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: 66 advected tracers, our default simulation.
2. SOA: 93 advected tracers, with secondary organic aerosols
3. SOA with semivolatile POA: 100 advected tracers, with secondary organic aerosols with semivolatile primary organic aerosols
4. dicarbonyls: 107 advected tracers, with dicarbonyl chemistry (NOTE: this simulation is in need of updating)

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 concentrations of the transported tracers specified in the Tracer Menu. You can change the name of the restart file to match the file that you have. 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 (stored in Input_Opt%DATA_DIR). 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 Input_Opt%GCAP_DIR.

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 Input_Opt%GEOS_4_DIR.

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 Input_Opt%GEOS_5_DIR.

Specify the directory path where GEOS–FP met fields are stored. You may include the YYYY and MM tokens as described above. This is stored in the variable Input_Opt%GEOS_FP_DIR.

Specify DATA_DIR_1x1 (stored in Input_Opt%DATA_DIR_1x1). 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. As of v9–01–03, GEOS–Chem 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 (stored in Input_Opt%TEMP_DIR). 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 (stored in Input_Opt%LUNZIP). 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 (stored in Input_Opt%LWAIT). 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 files 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 (stored in Input_Opt%IO, Input_Opt%JO). 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 simulation is 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 simulation is in need of updating)
14. POPs simulation

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

Specify N_TRACERS (stored in Input_Opt%N_TRACERS). 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 66 (as shown in the example above).
2. with secondary organic aerosols (SOA), then set N_TRACERS to 93.
3. with dicarbonyl chemistry, then set N_TRACERS to 107. (NOTE: this simulation is in need of updating)

Entry for the NO 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. NO is not a family tracer (i.e. it has no constituent species other than itself).

• You must also denote species which have emission reactions in the SMVGEAR chemical mechanism by placing parentheses around the species name. In this case, NO is an emitted species in the SMVGEAR chemical mechanism, 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. NO has a coefficient of one, and thus the number may be omitted.

Entry for the O3 tracer. As with NO, you must list the tracer number, name, and molecular weight. O3 has an emission reaction defined in the SMVGEAR chemical mechanism, so you need to list (O3) in parenthesis after the molecular weight in g/mole.

Entry for the PAN tracer: As with NO, you must list the tracer number, name, and molecular weight. However, PAN is not a family tracer and it 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 NO you must list the tracer number, name, and molecular weight. CO has an emission reaction defined in the SMVGEAR chemical mechanism, so you need to list (CO) in parentheses after the molecular weight in g/mole.

Entry for the ALK4 (C4 lumped alkanes) tracer: As with NO 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. 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 and has an emission reaction defined in the SMVGEAR chemical mechanism.

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 GEOS–Chem aerosol tracers.

Entries for the GEOS–Chem sea salt tracers.

NOTE: The molecular weight of 31.4 g/mole is consistent with actual average composition of sea salt, and international guidelines from the IAPWS. You may use the molecular weight of any individual constituent of interest.

Entries for the GEOS–Chem bromine tracers.

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

Entry for the MPN tracer.

Entries for the GEOS–Chem isoprene tracers.

• ISOPN is a family tracer (which consists of ISOPND + ISOPNB). Therefore, you must list the constituent species as shown above.

• MMN is a family tracer (which consists of MVKN + MACRN). Therefore, you must list the constituent species as shown above.

Entries for NO2, NO3, HNO2.

Header line

Specify LTRAN (stored in Input_Opt%LTRAN). Set LTRAN to T to turn on TPCORE transport, or set to F to turn off TPCORE transport.

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

Specify the IORD, JORD, KORD transport options for TPCORE (stored in Input_Opt%TPCORE_IORD, Input_Opt%TPCORE_JORD, Input_Opt%TPCORE_KORD). 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, stored in Input_Opt%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 (stored in Input_Opt%LCONV). Set LCONV to T to turn on cloud convection.

Specify LTURB (stored in Input_Opt%LTURB). Set LTURB to T to turn on PBL mixing.

Specify LNLPBL (stored in Input_Opt%LNLPBL). 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, stored in Input_Opt%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 (stored in Input_Opt%LEMIS). 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, stored in Input_Opt%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 (stored in Input_Opt%LANTHRO). Set LANTHRO to T to include anthropogenic emission, or to F to shut off all anthropogenic emission.

