GEOS–Chem v9–02 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 can finally run GEOS–Chem. But first doublecheck that you have customized the input files in your run directory for the simulation that you wish to perform. We provide below some convenient checklists that you can follow..
6.1.1 Checklist for NOx–Ox–Hydrocarbon–aerosol chemistry simulation with SMVGEAR or KPP
You have several chemistry mechanism options for the NOx–Ox–Hydrocarbon–aerosol (a.k.a. "full-chemistry") simulation:
We present a checklist of how to select options for each of these mechanisms in your input.geos file.
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 : 66And then list the tracer names, molecular weights, and constituent species as described in the Tracer Menu section of Chapter 5.
To run the SOA mechanism, increase the number of transported tracers to 93 (or 100 if using the semivolatile POA option). A list of the tracer names can be found HERE.
To run the dicarbonyls mechanism, increase the number of transported tracers to 107. 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 => Semivolatile POA? : F => NAP emiss (TgC/yr) : 1.0 => POA emission scale : 1.27 Online DUST AEROSOLS : T => Use DEAD emissions? : T Online SEASALT AEROSOLS : T => SALA radius bin [um]: 0.01 0.5 => SALC radius bin [um]: 0.5 8.0 Online dicarb. chem. : FIf you have included the SOA mechanism, you must toggle the 4th entry:
Online 2dy ORG AEROSOLS : TIf you want to use the semivolatile POA option in the SOA mechanism, you must toggle the following entry:
=> Semivolatile POA? : TIf you have included the dicarbonyls mechanism, you must toggle the 4th and 11th entries:
Online 2dy ORG AEROSOLS : T Online dicarb. chem. : TIf you switch the other aerosol types (sulfate, carbon, dust, seasalt) to to F (false), GEOS–Chem will attempt to read these from disk as monthly-mean quantities. NOTE: These offline aerosol fields may not be archived for the GEOS–5 / MERRA / GEOS–FP vertical grids.
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 => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution).
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.
Select the non-local PBL mixing option, which performs the boundary layer mixing more accurately.
Chemistry Menu:
Turn on Chemistry? : T Use linear. strat. chem?: T => Use Linoz for O3? : T Chemistry Timestep [min]: 60 Read and save CSPEC_FULL: T => CSPEC rst filename? : restart.cspec.YYYYMMDDhh USE solver coded by KPP : F Gamma HO2 : 0.2We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
Select the linear stratospheric chemistry option. We also recommend choosing the Linoz stratospheric ozone chemistry option as well. If you turn off Linoz, then GEOS–Chem will revert to using Synoz (synthetic stratospheric ozone algorithm) instead.
We recommend that you generate chemical species restart files by setting Read and save CSPEC_FULL to T (true). You may have to split your GEOS–Chem simulation into several stages in order to fit within the time limits imposed by your batch queuing system. Turning this option on will preserve the chemical species concentrations (stored in the CSPEC array) for the start of the next run stage.
You can switch from SMVGEAR II to KPP by toggling the USE solver coded by KPP option to T (true). If you use KPP, pick the Rosenbrock solver option. The Rosenbrock solver scales better than the SMVGEAR II solver.
Deposition Menu:
Turn on Dry Deposition? : T Turn on Wet Deposition? : TDry deposition occurs on every chemistry timestep (typically 60 minutes). Wet deposition takes place on every transport timestep (see above).
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 AEIC emissions? : T Use RCP emiss (anth+bf)?: F => RCP scenario? : RCP60 => RCP year? : 2000 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 => daily GFED3? : F => 3-hr GFED3? : F Individual NOx sources :--- => Use RCP aircraft NOx: F => Use lightning NOx? : T => Spat-seas constr?: T => Use soil NOx : T => soilNOx rst file?: restart.soilnox.YYYYMMDDhh => Use fertilizer NOx : T NOx scaling : 1 Use ship SO2 emissions? :--- => global EDGAR ? : T => global ICOADS ? : T => global RCP ? : F => EMEP over EUROPE ? : T => ship SO2 Corbett ? : F => ship SO2 Arctas ? : T Use COOKE BC/OC (N. Am.): F Use historical emiss? : F => What decade? : 2000 Bromine switches :--- => Use Warwick VSLS? : T => Use seasalt Br2? : T => 1ppt MBL BRO Sim.? : F => Bromine scaling : 1You 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). See the Emissions Menu section of Chapter 5 for a detailed description of each of these options.
Set the emission timestep to the same value as the chemistry timestep. The chemistry solver treats emissions as reactions having net production; therefore, emissions must be done as often as 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 : 3000000000000000000000000000000Place a 3 in the column corresponding to the months and days for which you want output.
