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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:
  
In the sections below, we present a '''''list of naming conventions''''' for netCDF diagnostics that we developed last year. GCST member [[User:bmy|Bob Yantosca]] will be working on the transition to netCDF diagnostics very soon so feel free to follow up with him on suggested names.
+
{| 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
  
=== An introduction to netCDF diagnostics ===
+
|-valign='top'
 
+
|ACO3
Bob Yantosca has created [[Media:Netcdf_Diagnostics.pdf|an overview presentation about the new netCDF diagnostics for v11-02]]. 
+
|C3H3O3
 
+
|Peroxyacetyl radical for APAN
=== 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.  The names for netCDF diagnostic quantities follow the [[#Naming convention|naming convention listed above]].
+
 
+
COLLECTIONS: <span style="color:red">'SpeciesConc'</span>,
+
              <span style="color:blue">'ConcAfterChem'</span>,
+
              ::
+
  <span style="color:red">SpeciesConc</span>.template:    '%y4%m2%d2_%h2%n2z.nc4',
+
  <span style="color:red">SpeciesConc</span>.<span style="color:darkorange">frequency:    060000</span>,
+
  <span style="color:red">SpeciesConc</span>.format:      'CFIO',
+
  <span style="color:red">SpeciesConc</span>.<span style="color:purple">duration:    240000</span>,
+
  <span style="color:red">SpeciesConc</span>.<span style="color:brown">mode:        'instantaneous'</span>,
+
  <span style="color:red">SpeciesConc</span>.<span style="color:green">fields:      'SpeciesConc_?ADV?'</span>,  'GIGCchem',
+
                            ::
+
  <span style="color:blue">ConcAfterChem</span>.template:  '%y4%m2%d2_%h2%n2z.nc4',
+
  <span style="color:blue">ConcAfterChem</span>.<span style="color:magenta">frequency:  000100 000000</span>,
+
  <span style="color:blue">ConcAfterChem</span>.format:    'CFIO',
+
  <span style="color:blue">ConcAfterChem</span>.<span style="color:purple">duration:  000100 000000</span>,
+
  <span style="color:blue">ConcAfterChem</span>.<span style="color:darkcyan">mode:      'time-averaged'</span>,
+
  <span style="color:blue">ConcAfterChem</span>.<span style="color:green">fields:    'OHconcAfterChem'</span>,    'GIGCchem',
+
                            <span style="color:green">'HO2concAfterChem'</span>,    'GIGCchem',
+
                            <span style="color:green">'O1DconcAfterChem'</span>,    ‘GIGCchem’,
+
                            <span style="color:green">'O3PconcAfterChem'</span>,    ‘GIGCchem’,
+
                            ::
+
 
+
In this HISTORY.rc file, we are requesting two collections, or types of netCDF file output.
+
 
+
#The first collection (<span style="color:red">SpeciesConc</span>) is <span style="color:brown">instantaneous (aka timeseries) output</span> with <span style="color:darkorange">a 6-hour frequency</span>. A new file will be created <span style="color:purple">every 24 hours</span>.
+
#The second collection (<span style="color:blue">ConcAfterChem</span>) is <span style="color:darkcyan">time-averaged output</span>. Data will be updated at the dynamic timestep (= 10 minutes for most GEOS-Chem simulations) by default and <span style="color:magenta">averaged into monthly-mean output</span>. A new file will be created <span style="color:purple">at the start of each new month</span>.
+
#<span style="color:green">The diagnostic quantities (aka "fields")</span> that will be archived in each collection are listed after the “fields” tag. These diagnostic quantities follow the naming convention described in the previous section.
+
#*For GEOS-Chem “Classic” simulations, you may use wildcards to request a multiple quantities. For example, instead of listing <tt>SpeciesConc_NO</tt>, <tt>SpeciesConc_O3</tt>, <tt>SpeciesConc_PAN</tt>, <tt>SpeciesConc_CO</tt>, etc. individually, you can use <tt>SpeciesConc_?ADV?</tt> to request all of the advected GEOS_Chem species.
+
#*The "GIGCchem" text is only relevant for GCHP and will be ignored for GEOS-Chem “Classic” simulations.
+
 
+
For more examples, please see [[Media:Netcdf_Diagnostics.pdf|Bob Yantosca’s netCDF diagnostics overview presentation]]. We will also add more documentation to the GEOS-Chem wiki in the coming weeks.
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:14, 8 February 2018 (UTC)
+
 
+
=== Legend ===
+
 
+
The following terms are used in the tables below.
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="175px"|Term
+
!width="600px"|Explanation
+
!width="225px"|Example
+
 
+
|-valign="top"
+
|<tt><spcname></tt>
+
|Short name of a GEOS-Chem species, used in several diagnostics listed below. 
+
 
