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 and 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 for FAST-JX photolysis species.

Links "GEOS-Chem species" to "FAST-JX" species. FAST-JX photolysis species are defined in the data file FJX_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 emissions and boundary conditions

NOTE: This menu is now mostly obsolete because of HEMCO. We now use the HEMCO_Config.rc file to set the emission inventories.

Specifies options for future emissions scenarios for GCAP simulations

NOTE: This menu is now mostly obsolete because of HEMCO. We now use the HEMCO_Config.rc file to set the emission inventories.

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

Radiation Menu

Specifies options for radiation

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

Benchmark Menu

Specifies options for the benchmark diagnostic

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 instantaneous concentrations of the transported tracers specified in the Tracer Menu. This file is used to initialize tracer concentrations at the start of your simulation.

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. 2013)
• 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: Using YYYYMMDDhhmm in the restart file names allow for test simulations of less than one hour to be performed.

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. The met fields are also stored in subdirectories of DATA_DIR.

For more information, please see our Setting up the ExtData directory wiki page.

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.

NOTE: This directory is obsolete in GEOS-Chem v10-01 and later versions. We now read emissions data on their native grids from the HEMCO data directories.

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. See our Setting up GEOS-Chem nested grid simulations wiki page for more information.

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 (NOTE: this is simulation is in need of updating)
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 UCX chemistry, then set N_TRACERS to 92.
3. with secondary organic aerosols (SOA), then set N_TRACERS to 93.
4. 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:

• 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°), 10 min (0.5° x 0.666°), or 5 min (0.25° x 0.3125°). 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 the name of the HEMCO configuration file (stored in Input_Opt%HcoConfigFile). The emission inventories that your simulation will use are set in this file.

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.

Header line

Specify LCH4EMIS (stored in Input_Opt%LCH4EMIS). Set LCH4EMIS to T to use online methane emissions.

Header line

Specify LCH4SBC (stored in Input_Opt%LCH4SBC). Set LCH4SBC to T to fix surface mixing ratio of methane.

Specify LOCSEMIS (stored in Input_Opt%LOCSEMIS). Set LOCSEMIS to T to fix surface mixing ratios of OCS.

Specify LCFCEMIS (stored in Input_Opt%LCFCEMIS). Set LCFCEMIS to T to fix surface mixing ratios of CFCs, HCFCs, and halons to match WMO projections under the Montreal Protocol.

Specify LCLEMIS (stored in Input_Opt%LCLEMIS). Set LCLEMIS to T to fix surface mixing ratios of other chlorinated carbon and inorganic chlorine species to match WMO projections under the Montreal Protocol.

Specify LBREMIS (stored in Input_Opt%LBREMIS). Set LBREMIS to T to fix surface mixing ratios of bromine species. Not recommended if other bromine emissions are enabled.

Specify LN2OEMIS (stored in Input_Opt%LN2OEMIS). Set LN2OEMIS to T to fix surface mixing ratios of N2O.

Header line

Specify LSETH2O (stored in Input_Opt%LSETH2O). Set LSETH2O to T to initialize stratospheric H2O mixing ratios based on meteorology data for the first timestep, overriding any restart file values.

Specify LSETCH4 (stored in Input_Opt%LSETH2O). Set LSETCH4 to T to initialize CH4 from the default GEOS-Chem climatology for the first timestep, overriding any restart file values.

Specify LSETOCS (stored in Input_Opt%LSETOCS). Set LSETOCS to T to initialize OCS distribution based on zonal means from a 2D model.

Specify LSETCFC (stored in Input_Opt%LSETCFC). Set LSETCFC to T to initialize CFCs, HCFCs, and halocarbons based on zonal means from a 2D model.

Specify LSETCL (stored in Input_Opt%LSETCL). Set LSETCL to T to initialize other chlorinated carbon and inoragnic chlorine species based on zonal means from a 2D model.

Specify LSETBRGCCM (stored in Input_Opt%LSETBRGCCM). Set LSETBRGCCM to T to initialize stratospheric bromine species to GCCM baseline.

Specify LSETBR (stored in Input_Opt%LSETBR). Set LSETBR to T to initialize bromine species based on zonal means from a 2D model.

Specify LSETBRSTRAT (stored in Input_Opt%LSETBRSTRAT). Set LSETBRSTRAT to T to initialize stratospheric bromine species based on zonal means from a 2D model.

