Difference between revisions of "List of diagnostics archived to netCDF format"
(→The MercuryChem collection) |
(→The Budget collection) |
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Here is a sample definition section for the Budget collection such that 1-month averages are output per species. To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name. This will prevent the diagnostic arrays from being initialized and therefore reduce required memory. You may also replace the species wildcards with individual species names, e.g. BudgetChemistryFull_O3 for full column ozone. | Here is a sample definition section for the Budget collection such that 1-month averages are output per species. To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name. This will prevent the diagnostic arrays from being initialized and therefore reduce required memory. You may also replace the species wildcards with individual species names, e.g. BudgetChemistryFull_O3 for full column ozone. | ||
+ | #============================================================================== | ||
# %%%%% THE Budget COLLECTION %%%%% | # %%%%% THE Budget COLLECTION %%%%% | ||
# | # | ||
− | GEOS-Chem budget diagnostics defined as species kg/s in the column | + | # GEOS-Chem budget diagnostics defined as species kg/s in the column |
# (full, troposphere, or PBL) due to a single component (e.g. chemistry) | # (full, troposphere, or PBL) due to a single component (e.g. chemistry) | ||
# (default = advected species) | # (default = advected species) | ||
Line 1,849: | Line 1,850: | ||
Budget.duration: 00000100 000000 | Budget.duration: 00000100 000000 | ||
Budget.mode: 'time-averaged' | Budget.mode: 'time-averaged' | ||
− | Budget.fields: | + | Budget.fields: 'BudgetChemistryFull_?ADV? ', 'GIGCchem', |
'BudgetChemistryPBL_?ADV? ', 'GIGCchem', | 'BudgetChemistryPBL_?ADV? ', 'GIGCchem', | ||
'BudgetChemistryTrop_?ADV? ', 'GIGCchem', | 'BudgetChemistryTrop_?ADV? ', 'GIGCchem', |
Revision as of 15:48, 29 October 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 Budget collection
- 3.6 The CH4 collection
- 3.7 The CloudConvFlux collection
- 3.8 The ConcAfterChem collection
- 3.9 The DryDep collection
- 3.10 The JValues collection
- 3.11 The JValuesLocalNoon collection
- 3.12 The LevelEdgeDiags collection
- 3.13 The MercuryChem collection
- 3.14 The MercuryEmis Collection
- 3.15 The MercuryOcean collection
- 3.16 The POPS collection
- 3.17 The ProdLoss Collection
- 3.18 The RadioNuclide Collection
- 3.19 The StateChm Collection
- 3.20 The StateMet collection
- 3.21 The WetLossConv collection
- 3.22 The WetLossLS collection
- 4 Replicating the existing specialty diagnostics
- 5 Diagnostics that are currently archived by HEMCO
- 6 Validating the netCDF diagnostics
- 7 Adding New Diagnostics
Overview
An introduction to netCDF diagnostics
GEOS-Chem v11-02 (aka 12.0.0) and later versions can save diagnostic output to netCDF format. There are two types of netCDF diagnostic output files:
- Emissions diagnostics archived directly by HEMCO
- Non-emissions diagnostics computed by GEOS-Chem
The GEOS-Chem Support Team has developed a new netCDF diagnostic capability for GEOS-Chem "Classic" (point #2 above) that replicates how the existing netCDF diagnostics work in GCHP (aka "History"). A common input file named HISTORY.rc can be used for both GEOS-Chem "Classic" and GCHP.
Bob Yantosca has created an overview presentation about the new netCDF diagnostics for v11-02.
