File containing all GEOS–Chem user options. In this file, you may specify the following options:

• Start & end time of the simulation
• Names of the input & output files
• Which diagnostics to save to disk
• Which processes (e.g. chemistry, transport, dry deposition, etc.) to turn on, etc.

File that defines the GEOS–Chem NOx-Ox-hydrocarbon-aerosol chemical mechanism. This file contains the list of chemical species and reactions used by the chemical solver (SMVGEAR II or KPP).

At present, you may pick from a few different chemistry mechanisms:

1. standard: 53 advected tracers, our default simulation.
2. SOA: 59 advected tracers, with secondary organic aerosols
3. dicarbonyls: 75 advected tracers, with dicarbonyl chemistry
4. isoprene: 56 advected tracers, with the Caltech isoprene scheme.
   NOTE: This scheme has not been fully tested yet!

Setup file for SMVGEAR II, containing convergence criteria and other parameters.

Contains cross-section and quantum yields (at 400nm) for FAST–JX photolysis species.

Links "GEOS–Chem species" to "FAST–JX" species. FAST–JX photolysis species are defined in the data file jv_spec.dat, GEOS–Chem species in globchem.dat.

Simulation Menu

Specifies the start & stop times of the run, the restart file names, and the directory path information.

Tracer Menu

Specifies information about each tracer, including name, molecular weight, and, for family tracers, individual constituent species.

Transport Menu

Specifies options for TPCORE transport.

Convection Menu

Specifies options for cloud convection and PBL mixing.

Emissions Menu

Specifies options for anthropogenic, biomass, biofuel, and biogenic emissions.

Specifies options for future emissions scenarios.

NOTE: This is currently only implemented for use with the GCAP met fields.

Aerosol Menu

Specifies options for emissions and chemistry of sulfate, carbon, secondary organic, dust, and sea salt aerosols.

Deposition Menu

Specifies options for both dry deposition and wet deposition.

Chemistry Menu

Specifies options for chemistry.

Specifies options for the mercury simulation, with or without the Global Terrestrial Mercury Model.

Output Menu

Specifies dates on which diagnostic output will be saved to the binary punch file.

Diagnostic Menu

Specifies which binary punch file diagnostics to turn on, and which tracers to save to disk.

Planeflight Menu

Specifies the names of the files for the ND40 plane flight diagnostic.

ND48 Menu

Specifies options for the ND48 station timeseries diagnostic.

ND49 Menu

Specifies options for the ND49 instantaneous timeseries diagnostic.

ND50 Menu

Specifies options for the ND50 24-hour average timeseries diagnostic.

ND51 Menu

Specifies options for the ND51 "satellite" timeseries diagnostic.

Prod & Loss Menu

Specifies options for the ND65 (chemical prod & loss) and ND20 (save PO3, LO3 to disk for tagged Ox simulation) diagnostics.

Archived OH Menu

Specifies the directory path for offline OH data files.

O3 P/L Menu

Specifies the directory path for PO3 and LO3 rate files (for tagged Ox simulation)

Nested Grid Menu

Specifies options for the nested grid simulations

Unix Cmds Menu

Specifies Unix commands which are used for unzipping data on the fly.

Header line

Specify the starting date and time of the GEOS–Chem simulation. The date must be in YYYYMMDD format (4-digit year, month, and day). The time must be in hhmmss format (hour, minute, and seconds). Note that since the GEOS–Chem dynamic timestep (see Transport Menu) is usually 10, 15, or 30 minutes, you can always set the seconds to zero.

Specify the ending date (YYYYMMDD format) and time (hhmmss format) of the GEOS–Chem simulation.

Specify the name of the GEOS–Chem run directory (e.g. where the executable file and input files reside).

Specify the name of the restart file, which contains the initial tracer concentrations. If you just specify the file name, GEOS–Chem will look for the restart file in the run directory. You may also specify an entire directory path. Also, you may include the following tokens in the file name:

• YYYY: Replaced by 4-digit year (e.g. 2008)
• MM: Replaced by 2-digit month (01-12)
• DD: Replaced by 2-digit day (01-31)
• hh: Replaced by 2-digit hour (0-23)
• mm: Replaced by 2-digit minutes (0-59)
• ss: Replaced by 2-digit seconds (0-59)

NOTE: Since the typical GEOS–Chem simulations start and end at the top of the hour, a restart file name such as restart.YYYYMMDDhh should suffice for most applications.

If you want to create new restart files then set this to T. A new restart file will be saved at the same time when diagnostics are saved to the binary punch file. See Output Menu for more information.

Specify the name or file path for the output restart file(s). As described above, GEOS–Chem will replace the YYYY, MM, DD, hh, mm, ss tokens in the file name with the appropriate date or time values.

Specify DATA_DIR (located in source code file directory_mod.F). DATA_DIR is the root-level data directory path. The various shared data inputs (e.g. emissions, offline OH, offline dust & aerosol concentrations, etc). are stored in subdirectories of DATA_DIR. Also, the met fields are stored in subdirectories of DATA_DIR.

Specify the directory path where GCAP met fields are stored. You may include the YYYY and MM tokens as described above. This is stored in the variable GEOS_1_DIR in source code file directory_mod.F.)

Specify the directory path where GEOS–4 met fields are stored. You may include the YYYY and MM tokens as described above. This is stored in the variable GEOS_4_DIR in source code file directory_mod.F.

Specify the directory path where GEOS–5 met fields are stored. You may include the YYYY and MM tokens as described above. This is stored in the variable GEOS_5_DIR in source code file directory_mod.F.

Specify the directory path where GEOS–5.7.2 met fields are stored. You may include the YYYY and MM tokens as described above. This is stored in the variable GEOS_57_DIR in source code file directory_mod.F.

Specify DATA_DIR_1x1 (located in source code file directory_mod.F). DATA_DIR_1x1 is the root-level data directory path where emission files on the GMAO 1° x 1°, generic 1° x 1°, and native grids are stored. GEOS–Chem v9–01–03 has the ability to regrid emissions (etc.) files on-the-fly from these 1° x 1° and native grids to the current model grid using the MAP A2A regridding algorithm.

Specify TEMP_DIR (located in source code file directory_mod.F). TEMP_DIR is the path of a temporary directory into which met field files will be unzipped.

NOTE: You only need to specify this if you are unzipping met fields on the fly. This was usually done with GEOS–3 met fields, which are now obsolete.

Specify LUNZIP (located in source code file logical_mod.F). LUNZIP determines whether GEOS–Chem will unzip met field files on the fly. If you have stored your met fields in gzipped format in order to save space, then you must set LUNZIP to T. If you have stored your met fields as unzipped, then set LUNZIP to F.

NOTE: You only need to specify this if you are unzipping met fields on the fly. This was usually done with GEOS–3 met fields, which are now obsolete.

Specify LWAIT (located in source code file logical_mod.F). If you are unzipping met field files on the fly (i.e. if LUNZIP is set to T), then you may also specify if you want GEOS–Chem to wait until the met field fi les are completely unzipped before proceeding. It may be necessary to set LWAIT to T if you are using a simulation such as Radon or Tagged Ox where the chemistry takes less time than it does to unzip the met fields.

NOTE: You only need to specify this if you are unzipping met fields on the fly. This was usually done with GEOS–3 met fields, which are now obsolete.