Specify FSCALYR (stored in Input_Opt%FSCALYR), the emission year for anthropogenic emissions. 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 1985-2010. Before 1985, 1985 is used and after 2010, 2010 is used. It is recommended to set this input to -1 to let GEOS–Chem automatically scale data to the year simulated.

Specify LEMEP (stored in Input_Opt%LEMEP). Set LEMEP to T to include EMEP European anthropogenic emissions, or to F otherwise.

Specify LBRAVO (stored in Input_Opt%LBRAVO). Set LBRAVO to T to include BRAVO anthropogenic emissions over Mexico, or to F otherwise.

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

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

Specify LNEI05 (located in source code file Input_Opt%LNEI05). 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 (stored in Input_Opt%LNEI99). 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 (stored in Input_Opt%LBIOFUEL). Set LBIOFUEL to T to include biofuel emissions, or to F to shut off all biofuel emission.

Specify LBIOGENIC (stored in Input_Opt%LBIOGENIC). Set LBIOGENIC to T to include biogenic emissions (e.g. ISOPRENE, MONOTERPENES), or to F to shut off all biogenic emission.

Specify LMEGAN (stored in Input_Opt%LMEGAN). 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 were removed in GEOS–Chem v9–01–03.

Specify LPECCA (stored in Input_Opt%LPECCA).

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 (stored in Input_Opt%ISOP_SCALING). 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 (stored in Input_Mod%LBIOMASS). Set LBIOMASS to T to include biomass burning emissions, or to F to shut off all biomass burning emissions.

Specify LBBSEA (stored in Input_Opt%LBBSEA). 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 (stored in Input_Mod%LTOMSAI). 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 (stored in Input_Opt%LGFED2BB). 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 (stored in Input_Opt%LGFED3BB). 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 (stored in Input_Opt%LDAYBB). 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 (stored in Input_Opt%L3HRBB3). 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 LRCPAIR (stored in Input_Opt%LRCPAIR). Set LRCPAIR to T to include aircraft emissions from the RCP future emission scenarios, or to F to shut off RCP aircraft NOx emissions.

NOTE: This option requires that the LAEIC option be turned off.

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

Specify LOTDSCALE (stored in Input_Opt%LOTDSCALE) 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 (stored in Input_Opt%LSOILNOX). Set LSOILNOX to T to include soil NOx emissions, or to F to shut off soil NOx emissions other than fertilizer NOx emissions.

• 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 soil NOx restart file name such as restart.soilnox.YYYYMMDDhh should suffice for most applications.

Specify LICOADSSHIP (stored in Input_Opt%LICOADSSHIP). Set LICOADSSHIP to T to use ICOADS ship emissions, or to F otherwise.

NOTE: If LEDGARSHIP and LICOADSSHIP are both set to T, then LICOADSSHIP will be used.

Specify LRCPSHIP (stored in Input_Opt%LRCPSHIP). Set LRCPSHIP to T to use ship emissions from the RCP future emission scenarios, or to F otherwise.

NOTE: This option requires that both LEDGARSHIP and LICOADSSHIP be turned off.

Specify LEMEPSHIP (stored in Input_Opt%LEMEPSHIP). Set LEMEPSHIP to T to use EMEP ship emissions for Europe, or to F otherwise.

NOTE: This option requires that LEMEP be turned on.

Specify LSHIPSO2 (stored in Input_Opt%LSHIPSO2). Set LSHIPSO2 to T to include SO2 emissions from ship exhaust, or to F to shut off SO2 emissions from ship exhaust.

Specify LARCSHIP (stored in Input_Opt%LARCSHIP). Set LARCSHIP to T to include ARCTAS SO2 and CO2 ship emissions, or to F otherwise.

Specify LWARWICK_VSLS (stored in Input_Opt%LWARWICK_VSLS). Set LWARWICK_VSLS to T to use surface CHBr3 emissions from Warwick et al. (2006), scenario 3 (400 Gg CHBr3/year).

Specify LSSABr2 (stored in Input_Opt%LSSABr2). 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 (stored in Input_Opt%LFIX_PBL_BrO). Set LFIX_PBL_BrO to T to set Bro concentrations in the PBL equal to 1 ppt during the day.

Set Br_SCALING (stored in 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. To turn off bromine emissions, set Br_SCALING to 0.

Header line

Specify LFUTURE (stored in Input_Opt%LFUTURE). Set LFUTURE to T to scale present-day emissions to one of the IPCC future scenarios, or F otherwise.