--Bob Yantosca (talk) 13:20, 8 June 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. # #============================================================================ EXPID: ./GEOSChem #============================================================================== # %%%%% COLLECTION NAME DECLARATIONS %%%%% # # To disable a collection, place a "#" character in front of its name # # NOTE: These are the "default" collections for GEOS-Chem. # But you can create your own custom diagnostic collections as well. #============================================================================== COLLECTIONS: 'SpeciesConc', '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 and prefixes
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:
|
|
<photobin> | Number of a given wavelength bin for FAST-JX photolysis |
|
Chem_ | To request diagnostic output for fields of the State_Chm object (other than SpeciesConc), add this prefix in front of the field name. (Prefix is case-insensitive.) |
|
Met_ | To request diagnostic output for fields of the State_Met object, add this prefix in front of the field name. (Prefix is case-insensitive.) |
|
--Bob Yantosca (talk) 14:00, 8 June 2018 (UTC)
Diagnostic collections
The diagnostic collections described in the sections below are used by default in GEOS-Chem simulations. You can create your own customized collections by modifying the 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. # #============================================================================ EXPID: ./GEOSChem #============================================================================== # %%%%% COLLECTION NAME DECLARATIONS %%%%% # # To disable a collection, place a "#" character in front of its name # # NOTE: These are the "default" collections for GEOS-Chem. # But you can create your own custom diagnostic collections as well. #============================================================================== COLLECTIONS: 'SpeciesConc', 'AerosolMass', 'Aerosols', 'CloudConvFlux', 'ConcAfterChem', 'DryDep', 'JValues', 'JValuesLocalNoon', 'LevelEdgeDiags', 'ProdLoss', 'StateChm', 'StateMet', 'WetLossConv', 'WetLossLS', ::
We have already discussed how 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 |
|
|||
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 |
|
| ||
TotalOC | Sum of all organic carbon | ug/m3 |
|
| ||
BetaNO | NO branching ratio | ug/m3 |
|
| ||
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 |
|
| ||
AerMassSOAGX | Aerosol-phase glyoxal | ug/m3 |
|
| ||
AerMassSOAMG | Aerosol-phase methylglyoxal | ug/m3 |
|
| ||
AerMassSOAIE | Aerosol-phase IEPOX | ug/m3 |
|
| ||
AerMassSOAME | Aerosol-phase IMAE | ug/m3 |
|
| ||
AerMassINDIOL | Generic aerosol-phase organonitrate hydrolysis product | ug/m3 |
|
| ||
AerMassLVOCOA | Aerosol-phase low-volatility non-IEPOX product of ISOPOOH (RIP) oxidation | ug/m3 |
|
| ||
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 |
|
|||
AODDust_WL1_?DUSTBIN? | AOD for 1st wavelength specified in Radiation Menu, for each dust bin | 1 | ?DUSTBIN? |
|
||
AODHygWL1_<spcname> | Optical depth for selected species (SO4, BC, OC, SALA, SALC) at the 1st wavelength specified in the Radiation Menu | 1 | ?HYG? |
|
||
AODSOAfromAqIsopreneWL1 | Optical depth of SOA from aqueous isoprene optical depth | 1 |
|
| ||
AODStratLiquidAerWL1 | Stratospheric liquid aerosol optical depth (600 nm) |
|
| |||
AODPolarStratCloudWL1 | Polar stratospheric cloud type 1a/2 optical depth (600 nm) | 1 |
|
|||
AerHygroscopicGrowth_<spcname> | Hygroscopic growth of selected species (SO4, BC, OC, SALA, SALC) | 1 | ?HYG? |
|
||
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 Budget collection
The Budget diagnostic collection was introduced in GEOS-Chem 12.1.0. It is a 2D diagnostic containing the mass tendencies per grid cell, in kg/s, for each species within a region of the column and across each GEOS-Chem component. The diagnostic is calculated by taking the difference in vertically summed column mass before and after major GEOS-Chem components.
There are three column regions defined for this diagnostic: troposphere-only, PBL-only, and full column. By post-processing this diagnostic you can calculate global mass change or mass change across regions by summing the diagnostic values for the relevant grid cells. You can also retrieve the mass change across a longer chunk of time by multiplying the time-averaged output by the number of seconds in the averaging period.
While there are seven major components in GEOS-Chem, there are only six implemented for the budget diagnostics. Emissions and dry deposition components are combined together for this diagnostic because of the way they are applied at the same time. Furthermore, if using non-local PBL mixing then the emissions and dry deposition budget diagnostic will not capture all fluxes from these sources and sinks. This is because emissions and dry deposition tendencies below the PBL are applied within mixing instead. When using full mixing, however, mixing and emissions/dry deposition budget diagnostics are fully separated.
Here is a sample definition section for the Budget collection such that 1-month averages are output per species. To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name. This will prevent the diagnostic arrays from being initialized and therefore reduce required memory. You may also replace the species wildcards with individual species names, e.g. BudgetChemistryFull_O3 for full column ozone.
#============================================================================== # %%%%% THE Budget COLLECTION %%%%% # # GEOS-Chem budget diagnostics defined as species kg/s in the column # (full, troposphere, or PBL) due to a single component (e.g. chemistry) # (default = advected species) # # Available for all simulations #============================================================================== Budget.template: '%y4%m2%d2_%h2%n2z.nc4', Budget.format: 'CFIO', Budget.frequency: 00000100 000000 Budget.duration: 00000100 000000 Budget.mode: 'time-averaged' Budget.fields: 'BudgetChemistryFull_?ADV? ', 'GIGCchem', 'BudgetChemistryPBL_?ADV? ', 'GIGCchem', 'BudgetChemistryTrop_?ADV? ', 'GIGCchem', 'BudgetEmisDepFull_?ADV? ', 'GIGCchem', 'BudgetEmisDepTrop_?ADV? ', 'GIGCchem', 'BudgetEmisDepPBL_?ADV? ', 'GIGCchem', 'BudgetTransportFull_?ADV? ', 'GIGCchem', 'BudgetTransportTrop_?ADV? ', 'GIGCchem', 'BudgetTransportPBL_?ADV? ', 'GIGCchem', 'BudgetMixingFull_?ADV? ', 'GIGCchem', 'BudgetMixingTrop_?ADV? ', 'GIGCchem', 'BudgetMixingPBL_?ADV? ', 'GIGCchem', 'BudgetConvectionFull_?ADV? ', 'GIGCchem', 'BudgetConvectionTrop_?ADV? ', 'GIGCchem', 'BudgetConvectionPBL_?ADV? ', 'GIGCchem', 'BudgetWetDepFull_?WET? ', 'GIGCchem', 'BudgetWetDepTrop_?WET? ', 'GIGCchem', 'BudgetWetDepPBL_?WET? ', 'GIGCchem',
This table describes the diagnostic quantities belonging to the Budget collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
BudgetXY_<spcname> | Mass tendency across component X in column region Y | kg/s |
|
All simulations |
None |
Components X include:
Column regions Y include:
|
1The mixing budget diagnostics includes the application of emissions and dry deposition below the PBL if using the non-local PBL mixing scheme (vdiff).
