GEOS-Chem input files for v11-01

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On this page we describe the input files that ship with the various GEOS-Chem run directories. For a list of files created by GEOS-Chem, please see our GEOS-Chem Output Files wiki page.

Overview

This page describes the input files that are read by GEOS-Chem. These files will reside in the various GEOS-Chem run directories. Each run directory is customized for a unique combination of simulation, horizontal resolution, and met field type, and contains the various input files with which you select options for your GEOS-Chem simulation.

You can generate GEOS-Chem run directories from the GEOS-Chem Unit Tester. Please see our our Creating GEOS-Chem run directories wiki page for detailed instructions. We recommend that you create a different run directory for each of your GEOS-Chem simulations to avoid overwriting output with subsequent model runs.

Note that run directories compatible with previous versions of GEOS-Chem will not work with [[GEOS-Chem v11-01]|v11-01]].

List of GEOS-Chem input files

Below is a table listing GEOS-Chem input files that reside in the run directory.

GEOS-Chem user input files
input.geos 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.
HEMCO_Config.rc Specifies emission inventories that you want to include in GEOS-Chem via the HEMCO emissions component.
Planeflight.dat Specifies flight tracks for which you want to save out specific tracers, chemical species, or met field quantities.
GEOS-Chem photolysis mechanism files
These are only found in the run directories for the various full-chemistry and aerosol-only simulations.
FJX_spec.dat Contains cross-section and quantum yields for FAST-JX photolysis species.
FJX_j2j.dat 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.spc. See this post for more information.
jv_spec_mie.dat Contains aerosol optical properties at 5 wavelengths.
dust.dat Contains aerosol optical properties for dust at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
org.dat Contains aerosol optical properties for organic carbon at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
so4.dat Contains aerosol optical properties for sulfate at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
soot.dat Contains aerosol optical properties for black carbon at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
ssa.dat Contains aerosol optical properties for accumulation mode sea salt aerosol at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
ssc.dat Contains aerosol optical properties for coarse mode sea salt aerosol at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).

--Bob Yantosca (talk) 17:04, 16 November 2016 (UTC)

Chemical mechanism files now ship with the GEOS-Chem source code

In GEOS-Chem v10-01 and prior versions, the chemical mechanism files globchem.dat, mglob.dat, and chemga.dat were contained in the GEOS-Chem run directories. But GEOS-Chem v11-01 and higher versions now uses the FlexChem implementation of the KPP chemical solver. Thus, the chemical mechanism is pre-processed and pre-compiled instead of being initialized at run-time. Please see our our FlexChem wiki page for more information about this.

For your reference, we now store the master KPP equation files (globchem.def, globchem.eqn, and globchem.spc) in the various subfolders of the GEOS-Chem source code directory, i.e.

  • KPP/Standard
  • KPP/Tropchem
  • KPP/UCX
  • KPP/SOA
  • KPP/SOA_SVPOA

If you need to add new species or reactions, you can modify these globchem.* files and then rebuild the KPP code. You can ask the GEOS-Chem Support Team for assistance with this.

In the very near future, we hope to build KPP fresh each time when GEOS-Chem is compiled. This will make it much easier to change the existing chemical mechanisms.

--Bob Yantosca (talk) 17:03, 16 November 2016 (UTC)

The input.geos file

GEOS-Chem combines all the input options and switches into a single input file, input.geos. All user-defined input switches and settings which customize GEOS-Chem output options are now defined within this file.

An input.geos file ships with each GEOS-Chem run directory. We invite you to create the run directory for the simulation(s) that you are interested in and view the corresponding input.geos file. You will note that the input.geos file is grouped into menus. Each menu controls the options for a particular aspect of a GEOS-Chem simulation. The sections below contain a list of the menus and the options that they control.

Most of the information listed in input.geos will be stored as fields of the Input_Opt derived-type object.

Simulation Menu

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% SIMULATION MENU %%% :
02: Start YYYYMMDD, hhmmss  : 20130701 000000
03: End   YYYYMMDD, hhmmss  : 20130801 000000
04: Run directory           : ./
05: Input restart file      : GEOSChem_restart.YYYYMMDDhhmm.nc
06: Root data directory     : /path/to/data/
07:  => GCAP    subdir      : AGRID/YYYY/MM/
08:  => GEOS-4  subdir      : GEOS_4_v4/YYYY/MM/
09:  => GEOS-5  subdir      : GEOS_5/YYYY/MM/
10:  => GEOS-FP subdir      : GEOS_FP/YYYY/MM/
11:  => MERRA   subdir      : MERRA/YYYY/MM/
12:  => MERRA2  subdir      : MERRA2/YYYY/MM/
13: Dir w/ 1x1 emissions etc: /path/to/data/GEOS_NATIVE/
14: Temporary directory     : ./
15: Unzip met fields?       : F
16: Wait for met fields?    : F
17: Use variable tropopause?: T
18: Global offsets I0, J0   : 0 0

Note: /path/to/data/ indicates the path to the root data folder on your system. If you don't know where this is, ask your IT staff.

