Difference between revisions of "List of diagnostics archived to netCDF format"
(→The Aerosols collection) |
(→The Aerosols collection) |
||
Line 961: | Line 961: | ||
'Chem_KhetiSLAHOBrHBr ', 'GIGCchem', | 'Chem_KhetiSLAHOBrHBr ', 'GIGCchem', | ||
:: | :: | ||
+ | |||
+ | |||
+ | {| border=1 cellspacing=0 cellpadding=5 | ||
+ | |-valign="top" bgcolor="#CCCCCC" | ||
+ | !width="225px"|Diagnostic name | ||
+ | !width="225px"|Description | ||
+ | !width="125px"|Units | ||
+ | !width="80px"|Wildcards | ||
+ | !width="150px"|Simulations | ||
+ | !width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]] | ||
+ | !width="150px"|Notes | ||
+ | |||
+ | |-valign="top" | ||
+ | |AerMassTSOA | ||
+ | |Aerosol products of terpene oxidation | ||
+ | |ug/m3 | ||
+ | |none | ||
+ | | | ||
+ | *benchmark | ||
+ | *complexSOA | ||
+ | *complexSOA_SVPOA | ||
+ | | | ||
=== The CloudConvFlux collection === | === The CloudConvFlux collection === |
Revision as of 14:48, 7 June 2018
On this page we list the information about the new netCDF diagnostics that will be introduced in GEOS-Chem v11-02.
NOTE: We will NOT retire the legacy bpch diagnostics in GEOS-Chem v11-02. We will preserve the bpch diagnostic output until we can find alternatives for specialty diagnostics, especially those which involve averaging in a local solar time window.
Contents
- 1 Overview
- 2 Legend to sections below
- 3 Diagnostic collections
- 3.1 The master collection list
- 3.2 The SpeciesConc collection
- 3.3 The AerosolMass collection
- 3.4 The Aerosols collection
- 3.5 The CloudConvFlux collection
- 3.6 The ConcAfterChem collection
- 3.7 The DryDep collection
- 3.8 The JValues collection
- 3.9 The JValuesLocalNoon collection
- 3.10 The LevelEdgeDiags collection
- 3.11 The ProdLoss Collection
- 3.12 The RadioNuclide Collection
- 3.13 The StateChm Collection
- 3.14 The StateMet collection
- 3.15 The WetLossConv collection
- 3.16 The WetLossLS collection
- 4 Proposed diagnostic names for specialty simulations
- 5 Diagnostics that are currently archived by HEMCO
- 6 Replicating the existing specialty diagnostics
- 7 Validating the netCDF diagnostics
Overview
An introduction to netCDF diagnostics
Bob Yantosca has created an overview presentation about the new netCDF diagnostics for v11-02.
--Bob Yantosca (talk) 22:12, 8 February 2018 (UTC)
Sample HISTORY.rc diagnostic input file
Here is a sample HISTORY.rc file that is used to request netCDF diagnostic output from a GEOS-Chem “Classic” simulation.
#============================================================================ # EXPID allows you to specify the beginning of the file path corresponding # to each diagnostic collection. For example: # # EXPID: ./GEOSChem # Will create netCDF files whose names begin "GEOSChem", # in this run directory. # # EXPID: ./OutputDir/GEOSChem # Will create netCDF files whose names begin with "GEOSChem" # in the OutputDir sub-folder of this run directory. # # EXPDSC and CoresPerNode are only used by GCHP simulations. #============================================================================ EXPID: ./GEOSChem EXPDSC: GEOS-Chem_devel CoresPerNode: 6 #============================================================================== # %%%%% COLLECTION NAME DECLARATIONS %%%%% # # To disable a collection, place a "#" character in front of its name # # NOTE: These are the "default" collections for GEOS-Chem. # But you can create your own custom diagnostic collections as well. #============================================================================== COLLECTIONS: 'SpeciesConc', 'ConcAfterChem', :: @============================================================================== # %%%%% THE SpeciesConc COLLECTION %%%%% # # GEOS-Chem species concentrations (default = advected species) # # Available for all simulations #============================================================================== SpeciesConc.template: '%y4%m2%d2_%h2%n2z.nc4', SpeciesConc.frequency: 060000, SpeciesConc.format: 'CFIO', SpeciesConc.duration: 240000, SpeciesConc.mode: 'instantaneous', SpeciesConc.fields: 'SpeciesConc_?ADV?', 'GIGCchem', :: #============================================================================== # %%%%% THE ConcAfterChem COLLECTION %%%%% # # Concentrations of OH, HO2, O1D, O3P immediately after exiting the KPP solver # or OH after the CH4 specialty-simulation chemistry routine. # # OH: Available for all full-chemistry simulations and CH4 specialty sim # HO2: Available for all full-chemistry simulations # O1D, O3P: Availalbe for full-chemistry simulations using UCX mechanism #============================================================================== ConcAfterChem.template: '%y4%m2%d2_%h2%n2z.nc4', ConcAfterChem.frequency: 00000100 000000, ConcAfterChem.format: 'CFIO', ConcAfterChem.duration: 00000100 000000, ConcAfterChem.mode: 'time-averaged', ConcAfterChem.fields: 'OHconcAfterChem', 'GIGCchem', 'HO2concAfterChem', 'GIGCchem', 'O1DconcAfterChem', ‘GIGCchem’, 'O3PconcAfterChem', ‘GIGCchem’, ::
In this HISTORY.rc file, we are requesting two collections, or types of netCDF file output. The table below explains in more detail parameters shown in the HISTORY.rc file above.