2The emissions and dry deposition budget diagnostics will not capture all fluxes if using the non-local PBL mixing scheme since these tendencies are applied within mixing in vdiff_mod below the PBL. When using full mixing, however, mixing and emissions/dry deposition are fully separated.
--Lizzie Lundgren (talk) 21:33, 9 October 2018 (UTC)
The CH4 collection
The CH4 collection contains diagnostics for loss of CH4 and OH concentration for the CH4 specialty simulation.
Here is a sample definition section for the CH4 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.
CH4.template: '%y4%m2%d2_%h2%n2z.nc4', CH4.format: 'CFIO', CH4.frequency: 00000100 000000 CH4.duration: 00000100 000000 CH4.mode: 'time-averaged' CH4.fields: 'OHconcAfterChem ', 'GIGCchem', 'LossCH4byClinTrop ', 'GIGCchem', 'LossCH4byOHinTrop ', 'GIGCchem', 'LossCH4inStrat ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the CH4 collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
LossCH4byClinTrop | Loss of CH4 by reaction with Cl in the troposphere | kg/s |
| |||
LossCH4byOHinTrop | Loss of CH4 by reaction with OH in the troposphere | kg/s |
| |||
LossCH4inStrat | Loss of CH4 in the stratosphere | kg/s |
| |||
OHconcAfterChem | OH concentration after chemistry | kg/s |
--Bob Yantosca (talk) 20:20, 19 October 2018 (UTC)
The CloudConvFlux collection
The CloudConvFlux collection contains diagnostics for mass fluxes in cloud convection.
Here is a sample definition section for the CH4 collection. If this collection is not already present in the 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.
JValuesLocalNoon.template: '%y4%m2%d2_%h2%n2z.nc4', JValuesLocalNoon.format: 'CFIO', JValuesLocalNoon.frequency: 00000100 000000 JValuesLocalNoon.duration: 00000100 000000 JValuesLocalNoon.mode: 'time-averaged' JValuesLocalNoon.fields: 'JNoon_?PHO? ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the JValuesLocalNoon collection:
NOTE: All fullchem refers to all simulations that use 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 MercuryChem collection
NOTE: This collection is currently under development and is slated to be introduced into GEOS-Chem 12.1.0.
The 'MercuryChem collection contains concentrations and prod/loss diagnostic outputs for the Hg specialty simulationl
Here is a sample definition section for the MercuryEmis 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.
MercuryChem.template: '%y4%m2%d2_%h2%n2z.nc4', MercuryChem.format: 'CFIO', MercuryChem.frequency: 00000000 040000 MercuryChem.duration: 00000000 040000 MercuryChem.mode: 'time-averaged' MercuryChem.fields: 'ConcBr ', 'GIGCchem', 'ConcBrO ', 'GIGCchem', 'LossHg2bySeaSalt ', 'GIGCchem', 'LossRateHg2bySeaSalt ', 'GIGCchem', 'PolarConcBr ', 'GIGCchem', 'PolarConcBrO ', 'GIGCchem', 'PolarConcO3 ', 'GIGCchem', 'ProdHg2fromBr ', 'GIGCchem', 'ProdHg2fromBrY ', 'GIGCchem', 'ProdHg2fromClY ', 'GIGCchem', 'ProdHg2fromHg0 ', 'GIGCchem', 'ProdHg2fromHgBrPlusBr2 ', 'GIGCchem', 'ProdHg2fromHgBrPlusBrBrO ', 'GIGCchem', 'ProdHg2fromHgBrPlusBrClO ', 'GIGCchem', 'ProdHg2fromHgBrPlusBrHO2 ', 'GIGCchem', 'ProdHg2fromHgBrPlusBrNO2 ', 'GIGCchem', 'ProdHg2fromHgBrPlusBrOH ', 'GIGCchem', 'ProdHg2fromO3 ', 'GIGCchem', 'ProdHg2fromOH ', 'GIGCchem', 'ParticulateBoundHg ', 'GIGCchem', 'ReactiveGaseousHg ', 'GIGCchem', ::
The table below describes the diagnostic quantities belonging to the MercuryChem collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
ConcBr | Br concentration | molec/cm3 |
|
|||
ConcBrO | BrO concentration | molec/cm3 |
|
|||
LossHg2bySeaSalt | Loss of Hg2 by reaction with sea salt aerosols | kg/s |
|
|||