Most of the time you will want to generate 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:
We list below the most important diagnostics for the full-chemistry simulation. We assume GEOS–5 meteorology with the "reduced" grid (47 vertical levels).
%%% 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 64 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 2 4 5 7 9 10 11 18 19 20 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 ND44: Drydep flx/vel : 1 2 3 7 8 9 11 13 14 15 16 17 20 22 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 47 48 50 55 57 58 59 60 61 62 63 64 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 these options, please see the Diagnostic Menu section of Chapter 5.
Prod & Loss Menu:
At present, you can only use this diagnostic with the SMVGEAR II solver. If you turn on this diagnostic while using the KPP solver, you will receive an error message asking you to change the settings in input.geos. We are looking to implement this diagnostic into KPP, so stay tuned!
%%% 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 : 7 1st chemical family : POX: O3 NO2 2NO3 PAN PMN PPN HNO4 3N2O5 HNO3 BrO HOBr BrNO2 2BrNO3 MPN 2nd chemical family : LOX: O3 NO2 2NO3 PAN PMN PPN HNO4 3N2O5 HNO3 BrO HOBr BrNO2 2BrNO3 MPN 3rd chemical family : PCO: CO 4th chemical family : LCO: CO 5th chemical family : PBrOx: Br BrO 6th chemical family : PBry: 2Br2 Br BrO HOBr HBr BrNO2 BrNO3 7th chemical family : LBry: 2Br2 Br BrO HOBr HBr BrNO2 BrNO3You should save the chemical production and loss of at least the Ox family tracer and CO tracer. List the constituent species of each family.
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 these options, please see the Prod & Loss Menu section of Chapter 5.
Input files
Make sure you have properly modified these input files. Most of the time these will be preset for the particular mechanism you are using.
Restart files:
For each full-chemistry simulation, you need at least the tracer restart file and the soil NOx restart file. We also recommend saving out the chemical species restart file as well (refer to the Chemistry Menu section above). If there is no CSPEC file available at the start of a simulation, GEOS–Chem will use background values from globchem.dat. Use the gamap routine from the GAMAP package to check the integrity of your restart file before starting a simulation.
6.1.2 Checklist for Radon–Lead–Beryllium simulation
We present a checklist of how to customize input.geos for the 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 in this menu.
Aerosol Menu:
None of the options in this menu affect the Radon-Lead-Beryllium simulation, so set these to F (false).
Transport Menu:
Turn on Transport : T => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution).
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 Use linear. strat. chem?: F => Use Linoz for O3? : F Chemistry Timestep [min]: 60 Read and save CSPEC_FULL: F => CSPEC rst filename? : none USE solver coded by KPP : F Gamma HO2 : 0.2We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
The other chemistry options do not affect the Radon–Lead–Beryllium simulation, so set them all to F (false).
Deposition Menu:
Turn on Dry Deposition? : T Turn on Wet Deposition? : TDry deposition occurs on every chemistry timestep. Wet deposition takes place on every transport timestep.
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 do not affect the Radon–Lead–Beryllium simulation, so set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above.
Diagnostic Menu:
We list below the most important diagnostics for the Radon-Lead-Beryllium simulation. We assume GEOS–5 meteorology with the "reduced" grid (47 vertical levels).
%%% 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 these options, please see the Diagnostic Menu section of Chapter 5.
6.1.3 Checklist for Total Ox and Tagged Ox simulations
We present a checklist of how to customize input.geos for the Tagged Ox simulation. NOTE: We will update this simulation in a future model version.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
You need to carry 2 tracers to run the total Ox simulation: Total O3 and Stratospherically produced O3. 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 O3 48.0 Tracer #2 : 2 O3Strt 48.0You may also specify geographically-tagged tracers:
%%% TRACER MENU %%% : Type of simulation : 6 Number of Tracers : 13 Tracer Entries -------> : TR# Name g/mole Tracer Members; () = emitted Tracer #1 : 1 O3 48.0 Tracer #2 : 2 O3UT 48.0 Tracer #3 : 3 O3MT 48.0 Tracer #4 : 4 O3ROW 48.0 Tracer #5 : 5 O3PacBL 48.0 Tracer #6 : 6 O3NABL 48.0 Tracer #7 : 7 O3AtlBL 48.0 Tracer #8 : 8 O3EurBL 48.0 Tracer #9 : 9 O3AfrBL 48.0 Tracer #10 : 10 O3AsBL 48.0 Tracer #11 : 11 O3Strat 48.0 Tracer #12 : 12 O3Init 48.0 Tracer #13 : 13 O3USA 48.0
Aerosol Menu:
None of the options in this menu affect the tagged Ox simulation. Set all of these to F (false).
Transport Menu:
Turn on Transport : T => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution).
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.
At present you cannot use the non-local PBL mixing scheme with the tagged Ox simulation. We are working to correct this.