Line What gets defined Description
1 nothing Header line
2 Input_Opt%NYMDb
Input_Opt%NHMSb
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.
3 Input_Opt%NYMDe
Input_Opt%NHMSe
Specify the ending date (YYYYMMDD format) and time (hhmmss format) of the GEOS-Chem simulation.
4 Input_Opt%RUN_DIR The name of the GEOS-Chem run directory (e.g. where the executable file and input files reside).
  • NOTE: This can usually be set to the current directory (i.e. ./).
5 Input_Opt%IN_RST_FILE The name of GEOS-Chem input restart file, which contains the instantaneous concentrations of the advected species specified in the Advected Species Menu. This file is used to initialize the species 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.

6 Input_Opt%DATA_DIR The 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 Input_Opt%DATA_DIR. The met fields are also stored in subdirectories of Input_Opt%DATA_DIR.

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

7 Input_Opt%GCAP_DIR The directory path where GCAP met fields are stored. You may include the YYYY and MM tokens as described above.
8 Input_Opt%GEOS_4_DIR The directory path where GEOS-4 met fields are stored. You may include the YYYY and MM tokens as described above.
9 Input_Opt%GEOS_5_DIR The directory path where GEOS-5 met fields are stored. You may include the YYYY and MM tokens as described above.
10 Input_Opt%GEOS_FP_DIR The directory path where GEOS-FP met fields are stored. You may include the YYYY and MM tokens as described above.
11 Input_Opt%MERRA_DIR The directory path where MERRA met fields are stored. You may include the YYYY and MM tokens as described above.
12 Input_Opt%MERRA2_DIR The directory path where MERRA-2 met fields are stored. You may include the YYYY and MM tokens as described above.
13 nothing Now obsolete
14 nothing Now obsolete
15 nothing Now obsolete
16 nothing Now obsolete
17 Input_Opt%LVARTROP Set this to T to use the dynamic tropopause (i.e. to compute the tropopause height directly from the met fields), or F if you want to use an annual mean tropopause
  • NOTE: This should always be set to T if you are using GEOS-4, GEOS-5, or GEOS-FP, MERRA, or MERRA-2 met fields.
18 Input_Opt%NESTED_I0
Input_Opt%NESTED_J0
Nested grid offsets. 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.

--Bob Yantosca (talk) 18:14, 17 November 2016 (UTC)

Advected Species Menu

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% ADVECTED SPECIES MENU %%%:
02: Type of simulation      : 3
03: Number of Advected Spec.: 125
04: Species Entries ------->: Name
05: Species #1              : NO
06: Species #2              : O3
07: Species #3              : PAN
08: Species #4              : CO
... etc not shown here ...
Line What gets defined Description
1 nothing Header line
2 Input_Opt%SIM_TYPE 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. One of the NOx-Ox-Hydrocarbon-aerosol (aka "full chemistry") simulations
  4. HCN simulation (NOTE: this simulation is in need of updating)
  5. UNUSED
  6. Tagged O3 simulation
  7. Tagged CO simulation
  8. C2H6 simulation
  9. CH4 simulation
  10. Aerosol-only simulation
  11. Mercury simulation
  12. CO2 simulation
  13. H2 and HD simulation (NOTE: this simulation is in need of updating)
  14. POPs simulation

NOTE: In this example, the ADVECTED SPECIES MENU is set up for a "Standard" full chemistry simulation. This is the simulation we use to generate the GEOS-Chem benchmark output.

3 Input_Opt%nAdvect The number of advected species that will be included in the GEOS-Chem simulation.

If you are performing one of the GEOS-Chem v11-01 "full-chemistry" simulations, then make sure this is set to:

  • 68 (Tropchem)
  • 95 (SOA)
  • 102 (SOA with semi-volatile POA)
  • 125 (Standard, aka the mechanism we use to benchmark GEOS-Chem)
  • 127 (Marine POA)
  • 137 (Acid Uptake)
4 nothing Header line
5 - Input_Opt%AdvectSpc_Name A list of the advected species names. Place only one species name on each line. These entries are used to populate the species database.

