GEOS–Chem v9–01–02 Online User's Guide
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6. Running the GEOS–Chem Model
6.1 Input File Checklists for GEOS–Chem Model Simulations
After you have completed the following steps:
you may start a GEOS–Chem simulation. The first thing you will want to do is to ensure that all of the input files in your run directory are set correctly for the type of GEOS–Chem simulation that you want to do. Here follows some convenient checklists that you may use as a guide before starting your model runs.
6.1.1 Checklist for NOx–Ox–Hydrocarbon–aerosol chemistry simulation with SMVGEAR or KPP
There are several options for the chemistry mechanism used for a NOx–Ox–Hydrocarbon–aerosol chemistry simulation: the standard mechanism, the secondary organic aerosol (SOA) mechanism, the the dicarbonyls mechanism, and the Caltech isoprene mechanism . Following is a quick check list of how various options should be set in the input.geos file for each of these options.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
Type of simulation : 3
Number of Tracers : 43And then list the tracer names, molecular weights, and constituent species as described in Chapter 5.2.1.2.
To run the SOA mechanism, increase the number of transported tracers to 59. A list of the tracer names can be found HERE.
To run the dicarbonyls mechanism, increase the number of transported tracers to 75. A list of the tracer names can be found HERE.
To run the Caltech isoprene mechanism, increase the number of transported tracers to 56. A list of the tracer names can be found HERE.
Aerosol Menu:
Online SULFATE AEROSOLS : T Online CRYST/AQ AEROSOLS: F Online CARBON AEROSOLS : T Online 2dy ORG AEROSOLS : F Online DUST AEROSOLS : T => Use DEAD emissions? : T Online SEASALT AEROSOLS : T => SALA radius bin [um]: 0.1 0.5 => SALC radius bin [um]: 0.5 4.0 Online dicarb. chem. : FIf you have included the SOA mechanism, you must switch the 4th entry:
Online 2dy ORG AEROSOLS : TIf you have included the dicarbonyls mechanism, you must switch the 4th and 11th entries:
Online 2dy ORG AEROSOLS : T Online dicarb. chem. : TAlso, if you turn off any of the other aerosol types (sulfate, carbon, dust, seasalt), then GEOS–Chem will read these from disk as monthly mean quantities instead of carrying them as transported tracers.
The crystalline sulfur and aqueous aerosols have not been implemented into GEOS–Chem at this point. They will be added into a future version.
Transport Menu:
Turn on Transport : T => Use Flux Correction?: F => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30 Use strat O3/NOy BC's : TSet the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution). Also you should not use FLUX correction since that is more computationally expensive.
You should also turn on the flux for O3 and NOy from the stratosphere.
Convection Menu:
Turn on Cloud Conv? : T Turn on PBL Mixing? : T => Use non-local PBL? : T Convect Timestep (min) : 30Set the convection timestep to the same value as the transport timestep.
Chemistry Menu:
Turn on Chemistry? : T Chemistry Timestep [min]: 60 Read and save CSPEC_FULL: T USE solver coded by KPP : FThe SMVGEAR II and KPP chemical solvers are computationally expensive. We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
We recommend that you turn on the reading and saving of CSPEC restart files by setting LSVCSPEC to T. If you are going to be splitting your GEOS–Chem simulation into several different stages (so that you can fit each stage into queue system time limits), then this will ensure that the chemical species concentrations (in the CSPEC array) will be preserved when then the next run stage begins.
You can switch from SMVGEAR II to any solver provided by KPP by turning LKPP to T. Note: Using Rosenbrock provided by KPP provides a better scalability of GEOS–Chem than using SMVGEAR II on several processors.
Deposition Menu:
Turn on Dry Deposition? : T Turn on Wet Deposition? : TDry deposition will be done on every chemistry timestep (typically 60 minutes). Wet deposition will be done on every transport timestep, which is typically 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1°). Therefore you do not have to list timesteps for these operations here.
Emissions Menu:
%%% EMISSIONS MENU %%% : Turn on emissions? : T Emiss timestep (min) : 60 Include anthro emiss? : T => Scale to (1985-2005): -1 => Use EMEP emissions? : T => Use BRAVO emissions?: T => Use EDGAR emissions?: T => Use STREETS emiss? : T => Use CAC emissions? : T => Use NEI2005 emiss? : T => Use RETRO emiss? : T Use EPA/NEI99 (anth+bf)?: F w/ ICARTT modif.? : F w/ VISTAS NOx emis? : F Include biofuel emiss? : T Include biogenic emiss? : T => Use MEGAN inventory?: T => Use PCEEA model? : F => Use MEGAN for MONO? : T => Isoprene scaling : 1 Include biomass emiss? : T => Seasonal biomass? : T => Scaled to TOMSAI? : F => Use GFED2 biomass? :--- => monthly GFED2? : F => 8-day GFED2? : F => 3-hr GFED2? : F => synoptic GFED2? : F => Use GFED3 biomass? :--- => monthly GFED3? : T => 8-day GFED3? : F => 3-hr GFED3? : F => synoptic GFED3? : F Individual NOx sources :--- => Use aircraft NOx? : T => Use lightning NOx? : T => Spat-seas constr?: T => Use soil NOx : T => Use fertilizer NOx : T NOx scaling : 1 Use ship SO2 emissions? :--- => global EDGAR ? : T => global ICOADS ? : T => EMEP over EUROPE ? : T => ship SO2 Corbett ? : F => ship SO2 Arctas ? : T Use COOKE BC/OC (N. Am.): F Use AVHRR-derived LAI? : F Use MODIS-derived LAI? : TFor a typical NOx–Ox–hydrocarbon–aerosol chemistry simulation simulation, you will want to turn on all of these different emission types, including the regional inventories (NEI05 for the USA, BRAVO for Mexico, STREETS for South-East Asia, EMEP for Europe).
Set the emission timestep to the same value as the chemistry timestep, which is suggested to be double the transport timestep. This is because emission rates are passed to SMVGEAR, which treats them as reactions with net production. So the emissions should be called at the same frequency as the chemistry.
Output Menu:
%%% OUTPUT MENU %%% : 123456789.123456789.123456789.1--1=ZERO+2=BPCH Schedule output for JAN : 3000000000000000000000000000000 Schedule output for FEB : 30000000000000000000000000000 Schedule output for MAR : 3000000000000000000000000000000 Schedule output for APR : 300000000000000000000000000000 Schedule output for MAY : 3000000000000000000000000000000 Schedule output for JUN : 300000000000000000000000000000 Schedule output for JUL : 3000000000000000000000000000000 Schedule output for AUG : 3000000000000000000000000000000 Schedule output for SEP : 300000000000000000000000000000 Schedule output for OCT : 3000000000000000000000000000000 Schedule output for NOV : 300000000000000000000000000000 Schedule output for DEC : 3000000000000000000000000000000Most of the time you will probably be interested in generating monthly mean diagnostic output. To do this, simply make sure that the first day of the each month has a "3" listed there.
For example, the above menu settings will direct GEOS–Chem to write the monthly-mean diagnostic output from January to disk at 0 GMT on February 1st, etc.
Diagnostic Menu:
Here is a list of some of the more important diagnostics that you can save out for a typical GEOS–Chem NOx–Ox–hydrocarbon–aerosol chemistry simulation. (NOTE: we are assuming a simulation with the 47-level "reduced" GEOS–5 or MERRA met fields. For GEOS–4 you can use "30" instead of " 47".)