Chemistry Menu:
Turn on Chemistry? : T Use linear. strat. chem?: T => Use Linoz for O3? : T Chemistry Timestep [min]: 60 Read and save CSPEC_FULL: F => CSPEC rst filename? : none USE solver coded by KPP : F Gamma HO2 : 0.2We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
Select the linear stratospheric chemistry and Linoz stratospheric ozone chemistry options. These will ensure that the stratospheric ozone gets computed correctly.
The other chemistry options do not have any effect on the tagged Ox simulation, so 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 do not affect the tagged Ox simulation, so set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above.
Diagnostic Menu:
We list below the most important diagnostics for the Tagged Ox simulation. We assume GEOS–5 meteorology with the "reduced" grid (47 vertical levels).
%%% 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 these options, please see the Diagnostic Menu section of Chapter 5.
Prod & Loss Menu:
IMPORTANT NOTE! For GEOS–Chem v9–02 and earlier versions, the Total Ox and Tagged Ox simulations will not work unless you switch on the PROD & LOSS diagnostic! We shall correct this issue in a future model version.
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: O3 Prod/Loss Family #2 : POxUT: O3Strt Prod/Loss Family #3 : LOx: O3 Prod/Loss Family #4 : LOxStrt: O3StrtIf, 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 : PO3: O3 Prod/Loss Family #2 : PO3UT: O3UT Prod/Loss Family #3 : PO3MT: O3Mt Prod/Loss Family #4 : PO3ROW: O3ROW Prod/Loss Family #5 : PO3PacBL: O3PacBL Prod/Loss Family #6 : PO3NABL: O3NABL Prod/Loss Family #7 : PO3AtlBL: O3AtlBL Prod/Loss Family #8 : PO3EurBL: O3EurBL Prod/Loss Family #9 : PO3AfrBL: O3AfrBL Prod/Loss Family #10 : PO3AsBL: O3AsBL Prod/Loss Family #11 : PO3Strat: O3Strat Prod/Loss Family #12 : PO3Init: O3Init Prod/Loss Family #13 : PO3USA: O3USA Prod/Loss Family #14 : LO3: O3 Prod/Loss Family #15 : LO3UT: O3UT Prod/Loss Family #16 : LO3MT: O3Mt Prod/Loss Family #17 : LO3ROW: O3ROW Prod/Loss Family #18 : LO3PacBL: O3PacBL Prod/Loss Family #19 : LO3NABL: O3NABL Prod/Loss Family #20 : LO3AtlBL: O3AtlBL Prod/Loss Family #21 : LO3EurBL: O3EurBL Prod/Loss Family #22 : LO3AfrBL: O3AfrBL Prod/Loss Family #23 : LO3AsBL: O3AsBL Prod/Loss Family #24 : LO3Strat: O3Strat Prod/Loss Family #25 : LO3Init: O3Init Prod/Loss Family #26 : LO3USA: O3USAThe order of the production and loss families should be the same as for the advected tracers (i.e. total O3 first, then O3UT, then O3MT, etc).
If you are running GEOS–5 or MERRA simulation with 47 levels, then typically the P(O3) and L(O3) 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 these options, please see the Prod & Loss Menu section of Chapter 5.
6.1.4 Checklist for Tagged CO simulation
We present a checklist of how to customize input.geos for the current "standard" 17-tracer Tagged CO simulation. In practice, the number of tagged CO tracers varies widely depending on which geographical regions are being studied.
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 names of the other tagged CO tracers specify the geographical region from which they are emitted.
Aerosol Menu:
None of the options in this menu affect the tagged CO simulation, so set them all to F (false).
Transport Menu:
Turn on Transport : T => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution).
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 Use linear. strat. chem?: T => Use Linoz for O3? : F Chemistry Timestep [min]: 60 Read and save CSPEC_FULL: F => CSPEC rst filename? : none USE solver coded by KPP : F Gamma HO2 : 0.2We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
Select the linear stratospheric chemistry option, which will properly set the stratospheric boundary conditions for CO. You can skip the Linoz stratospheric chemistry algorithm, which only applies to ozone.
The rest of the options in this menu have no affect on the tagged CO simulation, so set them 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. CO is not water-soluble, so turn off wet deposition.
