Difference between revisions of "List of diagnostics archived to netCDF format"
(→= HEMCO diagnostics for full-chemistry simulations) |
(→HEMCO diagnostics for full-chemistry simulations) |
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############################################################################### | ############################################################################### | ||
EmisMGLY_BioBurn MGLY 111 -1 -1 2 atomsC/cm2/s | EmisMGLY_BioBurn MGLY 111 -1 -1 2 atomsC/cm2/s | ||
+ | |||
+ | #EOC | ||
+ | |||
+ | === HEMCO diagnostics for the Rn-Pb-Be simulation === | ||
+ | |||
+ | The <tt>HEMCO_Diagn.rc</tt> file corresponding to the Rn-Pb-Be simulation is shown below. To disable a particular diagnostic quantity, simply place a <tt>#</tt> comment character in front of its name. | ||
+ | |||
+ | #------------------------------------------------------------------------------ | ||
+ | # GEOS-Chem Global Chemical Transport Model ! | ||
+ | #------------------------------------------------------------------------------ | ||
+ | #BOP | ||
+ | # | ||
+ | # !MODULE: HEMCO_Diagn.rc | ||
+ | # | ||
+ | # !DESCRIPTION: Configuration file for netCDF diagnostic output from HEMCO. | ||
+ | #\\ | ||
+ | #\\ | ||
+ | # !REMARKS: | ||
+ | # Customized for the RnPbBe simulation. | ||
+ | # TO DO: Add long names, which are used for netCDF variable attributes. | ||
+ | # | ||
+ | # !REVISION HISTORY: | ||
+ | # 13 Feb 2018 - E. Lundgren - Initial version | ||
+ | #EOP | ||
+ | #------------------------------------------------------------------------------ | ||
+ | #BOC | ||
+ | # Name Spec ExtNr Cat Hier Dim OutUnit LongName | ||
+ | |||
+ | ############################################################################### | ||
+ | ##### Rn emissions (in bpch ND01) ##### | ||
+ | ############################################################################### | ||
+ | EmisRn_Total Rn -1 -1 -1 3 kg/m2/s | ||
+ | EmisRn_Soil Rn 1001 1 -1 3 kg/m2/s | ||
+ | |||
+ | ############################################################################### | ||
+ | ##### Rn emissions (in bpch ND01) ##### | ||
+ | ############################################################################### | ||
+ | EmisBe7_Total Be7 -1 -1 -1 3 kg/m2/s | ||
+ | EmisBe7_Cosmic Be7 1001 1 -1 3 kg/m2/s | ||
#EOC | #EOC |
Revision as of 19:58, 7 June 2018
On this page we list the information about the new netCDF diagnostics that will be introduced in GEOS-Chem v11-02.
NOTE: We will NOT retire the legacy bpch diagnostics in GEOS-Chem v11-02. We will preserve the bpch diagnostic output until we can find alternatives for specialty diagnostics, especially those which involve averaging in a local solar time window.
Contents
- 1 Overview
- 2 Legend to sections below
- 3 Diagnostic collections
- 3.1 The master collection list
- 3.2 The SpeciesConc collection
- 3.3 The AerosolMass collection
- 3.4 The Aerosols collection
- 3.5 The CloudConvFlux collection
- 3.6 The ConcAfterChem collection
- 3.7 The DryDep collection
- 3.8 The JValues collection
- 3.9 The JValuesLocalNoon collection
- 3.10 The LevelEdgeDiags collection
- 3.11 The ProdLoss Collection
- 3.12 The RadioNuclide Collection
- 3.13 The StateChm Collection
- 3.14 The StateMet collection
- 3.15 The WetLossConv collection
- 3.16 The WetLossLS collection
- 4 Diagnostics that are currently archived by HEMCO
- 5 Replicating the existing specialty diagnostics
- 6 Validating the netCDF diagnostics
- 7 Proposed diagnostic names for specialty simulations
Overview
An introduction to netCDF diagnostics
Bob Yantosca has created an overview presentation about the new netCDF diagnostics for v11-02.
--Bob Yantosca (talk) 22:12, 8 February 2018 (UTC)
Sample HISTORY.rc diagnostic input file
Here is a sample HISTORY.rc file that is used to request netCDF diagnostic output from a GEOS-Chem “Classic” simulation.
#============================================================================ # EXPID allows you to specify the beginning of the file path corresponding # to each diagnostic collection. For example: # # EXPID: ./GEOSChem # Will create netCDF files whose names begin "GEOSChem", # in this run directory. # # EXPID: ./OutputDir/GEOSChem # Will create netCDF files whose names begin with "GEOSChem" # in the OutputDir sub-folder of this run directory. # # EXPDSC and CoresPerNode are only used by GCHP simulations. #============================================================================ EXPID: ./GEOSChem EXPDSC: GEOS-Chem_devel CoresPerNode: 6 #============================================================================== # %%%%% COLLECTION NAME DECLARATIONS %%%%% # # To disable a collection, place a "#" character in front of its name # # NOTE: These are the "default" collections for GEOS-Chem. # But you can create your own custom diagnostic collections as well. #============================================================================== COLLECTIONS: 'SpeciesConc', 'ConcAfterChem', :: @============================================================================== # %%%%% THE SpeciesConc COLLECTION %%%%% # # GEOS-Chem species concentrations (default = advected species) # # Available for all simulations #============================================================================== SpeciesConc.template: '%y4%m2%d2_%h2%n2z.nc4', SpeciesConc.frequency: 060000, SpeciesConc.format: 'CFIO', SpeciesConc.duration: 240000, SpeciesConc.mode: 'instantaneous', SpeciesConc.fields: 'SpeciesConc_?ADV?', 'GIGCchem', :: #============================================================================== # %%%%% THE ConcAfterChem COLLECTION %%%%% # # Concentrations of OH, HO2, O1D, O3P immediately after exiting the KPP solver # or OH after the CH4 specialty-simulation chemistry routine. # # OH: Available for all full-chemistry simulations and CH4 specialty sim # HO2: Available for all full-chemistry simulations # O1D, O3P: Availalbe for full-chemistry simulations using UCX mechanism #============================================================================== ConcAfterChem.template: '%y4%m2%d2_%h2%n2z.nc4', ConcAfterChem.frequency: 00000100 000000, ConcAfterChem.format: 'CFIO', ConcAfterChem.duration: 00000100 000000, ConcAfterChem.mode: 'time-averaged', ConcAfterChem.fields: 'OHconcAfterChem', 'GIGCchem', 'HO2concAfterChem', 'GIGCchem', 'O1DconcAfterChem', ‘GIGCchem’, 'O3PconcAfterChem', ‘GIGCchem’, ::
In this HISTORY.rc file, we are requesting two collections, or types of netCDF file output. The table below explains in more detail parameters shown in the HISTORY.rc file above.
Attribute | Explanation |
---|---|
SpeciesConc | Name of the first collection in this HISTORY.rc file. A collection is a series of files containing the same GEOS-Chem diagnostic quantities. |
SpeciesConc.template | Determines the date and time format for each netCDF file name belonging to the SpeciesConc collection.
|
SpeciesConc.frequency | Determines how often the diagnostic quantities belonging to SpeciesConc collection will be saved to a netCDF file.
|
SpeciesConc.format | For GCHP simulations only: indicates the I/O library that will be used. This can be omitted for GEOS-Chem "Classic" simualations. |
SpeciesConc.duration | Determines how often a new SpeciesConc netCDF file will be created.
|
SpeciesConc.mode | Determines the averaging method for the SpeciesConc collection
|
SpeciesConc.fields | Lists the diagnostic quantities to be included in the SpeciesConc collection.
See the sections below for in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format. NOTE: You may use wildcards to request a subset of all possible chemical species. See the next section for more information about wildcards. |
:: | Signifies the end of the SpeciesConc definition section.
|
ConcAfterChem | Name of the second collection in this HISTORY.rc file. |
ConcAfterChem.template | Determines the date and time format for each netCDF file name belonging to the ConcAfterChem collection. |
ConcAfterChem.frequency | Determines the length of the period in which the diagnostic quantities belonging to ConcAfterChem collection will be temporally-averaged, before being saved to a netCDF file.
|
ConcAfterChem.format | For GCHP simulations only: indicates the I/O library that will be used. This can be omitted for GEOS-Chem "Classic" simualations. |
ConcAfterChem.duration | Determines how often a new netCDF file belongng to the ConcAfterChem will be created.
|
ConcAfterChem.mode | Determines the averaging method for the ConcAfterChem collection
|
ConcAfterChem.fields | Lists the diagnostic quantities to be included in the ConcAfterChem collection.
See the sections below for in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format. NOTE: You may use wildcards to request a subset of all possible species. See the next section for more information about wildcards. |
:: | Signifies the end of the ConcAfterChem definition section.
|
For more examples, please see Bob Yantosca’s netCDF diagnostics overview presentation. We will also add more documentation to the GEOS-Chem wiki in the coming weeks.
--Bob Yantosca (talk) 22:12, 8 February 2018 (UTC)
netCDF filename convention
The names of the netCDF files corresponding to each collection will adhere to this convention:
EXPID.CollectionName.Template
Where EXPID can be specified at the very top of the HISTORY.rc file. This parameter controls the filename prefix. In the example from the previous section, EXPID is set to ./GEOSChem. This means that all netCDF output files will be placed in the current run directory (specified by ./) and will begin with GeosChem.
If you wish to send the netCDF diagnostic output to a sub-folder of the run directory (say named OutputDir), then you can set e.g. EXPID: ./OutputDir/GeosChem. (NOTE: You can also omit the ./, but we have included it to make it clear that the files will be placed in the same directory where the GEOS-Chem executable resides.)
The CollectionName and Template settings are defined as shown in our example HISTORY.rc file from the previous section, namely:
SpeciesConc.template: '%y4%m2%d2_%h2%n2z.nc4', . . . ConcAfterChem.template: '%y4%m2%d2_%h2%n2z.nc4',
In the template tags:
- The notation %y4%m2%d5_%h2%n2 specifies a in the format YYYYMMDD_hhmm into the netCDF filename.
- The lowercase zdenotes UTC time (aka "Zulu time").
- The .nc4 extension denotes that the file will be in netCDF-4 format.
Also recall that the duration tag of HISTORY.rc controls how often a new file will be written to disk, as we saw in our example from the previous section:
SpeciesConc.duration: 240000, # Write a new file each day . . . ConcAfterChem.duration: 00000100 000000, # Write a new file each month
Therefore, based on all of these settings in our example HISTORY.rc file, GEOS-Chem will write the following netCDF files to disk in the current run directory:
GEOSChem.SpeciesConc.20160101_0000z.nc4 GEOSChem.SpeciesConc.20160102_0000z.nc4 GEOSChem.SpeciesConc.20160103_0000z.nc4 GEOSChem.SpeciesConc.20160104_0000z.nc4 ... etc one file per day...
and
GEOSChem.ConcAfterChem.20160101_0000z.nc4 GEOSChem.ConcAfterChem.20160201_0000z.nc4 GEOSChem.ConcAfterChem.20160301_0000z.nc4 GEOSChem.ConcAfterChem.20160401_0000z.nc4 ... etc one file per month ...
--Bob Yantosca (talk) 18:45, 24 May 2018 (UTC)
Legend to sections below
This section contains a description of how the information about each diagnostic quantity is arranged in the sections below.
General information about each diagnostic
The tables below list the following parameters for each diagnostic that is archived to bpch format:
Diagnostic name | The name of the given diagnostic quantity that will be archived to netCDF file format.
|
---|---|
Description | A short overview of the given diagnostic. |
Units | The physical units of the given diagnostic quantity. |
Wildcards | A list of wildcards that can be used to specify all possible species, wavelength bins, etc. for the given diagnostic quantity. For a complete list of wildcards, please see the table below. |
Simulations | A list of simulations for which this particular diagnostic is valid. |
Bpch equivalent | The NDxx diagnostic number (and slot) under which the same diagnostic is available as bpch output. See the List of diagnostics archived to bpch format wiki page for more information. |
Notes | Lists supplemental information for the given diagnostic. |
Wildcards
The following terms are used in the tables below.
Term | Explanation | Example |
---|---|---|
<spcname> | Short name of a GEOS-Chem species, used in several diagnostics listed below.
NOTES:
|
SpeciesConc_NO SpeciesConc_CO SpeciesConc_?ADV? SpeciesConc_?AER? SpeciesConc_?ALL? SpeciesConc_?DRY? SpeciesConc_?FIX? SpeciesConc_?GAS? SpeciesConc_?KPP? SpeciesConc_?PHO? SpeciesConc_?VAR? SpeciesConc_?WET? ...etc... |
<photobin> | Number of a given wavelength bin for FAST-JX photolysis | 1-18 (with UCX on); 1-12 (with UCX off) |
--Bob Yantosca (talk) 19:10, 7 June 2018 (UTC)
Diagnostic collections
NOTE: The following collections are used by default in GEOS-Chem simulations. You can create your own customized collections by modifying the HISTORY.rc file.