%%% DIAGNOSTIC MENU %%% : Binary punch file name : ctm.bpch Diagnostic Entries ---> : L Tracers to print out for each diagnostic ... ND05: Sulfate prod/loss : 47 all ND06: Dust aer source : 1 all ND07: Carbon aer source : 47 all ND08: Seasalt aer source: 1 all ... ND11: Acetone sources : 47 all ... ND13: Sulfur sources : 47 all ...
ND21: Optical depths : 47 all ND22: J-Values : 47 1 7 8 20 99 => JV time range : 11 13 ND24: E/W transpt flx : 47 all ND25: N/S transpt flx : 47 all ND26: U/D transpt flx : 47 all ...
ND28: Biomass emissions : 1 1 4 5 9 10 11 18 19 20 21 26 30 34 35 ND29: CO sources : 1 all ... ND31: Surface pressure : 48 all ND32: NOx sources : 1 all ... ND34: Biofuel emissions : 1 1 4 5 9 10 11 18 19 20 21 ... ND36: Anthro emissions : 1 1 4 5 9 10 18 19 21 ...
ND38: Cld Conv scav loss: 47 all ND39: Wetdep scav loss : 47 7 8 20 24 26 27 28 29 30 31 32 34 35 36 37 38 39 40 41 42 43 ...
ND43: Chem OH,NO,HO2,NO2: 47 all ==> OH/HO2 time range : 0 24 ==> NO/NO2 time range : 10 14 ND44: Drydep flx/vel : 1 1 2 3 7 8 15 17 20 22 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 ND45: Tracer Conc's : 47 all ==> ND45 Time range : 0 24 ND46: Biogenic emissions: 1 all ... ND68: Airmass/Boxheight : 47 all ND69: Surface area : 1 allFor more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Prod & Loss Menu:
This diagnostic is not compatible with KPP. If LKPP and ND65 are both turned on, the run will stop with an error asking you to change at least one of the option.
%%% PROD & LOSS MENU %%%: Turn on P/L (ND65) diag?: T # of levels for ND65 : 47 Save O3 P/L (ND20)? : F Number of P/L families : 4 1st chemical family : POX: O3 NO2 2NO3 PAN PMN PPN HNO4 3N2O5 HNO3 2nd chemical family : LOX: O3 NO2 2NO3 PAN PMN PPN HNO4 3N2O5 HNO3 3rd chemical family : PCO: CO 4th chemical family : LCO: COWe recommend that you save the chemical production and loss of at least the Ox family tracer and CO tracer. You can denote which species constitute each family. It is possible to define additional tracers here.
If you also wish to archive the P(Ox) and L(Ox) rates for a future offline tagged Ox simulation, then you can set the SAVE O3 P/L (ND20)? switch to T and specify the number of levels to save to disk.
For more information about the Prod & Loss Menu, refer to Chapter 5.2.1.22.
Input files
Make sure you have properly set up the following input files:
- globchem.dat. (See Chapter 5.3.2)
- ratj.d. (See Chapter 5.4.1)
- jv_spec.dat. (See Chapter 5.4.3)
- mglob.dat (See Chapter 5.3.1).
Restart files:
You need need at least one restart file for all of the simulations. Make sure that the number of species in the restart file is equal to the number of tracers you want to run. For this you can use the gamap routine from the GAMAP package.
Also, for SOA and dicarbonyl simulations, you need a soaprod.YYYYMMDDhh restart file. Refer to Chapter 5.5.1 for more information.
6.1.2 Checklist for Radon–Lead–Beryllium simulation
Here is a quick checklist of how various options should be set in the input.geos file for a Radon–Lead–Beryllium simulation.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
Type of simulation : 1 Number of Tracers : 3 Tracer Entries -------> : TR# Name g/mole Tracer Members; () = emitted Tracer #1 : 1 Rn 222.0 Tracer #2 : 2 Pb 210.0 Tracer #3 : 3 Be7 7.0Specify each tracer and its molecular weight here.
Aerosol Menu:
The Radon–Lead–Beryllium simulation does not use any of the sulfate, carbon, etc. tracers, so you can set all of the switches in the Aerosol Menu section to F (false).
Transport Menu:
Turn on Transport : T => Use Flux Correction?: F => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30 Use strat O3/NOy BC's : FSet the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1°). Also you should not use FLUX correction since that is more computationally expensive.
You should also turn OFF the flux of O3 and NOy from the stratosphere, because we are not performing a simulation that includes O3 or NOy species.
Convection Menu:
Turn on Cloud Conv? : T Turn on PBL Mixing? : T => Use non-local PBL? : F Convect Timestep (min) : 30Set the convection timestep to the same value as the transport timestep. The non-local PBL scheme does not support the Radon–Lead–Beryllium simulation at the moment.
Chemistry Menu:
Turn on Chemistry? : T Chemistry Timestep [min]: 60We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). The other chemistry options do not have any effect on the Radon–Lead–Beryllium simulation, so you can set them all to F (false).
Deposition Menu:
Turn on Dry Deposition? : T Turn on Wet Deposition? : TDry deposition will be done on every chemistry timestep. Wet deposition will be done on every transport timestep. Therefore you do not have to list timesteps for these operations here.
Emissions Menu:
Turn on emissions? : T Emiss timestep (min) : 60Set the emission timestep to the same value as the chemistry timestep. The rest of the switches in the emissions menu will not have any affect on the Radon–Lead–Beryllium simulation, so you can set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
Here is a list of some of the more important diagnostics that you can save out for a typical GEOS–Chem Radon–Lead–Beryllium simulation. (Here we are assuming a 47–level GEOS-5 simulation.)
%%% DIAGNOSTIC MENU %%% : Binary punch file name : ctm.bpch Diagnostic Entries ---> : L Tracers to print out for each diagnostic ND01: Rn/Pb/Be source : 47 all ND02: Rn/Pb/Be decay : 47 all ... ND24: E/W transpt flx : 47 1 2 3 ND25: N/S transpt flx : 47 1 2 3 ND26: U/D transpt flx : 47 1 2 3 ... ND31: Surface pressure : 48 1 ... ND38: Cld Conv scav loss: 47 1 2 3 ND39: Wetdep scav loss : 47 1 2 3 ...
ND44: Drydep flx/vel : 1 all
ND45: Tracer Conc's : 47 all
--> ND45 Time range : 0 24
...
ND68: Airmass/Boxheight : 47 all
ND69: Surface area : 1 allFor more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
6.1.3 Checklist for Total Ox and Tagged Ox simulations
NOTE: The tagged Ox simulation will be updated in v9–01–03.
Here is a quick checklist of how various options should be set in the input.geos file for a typical tagged Ox simulation.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
If you wish to run the total Ox simulation, you need to carry 2 tracers: Total Ox and Stratospherically produced Ox. Specfify these in the Tracer Menu section as follows:
%%% TRACER MENU %%% : Type of simulation : 6 Number of Tracers : 2 Tracer Entries -------> : TR# Name g/mole Tracer Members; () = emitted Tracer #1 : 1 Ox 48.0 Tracer #2 : 2 OxStrt 48.0If you wish to run with all of the geographically-tagged Ox tracers, then your Tracer Menu should look like this:
%%% TRACER MENU %%% : Type of simulation : 6 Number of Tracers : 13 Tracer Entries -------> : TR# Name g/mole Tracer Members; () = emitted Tracer #1 : 1 Ox 48.0 Tracer #2 : 2 OxUT 48.0 Tracer #3 : 3 OxMT 48.0 Tracer #4 : 4 OxROW 48.0 Tracer #5 : 5 OxPacBL 48.0 Tracer #6 : 6 OxNABL 48.0 Tracer #7 : 7 OxAtlBL 48.0
Tracer #8 : 8 OxEurBL 48.0 Tracer #9 : 9 OxAfrBL 48.0 Tracer #10 : 10 OxAsBL 48.0 Tracer #11 : 11 OxStrat 48.0 Tracer #12 : 12 OxInit 48.0 Tracer #13 : 13 OxUSA 48.0
Aerosol Menu:
The tagged Ox simulation does not use any of the sulfate, carbon, etc. tracers, so you can set all of the switches in the Aerosol Menu section to F (false).