Specify FUTURE_YEAR (stored in Input_Opt%FUTURE_YEAR), which is the year to which the current emissions will be scaled. Current options are 2030 and 2050.

Specify FUTURE_SCEN (stored in Input_Opt%FUTURE_SCEN), which is the IPCC scenario to be used. Current options are: A1, B1.

Header line

Specify LSULF (stored in Input_Opt%LSULF). Set LSULF to T to turn on emissions and chemistry for sulfate aerosols (DMS, SO2, SO4, MSA, NH3, NH4, NIT).

Specify LCRYST (stored in Input_Opt%LCRYST). 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 (stored in Input_Opt%LCARB). Set LCARB to T to turn on emissions and chemistry for carbonaceous aerosols (BCPI, BCPO, OCPI, OCPO).

Specify LSOA (stored in Input_Opt%LSOA). Set LSOA to T to turn on emissions and chemistry for secondary organic aerosols. Turning on the secondary organic aerosols will add 27 tracers to the simulation.

Specify LSVPOA (stored in Input_Opt%LSVPOA). Set LSVPOA to T to use the semivolatile POA option.

Specify scale factor for the napthalene-like IVOC emissions (stored in Input_Opt%NAPEMISS). The recommended setting for NAPEMISS scaling is 1.0.

Specify scale factor for the POA emissions (stored in Input_Opt%POAEMISSSCALE). The recommended setting for POAEMISSSCALE is 1.27.

Specify LDUST (stored in Input_Opt%LDUST). Set LDUST to T to turn on emissions and chemistry for mineral dust aerosol tracers (DST1, DST2, DST3, DST4).

Specify LDEAD (stored in Input_Opt%LDEAD). 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 (stored in Input_Opt%LSSALT). 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 (stored in variable Input_Opt%SALA_REDGE_um). Recommended setting: 0.01 to 0.5 microns.

Specify the edges which denote coarse mode sea salt tracer in microns (stored in Input_Opt%SALC_REDGE_um). Recommended setting: 0.5 to 8 microns.

Header line

Specify LDRYD (stored in Input_Opt%LDRYD). Set LDRYD to T to turn on dry deposition, or F to turn off dry deposition.

Specify LWETD (stored in Input_Opt%LWETD). Set LWETD to T to turn on wet deposition, or F to turn off wet deposition.

Header line

Specify LCHEM (stored in Input_Opt%LCHEM). Set LCHEM to T to turn on chemistry, or F to turn off chemistry.

Specify LSCHEM (stored in Input_Opt%LSCHEM). Set LSCHEM to T to turn on stratospheric chemistry, or F to turn off stratospheric chemistry.

Specify LLINOZ (stored in Input_Opt%LLINOZ). Set LLINOZ to T to use Linoz for O3 chemistry in the stratosphere, otherwise Synoz will be used.

Specify the chemistry timestep (TS_CHEM, stored in Input_Opt%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 (stored in Input_Opt%LSVCSPEC). Set LSVCSPEC to T to save concentrations (stored in the CSPEC_FULL array) of all species listed in the globchem.dat file to a CSPEC restart file, or to F otherwise. The CSPEC restart file is saved in addition to the standard restart file, which saves only concentrations of transported tracers. If LSVCSPEC is F or if GEOS-Chem can't find a CSPEC restart file at the beginning of a simulation, then the chemical species will be set to the default concentrations specified in globchem.dat.

If the option Make new restart file is set to F in the Simulation Menu, then no CSPEC restart file will be saved regardless of the value of LSVCSPEC.

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 stay within the computational time limts of your system), then you should set LSVCSPEC to T. This will make sure that the chemical species concentrations are preserved when the next run stage starts. Otherwise, GEOS-Chem will use the default species concentrations specified in globchem.dat.

• 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 CSPEC restart file name such as restart.cspec.YYYYMMDDhh should suffice for most applications.

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]. This is stored in the variable Input_Opt%LGENFF.

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]. This is stored in the variable Input_Opt%LANNFF.

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]. This is stored in the variable Input_Opt%LMONFF.

3-D CO₂ chemical source from oxidation of CO, CH₄ and NMHCs based on Suntharalingam et al. [2005], with appropriate surface emission corrections. This is stored in the variable Input_Opt%LCHEMCO2.

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

Seasonally approximated biomass burning emissions from Duncan et al. [2003]. This is stored in the variable Input_Opt%LSEASBB.

Global Fire Emission Database (GFED) version 2 – monthly (1997-2008). This is stored in the variable Input_Opt%LGFED2BB.