Attribute | Explanation |
---|---|
SpeciesConc | Name of the first collection in this HISTORY.rc file. A collection is a series of files containing the same GEOS-Chem diagnostic quantities. |
SpeciesConc.template | Determines the date and time format for each netCDF file name belonging to the SpeciesConc collection.
|
SpeciesConc.frequency | Determines how often the diagnostic quantities belonging to SpeciesConc collection will be saved to a netCDF file.
|
SpeciesConc.format | For GCHP simulations only: indicates the I/O library that will be used. This can be omitted for GEOS-Chem "Classic" simualations. |
SpeciesConc.duration | Determines how often a new SpeciesConc netCDF file will be created.
|
SpeciesConc.mode | Determines the averaging method for the SpeciesConc collection
|
SpeciesConc.fields | Lists the diagnostic quantities to be included in the SpeciesConc collection.
See the sections below for in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format. NOTE: You may use wildcards to request a subset of all possible chemical species. See the next section for more information about wildcards. |
:: | Signifies the end of the SpeciesConc definition section.
|
ConcAfterChem | Name of the second collection in this HISTORY.rc file. |
ConcAfterChem.template | Determines the date and time format for each netCDF file name belonging to the ConcAfterChem collection. |
ConcAfterChem.frequency | Determines the length of the period in which the diagnostic quantities belonging to ConcAfterChem collection will be temporally-averaged, before being saved to a netCDF file.
|
ConcAfterChem.format | For GCHP simulations only: indicates the I/O library that will be used. This can be omitted for GEOS-Chem "Classic" simualations. |
ConcAfterChem.duration | Determines how often a new netCDF file belongng to the ConcAfterChem will be created.
|
ConcAfterChem.mode | Determines the averaging method for the ConcAfterChem collection
|
ConcAfterChem.fields | Lists the diagnostic quantities to be included in the ConcAfterChem collection.
See the sections below for in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format. NOTE: You may use wildcards to request a subset of all possible species. See the next section for more information about wildcards. |
:: | Signifies the end of the ConcAfterChem definition section.
|
For more examples, please see Bob Yantosca’s netCDF diagnostics overview presentation. We will also add more documentation to the GEOS-Chem wiki in the coming weeks.
--Bob Yantosca (talk) 22:12, 8 February 2018 (UTC)
netCDF filename convention
The names of the netCDF files corresponding to each collection will adhere to this convention:
EXPID.CollectionName.Template
Where EXPID can be specified at the very top of the HISTORY.rc file. This parameter controls the filename prefix. In the example from the previous section, EXPID is set to ./GEOSChem. This means that all netCDF output files will be placed in the current run directory (specified by ./) and will begin with GeosChem.
If you wish to send the netCDF diagnostic output to a sub-folder of the run directory (say named OutputDir), then you can set e.g. EXPID: ./OutputDir/GeosChem. (NOTE: You can also omit the ./, but we have included it to make it clear that the files will be placed in the same directory where the GEOS-Chem executable resides.)
The CollectionName and Template settings are defined as shown in our example HISTORY.rc file from the previous section, namely:
SpeciesConc.template: '%y4%m2%d2_%h2%n2z.nc4', . . . ConcAfterChem.template: '%y4%m2%d2_%h2%n2z.nc4',
In the template tags:
- The notation %y4%m2%d5_%h2%n2 specifies a in the format YYYYMMDD_hhmm into the netCDF filename.