--Bob Yantosca (talk) 18:17, 17 November 2016 (UTC)

Transport Menu

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% TRANSPORT MENU %%%  :
02: Turn on Transport       : T
03:  => Fill Negative Values: T
04:  => IORD, JORD, KORD    : 3  3  7
05: Transport Timestep [min]: 10
Line What gets defined Description
1 nothing Header line
2 Input_Opt%LTRAN Set this to T to turn on TPCORE transport, or set to F to turn off TPCORE transport.
3 Input_Opt%LFILL Set this to T to cause TPCORE to fill negative values with zeroes.
4 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.
5 Input_Opt%TS_DYN The transport timestep in minutes. This should be the smallest timestep used.

CAVEAT: Running GEOS-Chem with the recommended time steps from S. Philip et al (2016) has been shown to increase run times w/r/t v10-01 by approximately a factor of 2. To speed up GEOS-Chem simulations, users may choose to:

  • RUN WITH COARSER TIMESTEPS FOR FASTER TURNAROUND AND LOWER ACCURACY.
    • Using these transport timesteps (as was done prior to v11-01) should speed up your simulation by a factor of 2:
      • 30 min (4° x 5°)
      • 15 min (2° x 2.5°)
  • SELECT ONE OF THE MECHANISMS IN WHICH DETALED STRATOSPHERIC CHEMISTRY IS OMITTED:
    • These are: Tropchem, SOA, SOA-SVPOA.

--Bob Yantosca (talk) 15:54, 30 January 2017 (UTC)

Convection Menu

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% CONVECTION MENU %%% :
02: Turn on Cloud Conv?     : T
03: Turn on PBL Mixing?     : T
04:  => Use non-local PBL?  : T
05: Convect Timestep [min]  : 10
Line What gets defined Description
1 nothing Header line
2 Input_Opt%LCONV Set this to T to turn on cloud convection.
3 Input_Opt%LTURB Set this to T to turn on PBL mixing.
4 Input_Opt%LNLPBL The options are as follows:

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

CAVEAT: In this version, it has been noted that VDIFF (the non-local mixing option) does not strictly conserve mass. This will be more of a problem for long-lived species like CH4 and CO2. Therefore, if you are using the CH4 or CO2 specialty simulations, we recommend to use the full TURBDAY mixing by setting this Input_Opt%LNLPBL switch to F.

For more information please see these wiki posts below.

5 Input_Opt%TS_CONV Specify the convection timestep in minutes. The convection timestep should equal the the transport timestep. This is required for the central chemistry timestep algorithm.

CAVEAT: Running GEOS-Chem with the recommended time steps from S. Philip et al (2016) has been shown to increase run times w/r/t v10-01 by approximately a factor of 2. To speed up GEOS-Chem simulations, users may choose to:

  • RUN WITH COARSER TIMESTEPS FOR FASTER TURNAROUND AND LOWER ACCURACY.
    • Using these convection timesteps (as was done prior to v11-01) should speed up your simulation by a factor of 2:
      • 30 min (4° x 5°)
      • 15 min (2° x 2.5°)
  • SELECT ONE OF THE MECHANISMS IN WHICH DETALED STRATOSPHERIC CHEMISTRY IS OMITTED:
    • These are: Tropchem, SOA, SOA-SVPOA.

--Bob Yantosca (talk) 15:55, 30 January 2017 (UTC)

Emissions Menu

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% EMISSIONS MENU %%%  :
02: Turn on emissions?      : T
03: Emiss Timestep [min]    : 20
04: HEMCO Input file        : HEMCO_Config.rc
05:  => 1ppt MBL BRO Sim.?  : F
06: Switches for UCX        :---
07: => Use CH4 emissions?  : F
08: => Turn on surface BCs :---
09:    => CH4?             : T
10:    => OCS?             : T
11:    => CFCs?            : T
12:    => Cl species?      : T
13:    => Br species?      : F
14:    => N2O?             : T
15: => Set initial glob MRs:---
16:    => strat. H2O?      : T
17:    => CH4?             : T
18:    => OCS?             : T
19:    => CFCs?            : T
20:    => Cl species?      : T
21:    => strat Bry (GCCM)?: T
22:    => Br species?      : F
23:    => strat. Br?       : F
24:    => strat. NOx/HNO3? : T
25:    => N2O?             : T
26:    => strat. SO4?      : T
27: => CFC emission year   : 0
Line What gets defined Description
1 nothing Header Line
2 Input_Opt%LEMIS Set this to T to turn on emissions or F to turn off emissions.
3 Input_Opt%TS_EMIS The emission timestep, in minutes. The this should be the same as the chemistry time step. This is required for the central chemistry timestep algorithm.

