
|ProdPOPGfromOH
+
|Production of oxidized POPG from reaction with OH
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #21]]
+
|
+
 
+
|-valign="top"
+
|ProdPOPPOCPOfromO3
+
|Production of oxidized POPPOCPO from reaction with O3
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #22]]
+
|
+
 
+
|-valign="top"
+
|ProdPOPPOCPIfromO3
+
|Production of oxidized POPPOCPI from reaction with O3
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #23]]
+
|
+
 
+
|-valign="top"
+
|ProdPOPPBCPOfromO3
+
|Production of oxidized POPPBCPO from reaction with O3
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #24]]
+
|
+
 
+
|-valign="top"
+
|ProdPOPPBCPIfromO3
+
|Production of oxidized POPPBCPI from reaction with O3
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND53 #25]]
+
|
+
 
+
|-valign="top"
+
|ProdPOPPOCPOfromNO3
+
|Production of oxidized POPPOCPO from reaction with NO3
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND05 #26]]
+
|
+
 
+
|-valign="top"
+
|ProdPOPPOCPIfromNO3
+
|Production of oxidized POPPOCPI from reaction with NO3
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND05 #27]]
+
|
+
 
+
|-valign="top"
+
|ProdPOPPBCPOfromNO3
+
|Production of oxidized POPPBCPO from reaction with NO3
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND05 #28]]
+
|
+
 
+
|-valign="top"
+
|ProdPOPPBCPIfromNO3
+
|Production of oxidized POPPBCPI from reaction with NO3
+
|kg/s
+
|
+
|
+
*POPs
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND53:_POPs_diagnostics|ND05 #29]]
+
|
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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 [[GEOS-Chem_chemistry_mechanisms#Mechanisms_for_GEOS-Chem_v11-02|a full-chemistry mechanism]] (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).''
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign=top"
+
!colspan="7" bgcolor="#CCFFFF"|Diagnostics applicable only to the aciduptake simulation
+
 
+
|-valign="top"
+
|ProdSO4fromOxidationOnDust
+
|Production of SO4 from oxidation on dust aerosols
+
|kg S/s
+
|
+
|
+
*aciduptake
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #12]]
+
|
+
 
+
|-valign="top"
+
|ProdNITfromHNO3uptakeOnDust
+
|Production of NIT from HNO3 uptake on dust aerosols
+
|kg N/s
+
|
+
|
+
*aciduptake
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #13]]
+
|
+
 
+
|-valign="top"
+
|ProdSO4fromUptakeOfH2SO4g
+
|Production of SO4 from uptake of H2SO4(g)
+
||kg S/s
+
|
+
|
+
*aciduptake
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #14]]
+
|
+
 
+
|-valign=top"
+
!colspan="7" bgcolor="#CCFFFF"|Diagnostics applicable only to the aerosol-only simulation
+
 
+
|-valign="top"
+
|ProdSO2fromDMSandOH
+
|Production of SO2 from DMS + OH (in sulfate_mod.F)
+
|kg S/s
+
|
+
|
+
*aerosol
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #1]]
+
|
+
 
+
|-valign="top"
+
|ProdSO2fromDMSandNO3
+
|Production of SO2 from DMS + NO3R
+
|kg S/s
+
|
+
|
+
*aerosol
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #2]]
+
|
+
 
+
|-valign="top"
+
|ProdSO2fromDMS
+
|Total P(SO2) from DMS
+
|kg S/s
+
|
+
|
+
*aerosol
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #3]]
+
|
+
 
+
|-valign="top"
+
|ProdMSAfromDMS
+
|Production of MSA from DMS
+
|kg S/s
+
|
+
|
+
*aerosol
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #4]]
+
|
+
 
+
|-valign="top"
+
|ProdSO4fromGasPhase
+
|Production of SO4 in the gas phase
+
|kg S/s
+
|
+
|
+
*aerosol
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #5]]
+
|
+
 
+
|-valign=top"
+
!colspan="7" bgcolor="#CCFFFF"|Diagnostics applicable only to the aerosol-only and all fullchem simulations
+
 
+
|-valign="top"
+
|ProdBCPIfromBCPO
+
|Production of hydrophilic BC from hydrophobic BCs
+
|kg
+
|
+
|
+
*aerosol
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07 #4]]
+
|
+
 