Specify the global offsets I0 and J0 (located in source code file grid_mod.F). For a global run, I0 and J0 must both be set to zero. However, for nested grid runs, we must set I0 and J0 to the appropriate offsets.

Specify the type of GEOS–Chem simulation that you wish to perform. The choices are:

1. Rn–Pb–Be simulation
2. CH3I simulation (NOTE: this is old and in need of updating)
3. NOx–Ox–Hydrocarbon–aerosol simulation w/ SMVGEAR or KPP solver (a.k.a. "full chemistry")
4. HCN simulation
5. ### unused ###
6. Tagged Ox simulation
7. Tagged CO simulation
8. C2H6 simulation
9. CH4 simulation
10. Offline aerosol simulation (sulfate, carbon, secondary organics, dust, and sea salt aerosols)
11. Mercury simulation (with or without the Global Terrestrial Mercury Model option)
12. CO2 simulation
13. H2 and HD simulation (NOTE: this is in need of updating)

NOTE: In this example, the TRACER MENU is set up for a NOx–Ox–Hydrocarbon–aerosol (or "full chemistry") simulation.

Specify N_TRACERS (located in source code file tracer_mod.F). N_TRACERS is the number of tracers that will be included in the GEOS–Chem simulation.

NOTE: If you are performing a "full-chemistry" simulation:

1. with standard chemistry, then set N_TRACERS to 53 (as shown in the example above).
2. with secondary organic aerosols (SOA), then set N_TRACERS to 59.
3. with dicarbonyl chemistry, then set N_TRACERS to 75.
4. with the Caltech isoprene chemistry, then set N_TRACERS to 56.
   

Entry for the NOx tracer. You must list the following information:

• Tracer number
• Tracer name (up to 14 characters)
• Molecular weight in g/mole

For most types of simulations this is all you need to list. However, for the NOx–Ox–Hydrocarbon–aerosol simulation (a.k.a. "full chemistry") simulation, you must also list the following information, which will be passed to the SMVGEAR chemistry solver routines:

• If this is a family tracer, then you must specify the names of the individual species which constitute this tracer. In this example, NOx is a family consisting of NO2 + NO + NO3 + HNO2, so you must list these species names after the molecular weight as shown above. These can be separated by spaces (i.e. no commas or semicolons are needed).

• You must also denote species which have emission reactions in the SMVGEAR chemical mechanism by placing parentheses around the species name. In this case, all of the anthropogenic emissions which go into the NOx family are actually emissions of NO, so you must denote this by (NO).

• A number in front of an individual species name denotes the coefficient by which that species is to be multiplied. In the case of NOx, all of the species have a coefficient of one, and thus may be omitted.

Entry for the Ox tracer. As with NOx, you must list the tracer number, name, and molecular weight. You must also list this additional information:

• Ox is a family tracer (which consists of O3 + NO2 + 2NO3). Therefore in the example above, you must list constituent species as shown above. Note that the coefficient in front of the NO3 is 2, which denotes that 2 molecules of NO3 are included in the Ox family.

• You must also denote species which have emission reactions in the SMVGEAR chemical mechanism by placing parentheses around the species name. In this case, all of the anthropogenic emissions which go into the Ox family are actually emissions of O3, so you must denote this by (O3).

Entry for the PAN tracer: As with NOx, you must list the tracer number, name, and molecular weight. However, PAN is not a family tracer (i.e. it has no constituent species other than itself). It also does not have an emission reaction defined in the SMVGEAR chemical mechanism. So this is all the information you need to give.

Entry for the CO tracer: As with NOx you must list the tracer number, name, and molecular weight. Although CO is not a family tracer (i.e. it has no constituent species other than itself), it is an emitted tracer in the SMVGEAR chemical mechanism. Therefore you need to list (CO) in parentheses after the molecular weight in g/mole.

Entry for the ALK4 (C4 lumped alkanes) tracer: As with NOx you must list the tracer number, name, and molecular weight.

In GEOS–Chem, several of the hydrocarbon tracers are not carried in molecules of tracer, but in equivalent atoms of carbon. ALK4 is one of these types of hydrocarbon tracers. Also, ALK4 has an emission reaction defined within the SMVGEAR chemistry mechanism. You can therefore denote this by placing (4C) after the molecular weight in g/mole. The 4C denotes that ALK4 consists of 4 carbon atoms, and the parentheses denote that ALK4 has an emission reaction in the SMVGEAR chemistry mechanism.

Entry for the ISOP (isoprene) tracer. This is a hydrocarbon tracer which consists of 5 carbon atoms.

Entries for HNO3 and H2O2 tracers

Entries for hydrocarbon tracers: ACET (3 carbons), MEK (4 carbons), ALD2 (2 carbons)

Entries for RCHO, MVK, MACR, PMN, PPN, R4N2.

Entries for they hydrocarbon tracers PRPE (C3 lumped alkenes—3 carbons) and C3H8 (3 carbons).

Entry for CH2O (formaldehyde). This has an emission reaction defined in the SMVGEAR chemistry mechanism so we must list its name in parentheses after the molecular weight.

Entry for hydrocarbon tracer C2H6 (2 carbons).

Entries for the rest of the GEOS–Chem tracers.

Note: Br2, CHBr3, and CH2Br2 have emissions reactions defined within the SMVGEAR chemistry mechanism, so we must list these names in parentheses after the molecular weight.

Header line

Specify LTRAN (located in source code file logical_mod.F). Set LTRAN to T to turn on TPCORE transport, or set to F to turn off TPCORE transport.

Specify LMFCT (located in source code file logical_mod.F). Setting LFMCT to T turns on flux-corrected transport in TPCORE.

NOTE: This has no effect for GEOS–4 and GEOS–5 simulations.

Specify LFILL (located in source code file logical_mod.F). Setting LFILL to T will cause TPCORE to fill negative values with zeroes.

Specify the IORD, JORD, KORD transport options for TPCORE (located in source code file transport_mod.F). These settings determine how TPCORE performs transport in the E/W, N/S, and vertical directions. Recommended values are 3, 3, 7.

Specify the transport timestep (TS_DYN) in minutes. Recommended values: 30 min (4° x 5°), 15 min (2° x 2.5°) and 10 min (1° x 1° or higher resolution). The transport timestep should be the smallest timestep used.

Header line

Specify LCONV (located in source code file logical_mod.F). Set LCONV to T to turn on cloud convection.

Specify LTURB (located in source code file logical_mod.F). Set LTURB to T to turn on PBL mixing.

Specify LNLPBL (located in source code file logical_mod.F). The options are as follows:

• To use the non-local PBL mixing scheme (aka VDIFF), then LNLPBL to T.
• To use the full mixing in the PBL (aka TURBDAY), then set LNLPBL to F

NOTE: If LTURB (Line 3) is set to F, then neither PBL mixing option will be executed, regardless of the setting of LNLPBL.

Specify the convection timestep (TS_CONV) in minutes. The convection timestep should equal the the transport timestep (i.e. TS_CONV = TS_DYN). This is required for the central chemistry timestep algorithm.

Header line

Specify LEMIS (located in source code file logical_mod.F). Set LEMIS to T to turn on emissions in a GEOS–Chem simulation. Set LEMIS to F to turn off all emissions in a GEOS–Chem simulation.

Specify the emission timestep (TS_EMIS) in minutes. The emissions timestep should be the same as the chemistry time step (i.e. TS_EMIS = TS_CHEM). This is required for the central chemistry timestep algorithm.

