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==feel free to experiment here ==
=== Species added ===


== Overview ==
Species added between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:


=== An introduction to netCDF diagnostics ===
{| border=1 cellspacing=0 cellpadding=5
!width='100px' bgcolor='#CCCCCC'|Name
!width='100px' bgcolor='#CCCCCC'|Formula
!width='200px' bgcolor='#CCCCCC'|Fullname
!width='30px' bgcolor='#CCCCCC'|Advected
!width='30px' bgcolor='#CCCCCC'|Dry deposited
!width='30px' bgcolor='#CCCCCC'|Gas
!width='30px' bgcolor='#CCCCCC'|Photolyzed
!width='30px' bgcolor='#CCCCCC'|Wet deposited


Bob Yantosca has created [[Media:Netcdf_Diagnostics.pdf|an overview presentation about the new netCDF diagnostics for v11-02]]. 
|-valign='top'
 
|ACO3
=== Sample HISTORY.rc diagnostic input file ===
|C3H3O3
 
|Peroxyacetyl radical for APAN
Here is a sample <tt>HISTORY.rc</tt> file that is used to request netCDF diagnostic output from a GEOS-Chem “Classic” simulation. 
|
 
|
#===================================================================
|X
# Declare collection names.  Disable collections by commenting
|
# each collection name out with a "#" character.
|
  #===================================================================
COLLECTIONS: <span style="color:red">'SpeciesConc'</span>,
|-valign='top'
              <span style="color:blue">'ConcAfterChem'</span>,
|ACR
  ::
|C3H4O
#===================================================================
|Acrolein
# Collection to save out GEOS-Chem species concentrations
|X
  #===================================================================
|X
<span style="color:red">SpeciesConc</span>.<span style="color:gray">template:    '%y4%m2%d2_%h2%n2z.nc4'</span>,
|X
  <span style="color:red">SpeciesConc</span>.<span style="color:darkorange">frequency:    060000</span>,
|X
<span style="color:red">SpeciesConc</span>.format:      'CFIO',
|
<span style="color:red">SpeciesConc</span>.<span style="color:purple">duration:    240000</span>,
<span style="color:red">SpeciesConc</span>.<span style="color:brown">mode:        'instantaneous'</span>,
|-valign='top'
<span style="color:red">SpeciesConc</span>.<span style="color:green">fields:      'SpeciesConc_?ADV?'</span>, 'GIGCchem',
|ACRO2
::
|C3H5O4
#===================================================================
|Peroxy radical from ACR
# Collection to save out concentrations after chemistry
|
# (from the FlexChem/KPP solver)
|
#===================================================================
|X
<span style="color:blue">ConcAfterChem</span>.<span style="color:gray">template:  '%y4%m2%d2_%h2%n2z.nc4'</span>,
|
<span style="color:blue">ConcAfterChem</span>.<span style="color:magenta">frequency:  000100 000000</span>,
|
<span style="color:blue">ConcAfterChem</span>.format:    'CFIO',
<span style="color:blue">ConcAfterChem</span>.<span style="color:purple">duration:  000100 000000</span>,
|-valign='top'
<span style="color:blue">ConcAfterChem</span>.<span style="color:darkcyan">mode:      'time-averaged'</span>,
|ALK7
<span style="color:blue">ConcAfterChem</span>.<span style="color:green">fields:    'OHconcAfterChem'</span>,    'GIGCchem',
|C7H16
                          <span style="color:green">'HO2concAfterChem'</span>,    'GIGCchem',
|Lumped >= C6 Alkanes
                          <span style="color:green">'O1DconcAfterChem'</span>,    ‘GIGCchem’,
|X
                          <span style="color:green">'O3PconcAfterChem'</span>,    ‘GIGCchem’,
|
::
|X
 
|
In this <tt>HISTORY.rc</tt> file, we are requesting two collections, or types of netCDF file output.
|
 
{| border=1 cellspacing=0 cellpadding=5
|-valign='top'
|-valign="top" bgcolor="#CCCCCC"
|APAN
!width="200px"|Attribute
|C3H3NO5
!width="900px"|Explanation
|Peroxyacryloyl nitrate
 
|X
|-valign="top"
|X
|<tt><span style="color:red">SpeciesConc</span></tt>
|X
|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.
|X
 
|X
|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:gray">template</span></tt>
|-valign='top'
|Determines the date and time format for each netCDF file name belonging to the <tt><span style="color:red">SpeciesConc</span></tt> collection.
|APINN
*The string <tt>%y4%m2%d2_%h2%n2z.nc4</tt> will print <tt>YYYYMMDD_hhmmz.nc4</tt> to the end of each netCDF filename
|C10H17NO4
**<tt>YYYYMMDD</tt> is the date in year/month/day format
|1st gen organic nitrate from APIN
**<tt>hhmm</tt> is the time in hour:minutes format.
|X
**<tt>z</tt> denotes "Zulu", which is an abbreviation for UTC time.
|X
**<tt>.nc4</tt> denotes that the data file is in the netCDF-4 format.
|X
 
|X
|-valign="top"
|X
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:darkorange">frequency</span></tt>
|Determines how often the diagnostic quantities belonging to <tt><span style="color:red">SpeciesConc</span></tt> collection will be saved to a netCDF file.
|-valign='top'
*This can be specified as either "<tt>hhmmss</tt>" or "<tt>YYMMDD hhmmss</tt>".
|APINO2
*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.)
|C10H17O3
 
|Peroxy radical from APIN
|-valign="top"
|
|<tt><span style="color:red">SpeciesConc</span>.format</tt>
|
|Indicates the I/O library that will be used (for GCHP simulations only).
|X
 