Specify LSETNOYSTRAT (stored in Input_Opt%LSETNOYSTRAT). Set LSETNOYSTRAT to T to initialize stratospheric NOx and HNO3 based on zonal means from a 2D model.

Specify LSETN2O (stored in Input_Opt%LSETN2O). Set LSETN2O to T to initialize N2O distribution based on zonal means from a 2D model.

Specify LSETH2SO4 (stored in Input_Opt%LSETH2SO4). Set LSETH2SO4 to T to initialize stratospheric sulfates based on zonal means from a 2D model.

Specify the starting year for CFC emissions (stored in Input_Opt%CFCYEAR)

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 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 chemistry for crystalline sulfur and aqueous aerosols (AS, AHS, LET, SO4aq, NH4aq).

NOTE: This feature has not been implemented in GEOS-Chem v10-01. For the time being, set LCRYST to F.

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

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

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

NOTE: If the UCX chemistry mechanism is used (LUCX=T), then linearized chemistry is applied in the mesosphere.

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.

NOTE: If the UCX chemistry mechanism is used (LUCX=T), then Linoz is applied in the mesosphere.

Specify LUCX (stored in Input_Opt%LUCX). Set LUCX to T to use the UCX tropospheric-stratospheric chemistry mechanism, otherwise online chemistry will only be applied in the troposphere. To use this option you must compile GEOS-Chem with UCX=yes.

Specify LCH4CHEM (stored in Input_Opt%LCH4CHEM). Set LCH4CHEM to T to use online methane chemistry.

Specify LACTIVEH2O (stored in Input_Opt%LACTIVEH2O). Set LACTIVEH2O to T to allow the stratospheric H2O tracer to influence specific humidity and relative humidity. To use this option, you must also set LUCX to T.

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°), 20 min (0.5° x 0.666°), or 10 min (0.25° x 0.3125°). 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 our Centrailzed chemistry timestep 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 chemical 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 initialized with 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 start each simulation using the default species concentrations specified in globchem.dat.

• YYYY: Replaced by 4-digit year (e.g. 2013)
• 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, using YYYYMMDDhh in the CSPEC restart file name should suffice for most applications.

NOTE: When using the UCX mechanism, we recommend setting LKPP to T. SMVGEAR can be used with UCX, but it has been found to be extremely slow.

Header line

Specify wavelength(s) for the aerosol optical properties. Up to three wavelengths can be output. The wavelengths should be entered in nm with a space between each entry. The specified wavelengths are used for the Fast-JX photolysis mechanism, regardless of whether the RRTMG radiative transfer model is used.

Specify LRAD (stored in Input_Opt%LRAD). Set LRAD to T to turn on online radiative transfer using RRTMG, or F to turn off RRTMG.

Specify LLWRAD (stored in Input_Opt%LLWRAD). Set LLWRAD to T to turn on longwave radiation calculation.

Specify LSWRAD (stored in Input_Opt%LSWRAD). Set LSWRAD to T to turn on shortwave radiation calculation.

Specify LSKYRAD(1) (stored in Input_Opt%LSYKRAD(1)). Set LSKYRAD(1) to T to turn turn on calculation for clear-sky fluxes. This option will perform radiative calculations without clouds.

Specify LSKYRAD(2) (stored in Input_Opt%LSYKRAD(2)). Set LSKYRAD(2) to T to turn turn on calculation for all-sky fluxes. This option will perform radiative with clouds. Both clear sky and all-sky options can be turned on without signigicant increase to run time.

Specify the radiation timestep (TS_RAD, stored in Input_Opt%TS_RAD) in minutes. In all cases, the radiation timesetp should be a multiple of the transport timestep. The RRTMG calculation is instantaneous (i.e. not averaged over the period selected) and is set to occur at half the radiation timestep. We recommend using a radiation timestep of 180 min (producing RRTMG calls at 01:30, 4:30, etc.).

Specify the species for which radiative fluxes will be calculated. Set a value to 1 to calculate the radiative effect for that species, or 0 to turn off radiative calculations for that species. The first RRTMG call (the "baseline") contains all species switched on and each requested species calls RRTMG again with that species omitted, so that the difference can be calculated. The number of calls to RRTMG will be equal to the total sum of this line plus one (for the first "baseline" call), so this can substantially increase model run time.