- The lowercase zdenotes UTC time (aka "Zulu time").
- The .nc4 extension denotes that the file will be in netCDF-4 format.
Also recall that the duration tag of HISTORY.rc controls how often a new file will be written to disk, as we saw in our example from the previous section:
SpeciesConc.duration: 240000, # Write a new file each day . . . ConcAfterChem.duration: 00000100 000000, # Write a new file each month
Therefore, based on all of these settings in our example HISTORY.rc file, GEOS-Chem will write the following netCDF files to disk in the current run directory:
GEOSChem.SpeciesConc.20160101_0000z.nc4 GEOSChem.SpeciesConc.20160102_0000z.nc4 GEOSChem.SpeciesConc.20160103_0000z.nc4 GEOSChem.SpeciesConc.20160104_0000z.nc4 ... etc one file per day...
and
GEOSChem.ConcAfterChem.20160101_0000z.nc4 GEOSChem.ConcAfterChem.20160201_0000z.nc4 GEOSChem.ConcAfterChem.20160301_0000z.nc4 GEOSChem.ConcAfterChem.20160401_0000z.nc4 ... etc one file per month ...
--Bob Yantosca (talk) 18:45, 24 May 2018 (UTC)
Legend to sections below
This section contains a description of how the information about each diagnostic quantity is arranged in the sections below.
General information about each diagnostic
The tables below list the following parameters for each diagnostic that is archived to bpch format:
Diagnostic name | The name of the given diagnostic quantity that will be archived to netCDF file format.
|
---|---|
Description | A short overview of the given diagnostic. |
Units | The physical units of the given diagnostic quantity. |
Wildcards | A list of wildcards that can be used to specify all possible species, wavelength bins, etc. for the given diagnostic quantity. For a complete list of wildcards, please see the table below. |
Simulations | A list of simulations for which this particular diagnostic is valid. |
Bpch equivalent | The NDxx diagnostic number (and slot) under which the same diagnostic is available as bpch output. See the List of diagnostics archived to bpch format wiki page for more information. |
Notes | Lists supplemental information for the given diagnostic. |
Wildcards
The following terms are used in the tables below.
Term | Explanation | Example |
---|---|---|
<spcname> | Short name of a GEOS-Chem species, used in several diagnostics listed below.
NOTES:
|
SpeciesConc_NO SpeciesConc_CO SpeciesConc_?ADV? SpeciesConc_?AER? SpeciesConc_?ALL? SpeciesConc_?DRY? SpeciesConc_?FIX? SpeciesConc_?GAS? SpeciesConc_?KPP? SpeciesConc_?PHO? SpeciesConc_?VAR? SpeciesConc_?WET? ...etc... |
<metname> | Denotes a met field (or derived quantity such as total optical depth).
NOTES:
|
MET_U10M MET_PS MET_HFLUX MET_T ...etc... |
<photobin> | Number of a given wavelength bin for FAST-JX photolysis | 1-18 (with UCX on); 1-12 (with UCX off) |
<aername> | Aerosol quanatities included in the following array fields:
These do not always conform to GEOS-Chem species (for example, the mineral dust bins are the bins that are used as input for photolysis).
|
CHEM_AeroAreaMDUST1 CHEM_WetAeroRadiSSA ...etc...
|
--Bob Yantosca (talk) 17:05, 9 February 2018 (UTC)
Diagnostic collections
NOTE: The following collections are used by default in GEOS-Chem simulations. You can create your own customized collections by modifying the HISTORY.rc file.
The only restriction is that you cannot mix data that is placed on grid box layer edges in the same collection as data placed on grid box layer centers. This violates the netCDF convention that all data variables have to be defined with the same vertical dimension.