+
|-valign="top"
+
|ProdOCPIfromOCPO
+
|Production of hydrophilic BC from hydrophobic BCs
+
|kg
+
|
+
|
+
*aerosol
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07 #9]]
+
|
+
 
+
|-valign="top"
+
|ProdSO4fromH2O2inCloud
+
|Production of SO4 from aqueous oxidation of H2O2 in clouds
+
|kg S/s
+
|
+
|
+
*aerosol
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #6]]
+
|
+
 
+
|-valign="top"
+
|ProdSO4fromO2inCloudMetal
+
|Production of SO4 from aqueous oxidation of O2 from metals in cloud
+
|kg S/s
+
|
+
|
+
*aerosol
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #8]]
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|ProdSO4fromO3inCloud
+
|Production of SO4 from aqueous oxidation of O3 in clouds
+
|kg S/s
+
|
+
|
+
*aerosol
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #7]]
+
|
+
 
+
|-valign="top"
+
|ProdSO4fromO3inSeaSalt
+
|Production of SO4 from O3 in sea salt
+
|kg S/s
+
|
+
|
+
*aerosol
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #9]]
+
|
+
 
+
|-valign="top"
+
|ProdSO4fromO3s
+
|Production of SO4 from aqueous phase SO3-- loss by OH
+
|kg S/s
+
|
+
|
+
*aerosol
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #19]]
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|ProdSO4fromSRO3
+
|Production of SO4 from sulfur production rate of O3
+
|kg S/s
+
|
+
|
+
*aerosol
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #17]]
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|LossHNO3onSeaSalt
+
|Loss of HNO3 on sea salt aerosols
+
|kg S/s
+
|
+
|
+
*aerosol
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07 #15]]
+
|
+
 
+
|-valign=top"
+
!colspan="7" bgcolor="#CCFFFF"|Diagnostics applicable only to full-chemistry simulations
+
 
+
|-valign="top"
+
|ProdSO4fromHOBrinCloud
+
|Production of SO4 from aqueous oxidation of HOBr in clouds
+
|kg S/s
+
|
+
|
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #16]]
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|ProdSO4fromSRHOBr
+
|Production of SO4 from sulfur production rate of HOBr+O3
+
|kg S/s
+
|
+
|
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #18]]
+
|
+
*New in v11-02
+
 
+
|-valign=top"
+
!colspan="7" bgcolor="#CCFFFF"|Diagnostics for production and loss of species or chemical families (e.g. Ox)
+
 
+
|-valign="top"
+
|Prod_<spcname>
+
|Chemical production for a given species or family
+
|molec/cm3/s
+
|
+
*?PRD?
+
|
+
*all fullchem
+
*tagCO
+
*tagO3
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND65:_Chemical_production_and_loss_diagnostics|ND65]]
+
|
+
 
+
|-valign="top"
+
|Loss_<spcname>
+
|Chemical loss for a given species or family
+
|molec/cm3/s
+
|
+
*?LOS?
+
|
+
*all fullchem
+
*tagCO
+
*tagO3
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND65:_Chemical_production_and_loss_diagnostics|ND65]]
+
|
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:25, 17 May 2018 (UTC)
+
 
+
=== The RadioNuclide Collection ===
+
 
+
The '''RadioNuclide''' collection contains diagnostic outputs from the [[Rn-Pb-Be simulation|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|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 <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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.
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|PbFromRnDecay
+
|Production of 210Pb from 222Rn radioactive decay
+
|kg/s
+
|
+
|
+
*Rn-Pb-Be
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND01:_Rn-Pb-Be_sources|ND01 #2]]
+
|
+
 
+
|-valign="top"
+
|RadDecay_Rn
+
|Loss of 222Rn due to radiactive decay
+
|kg/s
+
|
+
|
+
*Rn-Pb-Be
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND01:_Rn-Pb-Be_decay|ND02 #1]]
+
|
+
 
+
|-valign="top"
+
|RadDecay_Pb
+
|Loss of 210Pb due to radiaoactive decay
+
|kg/s
+
|
+
|
+
*Rn-Pb-Be
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND01:_Rn-Pb-Be_decay|ND02 #2]]
+
|
+
 