Transport Menu:
Turn on Transport : T => Use Flux Correction?: F => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30 Use strat O3/NOy BC's : TSet the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1°). Also you should not use flux correction since that is more computationally expensive.
You should also turn on the flux of O3 and NOy from the stratosphere. We need to account for Ox which is transported down from the stratosphere.
Convection Menu:
Turn on Cloud Conv? : T Turn on PBL Mixing? : T => Use non-local PBL? : F Convect Timestep (min) : 30Set the convection timestep to the same value as the transport timestep.
Chemistry Menu:
Turn on Chemistry? : T Chemistry Timestep [min]: 60We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). The other chemistry options do not have any effect on the tagged Ox simulation, so you can set them all to F (false).
Deposition Menu:
Turn on Dry Deposition? : T Turn on Wet Deposition? : FDry deposition will be done on every chemistry timestep. Wet deposition is not done for the tagged Ox simulation because Ox is not water-soluble.
Emissions Menu:
Turn on emissions? : T Emiss timestep (min) : 60Set the emission timestep to the same value as the chemistry timestep. The rest of the switches in the Emissions Menu will not have any affect on the tagged Ox simulation, so you can set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
Here is a list of some of the more important diagnostics that you can save out for a typical GEOS–Chem tagged Ox simulation. (Here we assume a 47-layer GEOS–5 simulation.)
%%% DIAGNOSTIC MENU %%% : Binary punch file name : ctm.bpch Diagnostic Entries ---> : L Tracers to print out for each diagnostic
...
ND24: E/W transpt flx : 47 all ND25: N/S transpt flx : 47 all ND26: U/D transpt flx : 47 all ... ND31: Surface pressure : 1 all ... ND36: Anthro emissions : 0 1 4 5 9 10 18 19 21 ... ND44: Drydep flx/vel : 1 all ND45: Tracer Conc's : 47 all ==> ND45 Time range : 0 24 ... ND68: Airmass/Boxheight : 47 all ND69: Surface area : 1 allFor more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Prod & Loss Menu:
IMPORTANT NOTE! The Total Ox and Tagged Ox simulations will not work unless you switch on the PROD & LOSS diagnostic! This will be fixed in v9–01–03.
For the Ox simulation, the number of production & loss families is TWICE the number of advected tracers. Therefore, if you are using the Total Ox simulation, you should have 4 prod & loss families:
%%% PROD & LOSS MENU %%%: Turn on P/L (ND65) diag?: T # of levels for ND65 : 38 Save O3 P/L (ND20)? : F Number of P/L families : 26 Prod/Loss Family #1 : POx: Ox Prod/Loss Family #2 : POxUT: OxStrt Prod/Loss Family #3 : LOx: Ox Prod/Loss Family #4 : LOxStrt: OxStrtIf, on the other hand, you are using the full tagged Ox simulation, then you should have 26 prod & loss families:
%%% PROD & LOSS MENU %%%: Turn on P/L (ND65) diag?: T # of levels for ND65 : 47 Save O3 P/L (ND20)? : F Number of P/L families : 26 Prod/Loss Family #1 : POx: Ox Prod/Loss Family #2 : POxUT: OxUT Prod/Loss Family #3 : POxMT: OxMt Prod/Loss Family #4 : POxROW: OxROW Prod/Loss Family #5 : POxPacBL: OxPacBL Prod/Loss Family #6 : POxNABL: OxNABL Prod/Loss Family #7 : POxAtlBL: OxAtlBL Prod/Loss Family #8 : POxEurBL: OxEurBL Prod/Loss Family #9 : POxAfrBL: OxAfrBL Prod/Loss Family #10 : POxAsBL: OxAsBL Prod/Loss Family #11 : POxStrat: OxStrat Prod/Loss Family #12 : POxInit: OxInit Prod/Loss Family #13 : POxUSA: OxUSA Prod/Loss Family #14 : LOx: Ox Prod/Loss Family #15 : LOxUT: OxUT Prod/Loss Family #16 : LOxMT: OxMt Prod/Loss Family #17 : LOxROW: OxROW Prod/Loss Family #18 : LOxPacBL: OxPacBL Prod/Loss Family #19 : LOxNABL: OxNABL Prod/Loss Family #20 : LOxAtlBL: OxAtlBL Prod/Loss Family #21 : LOxEurBL: OxEurBL Prod/Loss Family #22 : LOxAfrBL: OxAfrBL Prod/Loss Family #23 : LOxAsBL: OxAsBL Prod/Loss Family #24 : LOxStrat: OxStrat Prod/Loss Family #25 : LOxInit: OxInit Prod/Loss Family #26 : LOxUSA: OxUSAThe order of the production and loss families should be the same as for the advected tracers (i.e. total Ox first, then OxUT, then OxMT, etc).
If you are running GEOS–5 or MERRA simulation with 47 levels, then typically the P(Ox) and L(Ox) data will be saved on 38 levels. The number of levels for ND65 also determines the size of the arrays used in the Total Ox and Tagged Ox simulation. This is why we use specify 38 levels in the text above.
For more information about the Prod & Loss Menu, refer to Chapter 5.2.1.22.
6.1.4 Checklist for Tagged CO simulation
Here is a quick checklist of how various options should be set in the input.geos file for a typical tagged CO simulation.
NOTE: in current practice, the number of tagged CO tracers can vary widely depending on which geographical regions are of interest. The example below describes how to set up the input.geos file for the current "standard" 17 tagged CO tracer simulation.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
%%% TRACER MENU %%% : Type of simulation : 7 Number of Tracers : 17 Tracer Entries -------> : TR# Name g/mole Tracer Members; () = emitted Tracer #1 : 1 CO 28.0 (CO) Tracer #2 : 2 COus 28.0 Tracer #3 : 3 COeur 28.0 Tracer #4 : 4 COasia 28.0 Tracer #5 : 5 COoth 28.0 Tracer #6 : 6 CObbam 28.0 Tracer #7 : 7 CObbaf 28.0 Tracer #8 : 8 CObbas 28.0 Tracer #9 : 9 CObboc 28.0 Tracer #10 : 10 CObbeu 28.0 Tracer #11 : 11 CObbna 28.0 Tracer #12 : 12 COch4 28.0 Tracer #13 : 13 CObiof 28.0 Tracer #14 : 14 COisop 28.0 Tracer #15 : 15 COmono 28.0 Tracer #16 : 16 COmeoh 28.0 Tracer #17 : 17 COacet 28.0Note that the first tracer is total CO and is just named CO. The other tagged CO tracers are named accordingly to reflect which geographical region they are emitted from.
Aerosol Menu:
The tagged CO simulation does not use any of the sulfate, carbon, etc. tracers, so you can set all of the switches in the Aerosol Menu section to F (false).
Transport Menu:
Turn on Transport : T => Use Flux Correction?: F => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30 Use strat O3/NOy BC's : FSet the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1°). Also you should not use flux correction since that is more computationally expensive.
You should also turn OFF the flux of O3 and NOy from the stratosphere, because the tagged CO run has no need of these.
Convection Menu:
Turn on Cloud Conv? : T Turn on PBL Mixing? : T => Use non-local PBL? : T Convect Timestep (min) : 30Set the convection timestep to the same value as the transport timestep.