CAVEAT: Running GEOS-Chem with the recommended time steps from S. Philip et al (2016) has been shown to increase run times w/r/t v10-01 by approximately a factor of 2. To speed up GEOS-Chem simulations, users may choose to:

  • RUN WITH COARSER TIMESTEPS FOR FASTER TURNAROUND AND LOWER ACCURACY.
    • Using these emission timesteps (as was done prior to v11-01) should speed up your simulation by a factor of 2:
      • 60 min (4° x 5°)
      • 30 min (2° x 2.5°)
  • SELECT ONE OF THE MECHANISMS IN WHICH DETALED STRATOSPHERIC CHEMISTRY IS OMITTED:
    • These are: Tropchem, SOA, SOA-SVPOA.
4 Input_Opt%HcoConfigFile The name of the HEMCO configuration file. The emission inventories that your simulation will use are set in this file.
5 Input_Opt%LFIX_PBL_BrO Set this to T to set Bro concentrations in the PBL equal to 1 ppt during the day.
6 nothing Header line.
The following lines contain settings specific to the UCX chemistry mechanism.
You can turn all of these options off if your simulation does not use the UCX mechanism.
7 Input_Opt%LCH4EMIS Set this T to use online methane emissions.
8 nothing Header line
9 Input_Opt%LCH4SBC Set this T to fix surface mixing ratio of methane.
10 Input_Opt%LOCSEMIS Set this to T to fix surface mixing ratios of OCS.
11 Input_Opt%LCFCEMIS Set this to T to fix surface mixing ratios of CFCs, HCFCs, and halons to match WMO projections under the Montreal Protocol.
12 Input_Opt%LCLEMIS Set this to T to fix surface mixing ratios of other chlorinated carbon and inorganic chlorine species to match WMO projections under the Montreal Protocol.
13 Input_Opt%LBREMIS Set this to T to fix surface mixing ratios of bromine species. Not recommended if other bromine emissions are enabled.
14 Input_Opt%LN2OEMIS Set this to T to fix surface mixing ratios of N2O.
15 nothing Header line
16 Input_Opt%LSETH2O Set this to T to initialize stratospheric H2O mixing ratios based on meteorology data for the first timestep, overriding any restart file values.
17 Input_Opt%LSETCH4 Set this to T to initialize CH4 from the default GEOS-Chem climatology for the first timestep, overriding any restart file values.
18 Input_Opt%LSETOCS Set this to T to initialize OCS distribution based on zonal means from a 2D model.
19 Input_Opt%LSETCFC Set this to T to initialize CFCs, HCFCs, and halocarbons based on zonal means from a 2D model.
20 Input_Opt%LSETCL Set this to T to initialize other chlorinated carbon and inoragnic chlorine species based on zonal means from a 2D model.
21 Input_Opt%LSETBRGCCM Set this to T to initialize stratospheric bromine species to GCCM baseline.
22 Input_Opt%LSETBR Set this to T to initialize bromine species based on zonal means from a 2D model.
23 Input_Opt%LSETBRSTRAT Set this o T to initialize stratospheric bromine species based on zonal means from a 2D model.
24 Input_Opt%LSETNOYSTRAT Set this to T to initialize stratospheric NOx and HNO3 based on zonal means from a 2D model.
25 Input_Opt%LSETN2O Set this to T to initialize N2O distribution based on zonal means from a 2D model.
26 Input_Opt%LSETH2SO4 Set this to T to initialize stratospheric sulfates based on zonal means from a 2D model.
27 Input_Opt%CFCYEAR Specify the starting year for CFC emissions.

--Bob Yantosca (talk) 20:23, 27 January 2017 (UTC)