LossRateHg2bySeaSalt | Rate of loss of Hg2 by reaction with sea salt aerosols | 1/s |
|
|||
PolarConcBr | Br concentration in polar regions | pptv |
|
|||
PolarConcBrO | BrO concentration in polar regions | molec/cm3 |
|
|||
PolarConcO3 | O3 concentration in polar regions | molec/cm3 |
|
|||
ProdHg2fromBr | Chemical production of Hg2 from Br | kg/s |
|
|||
ProdHg2fromBrY | Chemical production of Hg2 from reaction with BrY | kg/s |
|
|||
ProdHg2fromClY | Chemical production of Hg2 from reaction with ClY | kg/s |
|
|||
ProdHg2fromHg0 | Chemical production of Hg2 from reaction with Hg0 | kg/s |
|
|||
ProdHg2fromHgBrPlusBr2 | Chemical production of Hg2 from reaction with HgBr + Br2 | kg/s |
|
|||
ProdHg2fromHgBrPlusBrBrO | Chemical production of Hg2 from reaction with HgBr + BrBrO | kg/s |
|
|||
ProdHg2fromHgBrPlusBrClO | Chemical production of Hg2 from reaction with HgBr + BrClO | kg/s |
|
|||
ProdHg2fromHgBrPlusBrHO2 | Chemical production of Hg2 from reaction with HgBr + BrHO2 | kg/s |
|
|||
ProdHg2fromHgBrPlusBrNO2 | Chemical production of Hg2 from reaction with HgBr + BrNO2 | kg/s |
|
|||
ProdHg2fromHgBrPlusBrOH | Chemical production of Hg2 from reaction with HgBr + BrOH | kg/s |
|
|||
ProdHg2fromO3 | Chemical production of Hg2 from reaction with O3 | kg/s |
|
|||
ProdHg2fromO3 | Chemical production of Hg2 from reaction with O3 | kg/s |
|
|||
ParticulateBoundHg | Particulate bound mercury (PBM) | pptv |
|
|||
ParticulateBoundHg | Reactive gaseous mercury | pptv |
|
--Bob Yantosca (talk) 15:30, 29 October 2018 (UTC)
The MercuryEmis Collection
NOTE: This collection is currently under development and is slated to be introduced into GEOS-Chem 12.1.0.
The MercuryEmis collection contains emission diagnostics for the Hg specialty simulation.
Here is a sample definition section for the MercuryEmis 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.
MercuryEmis.template: '%y4%m2%d2_%h2%n2z.nc4', MercuryEmis.format: 'CFIO', MercuryEmis.frequency: 00000000 040000 MercuryEmis.duration: 00000000 040000 MercuryEmis.mode: 'time-averaged' MercuryEmis.fields: 'EmisHg0anthro ', 'GIGCchem', 'EmisHg0biomass ', 'GIGCchem', 'EmisHg0geogenic ', 'GIGCchem', 'EmisHg0land ', 'GIGCchem', 'EmisHg0ocean ', 'GIGCchem', 'EmisHg0soil ', 'GIGCchem', 'EmisHg0snow ', 'GIGCchem', 'EmisHg0vegetation ', 'GIGCchem', 'EmisHg2HgPanthro ', 'GIGCchem', 'EmisHg2snowToOcean ', 'GIGCchem', 'EmisHg2rivers ', 'GIGCchem', 'FluxHg2HgPfromAirToSnow ', 'GIGCchem', ::
The table below describes the diagnostic quantities belonging to the MercuryEmis collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
EmisHg0anthro | Emission of Hg0 from anthropogenic sources | kg/s |
|
|||
EmisHg0biomass | Emissions of Hg0 from biomass burning | kg/s |
|
|||
EmisHg0geogenic | Emissions of Hg0 from geogenic sources | kg/s |
|
|||
EmisHg0land | Re-emission of Hg0 from land | kg/s |
|
|||
EmisHg0ocean | Emissions of Hg0 from oceans | kg/s |
|
|||
EmisHg0snow | Emission of Hg0 from snowpack | kg/s |
|
|||
EmisHg0soil | Emissions of Hg0 from soils | kg/s |
|
|||
EmisHg0vegetation | Emission of Hg0 from vegetation | kg/s |
|
|||
EmisHg2HgPanthro | Emission of Hg2 + HgP from anthropogenic sources | kg/s |
|
| ||
EmisHg2snowToOcean | Hg2 delivered to oceans from melting snow | kg/s |
|
|||
EmisHg2rivers | Emissions of Hg2 from delivered to oceans from melting snow | kg/s |
|
|||
FluxHg2HgPfromAirToSnow | Deposition flux of Hg2 + HgP from the atmosphere onto snow | kg/s |
|
|
--Bob Yantosca (talk) 21:42, 26 October 2018 (UTC)
The MercuryOcean collection
NOTE: This collection is currently under development and is slated to be introduced into GEOS-Chem 12.1.0.