+
NOTES:
+
 
+
#The single-underscore (<tt>_</tt>) preceding the species name indicates that use of a species wildcard (e.g <tt>SpeciesConc_<span style="color:red">?ADV?</span></tt>, which only selects advected species) is possible.
+
#Allowable wild card values (case-insensitive) for species name are:
+
#*<tt>?ADV?</tt>: Only the advected species
+
#*<tt>?AER?</tt>: Only the aerosol species
+
#*<tt>?ALL?</tt>: All GEOS-Chem species
+
#*<tt>?DRY?</tt>: Only the dry-deposited species
+
#*<tt>?FIX?</tt>: Only the inactive (aka "fixed") species in the KPP chemical mechanism
+
#*<tt>?GAS?</tt>: Only the gas-phase species
+
#*<tt>?KPP?</tt>: Only the KPP species
+
#*<tt>?PHO</tt>: Only the photolyzed species
+
#*<tt>?VAR?</tt>: Only the active (aka "variable") species in the KPP chemical mechanism
+
#*<tt>?WET?</tt>: Only the wet-deposited species
+
#*<tt>?PRODLOSS?</tt>: Only prod/loss diagnostic species
+
#*<tt>?DUSTBIN</tt>: Only the dust bin number
+
#<tt><spcname></tt> should be case-insensitive.  In most places where species names are compared, species names are first converted to uppercase and then a string match test is done.  But because most species names represent a chemical formula (e.g. NO, CO),they will be mostly all uppercase. Some species names would have mixed-case, e.g. BrCl, Rn, Pb, Be7, etc.
+
|<tt>SpeciesConc_<span style="color:red">NO</span></tt><br><tt>SpeciesConc_<span style="color:red">CO</span></tt><br><tt>SpeciesConc_<span style="color:red">?ADV?</span></tt><br><tt>SpeciesConc_<span style="color:red">?AER?</span></tt><br><tt>SpeciesConc_<span style="color:red">?ALL?</span></tt><br><tt>SpeciesConc_<span style="color:red">?DRY?</span></tt><br><tt>SpeciesConc_<span style="color:red">?FIX?</span></tt><br><tt>SpeciesConc_<span style="color:red">?GAS?</span></tt><br><tt>SpeciesConc_<span style="color:red">?KPP?</span></tt><br><tt>SpeciesConc_<span style="color:red">?PHO?</span></tt><br><tt>SpeciesConc_<span style="color:red">?VAR?</span></tt><br><tt>SpeciesConc_<span style="color:red">?WET?</span></tt><br><tt>...etc...</tt>
+
 
+
|-valign="top" bgcolor="#CCFFFF"
+
|<tt><metname></tt>
+
|Denotes a met field (or derived quantity such as total optical depth).
+
 
+
NOTES:
+
#<tt>MET_</tt>, <tt>Met_</tt> or <tt>met_</tt> (case-insensitive) must precede <tt><metname></tt>.  This tells the diagnostic code to look for the corresponding field of the <tt>State_Met</tt> object.
+
|<tt>MET_<span style="color:red">U10M</span></tt><br><tt>MET_<span style="color:red">PS</span></tt><br><tt>MET_<span style="color:red">HFLUX</span></tt><br><tt>MET_<span style="color:red">T</span></tt><br><tt>...etc...</tt>
+
 
+
|-valign="top"
+
|<tt><photobin></tt>
+
|Number of a given wavelength bin for FAST-JX photolysis
+
|<tt>1-18</tt> (with UCX on);<br><tt>1-12</tt> (with UCX off)
+
 
+
|-valign="top"
+
|<tt><aername></tt>
+
|Aerosol quanatities included in the following array fields:
+
 
+
#<tt>State_Chm%AeroArea</tt>
+
#<tt>State_Chm%AeroRadi</tt>
+
#<tt>State_Chm%WetAeroArea</tt>
+
#<tt>State_Chm%WetAeroRadi</tt>
+
 
+
These do not always conform to GEOS-Chem species (for example, the mineral dust bins are the bins that are used as input for photolysis).
+
 
+
#<tt>MDUST1</tt>: Mineral dust (0.15&mu;m)
+
#<tt>MDUST2</tt>: Mineral dust (0.25&mu;m)
+
#<tt>MDUST3</tt>: Mineral dust (0.40&mu;m)
+
#<tt>MDUST4</tt>: Mineral dust (0.80&mu;m)
+
#<tt>MDUST5</tt>: Mineral dust (1.50&mu;m)
+
#<tt>MDUST6</tt>: Mineral dust (2.50&mu;m)
+
#<tt>MDUST7</tt>: Mineral dust (4.00&mu;m)
+
#<tt>SULF</tt>: Sulfate
+
#<tt>BC</tt>: Black Carbon
+
#<tt>OC</tt>: Organic Carbon
+
#<tt>SSA</tt>: Sea salt aerosol, accumulation mode
+
#<tt>SSC</tt>: Sea salt aerosol, coarse mode
+
#<tt>BGSULF</tt>: Background stratospheric sulfate
+
#<tt>ICEI</tt>: Irregular ice cloud (Mischenko)
+
|<tt>CHEM_AeroArea<span style="color:red">MDUST1</span></tt><br><tt>CHEM_WetAeroRadi<span style="color:red">SSA</span></tt><br><tt>...etc...</tt>
+
 