Aerosol Menu

01: %%% AEROSOL MENU %%%    :
02: Online SULFATE AEROSOLS : T
03: Online CRYST/AQ AEROSOLS: F
04: Online CARBON  AEROSOLS : T
05:  => Use Brown Carbon?   : F
06: Online 2dy ORG AEROSOLS : T
07:  => Semivolatile POA?   : F
08: Online DUST    AEROSOLS : T
09:  => Acidic uptake ?     : F
10: Online SEASALT AEROSOLS : T
11:  => SALA radius bin [um]: 0.01 0.5
12:  => SALC radius bin [um]: 0.5  8.0
13:  => MARINE ORG AEROSOLS : F
14: Online dicarb. chem.    : F
15: Settle strat. aerosols  : T
16: Online PSC AEROSOLS     : T
17: Allow homogeneous NAT?  : F
18: NAT supercooling req.(K): 3.0
19: Ice supersaturation req.: 1.2
20: Perform PSC het. chem.? : T
21: Calc. strat. aero. OD?  : T
Line What gets defined Description
1 nothing Header line
2 Input_Opt%LSULF Set this to T to turn on chemistry for sulfate aerosols (DMS, SO2, SO4, MSA, NH3, NH4, NIT).
3 nothing OBSOLETE
4 Input_Opt%LCARB Set this to T to turn on chemistry for carbonaceous aerosols (BCPI, BCPO, OCPI, OCPO).
5 Input_Opt%LBRC Set this to T to turn on brown carbon aerosols.
6 Input_Opt%LSOA Set this to T to turn on chemistry for secondary organic aerosols.
7 Input_Opt%LSVPOA Set this to T to use the semivolatile POA option.
8 Input_Opt%LDUST Set this to T to turn on removal for mineral dust aerosol species (DST1, DST2, DST3, DST4), as well as the dust uptake species.
9 Input_Opt%LDSTUP Set tis to T to turn on acid uptake on dust aerosols.
10 Input_Opt%LSSALT Set this to T to turn on chemistry for sea salt aerosols (SALA, SALC).
11 Input_Opt%SALA_REDGE_um The bin edges (in microns) that denote accumulation mode sea salt species.
  • Recommended setting: 0.01 to 0.5 microns.
12 Input_Opt%SALC_REDGE_um The bin edges (in microns) that denote coarse mode sea salt tracer in microns.
  • Recommended setting: 0.5 to 8 microns.
13 Input_Opt%LMOPA Set this to T top turn on marine organic aerosols.
14 nothing OBSOLETE
The following lines contain settings specific to the UCX chemistry mechanism.
You can turn all of these options off if your simulation does not use the UCX mechanism.
15 Input_Opt%LGRAVSTRAT Set this to T to apply gravitational settling to stratospheric solid particulate aerosols (SPA, trapezoidal scheme) and stratospheric liquid aerosols (SLA, corrected Stokes' Law).
16 Input_Opt%LSOLIDPSC Set this to T to use solid polar stratospheric clouds (PSCs).
17 Input_Opt%LHOMNUCNAT Set this to T to allow NAT to form homogeneously from freezing of HNO3.
18 Input_Opt%T_NAT_SUPERCOOL The degrees Kelvin of cooling required for homogeneous NAT nucleation.
19 Input_Opt%P_ICE_SUPERSAT The supersaturation factor required for ice nucleation.
  • Recommended values: 1.2 for coarse grids; 1.5 for fine grids.
20 Input_Opt%LPSCCHEM Set this to T to allow heterogeneous chemistry on stratospheric aerosols.
21 Input_Opt%LSTRATOD Set this to T to include online stratospheric aerosols in extinction calculations for photolysis.

--Bob Yantosca (talk) 17:57, 17 November 2016 (UTC)

Deposition Menu

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% DEPOSITION MENU %%% :
02: Turn on Dry Deposition? : T
03: Turn on Wet Deposition? : T
Line What gets defined Description
1 nothing Header line
2 Input_Opt%LDRYD Set this to T to turn on dry deposition, or F to turn off dry deposition.
3 Input_Opt%LWETD Set this to T to turn on wet deposition, or F to turn off wet deposition.

--Bob Yantosca (talk) 17:51, 17 November 2016 (UTC)

Chemistry Menu

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% CHEMISTRY MENU %%%  :
02: Turn on Chemistry?      : T
03: Use linear. strat. chem?: T
04:  => Use Linoz for O3?   : T
05: Use UCX strat. chem?    : T
06: Online CH4 chemistry?   : T
07: Active strat. H2O?      : T
08: Chemistry Timestep [min]: 20
09: Online O3 for FAST-JX?  : T
10: Gamma HO2               : 0.2
Line What gets defined Description
1 nothing Header line
2 Input_Opt%LCHEM Set this to T to turn on chemistry, or F to turn off chemistry.
3 Input_Opt%LSCHEM Set this to T to turn on linearized stratospheric chemistry, or F to turn off stratospheric chemistry.
4 Input_Opt%LLINOZ Set this to T to use Linoz stratospheric ozone chemistry, otherwise Synoz will be used.
  • NOTE: If the UCX chemistry mechanism is used (see line 5), then Linoz is applied in the mesosphere.
5 Input_Opt%LUCX Set this to T to use the UCX chemistry mechanism. Otherwise online chemistry will only be applied in the troposphere.
  • NOTE: To use this option you must also compile GEOS-Chem with UCX=yes.
6 Input_Opt%LCH4CHEM Set this to T to use online methane chemistry.
7 Input_Opt%LACTIVEH2O Set this to T to allow the stratospheric H2O tracer to influence specific humidity and relative humidity.
  • NOTE: To use this option, you must also turn on UCX (see line 5).
8 Input_Opt%TS_CHEM The chemistry timestep, in minutes. We suggest using a chemistry timestep double the transport time step (this is known as Strang operator splitting).

