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Overview
An introduction to netCDF diagnostics
Bob Yantosca has created an overview presentation about the new netCDF diagnostics for v11-02.
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. The names for netCDF diagnostic quantities follow the naming convention listed above.
#=================================================================== # Declare collection names. Disable collections by commenting # each collection name out with a "#" character. #=================================================================== COLLECTIONS: 'SpeciesConc', 'ConcAfterChem', :: #=================================================================== # Collection to save out GEOS-Chem species concentrations #=================================================================== 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', :: #=================================================================== # Collection to save out concentrations after chemistry # (from the FlexChem/KPP solver) #=================================================================== ConcAfterChem.template: '%y4%m2%d2_%h2%n2z.nc4', ConcAfterChem.frequency: 000100 000000, ConcAfterChem.format: 'CFIO', ConcAfterChem.duration: 000100 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.
| 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 filename in the in the SpeciesConc collection.
| ||
| SpeciesConc.frequency | For instantaneous collections (such as SpeciesConc), the frequency attribute determines the interval at which data will be saved to disk.
| ||
| 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 file will be written to disk.
| ||
| SpeciesConc.mode | Determines the averaging method for the SpeciesConc collection
| ||
| SpeciesConc.fields | A list of diagnostic quantities to be included in the SpeciesConc collection.
| ||
| :: | 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 filename in the in the SpeciesConc collection. | ||
| ConcAfterChem.frequency | For time-averaged collections (such as ConcAfterChem), the frequency attribute determines the length of the time-averaging period.
| ||
| ConcAfterChem.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 file will be written to disk.
| ||
| ConcAfterChem.mode | Determines the averaging method for the ConcAfterChem collection
| ||
| ConcAfterChem.fields | A list of diagnostic quantities to be included in the ConcAfterChem collection.
| ||
| :: | Signifies the end of the list of collections, as well as the end of each defined collection. "::" may be placed at any column in the file. | :: | 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) 20:14, 8 February 2018 (UTC)
Legend