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). This is stored in the variable Input_Opt%L8DAYBB.

NOTE: The choice of GFED emissions in the CO2 MENU must be consistent with the choice in the EMISSIONS MENU.

NOTE: The choice of GFED emissions in the CO2 MENU must be consistent with the choice in the EMISSIONS MENU.

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]. This is stored in the variable Input_Opt%LBIOFUEL.

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]. This is stored in the variable Input_Opt%LBIODAILY.

CASA model 3-hourly Net Ecosystem Production (balanced – no net annual flux) [Potter et al., 1993; Olsen and Randerson, 2004]. This is stored in the variable Input_Opt%LBIODIURNAL.

Net Terrestrial Exchange (original) of -1.01 PgC/yr. This is stored in the variable Input_Opt%LBIONETORIG.

Net Terrestrial Exchange (climatology) of -5.29 PgC/yr [Baker et al., 2006] adjusted for biomass/biofuel burning. This is stored in the variable Input_Opt%LBIONETCLIM.

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]. This is stored in the variable Input_Opt%LOCN1997.

Annual ocean flux climatology of non-El Niño years from Takahashi et al. [2009]. This is stored in the variable Input_Opt%LOCN2009ANN.

Monthly ocean flux climatology of non-El Niño years from Takahashi et al. [2009]. This is stored in the variable Input_Opt%LOCN2009MON.

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]. This is stored in the variable Input_Opt%LSHIPEDG.

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]. This is stored in the variable Input_Opt%LSHIPICO.

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. This is stored in the variable Input_Opt%LPLANE.

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

Save CO₂ background. This is stored in the variable Input_Opt%LFFBKGRD.

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. This is stored in the variable Input_Opt%LBIOSPHTAG.

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. This is stored in the variable Input_Opt%LFOSSILTAG.

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. This is stored in the variable Input_Opt%LSHIPTAG.

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. This is stored in the variable Input_Opt%LPLANETAG.

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 (stored in Input_Opt%ANTHRO_Hg_YEAR), which is the baseline year of the anthropogenic mercury emissions that are used in the tagged mercury simulation. Current options are either 2006 or 2050.

Specify Hg_SCENARIO (stored in Input_Opt%Hg_SCENARIO). Future emissions are based on the four IPCC SRES scenarios. Current options are PRESENT, A1B, A2, B1, or B2.

Specify USE_CHECKS (stored in Input_Opt%USE_CHECKS). 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 (stored in Input_Opt%LDYNOCEAN). 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.

Specify LPREINDHG (stored in Input_Opt%LPREINDHG). 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.

specify LGTMM (stored in Input_Opt%LGTMM). 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 POP_TYPE (stored in Input_Opt%POP_TYPE). Current options are PHE (phenanthrene), PYR (pyrene), or BAP (benzo[a]pyrene).

Specify CHEM_PROCESS (stored in Input_Opt%CHEM_PROCESS). Set CHEM_PROCESS to T to use POPs chemistry.

Specify the name of the POPs emission file. Current options are PHE_EM_1x1.bpch, PYR_EM_1x1.bpch, or BaP_EM_1x1.bpch.

Specify molecular weight of POP_TYPE in kg/mol (stored in Input_Opt%POP_XMW).

Specify the POP octanol-water partition coefficient (stored in Input_Opt%POP_KOA).

Specify the POP black carbon-air partition coefficient (stored in Input_Opt%POP_KBC).

Specify the POP reaction rate constant for reaction of gas phase POP with hydroxyl radical in cm3/molec/s (stored in Input_Opt%POP_K_POPG_OH).

Specify the POP reaction rate constant for reaction of particle phase POP with ozone in s-1 (stored in Input_Opt%POP_K_POPP_O3A).

Specify the POP reaction rate constant for reaction of particle phase POP with ozone in molec/cm3 (stored in Input_Opt%POP_K_POPP_O3B).

Specify the Henry's Law constant for POP_TYPE (stored in Input_Opt%POP_HSTAR).

Specify the enthalpy of air-water exchange in J/mol (stored in Input_Opt%POP_DEL_H).

Specify the enthalpy of phase transfer from gas phase to particle phase (stored in Input_Opt%POP_DEL_Hw).

Header line

Specify LCH4BUD (stored in Input_Opt%LCH4BUD). 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 (stored in Input_Opt%LGAO). Set LGAO to F to turn off CH4 emissions from gas and oil.