The master collection list
The top of each HISTORY.rc file will look similar to this:
############################################################################### ### HISTORY.rc file for GEOS-Chem ### ### Contact: GEOS-Chem Support Team (geos-chem-support@as.harvard.edu) ### ############################################################################### #============================================================================ # EXPID allows you to specify the beginning of the file path corresponding # to each diagnostic collection. For example: # # EXPID: ./GEOSChem # Will create netCDF files whose names begin "GEOSChem", # in this run directory. # # EXPID: ./OutputDir/GEOSChem # Will create netCDF files whose names begin with "GEOSChem" # in the OutputDir sub-folder of this run directory. # # EXPDSC and CoresPerNode are only used by GCHP simulations. #============================================================================ EXPID: ./GEOSChem EXPDSC: GEOS-Chem_devel CoresPerNode: 6 #============================================================================== # %%%%% COLLECTION NAME DECLARATIONS %%%%% # # To disable a collection, place a "#" character in front of its name # # NOTE: These are the "default" collections for GEOS-Chem. # But you can create your own custom diagnostic collections as well. #============================================================================== COLLECTIONS: 'SpeciesConc', 'AerosolMass', 'Aerosols', 'CloudConvFlux', 'ConcAfterChem', 'DryDep', 'JValues', 'JValuesLocalNoon', 'LevelEdgeDiags', 'ProdLoss', 'StateChm', 'StateMet', 'WetLossConv', 'WetLossLS', ::
We have already discussed how EXPID works in a previous section.
The COLLECTIONS: tag specifies all of the diagnostic collections that you wish to activate during a GEOS-Chem simulation. Each collection represents a group of diagnostic quantities that will be written to disk in netCDF file format. The collection name will be automatically added to the netCDF file name along with the date/or time, as we have seen above.
Each of the run directories for the various GEOS-Chem simulations will have its own customized HISTORY.rc file. Only the diagnostic collections pertaining to a particular GEOS-Chem simulation will be included in the corresponding HISTORY.rc file. (In other words, you will not find diagnostic collections for full-chemistry simulations in the HISTORY.rc file for the Rn-Pb-Be simulation.)
Each collection name must be bracketed by single quotes, and be followed by a comma.
To disable an entire diagnostic collection, simply put a # comment character in front of the collection name in the COLLECTIONS: section.
GEOS-Chem will expect to find a collection definition section for each of the activated collections listed under the COLLECTIONS: section. In other words, if you have SpeciesConc listed under COLLECTIONS:, but there is no further information provided about the SpeciesConc collection, then GEOS-Chem will halt with an error message.
The collections listed on this wiki page are the "default" diagnostic collections that we have created for GEOS-Chem. You are certainly not limited to just using these collections. We have created these default collections such that related quantities will be grouped together in the same netCDF files (to the greatest extent possible). But you can create your own customized diagnostic collections by referring to our sample HISTORY.rc file shown above.
--Bob Yantosca (talk) 18:51, 24 May 2018 (UTC)
The SpeciesConc collection
The SpeciesConc diagnostic collection contains advected species concentrations. This type of diagnostic output is used in all GEOS-Chem simulations; therefore, we have listed SpeciesConc first in the HISTORY.rc files that ship with each GEOS-Chem run directory.
Here is a sample definition section for the SpeciesConc collection. To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
SpeciesConc.template: '%y4%m2%d2_%h2%n2z.nc4', SpeciesConc.format: 'CFIO', SpeciesConc.frequency: 00000100 000000 SpeciesConc.duration: 00000100 000000 SpeciesConc.mode: 'time-averaged' SpeciesConc.fields: 'SpeciesConc_?ADV? ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the SpeciesConc collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
SpeciesConc_<spcname> | Chemical species concentrations | mol/mol dry air |
|
|
--Bob Yantosca (talk) 19:43, 16 May 2018 (UTC)
The AerosolMass collection
The AerosolMass collection contains diagnostics for aerosol mass and particulate matter from full-chemistry simulations.