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 AEIC emissions? : T Use RCP emiss (anth+bf)?: F => RCP scenario? : RCP60 => RCP year? : 2000 Use EPA/NEI99 (anth+bf)?: F w/ ICARTT modif.? : F w/ VISTAS NOx emis? : F Include biofuel emiss? : T Include biogenic emiss? : F => Use MEGAN inventory?: T => Use PCEEA model? : F => Use MEGAN for MONO? : T => Isoprene scaling : 1 Include biomass emiss? : T => Seasonal biomass? : F => 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 => daily GFED3? : F => 3-hr GFED3? : F Individual NOx sources :--- => Use RCP aircraft NOx: F => Use lightning NOx? : F => Spat-seas constr?: T => Use soil NOx : F => soilNOx rst file?: none => Use fertilizer NOx : F NOx scaling : 1 Use ship SO2 emissions? :--- => global EDGAR ? : F => global ICOADS ? : F => global RCP ? : F => EMEP over EUROPE ? : F => ship SO2 Corbett ? : F => ship SO2 Arctas ? : T Use COOKE BC/OC (N. Am.): F Use historical emiss? : F => What decade? : 2000 Bromine switches :--- => Use Warwick VSLS? : F => Use seasalt Br2? : F => 1ppt MBL BRO Sim.? : F => Bromine scaling : 1Set the emission timestep to the same value as the chemistry timestep.
You will want to turn on all of the different anthropogenic emission types, including the regional inventories (NEI05 for the USA, BRAVO for Mexico, STREETS for South-East Asia, EMEP for Europe). See the Emissions Menu section of Chapter 5 for a detailed description of each of these options. Turn off all options for species other than CO.
Output Menu:
Schedule days for diagnostic output as described above.
Diagnostic Menu:
We list below the most important diagnostics for the Tagged CO simulation. We assume GEOS–5 meteorology with the "reduced" grid (47 vertical levels).
%%% 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 these options, please see the Diagnostic Menu section of Chapter 5.
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 these options, please see the Prod & Loss Menu section of Chapter 5.
6.1.5 Checklist for H2–HD simulation
We present a checklist of how to customize input.geos for the 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:
None of the options in this menu affect the H2-HD simulation, so set them all to F (false).
Transport Menu:
Turn on Transport : T => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution).
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.
At present, you cannot use the non-local PBL mixing scheme with the H2–HD simulation.
Chemistry Menu:
Turn on Chemistry? : T Use linear. strat. chem?: T => Use Linoz for O3? : F Chemistry Timestep [min]: 60 Read and save CSPEC_FULL: F => CSPEC rst filename? : none USE solver coded by KPP : F Gamma HO2 : 0.2We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
Select the linear stratospheric chemistry option, which will apply the stratospheric boundary conditions for the H2-HD simulation.
All of the other Chemistry Menu options do not affect the H2-HD simulation, so 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 other switches in this menu do not affect the H2-HD simulation, so set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above.
Diagnostic Menu:
We list below the most important diagnostics for the H2-HD simulation. We assume GEOS–5 meteorology with the "reduced" grid (47 vertical levels).
%%% 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 these options, please see the Diagnostic Menu section of Chapter 5.
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 these options, please see the Prod & Loss Menu section of Chapter 5.
6.1.6 Checklist for offline aerosol simulation
We present a checklist of how to customize input.geos for the 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 : 47 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 SO4s 96.00 Tracer #5 : 5 MSA 96.00 Tracer #6 : 6 NH3 17.00 Tracer #7 : 7 NH4 18.00 Tracer #8 : 8 NIT 62.00 Tracer #9 : 9 NITs 62.00 Tracer #10 : 10 H2O2 34.00 Tracer #11 : 11 BCPI 12.00 Tracer #12 : 12 OCPI 12.00 Tracer #13 : 13 BCPO 12.00 Tracer #14 : 14 OCPO 12.00 Tracer #15 : 15 DST1 29.00 Tracer #16 : 16 DST2 29.00 Tracer #17 : 17 DST3 29.00 Tracer #18 : 18 DST4 29.00 Tracer #19 : 19 SALA 31.40 Tracer #20 : 20 SALC 31.40 Tracer #21 : 21 MTPA 136.23 Tracer #22 : 22 LIMO 136.23 Tracer #23 : 23 MTPO 136.23 Tracer #24 : 24 TSOG1 150.00 Tracer #25 : 25 TSOG2 150.00 Tracer #26 : 26 TSOG3 150.00 Tracer #27 : 27 TSOG0 150.00 Tracer #28 : 28 TSOA1 150.00 Tracer #29 : 29 TSOA2 150.00 Tracer #30 : 30 TSOA3 150.00 Tracer #31 : 31 TSOA0 150.00 Tracer #32 : 32 ISOG1 150.00 Tracer #33 : 33 ISOG2 150.00 Tracer #34 : 34 ISOG3 150.00 Tracer #34 : 35 ISOA1 150.00 Tracer #36 : 36 ISOA2 150.00 Tracer #37 : 37 ISOA3 150.00 Tracer #38 : 38 BENZ 12.00 (6C) Tracer #39 : 39 TOLU 12.00 (7C) Tracer #40 : 40 XYLE 12.00 (8C) Tracer #41 : 41 ASOG1 150.00 Tracer #42 : 42 ASOG2 150.00 Tracer #43 : 43 ASOG3 150.00 Tracer #44 : 44 ASOAN 150.00 Tracer #45 : 45 ASOA1 150.00 Tracer #46 : 46 ASOA2 150.00 Tracer #47 : 47 ASOA3 150.00The tracers above consist of sulfate, carbon, mineral dust, sea salt, and secondary organic aerosols. You do not have to use all 47 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 => Semivolatile POA? : F => NAP emiss (TgC/yr) : 1.0 => POA emission scale : 1.27 Online DUST AEROSOLS : T => Use DEAD emissions? : T Online SEASALT AEROSOLS : T => SALA radius bin [um]: 0.01 0.5 => SALC radius bin [um]: 0.5 8.0 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 (MTPA, LIMO, MTPO, TSOG0-3, TSOA0-3, ISOG1-3, ISOA1-3, ASOG1-3, ADOA1-3, ASOAN), 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.