Specify LANTHRO (located in source code file logical_mod.F). Set LANTHRO to T to include anthropogenic emission, or to F to shut off all anthropogenic emission.

Specify FSCALYR, the emission year for anthropogenic emissions (located in source code file CMN_O3). For each selected inventory (see below), if a dataset exists for that year, it is used. If not, the closest available year is used, and -for NOx, CO, and SOx only- emissions are scaled to the emission year. Scale factors are available for 1985-2006. Before 1985, 1985 is used and after 2006, 2006 is used. It is recommended to set this input to -1 to let GEOS–Chem automatically scale data to the year simulated.

Specify LEMEP (located in source code file logical_mod.F). Set LEMEP to T to include EMEP European anthropogenic emissions, or to F otherwise.

Specify LBRAVO (located in source code file logical_mod.F). Set LBRAVO to T to include BRAVO anthropogenic emissions over Mexico, or to F otherwise.

Specify LEDGAR (located in source code file logical_mod.F). Set LEDGAR to T to include EDGAR anthropogenic emissions, or to F otherwise.

Specify LSTREETS (located in source code file logical_mod.F). Set LSTREETS to T to include David Streets SE Asian anthropogenic emissions, or to F otherwise.

Specify LNEI05 (located in source code file logical_mod.F). Set LNEI05 to T to overwrite anthropogenic emissions over the continental USA with those from the EPA/NEI05 inventory, or F to keep the default emissions over the continental USA.

NOTE: We recommend using the newer EPA/NEI05 emissions rather than the EPA/NEI99 emissions.

Specify LNEI99 (located in source code file logical_mod.F). Set LNEI99 to T to overwrite anthropogenic and biofuel emissions over the continental USA with those from the EPA/NEI99 inventory, or F to keep the default emissions over the continental USA.

NOTE: If LNEI99 and LNEI05 are both set to T, then LNEI05 is used.

Specify LBIOFUEL (located in source code file logical_mod.F). Set LBIOFUEL to T to include biofuel emissions, or to F to shut off all biofuel emission.

Specify LBIOGENIC (located in source code file logical_mod.F). Set LBIOGENIC to T to include biogenic emissions (e.g. ISOPRENE, MONOTERPENES), or to F to shut off all biogenic emission.

Specify LMEGAN (located in source code file logical_mod.F). Set LMEGAN to T to use biogenic emissions from the MEGAN inventory for Isoprene and other VOC's.

NOTE: The GEIA biogenic emissions are now deprecated. They have been removed in GEOS–Chem v9–01–03.

Specify LPECCA (located in source code file logical_mod.F).

If you turn off the PCEEA model (by setting the line => Use PCEEA model? : F), then MEGAN will use the existing canopy model, but with updated leaf-age and temperature algorithms. This option is closest to the previous implementation of MEGAN in GEOS–Chem v8–02–03 and prior versions.

If you turn on the PCEEA model (by setting the line => Use PCEEA model? : T), then MEGAN will follow the approach of Guenther et al, 2006. It will not use a canopy model, but will take into account the light dependency of monoterpene emissions.

Set ISOP_SCALING (located in source code file emissions_mod.F). Set ISOP_SCALING to any REAL value to scale overall isoprene emissions. If you do not want to scale isoprene emissions, then leave ISOP_SCALING set to 1.

Specify LBIOMASS (located in source code file logical_mod.F). Set LBIOMASS to T to include biomass burning emissions, or to F to shut off all biomass burning emissions.

Specify LBBSEA (located in source code file logical_mod.F). Set LBBSEA to T if you wish to use seasonal (aka climatological) biomass burning emissions. Set LBBSEA to F if you wish to use biomass burning emissions for specific years (in order to establish interannual variability).

NOTE: This option is mostly obsolete. We recommend using the GFED3 biomass emissions.

Specify LTOMSAI (located in source code file logical_mod.F). Set LTOMSAI to T if you wish to scale biomass burning to TOMS Aerosol Index data.

NOTE: This option is mostly obsolete. We recommend using the GFED3 biomass emissions.

Specify LGFED2BB (located in source code file logical_mod.F). Set LGFED2BB to T if you wish to use the monthly-mean GFED2 biomass emissions, or to F otherwise.

NOTE: We recommend using the newer GFED3 biomass emissions rather than the GFED2 emissions.

Specify LGFED3BB (located in source code file logical_mod.F). Set LGFED3BB to T if you wish to use the monthly-mean GFED3 biomass emissions, or to F otherwise.

NOTE: For most applications, the monthly-mean GFED3 data should suffice.

Specify LDAYBB3 (located in source code file logical_mod.F). Set LDAYBB3 to T if you wish to use the daily-mean GFED3 biomass emissions, or to F otherwise.

NOTE: To use daily GFED3, you must also set LGFED3BB to T.

Specify L3HRBB3 (located in source code file logical_mod.F). Set L3HRBB3 to T if you wish to use the 3-hourly-mean GFED3 biomass emissions, or to F otherwise.

NOTE: To use 3-hourly GFED3, you must also set LGFED3BB and LDAYBB3 to T.

Header line

Specify LAIRNOX (located in source code file logical_mod.F). Set LAIRNOX to T to include aircraft NOx emissions, or to F to shut off all aircraft NOx emissions.

Specify LLIGHTNOX (located in source code file logical_mod.F). Set LLIGHTNOX to T to include lightning NOx emissions, or to F to shut off all lightning NOx emissions.

Specify LOTDSCALE (located in source code file logical_mod.F) to apply the OTD/LIS redistribution. This will place a spatial and seasonal constraint on lightning emissions.

NOTE: All of the other lightning redistribution options are now obsolete and have been removed.

Specify LSOILNOX (located in source code file logical_mod.F). Set LSOILNOX to T to include soil NOx emissions, or to F to shut off soil NOx emissions other than fertilizer NOx emissions.

Specify LSHIPSO2 (located in source code file logical_mod.F). Set LSHIPSO2 to T to include SO2 emissions from ship exhaust, or to F to shut off SO2 emissions from ship exhaust.

Specify LARCSHIP (located in source code file logical_mod.F). Set LARCSHIP to T to include ARCTAS SO2 and CO2 ship emissions, or to F otherwise.

Specify LAVHRRLAI (located in source code file logical_mod.F). Set LAVHRRLAI to T to use leaf area indices obtained from the AVHRR satellite, or F to continue using the default LAI inventory (from Yuhang Wang, 1998).

NOTE: This switch is now obsolete and is slated to be removed. GEOS–Chem now reads MODIS LAI data from netCDF files. The AVHRR LAI option has been removed.

Specify LMODISLAI (located in source code file logical_mod.F). Set LMODISLAI to T to use leaf area indices obtained from the MODIS satellite.

NOTE: This switch is now obsolete and is slated to be removed. GEOS–Chem now reads MODIS LAI data from netCDF files. The AVHRR LAI option has been removed.

Specify LWARWICK_VSLS (located in source code file logical_mod.F). Set LWARWICK_VSLS to T to use surface CHBr3 emissions from Warwick et al. (2006), scenario 3 (400 Gg CHBr3/year).

Specify LSSABr2 (located in source code file logical_mod.F). Set LSSABr2 to T to use sea salt Br2 emissions. Following Yang et al. (2005), sea-salt debromination is treated as emission of Br2.