Chemistry Menu:
Turn on Chemistry? : T Chemistry Timestep [min]: 60We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). The other options in the Chemistry Menu do not have any effect on the tagged CO simulation, so you can set them all to F (false).
Deposition Menu:
Turn on Dry Deposition? : T Turn on Wet Deposition? : FCO will dry-deposit to the surface, so you must turn dry deposition on to account for this.
You can turn off wet deposition. CO is not water soluble.
Emissions Menu:
Turn on emissions? : T Emiss timestep (min) : 60Set the emission timestep to the same value as the chemistry timestep. The rest of the switches in the emissions menu will not have any affect on the tagged CO simulation, so you can set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
Here is a list of some of the more important diagnostics that you can save out for a typical GEOS–Chem tagged CO simulation. (Here we assume a 47-layer GEOS–5 simulation.)
%%% DIAGNOSTIC MENU %%% : Binary punch file name : ctm.bpch Diagnostic Entries ---> : L Tracers to print out for each diagnostic ND24: E/W transpt flx : 47 all ND25: N/S transpt flx : 47 all ND26: U/D transpt flx : 47 all ND28: Biomass emissions : 1 4 ND29: CO sources : 1 all ND31: Surface pressure : 48 all ND34: Biofuel emissions : 1 4 ND36: Anthro emissions : 0 4 ND45: Tracer Conc's : 47 all ==> ND45 Time range : 0 24 ND68: Airmass/Boxheight : 47 all ND69: Surface area : 1 allFor more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Prod & Loss Menu:
%%% PROD & LOSS MENU %%%: Turn on P/L (ND65) diag?: T # of levels for ND65 : 47 Save O3 P/L (ND20)? : F
Number of P/L families : 22 Prod/Loss Family #1 : LCO: CO Prod/Loss Family #2 : PCOus: COus Prod/Loss Family #3 : PCOeur: COeur Prod/Loss Family #4 : PCOasia: COasia Prod/Loss Family #5 : PCOoth: COoth Prod/Loss Family #6 : PCObbam: CObbam Prod/Loss Family #7 : PCObbaf: CObbaf Prod/Loss Family #8 : PCObbas: CObbas Prod/Loss Family #9 : PCObboc: CObboc Prod/Loss Family #10 : PCObbeu: CObbeuP Prod/Loss Family #11 : PCObbna: CObbna Prod/Loss Family #12 : PCOch4: COch4 Prod/Loss Family #13 : PCObiof: CObiof Prod/Loss Family #14 : PCOisop: COisop Prod/Loss Family #15 : PCOmono: COmono Prod/Loss Family #16 : PCOmeoh: COmeoh Prod/Loss Family #17 : PCOacet: COacet Prod/Loss Family #18 : PISOP: ISOP Prod/Loss Family #19 : PCH4: CH4 Prod/Loss Family #20 : PCH3OH: CH3OH Prod/Loss Family #21 : PMONO: MONO Prod/Loss Family #22 : PACET: ACETFor the tagged CO simulation, you must define the following production and loss families:
- Loss of total CO by OH (LCO)
- Production of each of the tagged CO tracers
- Production of CO from Isoprene (PISOP)
- Production of CO from CH4 (PCH4)
- Production of CO from methanol (PCH3OH)
- Production of CO from monoterpenes (PMONO)
- Production of CO from Acetone (PACET)
For more information about the Prod & Loss menu, see Chapter 5.2.1.22.
6.1.5 Checklist for H2–HD simulation
Here is a quick checklist of how various options should be set in the input.geos file for a typical H2 -HD simulation.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
%%% TRACER MENU %%% : Type of simulation : 13 Number of Tracers : 2 Tracer Entries -------> : TR# Name g/mole Tracer Members; () = emitted Tracer #1 : 1 H2 2.0 Tracer #2 : 2 HD 3.0Specify each tracer and its molecular weight here.
Aerosol Menu:
The H2-HD simulation does not use any of the sulfate, carbon, etc. tracers, so you can set all of the switches in the Aerosol Menu section to F (false).
Transport Menu:
Turn on Transport : T => Use Flux Correction?: F => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30 Use strat O3/NOy BC's : TSet the transport timestep should be 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1°). Also you should not use flux correction since that is more computationally expensive.
You should turn on the switch labeled Use Strat/NOy BC's. This will turn on the stratospheric boundary conditions for the H2-HD simulation.
Convection Menu:
Turn on Cloud Conv? : T Turn on PBL Mixing? : T => Use non-local PBL? : F Convect Timestep (min) : 30Set the convection timestep to the same value as the transport timestep. The H2–HD simulation is not supported by the non-local PBL scheme.
Chemistry Menu:
Turn on Chemistry? : T Chemistry Timestep [min]: 60We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). The other options in the Chemistry Menu do not have any effect on the H2-HD simulation, so you can set them all to F (false).
Deposition Menu:
Turn on Dry Deposition? : T Turn on Wet Deposition? : TDry deposition will be done on every chemistry timestep. Wet deposition will be done on every transport timestep. Therefore you do not have to list timesteps for these operations here.
Emissions Menu:
Turn on emissions? : T Emiss timestep (min) : 60Set the emission timestep to the same value as the chemistry timestep. The rest of the switches in the Emissions Menu will not have any affect on the H2-HD simulation, so you can set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
Here is a list of some of the more important diagnostics that you can save out for a typical GEOS–Chem H2-HD simulation. (Here we assume a GEOS–5 47-layer simulation.)
%%% DIAGNOSTIC MENU %%% : Binary punch file name : ctm.bpch Diagnostic Entries ---> : L Tracers to print out for each diagnostic ND10: H2 prod/loss/emiss: 47 all ND24: E/W transpt flx : 47 all ND25: N/S transpt flx : 47 all ND26: U/D transpt flx : 47 all ND28: Biomass emissions : 1 4 ND29: CO sources : 1 all ND31: Surface pressure : 48 all ND34: Biofuel emissions : 1 4 ND36: Anthro emissions : 0 4 ND45: Tracer Conc's : 47 all ==> ND45 Time range : 0 24 ND68: Airmass/Boxheight : 47 all ND69: Surface area : 1 allFor more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Prod & Loss Menu:
%%% PROD & LOSS MENU %%%: Turn on P/L (ND65) diag?: FFor the H2-HD simulation, production and loss of H2 and Deuterium are archived with the ND10 diagnostic.
For more information about the Prod & Loss menu, see Chapter 5.2.1.22.
6.1.6 Checklist for offline aerosol chemistry simulation
Here is a quick checklist of how various options should be set in the input.geos file for a offline aerosol simulation, including secondary organic aerosols.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
Type of simulation : 10 Number of Tracers : 29 Tracer Entries -------> : TR# Name g/mole Tracer Members; () = emitted Tracer #1 : 1 DMS 62.00 Tracer #2 : 2 SO2 64.00 Tracer #3 : 3 SO4 96.00 Tracer #4 : 4 MSA 96.00 Tracer #5 : 5 NH3 17.00 Tracer #6 : 6 NH4 18.00 Tracer #7 : 7 NIT 62.00 Tracer #8 : 8 H2O2 34.00 Tracer #9 : 9 BCPI 12.00 Tracer #10 : 10 OCPI 12.00 Tracer #11 : 11 BCPO 12.00 Tracer #12 : 12 OCPO 12.00 Tracer #13 : 13 ALPH 136.23 Tracer #14 : 14 LIMO 136.23 Tracer #15 : 15 ALCO 142.00 Tracer #16 : 16 SOG1 150.00 Tracer #17 : 17 SOG2 160.00
Tracer #18 : 18 SOG3 220.00 Tracer #19 : 19 SOG4 130.00 Tracer #20 : 20 SOA1 150.00 Tracer #21 : 21 SOA2 160.00 Tracer #22 : 22 SOA3 220.00 Tracer #23 : 23 SOA4 130.00 Tracer #24 : 24 DST1 29.00 Tracer #25 : 25 DST2 29.00 Tracer #26 : 26 DST3 29.00
Tracer #27 : 27 DST4 29.00 Tracer #28 : 28 SALA 36.00 Tracer #29 : 29 SALC 36.00The tracers above consist of sulfate, carbon, mineral dust, sea salt, and secondary organic aerosols. You do not have to use all 23 tracers; you may define any subset of these as you wish. You must also set the appropriate flags T or F in the Aerosol Menu (described below).