|
|-valign="top"
|
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:purple">duration</span></tt>
|Determines how often a new <tt><span style="color:red">SpeciesConc</span></tt> netCDF file will be created. 
|-valign='top'
*This can be specified as either <tt>hhmmss</tt> or <tt>YYMMDD hhmmss</tt>.
|APINP
*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>.
|C10H18O3
 
|Hydroperoxide from APIN
|-valign="top"
|X
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:brown">mode</span></tt>
|X
|Determines the averaging method for the <tt><span style="color:red">SpeciesConc</span></tt> collection
|X
*In this example, <tt><span style="color:red">SpeciesConc</span></tt> is defined as an <tt><span style="color:brown">instantaneous</span></tt> (aka "time-series") collection. 
|
*Diagnostic quantities belonging to <tt><span style="color:red">SpeciesConc</span></tt> will be written directly to disk without any temporal averaging, at the specified <tt><span style="color:darkorange">frequency</span></tt>.
|X
 
|-valign="top"
|-valign='top'
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:green">fields</span></tt>
|AROMCHO
|Lists the diagnostic quantities to be included in the <tt><span style="color:red">SpeciesConc</span></tt> collection.
|C5H6O4
*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.
|ACCOMECHO from MCM
*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.
|X
 
|X
See the sections below contain in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format.
|X
 
|
NOTE: You may use wildcards to request a subset of all possible chemical species.  See the next section for more information about wildcards.
|X
 
|-valign="top"
|-valign='top'
|<tt>::</tt>
|AROMCO3
|Signifies the end of the <tt><span style="color:red">SpeciesConc</span></tt> definition section.
|C5H5O6
*"<tt>::</tt>" may be placed at any column in the file.
|Lumped aromatic peroxyacetyl radical
 
|
|-valign="top"
|
|<tt><span style="color:blue">ConcAfterChem</span></tt>
|X
|Name of the second collection in this <tt>HISTORY.rc</tt> file.
|
 
|
|-valign="top"
   
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:gray">template</span></tt>
|-valign='top'
|Determines the date and time format for each netCDF file name belonging to the <tt><span style="color:blue">ConcAfterChem</span></tt> collection.
|AROMPN
 
|C5H5NO8
|-valign="top"
|Lumped PN from aromatics
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:magenta">frequency</span></tt>
|X
|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.
|X
*This can be can be specified as either "<tt>hhmmss</tt>" or "<tt>YYMMDD hhmmss</tt>".
|X
*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>.
|X
 
|X
|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.format</tt>
|-valign='top'
|For GCHP simulations only: indicates the I/O library that will be used.  This can be omitted for GEOS-Chem "Classic" simualations.
|BPINN
 
|C10H17NO4
|-valign="top"
|Saturated 1st gen BPIN organic nitrate
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:purple">duration</span></tt>
|X
|Determines how often a new netCDF file belongng to the <tt><span style="color:blue">ConcAfterChem</span></tt> will be created.
|X
*The <tt><span style="color:purple">duration</span></tt> attribute can be specified as either <tt>hhmmss</tt> or <tt>YYMMDD hhmmss</tt>.
|X
*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>.
|X
 
|X
|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:darkcyan">mode</span></tt>
|-valign='top'
|Determines the averaging method for the <tt><span style="color:blue">ConcAfterChem</span></tt> collection
|BPINO
*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. 
|C9H14O
*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.
|Ketone from BPIN
 
|X
|-valign="top"
|X
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:green">fields</span></tt>
|X
|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>
|X
*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.
 
|-valign='top'
See the sections below contain in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format.
|BPINO2
 
|C10H17O3
NOTE: You may use wildcards to request a subset of all possible species.  See the next section for more information about wildcards.
|Peroxy radical from BPIN
 
|
|-valign="top"
|
|<tt>::</tt>
|X
|Signifies the end of the <tt><span style="color:blue">ConcAfterChem</span></tt> definition section.
|
*"<tt>::</tt>" may be placed at any column in the file.
|
 
|}
|-valign='top'
 
|BPINON
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.
|C9H13NO4
 
|Saturated 2nd gen BPIN organic nitrate
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:14, 8 February 2018 (UTC)
|X
 
|X
=== Legend ===
|X
 
|X
The following terms are used in the tables below.
|X
 
{| border=1 cellspacing=0 cellpadding=5
|-valign='top'
|-valign="top" bgcolor="#CCCCCC"
|BPINOO2
!width="175px"|Term
|C10H17O3
!width="600px"|Explanation
|2nd-gen peroxy radical from BPIN
!width="225px"|Example
|
 
|
|-valign="top"
|X
|<tt><spcname></tt>
|
|Short name of a GEOS-Chem species, used in several diagnostics listed below. 
|
 