Specify LFIX_PBL_BrO (located in source code file logical_mod.F). Set LFIX_PBL_BrO to T to set Bro concentrations in the PBL equal to 1 ppt during the day.

Set Br_SCALING (located in source code file bromocarb_mod.F). Set Br_SCALING to any REAL value to scale overall bromine emissions. If you do not want to scale bromine emissions, then leave Br_SCALING set to 1.

Header line

Specify LFUTURE (located in source code file logical_mod.F). Set LFUTURE to T to scale present-day emissions to one of the IPCC future scenarios, or F otherwise.

Specify FUTURE_YEAR, which is the year to which the current emissions will be scaled. Current options are 2030 and 2050.

Specify FUTURE_SCEN, which is the IPCC scenario to be used. Current options are: A1, B1.

Header line

Specify LSULF (located in source code file logical_mod.F). Set LSULF to T to turn on emissions and chemistry for sulfate aerosols (DMS, SO2, SO4, MSA, NH3, NH4, NIT).

Specify LCRYST (located in source code file logical_mod.F). Set LCRYST to T to turn on emissions and chemistry for crystalline sulfur and aqueous aerosols (AS, AHS, LET, SO4aq, NH4aq).

NOTE: This feature has not been implemented in GEOS–Chem v9–01–03. For the time being, set LCRYST to F.

Specify LCARB (located in source code file logical_mod.F). Set LCARB to T to turn on emissions and chemistry for carbonaceous aerosols (BCPI, BCPO, OCPI, OCPO).

Specify LSOA (located in source code file logical_mod.F). Set LSOA to T to turn on emissions and chemistry for secondary organic aerosols. Turning on the secondary organic aerosols will add 9 tracers to the simulation.

NOTE: If you are going to use the SOA tracers, you must also change the setting of LISOPOH in the "globchem.dat" file from "D" (dead) to "A" (active).

Specify LDUST (located in source code file logical_mod.F). Set LDUST to T to turn on emissions and chemistry for mineral dust aerosol tracers (DST1, DST2, DST3, DST4).

Specify LDEAD (located in source code file logical_mod.F). Set LDEAD to T to use the dust source function from the DEAD model (cf. C. Zender). Set LDEAD to F to use the dust source function from the GOCART (cf. Paul Ginoux).

Specify LSSALT (located in source code file logical_mod.F). Set LSSALT to T to turn on emissions and chemistry for sea salt aerosols (SALA, SALC).

Specify the edges which denote accumulation mode sea salt tracer in microns. (This is stored in variable SALA_REDGE_um in tracer_mod.F). Recommended setting: 0.01 to 0.5 microns.

Specify the edges which denote coarse mode sea salt tracer in microns. (This is stored in variable SALC_REDGE_um in tracer_mod.F). Recommended setting: 0.5 to 8 microns.

Header line

Specify LDRYD (located in source code file logical_mod.F). Set LDRYD to T to turn on dry deposition, or F to turn off dry deposition.

Specify LWETD (located in source code file logical_mod.F). Set LWETD to T to turn on wet deposition, or F to turn off wet deposition.

Header line

Specify LCHEM (located in source code file logical_mod.F). Set LCHEM to T to turn on chemistry, or F to turn off chemistry.

Specify LSCHEM (located in source code file logical_mod.F). Set LSCHEM to T to turn on stratospheric chemistry, or F to turn off stratospheric chemistry.

Specify LLINOZ (located in source code file logical_mod.F). Set LLINOZ to T to use Linoz for O3 chemistry in the stratosphere, otherwise Synoz will be used.

Specify the chemistry timestep (TS_CHEM) in minutes. We suggest using a chemistry timestep double the transport time step (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 should be a multiple of the transport timestep (i.e. TS_CHEM = X * TS_DYN, where X is an integer). See this wiki page for more information.

Specify LSVCSPEC (located in source code file logical_mod.F). Set LSVCSPEC to T to save all species (CSPEC_FULL array) in a restart file in addition to the standard restart file, which saves only the transported tracers or to F otherwise. If the option Make new restart file is set to F in the simulation menu, then no restart file will be saved regardless of LSVCSPEC value.

NOTE: If you are going to be running a very long GEOS–Chem simulation, and must split the job into several stages (i.e. in order to submit to a queue system), then you should set LSVCSPEC to T. This will make sure that the chemical species stored in the CSPEC array will not get reset to the background defaults (from globchem.dat) when the next run stage starts.

Header line

Fossil Fuel sub-header line (select only one option in this section)

Annually averaged fossil fuel emissions for 1995 from CDIAC [Andres et al., 1996]

Year-specific annually averaged fossil fuel emissions from CDIAC [Andres et al., 1996], with 2007-2009 scaled based on [Boden et al., 2009; LeQuere, 2009]

Month and year-specific monthly averaged fossil fuel emissions from CDIAC [Andres et al., 1996], with 2007-2009 scaled based on [Boden et al., 2009; LeQuere, 2009]

3-D CO₂ chemical source from oxidation of CO, CH₄ and NMHCs based on Suntharalingam et al. [2005], with appropriate surface emission corrections.

Biomass Burning sub-header line (select only one option in this section)

Seasonally approximated biomass burning emissions from Duncan et al. [2003]

Global Fire Emission Database (GFED) version 2 – monthly (1997-2008). NOTE: The choice of GFED emissions in the CO2 MENU must be consistent with the choice in the EMISSIONS MENU.

Global Fire Emission Database (GFED) version 2 – 8-day (2001-2007). NOTE: The choice of GFED emissions in the CO2 MENU must be consistent with the choice in the EMISSIONS MENU.

Biofuel Emissions – Yevich and Logan [2003]

Terrestrial Exchange sub-header line (select one balanced biosphere option and one Net Terrestrial Exchange option)

CASA model daily average Net Ecosystem Production (balanced – no net annual flux) [Potter et al., 1993; Olsen and Randerson, 2004]

CASA model 3-hourly Net Ecosystem Production (balanced – no net annual flux) [Potter et al., 1993; Olsen and Randerson, 2004]

Net Terrestrial Exchange (original) of -1.01 PgC/yr

Net Terrestrial Exchange (climatology) of -5.29 PgC/yr [Baker et al., 2006] adjusted for biomass/biofuel burning

Ocean Exchange sub-header line (select only one option in this section)

Annual ocean flux climatology of non-El Niño years from Takahashi et al. [1997]

Annual ocean flux climatology of non-El Niño years from Takahashi et al. [2009]

Monthly ocean flux climatology of non-El Niño years from Takahashi et al. [2009]

Ship and Plane sub-header (select no more than one ship option and one aviation option)

International ship CO₂ emissions (annually-averaged) with simplified distribution from EDGAR scaled to scaled to annual values for 1985-2006 [Endresen et al. 2007].

International ship CO₂ emissions based on the International Comprehensive Ocean Atmosphere Data Set (ICOADS) with monthly variability [Corbett & Koehler, 2003, 2004; Wang et al., 2008] scaled to annual values for 1985-2006 [Endresen et al. 2007].

Aviation emission 3-D distribution from fuel burn (GEOS–Chem sulfate aerosol simulation) scaled to annual CO₂ values for 1985-2002 [Sausen & Schumann, 2000; Kim et al., 2005; 2007; Wilkerson et al., 2010] and estimates for 2002-2009. An associated surface correction automatically removes domestic aviation emissions from the main fossil fuel source in continental size regions.