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... |
| nAdvect | Number of advected GEOS-Chem species | |
| nDryDep | Number of dry-depositing GEOS-Chem species | |
| nKppSpc | Number of species in the KPP chemistry mechanism | |
| nPhoto | Number of photolyzing GEOS-Chem species | |
| nTomas | Number of size-resolved TOMAS species | IBINS*(ICOMP-IDIAG+1) |
| nWetDep | Number of soluble, wet-depositing GEOS-Chem species |
--Bob Yantosca (talk) 20:32, 14 November 2017 (UTC)
Collection list
EXPID: OutputDir/GCHP EXPDSC: GEOS-Chem_devel CoresPerNode: 6
#===================================================================
# Declare collection names and toggle on/off
# by commenting out with a #
#===================================================================
COLLECTIONS: 'SpeciesConc',
'Aerosols',
'CloudConvFlux',
'ConcAfterChem',
'DryDep',
'JValues',
'JValuesLocalNoon',
'LevelEdgeDiags',
'ProdLoss',
'StateChm',
'StateMet',
'WetLossConv',
'WetLossLS',
Species concentrations
- Species concentrations (per advected species)
SpeciesConc.template: '%y4%m2%d2_%h2%n2z.nc4', SpeciesConc.format: 'CFIO', SpeciesConc.frequency: 010000 SpeciesConc.duration: 010000 SpeciesConc.mode: 'time-averaged' SpeciesConc.fields: 'SpeciesConc_?ADV? ', 'GIGCchem',
Aerosol diagnostics
#===================================================================
# Aerosol optical depth, surface area, number density, and hygroscopic growth
Aerosols.template: '%y4%m2%d2_%h2%n2z.nc4',
Aerosols.format: 'CFIO',
Aerosols.frequency: 010000
Aerosols.duration: 010000
Aerosols.mode: 'time-averaged'
Aerosols.fields: 'AODDust ', 'GIGCchem',
'AODDustWL1_?DUSTBIN? ', 'GIGCchem',
'AODHygWL1_?HYG? ', 'GIGCchem',
'AODSOAfromAqIsopreneWL1 ', 'GIGCchem',
'AODStratLiquidAerWL1 ', 'GIGCchem',
'AODPolarStratCloudWL1 ', 'GIGCchem',
'AerHygroscopicGrowth_?HYG? ', 'GIGCchem',
'AerNumDensityStratLiquid ', 'GIGCchem',
'AerNumDensityStratParticulate ', 'GIGCchem',
'AerAqueousVolume ', 'GIGCchem',
'AerSurfAreaDust ', 'GIGCchem',
'AerSurfAreaHyg_?HYG? ', 'GIGCchem',
'AerSurfAreaStratLiquid ', 'GIGCchem',
'AerSurfAreaPolarStratCloud ', 'GIGCchem',
'Chem_AeroAreaMDUST1 ', 'GIGCchem',
'Chem_AeroAreaMDUST2 ', 'GIGCchem',
'Chem_AeroAreaMDUST3' ', 'GIGCchem',
'Chem_AeroAreaMDUST4 ', 'GIGCchem',
'Chem_AeroAreaMDUST5 ', 'GIGCchem',
'Chem_AeroAreaMDUST6 ', 'GIGCchem',
'Chem_AeroAreaMDUST7 ', 'GIGCchem',
'Chem_AeroAreaSULF ', 'GIGCchem',
'Chem_AeroAreaBC ', 'GIGCchem',
'Chem_AeroAreaOC ', 'GIGCchem',
'Chem_AeroAreaSSA ', 'GIGCchem',
'Chem_AeroAreaSSC ', 'GIGCchem',
'Chem_AeroAreaBGSULF ', 'GIGCchem',
'Chem_AeroAreaICEI ', 'GIGCchem',
'Chem_AeroRadiMDUST1 ', 'GIGCchem',
'Chem_AeroRadiMDUST2 ', 'GIGCchem',
'Chem_AeroRadiMDUST3 ', 'GIGCchem',