NOTES:
|-valign='top'
 
|BPINOOH
#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.
|C9H14O3
#Allowable wild card values (case-insensitive) for species name are:
|2nd-gen peroxide from BPIN
#*<tt>?ADV?</tt>: Only the advected species
|X
#*<tt>?AER?</tt>: Only the aerosol species
|X
#*<tt>?ALL?</tt>: All GEOS-Chem species
|X
#*<tt>?DRY?</tt>: Only the dry-deposited species
|
#*<tt>?FIX?</tt>: Only the inactive (aka "fixed") species in the KPP chemical mechanism
|X
#*<tt>?GAS?</tt>: Only the gas-phase species
#*<tt>?KPP?</tt>: Only the KPP species
|-valign='top'
#*<tt>?PHO</tt>: Only the photolyzed species
|BPINP
#*<tt>?VAR?</tt>: Only the active (aka "variable") species in the KPP chemical mechanism
|C10H18O3
#*<tt>?WET?</tt>: Only the wet-deposited species
|Peroxide from BPIN
#*<tt>?PRODLOSS?</tt>: Only prod/loss diagnostic species
|X
#*<tt>?DUSTBIN</tt>: Only the dust bin number
|X
#<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.
|X
|<tt>SpeciesConc_<span style="color:red">NO</span></tt><br><tt>SpeciesConc_<span style="color:red">CO</span></tt><br><tt>SpeciesConc_<span style="color:red">?ADV?</span></tt><br><tt>SpeciesConc_<span style="color:red">?AER?</span></tt><br><tt>SpeciesConc_<span style="color:red">?ALL?</span></tt><br><tt>SpeciesConc_<span style="color:red">?DRY?</span></tt><br><tt>SpeciesConc_<span style="color:red">?FIX?</span></tt><br><tt>SpeciesConc_<span style="color:red">?GAS?</span></tt><br><tt>SpeciesConc_<span style="color:red">?KPP?</span></tt><br><tt>SpeciesConc_<span style="color:red">?PHO?</span></tt><br><tt>SpeciesConc_<span style="color:red">?VAR?</span></tt><br><tt>SpeciesConc_<span style="color:red">?WET?</span></tt><br><tt>...etc...</tt>
|
 
|X
|-valign="top" bgcolor="#CCFFFF"
|<tt><metname></tt>
|-valign='top'
|Denotes a met field (or derived quantity such as total optical depth).
|BUTN
 
|C4H7NO4
NOTES:
|C4H6 alkyl nitrate
#<tt>MET_</tt>, <tt>Met_</tt> or <tt>met_</tt> (case-insensitive) must precede <tt><metname></tt>.  This tells the diagnostic code to look for the corresponding field of the <tt>State_Met</tt> object.
|X
|<tt>MET_<span style="color:red">U10M</span></tt><br><tt>MET_<span style="color:red">PS</span></tt><br><tt>MET_<span style="color:red">HFLUX</span></tt><br><tt>MET_<span style="color:red">T</span></tt><br><tt>...etc...</tt>
|X
 
|X
|-valign="top"
|
|<tt><photobin></tt>
|X
|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'
 
|BUTO2
|-valign="top"
|C4H7O3
|<tt><aername></tt>
|peroxy radical from C4H6
|Aerosol quanatities included in the following array fields:
|
 
|
#<tt>State_Chm%AeroArea</tt>
|X
#<tt>State_Chm%AeroRadi</tt>
|
#<tt>State_Chm%WetAeroArea</tt>
|
#<tt>State_Chm%WetAeroRadi</tt>
 
|-valign='top'
These do not always conform to GEOS-Chem species (for example, the mineral dust bins are the bins that are used as input for photolysis).
|C4H6
 
|C4H6
#<tt>MDUST1</tt>: Mineral dust (0.15&mu;m)
|1,3-butadiene
#<tt>MDUST2</tt>: Mineral dust (0.25&mu;m)
|X
#<tt>MDUST3</tt>: Mineral dust (0.40&mu;m)
|
#<tt>MDUST4</tt>: Mineral dust (0.80&mu;m)
|X
#<tt>MDUST5</tt>: Mineral dust (1.50&mu;m)
|
#<tt>MDUST6</tt>: Mineral dust (2.50&mu;m)
|
#<tt>MDUST7</tt>: Mineral dust (4.00&mu;m)
#<tt>SULF</tt>: Sulfate
|-valign='top'
#<tt>BC</tt>: Black Carbon
|C96N
#<tt>OC</tt>: Organic Carbon
|C9H15NO4
#<tt>SSA</tt>: Sea salt aerosol, accumulation mode
|Saturated 2nd gen monoterpene organic nitrate
#<tt>SSC</tt>: Sea salt aerosol, coarse mode
|X
#<tt>BGSULF</tt>: Background stratospheric sulfate
|X
#<tt>ICEI</tt>: Irregular ice cloud (Mischenko)
|X
|<tt>CHEM_AeroArea<span style="color:red">MDUST1</span></tt><br><tt>CHEM_WetAeroRadi<span style="color:red">SSA</span></tt><br><tt>...etc...</tt>
|X
 
|X
|-valign="top" bgcolor="#CCFFFF"
|<tt>nAdvect</tt>
|-valign='top'
|Number of advected GEOS-Chem species
|C96O2
|C10H17O3
|2nd-gen peroxy radical from APIN
|
|
|X
|
|
   
|-valign='top'
|C96O2H
|C9H16O3
|Peroxide from APIN 2nd gen
|X
|X
|X
|
|X
|-valign='top'
|EBZ
|C8H10
|Ethylbenzene
|X
|
|X
|
|
|-valign='top'
|GCO3
|HOCH2CO3
|Peroxyacetyl radical for PHAN
|
|
|X
|
|
|-valign='top'
|HACTA
|HOCH2CO2H
|Hydroxyacetic/glycolic acid
|X
|X
|X
|
|X
|-valign='top'
|LIMAL
|C10H16O2
|Aldehyde from limonene
|X
|X
|X
|
|X
|-valign='top'
|LIMKB
|C10H16O3
|2nd gen ketone from limonene
|X
|X
|X
|
|X
|-valign='top'
|LIMKET
|C10H16O2
|Ketone from limonene
|X
|X
|X
|
|X
|-valign='top'
|LIMKO2
|C10H17O3
|2nd-gen peroxy radical from LIMO
|
|
|X
|
|
|-valign='top'
|LIMN
|C10H17NO4
|Saturated 1st gen limonene organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|LIMNB
|C10H15NO4
|Saturated 1st gen LIMO organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|LIMO2H
|C10H18O3
|Acid from LIMO
|X
|X
|X
|
|X
|-valign='top'
|LIMO3
|C10H17O3
|Acylperoxy radical from LIMO
|
|
|X
|
|
|-valign='top'
|LIMO3H
|C10H18O4
|Peracid from LIMO
|X
|X
|X
|
|X
   