+
|-valign="top" bgcolor="#CCFFFF"
+
|<tt>nAdvect</tt>
+
|Number of advected GEOS-Chem species
+
 
|
 
|
 
|-valign="top"
 
|<tt>nDryDep</tt>
 
|Number of dry-depositing GEOS-Chem species
 
 
|
 
|
 
+
|X
|-valign="top" bgcolor="#CCFFFF"
+
|<tt>nKppSpc</tt>
+
|Number of species in the KPP chemistry mechanism
+
 
|
 
|
 
|-valign="top"
 
|<tt>nPhoto</tt>
 
|Number of photolyzing GEOS-Chem species
 
 
|
 
|
 
+
|-valign="top" bgcolor="#CCFFFF"
+
|-valign='top'
|<tt>nTomas</tt>
+
|ACR
|Number of size-resolved TOMAS species
+
|C3H4O
|<tt>IBINS*(ICOMP-IDIAG+1)</tt>
+
|Acrolein
 
+
|X
|-valign="top"
+
|X
|<tt>nWetDep</tt>
+
|X
|Number of soluble, wet-depositing GEOS-Chem species
+
|X
 
|
 
|
 
+
 +
|-valign='top'
 +
|ACRO2
 +
|C3H5O4
 +
|Peroxy radical from ACR
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|ALK7
 +
|C7H16
 +
|Lumped >= C6 Alkanes
 +
|X
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|APAN
 +
|C3H3NO5
 +
|Peroxyacryloyl nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|APINN
 +
|C10H17NO4
 +
|1st gen organic nitrate from APIN
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|APINO2
 +
|C10H17O3
 +
|Peroxy radical from APIN
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|APINP
 +
|C10H18O3
 +
|Hydroperoxide from APIN
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|AROMCHO
 +
|C5H6O4
 +
|ACCOMECHO from MCM
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|AROMCO3
 +
|C5H5O6
 +
|Lumped aromatic peroxyacetyl radical
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|AROMPN
 +
|C5H5NO8
 +
|Lumped PN from aromatics
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|BPINN
 +
|C10H17NO4
 +
|Saturated 1st gen BPIN organic nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|BPINO
 +
|C9H14O
 +
|Ketone from BPIN
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|BPINO2
 +
|C10H17O3
 +
|Peroxy radical from BPIN
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|BPINON
 +
|C9H13NO4
 +
|Saturated 2nd gen BPIN organic nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|BPINOO2
 +
|C10H17O3
 +
|2nd-gen peroxy radical from BPIN
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|BPINOOH
 +
|C9H14O3
 +
|2nd-gen peroxide from BPIN
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|BPINP
 +
|C10H18O3
 +
|Peroxide from BPIN
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|BUTN
 +
|C4H7NO4
 +
|C4H6 alkyl nitrate
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|BUTO2
 +
|C4H7O3
 +
|peroxy radical from C4H6
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|C4H6
 +
|C4H6
 +
|1,3-butadiene
 +
|X
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|C96N
 +
|C9H15NO4
 +
|Saturated 2nd gen monoterpene organic nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|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'
 +
|ZRO2
 +
|C7H9O5
 +
|RO2 for making lumped aromatic nitrate
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 
|}
 
|}
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:32, 14 November 2017 (UTC)
+
 
+
=== Species removed===
== Collection list ==
+
 
+
  
EXPID:  OutputDir/GCHP
+
Species removed between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:
EXPDSC: GEOS-Chem_devel
+
CoresPerNode: 6
+
  
#===================================================================
+
{| border=1 cellspacing=0 cellpadding=5
# Declare collection names and toggle on/off
+
!width='100px' bgcolor='#CCCCCC'|Name
# by commenting out with a #
+
!width='100px' bgcolor='#CCCCCC'|Formula
#===================================================================
+
!width='200px' bgcolor='#CCCCCC'|Fullname
COLLECTIONS: 'SpeciesConc',
+
!width='30px' bgcolor='#CCCCCC'|Advected
              'Aerosols',
+
!width='30px' bgcolor='#CCCCCC'|Dry deposited
              'CloudConvFlux',
+
!width='30px' bgcolor='#CCCCCC'|Gas
              'ConcAfterChem',
+
!width='30px' bgcolor='#CCCCCC'|Photolyzed
              'DryDep',
+
!width='30px' bgcolor='#CCCCCC'|Wet deposited
              '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