Tagged CO₂ sub-header line (select all that apply)

Save CO₂ background

Tag biosphere regions (28), ocean regions (11) and the Rest of the World (ROW) as specified in the Regions_land.dat and Regions_ocean.dat files

NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.

Tag fossil fuel regions (28) as specified in the Regions_land.dat file and ROW

NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.

Tag global ship emissions as a single tracer

NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.

Tag global aviation emissions as a single tracer

NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.

Header line

Specify ANTHRO_Hg_YEAR (located in source code file mercury_mod.F), which is the baseline year of the anthropogenic mercury emissions that are used in the tagged mercury simulation. Current options are either 1995 or 2000.

Specify USE_CHECKS (located in source code file file ocean_mercury_mod.F). Set USE_CHECKS to T to stop with an error message if the sum of tagged tracers does not equal the total tracer, or F otherwise. This is useful for debugging.

Specify LDYNOCEAN (located in source code file logical_mod.F). Set LDYNOCEAN to T to use the online ocean mercury model (in source code file ocean_mercury_mod.F) or F to read ocean mercury concentrations from monthly mean files on disk.

Set to T if you want to run a preindustrial simulation (turn off anthropogenic emissions), to F otherwise.

If you have set LDYNOCEAN to T (i.e. you are using the online ocean mercury model), then you can specify the name of the ocean mercury restart file. This file saves the concentrations of oceanic mercury tracers for continuing the run at a later stage.

Set to T if you want to run GTMM online in GEOS–Chem. Note, that to use GTMM online, you need to first run GTMM offline up to equilibrium and to compile GEOS–Chem with GTMM enabled. For more information, please refer to this document.

If you are using the GTMM online, then you can specify the name of the GTMM mercury restart file. This file saves the monthly depositions of mercury tracers for continuing the run at a later stage.

Header line

Specify LCH4BUD (located in source code file logical_mod.F). Set LCH4BUD to T to calculate a monthly budget for CH4. The CH4 budget is not working well, we recommend setting LCH4BUD to F.

Specify LGAO (located in source code file logical_mod.F). Set LGAO to F to turn off CH4 emissions from gas and oil.

Specify LCOL (located in source code file logical_mod.F). Set LCOL to F to turn off CH4 emissions from coal.

Specify LLIV (located in source code file logical_mod.F). Set LLIV to F to turn off CH4 emissions from livestock.

Specify LWAST (located in source code file logical_mod.F). Set LWAST to F to turn off CH4 emissions from waste.

Specify LBFCH4 (located in source code file logical_mod.F). Set LBFCH4 to F to turn off CH4 emissions from biofuels.

Specify LRICE (located in source code file logical_mod.F). Set LRICE to F to turn off CH4 emissions from rice fields.

Specify LOTANT (located in source code file logical_mod.F). Set LOTANT to F to turn off other CH4 anthropogenic emissions.

Specify LBMCH4 (located in source code file logical_mod.F). Set LBMCH4 to F to turn off CH4 emissions from biomass burning.

Specify LWETL (located in source code file logical_mod.F). Set LWETL to F to turn off CH4 emissions from wetlands

Specify LSOABS (located in source code file logical_mod.F). Set LSOABS to F to turn off CH4 absorption by soils.

Specify LOTNAT (located in source code file logical_mod.F). Set LOTNAT to F to turn off other CH4 natural emissions.

Header line

Schedule diagnostic output for JANUARY. Place a 3 in the column corresponding to the day of the month (1–31) on which you want diagnostic output saved to the binary punch file.

In the example above, the columns which indicate January 1st and February 1st both have a 3 listed there. This will cause GEOS–Chem to archive diagnostic data for the entire month of January and then save it to disk at 0 GMT on February 1st. (GEOS–Chem is smart enough not to write anything to disk at 0 GMT on January 1st, since this is the starting time of the simulation.)

Schedule diagnostic output for FEBRUARY.

Schedule diagnostic output for MARCH.

Schedule diagnostic output for APRIL.

Schedule diagnostic output for MAY.

Schedule diagnostic output for JUNE.

Schedule diagnostic output for JULY.

Schedule diagnostic output for AUGUST.

Schedule diagnostic output for SEPTEMBER.

Schedule diagnostic output for OCTOBER.

Schedule diagnostic output for NOVEMBER.

Schedule diagnostic output for DECEMBER.

Header line

Path name of the diaginfo.dat file for GAMAP. GEOS–Chem will create this file, which will be customized to the particular simulation that is being done.

This may be either a relative path name (i.e. diaginfo.dat)
or absolute path name (i.e. /home/bmy/T/run.v9-01-03/diaginfo.dat).

Path name of the tracerinfo.dat file for GAMAP. GEOS–Chem will create this file, which will be customized to the particular simulation that is being done.

This may be either a relative path name (i.e. tracerinfo.dat)
or absolute path name (i.e. /home/bmy/T/run.v9-01-03/tracerinfo.dat).

Header line

Specify the name of the binary punch file. You may use date & time tokens YYYY, MM, DD, hh, mm, ss and GEOS–Chem will replace these with the appropriate values.

Header line.

ND01 (Rn–Pb–Be source) diagnostic settings. You must list the following information:

• Number of levels to save:
  
  • Entering 0 will turn off this diagnostic.
  • Entering 1 will archive data from level 1 (the surface level).
  • Entering 20 will archive data from level from 1 (surface) up to and including level 20.
  • Entering 30 will archive data from level from 1 (surface) up to and including level 30, etc.
    
    Note that the code is smart enough to prevent you from saving out more vertical levels than there are present for a given diagnostic.
    
    
• Tracer numbers to save. If you want to save all tracers for a given diagnostic, just type the word all. If you want to save specific tracer numbers then list them individually (separated by spaces).

You must list this information (number of levels and tracer numbers) for all other diagnostics in this menu. It is recommended to save out all tracers for a given diagnostic, unless you need to save disk space.

ND02 (Rn–Pb–Be decay) diagnostic settings.

ND03 (Mercury emissions, production & loss) diagnostic settings.

ND04 (CO2 prod/loss) diagnostic settings.

ND05 (sulfate prod & loss) diagnostic settings.

ND06 (mineral dust emissions) diagnostic settings.

ND07 (carbonaceous aerosol emissions) diagnostic settings.

ND08 (sea salt aerosol emissions) diagnostic settings.

ND10 (sources, production and loss of H2 and HD) diagnostic settings

ND11 (sea salt aerosol emissions) diagnostic settings.

ND12 (fraction of each layer in the PBL fraction) diagnostic settings.

ND13 (sulfate aerosol emissions) diagnostic settings.

ND14 (mass flux from cloud convection) diagnostic settings.

ND15 (mass flux from PBL mixing) diagnostic settings.

ND16 (fraction of grid box undergoing large scale & convective precip) diagnostic settings.

ND17 (fraction of soluble tracer lost to rainout) diagnostic settings.

ND18 (fraction of soluble tracer lost to washout) diagnostic settings.

ND19 (CH4 loss) diagnostic settings. For CH4 simulation only.

ND21 (optical depths of cloud, dust, and aerosols) diagnsotic settings.

ND22 (J-value photolysis rates) diagnostic settings.

Specify the averaging period (in local time) for the ND22 diagnostic. In the example above, J-value data from grid boxes where it is between 11:00 and 13:00 local time will be averaged and then saved to disk.