|-valign='top'
|LIMPAN
|C10H17NO4
|PAN from LIMO
|X
|X
|X
|X
|X
|-valign='top'
|MEKCO3
|C3H5O4
|False
|
|
|X
|
|
|-valign='top'
|MEKPN
|C3H5NO6
|MEK peroxyacetyl nitrate
|X
|X
|X
|X
|X
|-valign='top'
|MYRCO
|C10H18O3
|Aldehyde or ketone from myrcene
|X
|X
|X
|
|X
|-valign='top'
|PHAN
|C2H3NO6
|Peroxyhydroxyacetic nitric anhydride
|X
|X
|X
|X
|X
|-valign='top'
|PIN
|C10H17NO4
|Saturated 1st gen monoterpene organic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|PINAL
|C10H16O2
|Pinonaldehyde
|X
|X
|X
|
|X
|-valign='top'
|PINO3
|C10H17O3
|Acylperoxy radical from APIN
|
|
|X
|
|
|-valign='top'
|PINO3H
|C10H18O4
|Pinonic peracid
|X
|X
|X
|
|X
|-valign='top'
|PINONIC
|C10H18O3
|Pinonic acid
|X
|X
|X
|
|X
|-valign='top'
|PINPAN
|C10H17NO4
|PAN from pinonaldehyde
|X
|X
|X
|X
|X
|-valign='top'
|R7N1
|C7H15NO5
|Peroxy radical from R7N2
|
|
|X
|
|
   
|-valign='top'
|R7N2
|RO2NO
|C7 Lumped alkyl nitrate
|X
|X
|X
|X
|X
|-valign='top'
|R7O2
|C7H15O2
|Peroxy radical from ALK7
|
|
|X
|
|
|-valign='top'
|R7P
|C7H16O2
|Peroxide from R7O2
|X
|X
|X
|X
|X
   
|-valign='top'
|RNO3
|RO2NO
|Lumped aromatic nitrate
|X
|X
|X
|X
|X
|-valign='top'
|STYR
|C8H8
|Styrene
|X
|
|X
|
|
|-valign='top'
|TLFUO2
|C5H7O5
|False
|
|
|X
|
|
|-valign='top'
|TLFUONE
|C5H6O2
|Aromatic furanones
|X
|X
|X
|
|X
|-valign='top'
|TMB
|C8H10
|Trimethylbenzenes
|
|
|X
|
|
|
 
|-valign="top"
|-valign='top'
|<tt>nDryDep</tt>
|ZRO2
|Number of dry-depositing GEOS-Chem species
|C7H9O5
|RO2 for making lumped aromatic nitrate
|
|
|-valign="top" bgcolor="#CCFFFF"
|<tt>nKppSpc</tt>
|Number of species in the KPP chemistry mechanism
|
|
 
|X
|-valign="top"
|<tt>nPhoto</tt>
|Number of photolyzing GEOS-Chem species
|
|
|-valign="top" bgcolor="#CCFFFF"
|<tt>nTomas</tt>
|Number of size-resolved TOMAS species
|<tt>IBINS*(ICOMP-IDIAG+1)</tt>
|-valign="top"
|<tt>nWetDep</tt>
|Number of soluble, wet-depositing GEOS-Chem species
|
|
 
|}
|}


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:32, 14 November 2017 (UTC)
=== Species removed===


== Collection list ==
Species removed between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:


{| border=1 cellspacing=0 cellpadding=5
!width='100px' bgcolor='#CCCCCC'|Name
!width='100px' bgcolor='#CCCCCC'|Formula
!width='200px' bgcolor='#CCCCCC'|Fullname
!width='30px' bgcolor='#CCCCCC'|Advected
!width='30px' bgcolor='#CCCCCC'|Dry deposited
!width='30px' bgcolor='#CCCCCC'|Gas
!width='30px' bgcolor='#CCCCCC'|Photolyzed
!width='30px' bgcolor='#CCCCCC'|Wet deposited


EXPID:  OutputDir/GCHP
|}
EXPDSC: GEOS-Chem_devel
CoresPerNode: 6
 
#===================================================================
# Declare collection names and toggle on/off
# by commenting out with a #
#===================================================================
COLLECTIONS: 'SpeciesConc',
              'Aerosols',
              'CloudConvFlux',
              'ConcAfterChem',
              'DryDep',
              'JValues',
              'JValuesLocalNoon',
              'LevelEdgeDiags',     
              'ProdLoss',
              'StateChm',   
              'StateMet',     
              'WetLossConv',
              'WetLossLS',
 
== Species concentrations ==
 
# Species concentrations (per advected species)
  SpeciesConc.template:      '%y4%m2%d2_%h2%n2z.nc4',
  SpeciesConc.format:        'CFIO',
  SpeciesConc.frequency:      010000
  SpeciesConc.duration:      010000
  SpeciesConc.mode:          'time-averaged'
  SpeciesConc.fields:        'SpeciesConc_?ADV?            ', 'GIGCchem',
 