+
|-valign="top"
+
|RadDecay_Be7
+
|Loss of 7Be due to radioactive decay
+
|kg/s
+
|
+
|
+
*Rn-Pb-Be
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND02:_Rn-Pb-Be_decay|ND02 #3]]
+
|
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:56, 22 May 2018 (UTC)
+
 
+
=== The StateChm Collection ===
+
 
+
The '''StateChm ''' collection contains quantities from <tt>State_Chm</tt>, 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 <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name.
+
 
+
Other fields of the <tt>State_Chm</tt> object can be added to this collection by prefixing the field name with <tt>Chem_</tt>.
+
 
+
  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 [[GEOS-Chem_chemistry_mechanisms#Mechanisms_for_GEOS-Chem_v11-02|a full-chemistry mechanism]] (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).''
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|Chem_phSav
+
|ISORROPIA aerosol pH
+
|1
+
|
+
|
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND73:_ISORROPIA_diagnostics|ND73 #1]]
+
|
+
 
+
|-valign="top"
+
|Chem_HplusSav
+
|ISORROPIA H+ concentration
+
|M
+
|
+
|
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND73:_ISORROPIA_diagnostics|ND73 #2]]
+
|
+
 
+
|-valign="top"
+
|Chem_WaterSav
+
|ISORROPIA aerosol water
+
|&mu;g/m3
+
|
+
|
+
*all fullchem
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND73:_ISORROPIA_diagnostics|ND73 #3]]
+
|
+
 
+
|-valign="top"
+
|Chem_SulRatSav
+
|ISORROPIA sulfate concentration
+
|M
+
|
+
|
+
*all fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_NaRatSav
+
|ISORROPIA Na+ concentration
+
|M
+
|
+
|
+
*all fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_AcidPurSav
+
|ISORROPIA acidpur ?? concentration
+
|M
+
|
+
|
+
*all fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_BiSulSav
+
|ISORROPIA bisulfate (general acid) concentration
+
|M
+
|
+
|
+
*all fullchem
+
|
+
|
+
 
+
|-valign="top"
+
|Chem_phCloud
+
|Cloud PH
+
|1
+
|
+
|
+
*all fullchem
+
|
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|Chem_SSAlk
+
|Sea salt alkalinity
+
|1
+
|
+
|
+
*all fullchem
+
|
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|Chem_HSO3AQ
+
|Cloud bisulfite concentration
+
|mol/L
+
|
+
|
+
*all fullchem
+
|
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|Chem_SO3AQ
+
|Cloud sulfite concentration
+
|mol/L
+
|
+
|
+
*all fullchem
+
|
+
|
+
*New in v11-02
+
 
+
|-valign="top"
+
|Chem_fupdateHOBr
+
|Correction factor for HOBr removal by SO2
+
|mol/L
+
|
+
|
+
*all fullchem
+
|
+
|
+
*New in v11-02
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>State_Met</tt> object.
+
 
+
Here is a sample definition section for the '''StateMet''' collection.  If this collection is not already present in the <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
+
 
+
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name.
+
 
+
Other fields of the <tt>State_Met</tt> object can be added to this collection by prefixing the field name with <tt>Met_</tt>.
+
 
+
  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',
+
::
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="225px"|Diagnostic name
+
!width="225px"|Description
+
!width="125px"|Units
+
!width="80px"|Wildcards
+
!width="150px"|Simulations
+
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
+
!width="150px"|Notes
+
 
+
|-valign="top"
+
|Met_AD
+
|Visible surface albedo
+
|1
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND68: Air mass and related quantities|ND68 #2]]
+
|
+
 
+
|-valign="top"
+
|Met_AIRDEN
+
|Dry air density
+
|kg/m3
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_AIRVOL
+
|Grid box volume, dry air
+
|m3
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_ALBD
+
|Surface albedo
+
|1
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND67: GMAO 2-D met fields|ND67 #14]]
+
|
+
 
+
|-valign="top"
+
|Met_AREAM2
+
|Grid box area
+
|m2
+
|
+
|
+
*all simulations
+
|
+
|
+
*AREA is written to each netCDF file
+
 
+
|-valign="top"
+
|Met_AVGW
+
|Water vapor volume mixing ratio
+
|vol H2O/vol dry air
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND68: Air mass and related quantities|ND68 #3]]
+
|
+
 