The only restriction is that you cannot mix data that is placed on grid box layer edges in the same collection as data placed on grid box layer centers. This violates the netCDF convention that all data variables have to be defined with the same vertical dimension.
The master collection list
The top of each HISTORY.rc file will look similar to this:
############################################################################### ### HISTORY.rc file for GEOS-Chem ### ### Contact: GEOS-Chem Support Team (geos-chem-support@as.harvard.edu) ### ############################################################################### #============================================================================ # EXPID allows you to specify the beginning of the file path corresponding # to each diagnostic collection. For example: # # EXPID: ./GEOSChem # Will create netCDF files whose names begin "GEOSChem", # in this run directory. # # EXPID: ./OutputDir/GEOSChem # Will create netCDF files whose names begin with "GEOSChem" # in the OutputDir sub-folder of this run directory. # # EXPDSC and CoresPerNode are only used by GCHP simulations. #============================================================================ EXPID: ./GEOSChem EXPDSC: GEOS-Chem_devel CoresPerNode: 6 #============================================================================== # %%%%% COLLECTION NAME DECLARATIONS %%%%% # # To disable a collection, place a "#" character in front of its name # # NOTE: These are the "default" collections for GEOS-Chem. # But you can create your own custom diagnostic collections as well. #============================================================================== COLLECTIONS: 'SpeciesConc', 'AerosolMass', 'Aerosols', 'CloudConvFlux', 'ConcAfterChem', 'DryDep', 'JValues', 'JValuesLocalNoon', 'LevelEdgeDiags', 'ProdLoss', 'StateChm', 'StateMet', 'WetLossConv', 'WetLossLS', ::
We have already discussed how EXPID works in a previous section.
The COLLECTIONS: tag specifies all of the diagnostic collections that you wish to activate during a GEOS-Chem simulation. Each collection represents a group of diagnostic quantities that will be written to disk in netCDF file format. The collection name will be automatically added to the netCDF file name along with the date/or time, as we have seen above.
Each of the run directories for the various GEOS-Chem simulations will have its own customized HISTORY.rc file. Only the diagnostic collections pertaining to a particular GEOS-Chem simulation will be included in the corresponding HISTORY.rc file. (In other words, you will not find diagnostic collections for full-chemistry simulations in the HISTORY.rc file for the Rn-Pb-Be simulation.)
Each collection name must be bracketed by single quotes, and be followed by a comma.
To disable an entire diagnostic collection, simply put a # comment character in front of the collection name in the COLLECTIONS: section.
GEOS-Chem will expect to find a collection definition section for each of the activated collections listed under the COLLECTIONS: section. In other words, if you have SpeciesConc listed under COLLECTIONS:, but there is no further information provided about the SpeciesConc collection, then GEOS-Chem will halt with an error message.
The collections listed on this wiki page are the "default" diagnostic collections that we have created for GEOS-Chem. You are certainly not limited to just using these collections. We have created these default collections such that related quantities will be grouped together in the same netCDF files (to the greatest extent possible). But you can create your own customized diagnostic collections by referring to our sample HISTORY.rc file shown above.
--Bob Yantosca (talk) 18:51, 24 May 2018 (UTC)
The SpeciesConc collection
The SpeciesConc diagnostic collection contains advected species concentrations. This type of diagnostic output is used in all GEOS-Chem simulations; therefore, we have listed SpeciesConc first in the HISTORY.rc files that ship with each GEOS-Chem run directory.
Here is a sample definition section for the SpeciesConc collection. To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
SpeciesConc.template: '%y4%m2%d2_%h2%n2z.nc4', SpeciesConc.format: 'CFIO', SpeciesConc.frequency: 00000100 000000 SpeciesConc.duration: 00000100 000000 SpeciesConc.mode: 'time-averaged' SpeciesConc.fields: 'SpeciesConc_?ADV? ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the SpeciesConc collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
SpeciesConc_<spcname> | Chemical species concentrations | mol/mol dry air |
|
|
--Bob Yantosca (talk) 19:43, 16 May 2018 (UTC)
The AerosolMass collection
The AerosolMass collection contains diagnostics for aerosol mass and particulate matter from full-chemistry simulations.
Here is a sample definition section for the AerosolMass collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
AerosolMass.template: '%y4%m2%d2_%h2%n2z.nc4', AerosolMass.format: 'CFIO', AerosolMass.frequency: 00000100 000000 AerosolMass.duration: 00000100 000000 AerosolMass.mode: 'time-averaged' AerosolMass.fields: 'AerMassASOA ', 'GIGCchem', 'AerMassBC ', 'GIGCchem', 'AerMassINDIOL ', 'GIGCchem', 'AerMassISN1OA ', 'GIGCchem', 'AerMassISOA ', 'GIGCchem', 'AerMassLVOCOA ', 'GIGCchem', 'AerMassNH4 ', 'GIGCchem', 'AerMassNIT ', 'GIGCchem', 'AerMassOPOA ', 'GIGCchem', 'AerMassPOA ', 'GIGCchem', 'AerMassSAL ', 'GIGCchem', 'AerMassSO4 ', 'GIGCchem', 'AerMassSOAGX ', 'GIGCchem', 'AerMassSOAIE ', 'GIGCchem', 'AerMassSOAME ', 'GIGCchem', 'AerMassSOAMG ', 'GIGCchem', 'AerMassTSOA ', 'GIGCchem', 'BetaNO ', 'GIGCchem', 'PM25 ', 'GIGCchem', 'TotalBiogenicOA ', 'GIGCchem', 'TotalOA ', 'GIGCchem', 'TotalOC ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the AerosolMass collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
AerMassTSOA | Aerosol products of terpene oxidation | ug/m3 |
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AerMassISOA | Aerosol products of isoprene oxidation | ug/m3 |
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AerMassTSOA | Aerosol products of terpene oxidation | ug/m3 |
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AerMassASOA | Aerosol products of light aromatics + IVOC oxidation | ug/m3 |
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AerMassPOA | Aerosols from SVOCs | ug/m3 |
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AerMassTSOA | Aerosol products of terpene oxidation | ug/m3 |
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AerMassOPOA | Aerosol products of POG oxidation | ug/m3 |
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TotalOA | Sum of all organic aerosol | ug/m3 |
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TotalOC | Sum of all organic carbon | ug/m3 |
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BetaNO | NO branching ratio | ug/m3 |
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AerMassBC | Black carbon (BCPI + BCPO) | ug/m3 |
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AerMassSO4 | Sulfate | ug/m3 |
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AerMassNH4 | Ammonium | ug/m3 |
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AerMassNIT | Nitrate | ug/m3 |
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AerMassSAL | Sea salt aerosol (SALA + SALC) | ug/m3 |
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PM25 | Particulate matter (r < 2.5 μm) | ug/m3 |
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AerMassSOAGX | Aerosol-phase glyoxal | ug/m3 |
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AerMassSOAMG | Aerosol-phase methylglyoxal | ug/m3 |
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AerMassSOAIE | Aerosol-phase IEPOX | ug/m3 |
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AerMassSOAME | Aerosol-phase IMAE | ug/m3 |
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AerMassINDIOL | Generic aerosol-phase organonitrate hydrolysis product | ug/m3 |
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AerMassLVOCOA | Aerosol-phase low-volatility non-IEPOX product of ISOPOOH (RIP) oxidation | ug/m3 |
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AerMassISN1OA | Aerosol-phase 2nd generation hydroxynitrates formed from ISOP+NO3 reaction pathway | ug/m3 |
|
|
--Bob Yantosca (talk) 20:19, 16 May 2018 (UTC)
The Aerosols collection
The Aerosols collection contains diagnostics for aerosol optical depth and related quantities from full-chemistry simulations.
Here is a sample definition section for the Aerosols collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
Aerosols.template: '%y4%m2%d2_%h2%n2z.nc4', Aerosols.format: 'CFIO', Aerosols.frequency: 00000100 000000 Aerosols.duration: 00000100 000000 Aerosols.mode: 'time-averaged' Aerosols.fields: 'AODDust ', 'GIGCchem', 'AODDustWL1_?DUSTBIN? ', 'GIGCchem', 'AODHygWL1_?HYG? ', 'GIGCchem', 'AODSOAfromAqIsopreneWL1 ', 'GIGCchem', 'AODStratLiquidAerWL1 ', 'GIGCchem', 'AODPolarStratCloudWL1 ', 'GIGCchem', 'AerHygroscopicGrowth_?HYG? ', 'GIGCchem', 'AerNumDensityStratLiquid ', 'GIGCchem', 'AerNumDensityStratParticulate ', 'GIGCchem', 'AerAqueousVolume ', 'GIGCchem', 'AerSurfAreaDust ', 'GIGCchem', 'AerSurfAreaHyg_?HYG? ', 'GIGCchem', 'AerSurfAreaStratLiquid ', 'GIGCchem', 'AerSurfAreaPolarStratCloud ', 'GIGCchem', 'Chem_AeroAreaMDUST1 ', 'GIGCchem', 'Chem_AeroAreaMDUST2 ', 'GIGCchem', 'Chem_AeroAreaMDUST3' ', 'GIGCchem', 'Chem_AeroAreaMDUST4 ', 'GIGCchem', 'Chem_AeroAreaMDUST5 ', 'GIGCchem', 'Chem_AeroAreaMDUST6 ', 'GIGCchem', 'Chem_AeroAreaMDUST7 ', 'GIGCchem', 'Chem_AeroAreaSULF ', 'GIGCchem', 'Chem_AeroAreaBC ', 'GIGCchem', 'Chem_AeroAreaOC ', 'GIGCchem', 'Chem_AeroAreaSSA ', 'GIGCchem', 'Chem_AeroAreaSSC ', 'GIGCchem', 'Chem_AeroAreaBGSULF ', 'GIGCchem', 'Chem_AeroAreaICEI ', 'GIGCchem', 'Chem_AeroRadiMDUST1 ', 'GIGCchem', 'Chem_AeroRadiMDUST2 ', 'GIGCchem', 'Chem_AeroRadiMDUST3 ', 'GIGCchem', 'Chem_AeroRadiMDUST4 ', 'GIGCchem', 'Chem_AeroRadiMDUST5 ', 'GIGCchem', 'Chem_AeroRadiMDUST6 ', 'GIGCchem', 'Chem_AeroRadiMDUST7 ', 'GIGCchem', 'Chem_AeroRadiSULF ', 'GIGCchem', 'Chem_AeroRadiBC ', 'GIGCchem', 'Chem_AeroRadiOC ', 'GIGCchem', 'Chem_AeroRadiSSA ', 'GIGCchem', 'Chem_AeroRadiSSC ', 'GIGCchem', 'Chem_AeroRadiBGSULF ', 'GIGCchem', 'Chem_AeroRadiICEI ', 'GIGCchem', 'Chem_WetAeroAreaMDUST1 ', 'GIGCchem', 'Chem_WetAeroAreaMDUST2 ', 'GIGCchem', 'Chem_WetAeroAreaMDUST3 ', 'GIGCchem', 'Chem_WetAeroAreaMDUST4 ', 'GIGCchem', 'Chem_WetAeroAreaMDUST5 ', 'GIGCchem', 'Chem_WetAeroAreaMDUST6 ', 'GIGCchem', 'Chem_WetAeroAreaMDUST7 ', 'GIGCchem', 'Chem_WetAeroAreaSULF ', 'GIGCchem', 'Chem_WetAeroAreaBC ', 'GIGCchem', 'Chem_WetAeroAreaOC ', 'GIGCchem', 'Chem_WetAeroAreaSSA ', 'GIGCchem', 'Chem_WetAeroAreaSSC ', 'GIGCchem', 'Chem_WetAeroAreaBGSULF ', 'GIGCchem', 'Chem_WetAeroAreaICEI ', 'GIGCchem', 'Chem_WetAeroRadiMDUST1 ', 'GIGCchem', 'Chem_WetAeroRadiMDUST2 ', 'GIGCchem', 'Chem_WetAeroRadiMDUST3 ', 'GIGCchem', 'Chem_WetAeroRadiMDUST4 ', 'GIGCchem', 'Chem_WetAeroRadiMDUST5 ', 'GIGCchem', 'Chem_WetAeroRadiMDUST6 ', 'GIGCchem', 'Chem_WetAeroRadiMDUST7 ', 'GIGCchem', 'Chem_WetAeroRadiSULF ', 'GIGCchem', 'Chem_WetAeroRadiBC ', 'GIGCchem', 'Chem_WetAeroRadiOC ', 'GIGCchem', 'Chem_WetAeroRadiSSA ', 'GIGCchem', 'Chem_WetAeroRadiSSC ', 'GIGCchem', 'Chem_WetAeroRadiBGSULF ', 'GIGCchem', 'Chem_WetAeroRadiICEI ', 'GIGCchem', 'Chem_StatePSC ', 'GIGCchem', 'Chem_KhetiSLAN2O5H2O ', 'GIGCchem', 'Chem_KhetiSLAN2O5HCl ', 'GIGCchem', 'Chem_KhetiSLAClNO3H2O ', 'GIGCchem', 'Chem_KhetiSLAClNO3HCl ', 'GIGCchem', 'Chem_KhetiSLAClNO3HBr ', 'GIGCchem', 'Chem_KhetiSLABrNO3H2O ', 'GIGCchem', 'Chem_KhetiSLABrNO3HCl ', 'GIGCchem', 'Chem_KhetiSLAHOClHCl ', 'GIGCchem', 'Chem_KhetiSLAHOClHBr ', 'GIGCchem', 'Chem_KhetiSLAHOBrHCl ', 'GIGCchem', 'Chem_KhetiSLAHOBrHBr ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the Aerosols collection:
NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).