== Aerosol diagnostics ==
 
#===================================================================
# Aerosol optical depth, surface area, number density, and hygroscopic growth
  Aerosols.template:          '%y4%m2%d2_%h2%n2z.nc4',
  Aerosols.format:            'CFIO',
  Aerosols.frequency:        010000
  Aerosols.duration:          010000
  Aerosols.mode:              'time-averaged'
  Aerosols.fields:            'AODDust                      ', 'GIGCchem',
                              'AODDustWL1_?DUSTBIN?          ', 'GIGCchem',
                              'AODHygWL1_?HYG?              ', 'GIGCchem',
                              'AODSOAfromAqIsopreneWL1      ', 'GIGCchem',
                              'AODStratLiquidAerWL1          ', 'GIGCchem',
                              'AODPolarStratCloudWL1        ', 'GIGCchem',
                              'AerHygroscopicGrowth_?HYG?    ', 'GIGCchem',
                              'AerNumDensityStratLiquid      ', 'GIGCchem',
                              'AerNumDensityStratParticulate ', 'GIGCchem',
                              'AerAqueousVolume              ', 'GIGCchem',
                              'AerSurfAreaDust              ', 'GIGCchem',
                              'AerSurfAreaHyg_?HYG?          ', 'GIGCchem',
                              'AerSurfAreaStratLiquid        ', 'GIGCchem',
                              'AerSurfAreaPolarStratCloud    ', 'GIGCchem',
                              'Chem_AeroAreaMDUST1          ', 'GIGCchem',
                              'Chem_AeroAreaMDUST2          ', 'GIGCchem',
                              'Chem_AeroAreaMDUST3'          ', 'GIGCchem',
                              'Chem_AeroAreaMDUST4          ', 'GIGCchem',
                              'Chem_AeroAreaMDUST5          ', 'GIGCchem',
                              'Chem_AeroAreaMDUST6          ', 'GIGCchem',
                              'Chem_AeroAreaMDUST7          ', 'GIGCchem',
                              'Chem_AeroAreaSULF            ', 'GIGCchem',
                              'Chem_AeroAreaBC              ', 'GIGCchem',
                              'Chem_AeroAreaOC              ', 'GIGCchem',
                              'Chem_AeroAreaSSA              ', 'GIGCchem',
                              'Chem_AeroAreaSSC              ', 'GIGCchem',
                              'Chem_AeroAreaBGSULF          ', 'GIGCchem',
                              'Chem_AeroAreaICEI            ', 'GIGCchem',
                              'Chem_AeroRadiMDUST1          ', 'GIGCchem',
                              'Chem_AeroRadiMDUST2          ', 'GIGCchem',
                              'Chem_AeroRadiMDUST3          ', 'GIGCchem',
                              'Chem_AeroRadiMDUST4          ', 'GIGCchem',
                              'Chem_AeroRadiMDUST5          ', 'GIGCchem',
                              'Chem_AeroRadiMDUST6          ', 'GIGCchem',
                              'Chem_AeroRadiMDUST7          ', 'GIGCchem',
                              'Chem_AeroRadiSULF            ', 'GIGCchem',
                              'Chem_AeroRadiBC              ', 'GIGCchem',
                              'Chem_AeroRadiOC              ', 'GIGCchem',
                              'Chem_AeroRadiSSA              ', 'GIGCchem',
                              'Chem_AeroRadiSSC              ', 'GIGCchem',
                              'Chem_AeroRadiBGSULF          ', 'GIGCchem',
                              'Chem_AeroRadiICEI            ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST1        ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST2        ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST3        ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST4        ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST5        ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST6        ', 'GIGCchem',
                              'Chem_WetAeroAreaMDUST7        ', 'GIGCchem',
                              'Chem_WetAeroAreaSULF          ', 'GIGCchem',
                              'Chem_WetAeroAreaBC            ', 'GIGCchem',
                              'Chem_WetAeroAreaOC            ', 'GIGCchem',
                              'Chem_WetAeroAreaSSA          ', 'GIGCchem',
                              'Chem_WetAeroAreaSSC          ', 'GIGCchem',
                              'Chem_WetAeroAreaBGSULF        ', 'GIGCchem',
                              'Chem_WetAeroAreaICEI          ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST1        ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST2        ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST3        ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST4        ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST5        ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST6        ', 'GIGCchem',
                              'Chem_WetAeroRadiMDUST7        ', 'GIGCchem',
                              'Chem_WetAeroRadiSULF          ', 'GIGCchem',
                              'Chem_WetAeroRadiBC            ', 'GIGCchem',
                              'Chem_WetAeroRadiOC            ', 'GIGCchem',
                              'Chem_WetAeroRadiSSA          ', 'GIGCchem',
                              'Chem_WetAeroRadiSSC          ', 'GIGCchem',
                              'Chem_WetAeroRadiBGSULF        ', 'GIGCchem',
                              'Chem_WetAeroRadiICEI          ', 'GIGCchem',
                              'Chem_StatePSC                ', 'GIGCchem',
                              'Chem_KhetiSLAN2O5H2O          ', 'GIGCchem',
                              'Chem_KhetiSLAN2O5HCl          ', 'GIGCchem',
                              'Chem_KhetiSLAClNO3H2O        ', 'GIGCchem',
                              'Chem_KhetiSLAClNO3HCl        ', 'GIGCchem',
                              'Chem_KhetiSLAClNO3HBr        ', 'GIGCchem',
                              'Chem_KhetiSLABrNO3H2O        ', 'GIGCchem',
                              'Chem_KhetiSLABrNO3HCl        ', 'GIGCchem',
                              'Chem_KhetiSLAHOClHCl          ', 'GIGCchem',
                              'Chem_KhetiSLAHOClHBr          ', 'GIGCchem',
                              'Chem_KhetiSLAHOBrHCl          ', 'GIGCchem',
                              'Chem_KhetiSLAHOBrHBr          ', 'GIGCchem',
                              ::
 