Specify LCOL (stored in Input_Opt%LCOL). Set LCOL to F to turn off CH4 emissions from coal.

Specify LLIV (stored in Input_Opt%LLIV). Set LLIV to F to turn off CH4 emissions from livestock.

Specify LWAST (stored in Input_Opt%LWAST). Set LWAST to F to turn off CH4 emissions from waste.

Specify LBFCH4 (stored in Input_Opt%LBFCH4). Set LBFCH4 to F to turn off CH4 emissions from biofuels.

Specify LRICE (stored in Input_Opt%LRICE). Set LRICE to F to turn off CH4 emissions from rice fields.

Specify LOTANT (stored in Input_Opt%LOTANT). Set LOTANT to F to turn off other CH4 anthropogenic emissions.

Specify LBMCH4 (stored in Input_Opt%LBMCH4). Set LBMCH4 to F to turn off CH4 emissions from biomass burning.

Specify LWETL (stored in Input_Opt%LWETL). Set LWETL to F to turn off CH4 emissions from wetlands

Specify LSOABS (stored in Input_Opt%LSOABS). Set LSOABS to F to turn off CH4 absorption by soils.

Specify LOTNAT (stored in Input_Opt%LOTNAT). 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 an 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 an 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 for 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.

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.

ND53 (POPs emissions) diagnostic settings. For POPs simulation only.

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.

NOTE: The chemical family production & loss diagnostic must be turned off when using the KPP chemical solver.

• 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 (stored in Input_Opt%OH_DIR). OH_DIR is directory path where the offline monthly-mean OH files are stored.

Header line

Specify O3_PL_DIR (stored in Input_Opt%O3_PL_DIR). 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 (stored in Input_Opt%LWINDO). 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 (stored in Input_Opt%LWINDO2x25):

• 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 (stored in Input_Opt%TPBC_DIR_NA). 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 (stored in Input_Opt%TPBC_DIR_EU). TPBC_DIR_EU is the directory path where you have stored the boundary conditions for your European nested-grid simulation.

Specify TPBC_DIR_CH (stored in Input_Opt%TPBC_DIR_CH). 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 (stored in Input_Opt%TPBC_DIR_SE). TPBC_DIR_SE is the directory path where you have stored the boundary conditions for your SE Asia nested-grid simulation.

Specify TPBC_DIR_CU (stored in Input_Opt%TPBC_DIR_CU). 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 (stored in 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 (stored in 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 (stored in Input_Opt%BACKGROUND). Set BACKGROUND to the symbol which is used to place Unix jobs in the background. Recommended value: "&".

Specify REDIRECT (stored in Input_Opt%REDIRECT). 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 (stored in Input_Opt%REMOVE_CMD). Set REMOVE_CMD to the string which defines the Unix remove file command. Recommended value: "rm -f".

Specify SEPARATOR (stored in Input_Opt%SEPARATOR). Set SEPARATOR to the symbol which is used as the directory path separator. Recommended value: "/".

Specify STAR (stored in Input_Opt%STAR). Set STAR to the symbol which is used as the Unix wild card character. Recommended value: "*".

Specify UNZIP_CMD (stored in Input_Opt%UNZIP_CMD). Set UNZIP_CMD to the string which defines the file unzipping command. Recommended value: "gzip -dc".

Specify ZIP_SUFFIX (stored in Input_Opt%ZIP_SUFFIX). 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 transported tracers (listed in the Tracer Menu) 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 chemical species (listed in globchem.dat) 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 stay within the computational time limts of your system), then you should set LSVCSPEC to T. This will make sure that the chemical species concentrations are preserved when the next run stage starts. Otherwise, GEOS-Chem will use the default species concentrations specified in globchem.dat.

restart.soilnox.YYYYMMDDhh

Restart file (binary punch format) containing soil NOx information for year/month/day/hour YYYYMMDDhh.

This file saves the following information for continuation of the run at a later stage:

• DRYPERIOD: Time since soil moisture increased by 0.01. Unit is hours.
• PFACTOR: If soil pulsing, pulse factor from previous timestep (unitless).
• GWET_PR: Soil moisture from previous timestep (unitless).
• N_RESERVOIR: Contribution of wet and dry deposition to fertilizer N since previous last timestep. Unit is ng N/m2.

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.

NOTE: In GEOS–Chem v9-02 and later versions, the soaprod restart file no longer exists. The APROD and GPROD quantities were removed in the updated SOA simulation since different volatility species are not lumped together.

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.