NOTE: UCX fullchem refers to all full-chemistry simulations that use UCX (i.e. benchmark, standard, aciduptake, marinePOA).
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
AODDust | Mineral dust optical depth for 1st wavelength specified in Radiation Menu | 1 |
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AODDust_WL1_?DUSTBIN? | AOD for 1st wavelength specified in Radiation Menu, for each dust bin | 1 | ?DUSTBIN? |
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AODHygWL1_<spcname> | Optical depth for selected species (SO4, BC, OC, SALA, SALC) at the 1st wavelength specified in the Radiation Menu | 1 | ?HYG? |
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AODSOAfromAqIsopreneWL1 | Optical depth of SOA from aqueous isoprene optical depth | 1 |
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AODStratLiquidAerWL1 | Stratospheric liquid aerosol optical depth (600 nm) |
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AODPolarStratCloudWL1 | Polar stratospheric cloud type 1a/2 optical depth (600 nm) | 1 |
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AerHygroscopicGrowth_<spcname> | Hygroscopic growth of selected species (SO4, BC, OC, SALA, SALC) | 1 | ?HYG? |
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AerNumDensityStratLiquid | Stratospheric liquid aerosol number density (UCX simulation only) | 1/cm3 |
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AerSurfAreaStratLiquid | Stratospheric liquid aerosol surface area (UCX simulation only) | cm2/cm3 |
|
|||
AerSurfAreaPolarStratCloud | Polar stratospheric cloud type 1a/2 surface area (UCX simulation only) | cm2/cm3 |
|
|||
Chem_AeroAreaMDUST1 | Dry aerosol area for mineral dust (bin Reff = 0.15 μm) | cm2/cm3 |
|
|||
Chem_AeroAreaMDUST2 | Dry aerosol area for mineral dust (bin Reff = 0.25 μm) | cm2/cm3 |
|
|||
Chem_AeroAreaMDUST3 | Dry aerosol area for mineral dust (bin Reff = 0.4 μm) | cm2/cm3 |
|
|||
Chem_AeroAreaMDUST4 | Dry aerosol area for mineral dust (bin Reff = 0.8 μm) | cm2/cm3 |
|
|||
Chem_AeroAreaMDUST5 | Dry aerosol area for mineral dust (bin Reff = 1.5 μm) | cm2/cm3 |
|
|||
Chem_AeroAreaMDUST6 | Dry aerosol area for mineral dust (bin Reff = 2.5 μm) | cm2/cm3 |
|
|||
Chem_AeroAreaMDUST7 | Dry aerosol area for mineral dust (bin Reff = 4.0 μm) | cm2/cm3 |
|
|||
Chem_AeroAreaSULF | Dry aerosol area for sulfate | cm2/cm3 |
|
|||
Chem_AeroAreaBC | Dry aerosol area for black carbon | cm2/cm3 |
|
|||
Chem_AeroAreaOC | Dry aerosol area for organic carbon | cm2/cm3 |
|
|||
Chem_AeroAreaSSA | Dry aerosol area for sea salt, accumulation mode | cm2/cm3 |
|
|||
Chem_AeroAreaSSA | Dry aerosol area for sea salt, coarse mode | cm2/cm3 |
|
|||
Chem_AeroAreaBGSULF | Dry aerosol area for background stratospheric sulfate | cm2/cm3 |
|
|||
Chem_AeroAreaICEI | Dry aerosol area for irregular ice cloud (Mischenko) | cm2/cm3 |
|
|||
Chem_AeroRadiMDUST1 | Dry aerosol radius for mineral dust (bin Reff = 0.15 μm) | cm |
|
|||
Chem_AeroRadiMDUST2 | Dry aerosol radius for mineral dust (bin Reff = 0.25 μm) | cm |
|
|||
Chem_AeroRadiMDUST3 | Dry aerosol radius for mineral dust (bin Reff = 0.4 μm) | cm |
|
|||
Chem_AeroRadiMDUST4 | Dry aerosol radius for mineral dust (bin Reff = 0.8 μm) | cm |
|
|||
Chem_AeroRadiMDUST5 | Dry aerosol radius for mineral dust (bin Reff = 1.5 μm) | cm |
|
|||
Chem_AeroRadiMDUST6 | Dry aerosol radius for mineral dust (bin Reff = 2.5 μm) | cm |
|
|||
Chem_AeroRadiMDUST7 | Dry aerosol radius for mineral dust (bin Reff = 4.0 μm) | cm |
|
|||
Chem_AeroRadiSULF | Dry aerosol radius for sulfate | cm |
|
|||
Chem_AeroRadiBC | Dry aerosol radius for black carbon | cm |
|
|||
Chem_AeroRadiOC | Dry aerosol radius for organic carbon | cm |
|
|||
Chem_AeroRadiSSA | Dry aerosol radius for sea salt, accumulation mode | cm |
|
|||
Chem_AeroRadiusSSC | Dry aerosol radius for sea salt, coarse mode | cm |
|
|||
Chem_AeroRadiBGSULF | Dry aerosol radius for background stratospheric sulfate | cm |
|
|||
Chem_AeroRadiusICEI | Dry aerosol radius for irregular ice cloud (Mischenko) | cm |
|
|||
Chem_WetAeroAreaMDUST1 | Wet aerosol area for mineral dust (bin Reff = 0.15 μm) | cm2/cm3 |
|
|||
Chem_WetAeroAreaMDUST2 | Wet aerosol area for mineral dust (bin Reff = 0.25 μm) | cm2/cm3 |
|
|||
Chem_WetAeroAreaMDUST3 | Wet aerosol area for mineral dust (bin Reff = 0.4 μm) | cm2/cm3 |
|
|||
Chem_WetAeroAreaMDUST4 | Wet aerosol area for mineral dust (bin Reff = 0.8 μm) | cm2/cm3 |
|
|||
Chem_WetAeroAreaMDUST5 | Wet aerosol area for mineral dust (bin Reff = 1.5 μm) | cm2/cm3 |
|
|||
Chem_WetAeroAreaMDUST6 | Wet aerosol area for mineral dust (bin Reff = 2.5 μm) | cm2/cm3 |
|
|||
Chem_WetAeroAreaMDUST7 | Wet aerosol area for mineral dust (bin Reff = 4.0 μm) | cm2/cm3 |
|
|||
Chem_WetAeroAreaSULF | Wet aerosol area for sulfate | cm2/cm3 |
|
|||
Chem_WetAeroAreaBC | Wet aerosol area for black carbon | cm2/cm3 |
|
|||
Chem_WetAeroAreaOC | Wet aerosol area for organic carbon | cm2/cm3 |
|
|||
Chem_WetAeroAreaSSA | Wet aerosol area for sea salt, accumulation mode | cm2/cm3 |
|
|||
Chem_WetAeroAreaSSA | Wet aerosol area for sea salt, coarse mode | cm2/cm3 |
|
|||
Chem_WetAeroAreaBGSULF | Wet aerosol area for background stratospheric sulfate | cm2/cm3 |
|
|||
Chem_WetAeroAreaICEI | Wet aerosol area for irregular ice cloud (Mischenko) | cm2/cm3 |
|
|||
Chem_WetAeroRadiMDUST1 | Wet aerosol radius for mineral dust (bin Reff = 0.15 μm) | cm |
|
|||
Chem_WetAeroRadiMDUST2 | Wet aerosol radius for mineral dust (bin Reff = 0.25 μm) | cm |
|
|||
Chem_WetAeroRadiMDUST3 | Wet aerosol radius for mineral dust (bin Reff = 0.4 μm) | cm |
|
|||
Chem_WetAeroRadiMDUST4 | Wet aerosol radius for mineral dust (bin Reff = 0.8 μm) | cm |
|
|||
Chem_WetAeroRadiMDUST5 | Wet aerosol radius for mineral dust (bin Reff = 1.5 μm) | cm |
|
|||
Chem_WetAeroRadiMDUST6 | Wet aerosol radius for mineral dust (bin Reff = 2.5 μm) | cm |
|
|||
Chem_WetAeroRadiMDUST7 | Wet aerosol radius for mineral dust (bin Reff = 4.0 μm) | cm |
|
|||
Chem_WetAeroRadiSULF | Wet aerosol radius for sulfate | cm |
|
|||
Chem_WetAeroRadiBC | Wet aerosol radius for black carbon | cm |
|
|||
Chem_WetAeroRadiOC | Wet aerosol radius for organic carbon | cm |
|
|||
WetChem_AeroRadiSSA | Wet aerosol radius for sea salt, accumulation mode | cm |
|
|||
Chem_WetAeroRadiusSSC | Wet aerosol radius for sea salt, coarse mode | cm |
|
|||
Chem_WetAeroRadiBGSULF | Wet aerosol radius for background stratospheric sulfate | cm |
|
|||
Chem_WetAeroRadiusICEI | Wet aerosol radius for irregular ice cloud (Mischenko) | cm |
|
|||
Chem_StatePSC | Polar stratospheric cloud type (cf Kirner et al, 2011, GMD) | count |
|
|||
Chem_KhetiSLAN2O5H2O | Sticking coeff. for N2O5 + H2O rxn | 1 |
|
|||
Chem_KhetiSLAN2O5HCl | Sticking coeff. for N2O5 + HCl rxn | 1 |
|
|||
Chem_KhetiSLAClNO3H2O | Sticking coeff. for ClNO3 + H2O rxn | 1 |
|
|||
Chem_KhetiSLAClNO3HCl | Sticking coeff. for ClNO3 + HCl rxn | 1 |
|
|||
Chem_KhetiSLAClNO3HBr | Sticking coeff. for ClNO3 + HBr rxn | 1 |
|
|||
Chem_KhetiSLABrNO3H2O | Sticking coeff. for BrNO3 + H2O rxn | 1 |
|
|||
Chem_KhetiSLABrNO3HCl | Sticking coeff. for BrNO3 + HCl rxn | 1 |
|
|||
Chem_KhetiSLAHOClHCl | Sticking coeff. for HOCl + HCl rxn | 1 |
|
|||
Chem_KhetiSLAHOClBr | Sticking coeff. for HOCl + HBr rxn | 1 |
|
|||
Chem_KhetiSLAHOBrHCl | Sticking coeff. for HOBr + HCl rxn | 1 |
|
|||
Chem_KhetiSLAHOBrHCl | Sticking coeff. for HOBr + HBr rxn | 1 |
|
--Bob Yantosca (talk) 19:07, 7 June 2018 (UTC)
The CloudConvFlux collection
The CloudConvFlux collection contains diagnostics for mass fluxes in cloud convection.
Here is a sample definition section for the CloudConvFlux collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
CloudConvFlux.template: '%y4%m2%d2_%h2%n2z.nc4', CloudConvFlux.format: 'CFIO', CloudConvFlux.frequency: 00000100 000000 CloudConvFlux.duration: 00000100 000000 CloudConvFlux.mode: 'time-averaged' CloudConvFlux.fields: 'CloudConvFlux_?ADV? ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the CloudConvFlux collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
CloudConvFlux_<spcname> | Mass change due to cloud convection | kg/s |
|
|
|
--Bob Yantosca (talk) 19:18, 7 June 2018 (UTC)
The ConcAfterChem collection
The ConcAfterChem collection contains diagnostics for OH, HO2, etc. species immediately upon exiting the FlexChem solver.
Here is a sample definition section for the ConcAfterChem collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
ConcAfterChem.template: '%y4%m2%d2_%h2%n2z.nc4', ConcAfterChem.format: 'CFIO', ConcAfterChem.frequency: 00000100 000000 ConcAfterChem.duration: 00000100 000000 ConcAfterChem.mode: 'time-averaged' ConcAfterChem.fields: 'OHconcAfterChem ', 'GIGCchem', 'HO2concAfterChem ', 'GIGCchem', 'O1DconcAfterChem ', 'GIGCchem', 'O3PconcAfterChem ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the ConcAfterChem collection:
NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).