== Cloud convective flux ==
 
# Cloud convective flux (per advected species)
  CloudConvFlux.template:    '%y4%m2%d2_%h2%n2z.nc4',
  CloudConvFlux.format:      'CFIO',
  CloudConvFlux.frequency:    010000
  CloudConvFlux.duration:    010000
  CloudConvFlux.mode:        'time-averaged'
  CloudConvFlux.fields:      'CloudConvFlux_?ADV?          ', 'GIGCchem',
 
== Concentrations after chemistry ==
 
  # Concentrations after chemistry
  ConcAfterChem.template:    '%y4%m2%d2_%h2%n2z.nc4',
  ConcAfterChem.format:      'CFIO',
  ConcAfterChem.frequency:    010000
  ConcAfterChem.duration:    010000
  ConcAfterChem.mode:        'time-averaged'
  ConcAfterChem.fields:      'OHconcAfterChem              ', 'GIGCchem', 
                              'HO2concAfterChem              ', 'GIGCchem', 
                              'O1DconcAfterChem              ', 'GIGCchem', 
                              'O3PconcAfterChem              ', 'GIGCchem', 
::
 
== Dry deposition diagnostics ==
 
# Dry deposition flux velocity (per dry deposited species)
  DryDep.template:            '%y4%m2%d2_%h2%n2z.nc4',
  DryDep.format:              'CFIO',
  DryDep.frequency:          010000
  DryDep.duration:            010000
  DryDep.mode:                'time-averaged'
  DryDep.fields:              'DryDepVel_?DRY?              ', 'GIGCchem',
                              'DryDepMix_?DRY?              ', 'GIGCchem',
                              'DryDepChm_?DRY?              ', 'GIGCchem',
                              'DryDep_?DRY?                  ', 'GIGCchem',
::
 
== Photolysis diagnostics ==
 
# Photolysis rates (J-values)
  JValues.template:          '%y4%m2%d2_%h2%n2z.nc4',
  JValues.format:            'CFIO',
  JValues.frequency:          010000
  JValues.duration:          010000
  JValues.mode:              'time-averaged'
  JValues.fields:            'Jval_?PHO?                    ', 'GIGCchem',
::
# Photolysis rates at local noon (J-values)
  JValuesLocalNoon.template:  '%y4%m2%d2_%h2%n2z.nc4',
  JValuesLocalNoon.format:    'CFIO',
  JValuesLocalNoon.frequency: 010000
  JValuesLocalNoon.duration:  010000
  JValuesLocalNoon.mode:      'instantaneous'
  JValuesLocalNoon.fields:    'JNoon_?PHO?                  ', 'GIGCchem',
::
 
== Diagnostics on level edges ==
 
# Level edge diagnostics (73-level only)
  LevelEdgeDiags.template:    '%y4%m2%d2_%h2%n2z.nc4',
  LevelEdgeDiags.format:      'CFIO',
  LevelEdgeDiags.frequency:  010000
  LevelEdgeDiags.duration:    010000
  LevelEdgeDiags.mode:        'time-averaged'
  LevelEdgeDiags.fields:      'Met_CMFMC                    ', 'GIGCchem',
                              'Met_PEDGE                      ', 'GIGCchem',
                              'Met_PEDGEDRY                  ', 'GIGCchem',
                              'Met_PFICU                      ', 'GIGCchem',
                              'Met_PFILSAN                    ', 'GIGCchem',
                              'Met_PFLCU                      ', 'GIGCchem',
                              'Met_PFLLSAN                    ', 'GIGCchem',
::
 
== Production and loss rates ==
 
  # Prod/loss rates
  ProdLoss.template:          '%y4%m2%d2_%h2%n2z.nc4',
  ProdLoss.format:            'CFIO',
  ProdLoss.frequency:        010000
  ProdLoss.duration:          010000
  ProdLoss.mode:              'time-averaged'
  ProdLoss.fields:            'PROD_?PRD?                    ', 'GIGCchem',
                              'ProdBCPIfromBCPO              ', 'GIGCchem',
                              'ProdOCPIfromOCPO              ', 'GIGCchem',
                              'ProdSO4fromH2O2inCloud        ', 'GIGCchem',
                              'ProdSO4fromO3inCloud          ', 'GIGCchem',
                              'ProdSO4fromO3inSeaSalt        ', 'GIGCchem',
                              'ProdSO4fromHOBrInCloud        ', 'GIGCchem',
                              'ProdSO4fromSRO3              ', 'GIGCchem',
                              'ProdSO4fromSRHObr            ', 'GIGCchem',
                              'ProdSO4fromO3s                ', 'GIGCchem',
                              'LOSS_?LOS?                    ', 'GIGCchem',
                              'LossHNO3onSeaSalt            ', 'GIGCchem',
::
 