Aerosol Menu:
Online SULFATE AEROSOLS : T Online CRYST/AQ AEROSOLS: F Online CARBON AEROSOLS : T Online 2dy ORG AEROSOLS : T Online DUST AEROSOLS : T => Use DEAD emissions? : T Online SEASALT AEROSOLS : T => SALA radius bin [um]: 0.1 0.5 => SALC radius bin [um]: 0.5 4.0 Online dicarb. chem. : F
If you do NOT wish to include sulfate aerosols (DMS, SO2, SO4, MSA, NH3, NH4, NIT), then set the Online SULFATE AEROSOLS line to F (false). Also remove the lines for these tracers from the Tracer Menu above.
At this point, crystallline sulfur and aqueous aerosols have not been fully implemented into GEOS–Chem. Therefore for the time being, set ONLINE CRYST/AQ AEROSOLS to F (false).
If you do NOT wish to include carbonaceous aerosols (BCPI, BCPO, OCPI, OCPO), then set the Online CARBON AEROSOLS line to F (false). Also remove the lines for these tracers from the Tracer Menu above.
If you do NOT wish to include secondary organic aerosols (ALPH, LIMO, ALCO, SOG1, SOG2, SOG3, SOA4, SOA1, SOA2, SOA3, SOA4), then set the Online 2dy ORG AEROSOLS line to F (false). Also remove the lines for these tracers from the Tracer Menu above.
If you do NOT wish to include seasalt aerosols (SALA, SALC), then set the Online SEASALT AEROSOLS line to F (false). Also remove the lines for these tracers from the Tracer Menu above.
If you do not wish to include mineral dust aerosols (DST1, DST2, DST3, DST4), then set the Online DUST AEROSOLS line to F (false). Also remove the lines for these tracers from the Tracer Menu above.
NOTE: You may define the limits of the accumulation and coarse mode sea salt aerosol radius bins (in variables SALA_REDGE_um and SALC_REDGE_um) as you wish. However, the recommended values of 0.1–0.5 and 0.5–4 microns, respectively, were chosen in order to conform to the cross-sections and other optical settings as defined in the FAST–J input file jv_spec.dat. Therefore, unless you use the recommended values, you will not be able to archive aerosol optical depths for these aerosol types with the ND21, ND48, ND49, ND50, and ND51 diagnostics.
NOTE: The dicarbonyl chemistry is only implemented for fullchem simulations. So the Online dicarb. chem. line should be set to F.
Transport Menu:
Turn on Transport : T => Use Flux Correction?: F => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30 Use strat O3/NOy BC's : FSet the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1°). Also you should not use flux correction since that is more computationally expensive.
Turn OFF the flux of O3 and NOy from the stratosphere, since the offline aerosol simulation does not use these tracers.
Convection Menu:
Turn on Cloud Conv? : T Turn on PBL Mixing? : T => Use non-local PBL? : T Convect Timestep (min) : 30Set the convection timestep to the same value as the transport timestep.
Chemistry Menu:
Turn on Chemistry? : T Chemistry Timestep [min]: 60We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). The other chemistry options do not have any effect on the offline aerosols chemistry simulation, so you can set them all to F (false).
Deposition Menu:
Turn on Dry Deposition? : T Turn on Wet Deposition? : TDry deposition will be done on every chemistry timestep. Wet deposition will be done on every transport timestep. Therefore you do not have to list timesteps for these operations here.
Emissions Menu:
%%% EMISSIONS MENU %%% : Turn on emissions? : T Emiss timestep (min) : 60 Include anthro emiss? : T => Scale to (1985-2005): -1 => Use EMEP emissions? : T => Use BRAVO emissions?: T => Use EDGAR emissions?: T => Use STREETS emiss? : T => Use CAC emissions? : T => Use NEI2005 emiss? : T => Use RETRO emiss? : T Use EPA/NEI99 (anth+bf)?: F w/ ICARTT modif.? : F w/ VISTAS NOx emis? : F Include biofuel emiss? : T Include biogenic emiss? : T => Use MEGAN inventory?: T => Use PCEEA model? : F => Use MEGAN for MONO? : T => Isoprene scaling : 1 Include biomass emiss? : T => Seasonal biomass? : T => Scaled to TOMSAI? : F => Use GFED2 biomass? :--- => monthly GFED2? : F => 8-day GFED2? : F => 3-hr GFED2? : F => synoptic GFED2? : F => Use GFED3 biomass? :--- => monthly GFED3? : T => 8-day GFED3? : F => 3-hr GFED3? : F => synoptic GFED3? : F Individual NOx sources :--- => Use aircraft NOx? : T => Use lightning NOx? : T => Spat-seas constr?: T => Use soil NOx : T => Use fertilizer NOx : T NOx scaling : 1 Use ship SO2 emissions? :--- => global EDGAR ? : T => global ICOADS ? : T => EMEP over EUROPE ? : T => ship SO2 Corbett ? : F => ship SO2 Arctas ? : T Use COOKE BC/OC (N. Am.): F Use AVHRR-derived LAI? : F Use MODIS-derived LAI? : TSet the emission timestep to the same value as the chemistry timestep.
You will typically want to include anthropogenic, biomass, biogenic, and biofuel emissions for the aerosol tracers. You can turn off the sources of NOx emissions; these will have no effect on the aerosol simulation. You may also include SO2 emissions from ship exhaust.
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
Here is a list of some of the more important diagnostics that you can save out for a typical GEOS–Chem offline aerosol chemistry simulation. (Here we assume a GEOS–5 47-layer simulation.)%%% DIAGNOSTIC MENU %%% : Binary punch file name : ctm.bpch Diagnostic Entries ---> : L Tracers to print out for each diagnostic ... ND05: Sulfate prod/loss : 47 all ND06: Dust aer source : 1 all ND07: Carbon aer source : 47 all ND08: Seasalt aer source: 1 all ... ND13: Sulfur sources : 0 all ... ND21: Optical depths : 47 all ND22: J-Values : 47 all -- JV time range : 11 13 ND24: E/W transpt flx : 47 all ND25: N/S transpt flx : 47 all ND26: U/D transpt flx : 47 all ... ND28: Biomass emissions : 0 1 4 5 9 10 11 18 19 20 21 26 30 34 35 ... ND31: Surface pressure : 48 all ... ND34: Biofuel emissions : 0 1 4 5 9 10 11 18 19 20 21 ... ND36: Anthro emissions : 0 1 4 5 9 10 18 19 21 ... ND38: Cld Conv scav loss: 47 all ND39: Wetdep scav loss : 47 all ... ND44: Drydep flx/vel : 1 all ND45: Tracer Conc's : 47 all ==> ND45 Time range : 0 24 ND46: Biogenic emissions: 0 all ... ND68: Airmass/Boxheight : 47 all ND69: Surface area : 1 allFor more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Other files:
In order to use the aerosol and dust optical depth diagnostics (ND21, ND48, ND49, ND50, ND51), then GEOS–Chem must read in the chemistry mechanism and photolysis files.