Here is a sample definition section for the AerosolMass collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
AerosolMass.template: '%y4%m2%d2_%h2%n2z.nc4', AerosolMass.format: 'CFIO', AerosolMass.frequency: 00000100 000000 AerosolMass.duration: 00000100 000000 AerosolMass.mode: 'time-averaged' AerosolMass.fields: 'AerMassASOA ', 'GIGCchem', 'AerMassBC ', 'GIGCchem', 'AerMassINDIOL ', 'GIGCchem', 'AerMassISN1OA ', 'GIGCchem', 'AerMassISOA ', 'GIGCchem', 'AerMassLVOCOA ', 'GIGCchem', 'AerMassNH4 ', 'GIGCchem', 'AerMassNIT ', 'GIGCchem', 'AerMassOPOA ', 'GIGCchem', 'AerMassPOA ', 'GIGCchem', 'AerMassSAL ', 'GIGCchem', 'AerMassSO4 ', 'GIGCchem', 'AerMassSOAGX ', 'GIGCchem', 'AerMassSOAIE ', 'GIGCchem', 'AerMassSOAME ', 'GIGCchem', 'AerMassSOAMG ', 'GIGCchem', 'AerMassTSOA ', 'GIGCchem', 'BetaNO ', 'GIGCchem', 'PM25 ', 'GIGCchem', 'TotalBiogenicOA ', 'GIGCchem', 'TotalOA ', 'GIGCchem', 'TotalOC ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the AerosolMass collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes |
---|---|---|---|---|---|---|
AerMassTSOA | Aerosol products of terpene oxidation | ug/m3 | none |
|
||
AerMassISOA | Aerosol products of isoprene oxidation | ug/m3 | none |
|
||
AerMassTSOA | Aerosol products of terpene oxidation | ug/m3 | none |
|
||
AerMassASOA | Aerosol products of light aromatics + IVOC oxidation | ug/m3 | none |
|
||
AerMassPOA | Aerosols from SVOCs | ug/m3 | none |
|
||
AerMassTSOA | Aerosol products of terpene oxidation | ug/m3 | none |
|
||
AerMassOPOA | Aerosol products of POG oxidation | ug/m3 | none |
|
||
TotalOA | Sum of all organic aerosol | ug/m3 | none |
|
| |
TotalOC | Sum of all organic carbon | ug/m3 | none |
|
| |
BetaNO | NO branching ratio | ug/m3 | none |
|
| |
AerMassBC | Black carbon (BCPI + BCPO) | ug/m3 | none |
|
||
AerMassSO4 | Sulfate | ug/m3 | none |
|
||
AerMassNH4 | Ammonium | ug/m3 | none |
|
||
AerMassNIT | Nitrate | ug/m3 | none |
|
||
AerMassSAL | Sea salt aerosol (SALA + SALC) | ug/m3 | none |
|
||
PM25 | Particulate matter (r < 2.5 μm) | ug/m3 | none |
|
| |
AerMassSOAGX | Aerosol-phase glyoxal | ug/m3 | none |
|
| |
AerMassSOAMG | Aerosol-phase methylglyoxal | ug/m3 | none |
|
| |
AerMassSOAIE | Aerosol-phase IEPOX | ug/m3 | none |
|
| |
AerMassSOAME | Aerosol-phase IMAE | ug/m3 | none |
|
| |
AerMassINDIOL | Generic aerosol-phase organonitrate hydrolysis product | ug/m3 | none |
|
| |
AerMassLVOCOA | Aerosol-phase low-volatility non-IEPOX product of ISOPOOH (RIP) oxidation | ug/m3 | none |
|
| |
AerMassISN1OA | Aerosol-phase 2nd generation hydroxynitrates formed from ISOP+NO3 reaction pathway | ug/m3 | none |
|
|
--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', ::
Diagnostic name | Description | Units | Wildcards | Simulations | Bpch equiv. | Notes | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
AerMassTSOA | Aerosol products of terpene oxidation | ug/m3 | none |
|
The CloudConvFlux collectionThe CloudConvFlux collection contains diagnostics for mass fluxes in cloud convection. Here is a sample definition section for the CloudConvFlux collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly. To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name. CloudConvFlux.template: '%y4%m2%d2_%h2%n2z.nc4', CloudConvFlux.format: 'CFIO', CloudConvFlux.frequency: 00000100 000000 CloudConvFlux.duration: 00000100 000000 CloudConvFlux.mode: 'time-averaged' CloudConvFlux.fields: 'CloudConvFlux_?ADV? ', 'GIGCchem', :: This table describes the diagnostic quantities belonging to the CloudConvFlux collection:
--Bob Yantosca (talk) 20:21, 16 May 2018 (UTC) The ConcAfterChem collectionThe 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).
--Bob Yantosca (talk) 20:59, 16 May 2018 (UTC) The DryDep collectionThe 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:
--Bob Yantosca (talk) 20:33, 16 May 2018 (UTC) The JValues collectionThe 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).