== Fields of the State_Chm object ==
 
# State_Chm array diagnostics (see also Aerosols collection
  StateChm.template:          '%y4%m2%d2_%h2%n2z.nc4',
  StateChm.format:            'CFIO',
  StateChm.frequency:        010000
  StateChm.duration:          010000
  StateChm.mode:              'time-averaged'
  StateChm.fields:            'Chem_phSav                    ', 'GIGCchem', 
                              'Chem_HplusSav                ', 'GIGCchem', 
                              'Chem_WaterSav                ', 'GIGCchem', 
                              'Chem_SulRatSav                ', 'GIGCchem', 
                              'Chem_NaRatSav                ', 'GIGCchem', 
                              'Chem_AcidPurSav              ', 'GIGCchem', 
                              'Chem_BiSulSav                ', 'GIGCchem',
                              'Chem_pHCloud                  ', 'GIGCchem',
                              'Chem_SSAlk',                  ', 'GIGCchem',
                              'Chem_HSO3AQ                  ', 'GIGCchem',
                              'Chem_SO3AQ                    ', 'GIGCchem',
                              'Chem_fupdateHOBr              ', 'GIGCchem',
::
 
== Fields of the State_Met object ==
 
# State_Met array diagnostics
  StateMet.template:          '%y4%m2%d2_%h2%n2z.nc4',
  StateMet.format:            'CFIO',
  StateMet.frequency:        010000
  StateMet.duration:          010000
  StateMet.mode:              'time-averaged'
  StateMet.fields:            'Met_AD                        ', 'GIGCchem',
                              'Met_AIRDEN                    ', 'GIGCchem',
                              'Met_AIRVOL                    ', 'GIGCchem',
                              'Met_ALBD                      ', 'GIGCchem',
                              'Met_AREAM2                    ', 'GIGCchem',
                              'Met_AVGW                      ', 'GIGCchem',
                              'Met_BXHEIGHT                  ', 'GIGCchem',
                              'Met_ChemGridLev                ', 'GIGCchem',
                              'Met_CLDF                      ', 'GIGCchem',
                              'Met_CLDFRC                    ', 'GIGCchem',
                              'Met_CLDTOPS                    ', 'GIGCchem',
                              'Met_DELP                      ', 'GIGCchem',
                              'Met_DQRCU                      ', 'GIGCchem',
                              'Met_DQRLSAN                    ', 'GIGCchem',
                              'Met_DTRAIN                    ', 'GIGCchem',
                              'Met_EFLUX                      ', 'GIGCchem',
                              'Met_FRCLND                    ', 'GIGCchem',
                              'Met_FRLAKE                    ', 'GIGCchem',
                              'Met_FRLAND                    ', 'GIGCchem',
                              'Met_FRLANDIC                  ', 'GIGCchem',
                              'Met_FROCEAN                    ', 'GIGCchem',
                              'Met_FRSEAICE                  ', 'GIGCchem',
                              'Met_FRSNO                      ', 'GIGCchem',
                              'Met_GWETROOT                  ', 'GIGCchem',
                              'Met_GWETTOP                    ', 'GIGCchem',
                              'Met_HFLUX                      ', 'GIGCchem',
                              'Met_LAI                        ', 'GIGCchem',
                              'Met_LWI                        ', 'GIGCchem',
                              'Met_PARDR                      ', 'GIGCchem',
                              'Met_PARDF                      ', 'GIGCchem',
                              'Met_PBLTOPL                    ', 'GIGCchem',
                              'Met_PBLH                      ', 'GIGCchem',
                              'Met_PHIS                      ', 'GIGCchem',
                              'Met_PMID                      ', 'GIGCchem',
                              'Met_PMIDDRY                    ', 'GIGCchem',
                              'Met_PRECANV                    ', 'GIGCchem',
                              'Met_PRECCON                    ', 'GIGCchem',
                              'Met_PRECLSC                    ', 'GIGCchem',
                              'Met_PRECTOT                    ', 'GIGCchem',
                              'Met_PS1DRY                    ', 'GIGCchem',
                              'Met_PS1WET                    ', 'GIGCchem',
                              'Met_PS2DRY                    ', 'GIGCchem',
                              'Met_PS2WET                    ', 'GIGCchem',
                              'Met_PSC2WET                    ', 'GIGCchem',
                              'Met_PSC2DRY                    ', 'GIGCchem',
                              'Met_QI                        ', 'GIGCchem',
                              'Met_QL                        ', 'GIGCchem',
                              'Met_OMEGA                      ', 'GIGCchem',
                              'Met_OPTD                      ', 'GIGCchem',
                              'Met_REEVAPCN                  ', 'GIGCchem',
                              'Met_REEVAPLS                  ', 'GIGCchem',
                              'Met_SLP                        ', 'GIGCchem',
                              'Met_SNODP                      ', 'GIGCchem',
                              'Met_SNOMAS                    ', 'GIGCchem',
                              'Met_SPHU                      ', 'GIGCchem',
                              'Met_SPHU1                      ', 'GIGCchem',
                              'Met_SPHU2                      ', 'GIGCchem',
                              'Met_SUNCOS                    ', 'GIGCchem',
                              'Met_SUNCOSmid                  ', 'GIGCchem',
                              'Met_SWGDN                      ', 'GIGCchem',
                              'Met_T                          ', 'GIGCchem',
                              'Met_TAUCLI                    ', 'GIGCchem',
                              'Met_TAUCLW                    ', 'GIGCchem',
                              'Met_THETA                      ', 'GIGCchem',
                              'Met_TMPU1                      ', 'GIGCchem',
                              'Met_TMPU2                      ', 'GIGCchem',
                              'Met_TO3                        ', 'GIGCchem',
                              'Met_TropHt                    ', 'GIGCchem',
                              'Met_TropLev                    ', 'GIGCchem',
                              'Met_TropP                      ', 'GIGCchem',
                              'Met_TS                        ', 'GIGCchem',
                              'Met_TSKIN                      ', 'GIGCchem',
                              'Met_TV                        ', 'GIGCchem',
                              'Met_U                          ', 'GIGCchem',
                              'Met_U10M                      ', 'GIGCchem',
                              'Met_USTAR                      ', 'GIGCchem',
                              'Met_UVALBEDO                  ', 'GIGCchem',
                              'Met_V                          ', 'GIGCchem',
                              'Met_V10M                      ', 'GIGCchem',
                              'Met_Z0                        ', 'GIGCchem',
::
 