Make sure you are using the proper globchem.dat and chemga.dat files. For more information, refer to Chapter 5.3.2 and Chapter 5.3.3.
Make sure that you have the proper ratj.d file. For more information, refer to Chapter 5.4.1.
Creating your own oxidant files for an offline aerosol simulation
Thanks to Eric Sofen (U. Washington) for compiling this information!
NOTE: this assumes a GEOS4 30-level simulation.
The JH2O2, PH2O2, O3, and NO3 bpch files must extend only up to the tropopause. When you extract the data from the bpch file that is produced by a full chemistry simulation, these files will be either 22 or 30 vertical levels and the tropopause extends up to 17 levels. Use the routine /gamap2/regridding/trop_cut.pro to remove these upper levels.
THNO3 is a full 30 levels, and consists of HNO3+NIT.
OH needs to be 55 levels. 22 levels will come from the full-chem simulation, then this gets paired with the stratospheric data from the current OH file in the data directories (e.g. .../data/GEOS_4x5/stratOH_200203/stratOH.geos4.4x5). This is done using IDL routine gamap2/regridding/merge_o3.pro. Bob said of this IDL code, "NOTE, this file is somewhat hardwired, be prepared to dive in & tinker w/ it accordingly."
You'll also need to modify the GEOS–Chem code so that it looks for your new oxidant files (or, I suppose, overwrite the existing ones). This requires making changes in sulfate_mod.F, global_no3_mod.F, and global_hno3_mod.F. The easiest way to change where the model looks for OH is in the input.geos file.
6.1.7 Checklist for Total Hg and Tagged Hg simulations
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
%%% TRACER MENU %%% : Type of simulation : 11 Number of Tracers : 21 Tracer Entries -------> : TR# Name g/mole Tracer Members; () = emitted Tracer #1 : 1 Hg0 201.0 Tracer #2 : 2 Hg2 201.0 Tracer #3 : 3 HgP 201.0 Tracer #4 : 4 Hg0_an_na 201.0 Tracer #5 : 5 Hg0_an_eu 201.0 Tracer #6 : 6 Hg0_an_as 201.0 Tracer #7 : 7 Hg0_an_rw 201.0 Tracer #8 : 8 Hg0_oc 201.0 Tracer #9 : 9 Hg0_ln 201.0 Tracer #10 : 10 Hg0_nt 201.0 Tracer #11 : 11 Hg2_an_na 201.0 Tracer #12 : 12 Hg2_an_eu 201.0 Tracer #13 : 13 Hg2_an_as 201.0 Tracer #14 : 14 Hg2_an_rw 201.0 Tracer #15 : 15 Hg2_oc 201.0 Tracer #16 : 16 Hg2_ln 201.0 Tracer #17 : 17 Hg2_nt 201.0 Tracer #18 : 18 HgP_an_na 201.0 Tracer #19 : 19 HgP_an_eu 201.0 Tracer #20 : 20 HgP_an_as 201.0 Tracer #21 : 21 HgP_an_rw 201.0Tracers 1-3 are global totals of Hg0, Hg2, HgP.
Tracers 4-21 are geographically tagged tracers of Hg0, Hg2, HgP. These are named accordingly to reflect which geographical region they are emitted from.
If you wish to set up a simulation with only the total Hg tracers, then:
- List Tracers 1-3 in the input.geos file
- Omit Tracers 4-21 from the input.geos file
- You also have the option to run with the Global Terrestrial Mercury Model option (if you have compiled GEOS–Chem with the GTMM_Hg C–preprocessor switch).
- For more information about the Global model, please refer to this document.
If you wish to set up a simulation with the tagged tracers, then
- Specify Tracers 1-21 in the input.geos file
- NOTE: The Global Terrestrial Mercury Model is not enabled for tagged simulation. GTMM can be used when running the total tracers only.
Aerosol Menu:
The tagged mercury simulation does not use any of the sulfate, carbon, etc. tracers, so you can set all of the switches in the Aeroosl Menu section to F (false).
Transport Menu:
Turn on Transport : T => Use Flux Correction?: F => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30 Use strat O3/NOy BC's : FSet the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1°). Also you should not use flux correction since that is more computationally expensive.
You should also turn OFF the flux of O3 and NOy from the stratosphere, because the mercury simulation does not have need of these.
Convection Menu:
Turn on Cloud Conv? : T Turn on PBL Mixing? : T => Use non-local PBL? : F Convect Timestep (min) : 30Set the convection timestep to the same value as the transport timestep.
Chemistry Menu:
Turn on Chemistry? : T Chemistry Timestep [min]: 60We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting).
Mercury Menu:
%%% MERCURY MENU %%% : Use anthro Hg emiss for : 2000 Error check tag/tot Hg? : F Use dynamic ocean Hg? : T Preindustrial sim? : F Ocean Hg restart file : ocean.totHg.YYYYMMDDhh Use GTMM soil model? : F GTMM Hg restart file : GTM.totHg.YYYYMMDDhhWhenever you use the dynamic ocean, you need to specify an ocean restart file.
For more information about the GTMM model, please refer to this document.
Deposition Menu:
Turn on Dry Deposition? : T Turn on Wet Deposition? : TDry deposition will be done on every chemistry timestep. Wet deposition will be done on every transport timestep. Therefore you do not have to list timesteps for these operations here.
Emissions Menu:
Turn on emissions? : T Emiss timestep (min) : 60Set the emission timestep to the same value as the chemistry timestep. The rest of the switches in the Emissions mMnu will not have any affect on the tagged mercury simulation, so you can set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
Here is a list of some of the more important diagnostics that you can save out for a typical GEOS–Chem tagged mercury simulation.
%%% DIAGNOSTIC MENU %%% : Binary punch file name : ctm.bpch Diagnostic Entries ---> : L Tracers to print out for each diagnostic ... ND03: Hg emissions, P/L : 47 all ... ND24: E/W transpt flx : 47 all ND25: N/S transpt flx : 47 all ND26: U/D transpt flx : 47 all ... ND31: Surface pressure : 48 all ... ND38: Cld Conv scav loss: 47 all ND39: Wetdep scav loss : 47 all ... ND44: Drydep flx/vel : 1 all ND45: Tracer Conc's : 47 all ==> ND45 Time range : 0 24 ... ND68: Airmass/Boxheight : 47 all ND69: Surface area : 1 allFor more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Prod & Loss Menu:
%%% PROD & LOSS MENU %%%: Turn on P/L (ND65) diag?: F # of levels for ND65 : 30 Save O3 P/L (ND20)? : F Number of P/L families : 0Production & loss of tagged mercury tracers are handled in the ND03 diagnostic, so you can turn off all the switches in the Prod & Loss Menu as shown above.
For more information about the Prod & Loss Menu, refer to Chapter 5.2.1.22.
6.1.8 Checklist for a CH4 offline simulation
Here is a quick checklist of how various options should be set in the input.geos file for a typical CH4 simulation.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
%%% TRACER MENU %%% : Type of simulation : 9 Number of Tracers : 12 Tracer Entries -------> : TR# Name g/mole Tracer Members; () = emitted Tracer #1 : 1 CH4_tot 16.0 CH4 Tracer #2 : 2 CH4_ga 16.0 CH4 Tracer #3 : 3 CH4_co 16.0 CH4 Tracer #4 : 4 CH4_ef 16.0 CH4 Tracer #5 : 5 CH4_wa 16.0 CH4 Tracer #6 : 6 CH4_bf 16.0 CH4 Tracer #7 : 7 CH4_ri 16.0 CH4 Tracer #8 : 8 CH4_oa 16.0 CH4 Tracer #9 : 9 CH4_bb 16.0 CH4 Tracer #10 : 10 CH4_wl 16.0 CH4 Tracer #11 : 11 CH4_sa 16.0 CH4 Tracer #12 : 12 CH4_on 16.0 CH4Tracers 1 is global total of CH4. Tracers 2-12 are tagged tracers for each type of emission and are named accordingly.