'Chem_AeroRadiMDUST4 ', 'GIGCchem',
'Chem_AeroRadiMDUST5 ', 'GIGCchem',
'Chem_AeroRadiMDUST6 ', 'GIGCchem',
'Chem_AeroRadiMDUST7 ', 'GIGCchem',
'Chem_AeroRadiSULF ', 'GIGCchem',
'Chem_AeroRadiBC ', 'GIGCchem',
'Chem_AeroRadiOC ', 'GIGCchem',
'Chem_AeroRadiSSA ', 'GIGCchem',
'Chem_AeroRadiSSC ', 'GIGCchem',
'Chem_AeroRadiBGSULF ', 'GIGCchem',
'Chem_AeroRadiICEI ', 'GIGCchem',
'Chem_WetAeroAreaMDUST1 ', 'GIGCchem',
'Chem_WetAeroAreaMDUST2 ', 'GIGCchem',
'Chem_WetAeroAreaMDUST3 ', 'GIGCchem',
'Chem_WetAeroAreaMDUST4 ', 'GIGCchem',
'Chem_WetAeroAreaMDUST5 ', 'GIGCchem',
'Chem_WetAeroAreaMDUST6 ', 'GIGCchem',
'Chem_WetAeroAreaMDUST7 ', 'GIGCchem',
'Chem_WetAeroAreaSULF ', 'GIGCchem',
'Chem_WetAeroAreaBC ', 'GIGCchem',
'Chem_WetAeroAreaOC ', 'GIGCchem',
'Chem_WetAeroAreaSSA ', 'GIGCchem',
'Chem_WetAeroAreaSSC ', 'GIGCchem',
'Chem_WetAeroAreaBGSULF ', 'GIGCchem',
'Chem_WetAeroAreaICEI ', 'GIGCchem',
'Chem_WetAeroRadiMDUST1 ', 'GIGCchem',
'Chem_WetAeroRadiMDUST2 ', 'GIGCchem',
'Chem_WetAeroRadiMDUST3 ', 'GIGCchem',
'Chem_WetAeroRadiMDUST4 ', 'GIGCchem',
'Chem_WetAeroRadiMDUST5 ', 'GIGCchem',
'Chem_WetAeroRadiMDUST6 ', 'GIGCchem',
'Chem_WetAeroRadiMDUST7 ', 'GIGCchem',
'Chem_WetAeroRadiSULF ', 'GIGCchem',
'Chem_WetAeroRadiBC ', 'GIGCchem',
'Chem_WetAeroRadiOC ', 'GIGCchem',
'Chem_WetAeroRadiSSA ', 'GIGCchem',
'Chem_WetAeroRadiSSC ', 'GIGCchem',
'Chem_WetAeroRadiBGSULF ', 'GIGCchem',
'Chem_WetAeroRadiICEI ', 'GIGCchem',
'Chem_StatePSC ', 'GIGCchem',
'Chem_KhetiSLAN2O5H2O ', 'GIGCchem',
'Chem_KhetiSLAN2O5HCl ', 'GIGCchem',
'Chem_KhetiSLAClNO3H2O ', 'GIGCchem',
'Chem_KhetiSLAClNO3HCl ', 'GIGCchem',
'Chem_KhetiSLAClNO3HBr ', 'GIGCchem',
'Chem_KhetiSLABrNO3H2O ', 'GIGCchem',
'Chem_KhetiSLABrNO3HCl ', 'GIGCchem',
'Chem_KhetiSLAHOClHCl ', 'GIGCchem',
'Chem_KhetiSLAHOClHBr ', 'GIGCchem',
'Chem_KhetiSLAHOBrHCl ', 'GIGCchem',
'Chem_KhetiSLAHOBrHBr ', 'GIGCchem',
::
Cloud convective flux
- Cloud convective flux (per advected species)
CloudConvFlux.template: '%y4%m2%d2_%h2%n2z.nc4', CloudConvFlux.format: 'CFIO', CloudConvFlux.frequency: 010000 CloudConvFlux.duration: 010000 CloudConvFlux.mode: 'time-averaged' CloudConvFlux.fields: 'CloudConvFlux_?ADV? ', 'GIGCchem',
Concentrations after chemistry
# Concentrations after chemistry
ConcAfterChem.template: '%y4%m2%d2_%h2%n2z.nc4',
ConcAfterChem.format: 'CFIO',
ConcAfterChem.frequency: 010000
ConcAfterChem.duration: 010000
ConcAfterChem.mode: 'time-averaged'
ConcAfterChem.fields: 'OHconcAfterChem ', 'GIGCchem',
'HO2concAfterChem ', 'GIGCchem',
'O1DconcAfterChem ', 'GIGCchem',
'O3PconcAfterChem ', 'GIGCchem',
Dry deposition diagnostics
- Dry deposition flux velocity (per dry deposited species)
DryDep.template: '%y4%m2%d2_%h2%n2z.nc4',
DryDep.format: 'CFIO',