NOTE: UCX fullchem refers to all full-chemistry simulations that use UCX (i.e. benchmark, standard, aciduptake, marinePOA).
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
OHconcAfterChem | OH concentration immediately after exiting the FlexChem solver | molec/cm3 |
|
|
||
HO2concAfterChem | HO2 concentration immediately after exiting the FlexChem solver | molec/cm3 |
|
|
||
O1DconcAfterChem | O1D concentration immediately after exiting the FlexChem solver | molec/cm3 |
|
|
||
O3PconcAfterChem | O3P concentration immediately after exiting the FlexChem solver | molec/cm3 |
|
|
--Bob Yantosca (talk) 19:12, 7 June 2018 (UTC)
The DryDep collection
The DryDep collection contains diagnostics for the flux and velocity of each species lost to dry-deposition.
Here is a sample definition section for the DryDep collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
DryDep.template: '%y4%m2%d2_%h2%n2z.nc4', DryDep.format: 'CFIO', DryDep.frequency: 00000100 000000 DryDep.duration: 00000100 000000 DryDep.mode: 'time-averaged' DryDep.fields: 'DryDepVel_?DRY? ', 'GIGCchem', 'DryDepMix_?DRY? ', 'GIGCchem', 'DryDepChm_?DRY? ', 'GIGCchem', 'DryDep_?DRY? ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the DryDep collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
DryDepVel_<spcname> | Dry deposition velocity | cm/s |
|
|
||
DryDepMix_<spcname> | Dry deposition flux (computed in PBL mixing) |
molec/cm2/s |
|
|
||
DryDepChm_<spcname> | Dry deposition flux (computed in chemistry) |
molec/cm2/s |
|
|
||
DryDep_<spcname> | Total dry deposition flux | molec/cm2/s |
|
|
|
--Bob Yantosca (talk) 20:33, 16 May 2018 (UTC)
The JValues collection
The JValues collection contains diagnostics for photolysis rates for various chemical species, obtained from the FAST-JX photolysis mechanism.
Here is a sample definition section for the JValues collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
JValues.template: '%y4%m2%d2_%h2%n2z.nc4', JValues.format: 'CFIO', JValues.frequency: 00000000 010000 JValues.duration: 00000000 010000 JValues.mode: 'instantaneous' JValues.fields: 'Jval_?PHO? ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the JValues collection:
NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
Jval_<spcname> | Photolysis rates | 1/s |
|
|
|
--Bob Yantosca (talk) 20:38, 16 May 2018 (UTC)
The JValuesLocalNoon collection
NOTE: At present, we are debugging an issue in how the noontime J-values are archived for netCDF. Until further notice, we recommend that you use the ND22 bpch diagnostic to archive noontime J-values. (Bob Yantosca, 16 May 2018)
The JValuesLocalNoon collection contains diagnostics for photolysis rates for various chemical species, obtained from the FAST-JX photolysis mechanism, at the grid box where it is nearest to local solar noon.
Here is a sample definition section for the JValuesLocalNoon collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
JValues.template: '%y4%m2%d2_%h2%n2z.nc4', JValues.format: 'CFIO', JValues.frequency: 00000100 000000 JValues.duration: 00000100 000000 JValues.mode: 'time-averaged' JValues.fields: 'JNoon_?PHO? ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the JValuesLocalNoon collection:
NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
JNoon_<spcname> | Photolysis rates (archived where it is local noon) | 1/s |
|
|
|
--Bob Yantosca (talk) 21:07, 16 May 2018 (UTC)
The LevelEdgeDiags collection
The LevelEdgeDiags collection contains diagnostics for quantities (mostly met fields) that are defined on the vertical edges of each grid box. According to the COARDS convention, all of the data variables in a netCDF file must be defined with the same vertical dimension.
Here is a sample definition section for the LevelEdgeDiags collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
LevelEdgeDiags.template: '%y4%m2%d2_%h2%n2z.nc4', LevelEdgeDiags.format: 'CFIO', LevelEdgeDiags.frequency: 00000100 000000 LevelEdgeDiags.duration: 00000100 000000 LevelEdgeDiags.mode: 'time-averaged' LevelEdgeDiags.fields: 'Met_CMFMC ', 'GIGCchem', 'Met_PEDGE ', 'GIGCchem', 'Met_PEDGEDRY ', 'GIGCchem', 'Met_PFICU ', 'GIGCchem', 'Met_PFILSAN ', 'GIGCchem', 'Met_PFLCU ', 'GIGCchem', 'Met_PFLLSAN ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the JValuesLocalNoon collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
Met_CMFMC | Upward moist convective mass flux | kg/m2/s |
|
|||
Met_PEDGE | Surface pressure at level edges (based on moist air) | hP |
|
|||
Met_PEDGEDRY | Surface pressure at level edges (based on dry air) | hP |
|
|||
Met_PFICU | 3d flux of ice convective precipitation | kg/m2/s |
|
|||
Met_PFILSAN | 3d flux of ice non-convective precipitation | kg/m2/s |
|
|||
Met_PFLCU | 3d flux of liquid convective precipitation | kg/m2/s |
|
|||
Met_PFLLSAN | 3d flux of liquid non-convective precipitation | kg/m2/s |
|
--Bob Yantosca (talk) 21:23, 16 May 2018 (UTC)
The ProdLoss Collection
The ProdLoss collection contains chemical production and loss rates.
Here is a sample definition section for the ProdLoss collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
NOTE: This example is for the benchmark simulation. Some quantities in this collection are not applicable to certain simulations.
ProdLoss.template: '%y4%m2%d2_%h2%n2z.nc4', ProdLoss.format: 'CFIO', ProdLoss.frequency: 00000100 000000 ProdLoss.duration: 00000100 000000 ProdLoss.mode: 'time-averaged' ProdLoss.fields: 'Prod_?PRD? ', 'GIGCchem', 'ProdBCPIfromBCPO ', 'GIGCchem', 'ProdOCPIfromOCPO ', 'GIGCchem', 'ProdSO4fromH2O2inCloud ', 'GIGCchem', 'ProdSO4fromO2inCloudMetal ', 'GIGCchem', 'ProdSO4fromO3inCloud ', 'GIGCchem', 'ProdSO4fromO3inSeaSalt ', 'GIGCchem', 'ProdSO4fromHOBrInCloud ', 'GIGCchem', 'ProdSO4fromSRO3 ', 'GIGCchem', 'ProdSO4fromSRHObr ', 'GIGCchem', 'ProdSO4fromO3s ', 'GIGCchem', 'Loss_?LOS? ', 'GIGCchem', 'LossHNO3onSeaSalt ', 'GIGCchem', ::
The table below describes diagnostic quantities belonging to the ProdLoss collection.
NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
Diagnostics applicable only to the aciduptake simulation | ||||||
ProdSO4fromOxidationOnDust | Production of SO4 from oxidation on dust aerosols | kg S/s |
|
|||
ProdNITfromHNO3uptakeOnDust | Production of NIT from HNO3 uptake on dust aerosols | kg N/s |
|
|||
ProdSO4fromUptakeOfH2SO4g | Production of SO4 from uptake of H2SO4(g) | kg S/s |
|
|||
Diagnostics applicable only to the aerosol-only simulation | ||||||
ProdSO2fromDMSandOH | Production of SO2 from DMS + OH (in sulfate_mod.F) | kg S/s |
|
|||
ProdSO2fromDMSandNO3 | Production of SO2 from DMS + NO3 | kg S/s |
|
|||
ProdSO2fromDMS | Total P(SO2) from DMS | kg S/s |
|
|||
ProdMSAfromDMS | Production of MSA from DMS | kg S/s |
|
|||
ProdSO4fromGasPhase | Production of SO4 in the gas phase | kg S/s |
|
|||
Diagnostics applicable only to the aerosol-only and all fullchem simulations | ||||||
ProdBCPIfromBCPO | Production of hydrophilic BC from hydrophobic BCs | kg |
|
|||
ProdOCPIfromOCPO | Production of hydrophilic BC from hydrophobic BCs | kg |
|
|||
ProdSO4fromH2O2inCloud | Production of SO4 from aqueous oxidation of H2O2 in clouds | kg S/s |
|
|||
ProdSO4fromO2inCloudMetal | Production of SO4 from aqueous oxidation of H2O2 in clouds | kg S/s |
|
| ||
ProdSO4fromO3inCloud | Production of SO4 from aqueous oxidation of O3 in clouds | kg S/s |
|
|||
ProdSO4fromO3inSeaSalt | Production of SO4 from O3 in sea salt | kg S/s |
|
|||
ProdSO4fromO3s | Production of SO4 from aqueous phase SO3-- loss by OH | kg S/s |
|
| ||
ProdSO4fromSRO3 | Production of SO4 from sulfur production rate of O3 | kg S/s |
|
| ||
LossHNO3onSeaSalt | Loss of HNO3 on sea salt aerosols | kg S/s |
|
|||
Diagnostics applicable only to full-chemistry simulations | ||||||
ProdSO4fromHOBrinCloud | Production of SO4 from aqueous oxidation of HOBr in clouds | kg S/s |
|
| ||
ProdSO4fromSRHOBr | Production of SO4 from sulfur production rate of HOBr+O3 | kg S/s |
|
| ||
Diagnostics for production and loss of species or chemical families (e.g. Ox) | ||||||
Prod_<spcname> | Chemical production for a given species or family | molec/cm3/s |
|
|
||
Loss_<spcname> | Chemical loss for a given species or family | molec/cm3/s |
|
|
--Bob Yantosca (talk) 19:25, 17 May 2018 (UTC)
The RadioNuclide Collection
The RadioNuclide collection contains diagnostic ouputs from the Radon-Lead-Beryllium specialty simulation.
Here is a sample definition section for the RadioNuclide collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
RadioNuclide.template: '%y4%m2%d2_%h2%n2z.nc4', RadioNuclide.format: 'CFIO', RadioNuclide.frequency: 00000100 000000 RadioNuclide.duration: 00000100 000000 RadioNuclide.mode: 'time-averaged' RadioNuclide.fields: 'PbFromRnDecay ', 'GIGCchem', 'RadDecay_Rn ', 'GIGCchem', 'RadDecay_Pb ', 'GIGCchem', 'RadDecay_Be7 ', 'GIGCchem', ::
The table below describes diagnostic quantities belonging to the RadioNuclide collection.
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
PbFromRnDecay | Production of 210Pb from 222Rn radioactive decay | kg/s |
|
|||
RadDecay_Rn | Loss of 222Rn due to radiactive decay | kg/s |
|
|||
RadDecay_Pb | Loss of 210Pb due to radiaoactive decay | kg/s |
|
|||
RadDecay_Be7 | Loss of 7Be due to radioactive decay | kg/s |
|
--Bob Yantosca (talk) 20:56, 22 May 2018 (UTC)
The StateChm Collection
The StateChm collection contains quantities from State_Chm, the Chemistry state object (other than the species concentrations, which are stored in the SpeciesConc collection).
Here is a sample definition section for the StateChm collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
Other fields of the State_Chm object can be added to this collection by prefixing the field name with Chem_.
StateChm.template: '%y4%m2%d2_%h2%n2z.nc4', StateChm.format: 'CFIO', StateChm.frequency: 00000100 000000 StateChm.duration: 00000100 000000 StateChm.mode: 'time-averaged' StateChm.fields: 'Chem_phSav ', 'GIGCchem', 'Chem_HplusSav ', 'GIGCchem', 'Chem_WaterSav ', 'GIGCchem', 'Chem_SulRatSav ', 'GIGCchem', 'Chem_NaRatSav ', 'GIGCchem', 'Chem_AcidPurSav ', 'GIGCchem', 'Chem_BiSulSav ', 'GIGCchem', 'Chem_pHCloud ', 'GIGCchem', 'Chem_SSAlk', ', 'GIGCchem', 'Chem_HSO3AQ ', 'GIGCchem', 'Chem_SO3AQ ', 'GIGCchem', 'Chem_fupdateHOBr ', 'GIGCchem', ::
The table below describes diagnostic quantities belonging to the StateChm collection.
NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
Chem_phSav | ISORROPIA aerosol pH | 1 |
|
|||
Chem_HplusSav | ISORROPIA H+ concentration | M |
|
|||
Chem_WaterSav | ISORROPIA aerosol water | μg/m3 |
|
|||
Chem_SulRatSav | ISORROPIA sulfate concentration | M |
|
|||
Chem_NaRatSav | ISORROPIA Na+ concentration | M |
|
|||
Chem_AcidPurSav | ISORROPIA acidpur ?? concentration | M |
|
|||
Chem_BiSulSav | ISORROPIA bisulfate (general acid) concentration | M |
|
|||
Chem_phCloud | Cloud PH | 1 |
|
| ||
Chem_SSAlk | Sea salt alkalinity | 1 |
|
| ||
Chem_HSO3AQ | Cloud bisulfite concentration | mol/L |
|
| ||
Chem_SO3AQ | Cloud sulfite concentration | mol/L |
|
| ||
Chem_fupdateHOBr | Correction factor for HOBr removal by SO2 | mol/L |
|
|
--Bob Yantosca (talk) 19:55, 17 May 2018 (UTC)
The StateMet collection
The StateMet collection contains met fields and other derived quantities that are carried in the State_Met object.