It is also possible to run a simulation with just the global total tracer CH4_tot.
Aerosol Menu:
The CH4 simulation does not use any of the sulfate, carbon, etc. tracers, so you can set all of the switches in the Aerosol Menu section to F (false).
Transport Menu:
Turn on Transport : T => Use Flux Correction?: F => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30 Use strat O3/NOy BC's : FSet the timestep should be 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1°). Also you should not select the flux correction option since this option is more computationally expensive.
The stratospheric flux boundary conditions can be turned off, because the CH4 simulation has no need of these.
Convection Menu:
Turn on Cloud Conv? : T Turn on PBL Mixing? : T => Use non-local PBL? : F Convect Timestep (min) : 30The convection timestep should be the same as the transport timestep.
Chemistry Menu:
Turn on Chemistry? : T Chemistry Timestep [min]: 1440The chemistry timestep for methane must be 1440 min (24 hours). The first chemistry calculation occurs at the beginning of the second day of the run. Other chemistry options have no effect on the methane simulation, so you can set them all to F (false).
It is recommended to turn KPP off (F) to save memory.
Methane Menu:
Compute CH4 budget? : F Use Gas & Oil emis? : T Use Coal Mine emis? : T Use Livestock emis? : T Use Waste emis? : T Use Biofuel emis? : T Use Rice emis? : T Use Ot. Anthro emis? : T Use Biomass emis? : T Use Wetlands emis? : T Use Soil Absorption? : T Use Ot. Natural emis? : TThis menu allows you to turn on/off the individual emission categories for CH4. The CH4 budget computation is thought to be unreliable. If you want to use it anyway, it only works for full month simulations (i.e. you have to start the simulation on the first day of a month and end on a last day of a month).
Deposition Menu:
Turn on Dry Deposition? : F Turn on Wet Deposition? : FMethane is not subject to deposition, so you can turn these off.
Emissions Menu:
Turn on emissions? : T Emiss timestep (min) : 60We recommend that you set the emissions timestep to double the transport timestep (this is known as Strang operator splitting). The rest of the switches in the emissions menu will not have any effect on the tagged methane simulation, so you can set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
Here is a list of more important diagnostics that you can save to output for a typical GEOS–Chem methane simulation.
%%% DIAGNOSTIC MENU %%% : Binary punch file name : ctm.bpch Diagnostic Entries ---> : L Tracers to print out for each diagnostic ... ND19: CH4 loss : 47 all ... ND24: E/W transpt flx : 47 all ND25: N/S transpt flx : 47 all ND26: U/D transpt flx : 47 all ... ND31: Surface pressure : 48 all ... ND45: Tracer Conc's : 47 all ==> ND45 Time range : 0 24 ... ND58: CH4 Emissions : 1 all ND60: Wetland Fraction : 1 all ND68: Airmass/Boxheight : 47 all ND69: Surface area : 1 allFor more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Prod & Loss Menu:
%%% PROD & LOSS MENU %%%: Turn on P/L (ND65) diag?: F # of levels for ND65 : 30 Save O3 P/L (ND20)? : F Number of P/L families : 0Loss of methane tracers are handled in the ND19 diagnostic, so you can turn off all the switches in the Prod & Loss Menu as shown above.
For more information about the Prod & Loss Menu, refer to Chapter 5.2.1.22.
6.1.9 Checklist for Total CO2 and Tagged CO2 simulations
Here is a quick checklist of how various options should be set in the input.geos file for a typical CO2 simulation.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
%%% TRACER MENU %%% : Type of simulation : 12 Number of Tracers : 1 Tracer Entries ------- : TR# Name g/mole Tracer Members; () = emitted Tracer #1 : 1 CO2 44.0More source tracers can be used if desired for example in the alternate selection, where emission from 1) Total CO2; 2) Fossil Fuel (land) and cement manufacture, 3) Ocean exchange, 4) Balanced Biosphere; 5) Biomass Burning Emissions; 6) Biofuel Burning Emissions; 7) Net Terrestrial Exchange; 8) Ship Emissions; 9) Aviation Emissions; 10) Chemical Source; 11) Chemical Source surface correction. NOTE: If the restart file and input.geos do not have the same number of tracers, the run will crash before completion.
Type of simulation : 12 Number of Tracers : 10 Tracer Entries -------> : TR# Name g/mole Tracer Members; () = emitted Tracer #1 : 1 CO2 44.0 Tracer #2 : 2 CO2 44.0 Tracer #3 : 3 CO2 44.0 Tracer #4 : 4 CO2 44.0 Tracer #5 : 5 CO2 44.0 Tracer #6 : 6 CO2 44.0 Tracer #7 : 7 CO2 44.0 Tracer #8 : 8 CO2 44.0 Tracer #9 : 9 CO2 44.0 Tracer #10 : 10 CO2 44.0 Tracer #11 : 11 CO2 44.0Configuration for a full tagged-CO2 run is shown below (appropriate selections at the end of the CO2 menu are also required). Tracers 1-11 are as above. Tracer 12 is the background including only Fossil Fuel CO2. Tracers 13-52 are for 40 geographical regions, tracer 53 is shipping and tracer 54 is aviation. Remember, if the restart file and input.geos do not have the same number of tracers, the run will crash before completion.
Type of simulation : 12 Number of Tracers : 52 Tracer Entries -------> : TR# Name g/mole Tracer Members; () = emitted Tracer #1 : 1 CO2 44.0 Tracer #2 : 2 CO2 44.0 .. Tracer #53 : 53 CO2 44.0 Tracer #54 : 54 CO2 44.0
Transport Menu:
Turn on Transport : T => Use Flux Correction?: F => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 15 Use strat O3/NOy BC's : FSe the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1°). Also you should not use flux correction since that is more computationally expensive.
Convection Menu:
Turn on Cloud Conv? : T Turn on PBL Mixing? : T Convect Timestep (min) : 15Set the convection timestep to the same value as the transport timestep.
Chemistry Menu:
Turn on Chemistry? : T Chemistry Timestep [min]: 30We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). The rest of the switches in the Chemistry Menu will not have any effect on the CO2 simulation, so you can set them all to F (false).
Emissions Menu:
Turn on emissions? : T Emiss timestep (min) : 30Set the emission timestep to the same value as the chemistry timestep.
Only the GFED switches in the Emissions Menu can affect the simulation. They must be consistent with the choice made in the CO2 Menu for the sake of redundancy. The rest of the switches in the Emissions Menu will not have any affect on the CO2 simulation, so you can set them all to F (false).
CO2 Menu:
%%% CO2 SIM MENU %%% : Fossil Fuel Emissions :--- Generic FF emissions : F Annual FF emissions : F Monthly FF emissions : T 3-D Chemical Oxid Source: F Biomass Burn emissions :--- Seasonal only biomass : F GFED2 monthly biomass : F GFED2 8-day biomass : T GFED3 monthly biomass : F GFED3 8-day biomass : F Biofuel emissions : T Terrestrial Exchange :--- CASA daily avg NEP : F CASA diurnal cycle NEP: T Net Ter Ex original : F Net Ter Ex climatology: T Ocean Exchange :--- Takahashi 1997 : F Takahashi 2009 annual : F Takahashi 2009 monthly: T Ship & Plane Emissions :--- EDGAR ship emissions : F ICOADS ship emissions : T Aviation emissions 3-D: T Tagged CO2 runs :--- Save Fossil CO2 Bkgrd : F Tag Bios/Ocean CO2 reg: F Tag Land FF CO2 reg : F Tag Global Ship CO2 : F Tag Global Plane CO2 : FThe above CO2 menu configuration is the default for a single tracer run. Other options like the chemical source can be selected by the user.
