Sandbox
Contents
- 1 feel free to experiment here
- 2 Overview
- 3 Collection list
- 4 Species concentrations
- 5 Aerosol diagnostics
- 6 Cloud convective flux
- 7 Concentrations after chemistry
- 8 Dry deposition diagnostics
- 9 Photolysis diagnostics
- 10 Diagnostics on level edges
- 11 Production and loss rates
- 12 Fields of the State_Chm object
- 13 Fields of the State_Met object
- 14 Loss of soluble species in cloud updrafts
- 15 Loss of soluble species in large-scale wet deposition
feel free to experiment here
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 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.
|
:: | 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',