Here is a sample definition section for the StateMet collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
Other fields of the State_Met object can be added to this collection by prefixing the field name with Met_.
StateMet.template: '%y4%m2%d2_%h2%n2z.nc4', StateMet.format: 'CFIO', StateMet.frequency: 00000100 000000 StateMet.duration: 00000100 000000 StateMet.mode: 'time-averaged' StateMet.fields: 'Met_AD ', 'GIGCchem', 'Met_AIRDEN ', 'GIGCchem', 'Met_AIRVOL ', 'GIGCchem', 'Met_ALBD ', 'GIGCchem', 'Met_AREAM2 ', 'GIGCchem', 'Met_AVGW ', 'GIGCchem', 'Met_BXHEIGHT ', 'GIGCchem', 'Met_ChemGridLev ', 'GIGCchem', 'Met_CLDF ', 'GIGCchem', 'Met_CLDFRC ', 'GIGCchem', 'Met_CLDTOPS ', 'GIGCchem', 'Met_DELP ', 'GIGCchem', 'Met_DQRCU ', 'GIGCchem', 'Met_DQRLSAN ', 'GIGCchem', 'Met_DTRAIN ', 'GIGCchem', 'Met_EFLUX ', 'GIGCchem', 'Met_FRCLND ', 'GIGCchem', 'Met_FRLAKE ', 'GIGCchem', 'Met_FRLAND ', 'GIGCchem', 'Met_FRLANDIC ', 'GIGCchem', 'Met_FROCEAN ', 'GIGCchem', 'Met_FRSEAICE ', 'GIGCchem', 'Met_FRSNO ', 'GIGCchem', 'Met_GWETROOT ', 'GIGCchem', 'Met_GWETTOP ', 'GIGCchem', 'Met_HFLUX ', 'GIGCchem', 'Met_LAI ', 'GIGCchem', 'Met_LWI ', 'GIGCchem', 'Met_PARDR ', 'GIGCchem', 'Met_PARDF ', 'GIGCchem', 'Met_PBLTOPL ', 'GIGCchem', 'Met_PBLH ', 'GIGCchem', 'Met_PHIS ', 'GIGCchem', 'Met_PMID ', 'GIGCchem', 'Met_PMIDDRY ', 'GIGCchem', 'Met_PRECANV ', 'GIGCchem', 'Met_PRECCON ', 'GIGCchem', 'Met_PRECLSC ', 'GIGCchem', 'Met_PRECTOT ', 'GIGCchem', 'Met_PS1DRY ', 'GIGCchem', 'Met_PS1WET ', 'GIGCchem', 'Met_PS2DRY ', 'GIGCchem', 'Met_PS2WET ', 'GIGCchem', 'Met_PSC2WET ', 'GIGCchem', 'Met_PSC2DRY ', 'GIGCchem', 'Met_QI ', 'GIGCchem', 'Met_QL ', 'GIGCchem', 'Met_OMEGA ', 'GIGCchem', 'Met_OPTD ', 'GIGCchem', 'Met_REEVAPCN ', 'GIGCchem', 'Met_REEVAPLS ', 'GIGCchem', 'Met_SLP ', 'GIGCchem', 'Met_SNODP ', 'GIGCchem', 'Met_SNOMAS ', 'GIGCchem', 'Met_SPHU ', 'GIGCchem', 'Met_SPHU1 ', 'GIGCchem', 'Met_SPHU2 ', 'GIGCchem', 'Met_SUNCOS ', 'GIGCchem', 'Met_SUNCOSmid ', 'GIGCchem', 'Met_SWGDN ', 'GIGCchem', 'Met_T ', 'GIGCchem', 'Met_TAUCLI ', 'GIGCchem', 'Met_TAUCLW ', 'GIGCchem', 'Met_THETA ', 'GIGCchem', 'Met_TMPU1 ', 'GIGCchem', 'Met_TMPU2 ', 'GIGCchem', 'Met_TO3 ', 'GIGCchem', 'Met_TropHt ', 'GIGCchem', 'Met_TropLev ', 'GIGCchem', 'Met_TropP ', 'GIGCchem', 'Met_TS ', 'GIGCchem', 'Met_TSKIN ', 'GIGCchem', 'Met_TV ', 'GIGCchem', 'Met_U ', 'GIGCchem', 'Met_U10M ', 'GIGCchem', 'Met_USTAR ', 'GIGCchem', 'Met_UVALBEDO ', 'GIGCchem', 'Met_V ', 'GIGCchem', 'Met_V10M ', 'GIGCchem', 'Met_Z0 ', 'GIGCchem', ::
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
Met_AD | Visible surface albedo | 1 |
|
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Met_AIRDEN | Dry air density | kg/m3 |
|
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Met_AIRVOL | Grid box volume, dry air | m3 |
|
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Met_ALBD | Surface albedo | 1 |
|
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Met_AREAM2 | Grid box area | m2 |
|
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Met_AVGW | Water vapor volume mixing ratio | vol H2O/vol dry air |
|
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Met_BXHEIGHT | Grid box height | m |
|
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Met_ChemGridLev | Chemistry grid level | 1 |
|
| ||
Met_CLDF | 3-D cloud fraction | 1 |
|
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Met_CLDFRC | Column cloud fraction | 1 |
|
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Met_CLDTOPS | Maximum cloud top height | 1 |
|
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Met_DELP | Delta-pressure between top and bottom edges of grid box (wet air) | hPa |
|
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Met_DQRCU | Convective precipitation production rate (dry air) | kg/kg/s |
|
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Met_DTRAIN | Detrainment flux | kg/m2/s |
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Met_EFLUX | Latent heat flux | W/m2 |
|
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Met_FRCLND | Olson land fraction | 1 |
|
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Met_FRLAKE | Fraction of grid box covered by lakes | 1 |
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Met_FRLAND | Fraction of grid box covered by land | 1 |
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Met_FRLANDIC | Fraction of grid box covered by land ice | 1 |
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Met_FROCEAN | Fraction of grid box covered by ocean | 1 |
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Met_FRSEAICE | Fraction of grid box covered by sea ice | 1 |
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Met_FRSNO | Fraction of grid box covered by snow | 1 |
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Met_GWETROOT | Root soil moisture | 1 |
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Met_GWETTOP | Topsoil moisture | 1 |
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Met_HFLUX | Sensible heat flux | W/m2 |
|
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Met_LAI | Leaf area index from met field archive | m2/m2 |
|
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Met_LWI | Land-water-ice indices | 1 |
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Met_PARDF | Diffuse photosynthetically active radiation | W/m2 |
|
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Met_PARDR | Diffuse photosynthetically active radiation | W/m2 |
|
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Met_PBLTOPL | PBL top layer | 1 |
|
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Met_PBLH | PBL height | m |
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Met_PHIS | Surface geopotential height | m2/s2 |
|
= Height * g | ||
Met_PMID | Pressure at midpoint of model layers, defined as arithmetic average of edge pressures (wet air) | hPa |
|
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Met_PMIDDRY | Pressure at midpoint of model layers, defined as arithmetic average of edge pressures (dry air) | hPa |
|
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Met_PRECANV | Anvil precipitation (at surface) | kg/m2/s |
|
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Met_PRECCON | Convective precipitation (at surface) | kg/m2/s |
|
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Met_PRECLSC | Large-scale precipitation (at surface) | kg/m2/s |
|
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Met_PRECTOT | Total precipitation (at surface) | kg/m2/s |
|
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Met_PS1DRY | Instantaneous surface pressure at start of 3-hr met field interval (dry air) | hPa |
|
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Met_PS2DRY | Instantaneous surface pressure at end of 3-hr met field interval (dry air) | hPa |
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Met_PSC2DRY | Surface pressure interpolated to current time (dry air) | hPa |
|
| ||
Met_PS1WET | Instantaneous surface pressure at start of 3-hr met field interval (wet air) | hPa |
|
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Met_PS2WET | Instantaneous surface pressure at end of 3-hr met field interval (wet air) | hPa |
|
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Met_PSC2WET | Surface pressure interpolated to current time (wet air) | hPa |
|
| ||
Met_QI | Ice mixing ratio (dry air) | kg/kg dry air |
|
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Met_QL | Liquid water mixing ratio (dry air) | kg/kg dry air |
|
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Met_OMEGA | Updraft velocity | Pa/s |
|
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Met_OPTD | Visible optical depth | 1i |
|
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Met_REEVAPCN | Evaporation of convective precipitation (dry air) | kg/kg/s |
|
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Met_REEVAPLS | Evaporation of large-scale + anvil precipitation (dry air) | kg/kg/s |
|
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Met_SLP | Sea level pressure | hPa |
|
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Met_SNODP | Snow depth | m |
|
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Met_SNOMAS | Snow mass | kg/m2 |
|
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Met_SPHU1 | Instantaneous specific humidity at start of 3 hr met field interval (wet air) | kg/kg |
|
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Met_SPHU2 | Instantaneous specific humidity at end of 3-hr met field interval (wet air) | kg/kg |
|
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Met_SPHU | Specific humidity interpolated to current time (wet air) | g H2O/kg air |
|
| ||
Met_SUNCOS | Cosine of solar zenith angle at current time | 1 |
|
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Met_SUNCOSMID | Cosine of solar zenith angle at midpoint of chemistry timestep | 1 |
|
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Met_SWGDN | Incident shortwave radiation at ground | W/m2 |
|
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Met_TAUCLI | Visible optical depth of ice clouds | 1 |
|
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Met_TAUCLW | Visible optical depth of water clouds | 1 |
|
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Met_THETA | Potential temperature | K |
|
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Met_TMPU1 | Instantaneous temperature at start of 3-hr met field interval | K |
|
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Met_TMPU2 | Instantaneous temperature at end of 3-hr met field interval | K |
|
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Met_T | Temperature interpolated to current time | K |
|
| ||
Met_TO3 | Total overhead ozone column | Dobsons |
|
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Met_TropHt | Tropopause height | u |
|
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Met_TropLev | Tropopause height | km |
|
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Met_TROPP | Tropopause pressure | hPa |
|
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Met_TS | Surface temperature | K |
|
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Met_TSKIN | Surface skin temperature | K |
|
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Met_U | East-west ccomponent of wind | m/s |
|
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Met_U10M | East-west component of wind at 10 m height above surface | m/s |
|
|||
Met_USTAR | Friction velocity | m/s |
|
|||
Met_UVALBEDO | Ultraviolet surface albedo | 1 |
|
|||
Met_V | North-south ccomponent of wind | m/s |
|
|||
Met_V10M | North-south component of wind at 10 m height above surface | m/s |
|
|||
Met_Z0 | Surface roughness height | m |
|
--Bob Yantosca (talk) 20:40, 22 May 2018 (UTC)
The WetLossConv collection
The WetLossConv collection contains diagnostics fluxes of soluble species lost to wet scaveinging in convective updrafts.
Here is a sample definition section for the WetLossConv collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
WetLossConv.template: '%y4%m2%d2_%h2%n2z.nc4', WetLossConv.format: 'CFIO', WetLossConv.frequency: 00000100 000000 WetLossConv.duration: 00000100 000000 WetLossConv.mode: 'time-averaged' WetLossConv.fields: 'WetLossConv_?WET? ', 'GIGCchem', 'WetLossConvFrac_?WET? ', 'GIGCchem', ::
The table below describes diagnostic quantities belonging to the WetLossConv collection.
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
WetLossConv_<spcname> | Loss of soluble species scavenged by cloud updrafts in moist convection | kg/s |
|
|
||
WetLossConvFrac_<spcname> | Fraction of species scavenged by cloud updrafts in moist convection | 1 |
|
|
--Bob Yantosca (talk) 20:23, 17 May 2018 (UTC)
The WetLossLS collection
The WetLossLS collection contains diagnostics fluxes of soluble species lost to rainout and washout in large-scale wet deposition.
Here is a sample definition section for the WetLossConv collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
WetLossLS.template: '%y4%m2%d2_%h2%n2z.nc4', WetLossLS.format: 'CFIO', WetLossLS.frequency: 010000 WetLossLS.duration: 010000 WetLossLS.mode: 'time-averaged' WetLossLS.fields: 'WetLossLS_?WET? ', 'GIGCchem', ::
The table below describes diagnostic quantities belonging to the WetLossLS collection.
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
WetLossLS_<spcname> | Loss of soluble species in large-scale precipitation | kg/s |
|
|
||
WetLossConvFrac_<spcname> | Fraction of species scavenged by cloud updrafts in moist convection | 1 |
|
|
--Bob Yantosca (talk) 20:23, 17 May 2018 (UTC)
Diagnostics that are currently archived by HEMCO
The diagnostic collections described in the previous section do not contain any emissions diagnostics. These are archived by the HEMCO emissions component.