DryDep.frequency: 010000
DryDep.duration: 010000
DryDep.mode: 'time-averaged'
DryDep.fields: 'DryDepVel_?DRY? ', 'GIGCchem',
'DryDepMix_?DRY? ', 'GIGCchem',
'DryDepChm_?DRY? ', 'GIGCchem',
'DryDep_?DRY? ', 'GIGCchem',
Photolysis diagnostics
- Photolysis rates (J-values)
JValues.template: '%y4%m2%d2_%h2%n2z.nc4', JValues.format: 'CFIO', JValues.frequency: 010000 JValues.duration: 010000 JValues.mode: 'time-averaged' JValues.fields: 'Jval_?PHO? ', 'GIGCchem',
- Photolysis rates at local noon (J-values)
JValuesLocalNoon.template: '%y4%m2%d2_%h2%n2z.nc4', JValuesLocalNoon.format: 'CFIO', JValuesLocalNoon.frequency: 010000 JValuesLocalNoon.duration: 010000 JValuesLocalNoon.mode: 'instantaneous' JValuesLocalNoon.fields: 'JNoon_?PHO? ', 'GIGCchem',
Diagnostics on level edges
- Level edge diagnostics (73-level only)
LevelEdgeDiags.template: '%y4%m2%d2_%h2%n2z.nc4',
LevelEdgeDiags.format: 'CFIO',
LevelEdgeDiags.frequency: 010000
LevelEdgeDiags.duration: 010000
LevelEdgeDiags.mode: 'time-averaged'
LevelEdgeDiags.fields: 'Met_CMFMC ', 'GIGCchem',
'Met_PEDGE ', 'GIGCchem',
'Met_PEDGEDRY ', 'GIGCchem',
'Met_PFICU ', 'GIGCchem',
'Met_PFILSAN ', 'GIGCchem',
'Met_PFLCU ', 'GIGCchem',
'Met_PFLLSAN ', 'GIGCchem',
Production and loss rates
# Prod/loss rates
ProdLoss.template: '%y4%m2%d2_%h2%n2z.nc4',
ProdLoss.format: 'CFIO',
ProdLoss.frequency: 010000
ProdLoss.duration: 010000
ProdLoss.mode: 'time-averaged'
ProdLoss.fields: 'PROD_?PRD? ', 'GIGCchem',
'ProdBCPIfromBCPO ', 'GIGCchem',
'ProdOCPIfromOCPO ', 'GIGCchem',
'ProdSO4fromH2O2inCloud ', 'GIGCchem',
'ProdSO4fromO3inCloud ', 'GIGCchem',
'ProdSO4fromO3inSeaSalt ', 'GIGCchem',
'ProdSO4fromHOBrInCloud ', 'GIGCchem',
'ProdSO4fromSRO3 ', 'GIGCchem',
'ProdSO4fromSRHObr ', 'GIGCchem',
'ProdSO4fromO3s ', 'GIGCchem',
'LOSS_?LOS? ', 'GIGCchem',
'LossHNO3onSeaSalt ', 'GIGCchem',
Fields of the State_Chm object
- State_Chm array diagnostics (see also Aerosols collection
StateChm.template: '%y4%m2%d2_%h2%n2z.nc4',
StateChm.format: 'CFIO',
StateChm.frequency: 010000
StateChm.duration: 010000
StateChm.mode: 'time-averaged'
StateChm.fields: 'Chem_phSav ', 'GIGCchem',
'Chem_HplusSav ', 'GIGCchem',
'Chem_WaterSav ', 'GIGCchem',
'Chem_SulRatSav ', 'GIGCchem',
'Chem_NaRatSav ', 'GIGCchem',
'Chem_AcidPurSav ', 'GIGCchem',
'Chem_BiSulSav ', 'GIGCchem',
'Chem_pHCloud ', 'GIGCchem',
'Chem_SSAlk', ', 'GIGCchem',
'Chem_HSO3AQ ', 'GIGCchem',
'Chem_SO3AQ ', 'GIGCchem',
'Chem_fupdateHOBr ', 'GIGCchem',
Fields of the State_Met object
# State_Met array diagnostics
StateMet.template: '%y4%m2%d2_%h2%n2z.nc4',
StateMet.format: 'CFIO',
StateMet.frequency: 010000
StateMet.duration: 010000
StateMet.mode: 'time-averaged'
StateMet.fields: 'Met_AD ', 'GIGCchem',