If you are using the UCX chemistry mechanism, then you will need to add an additional entry (0 or 1) at the end of this line for stratospheric aerosols for a total of 11 possible species.

This line lists species available for output from the flux calculations. This line is here for reference and is not actually read by GEOS-Chem.

Available species are:

1. O3 (Ozone)
2. ME (Methane)
3. SU (Sulfate)
4. NI (Nitrate)
5. AM (Ammonium)
6. BC (Black carbon)
7. OA (Organic aerosol)
8. SS (Sea salt)
9. DU (Mineral dust)
10. PM (All particulate matter)
11. ST (Stratospheric aerosol, UCX simulation only)

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.

NOTE: The choice of fossil fuel emissions in the CO2 Menu must be consistent with the choice in the HEMCO_Config.rc file.

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.

NOTE: The choice of fossil fuel emissions in the CO2 Menu must be consistent with the choice in the HEMCO_Config.rc file.

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.

NOTE: The choice of fossil fuel emissions in the CO2 Menu must be consistent with the choice in the HEMCO_Config.rc file.

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.

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.

NOTE: The choice of ship emissions in the CO2 Menu must be consistent with the choice in the HEMCO_Config.rc file.

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.

NOTE: The choice of ship emissions in the CO2 Menu must be consistent with the choice in the HEMCO_Config.rc file.

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.

NOTE: The choice of aircraft emissions in the CO2 Menu must be consistent with the choice in the HEMCO_Config.rc file.

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. You may use date & time tokens YYYY, MM, DD, hh, mm, ss and GEOS-Chem will replace these with the appropriate values.

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. You may use date & time tokens YYYY, MM, DD, hh, mm, ss and GEOS-Chem will replace these with the appropriate values.

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 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.) If you would like to save daily diagnostic output to the binary punch file, put a 3 for each day of each month.

NOTE: You must place a 3 in the location corresponding to the simulation end date. Otherwise, the GEOS-Chem simulation will crash immediately with the error No output scheduled on last day of run!

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

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

ND09 (HCN/CH3CN sources) diagnostic settings

NOTE: This diagnostic is more or less obsolete.

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

NOTE: This diagnostic is more or less obsolete.

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 the CH4 simulation only

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

ND22 (J-value photolysis rates) diagnostic settings

NOTE: The only tracers that have J-values defined are:

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 diagnostic 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

ND52 (gamma(HO2) for the HO2 uptake by aerosols)

ND53 (POPs emissions) diagnostic settings for POPs simulation only

ND54 diagnostic settings (computes the time that a given grid box spends in the troposphere)

ND55 (tropopause height) diagnostic settings

ND56 (lightning flashes) diagnostic settings

ND57 (Potential temperature) diagnostic settings

ND58 (CH4 Emissions) diagnostic settings for CH4 and UCX simulations only

ND59 (TOMAS aerosol emissions) diagnostic settings

ND60 (Wetland Frac) diagnotic settings for CH4 simulation only

ND61 (TOMAS 3D rate) diagnostic settings

ND62 (instantaneous column maps) diagnostic settings

ND64 (Radiative flux) diagnostic settings

ND66 (3-D met fields) diagnostic settings

ND67 (2-D met fields) diagnostic settings

ND68 (boxheight & air mass) diagnostic setting.

ND69 (grid box surface area) diagnostic settings

ND70 (turn on debug output) diagnostic settings

ND71 (Hourly maximum mixing ratio) diagnostic settings

ND72 (Radiative 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 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) defined 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 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 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(s)

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 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 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 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 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 enter 1, it will just save the surface level.
• If you enter 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

Set this switch to T if you wish to save out benchmark diagnostics, or F otherwise. This option will save out initial and final tracer masses needed for the 1-month benchmark simulation plotting routines.

Specify name of file that will contain initial tracer mass.

Specify name of file that will contain final tracer mass.

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, J0_W, I0_E, and J0_E (located in source code file tpcore_bc_mod.F). I0_W and J0_W are the 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 window is smaller than the actual size of them 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. We have set I0_E=3 and J0_E=3, but for some grids (e.g. SE Asia) you may want to use I0_E=2 and J0_E=2.

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.

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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.

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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.

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