ND24 (E/W transport mass fluxes) diagnostic settings

ND25 (N/S transport mass fluxes) diagnostic settings

ND26 (vertical transport mass fluxes) diagnostic settings

ND27 (flux of tracer from the stratosphere) diagnostic settings

ND28 (biomass burning emissions) diagnostic settings. NOTE: the only tracers that have biomass burning emissions defined are:

ND29 (sources of CO) diagnostic settings

ND30 (surface map) diagnostic settings

ND31 (surface pressure) diagnostic settings.

ND32 (sources of NOx) diagnostic settings.

ND33 (column tracer) diagnostic settings. NOTE: This is more or less obsolete.

ND34 (biofuel emissions) diagnostic settings. NOTE: the only tracers that have biofuel emissions defined are:

ND35 (500 hPa tracers) diagnostic settings. NOTE: This is more or less obsolete now.

ND36 (anthropogenic emissions) diagnostic settings. NOTE: the only tracers that have anthropogenic emissions defined are:

ND37 (fraction of soluble tracer scavenged in updrafts in cloud convection) diagnostic settings.

ND38 (rainout loss of soluble tracer in convective updrafts) diagnostic settings.

ND39 (washout loss of soluble tracer in convective updrafts) diagnostic settings.

ND41 (afternoon PBL height) diagnostic settings.

ND42 (secondary organic aerosol concentration) diagnostic settings.

ND43 (chemically produced quantities) diagnostic settings.

Specify the averaging period (in local time) for OH and HO2 in the ND43 diagnostic. It is recommended to average OH and HO2 from 00:00 to 24:00 hours local time (i.e. all day long). This is shown in the example above.

Specify the averaging period (in local time) for NO and NO2 in the ND43 diagnostic. It is recommended to average NO and NO2 from 10:00 to 14:00 hours local time (i.e. around noon time). This is shown in the example above.

ND44 (dry deposition fluxes & velocities) diagnostic settings.

ND45 (tracer concentrations) diagnostic settings.

Specify the averaging period (in local time) for tracers in the ND45 diagnostic. It is recommended to average tracers from 00:00 to 24:00 hours local time (i.e. all day long). This is shown in the example above.

ND46 (biogenic emissions) diagnostic settings.

ND47 (24-hour tracer concentrations) diagnostic settings.

Free diagnostic (reserved for future use)

ND55 (tropopause height) diagnostic settings.

ND56 (lightning flashes) diagnostic settings.

ND62 (instantaneous column maps) diagnostic settings.

Free diagnostic (reserved for future use).

ND66 (3-D met fields) diagnostic settings.

ND67 (2-D met fields) diagnostic settings.

ND68 (boxheight & air mass) diagnostic settings.

ND69 (grid box surface area) diagnostic settings.

ND70 (turn on debug output) diagnostic settings.

Header line

Set this to T to turn on the plane flight following diagnostic (a.k.a. ND40 diagnostic). Set this switch to F to turn off the plane flight diagnostic.

Specify the name of the input file (usually called Planeflight.dat.YYYYMMDD) for the plane flight diagnostic. This file is described below. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS–Chem will replace these with the appropriate values.

If the plane flight diagnostic is turned on, then GEOS–Chem will look for a new Planeflight.dat.YYYYMMDD file for each YYYYMMDD date. Then it will save out various quantities along the flight track(s) define within the Planeflight.dat.YYYYMMDD file.

Specify the name of the output file (usually called plane.log) for the plane flight diagnostic. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS–Chem will replace these with the appropriate values.

Header line

Set this to T to turn on the ND48 station timeseries diagnostic. This allows you to save timeseries data of various quantities at specific grid boxes. Set this to F to turn off the ND48 station timeseries diagnostic.

Specify the name of the file which will contain output from the ND48 station timeseries diagnostic. This file will be in binary punch format and can be read by GAMAP. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS–Chem will replace these with the appropriate values.

Specify the frequency in minutes at which data will be archived by the ND48 station timeseries diagnostic. Recommended values: 60 minutes or 120 minutes.

Specify the number of ND48 stations at which timeseries data will be saved to disk.

For each ND48 station, you must provide the following information (separated by spaces):

• Longitude index
• Latitude index
• Number of levels to save
  • If you type 1, it will just save the surface level.
  • If you type 10, then it will save all levels from level 1 (surface) to level 10.
• ND48 diagnostic quantity number

Header line

Set this to T to turn on the ND49 instantaneous 3D timeseries diagnostic. This allows you to archive instantaneous timeseries data for various quantities from a 3D region of the globe.

Specify the name of the file which will contain output from the ND49 station timeseries diagnostic. This file will be in binary punch format and can be read by GAMAP. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS–Chem will replace these with the appropriate values.

Specify the ND49 diagnostic quantities to save to disk. Separate each number with a space.

Specify the frequency (in minutes) at which ND49 will save data for a 3D region of the globe data to disk. Recommended value: 180 min (3 hours). You may save data at a higher temporal resolution (e.g. every 60 min) but this will create HUGE data files!

Specify IMIN and IMAX, the indices which determine the longitude extent of the 3D region of the globe. Note that these are indices and not actual longitude values. To specify all 360 degrees of longitude, type the following:

• For GCAP 4° x 5° grid: 1 72
• For GMAO 4° x 5° grid: 1 72
• For GMAO 2° x 2.5° grid: 1 144

Also, note you can wrap around the date line. In the example shown above, IMIN=70 and IMAX=30. This will create a 3D region (assuming 4x5 grid) which starts at 165° E longitude and extends across the date line to 35° W longitude.

Specify JMIN and JMAX, the indices which determine the latitude extent of the 3D region of the globe. Note that these are indices and not actual latitude values. To specify all 180 degrees of latitude, type the following:

• For GCAP 4° x 5° grid: 1 45
• For GMAO 4° x 5° grid: 1 46
• For GMAO 2° x 2.5° grid: 1 91

Specify LMIN and LMAX, the indices which determine the vertical extent of the 3D region of the globe.

Header line

Set this to T to turn on the ND50 24-hour 3D timeseries diagnostic. This allows you save to archive 24-hour averaged data from a 3D region of the globe.

Specify the name of the file which will contain output from the ND49 station timeseries diagnostic. This file will be in binary punch format and can be read by GAMAP. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS–Chem will replace these with the appropriate values.

To output the ND50 diagnostic quantities in HDF5 format.

Note: HDF5 must be installed on your system for using this option.
(The GEOS–Chem support team does not provide help for the installation of this library)

Specify the ND50 diagnostic quantities to save to disk. Separate each number with a space.

Specify IMIN and IMAX, the indices which determine the longitude extent of the 3D region of the globe. Note that these are indices and not actual longitude values. To specify all 360 degrees of longitude, type the following:

• For GCAP 4° x 5° grid: 1 72
• For GMAO 4° x 5° grid: 1 72
• For GMAO 2° x 2.5° grid: 1 144

Also, note you can wrap around the date line. In the example shown above, IMIN=70 and IMAX=30. This will create a 3D region (assuming 4x5 grid) which starts at 165° E longitude and extends across the date line to 35° W longitude.

Specify JMIN and JMAX, the indices which determine the latitude extent of the 3D region of the globe. Note that these are indices and not actual latitude values. To specify all 180 degrees of latitude, type the following:

• For GCAP 4° x 5° grid: 1 45
• For GMAO 4° x 5° grid: 1 46
• For GMAO 2° x 2.5° grid: 1 91

Specify LMIN and LMAX, the indices which determine the vertical extent of the 3D region of the globe.

