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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.
| Term | Explanation |
|---|---|
| SpeciesConc | Name of the first collection. A collection is a series of files that will be produced containing the same 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), frequency determines the interval at which data will be saved to disk. In this example, advected species concentration values will be written to the file
every 6 hours. |
| 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, | For GCHP simulations only: indicates the I/O library that will be used. This can be ignored for GEOS-Chem "Classic" simualations. |
| :: | 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. |
- The first collection is instantaneous (aka timeseries) output with a 6-hour frequency. A new file will be created every 24 hours.
- The second collection (ConcAfterChem) is time-averaged output. Data will be updated at the dynamic timestep (= 10 minutes for most GEOS-Chem simulations) by default and averaged into monthly-mean output. A new file will be created at the start of each new month.
- The diagnostic quantities (aka "fields") that will be archived in each collection are listed after the “fields” tag. These diagnostic quantities follow the naming convention described in the previous section.
- For GEOS-Chem “Classic” simulations, you may use wildcards to request a multiple quantities. For example, instead of listing SpeciesConc_NO, SpeciesConc_O3, SpeciesConc_PAN, SpeciesConc_CO, etc. individually, you can use SpeciesConc_?ADV? to request all of the advected GEOS_Chem species.
- The "GIGCchem" text is only relevant for GCHP and will be ignored for GEOS-Chem “Classic” simulations.
- The template setting sets the date and time format for each output file in the collection.
- The string %y4%m2%d2_%h2%n2z.nc4 will print YYYYMMDD_hhmmz.nc4 to the end of each netCDF filename, where YYYYMMDD is the date in year/month/day format and hhmm is the time in hour:minutes format.
- The z character denotes "Zulu", which is an abbreviation for UTC time.
- The :: signifies the end of the list of collections, as well as the end of each defined collection. The :: may be placed at any column in the HISTORY.rc file.
- The format setting only applies to GCHP simulations.
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',