Brief overview of HEMCO diagnostics
A file named HEMCO_Diagn.rc will be included in each GEOS-Chem run directory that you create. This file lists the quantities that you would like archived to diagnostic output. You can archive any quantity computed by HEMCO (i.e. the container names listed in the HEMCO.log file) to diagnostic output. Typically you will want to save the following types of diagnostic quantities:
- Emissions for a given species, summed over all inventories and sectors (e.g. EmisCO_Total)
- Emissions for a given species, for a single emissions sector (e.g. EmisCO_Bioburn)
- Emissions for a given species, from a single inventory (e.g. EmisCO_EMEP)
The HEMCO diagnostic file name and archival frequency can be specified at the top of your HEMCO_Config.rc file. Usually the HEMCO diagnostic files are named HEMCO_diagnostics.YYYYMMDDhhmm.nc and the archival frequency is set to End (which will write out files when the simulation ends). You can change the archival frequency to e.g. monthly with e.g. 00000100 000000, etc.
For more information about HEMCO diagnostics, please see The HEMCO User's Guide: Diagnostics section.
HEMCO diagnostics for full-chemistry simulations
The HEMCO_Diagn.rc file corresponding to most GEOS-Chem full-chemistry simulations is shown below. To disable a particular diagnostic quantity, simply place a # comment character in front of its name.
#------------------------------------------------------------------------------ # GEOS-Chem Global Chemical Transport Model ! #------------------------------------------------------------------------------ #BOP # # !MODULE: HEMCO_Diagn.rc # # !DESCRIPTION: Configuration file for netCDF diagnostic output from HEMCO. #\\ #\\ # !REMARKS: # Customized for the benchmark simulation. # TO DO: Add long names, which are used for netCDF variable attributes. # # !REVISION HISTORY: # 13 Feb 2018 - E. Lundgren - Initial version #EOP #------------------------------------------------------------------------------ #BOC # Name Spec ExtNr Cat Hier Dim OutUnit LongName ############################################################################### ##### ACET emissions (in bpch ND11, ND28, ND34, ND36, ND46) ##### ############################################################################### EmisACET_Total ACET -1 -1 -1 3 molec/cm2/s EmisACET_Anthro ACET 0 1 -1 3 atomsC/cm2/s EmisACET_BioBurn ACET 111 -1 -1 2 atomsC/cm2/s EmisACET_Biofuel ACET 0 2 -1 2 atomsC/cm2/s EmisACET_Biogenic ACET 108 -1 -1 2 atomsC/cm2/s EmisACET_DirectBio ACET 108 -1 -1 2 atomsC/cm2/s ACET_from_direct_emissions EmisACET_MethylBut ACET 108 -1 -1 2 atomsC/cm2/s ACET_from_methyl_butenol EmisACET_Monoterp ACET 108 -1 -1 2 atomsC/cm2/s ACET_from_monoterpenes EmisACET_Ocean ACET 101 -1 -1 2 atomsC/cm2/s ACET_from_ocean_source ############################################################################### ##### ALD2 emissions (in bpch ND28, ND34, ND36, ND46. ALD2_Ocean ##### ##### and is new) ##### ############################################################################### EmisALD2_Total ALD2 -1 -1 -1 3 molec/cm2/s EmisALD2_Anthro ALD2 0 1 -1 3 atomsC/cm2/s EmisALD2_BioBurn ALD2 111 -1 -1 2 atomsC/cm2/s EmisALD2_Biofuel ALD2 0 2 -1 2 atomsC/cm2/s EmisALD2_Biogenic ALD2 108 -1 -1 2 atomsC/cm2/s EmisALD2_Ocean ALD2 101 -1 -1 2 atomsC/cm2/s EmisALD2_Senesc ALD2 0 4 -1 2 atomsC/cm2/s ############################################################################### ##### ALK4 emissions (in bpch ND28, ND34, ND36) ##### ############################################################################### EmisALK4_Total ALK4 -1 -1 -1 3 molec/cm2/s EmisALK4_Anthro ALK4 0 1 -1 3 atomsC/cm2/s EmisALK4_BioBurn ALK4 111 -1 -1 2 atomsC/cm2/s EmisALK4_Biofuel ALK4 0 2 -1 2 atomsC/cm2/s ############################################################################### ##### C2H6 emissions (in bpch ND28, ND34, ND36 ) ###### ############################################################################### EmisC2H6_Total C2H6 -1 -1 -1 3 molec/cm2/s EmisC2H6_Anthro C2H6 0 1 -1 3 atomsC/cm2/s EmisC2H6_BioBurn C2H6 111 -1 -1 2 atomsC/cm2/s EmisC2H6_Biofuel C2H6 0 2 -1 2 atomsC/cm2/s ############################################################################### ##### C3H8 emissions (in bpch ND28, ND34, ND36) ##### ############################################################################### EmisC3H8_Total C3H8 -1 -1 -1 3 molec/cm2/s EmisC3H8_Anthro C3H8 0 1 -1 3 atomsC/cm2/s EmisC3H8_BioBurn C3H8 111 -1 -1 2 atomsC/cm2/s EmisC3H8_Biofuel C3H8 0 2 -1 2 atomsC/cm2/s ############################################################################### ##### CH2O emissions (in bpch ND28, ND34, ND36 ) ##### ############################################################################### EmisCH2O_Total CH2O -1 -1 -1 3 molec/cm2/s EmisCH2O_Anthro CH2O 0 1 -1 3 atomsC/cm2/s EmisCH2O_BioBurn CH2O 111 -1 -1 2 atomsC/cm2/s EmisCH2O_Biofuel CH2O 0 2 -1 2 atomsC/cm2/s ############################################################################### ##### CO sources (in bpch ND29) ##### ############################################################################### EmisCO_Total CO -1 -1 -1 3 molec/cm2/s EmisCO_Anthro CO 0 1 -1 3 molec/cm2/s EmisCO_BioBurn CO 111 -1 -1 2 molec/cm2/s EmisCO_Biofuel CO 0 2 -1 2 molec/cm2/s EmisCO_Monoterp CO 109 -1 -1 2 molec/cm2/s EmisCO_Ship CO 0 10 -1 2 molec/cm2/s ############################################################################### ##### DMS emissions (in bpch ND13) ##### ############################################################################### EmisDMS_Ocean DMS 101 -1 -1 2 kg ############################################################################### ##### Dust emissions (in bpch ND06) ##### ############################################################################### EmisDST1_Natural DST1 105 -1 -1 2 kg EmisDST2_Natural DST2 105 -1 -1 2 kg EmisDST3_Natural DST3 105 -1 -1 2 kg EmisDST4_Natural DST4 105 -1 -1 2 kg ############################################################################### ##### OCPI emissions (in bpch ND07 combined with OCPO) ##### ############################################################################### EmisOCPI_Total OCPI -1 -1 -1 3 kgC EmisOCPI_Anthro OCPI 0 1 -1 3 kgC EmisOCPI_BioBurn OCPI 111 -1 -1 2 kgC EmisOCPI_Biofuel OCPI 0 2 -1 2 kgC EmisOCPI_Biogenic OCPI 109 -1 -1 2 kgC ############################################################################### ##### OCPO emissions (in bpch ND07 combined with OCPI) ##### ############################################################################### EmisOCPO_Total OCPO -1 -1 -1 3 kgC EmisOCPO_Anthro OCPO 0 1 -1 3 kgC EmisOCPO_BioBurn OCPO 111 -1 -1 2 kgC EmisOCPO_Biofuel OCPO 0 2 -1 2 kgC ############################################################################### ##### Sea salt emissions (in bpch ND08) ##### ############################################################################### EmisSALA_Natural SALA 107 -1 -1 2 kg EmisSALC_Natural SALC 107 -1 -1 2 kg ############################################################################### ##### SO2 emissions (in bpch ND13, ND28) ##### ############################################################################### EmisSO2_Total SO2 -1 -1 -1 3 kg EmisSO2_Aircraft SO2 0 20 -1 3 kg EmisSO2_Anthro SO2 0 1 -1 3 kg EmisSO2_BioBurn SO2 111 -1 -1 2 kg EmisSO2_Biofuel SO2 0 2 -1 2 kg EmisSO2_EVOL SO2 0 51 -1 2 kg EmisSO2_NVOL SO2 0 52 -1 2 kg EmisSO2_Ship SO2 0 10 -1 2 kg ############################################################################### ##### SO4 emissions (in bpch ND13) ##### ############################################################################### EmisSO4_Total SO4 -1 -1 -1 3 kg EmisSO4_Anthro SO4 0 1 -1 3 kg EmisSO4_Biofuel SO4 0 2 -1 2 kg ############################################################################### ##### NH3 emissions (in bpch ND13, ND28 ) ##### ############################################################################### EmisNH3_Total NH3 -1 -1 -1 3 kg EmisNH3_Anthro NH3 0 1 -1 3 kg EmisNH3_BioBurn NH3 111 -1 -1 2 kg EmisNH3_Biofuel NH3 0 2 -1 2 kg EmisNH3_Natural NH3 0 3 -1 2 kg ############################################################################### ##### NOx emissions (in bpch ND28, ND32, ND36) ##### ############################################################################### EmisNO_Total NO -1 -1 -1 3 molec/cm2/s EmisNO_Aircraft NO 0 20 -1 3 molec/cm2/s EmisNO_Anthro NO 0 1 -1 3 molec/cm2/s EmisNO_BioBurn NO 111 -1 -1 2 molec/cm2/s EmisNO_Biofuel NO 0 2 -1 2 molec/cm2/s EmisNO_Fert NO 104 -1 -1 2 molec/cm2/s EmisNO_Lightning NO 103 -1 -1 2 molec/cm2/s EmisNO_Ship NO 102 -1 -1 2 molec/cm2/s EmisNO_Soil NO 104 -1 -1 2 molec/cm2/s ############################################################################### ##### MEK emissions (in bpch ND28, ND34, ND36) ##### ############################################################################### EmisMEK_Total MEK -1 -1 -1 3 molec/cm2/s EmisMEK_Anthro MEK 0 1 -1 3 atomsC/cm2/s EmisMEK_BioBurn MEK 111 -1 -1 2 atomsC/cm2/s EmisMEK_Biofuel MEK 0 2 -1 2 atomsC/cm2/s ############################################################################### ##### RCHO emissions (in bpch ND34?, ND36?) ##### ############################################################################### EmisRCHO_Total RCHO -1 -1 -1 3 molec/cm2/s EmisRCHO_Anthro RCHO 0 1 -1 3 atomsC/cm2/s EmisRCHO_Biofuel RCHO 0 2 -1 2 atomsC/cm2/s ############################################################################### ##### MACR emissions (in bpch ND34?, ND36?) ##### ############################################################################### EmisMACR_Total MACR -1 -1 -1 3 molec/cm2/s EmisMACR_Anthro MACR 0 1 -1 3 atomsC/cm2/s EmisMACR_Biofuel MACR 0 2 -1 2 atomsC/cm2/s ############################################################################### ##### PRPE emissions (in bpch ND28, ND34, ND36, ND46) ##### ############################################################################### EmisPRPE_Total PRPE -1 -1 -1 3 molec/cm2/s EmisPRPE_Anthro PRPE 0 1 -1 3 atomsC/cm2/s EmisPRPE_BioBurn PRPE 111 -1 -1 2 atomsC/cm2/s EmisPRPE_Biofuel PRPE 0 2 -1 2 atomsC/cm2/s EmisPRPE_Biogenic PRPE 108 -1 -1 2 atomsC/cm2/s ############################################################################### ##### ISOP emissions (in bpch ND46) ##### ############################################################################### EmisISOP_Biogenic ISOP 108 -1 -1 2 atomsC/cm2/s ############################################################################### ##### BC emissions (combined with BCPO in bpch ND07, ND28) ##### ############################################################################### EmisBCPI_Total BCPI -1 -1 -1 3 kgC EmisBCPI_Anthro BCPI 0 1 -1 3 kgC EmisBCPI_BioBurn BCPI 111 -1 -1 2 kgC EmisBCPI_Biofuel BCPI 0 2 -1 2 kgC ############################################################################### ##### BC emissions (combined with BCPI in bpch ND07, ND28) ###### ############################################################################### EmisBCPO_Total BCPO -1 -1 -1 3 kgC EmisBCPO_Anthro BCPO 0 1 -1 3 kgC EmisBCPO_BioBurn BCPO 111 -1 -1 2 kgC EmisBCPO_Biofuel BCPO 0 2 -1 2 kgC ############################################################################### ##### CHBr3 emissions (in bpch ND46) ##### ############################################################################### EmisCHBr3_Ocean CHBr3 0 1 -1 2 kg/m2/s ############################################################################### ##### CH2Br2 emissions (in bpch ND46) ##### ############################################################################### EmisCH2Br2_Ocean CH2Br2 0 1 -1 2 kg/m2/s ############################################################################### ##### Br2 emissions (in bpch ND46) ##### ############################################################################### EmisBr2_Ocean Br2 107 -1 -1 2 kg/m2/s ############################################################################### ##### NO2 emissions (in bpch ND36?) ##### ############################################################################### EmisNO2_Anthro NO2 0 1 -1 3 molec/cm2/s ############################################################################### ##### HNO2 emissions (in bpch ND36?) ##### ############################################################################### EmisHNO2_Anthro HNO2 0 1 -1 3 molec/cm2/s ############################################################################### ##### BENZ emissions (in bpch ND34?, ND36?) ##### ############################################################################### EmisBENZ_Total BENZ -1 -1 -1 3 atomsC/cm2/s EmisBENZ_Anthro BENZ 0 1 -1 3 atomsC/cm2/s EmisBENZ_BioBurn BENZ 111 -1 -1 2 atomsC/cm2/s EmisBENZ_Biofuel BENZ 0 2 -1 2 atomsC/cm2/s ############################################################################### ##### TOLU emissions (in bpch ND34?, ND36?) ##### ############################################################################### EmisTOLU_Total TOLU -1 -1 -1 3 atomsC/cm2/s EmisTOLU_Anthro TOLU 0 1 -1 3 atomsC/cm2/s EmisTOLU_BioBurn TOLU 111 -1 -1 2 atomsC/cm2/s EmisTOLU_Biofuel TOLU 0 2 -1 2 atomsC/cm2/s ############################################################################### ##### XYLE emissions (in bpch ND34?, ND36?) ##### ############################################################################### EmisXYLE_Total XYLE -1 -1 -1 3 atomsC/cm2/s EmisXYLE_Anthro XYLE 0 1 -1 3 atomsC/cm2/s EmisXYLE_BioBurn XYLE 111 -1 -1 2 atomsC/cm2/s EmisXYLE_Biofuel XYLE 0 2 -1 2 atomsC/cm2/s ############################################################################### ##### EOH emissions (in bpch ND34?, ND36?, ND46?) ##### ############################################################################### EmisEOH_Total EOH -1 -1 -1 3 atomsC/cm2/s EmisEOH_Anthro EOH 0 1 -1 3 atomsC/cm2/s EmisEOH_BioBurn EOH 111 -1 -1 2 atomsC/cm2/s EmisEOH_Biofuel EOH 0 2 -1 2 atomsC/cm2/s EmisEOH_Biogenic EOH 108 -1 -1 2 atomsC/cm2/s EmisEOH_Senesc EOH 0 4 -1 2 atomsC/cm2/s ############################################################################### ##### MGLY emissions (new?) ##### ############################################################################### EmisMGLY_BioBurn MGLY 111 -1 -1 2 atomsC/cm2/s #EOC
HEMCO diagnostics for the Rn-Pb-Be simulation
The HEMCO_Diagn.rc file corresponding to the Rn-Pb-Be simulation is shown below. To disable a particular diagnostic quantity, simply place a # comment character in front of its name.