CAVEAT: Running GEOS-Chem with the recommended time steps from S. Philip et al (2016) has been shown to increase run times w/r/t v10-01 by approximately a factor of 2. To speed up GEOS-Chem simulations, users may choose to:

  • RUN WITH COARSER TIMESTEPS FOR FASTER TURNAROUND AND LOWER ACCURACY.
    • Using these chemistry timesteps (as was done prior to v11-01) should speed up your simulation by a factor of 2:
      • 60 min (4° x 5°)
      • 30 min (2° x 2.5°)
  • SELECT ONE OF THE MECHANISMS IN WHICH DETALED STRATOSPHERIC CHEMISTRY IS OMITTED:
    • These are: Tropchem, SOA, SOA-SVPOA.
9 Input_Opt%LO3_FJX Set this to T to use online O3 from GEOS-Chem in the extinction calculations for FAST-JX photolysis.
10 Input_Opt%GAMMA_HO2 The recommended setting is 0.2.

--Bob Yantosca (talk) 20:21, 27 January 2017 (UTC)

Output Menu

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% OUTPUT MENU %%%     : 123456789.123456789.123456789.1--1=ZERO+2=BPCH
02: Schedule output for JAN : 3000000000000000000000000000000
03: Schedule output for FEB : 30000000000000000000000000000
04: Schedule output for MAR : 3000000000000000000000000000000
05: Schedule output for APR : 300000000000000000000000000000
06: Schedule output for MAY : 3000000000000000000000000000000
07: Schedule output for JUN : 300000000000000000000000000000
08: Schedule output for JUL : 3000000000000000000000000000000
09: Schedule output for AUG : 3000000000000000000000000000000
10: Schedule output for SEP : 300000000000000000000000000000
11: Schedule output for OCT : 3000000000000000000000000000000
12: Schedule output for NOV : 300000000000000000000000000000
13: Schedule output for DEC : 3000000000000000000000000000000
Line What gets defined Description
1 nothing Header line
2 Input_Opt%NJDAY 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!
3 Schedule diagnostic output for FEBRUARY
4 Schedule diagnostic output for MARCH
5 Schedule diagnostic output for APRIL
6 Schedule diagnostic output for MAY
7 Schedule diagnostic output for JUNE
8 Schedule diagnostic output for JULY
9 Schedule diagnostic output for AUGUST
10 Schedule diagnostic output for SEPTEMBER
11 Schedule diagnostic output for OCTOBER
12 Schedule diagnostic output for NOVEMBER
13 Schedule diagnostic output for DECEMBER

--Bob Yantosca (talk) 20:13, 16 November 2016 (UTC)

GAMAP Menu

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% GAMAP MENU %%%      :
02: diaginfo.dat path       : diaginfo.dat
03: tracerinfo.dat path     : tracerinfo.dat
Line What gets defined Description
1 nothing Header line
2 Input_Opt%GAMAP_DIAGINFO 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 or an absolute path name.
3 Input_Opt%GAMAP_TRACERINFO 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 or an absolute path name.

--Bob Yantosca (talk) 17:44, 17 November 2016 (UTC)

Diagnostic Menu

NOTE: The binary punch file format is slated to be removed from the next version of GEOS-Chem (i.e., v11-02).

This menu lets you specify which GEOS_Chem diagnostic quantities will be archived to disk. For a complete list of diagnostic settings, please see our List of diagnostics for v11-01 wiki page.