The MercuryOcean collection contains diagnostics from the mercury ocean model, used in the Hg specialty simulaton.
Here is a sample definition section for the MercuryOcean 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.
MercuryOcean.template: '%y4%m2%d2_%h2%n2z.nc4', MercuryOcean.format: 'CFIO', MercuryOcean.frequency: 00000000 040000 MercuryOcean.duration: 00000000 040000 MercuryOcean.mode: 'time-averaged' MercuryOcean.fields: 'FluxHg0fromAirToOcean ', 'GIGCchem', 'FluxHg0fromOceanToAir ', 'GIGCchem', 'FluxHg2HgPfromAirToOcean ', 'GIGCchem', 'FluxHg2toDeepOcean ', 'GIGCchem', 'FluxOCtoDeepOcean ', 'GIGCchem', 'MassHg0inOcean ', 'GIGCchem', 'MassHg2inOcean ', 'GIGCchem', 'MassHgPinOcean ', 'GIGCchem', 'MassHgTotalInOcean ', 'GIGCchem', ::
The table below describes diagnostic quantities belonging to the MercuryOcean collection
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
FluxHg0fromAirToOcean | Deposition flux of Hg0 from the atmosphere to the ocean | kg/s |
|
|||
FluxHg0fromOceanToAir | Volatilizatoin flux of Hg0 from the ocean to the atmosphere | kg/s |
|
|||
FluxHg2HgPfromAirToOcean | Deposition flux of Hg2 + HgP from the atmosphere to the ocean | kg/s |
|
|||
FluxHg2toDeepOcean | Flux of Hg2 sunk to the deep ocean | kg/s |
|
|||
MassHg0inOcean | Total mass of oceanic Hg0 | kg |
|
|||
MassHg2inOcean | Total mass of oceanic Hg2 | kg |
|
|||
MassHgPinOcean | Total mass of oceanic Hg2 | kg |
|
|||
MassHgTotalInOcean | Total mass of all organic mercury | kg |
|
--Bob Yantosca (talk) 19:56, 26 October 2018 (UTC)
The POPS collection
NOTE: This collection is currently under development and is slated to be introduced into GEOS-Chem 12.1.0.
The POPS collection contains diagnostic quantities for the Persistent Organic Pollutants (aka POPs) specialty simulation.
Here is a sample definition section for the POPS collection. If this collection is not already present in the 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.
POPS.template: '%y4%m2%d2_%h2%n2z.nc4', POPS.format: 'CFIO', POPS.frequency: 00000100 000000 POPS.duration: 00000100 000000 POPS.mode: 'time-averaged' POPS.fields: 'EmisPOPPOCPO ', 'GIGCchem', 'EmisPOPPBCPO ', 'GIGCchem', 'EmisPOPG ', 'GIGCchem', 'EmisPOPGfromSoil ', 'GIGCchem', 'EmisPOPGfromLake ', 'GIGCchem', 'EmisPOPGfromLeaf ', 'GIGCchem', 'FluxPOPGfromSoilToAir ', 'GIGCchem', 'FluxPOPGfromAirToSoil ', 'GIGCchem', 'FluxPOPGfromLakeToAir ', 'GIGCchem', 'FluxPOPGfromAirtoLake ', 'GIGCchem', 'FluxPOPGfromLeafToAir ', 'GIGCchem', 'FluxPOPGfromAirToLeaf ', 'GIGCchem', 'FugacitySoilToAir ', 'GIGCchem', 'FugacityLakeToAir ', 'GIGCchem', 'FugacityLeafToAir ', 'GIGCchem', 'LossPOPPOCPObyGasPhase ', 'GIGCchem', 'ProdPOPPOCPOfromGasPhase ', 'GIGCchem', 'LossPOPPBPOCbyGasPhase ', 'GIGCchem', 'ProdPOPPBCPOfromGasPhase ', 'GIGCchem', 'ProdPOPGfromOH ', 'GIGCchem', 'ProdPOPPOCPOfromO3 ', 'GIGCchem', 'ProdPOPPOCPIfromO3 ', 'GIGCchem', 'ProdPOPPBCPIfromO3 ', 'GIGCchem', 'ProdPOPPBCPOfromO3 ', 'GIGCchem', 'ProdPOPPOCPOfromNO3 ', 'GIGCchem', 'ProdPOPPOCPIfromNO3 ', 'GIGCchem', 'ProdPOPPBCPIfromNO3 ', 'GIGCchem', 'ProdPOPPBCPOfromNO3 ', 'GIGCchem', ::
The table below describes diagnostic quantities belonging to the POPS collection.