#------------------------------------------------------------------------------ # GEOS-Chem Global Chemical Transport Model ! #------------------------------------------------------------------------------ #BOP # # !MODULE: HEMCO_Diagn.rc # # !DESCRIPTION: Configuration file for netCDF diagnostic output from HEMCO. #\\ #\\ # !REMARKS: # Customized for the RnPbBe simulation. # TO DO: Add long names, which are used for netCDF variable attributes. # # !REVISION HISTORY: # 13 Feb 2018 - E. Lundgren - Initial version #EOP #------------------------------------------------------------------------------ #BOC # Name Spec ExtNr Cat Hier Dim OutUnit LongName ############################################################################### ##### Rn emissions (in bpch ND01) ##### ############################################################################### EmisRn_Total Rn -1 -1 -1 3 kg/m2/s EmisRn_Soil Rn 1001 1 -1 3 kg/m2/s ############################################################################### ##### Rn emissions (in bpch ND01) ##### ############################################################################### EmisBe7_Total Be7 -1 -1 -1 3 kg/m2/s EmisBe7_Cosmic Be7 1001 1 -1 3 kg/m2/s #EOC
--Bob Yantosca (talk) 19:26, 7 June 2018 (UTC)
Replicating the existing specialty diagnostics
Here we discuss our plans to replicate specialty diagnostic outputs (timeseries, local-time diagnostics, etc.) in the new GEOS-Chem netCDF diagnostic package.
NOTE: We will NOT retire the legacy bpch diagnostics in GEOS-Chem v11-02. We will preserve the bpch diagnostic output until we can find alternatives for specialty diagnostics, especially those which involve averaging in a local solar time window.
ND40 planeflight diagnostic
Tomas Sherwen wrote:
Please could I ask if there is s position on/plan for restoring the chemical rate tracking (REA_??) functionality of the planeflight diagnostic?In v11-01/ v11-02d REA_?? has been deactivated due to FlexChem.
I use this functionality (and I suspect many others do) for tracking rates (e.g. JNO2) along plane/ship/station tracks/timeseries at instrument resolution.
Melissa Sulprizio replied:
Yes, we will eventually restore the chemical rates in the planeflight diagnostic. One issue is that we're currently developing netCDF diagnostics and that will mess up the planeflight diagnostics even more. Bob wrote to the GCSC:For the “planeflight” diagnostic, we will investigate using a separate package (such as NOAA ObsPack, as recommended by Andy Jacobsen at IGC8) that can more efficiently store point data. Then new diagnostic package we are developing works well for array data but not as well for point data.Once the netCDF diagnostics are in place, we will reconsider how to fix/update planeflight_mod.F. If you need these diagnostics in the meantime, you should be able to hack it into the chemical mechanism by adding dummy species to the reactions you want to track and then rebuilding the mechanism based on these instructions. In flexchem_mod.F90, you can then obtain the rate from KPP using the C array (e.g. Rate = C(ind_NEWSPC) / DT to get molec/cm3/s).
Mat Evans replied:
I’ve had a quick look at obspack. I’m not sure its well suited to our needs.
I personally don’t see much need to update the plane flight files. They are easy to understand at the moment and easy to manipulate being in ascii. The biggest problem at the moment is that the rate constants have fallen out of them because of the move to FlexChem. If we can get that sorted I don’t think there is a pressing need to update the format.
--Bob Yantosca (talk) 16:20, 15 November 2017 (UTC)
ND48 station diagnostics
We will keep the current ND48 station diagnostics (bpch format) in GEOS-Chem v11-02 until we can find a suitable replacement.
Jenny Fisher wrote:
It seems we are losing compatibility for both ND48 (station) and ND51 (satellite) diagnostics. These are probably the two my group uses most frequently (and replacing with e.g. hourly output everywhere will require a lot of extra disk space). If we are going to have regional subsetting of diagnostics available, then ND48 can probably be dealt with by subsetting down to the level of a single box – but ND51 is harder.
ND49 instantaneous timeseries diagnostic
You can replicate the ND49 bpch diagnostic (instantaneous timeseries) as follows:
- Define a diagnostic collection in HISTORY.rc:
- Specify instantaneous output:
- Set mode: instantaneous
- Specify the desired output frequency:
- Set frequency: 010000 for hourly output
- Set frequency: 030000 for 3-hourly output
- Set frequency: 120000 for 12-hourly output, etc.
- Specify that a new netCDF file should be created every 24 hours:
- Set duration: 240000
- Specify instantaneous output:
- Within this diagnostic collection, you can add archive any available quantity from the State_Met, State_Chm, or State_Diag objects.
Example:
COLLECTIONS: inst3hr', :: inst3hr.filename: './GEOSChem.inst3hr.%y4%m2%d2.nc4', inst3hr.frequency: 030000, inst3hr.duration: 240000, inst3hr.mode: 'instantaneous', inst3hr.fields: 'SpeciesConc_?ADV?', 'GIGCchem', 'Met_T', 'GIGCchem', 'DryDepVel_?DRY?', 'GIGCchem',
--Bob Yantosca (talk) 15:57, 15 November 2017 (UTC)
ND50 24-hr average timeseries diagnostic
You can replicate the ND50 bpch diagnostic (24-hr average timeseries) as follows:
- Define a diagnostic collection in HISTORY.rc:
- Specify time-averaged output:
- Set mode: time-averaged
- Specify daily output frequency. This will also set the averaging interval to be daily.
- Set frequency: 240000
- Specify that a new netCDF file should be created every 24 hours:
- Set duration: 240000
- Specify time-averaged output:
- Within this diagnostic collection, you can add archive any available quantity from the State_Met, State_Chm, or State_Diag objects.
Example:
COLLECTIONS: avg24hr', :: avg24hr.filename: './GEOSChem.avg24hr.%y4%m2%d2.nc4', avg24hr.frequency: 240000, avg24hr.duration: 240000, avg24hr.mode: 'time-averaged', avg24hr.fields: 'SpeciesConc_?ADV?', 'GIGCchem', 'Met_T', 'GIGCchem', 'DryDepVel_?DRY?', 'GIGCchem',
--Bob Yantosca (talk) 16:06, 15 November 2017 (UTC)
ND51 satellite diagnostic
Aaron van Donkelaar wrote:
I wanted to double check about how the satellite-overpass diagnostic (ND51) was being included. There was some mention of it within the (netCDF diagnostic) presentation, but I wasn’t clear to me how the time-averaged netcdf collection could be made to output something similar to the current ND51.My main concern was that ND51 samples between two defined local times once each day. From what I understood of the time-averaged collection via netcdf, it could be set to regularly sample between a defined interval of time (e.g. every six hours), but I didn’t understand how this could be set to sample between, say, 10am-12pm local time each day. Neither local time, nor once per day seemed an option.
Apologies if I’ve just misunderstood, but I thought I should check that an ND51-type output would still be possible.
Bob Yantosca replied:
At this time we don't yet have a good substitute for the ND51 satellite timeseries diagnostics. We may be able to replicate this with some type of satellite simulator package, but that remains to be seen as of yet. Right now we are focusing our efforts on implementing the netCDF diagnostics that are required for benchmarking. (Specialty diagnostics will be added later.)We have designed the netCDF diagnostics for GC-Classic to replicate the behavior of the diagnostics in GCHP. Having the diagnostics work the same way in both configurations of GC facilitates benchmarking and comparing GC-Classic to GCHP. It also makes it easier for users to switch between GC-Classic to GCHP. But GCHP does not allow for local-time diagnostics. GCHP relies on the MAPL library, and its diagnostic package (aka "History") only allows for instantaneous or time-averaged output.
One could save e.g hourly timeseries, along with a local time field, to netCDF, and apply the local time comparison in post-processing. This would be doable but it would also end up generating a ton of output.
The good news is that we will preserve the bpch diagnostics in v11-02 (I need to update the wiki better to reflect that). We will not remove the bpch diagnostics until we have found a suitable replacement for the local-time diagnostics. So for the time being you can still rely on ND51.
--Bob Yantosca (talk) 15:33, 15 November 2017 (UTC)
Validating the netCDF diagnostics
In GEOS-Chem Classic
We invite you to view the the presentation NetCDF diagnostic validation in GEOS-Chem "Classic" by Bob Yantosca and the GCST which summarizes the initial validation process. A more robust validation will take place shortly.
One of the take-aways of the validation is that the timestep at which diagnostics are update could cause non-negligble differences. For example, several GEOS-Chem time-averaged diagnostics are updated on each chemistry timestep, which is 20 minutes for most GEOS-Chem simulations. But the default behavior of the new netCDF diagnostics in GEOS-Chem updates time-averaged diagnostic quantities every "heartbeat" timestep, which is 10 minutes for most simulations. Therefore, the netCDF diagnostics will capture the state of the atmopshere on those timesteps where chemistry does not happen. As shown in the presentation, this could cause non-negligible differences when comparing to the legacy diagnostics.
The GCST recommends that time-averaged diagnostic quantities in GEOS-Chem "Classic" be updated on each "heartbeat" timestep, as this mimics the behavior the diagnostics in GCHP.
--Bob Yantosca (talk) 20:14, 27 November 2017 (UTC)
In GCHP
Lizzie Lundgren (GCST) and Colin Lee (Dalhousie) are validating the new diagnostics in GCHP. Stay tuned for more information.
--Bob Yantosca (talk) 20:14, 27 November 2017 (UTC)
Proposed diagnostic names for specialty simulations
Here is a list of our proposed netCDF diagnostic names for quantities archived in the GEOS-Chem specialty simulations. This list is by no means exhaustive or complete. Contact Bob Yantosca with any suggestions or concerns.
CO2 simulation
NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.
NOTE: For consistency with the HEMCO emissions diagnostics, we propose changing the units of these diagnostics from [atoms C/cm2/s] to [kg/m2/s].