Header line

Set this to T to turn on the ND51 "satellite" 3D timeseries diagnostic. ND51 allows you to archive 3D data blocks for various quantities which have been time-averaged between 2 local times. This is useful for comparing model data to sun-synchronous satellites such as GOME or MOPITT which have morning overpass times.

Specify the name of the file which will contain output from the ND51 station timeseries diagnostic. This file will be in binary punch format and can be read by GAMAP. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS–Chem will replace these with the appropriate values.

To output the ND50 diagnostic quantities in HDF format.

Note: HDF5 must be installed on your system for using this option.
(The GEOS–Chem support team does not provide help for the installation of this library)

Specify the ND51 diagnostic quantities to save to disk. Separate each number with a space.

6

Specify the time of day (in GMT hours) at which the ND51 timeseries file will be written to disk. Recommended value: 0 GMT each day.

Specify the ND51 time averaging window (in local time hours). Only data from grid boxes where the local time falls within this window will be included in the diagnostic averaging process. Recommended values: 10:00 to 12:00 LT. This will cover both GOME and MOPITT overpasses.

Specify IMIN and IMAX, the indices which determine the longitude extent of the 3D region of the globe. Note that these are indices and not actual longitude values. To specify all 360 degrees of longitude, type the following:

• For GCAP 4° x 5° grid: 1 72
• For GMAO 4° x 5° grid: 1 72
• For GMAO 2° x 2.5° grid: 1 144

Also, note you can wrap around the date line. In the example shown above, IMIN=70 and IMAX=30. This will create a 3D region (assuming 4x5 grid) which starts at 165° E longitude and extends across the date line to 35° W longitude.

Specify JMIN and JMAX, the indices which determine the latitude extent of the 3D region of the globe. Note that these are indices and not actual latitude values. To specify all 180 degrees of latitude, type the following:

• For GCAP 4° x 5° grid: 1 45
• For GMAO 4° x 5° grid: 1 46
• For GMAO 2° x 2.5° grid: 1 91

Specify LMIN and LMAX, the indices which determine the vertical extent of the 3D region of the globe.

Header line

Set this to T to turn on the ND63 ship timeseries diagnostic.

Specify the name of the file which will contain output from the ND63 timeseries diagnostic. This file will be in binary punch format and can be read by GAMAP. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS–Chem will replace these with the appropriate values.

Specify the ND63 diagnostic quantities to save to disk.

5

Specify the frequency (in minutes) at which the ND63 timeseries file will be written to disk.

Specify IMIN and IMAX, the indices which determine the longitude extent of the 3D region of the globe. Note that these are indices and not actual longitude values. To specify all 360 degrees of longitude, type the following:

• For GCAP 4° x 5° grid: 1 72
• For GMAO 4° x 5° grid: 1 72
• For GMAO 2° x 2.5° grid: 1 144

Also, note you can wrap around the date line. In the example shown above, IMIN=70 and IMAX=30. This will create a 3D region (assuming 4x5 grid) which starts at 165° E longitude and extends across the date line to 35° W longitude.

Specify JMIN and JMAX, the indices which determine the latitude extent of the 3D region of the globe. Note that these are indices and not actual latitude values. To specify all 180 degrees of latitude, type the following:

• For GCAP 4° x 5° grid: 1 45
• For GMAO 4° x 5° grid: 1 46
• For GMAO 2° x 2.5° grid: 1 91

Header line

Set this switch to T if you wish to save out chemical production for family tracers (a.k.a. the ND65 diagnostic), or F otherwise.

• If you type 1, it will just save the surface level.
• If you type 20, then it will save all levels from level 1 (surface) to level 20, etc.

If you are performing a full-chemistry simulation, then you may only archive production and loss data within the troposphere. This is because SMVGEAR does not do chemistry in the stratosphere. For other types of simulations (e.g. tagged Ox, tagged CO), you may archive production and loss data from all levels.

Set this switch to T if you wish to archive P(Ox) and L(Ox) rates from a full chemistry simulation into binary punch format, so that these rates can be used to drive a future tagged Ox simulation (a.k.a. ND20 diagnostic).

Specify the number of production and loss families to archive. You must list each family below.

Entry for the POx chemical production family (assuming we are performing a full-chemistry simulation). The family name comes first and must be followed by a colon. Then you must list the individual species which constitute the POx family. A number in front of a species name is the coefficient by which that species will be multiplied. (You do not have to list the coefficient if it is 1.) Since the family name POx begins with a P, it is interpreted to be a chemical production family.

Entry for the LOx chemical production family (assuming we are performing a full-chemistry simulation). You may proceed as described above. Since the family name LOx begins with an L, it is interpreted to be a chemical loss family.

Entry for the PCO chemical production family.

Entry for the LCO chemical production family.

Entry for the PBrOx chemical production family.

Entry for the PBry chemical production family.

Entry for the LBry chemical production family.

Header line

Specify OH_DIR (located in source code file directory_mod.F). OH_DIR is directory path where the offline monthly-mean OH files are stored.

Header line

Specify O3_PL_DIR (located in source code file directory_mod.F). O3_PL_DIR is directory path where the P(Ox) and L(Ox) rates are stored, or where they will be created. These rates, which have been archived from a full-chemistry simulation, are required to drive a tagged Ox simulation.

Header line

Specify LWINDO (located in source code file logical_mod.F). Set LWINDO to T if you wish to save out boundary conditions from a GEOS–Chem simulation, or F otherwise. Before you run at the nested-grid resolution, you must first save out boundary conditions from a global GEOS–Chem simulation (usually 2° x 2.5°).

Specify LWINDO2x25 (located in source code file logical_mod.F):

• If you are using boundary conditions saved from a 2° x 2.5° GEOS–Chem simulation, then set Set LWINDO2x25 to T.
• If you are using boundary conditions saved from a 4° x 5° GEOS–Chem simulation, then set Set LWINDO2x25 to F.

Specify TPBC_DIR_NA (located in source code file directory_mod.F). TPBC_DIR_NA is the directory path where you have stored the boundary conditions for your North American nested-grid simulation.

Specify TPBC_DIR_EU (located in source code file directory_mod.F). TPBC_DIR_EU is the directory path where you have stored the boundary conditions for your European nested-grid simulation.

Specify TPBC_DIR_CH (located in source code file directory_mod.F). TPBC_DIR_CH is the directory path where you have stored the boundary conditions for your China/SE Asia nested-grid simulation.

Specify TPBC_DIR_SE (located in source code file directory_mod.F). TPBC_DIR_SE is the directory path where you have stored the boundary conditions for your SEAC4RS nested-grid simulation.

Specify TPBC_DIR_CU (located in source code file directory_mod.F). TPBC_DIR_CU is the directory path where you have stored the boundary conditions for your custom-domain nested-grid simulation.

Specify the frequency in minutes at which the 2° x 2.5° or 4° x 5° boundary conditions will be saved to disk. Recommended value: 180 min (3 hours).

Specify I1_BC and J1_BC (located in source code file tpcore_bc_mod.F). I1_BC and J1_BC are the longitude and latitude indices of the grid box at the LOWER LEFT CORNER of the region in which 4° x 5° boundary conditions are being saved. In the example listed above, I1_BC=51 and J1_BC=21 denotes the grid box (70°E, 10°S).