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
EmisPOPPOCPO | Particulate (hydrophobic organic carbon) POPS emissions | kg/m2/s |
|
|||
EmisPOPPBCPO | Particulate (hydrophobic black carbon) POPS emissions | kg/m2/s |
|
| ||
EmisPOPG | POPG (gas-phase) POPS emissions | kg/m2/s |
|
|||
EmisPOPGfromSoil | Secondary emission of POPG from soils | kg/s |
|
|||
EmisPOPGfromLake | Secondary emission of POPG from lakes | kg/s |
|
|||
EmisPOPGfromLeaf | Secondary emission of POPG from leaves | kg/m2/s |
|
|||
FluxPOPGfromSoilToAir | Secondary (positive) flux of POPG from soils to air | ng/m2/day |
|
|||
FluxPOPGfromAirToSoil | Secondary (negative) flux of POPG from air to soil | ng/m2/day |
|
|||
FluxPOPGfromLakeToAir | Secondary (positive) flux of POPG from lakes to air | ng/m2/day |
|
|||
FluxPOPGfromAirToLake | Secondary (negative) flux of POPG from air to lakes | ng/m2/day |
|
|||
FluxPOPGfromLeafToAir | Secondary (positive) flux of POPG from leaves to air | ng/m2/day |
|
|||
FluxPOPGfromAirToLeaf | Secondary (negative) flux of POPG from air to leaves | ng/m2/day |
|
|||
FugacitySoilToAir | Fugacity ratio: soil/air | 1 |
|
|||
FugacityLakeToAir | Fugacity ratio: lake/air | 1 |
|
|||
FugacityLeafToAir | Fugacity ratio: leaf/air | 1 |
|
|||
LossPOPPOCPObyGasPhase | Gross POP OC lost to gas | kg/s |
|
|||
LossPOPPOCPObyGasPhase | Gross POP OC produced from gas | kg/s |
|
|||
LossPOPPBCPObyGasPhase | Gross POP BC lost to gas | kg/s |
|
|||
LossPOPPBCPObyGasPhase | Gross POP BC produced from gas | kg/s |
|
|||
ProdPOPGfromOH | Production of oxidized POPG from reaction with OH | kg/s |
|
|||
ProdPOPPOCPOfromO3 | Production of oxidized POPPOCPO from reaction with O3 | kg/s |
|
|||
ProdPOPPOCPIfromO3 | Production of oxidized POPPOCPI from reaction with O3 | kg/s |
|
|||
ProdPOPPBCPOfromO3 | Production of oxidized POPPBCPO from reaction with O3 | kg/s |
|
|||
ProdPOPPBCPIfromO3 | Production of oxidized POPPBCPI from reaction with O3 | kg/s |
|
|||
ProdPOPPOCPOfromNO3 | Production of oxidized POPPOCPO from reaction with NO3 | kg/s |
|
|||
ProdPOPPOCPIfromNO3 | Production of oxidized POPPOCPI from reaction with NO3 | kg/s |
|
|||
ProdPOPPBCPOfromNO3 | Production of oxidized POPPBCPO from reaction with NO3 | kg/s |
|
|||
ProdPOPPBCPIfromNO3 | Production of oxidized POPPBCPI from reaction with NO3 | kg/s |
|
--Bob Yantosca (talk) 18:09, 17 October 2018 (UTC)
The ProdLoss Collection
The ProdLoss collection contains chemical production and loss rates.
Here is a sample definition section for the ProdLoss collection. If this collection is not already present in the 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 + NO3R | 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 O2 from metals in cloud | 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 outputs from the Radon-Lead-Beryllium specialty simulation.
NOTE: Emissions of Rn and Be7 are archived to diagnostic output by HEMCO, and are thus not contained in this collection. For more information, please see the HEMCO diagnostics for the Rn-Pb-Be simulation below.