+
|-valign="top"
+
|Met_BXHEIGHT
+
|Grid box height
+
|m
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND68: Air mass and related quantities|ND68 #1]]
+
|
+
 
+
|-valign="top"
+
|Met_ChemGridLev
+
|Chemistry grid level
+
|1
+
|
+
|
+
*all simulations
+
|
+
|
+
*Equivalent to ITS_IN_THE_CHEMGRID
+
 
+
|-valign="top"
+
|Met_CLDF
+
|3-D cloud fraction
+
|1
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND21: Cloud diagnostics|ND21 #2]]
+
|
+
 
+
|-valign="top"
+
|Met_CLDFRC
+
|Column cloud fraction
+
|1
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND67: GMAO 2-D met fields|ND67 #10]]
+
|
+
 
+
|-valign="top"
+
|Met_CLDTOPS
+
|Maximum cloud top height
+
|1
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND67: GMAO 2-D met fields|ND67 #16]]
+
|
+
 
+
|-valign="top"
+
|Met_DELP
+
|Delta-pressure between top and bottom edges of grid box (wet air)
+
|hPa
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_DQRCU
+
|Convective precipitation production rate (dry air)
+
|kg/kg/s
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_DTRAIN
+
|Detrainment flux
+
|kg/m2/s
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND66: GMAO 3-D met fields|ND66 #6]]
+
|
+
 
+
|-valign="top"
+
|Met_EFLUX
+
|Latent heat flux
+
|W/m2
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND67: GMAO 2-D met fields|ND67 #2]]
+
|
+
 
+
|-valign="top"
+
|Met_FRCLND
+
|Olson land fraction
+
|1
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_FRLAKE
+
|Fraction of grid box covered by lakes
+
|1
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_FRLAND
+
|Fraction of grid box covered by land
+
|1
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_FRLANDIC
+
|Fraction of grid box covered by land ice
+
|1
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_FROCEAN
+
|Fraction of grid box covered by ocean
+
|1
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_FRSEAICE
+
|Fraction of grid box covered by sea ice
+
|1
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_FRSNO
+
|Fraction of grid box covered by snow
+
|1
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_GWETROOT
+
|Root soil moisture
+
|1
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_GWETTOP
+
|Topsoil moisture
+
|1
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND67: GMAO 2-D met fields|ND67 #2]]
+
|
+
 
+
|-valign="top"
+
|Met_HFLUX
+
|Sensible heat flux
+
|W/m2
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND67: GMAO 2-D met fields|ND67 #1]]
+
|
+
 
+
|-valign="top"
+
|Met_LAI
+
|Leaf area index from met field archive
+
|m2/m2
+
|
+
|
+
*all simulations
+
|
+
|
+
*Lacks interannual variability; use MODIS LAI instead
+
 
+
|-valign="top"
+
|Met_LWI
+
|Land-water-ice indices
+
|1
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND30:_Land_map|ND30 #1]]
+
|
+
 
+
|-valign="top"
+
|Met_PARDF
+
|Diffuse photosynthetically active radiation
+
|W/m2
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND67: GMAO 2-D met fields|ND67 #20]]
+
|
+
 
+
|-valign="top"
+
|Met_PARDR
+
|Diffuse photosynthetically active radiation
+
|W/m2
+
|
+
|
+
*all simulations
+
|
+
*[[List_of_diagnostics_archived_to_bpch_format#ND67: GMAO 2-D met fields|ND67 #21]]
+
|
+
 
+
|-valign="top"
+
|Met_PBLTOPL
+
|PBL top layer
+
|1
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_PBLH
+
|PBL height
+
|m
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_PHIS
+
|Surface geopotential height
+
|m2/s2
+
|
+
|
+
*all simulations
+
|
+
|
+
= Height * g
+
 
+
|-valign="top"
+
|Met_PMID
+
|Pressure at midpoint of model layers, defined as arithmetic average of edge pressures (wet air)
+
|hPa
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+
|-valign="top"
+
|Met_PMIDDRY
+
|Pressure at midpoint of model layers, defined as arithmetic average of edge pressures (dry air)
+
|hPa
+
|
+
|
+
*all simulations
+
|
+
|
+
 
+