== Loss of soluble species in cloud updrafts ==
 
# Loss due to convection (per wet deposited species)
  WetLossConv.template:      '%y4%m2%d2_%h2%n2z.nc4',
  WetLossConv.format:        'CFIO',
  WetLossConv.frequency:      010000
  WetLossConv.duration:      010000
  WetLossConv.mode:          'time-averaged'
  WetLossConv.fields:        'WetLossConv_?WET?            ', 'GIGCchem',
::
 
== Loss of soluble species in large-scale wet deposition ==
 
# Loss due to rainout and washout (per deposited species)
  WetLossLS.template:        '%y4%m2%d2_%h2%n2z.nc4',
  WetLossLS.format:          'CFIO',
  WetLossLS.frequency:        010000
  WetLossLS.duration:        010000
  WetLossLS.mode:            'time-averaged'
  WetLossLS.fields:          'WetLossLS_?WET?              ', 'GIGCchem',
::

Latest revision as of 19:10, 3 October 2024

Species added

Species added between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:

Name Formula Fullname Advected Dry deposited Gas Photolyzed Wet deposited
ACO3 C3H3O3 Peroxyacetyl radical for APAN X
ACR C3H4O Acrolein X X X X
ACRO2 C3H5O4 Peroxy radical from ACR X
ALK7 C7H16 Lumped >= C6 Alkanes X X
APAN C3H3NO5 Peroxyacryloyl nitrate X X X X X
APINN C10H17NO4 1st gen organic nitrate from APIN X X X X X
APINO2 C10H17O3 Peroxy radical from APIN X
APINP C10H18O3 Hydroperoxide from APIN X X X X
AROMCHO C5H6O4 ACCOMECHO from MCM X X X X
AROMCO3 C5H5O6 Lumped aromatic peroxyacetyl radical X
AROMPN C5H5NO8 Lumped PN from aromatics X X X X X
BPINN C10H17NO4 Saturated 1st gen BPIN organic nitrate X X X X X
BPINO C9H14O Ketone from BPIN X X X X
BPINO2 C10H17O3 Peroxy radical from BPIN X
BPINON C9H13NO4 Saturated 2nd gen BPIN organic nitrate X X X X X
BPINOO2 C10H17O3 2nd-gen peroxy radical from BPIN X
BPINOOH C9H14O3 2nd-gen peroxide from BPIN X X X X
BPINP C10H18O3 Peroxide from BPIN X X X X
BUTN C4H7NO4 C4H6 alkyl nitrate X X X X
BUTO2 C4H7O3 peroxy radical from C4H6 X
C4H6 C4H6 1,3-butadiene X X
C96N C9H15NO4 Saturated 2nd gen monoterpene organic nitrate X X X X X
C96O2 C10H17O3 2nd-gen peroxy radical from APIN X
C96O2H C9H16O3 Peroxide from APIN 2nd gen X X X X
EBZ C8H10 Ethylbenzene X X
GCO3 HOCH2CO3 Peroxyacetyl radical for PHAN X
HACTA HOCH2CO2H Hydroxyacetic/glycolic acid X X X X
LIMAL C10H16O2 Aldehyde from limonene X X X X
LIMKB C10H16O3 2nd gen ketone from limonene X X X X
LIMKET C10H16O2 Ketone from limonene X X X X
LIMKO2 C10H17O3 2nd-gen peroxy radical from LIMO X
LIMN C10H17NO4 Saturated 1st gen limonene organic nitrate X X X X X
LIMNB C10H15NO4 Saturated 1st gen LIMO organic nitrate X X X X X
LIMO2H C10H18O3 Acid from LIMO X X X X
LIMO3 C10H17O3 Acylperoxy radical from LIMO X
LIMO3H C10H18O4 Peracid from LIMO X X X X
LIMPAN C10H17NO4 PAN from LIMO X X X X X
MEKCO3 C3H5O4 False X
MEKPN C3H5NO6 MEK peroxyacetyl nitrate X X X X X
MYRCO C10H18O3 Aldehyde or ketone from myrcene X X X X
PHAN C2H3NO6 Peroxyhydroxyacetic nitric anhydride X X X X X
PIN C10H17NO4 Saturated 1st gen monoterpene organic nitrate X X X X X
PINAL C10H16O2 Pinonaldehyde X X X X
PINO3 C10H17O3 Acylperoxy radical from APIN X
PINO3H C10H18O4 Pinonic peracid X X X X
PINONIC C10H18O3 Pinonic acid X X X X
PINPAN C10H17NO4 PAN from pinonaldehyde X X X X X
R7N1 C7H15NO5 Peroxy radical from R7N2 X
R7N2 RO2NO C7 Lumped alkyl nitrate X X X X X
R7O2 C7H15O2 Peroxy radical from ALK7 X
R7P C7H16O2 Peroxide from R7O2 X X X X X
RNO3 RO2NO Lumped aromatic nitrate X X X X X
STYR C8H8 Styrene X X
TLFUO2 C5H7O5 False X
TLFUONE C5H6O2 Aromatic furanones X X X X
TMB C8H10 Trimethylbenzenes X
ZRO2 C7H9O5 RO2 for making lumped aromatic nitrate X


Species removed

Species removed between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:

Name Formula Fullname Advected Dry deposited Gas Photolyzed Wet deposited
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