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 |
|
|||
Met_AIRDEN | Dry air density | kg/m3 |
|
|||
Met_AIRVOL | Grid box volume, dry air | m3 |
|
|||
Met_ALBD | Surface albedo | 1 |
|
|||
Met_AREAM2 | Grid box area | m2 |
|
| ||
Met_AVGW | Water vapor volume mixing ratio | vol H2O/vol dry air |
|
|||
Met_BXHEIGHT | Grid box height | m |
|
|||
Met_ChemGridLev | Chemistry grid level | 1 |
|
| ||
Met_CLDF | 3-D cloud fraction | 1 |
|
|||
Met_CLDFRC | Column cloud fraction | 1 |
|
|||
Met_CLDTOPS | Maximum cloud top height | 1 |
|
|||
Met_DELP | Delta-pressure between top and bottom edges of grid box (wet air) | hPa |
|
|||
Met_DQRCU | Convective precipitation production rate (dry air) | kg/kg/s |
|
|||
Met_DTRAIN | Detrainment flux | kg/m2/s |
|
|||
Met_EFLUX | Latent heat flux | W/m2 |
|
|||
Met_FRCLND | Olson land fraction | 1 |
|
|||
Met_FRLAKE | Fraction of grid box covered by lakes | 1 |
|
|||
Met_FRLAND | Fraction of grid box covered by land | 1 |
|
|||
Met_FRLANDIC | Fraction of grid box covered by land ice | 1 |
|
|||
Met_FROCEAN | Fraction of grid box covered by ocean | 1 |
|
|||
Met_FRSEAICE | Fraction of grid box covered by sea ice | 1 |
|
|||
Met_FRSNO | Fraction of grid box covered by snow | 1 |
|
|||
Met_GWETROOT | Root soil moisture | 1 |
|
|||
Met_GWETTOP | Topsoil moisture | 1 |
|
|||
Met_HFLUX | Sensible heat flux | W/m2 |
|
|||
Met_LAI | Leaf area index from met field archive | m2/m2 |
|
| ||
Met_LWI | Land-water-ice indices | 1 |
|
|||
Met_PARDF | Diffuse photosynthetically active radiation | W/m2 |
|
|||
Met_PARDR | Diffuse photosynthetically active radiation | W/m2 |
|
|||
Met_PBLTOPL | PBL top layer | 1 |
|
|||
Met_PBLH | PBL height | m |
|
|||
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 |
|
|||
Met_PMIDDRY | Pressure at midpoint of model layers, defined as arithmetic average of edge pressures (dry air) | hPa |
|
|||
Met_PRECANV | Anvil precipitation (at surface) | kg/m2/s |
|
|||
Met_PRECCON | Convective precipitation (at surface) | kg/m2/s |
|
|||
Met_PRECLSC | Large-scale precipitation (at surface) | kg/m2/s |
|
|||
Met_PRECTOT | Total precipitation (at surface) | kg/m2/s |
|
|||
Met_PS1DRY | Instantaneous surface pressure at start of 3-hr met field interval (dry air) | hPa |
|
|||
Met_PS2DRY | Instantaneous surface pressure at end of 3-hr met field interval (dry air) | hPa |
|
|||
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 |
|
|||
Met_PS2WET | Instantaneous surface pressure at end of 3-hr met field interval (wet air) | hPa |
|
|||
Met_PSC2WET | Surface pressure interpolated to current time (wet air) | hPa |
|
| ||
Met_QI | Ice mixing ratio (dry air) | kg/kg dry air |
|
|||
Met_QL | Liquid water mixing ratio (dry air) | kg/kg dry air |
|
|||
Met_OMEGA | Updraft velocity | Pa/s |
|
|||
Met_OPTD | Visible optical depth | 1i |
|
|||
Met_REEVAPCN | Evaporation of convective precipitation (dry air) | kg/kg/s |
|
|||
Met_REEVAPLS | Evaporation of large-scale + anvil precipitation (dry air) | kg/kg/s |
|
|||
Met_SLP | Sea level pressure | hPa |
|
|||
Met_SNODP | Snow depth | m |
|
|||
Met_SNOMAS | Snow mass | kg/m2 |
|
|||
Met_SPHU1 | Instantaneous specific humidity at start of 3 hr met field interval (wet air) | kg/kg |
|
|||
Met_SPHU2 | Instantaneous specific humidity at end of 3-hr met field interval (wet air) | kg/kg |
|
|||
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 |
|
|||
Met_SUNCOSMID | Cosine of solar zenith angle at midpoint of chemistry timestep | 1 |
|
|||
Met_SWGDN | Incident shortwave radiation at ground | W/m2 |
|
|||
Met_TAUCLI | Visible optical depth of ice clouds | 1 |
|
|||
Met_TAUCLW | Visible optical depth of water clouds | 1 |
|
|||
Met_THETA | Potential temperature | K |
|
|||
Met_TMPU1 | Instantaneous temperature at start of 3-hr met field interval | K |
|
|||
Met_TMPU2 | Instantaneous temperature at end of 3-hr met field interval | K |
|
|||
Met_T | Temperature interpolated to current time | K |
|
| ||
Met_TO3 | Total overhead ozone column | Dobsons |
|
|||
Met_TropHt | Tropopause height | u |
|
|||
Met_TropLev | Tropopause height | km |
|
|||
Met_TROPP | Tropopause pressure | hPa |
|
|||
Met_TS | Surface temperature | K |
|
|||
Met_TSKIN | Surface skin temperature | K |
|
|||
Met_U | East-west ccomponent of wind | m/s |
|
|||
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)
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
Bob Yansotca wrote:
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.
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.
- You can also use the full date/time descriptor (00000000 010000, etc.)