The tagged tracer options have not been selected. A standard tagged tracer configuration is available in the code for 2° x 2.5° simulations but this can be customized by the user or set up for other resolutions by modification of the code and the Regions_land.dat and Regions_ocean.dat files, which reside in the CO2 run directory.
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
The only diagnostic here which is unique to the CO2 simulation is ND04, the CO2. Sources 1-7, and 10 are 2-D (surface level) and sources 8-10 are 3-D with all model levels.
%%% DIAGNOSTIC MENU %%% :
ND04: CO2 Sources : 1 1 2 3 4 5 6 7 8 9 10For more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
6.2 Running a Regular GEOS–Chem Job
The following section describes how to run the GEOS–Chem model for either the LSF, PBS or SGE batch queue systems.
Also, it is STRONGLY RECOMMENDED to test your simulation with a short (1-day or 2-day) run before submitting a very long-term GEOS–Chem simulation. A shorter run will make it easier to detect errors or problems without tying up precious computer time.
6.2.1 Interactive jobs (no queue system)
The most basic way to run GEOS–Chem is to type the executable name at the shell prompt (do not do it, keep reading):
geos
However default outputs are printed to the screen! So you will need to redirect outputs to files. For example, a typical Linux (bash) redirection would be:
geos 1>gc.log 2>gc.error &
The & is for the code to run in the background. The 1 (standard output) and 2 (error output) can be combined in the same file:
geos 1>gc.log 2>&1
or
geos >& gc.log
Double check the syntax, it depends on your shell (see here for a more detailed discussion about redirection). This is basically it. You will have a log file that will help understanding what went wrong.
If your platform uses the LSF batch queue system, you can use the following commands to submit, delete, and check the status of GEOS–Chem jobs:
bman # prints LSF man pages to stdout
bsub or submit # submit a batch jobs to a queue
bkill # kill batch jobs
bjobs # Lists all jobs currently running
bqueues # Lists available batch queues
bhist # shows history list of submitted jobs
lsload # shows % of each machine's resources that
# is currently utilized
Perhaps the best way to submit batch jobs to the queues is to write a simple job script, such as:
#!/bin/tcsh -f # Script definition line
cd /scratch/bmy/run.v8–03–01 # cd to your run dir
rm -f log # clear pre-existing log files
time geos > log # time job; pipe output to log file
exit(0) # exit normally
and then save that to a file named job. To submit the job script to the queue system, pick a queue in which to run the GEOS–Chem, and type:
bsub -q queue-name job
at the Unix prompt. You can check the status of the run by looking at the log file. LSF should also email you when your job is done, or if for any reason it dies prematurely.
If your platform uses the PBS batch queue system, you can use the following commands to submit, delete, and check the status of GEOS–Chem jobs:
qsub # submits a PBS job
qstat -Q # list all available batch queues
qstat -a @machine # list all PBS jobs that are running on 'machine'
qstat -f jobid # list information about PBS Job jobid
qdel jobid # Kills PBS Job jobid
xpbs # Graphical user interface for PB
Then create a simple GEOS–Chem job script (named job), similar to the above example for LSF:
#!/bin/tcsh -f # Script definition line
cd run.v8–03–01 # cd to your run dir
rm -f log # clear pre-existing log files
time geos > log # time job; pipe output to log file
exit(0) # exit normally
and then submit this with the qsub command:
qsub -q queue-name -o output-file-name job
at the Unix prompt.
The job status command qstat -f jobid sometimes provides a little too much information. Bob Yantosca has written a script called pbstat (this is already installed at Harvard) which condenses the output you get from qstat -f jobid. If you type pbstat at the Unix prompt, you will output similar to:
-------------------------------------------------------- PBS Job ID number : 10929.sol Job owner : pip@sol Job name : run.sh Job started on : Sun Aug 10 17:22:21 2003 Job status : Running PBS queue and server : q4x64 on amalthea Job is running on : hera/0*4 (R12K processors) # of CPUs being used : 4 (max allowed is 4) CPU utilization : 394% (ideal max is 400%) Elapsed walltime : 22:14:43 (max allowed is 64:00:00) Elapsed CPU time : 76:20:40 Memory usage : 10475844kb (max allowed is 1700Mb) VMemory usage : 8244704kb
This allows you to obtain information about your run much more easily. If you type pbstat all, you will obtain information about every job which is running. If you type pbstat userid, then you will get information about all of the jobs that user userid is running.
If your platform uses the SGE batch queue system, you can use the following commands to submit, delete, and check the status of GEOS–Chem jobs:
qsub # submits a PBS job
qconf -spl # list all available batch queues
qstat -f # list execution queues and shows the status
# of all your jobs on the current cluster
qstat -f -j jobid # list information about SGE Job jobid
qdel jobid # Kills PBS Job jobid
qmon # Graphical user interface for PB
Then create a simple GEOS–Chem job script (named job), similar to the above example for PBS:
#!/bin/tcsh -f # Script definition line cd run.v8–03–01 # cd to your run dir rm -f log # clear pre-existing log files time geos > log # time job; pipe output to log file exit(0) # exit normally
and then submit this with the qsub command:
qsub -pe queue-name NCPUs -o output-file-name job
at the Unix prompt.
Here we shall provide some general information on GEOS–Chem errors. For more up-to-date information about specific GEOS–Chem errors and their solutions, please be sure to consult the following resources:
6.3.1 I/O (input/output) errors
Almost all of the GEOS–Chem code supports I/O error trapping. In other words, if an error occurs while reading from a file or writing to a file, the run will stop and an appropriate error message will be displayed. Many of the error messages have the following format:
===============================================================
I/O Error Number 4001 in file unit 10
Encountered in routine read_bpch2:3
===============================================================
This means that an error (#4001) has occurred while reading from logical file unit 10. The routine where the error occurred is routine READ_BPCH2 (which happens to belong to bpch2_mod.F). The string read_bpch2:3 indicates that the third error trap within READ_BPCH2 was where the error occurred. If you grep for the string read_bpch2:3 in bpch2_mod.F, you will be taken to the offending line of code.
In general, Fortran I/O errors fall into 3 classes:
| Error number | Meaning |
|---|---|
| Greater than 0 | An I/O error has occurred. Something went wrong during reading or writing. |
| Equal to 0 | The file was read or written normally. No I/O error has occurred. |
| Less than 0 | The end-of-file was reached normally. |
For Fortran I/O errors greater than zero, the error numbers may be used to deduce the nature of the error. For example, if you compile GEOS–Chem with the Intel Fortran Compiler, the code will die with error #29 if it tries to read a file that is not on disk (i.e. a "file-not-found" error). However, if you compile GEOS–Chem with the a different compiler, then the same "file-not-found" error will cause the code to die with a different error number. The number that corresponds to each error depends on the compiler that you are using. Therefore, you should check your compiler documentation for a list of the error codes.
Also be sure to visit the GEOS–Chem wiki for the latest information about bugs and fixes!
Other kind of errors may occur. For a more detailled discussion about catching and debugging them, visit the GEOS–Chem Debugging page.