'Met_AIRDEN ', 'GIGCchem',
'Met_AIRVOL ', 'GIGCchem',
'Met_ALBD ', 'GIGCchem',
'Met_AREAM2 ', 'GIGCchem',
'Met_AVGW ', 'GIGCchem',
'Met_BXHEIGHT ', 'GIGCchem',
'Met_ChemGridLev ', 'GIGCchem',
'Met_CLDF ', 'GIGCchem',
'Met_CLDFRC ', 'GIGCchem',
'Met_CLDTOPS ', 'GIGCchem',
'Met_DELP ', 'GIGCchem',
'Met_DQRCU ', 'GIGCchem',
'Met_DQRLSAN ', 'GIGCchem',
'Met_DTRAIN ', 'GIGCchem',
'Met_EFLUX ', 'GIGCchem',
'Met_FRCLND ', 'GIGCchem',
'Met_FRLAKE ', 'GIGCchem',
'Met_FRLAND ', 'GIGCchem',
'Met_FRLANDIC ', 'GIGCchem',
'Met_FROCEAN ', 'GIGCchem',
'Met_FRSEAICE ', 'GIGCchem',
'Met_FRSNO ', 'GIGCchem',
'Met_GWETROOT ', 'GIGCchem',
'Met_GWETTOP ', 'GIGCchem',
'Met_HFLUX ', 'GIGCchem',
'Met_LAI ', 'GIGCchem',
'Met_LWI ', 'GIGCchem',
'Met_PARDR ', 'GIGCchem',
'Met_PARDF ', 'GIGCchem',
'Met_PBLTOPL ', 'GIGCchem',
'Met_PBLH ', 'GIGCchem',
'Met_PHIS ', 'GIGCchem',
'Met_PMID ', 'GIGCchem',
'Met_PMIDDRY ', 'GIGCchem',
'Met_PRECANV ', 'GIGCchem',
'Met_PRECCON ', 'GIGCchem',
'Met_PRECLSC ', 'GIGCchem',
'Met_PRECTOT ', 'GIGCchem',
'Met_PS1DRY ', 'GIGCchem',
'Met_PS1WET ', 'GIGCchem',
'Met_PS2DRY ', 'GIGCchem',
'Met_PS2WET ', 'GIGCchem',
'Met_PSC2WET ', 'GIGCchem',
'Met_PSC2DRY ', 'GIGCchem',
'Met_QI ', 'GIGCchem',
'Met_QL ', 'GIGCchem',
'Met_OMEGA ', 'GIGCchem',
'Met_OPTD ', 'GIGCchem',
'Met_REEVAPCN ', 'GIGCchem',
'Met_REEVAPLS ', 'GIGCchem',
'Met_SLP ', 'GIGCchem',
'Met_SNODP ', 'GIGCchem',
'Met_SNOMAS ', 'GIGCchem',
'Met_SPHU ', 'GIGCchem',
'Met_SPHU1 ', 'GIGCchem',
'Met_SPHU2 ', 'GIGCchem',
'Met_SUNCOS ', 'GIGCchem',
'Met_SUNCOSmid ', 'GIGCchem',
'Met_SWGDN ', 'GIGCchem',
'Met_T ', 'GIGCchem',
'Met_TAUCLI ', 'GIGCchem',
'Met_TAUCLW ', 'GIGCchem',
'Met_THETA ', 'GIGCchem',
'Met_TMPU1 ', 'GIGCchem',
'Met_TMPU2 ', 'GIGCchem',
'Met_TO3 ', 'GIGCchem',
'Met_TropHt ', 'GIGCchem',
'Met_TropLev ', 'GIGCchem',
'Met_TropP ', 'GIGCchem',
'Met_TS ', 'GIGCchem',
'Met_TSKIN ', 'GIGCchem',
'Met_TV ', 'GIGCchem',
'Met_U ', 'GIGCchem',
'Met_U10M ', 'GIGCchem',
'Met_USTAR ', 'GIGCchem',
'Met_UVALBEDO ', 'GIGCchem',
'Met_V ', 'GIGCchem',
'Met_V10M ', 'GIGCchem',
'Met_Z0 ', 'GIGCchem',
Loss of soluble species in cloud updrafts
- Loss due to convection (per wet deposited species)
WetLossConv.template: '%y4%m2%d2_%h2%n2z.nc4', WetLossConv.format: 'CFIO', WetLossConv.frequency: 010000 WetLossConv.duration: 010000 WetLossConv.mode: 'time-averaged' WetLossConv.fields: 'WetLossConv_?WET? ', 'GIGCchem',
Loss of soluble species in large-scale wet deposition
- Loss due to rainout and washout (per deposited species)
WetLossLS.template: '%y4%m2%d2_%h2%n2z.nc4', WetLossLS.format: 'CFIO', WetLossLS.frequency: 010000 WetLossLS.duration: 010000 WetLossLS.mode: 'time-averaged' WetLossLS.fields: 'WetLossLS_?WET? ', 'GIGCchem',