Proposed diagnostic name | Description | replaces NDXX |
with CATEGORY |
and TRACERS |
and FREQUENCY |
from this bpch file |
---|---|---|---|---|---|---|
BalanceBiosph_<spcname> | CO2 balanced biospheres [atoms C/cm2/s]
NOTE: For tagged CO2 simuations you may specify all of the advected species. |
ND04 | CO2-SRCE | 3 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
ChemSource_<spcname> | CO2 chemical source [atoms C/cm2/s] | ND04 | CO2-SRCE | 9 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
ChemSurfaceCorr_<spcname> | CO2 chemical source surface correction [atoms C/cm2/s] | ND04 | CO2-SRCE | 10 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
EmisAircraft_<spcname> | CO2 aircraft emissions [atoms C/cm2/s]
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND04 | CO2-SRCE | 8 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
EmisAnthro_<spcname> | CO2 anthropogenic emissions [atoms C/cm2/s]
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND04 | CO2-SRCE | 1 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
EmisBiofuel_<spcname> | CO2 biofuel emissions [atoms C/cm2/s]
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND04 | CO2-SRCE | 5 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Biomass_<spcname> | CO2 biomass burning emissions [atoms C/cm2/s]
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND04 | CO2-SRCE | 4 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
EmisOcean_<spcname> | CO2 ocean emissions [atoms C/cm2/s]
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND04 | CO2-SRCE | 2 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
EmisShip_<spcname> | CO2 ship emissions [atoms C/cm2/s]
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND04 | CO2-SRCE | 7 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
NetTerrExch_<spcname> | CO2 net terrestrial exchange [atoms C/cm2/s] | ND04 | CO2-SRCE | 6 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
--Bob Yantosca (talk) 15:42, 15 November 2017 (UTC)
Hg simulation
NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability. ALSO NOTE: We will eliminate underscore characters within the variable name (except to separate the name from the species name or wildcard) at a later date.
NOTE: We will probably delay implementation of new diagnostics for the Hg simulation until we receive updated Hg simulation source code from the Hg and POPs Working Group. Also we look to the Hg and POPs working group to inform us if any of these diagnostics are no longer necessary.
Proposed diagnostic name | Description | replaces NDXX |
with CATEGORY |
and TRACERS |
and FREQUENCY |
from this bpch file |
---|---|---|---|---|---|---|
Emis_Anthro_Hg0 | Anthropogenic Hg0 emissions
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND03 | HG-SRCE | 1 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Mass_Ocean_Hg0 | Mass of oceanic Hg0 | ND03 | HG-SRCE | 2 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Ocean_Hg0 | Oceanic Hg0 emissions
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND03 | HG-SRCE | 3 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_LandReem_Hg0 | Land Hg0 re-emission
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND03 | HG-SRCE | 4 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Natural_Hg0 | Natural Hg0 emissions (from land)
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND03 | HG-SRCE | 5 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Anthro_Hg2 | Anthropogenic Hg2 emissions
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND03 | HG-SRCE | 6 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Mass_Ocean_Hg2 | Oceanic Hg2 mass | ND03 | HG-SRCE | 7 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Sink_Ocean_Hg2 | Sink of Hg2 into deep ocean | ND03 | HG-SRCE | 8 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Anthro_HgP | Anthropogenic HgP emissions
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND03 | HG-SRCE | 9 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Mass_Total_Hg | Mass of oceanic Hg | ND03 | HG-SRCE | 10 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Mass_Ocean_HgP | Mass of oceanic HgP | ND03 | HG-SRCE | 11 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Ocean_OC | Sink of organic carbon to the ocean
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND03 | HG-SRCE | 12 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Biomass_Hg0 | Hg0 emissions from biomass burning
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND03 | HG-SRCE | 13 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Vegetation_Hg0 | Hg0 emissions from vegetation
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND03 | HG-SRCE | 14 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Soil_Hg0 | Hg0 emissions from soils
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND03 | HG-SRCE | 15 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Hg0_Flux_from_Ocean | Upwelling flux of Hg0 volatized from the ocean | ND03 | HG-SRCE | 16 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Hg0_Flux_to_Ocean | Drydep flux of Hg0 to the ocean | ND03 | HG-SRCE | 17 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Snow_Hg | Emission of Hg from snowpack
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND03 | HG-SRCE | 18 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Hg2_Prod_from_Hg0 | Production of Hg2 from Hg0 | ND03 | PL-HG2-$ | 19 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Hg2_Prod_from_OH | Production of Hg2 from rxn with OH | ND03 | PL-HG2-$ | 20 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Hg2_Prod_from_O3 | Production of Hg2 from rxn with O3 | ND03 | PL-HG2_$ | 21 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Hg2_Loss_by_Seasalt | Loss of Hg2 from reaction with sea salt | ND03 | PL-HG2-$ | 22 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
RxnRate_Seasalt_Hg2 | Loss rate of Hg2 from rxn with sea salt | ND03 | PL-HG2-$ | 23 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Br2_Prod_from_Br | Production of Br2 from Br | ND03 | PL-Hg2-$ | 24 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Concentration_Br | Br concentration NOTE: We can probably get this from the species concentration diagnostic; maybe no need to replicate it here. |
ND03 | HG-SRCE | 25 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Concentration_BrO | BrO concentration NOTE: We can probably get this from the species concentration diagnostic; maybe no need to replicate it here. |
ND03 | HG-SRCE | 26 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Concentration_HgP | Particulate bound mercury
NOTE: Is this any different from the HgP species?' |
ND03 | PL-HG2-$ | 27 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Concentratioin_RGM | Reactive gaseous mercury
NOTE: Can this be obtained by summing Hg0 + Hg2?' |
ND03 | PL-HG2-$ | 28 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Mass_Ocean_Hg0 | Mass of oceanic Hg0
Is this needed anymore? Does the Hg simulation still need the slab ocean? |
ND03 | OCEAN-HG | 29 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Mass_Ocean_Hg2 | Mass of oceanic Hg2
Is this needed anymore? Does the Hg simulation still need the slab ocean? |
ND03 | OCEAN-Hg | 30 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Mass_Ocean_HgP | Mass of oceanic Hg
Is this needed anymore? Does the Hg simulation still need the slab ocean? |
ND03 | HG-SRCE | 31 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Mass_SnowPack_Hg | Mass of Hg in snowpack
Is this needed anymore? Does the Hg simulation still need the slab ocean? |
ND03 | <ttOCEAN_Hg</tt> | 32 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
--Bob Yantosca (talk) 16:57, 20 October 2017 (UTC)
POPs simulation
NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.
NOTE: We will probably delay implementation of new diagnostics for the POPs simulation until we receive updated Hg simulation source code from the Hg and POPs Working Group.
Proposed diagnostic name | Description | replaces NDXX |
with CATEGORY |
and TRACERS |
and FREQUENCY |
from this bpch file |
---|---|---|---|---|---|---|
Emis_POP | Total POPs emissions | ND53 | PG-SRCE | 1 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_POPOC | POP OC emissions
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND53 | PG-SRCE | 2 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_POPBC | POP BC emissions
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND53 | PG-SRCE | 3 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_POPG | Gas-phase POPs emissions
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND53 | PG-SRCE | 4 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Soil_POP | Secondary emissions from soil
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND53 | PG-SRCE | 5 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Lake_POP | Secondary emissions from lakes
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND53 | PG-SRCE | 6 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Emis_Vegetation_POP | Secondary emissions from vegetation (leaves)
NOTE: Could we use HEMCO's diagnostic capability to archive this? |
ND53 | PG-SRCE | 7 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
FluxFromSoil_Pos_POP | Secondary positive soil flux | ND53 | PG-SRCE | 8 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
FluxFromSoil_Neg_POP | Secondary negative soil flux | ND53 | PG-SRCE | 9 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
FluxFromLake_Pos_POP | Secondary positive lake flux | ND53 | PG-SRCE | 10 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
FluxFromLake_Neg_POP | Secondary negative lake flux | ND53 | PG-SRCE | 11 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
FluxFromVegetation_Pos_POP | Secondary positive vegetation flux | ND53 | PG-SRCE | 12 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
FluxFromVegetation_Neg_POP | Secondary negative leaf flux | ND53 | PG-SRCE | 13 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Fugacity_Soil_Air | Fugacity ratio: soil / air | ND53 | PG-SRCE | 14 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Fugacity_Lake_Air | Fugacity ratios: lake/air | ND53 | PG-SRCE | 15 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Fugacity_Leaf_Air | Fugacity ratios: leaf/air | ND53 | PG-SRCE | 16 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPOC_Loss_to_Gas | Gross POPOC lost to gas | ND53 | PG-PP | 17 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPOC_Prod_from_Gas | Gross POPOC formed from gas | ND53 | PG-PP | 18 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPBC_Loss_to_Gas | Gross POPBC lost to gas | ND53 | PG-PP | 19 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPBC_Prod_from_Gas | Gross POPBC formed from gas | ND53 | PG-PP | 20 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPG_Prod_from_OH | Production of oxidized POPG from reaction with OH | ND53 | PG-PP | 21 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPPOCPO_Prod_from_O3 | Production of oxidized POPPOCPO from reaction with O3 | ND53 | PG-PP | 22 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPPPOCPI_Prod_from_O3 | Production of oxidized POPPOCPI from reaction with O3 | ND53 | PG-PP | 23 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPPBCPO_Prod_from_O3 | Production of oxidized POPPBCPO from reaction with O3 | ND53 | PG-PP | 24 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPPBCPI_Prod_from_O3 | Production of oxidized POPBCPI from reaction with O3 | ND53 | PG-PP | 25 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPPOCPO_Prod_from_NO3 | Production of oxidized POPPOCPO from reaction with NO3 | ND53 | PG-PP | 26 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPPOCPI_Prod_from_NO3 | Production of oxidized POPPOCPI from reaction with NO3 | ND53 | PG-PP | 27 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPPBCPO_Prod_from_NO3 | Production of oxidized POPPBCPO from reaction with NO3 | ND53 | PG-PP | 28 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
POPPBCPI_Prod_from_NO3 | Production of oxidized POPPBCPI from reaction with NO3 | ND53 | PG-PP | 29 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
--Bob Yantosca (talk) 17:02, 20 October 2017 (UTC)
RRTMG radiative transfer model
NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.
Proposed diagnostic name | Description | replaces NDXX |
with CATEGORY |
and TRACERS |
and FREQUENCY |
from this bpch file |
---|---|---|---|---|---|---|
RadAllSkyLWSurf | All-sky long-wave radiation @ surface [W/m2] | ND72 | RADMAP-$ | 4 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
RadAllSkyLWTOA | All-sky long-wave radiation @ top of atm [W/m2] | ND72 | RADMAP-$ | 3 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
RadAllSkySWSurf | All-sky short-wave radiation @ surface [W/m2] | ND72 | RADMAP-$ | 2 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
RadAllSkySWTOA | All-sky short-wave radiation @ top of atm [W/m2] | ND72 | RADMAP-$ | 1 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
RadClrSkyLWSurf | Clear-sky long-wave radiation @ surface [W/m2] | ND72 | RADMAP-$ | 8 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
RadClrSkyLWTOA | Clear-sky long-wave radiation @ top of atm [W/m2] | ND72 | RADMAP-$ | 7 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
RadClrSkySWSurf | Clear-sky short-wave radiation @ surface [W/m2] | ND72 | RADMAP-$ | 6 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
RadClrSkySWTOA | Clear-sky short-wave radiation @ top of atm [W/m2] | ND72 | RADMAP-$ | 5 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
--Bob Yantosca (talk) 15:44, 2 November 2017 (UTC)
TOMAS aerosol microphysics
NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.
NOTE: We invite the TOMAS team to review these diagnostic names for accuracy.
Proposed diagnostic name | Description | replaces NDXX |
with CATEGORY |
and TRACERS |
and FREQUENCY |
from this bpch file |
---|---|---|---|---|---|---|
RateCond_<spcname> | Condensation rate | ND60 | TMS-COND | 1-nTomas | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
RateCoag_<spcname> | Coagulation rate | ND60 | TMS-COAG | 1-nTomas | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
RateNucl_<spcname> | Nucleation rate | ND60 | TMS-NUCL | 1-nTomas | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
RateAqOx_<spcname> | Aqueous oxidation rate | ND60 | TMS-NUCL | 1-nTomas | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
ErrorAccumFix_<spcname> | Accumulated error fixed | ND60 | AERO-FIX | 1-nTomas | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
RateCond_SOA | SOA condensation rate | ND60 | TMS-SOA | 1-nTomas | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Rate3dForm | Formation of particles with a diameter > 10nm | ND61 | TOMAS-3D | 1 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
Rate3dNucl | Nucleation rate (cluster size) | ND61 | TOMAS-3D | 2 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
--Bob Yantosca (talk) 20:43, 14 November 2017 (UTC)