Specify I2_BC and J2_BC (located in source code file tpcore_bc_mod.F). I2_BC and J2_BC are the longitude and latitude indices of the grid box at the UPPER RIGHT CORNER of the 4° x 5° window region in which boundary conditions are being saved. In the example listed above, I2_BC=67 and J2_BC=37 denotes the grid box (150°E, 54°N).

Specify I0_W and J0_W (located in source code file tpcore_bc_mod.F). I0_W and J0_W are the 1° x 1° nested grid longitude and latitude offsets (in # of boxes) of the which are used to define an inner window reion in which transport is actually done. The region in which transport is done in the 1° x 1° window is smaller than the actual size of them 1° x 1° nested grid met fields in order to account for the boundary conditions. Please see the comments to the source code file tpcore_bc_mod.F for more information. Recommended values: I0_W=3 and J0_W=3.

Header line

Specify BACKGROUND (located in source code file unix_cmds_mod.F). Set BACKGROUND to the symbol which is used to place Unix jobs in the background. Recommended value: "&".

Specify REDIRECT (located in source code file unix_cmds_mod.F). Set REDIRECT to the symbol which is used to redirect output from one file to another. Recommended value: "  >". (NOTE: leave a space before the greater than sign.)

Specify REMOVE_CMD (located in source code file unix_cmds_mod.F). Set REMOVE_CMD to the string which defines the Unix remove file command. Recommended value: "rm -f".

Specify SEPARATOR (located in source code file unix_cmds_mod.F). Set SEPARATOR to the symbol which is used as the directory path separator. Recommended value: "/".

Specify STAR (located in source code file unix_cmds_mod.F). Set STAR to the symbol which is used as the Unix wild card character. Recommended value: "*".

Specify UNZIP_CMD (located in source code file unix_cmds_mod.F). Set UNZIP_CMD to the string which defines the file unzipping command. Recommended value: "gzip -dc".

Specify ZIP_SUFFIX (located in source code file unix_cmds_mod.F). Set ZIP_SUFFIX to the file extension string which is used to denote compressed files. Recommended value: ".gz".

Header lines with comments

Number of diagnostic quantities to print out.

Separator line

Here we list the diagnostic quantities that we want to print out at each flight track location. (For clarity, only a few flight track locations are listed, but in reality, you can list thousands of locations.)

As shown above, you may specify multiple flight tracks in a Planeflight.dat file. The only restriction is that flight track locations must be listed in increasing order of GMT.

Separator Lines

Comment line which shows you where to line up each column field of the flight track points.

Here we list quantities which define each flight track point. Make sure that each field lines up with the guides in the line above.

GEOS–Chem will loop through each of the flight track points listed in Planeflight.dat and print out each of the diagnostic quantities. GEOS–Chem will pick the nearest model box to each flight track point for comparison. In the future we may introduce a more intelligent interpolation scheme.

Note that it is OK to list flight track points from more than one aircraft in the same Planeflight.dat.YYYYMMDD file (as is shown above). However, all flight track points must be listed in increasing order of GMT time or else they will not be interpreted correctly by GEOS–Chem.

Ending line

Output file (binary punch format) from the ND63 ship timeseries.

A new file (timestamped with YYYYMMDD) will be created for each new day.

Output file (binary punch format) from the ND48 station timeseries diagnostic.

A new file (timestamped with YYYYMMDD) will be created for each new day.

NOTE: You can use the GAMAP routine GC_COMBINE_ND48 to work with this file. Click here for more information. This diagnostic is somewhat obsolete. We recommend using ND49 to save a region of the world and post-process the output to get the output at the stations positions.

Output file (binary punch format) from the ND49 instantaneous timeseries diagnostic.

A new file (timestamped with YYYYMMDD) will be created for each new day.

NOTE: You can use the GAMAP routine GC_COMBINE_ND49 to work with this file. Click here for more information.

Output file (binary punch format) from the ND50 24-hr average timeseries diagnostic.

A new file (timestamped with YYYYMMDD) will be created for each new day.

NOTE: You can use the GAMAP routine GC_COMBINE_ND49 to work with this file. Click here for more information.

Output file (binary punch format) from the ND51 local-time-averaged timeseries, also known as satellite timeseries).

A new file (timestamped with YYYYMMDD) will be created for each new day.

NOTE: You can use the GAMAP routine GC_COMBINE_ND49 to work with this file. Click here for more information.

Restart file (binary punch format) for gas-phase and aerosol tracers for year/month/date YYYYMMDD.

This file saves instantaneous concentrations of all tracers on all levels for continuation of the run at a later stage.

NOTE: You may use the GAMAP routines REGRIDV_RESTART and REGRIDH_RESTART to vertically and horizontally regrid restart files from one grid to another.

restart.cspec.YYYYMMDDhh

Restart file (binary punch format) for all chemical species for year/month/day/hour YYYYMMDDhh.

This file saves instantaneous concentrations of all tracers on all levels for continuation of the run at a later stage.

NOTE: If you are going to be running a very long GEOS–Chem simulation, and must split the job into several stages (i.e. in order to submit to a queue system), then you should set LSVCSPEC to T. This will make sure that the chemical species stored in the CSPEC array will not get reset to the background defaults (from globchem.dat) when the next run stage starts.

Restart file (binary punch format) for APROD and GPROD quantities for year/month/date YYYYMMDD.

This file saves the various quantities stored in the APROD and GPROD arrays in GEOS–Chem source code file carbon_mod.F for continuation of the run at a later stage.

This is necessary if you are performing a simulation with secondary organic aerosol tracers or with dicarbonyls.

NOTE: You can use the GAMAP routines REWRITE_AGPROD, REGRIDV_RESTART, and REGRIDH_RESTART to regrid these files from one horizontal resolution to another. Click here for more information.

Restart file (binary punch format) for the online mercury model for year/month/date YYYYMMDD.

This file saves the concentrations of tagged mercury tracers in the ocean (from GEOS–Chem source code file ocean_mercury_mod.F) for continuation of the run at a later stage.

NOTE: You may use the GAMAP routines REGRIDV_RESTART and REGRIDH_RESTART to vertically and horizontally regrid restart files from one grid to another.

File (binary punch format) containing time-averaged diagnostic output from GEOS–Chem. Most of the GEOS–Chem diagnostics will place their output in this file.

A single file containing multiple data blocks will be created.

File (text format) that lists diagnostic categories contained in the ctm.bpch file. This file facilitates reading and plotting of the data with the GAMAP package.

For more information, please see the GAMAP Online User's Guide, Chapter 7.2.

File (text format) that lists the tracer numbers for each diagnostic category contained in the ctm.bpch file. This file facilitates reading and plotting of the data with the GAMAP package.

For more information, please see the GAMAP Online User's Guide, Chapter 7.3.

File (text format) containing echo-back of input from SMVGEAR II. Check this file to see if SMVGEAR read the globchem.dat file properly.

This file will also contain information about reactions and species used by the ND65 prod-loss diagnostic. (This file is only produced when SMVGEAR is used, i.e. for full NOx-Ox-hydrocarbon chemistry only.)

File (text format) containing output from the ND40 planeflight diagnostic, scheduled via the Planeflight.dat file (see above).

NOTE: You can use GAMAP routines CTM_READ_PLANEFLlGHT and PLANE_PLOT to read and plot output from this file.