%%% DIAGNOSTIC MENU %%% :
Binary punch file name  : trac_avg.geosfp_4x5_standard.YYYYMMDDhhmm
Diagnostic Entries ---> :  L   Tracers to print out for each diagnostic
ND01: Rn/Pb/Be source   :  0   all
ND02: Rn/Pb/Be decay    :  0   all
ND03: Hg emissions, P/L :  0   all
ND04: CO2 Sources       :  0   all
ND05: Sulfate prod/loss : 72   all
ND06: Dust aer source   :  1   all
ND07: Carbon aer source : 72   all
ND08: Seasalt aer source:  1   all
ND09: -                 :  0   all
ND10: -                 :  0   all
ND11: Acetone sources   :  1   all
ND12: BL fraction       :  0   all
ND13: Sulfur sources    : 72   all
ND14: Cld conv mass flx :  0   all
ND15: BL mix mass flx   :  0   all
ND16: LS/Conv prec frac :  0   all
ND17: Rainout fraction  :  0   all
ND18: Washout fraction  :  0   all
ND19: CH4 loss          :  0   all
ND21: Optical depths    : 72   all
ND22: J-Values          : 72   1 2 7 8 9 11 13 14 20 44 46 47 49 50 51 59 60 66 67 69 74 75 83 84 -1
      => JV time range  :      11 13
ND24: E/W transpt flx   :  0   all
ND25: N/S transpt flx   :  0   all
ND26: U/D transpt flx   :  0   all
ND27: Strat NOx,Ox,HNO3 :  0   1 2 7
ND28: Biomass emissions :  1   1 4 5 9 10 11 18 19 20 21 26 30 34 35 71
ND29: CO sources        :  1   all
ND30: Land Map          :  0   all
ND31: Pressure edges    : 73   all
ND32: NOx sources       :  1   all
ND33: Column tracer     :  0   all
ND34: Biofuel emissions :  1   1 4 5 9 10 11 18 19 20 21
ND35: Tracers at 500 mb :  0   all
ND36: Anthro emissions  :  1   1 2 4 5 7 9 10 11 18 19 20 21 71
ND37: Updraft scav frac :  0   all
ND38: Cld Conv scav loss: 72   all
ND39: Wetdep scav loss  : 72   all
ND41: Afternoon PBL ht  :  0   all
ND42: SOA concentrations: 72   all
ND43: Chem prod OH, HO2 : 72   all
  ==> OH/HO2 time range :       0 24
ND44: Drydep flx/vel    :  1   2 3 7 8 9 11 13 14 15 16 17 20 22 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 47 48 50  55 56 58 59 60 61 62 63 64 65 66 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 119 120 121 122 123 124 125
ND45: Tracer Conc's     : 72   all
  ==> ND45 Time range   :       0 24
ND46: Biogenic emissions:  1   all
ND47: 24-h avg trc conc :  0   all
ND52: GAMMA HO2         :  0   all
ND53: POPs Emissions    :  0   all
ND54: Time in t'sphere  : 72   all
ND55: Tropopause height : 72   all
ND56: Lightning flashes :  0   all
ND57: Potential T       :  0   all
ND58: CH4 Emissions     :  0   all
ND59: TOMAS aerosol emis:  0   all
ND60: Wetland Frac      :  0   all
ND61: TOMAS 3D rate     :  0   all
ND62: Inst column maps  :  0   all
ND64: Radiative flux    :  0   all
ND66: DAO 3-D fields    : 72   all
ND67: DAO 2-D fields    : 72   all
ND68: Airmass/Boxheight : 72   all
ND69: Surface area      :  1   all
ND70: Debug output      :  0   all
ND71: Hourly max ppbv   :  0   2
ND72: Radiative output  :  0   all

--Bob Yantosca (talk) 20:48, 16 November 2016 (UTC)

Planeflight Menu

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% PLANEFLIGHT MENU %%%:
02: Turn on plane flt diag? : F
03: Flight track info file  : Planeflight.dat.YYYYMMDD
04: Output file name        : plane.log.YYYYMMDD
Line What gets defined Description
1 nothing Header line
2 Input_Opt%DO_PF Set this to T to turn on the planeflight diagnostic (aka ND40).
3 Input_Opt%PF_IFILE 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.

4 Input_Opt%PF_OFILE Specify the name of the output file (usually called plane.log.YYYYMMDD) 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.

ND48 Menu

NOTE: The binary punch file format is slated to be removed from the next version of GEOS-Chem (i.e., v11-02).

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% ND48 MENU %%%       :
02: Turn on ND48 stations   : F
03: Station Timeseries file : stations.YYYYMMDD
04: Frequency [min]         :  60
05: Number of stations      :   1
06: Station #1 (I,J,Lmax,N) : 133 29 15 2
Line What gets defined Description
1 nothing Header line
2 Input_Opt%DO_ND48 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.
3 Input_Opt%ND48_FILE 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.
4 Input_Opt%ND48_FILE The frequency in minutes at which data will be archived by the ND48 station timeseries diagnostic. Recommended values: 60 minutes or 120 minutes.
5 Input_Opt%ND48_N_STA The number of ND48 stations at which timeseries data will be saved to disk.
6 Input_Opt%ND48_IARR
Input_Opt%ND48_JARR
Input_Opt%ND48_LARR
Input_Opt%ND48_NARR
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)

--Melissa Sulprizio (talk) 21:30, 13 March 2017 (UTC)

ND49 Menu

NOTE: The binary punch file format is slated to be removed from the next version of GEOS-Chem (i.e., v11-02).

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% ND49 MENU %%%       :
02: Turn on ND49 diagnostic : F
03: Inst 3-D timeser. file  : tsYYYYMMDD.bpch
04: Tracers to include      : 94
05: Frequency [min]         : 120
06: IMIN, IMAX of region    :  70  30
07: JMIN, JMAX of region    :  23  46
08: LMIN, LMAX of region    :   1   1
Line What gets defined Description
1 nothing Header line
2 Input_Opt%DO_ND49 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.
3 Input_Opt%ND49_FILE 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.
4 Input_Opt%ND49_TRACERS The ND49 diagnostic quantities that you wish to save to disk. Separate each number with a space.
5 Input_Opt%ND49_FREQ 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!
6 Input_Opt%ND49_IMIN
Input_Opt%ND49_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 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.