If you do not wish to include acid uptake on dust aerosols (NITD1-4, SO4D1-4, DAL1-4), 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 0.01–0.5 and 0.5–8 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 set the Online dicarb. chem.to F.
Transport Menu:
Turn on Transport : T => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution).
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.
Select the non-local PBL mixing option, which performs the boundary layer mixing more accurately.
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). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
The other chemistry options do not affect the offline aerosols chemistry simulation, so set them to F (false).
Deposition Menu:
Turn on Dry Deposition? : T Turn on Wet Deposition? : TDry deposition occurs on every chemistry timestep. Wet deposition takes place on every transport timestep.
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 AEIC emissions? : T Use RCP emiss (anth+bf)?: F => RCP scenario? : RCP60 => RCP year? : 2000 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 => daily GFED3? : F => 3-hr GFED3? : F Individual NOx sources :--- => Use RCP aircraft NOx: F => Use lightning NOx? : T => Spat-seas constr?: T => Use soil NOx : T => soilNOx rst file?: none => Use fertilizer NOx : T NOx scaling : 1 Use ship SO2 emissions? :--- => global EDGAR ? : T => global ICOADS ? : T => global RCP ? : F => EMEP over EUROPE ? : T => ship SO2 Corbett ? : F => ship SO2 Arctas ? : T Use COOKE BC/OC (N. Am.): F Use historical emiss? : F => What decade? : 2000 Bromine switches :--- => Use Warwick VSLS? : F => Use seasalt Br2? : F => 1ppt MBL BRO Sim.? : F => Bromine scaling : 0Set the emission timestep to the same value as the chemistry timestep.
You will want to turn on all of the different anthropogenic emission types for aerosols, including the regional inventories (NEI05 for the USA, BRAVO for Mexico, STREETS for South-East Asia, EMEP for Europe). See the Emissions Menu section of Chapter 5 for a detailed description of each of these options. Turn off all options for species other than aerosols.
Output Menu:
Schedule days for diagnostic output as described above.
Diagnostic Menu:
We list below the most important diagnostics for the offline aerosol simulation. We assume GEOS–5 meteorology with the "reduced" grid (47 vertical levels).%%% 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 these options, please see the Diagnostic Menu section of Chapter 5.
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.
Make sure that you have the proper ratj.d file.