--Bob Yantosca (talk) 20:38, 16 May 2018 (UTC) The JValuesLocalNoon collectionNOTE: At present, we are debugging an issue in how the noontime J-values are archived for netCDF. Until further notice, we recommend that you use the ND22 bpch diagnostic to archive noontime J-values. (Bob Yantosca, 16 May 2018) The JValuesLocalNoon collection contains diagnostics for photolysis rates for various chemical species, obtained from the FAST-JX photolysis mechanism, at the grid box where it is nearest to local solar noon. Here is a sample definition section for the JValuesLocalNoon collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly. To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name. JValues.template: '%y4%m2%d2_%h2%n2z.nc4', JValues.format: 'CFIO', JValues.frequency: 00000100 000000 JValues.duration: 00000100 000000 JValues.mode: 'time-averaged' JValues.fields: 'JNoon_?PHO? ', 'GIGCchem', :: This table describes the diagnostic quantities belonging to the JValuesLocalNoon collection: NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).
--Bob Yantosca (talk) 21:07, 16 May 2018 (UTC) The LevelEdgeDiags collectionThe 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:
--Bob Yantosca (talk) 21:23, 16 May 2018 (UTC) The ProdLoss CollectionThe 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).
--Bob Yantosca (talk) 19:25, 17 May 2018 (UTC) The RadioNuclide CollectionThe RadioNuclide collection contains diagnostic ouputs from the Radon-Lead-Beryllium specialty simulation. Here is a sample definition section for the RadioNuclide collection. If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly. To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name. RadioNuclide.template: '%y4%m2%d2_%h2%n2z.nc4', RadioNuclide.format: 'CFIO', RadioNuclide.frequency: 00000100 000000 RadioNuclide.duration: 00000100 000000 RadioNuclide.mode: 'time-averaged' RadioNuclide.fields: 'PbFromRnDecay ', 'GIGCchem', 'RadDecay_Rn ', 'GIGCchem', 'RadDecay_Pb ', 'GIGCchem', 'RadDecay_Be7 ', 'GIGCchem', :: The table below describes diagnostic quantities belonging to the RadioNuclide collection.
--Bob Yantosca (talk) 20:56, 22 May 2018 (UTC) The StateChm CollectionThe 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).
--Bob Yantosca (talk) 19:55, 17 May 2018 (UTC) The StateMet collectionThe 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', ::
--Bob Yantosca (talk) 20:40, 22 May 2018 (UTC) The WetLossConv collectionThe 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.
--Bob Yantosca (talk) 20:23, 17 May 2018 (UTC) The WetLossLS collectionThe 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.
--Bob Yantosca (talk) 20:23, 17 May 2018 (UTC) Proposed diagnostic names for specialty simulationsHere is a list of our proposed netCDF diagnostic names for quantities archived in the GEOS-Chem specialty simulations. This list is by no means exhaustive or complete. Contact Bob Yantosca with any suggestions or concerns. CH4 simulationNOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.
--Bob Yantosca (talk) 18:57, 21 November 2017 (UTC) CO2 simulationNOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability. NOTE: For consistency with the HEMCO emissions diagnostics, we propose changing the units of these diagnostics from [atoms C/cm2/s] to [kg/m2/s].
--Bob Yantosca (talk) 15:42, 15 November 2017 (UTC) Hg simulationNOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability. ALSO NOTE: We will eliminate underscore characters within the variable name (except to separate the name from the species name or wildcard) at a later date. NOTE: We will probably delay implementation of new diagnostics for the Hg simulation until we receive updated Hg simulation source code from the Hg and POPs Working Group. Also we look to the Hg and POPs working group to inform us if any of these diagnostics are no longer necessary.
--Bob Yantosca (talk) 16:57, 20 October 2017 (UTC) POPs simulationNOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability. NOTE: We will probably delay implementation of new diagnostics for the POPs simulation until we receive updated Hg simulation source code from the Hg and POPs Working Group.
--Bob Yantosca (talk) 17:02, 20 October 2017 (UTC) RRTMG radiative transfer modelNOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.
--Bob Yantosca (talk) 15:44, 2 November 2017 (UTC) TOMAS aerosol microphysicsNOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability. NOTE: We invite the TOMAS team to review these diagnostic names for accuracy.
--Bob Yantosca (talk) 20:43, 14 November 2017 (UTC) Diagnostics that are currently archived by HEMCOThe following is a list of diagnostics that are archived by HEMCO. Usually, these diagnostics are written to the bpch file trac_avg_YYYYMMDDhhmm.bpch. But they can also be sent to the HEMCO_diagnostics.YYYYMMDDhhmm.nc file if you list them specifically in the HEMCO_Diagnostics.rc file. We will preserve the HEMCO diagnostic naming structure for the time being.