- Specify that a new netCDF file should be created every 24 hours:
- Set duration: 240000
- You can also use the full date/time descriptor (00000001 000000)
- 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:
#=================================================================== # Add an instantaneous timeseries collection to the master list #=================================================================== COLLECTIONS: inst3hr', :: #==================================================================== # Define the properties of the instantaneous timeseries collection #==================================================================== inst3hr.template: '%y4%m2%d2_%h2%n2z.nc4', inst3hr.frequency: 030000, inst3hr.duration: 240000, inst3hr.mode: 'instantaneous', inst3hr.fields: 'SpeciesConc_?ADV?', 'GIGCchem', 'Met_T', 'GIGCchem', 'DryDepVel_?DRY?', 'GIGCchem', ::
--Bob Yantosca (talk) 21:55, 7 June 2018 (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
- You can also use the full date/time descriptor: 00000001 000000
- Set frequency: 240000
- Specify that a new netCDF file should be created every 24 hours:
- Set duration: 240000
- You can also use the full date/time descriptor: 00000001 000000
- 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:
#=================================================================== # Add an 24-hr average timeseries collection to the master list #=================================================================== COLLECTIONS: avg24hr', :: #=================================================================== # Define the properties of the 24-hr average timeseries collection #=================================================================== avg24hr.template: '%y4%m2%d2_%h2%n2z.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) 21:58, 7 June 2018 (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)
netCDF diagnostics for GEOS-Chem specialty simulations
In order to prioritize the GEOS-Chem v11-02 (aka 12.0.0) release, we focused on creating netCDF diagnostics that correspond to the bpch diagnostics used for benchmarking GEOS-Chem. Following v11-02 we will start to add the netCDF diagnostics for the following specialty simulations.
NOTE: Emissions for any specialty simulation can be archived as diagnostic output directly by HEMCO. See the following section for more information.
--Bob Yantosca (talk) 13:50, 8 June 2018 (UTC)
Diagnostics that are currently archived by HEMCO
The diagnostic collections described above 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 want to archive as 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, as shown here:
DiagnPrefix: HEMCO_diagnostics DiagnFreq: End
This will send HEMCO diagnostic output to netCDF files named HEMCO_diagnostics.YYYYMMDDhhmm.nc. You can also change the archival frequency to e.g. monthly with
DiagnFreq: 00000100 000000
or to any other interval.
For more information about HEMCO diagnostics, please see The HEMCO User's Guide: Diagnostics section.
--Bob Yantosca (talk) 20:10, 7 June 2018 (UTC)
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. You can of course add more diagnostics to this list.
For more information how to add new diagnostic fields to the HEMCO_Diagn.rc file, please see The HEMCO User's Guide: Diagnostics section.
#------------------------------------------------------------------------------ # 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 specialty 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) 20:00, 7 June 2018 (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)
Adding New Diagnostics
To add your own diagnostics we recommend that you find a similar existing diagnostic and use its implementation as a template. Most of the work is done in Headers/state_diag_mod.F90. Briefly, the following updates to that file are essential for adding in your own netcdf diagnostics:
- Declare diagnostic array at top of module
- Set diagnostic array pointer to null in Init_State_Diag subroutine
- Create a section in Init_State_Diag subroutine to allocate and register the array
- Deallocate the diagnostic array in subroutine Cleanup_State_Diag
- Add an if block for the diagnostic within subroutine Get_Metadata_State_Diag to define its metadata
Good diagnostics to use as templates are SpeciesConc for 3-dimensional arrays that are for all species and DryDepVel for 2-dimensional arrays that are for a subset of species. If your diagnostic is not per species then AODDust is a good diagnostic to look at. Search the file Headers/state_diag_mod.F90 for any of these strings to find all instances of code related to their implementation.
Note that information about the dimensions and species collection the diagnostic will include must be specified when allocating the array in Init_State_Diag and in Get_Metadata_State_Diag. In the latter subroutine the Rank is the integer number of dimensions of the diagnostic (not including species) and the TagID string, if any, specifies the species collection to output the diagnostic per. TagIDs are defined in subroutine Get_TagInfo. Each TagID string can also be used as a wildcard within HISTORY.rc to simplify diagnostic name specification (for GEOS-Chem classic only).
Once you have implemented your diagnostic in Headers/state_diag_mod.F90 and checked that it compiles using NC_DIAG=y, try adding it to HISTORY.rc and running. You should get your diagnostic output in the netcdf output file as all zeros. The next step is to populate the array with whatever value you want to output. You should do this by passing the State_Diag array to the location where you want to set the values. Then write code to fill the array being sure to wrap it in #if defined( NC_DIAG ) and #endif C-preprocessor code (no indent). A simple test of your understanding is to initially set values to a constant other than zero and see if that works.
--Lizzie Lundgren (talk) 17:45, 24 August 2018 (UTC)