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
We present a checklist of how to customize input.geos for the mercury 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 : 11 Number of Tracers : 87 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_can 201.0 Tracer #5 : 5 Hg0_usa 201.0 Tracer #6 : 6 Hg0_cam 201.0 Tracer #7 : 7 Hg0_sam 201.0 Tracer #8 : 8 Hg0_waf 201.0 Tracer #9 : 9 Hg0_eaf 201.0 Tracer #10 : 10 Hg0_saf 201.0 Tracer #11 : 11 Hg0_naf 201.0 Tracer #12 : 12 Hg0_eur 201.0 Tracer #13 : 13 Hg0_eeu 201.0 Tracer #14 : 14 Hg0_sov 201.0 Tracer #15 : 15 Hg0_mde 201.0 Tracer #16 : 16 Hg0_sas 201.0 Tracer #17 : 17 Hg0_eas 201.0 Tracer #18 : 18 Hg0_sea 201.0 Tracer #19 : 19 Hg0_jpn 201.0 Tracer #20 : 20 Hg0_oce 201.0 Tracer #21 : 21 Hg0_so 201.0 Tracer #22 : 22 Hg0_bb 201.0 Tracer #23 : 23 Hg0_geo 201.0 Tracer #24 : 24 Hg0_atl 201.0 Tracer #25 : 25 Hg0_nat 201.0 Tracer #26 : 26 Hg0_sat 201.0 Tracer #27 : 27 Hg0_npa 201.0 Tracer #28 : 28 Hg0_arc 201.0 Tracer #29 : 29 Hg0_ant 201.0 Tracer #30 : 30 Hg0_ocn 201.0 Tracer #31 : 31 Hg0_str 201.0 Tracer #32 : 32 Hg2_can 201.0 Tracer #33 : 33 Hg2_usa 201.0 Tracer #34 : 34 Hg2_cam 201.0 Tracer #35 : 35 Hg2_sam 201.0 Tracer #36 : 36 Hg2_waf 201.0 Tracer #37 : 37 Hg2_eaf 201.0 Tracer #38 : 38 Hg2_saf 201.0 Tracer #39 : 39 Hg2_naf 201.0 Tracer #40 : 40 Hg2_eur 201.0 Tracer #41 : 41 Hg2_eeu 201.0 Tracer #42 : 42 Hg2_sov 201.0 Tracer #43 : 43 Hg2_mde 201.0 Tracer #44 : 44 Hg2_sas 201.0 Tracer #45 : 45 Hg2_eas 201.0 Tracer #46 : 46 Hg2_sea 201.0 Tracer #47 : 47 Hg2_jpn 201.0 Tracer #48 : 48 Hg2_oce 201.0 Tracer #49 : 49 Hg2_so 201.0 Tracer #50 : 50 Hg2_bb 201.0 Tracer #51 : 51 Hg2_geo 201.0 Tracer #52 : 52 Hg2_atl 201.0 Tracer #53 : 53 Hg2_nat 201.0 Tracer #54 : 54 Hg2_sat 201.0 Tracer #55 : 55 Hg2_npa 201.0 Tracer #56 : 56 Hg2_arc 201.0 Tracer #57 : 57 Hg2_ant 201.0 Tracer #58 : 58 Hg2_ocn 201.0 Tracer #59 : 59 Hg2_str 201.0 Tracer #60 : 60 HgP_can 201.0 Tracer #61 : 61 HgP_usa 201.0 Tracer #62 : 62 HgP_cam 201.0 Tracer #63 : 63 HgP_sam 201.0 Tracer #64 : 64 HgP_waf 201-0 Tracer #65 : 65 HgP_eaf 201.0 Tracer #66 : 66 HgP_saf 201.0 Tracer #67 : 67 HgP_naf 201.0 Tracer #68 : 68 HgP_eur 201.0 Tracer #69 : 69 HgP_eeu 201.0 Tracer #70 : 70 HgP_sov 201.0 Tracer #71 : 71 HgP_mde 201.0 Tracer #72 : 72 HgP_sas 201.0 Tracer #73 : 73 HgP_eas 201.0 Tracer #74 : 74 HgP_sea 201.0 Tracer #75 : 75 HgP_jpn 201.0 Tracer #76 : 76 HgP_oce 201.0 Tracer #77 : 77 HgP_so 201.0 Tracer #78 : 78 HgP_bb 201.0 Tracer #79 : 79 HgP_geo 201.0 Tracer #80 : 80 HgP_atl 201.0 Tracer #81 : 81 HgP_nat 201.0 Tracer #82 : 82 HgP_sat 201.0 Tracer #83 : 83 HgP_npa 201.0 Tracer #84 : 84 HgP_arc 201.0 Tracer #85 : 85 HgP_ant 201.0 Tracer #86 : 86 HgP_ocn 201.0 Tracer #87 : 87 HgP_str 201.0Tracers 1-3 are global totals of Hg0, Hg2, HgP.
Tracers 4-87 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 4-87 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 GTMM model, please refer to this document.
If you wish to set up a simulation with the tagged tracers, then
- Specify Tracers 1-87 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:
None of the switches in this menu affect the mercury simulation, so set them to F (false).
Transport Menu:
Turn on Transport : T => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution).
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.
Select the non-local PBL mixing option, which performs the boundary layer mixing more accurately.
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). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
All of the other options in this menu do not affect the mercury simulation, so set them all to F (false).
Mercury Menu:
%%% MERCURY MENU %%% : Use anthro Hg emiss for : 2006 Use future emissions? : PRESENT 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 occurs on every chemistry timestep. Wet deposition takes place on every transport timestep.
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 do not affect the mercury simulation, so set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above.
Diagnostic Menu:
We list below the most important diagnostics for the mercury simulation. We assume GEOS–5 meteorology with the "reduced" grid (47 vertical levels).
%%% 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 these options, please see the Prod & Loss Menu section of Chapter 5.
6.1.8 Checklist for POPs simulation
We present a checklist of how to customize input.geos for the POPs simulation:
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
You need to use 3 tracers for the POPs simulations: gas-phase POP, OC-bound POP, and BC-bound POP. As of GEOS–Chem v9-02, three polycyclic aromatic hydrocarbons (PAHS) can be modeled.