--Bob Yantosca (talk) 14:16, 19 October 2017 (UTC) Replicating the existing specialty diagnosticsHere 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 diagnosticTomas Sherwen wrote: Please could I ask if there is s position on/plan for restoring the chemical rate tracking (REA_??) functionality of the planeflight diagnostic? Melissa Sulprizio replied: Yes, we will eventually restore the chemical rates in the planeflight diagnostic. One issue is that we're currently developing netCDF diagnostics and that will mess up the planeflight diagnostics even more. Bob wrote to the GCSC:For the “planeflight” diagnostic, we will investigate using a separate package (such as NOAA ObsPack, as recommended by Andy Jacobsen at IGC8) that can more efficiently store point data. Then new diagnostic package we are developing works well for array data but not as well for point data.Once the netCDF diagnostics are in place, we will reconsider how to fix/update planeflight_mod.F. If you need these diagnostics in the meantime, you should be able to hack it into the chemical mechanism by adding dummy species to the reactions you want to track and then rebuilding the mechanism based on these instructions. In flexchem_mod.F90, you can then obtain the rate from KPP using the C array (e.g. Rate = C(ind_NEWSPC) / DT to get molec/cm3/s). Mat Evans replied: I’ve had a quick look at obspack. I’m not sure its well suited to our needs. I personally don’t see much need to update the plane flight files. They are easy to understand at the moment and easy to manipulate being in ascii. The biggest problem at the moment is that the rate constants have fallen out of them because of the move to FlexChem. If we can get that sorted I don’t think there is a pressing need to update the format. --Bob Yantosca (talk) 16:20, 15 November 2017 (UTC) ND48 station diagnosticsWe 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 diagnosticYou can replicate the ND49 bpch diagnostic (instantaneous timeseries) as follows:
Example: COLLECTIONS: inst3hr', :: inst3hr.filename: './GEOSChem.inst3hr.%y4%m2%d2.nc4', inst3hr.frequency: 030000, inst3hr.duration: 240000, inst3hr.mode: 'instantaneous', inst3hr.fields: 'SpeciesConc_?ADV?', 'GIGCchem', 'Met_T', 'GIGCchem', 'DryDepVel_?DRY?', 'GIGCchem', --Bob Yantosca (talk) 15:57, 15 November 2017 (UTC) ND50 24-hr average timeseries diagnosticYou can replicate the ND50 bpch diagnostic (24-hr average timeseries) as follows:
Example: COLLECTIONS: avg24hr', :: avg24hr.filename: './GEOSChem.avg24hr.%y4%m2%d2.nc4', avg24hr.frequency: 240000, avg24hr.duration: 240000, avg24hr.mode: 'time-averaged', avg24hr.fields: 'SpeciesConc_?ADV?', 'GIGCchem', 'Met_T', 'GIGCchem', 'DryDepVel_?DRY?', 'GIGCchem', --Bob Yantosca (talk) 16:06, 15 November 2017 (UTC) ND51 satellite diagnosticAaron 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. 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.) --Bob Yantosca (talk) 15:33, 15 November 2017 (UTC) Validating the netCDF diagnosticsIn GEOS-Chem ClassicWe invite you to view the the presentation NetCDF diagnostic validation in GEOS-Chem "Classic" by Bob Yantosca and the GCST which summarizes the initial validation process. A more robust validation will take place shortly. One of the take-aways of the validation is that the timestep at which diagnostics are update could cause non-negligble differences. For example, several GEOS-Chem time-averaged diagnostics are updated on each chemistry timestep, which is 20 minutes for most GEOS-Chem simulations. But the default behavior of the new netCDF diagnostics in GEOS-Chem updates time-averaged diagnostic quantities every "heartbeat" timestep, which is 10 minutes for most simulations. Therefore, the netCDF diagnostics will capture the state of the atmopshere on those timesteps where chemistry does not happen. As shown in the presentation, this could cause non-negligible differences when comparing to the legacy diagnostics. The GCST recommends that time-averaged diagnostic quantities in GEOS-Chem "Classic" be updated on each "heartbeat" timestep, as this mimics the behavior the diagnostics in GCHP. --Bob Yantosca (talk) 20:14, 27 November 2017 (UTC) In GCHPLizzie Lundgren (GCST) and Colin Lee (Dalhousie) are validating the new diagnostics in GCHP. Stay tuned for more information. --Bob Yantosca (talk) 20:14, 27 November 2017 (UTC) |