For phenanthrene (PHE), use:
%%% TRACER MENU %%% : Type of simulation : 14 Number of Tracers : 3 Tracer Entries -------> : TR# Name g/mole Tracer #1 : 1 POPG 178.23 Tracer #2 : 2 POPPOC 178.23 Tracer #3 : 3 POPPBC 178.23For pyrene (PYR), use:
%%% TRACER MENU %%% : Type of simulation : 14 Number of Tracers : 3 Tracer Entries -------> : TR# Name g/mole Tracer #1 : 1 POPG 202.25 Tracer #2 : 2 POPPOC 202.25 Tracer #3 : 3 POPPBC 202.25For benzo[a]pyrene (BaP), use:
%%% TRACER MENU %%% : Type of simulation : 14 Number of Tracers : 3 Tracer Entries -------> : TR# Name g/mole Tracer #1 : 1 POPG 252.31 Tracer #2 : 2 POPPOC 252.31 Tracer #3 : 3 POPPBC 252.31
Aerosol Menu:
None of the switches in this menu affect the POPs simulation, so set them to F (false).
Transport Menu:
Turn on Transport : T => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution).
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.
Select the non-local PBL mixing option, which performs the boundary layer mixing more accurately.
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). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
All of the other options in this menu do not affect the POPs simulation, so set them all to F (false).
POPs Menu:
For phenanthrene (PHE), use:
%%% POPS MENU %%% : POP type [PHE,PYR,BAP] : PHE Chemistry proceesing on?: T POPs emiss file : PHE_EM_1x1.bpch POP_XMW : 178d-3 POP_KOA : 4.37d7 POP_KBC : 1d10 POP_K_POPG_OH : 2.70d-11 POP_K_POPG_O3A : 5d-4 POP_K_POPG_O3B : 2.15d15 POP_HSTAR : 2.35d1 POP_DEL_H : -74d3 POP_DEL_Hw : -5.65d3For pyrene (PYR), use:
%%% POPS MENU %%% : POP type [PHE,PYR,BAP] : PYR Chemistry proceesing on?: T POPs emiss file : PYR_EM_1x1.bpch POP_XMW : 202d-3 POP_KOA : 7.24d8 POP_KBC : 1d11 POP_K_POPG_OH : 5.00d-11 POP_K_POPG_O3A : 7d-4 POP_K_POPG_O3B : 3d15 POP_HSTAR : 7.61d1 POP_DEL_H : -87d3 POP_DEL_Hw : -5.17d3For benzo[a]pyrene (BaP), use:
%%% POPS MENU %%% : POP type [PHE,PYR,BAP] : BAP Chemistry proceesing on?: T POPs emiss file : BaP_EM_1x1.bpch POP_XMW : 252d-3 POP_KOA : 3.02d11 POP_KBC : 7.94d13 POP_K_POPG_OH : 50d-12 POP_K_POPG_O3A : 5.5d-3 POP_K_POPG_O3B : 2.8d15 POP_HSTAR : 1.23d3 POP_DEL_H : -11d4 POP_DEL_Hw : -5.65d3
Deposition Menu:
Turn on Dry Deposition? : T Turn on Wet Deposition? : TDry deposition occurs on every chemistry timestep. Wet deposition takes place on every transport timestep.
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 do not affect the POPs simulation, so set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above.
Diagnostic Menu:
We list below the most important diagnostics for the POPs simulation. We assume GEOS–5 meteorology with the "reduced" grid (47 vertical levels).
%%% 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 ... ND37: Updraft scav frac : 47 all ND38: Cld Conv scav loss: 47 2 3 ND39: Wetdep scav loss : 47 2 3 ... ND44: Drydep flx/vel : 1 all ND45: Tracer Conc's : 47 all ==> ND45 Time range : 0 24 ... ND53: POPs Emissions : 47 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 : 0Production & loss of POPs tracers are handled in the ND53 diagnostic, so you can turn off all the switches in the Prod & Loss Menu as shown above.
For more information about these options, please see the Prod & Loss Menu section of Chapter 5.
6.1.9 Checklist for a CH4 offline simulation
We present a checklist of how to customize input.geos for the methane 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 (or just CH4).
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 => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution).
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]: 60We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
Other chemistry options have no effect on the methane simulation, so set them all to F (false).
Methane Menu:
%%% CH4 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:
%%% EMISSIONS MENU %%% : Turn on emissions? : T Emiss timestep (min) : 60 Include anthro emiss? : T => Scale 1985 to year : -1 => Use EMEP emissions? : F => Use BRAVO emissions?: F => Use EDGAR emissions?: F => Use STREETS emiss? : F => Use CAC emissions? : F => Use NEI2005 emiss? : F => Use RETRO emiss? : F => Use AEIC emissions? : F Use RCP emiss (anth+bf)?: F => RCP scenario? : RCP60 => RCP year? : 2000 Use EPA/NEI99 (anth+bf)?: F w/ ICARTT modif.? : F w/ VISTAS NOx emis? : F Include biofuel emiss? : F Include biogenic emiss? : F => Use MEGAN inventory?: F => Use PCEEA model? : F => Use MEGAN for MONO? : F => Isoprene scaling : 1 Include biomass emiss? : T => Seasonal biomass? : F => 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 => daily GFED3? : T => 3-hr GFED3? : F Individual NOx sources :--- => Use RCP aircraft NOx: F => Use lightning NOx? : F => Spat-seas constr?: F => Use soil NOx : F => soilNOx rst file?: none => Use fertilizer NOx : F NOx scaling : 1 Use ship SO2 emissions? :--- => global EDGAR ? : F => global ICOADS ? : F => global RCP ? : F => EMEP over EUROPE ? : F => ship SO2 Corbett ? : F => ship SO2 Arctas ? : F Use COOKE BC/OC (N. Am.): F Use historical emiss? : F => What decade? : 2000 Bromine switches :--- => Use Warwick VSLS? : F => Use seasalt Br2? : F => 1ppt MBL BRO Sim.? : F => Bromine scaling : 1Set the emissions 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 CH4 Menu for the sake of redundancy.
The rest of the switches in the emissions menu do not affect the tagged methane simulation, so set them to F (false).
Output Menu:
Schedule days for diagnostic output as described above.
Diagnostic Menu:
We list below the most important diagnostics for the methane simulation. We assume GEOS–5 meteorology with the "reduced" grid (47 vertical levels).
%%% 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.
6.1.10 Checklist for Total CO2 and Tagged CO2 simulations
We present a checklist of how to customize input.geos for the 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 shown 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 => Fill Negative Values: T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 15Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution).
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). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
The rest of the switches in this menu do not affect the CO2 simulation, so 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 do not affect on the CO2 simulation, so 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 : F GFED3 monthly biomass : T GFED3 daily 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 shows the defaults for a single tracer run. You can select other options (e.g. the chemical source)..
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.
Diagnostic Menu:
The CO2 simulation has its own unique diagnostic (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 10Also see the Diagnostic Menu section in Chapter 5.
6.2 Running a Regular GEOS–Chem Job
We describe below how to run the GEOS–Chem model with the LSF, PBS, and SGE batch queue systems.
Furthermore, we STRONGLY RECOMMEND that you test your simulation with a short (1-day or 2-day) run before submitting a very long-term GEOS–Chem simulation. You will be better able to detect errors or problems in a short run. You will also avoid wasting precious computer time.
6.2.1 Interactive jobs (no queue system)
If your computer system supports interactive access, then you can run GEOS–Chem from the Unix prompt. (Don't do it yet, please keep reading!)
At the Unix prompt, type:
geos
You will find that the output from GEOS–Chem is printed to the screen! Therefore, you will need to redirect the screen output to log files. If you use Bourne-again shell (bash), you can type::
geos 1>gc.log 2>gc.error &
This will send program output (the Unix stdout stream, aka "1") to gc.log and error output (the Unix stderr stream, aka "2") to gc.error. The & specifies that the job will run in the Unix background.
You can combine these into the same file:
geos 1>gc.log 2>&1
or
geos >& gc.log
This last syntax will also work if you use C-shell (csh) or T-shell (tcsh). Of course, the commands that you use for Unix redirection vary depending on which shell you use. Follow this link for a more detailed discussion about Unix redirection.
If your computational cluster 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
You can write a simple GEOS–Chem job script to run GEOS–Chem:
#!/bin/tcsh -f # Script definition line cd /scratch/bmy/run.v9–02 # 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. Select the queue in which you will run GEOS–Chem, and type:
bsub -q queue-name job
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 comptational cluster 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
Create a simple GEOS–Chem job script (named job), similar to the above example for LSF:
#!/bin/tcsh -f # Script definition line cd run.v9–02 # 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
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 computational cluster 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 SGE 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 SGE Job jobid
qmon # Graphical user interface for SGE
Create a simple GEOS–Chem job script (named job), similar to the above examples for LSF and PBS:
#!/bin/tcsh -f # Script definition line cd run.v9–02 # 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
We provide below some general information about GEOS–Chem errors. For the most up-to-date information about specific GEOS–Chem errors and their solutions, please consult the following resources:
6.3.1 I/O (input/output) errors
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 display an error message and then exit. 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, you can deduce the nature of the error from the error number. 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. 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.