7 Input_Opt%ND49_JMIN
Input_Opt%ND49_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 GMAO 4° x 5° grid: 1 46
  • For GMAO 2° x 2.5° grid: 1 91
8 Input_Opt%ND51_LMIN
Input_Opt%ND51_LMAX
The indices which determine the vertical extent of the 3D region of the globe.

--Bob Yantosca (talk) 17:41, 17 November 2016 (UTC)

ND50 Menu

NOTE: The binary punch file format is slated to be removed from the next version of GEOS-Chem (i.e., v11-02).

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% ND50 MENU %%%       :
02: Turn on ND50 diagnostic : F
03: 24-hr avg timeser. file : ts_24h_avg.YYYYMMDD.bpch
04: Output as HDF5?         : F
05: Tracers to include      : 82 83 84 85 86 87
06: IMIN, IMAX of region    :   1  72
07: JMIN, JMAX of region    :   1  46
08: LMIN, LMAX of region    :   1   1
Line What gets defined Description


1 nothing Header line
2 Input_Opt%DO_ND50 Set this to T to turn on the ND50 24-hr average 3D timeseries diagnostic. This allows you to archive 24-hour time-averaged timeseries data for various quantities from a 3D region of the globe.
3 Input_Opt%ND50_FILE The name of the file which will contain output from the ND50 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.
4 nothing OBSOLETE
5 Input_Opt%ND50_TRACERS The ND50 diagnostic quantities that you wish to save to disk. Separate each number with a space.
6 Input_Opt%ND50_IMIN
Input_Opt%ND50_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 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.

7 Input_Opt%ND50_JMIN
Input_Opt%ND50_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 GMAO 4° x 5° grid: 1 46
  • For GMAO 2° x 2.5° grid: 1 91
8 Input_Opt%ND50_LMIN
Input_Opt%ND50_LMAX
The indices which determine the vertical extent of the 3D region of the globe.

--Bob Yantosca (talk) 17:37, 17 November 2016 (UTC)

ND51 and ND51b Menus

NOTE: The binary punch file format is slated to be removed from the next version of GEOS-Chem (i.e., v11-02).

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% ND51 MENU %%%       :
02: Turn on ND51 diagnostic : F
03: LT avg timeseries file  : ts_satellite.YYYYMMDD.bpch
04: Output as HDF5?         : F
05: Tracers to include      : 82 83 84 85 86 87
06: GMT Hour for disk write :   0
07: Avg Period [LT hours]   :  10  12
08: IMIN, IMAX of region    :   1 151
09: JMIN, JMAX of region    :   1 121
10: LMIN, LMAX of region    :   1  40

01: %%% ND51b MENU %%%      :
02: Turn on ND51b diagnstic : F
03: LT avg timeseries file  : ts_13_15.NA.YYYYMMDD.h5
04: Output as HDF5?         : F
05: Tracers to include      : 1 4 20 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44
06: GMT Hour for disk write :  1
07: Avg Period [LT hours]   :  13  15
08: IMIN, IMAX of region    :   1  72
09: JMIN, JMAX of region    :   1  46
10: LMIN, LMAX of region    :   1   1
Line What gets defined Description
1 nothing Header line
2 Input_Opt%DO_ND51
Input_Opt%DO_ND51b
Set this to T to turn on the ND51 and/or ND51b "satellite" 3D timeseries diagnostic. ND51 and/or ND51b 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.
  • NOTE: The ND51 and ND51b diagnostics allow you to archive two separate time-averaged timeseries files simultaneously in GEOS-Chem. This is useful if you want to only run GEOS-Chem once, but create timeseries output corresponding to 2 different satellite instruments simultaneously.
3 Input_Opt%ND51_FILE
Input_Opt%ND51b_FILE
The name of the ND51 and/or ND51b files which will contain output from the ND51 and/or ND51b 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.
4 nothing OBSOLETE
5 Input_Opt%ND51_TRACERS
Input_Opt%ND51b_TRACERS
The ND51 and/or ND51b diagnostic quantities to save to disk. Separate each number with a space.
6 Input_Opt%ND51_HR_WRITE
Input_Opt%ND51b_HR_WRITE
The time of day (in GMT hours) at which the ND51 timeseries file will be written to disk. Recommended value: 0 GMT each day.
7 Input_Opt%ND51_HR_1
Input_Opt%ND51_HR2
Input_Opt%ND51b_HR_1
Input_Opt%ND51b_HR2
The ND51 and/or ND51b 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.
8 Input_Opt%ND51_IMIN
Input_Opt%ND51_IMAX
Input_Opt%ND51b_IMIN
Input_Opt%ND51b_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 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.

9 Input_Opt%ND51_JMIN
Input_Opt%ND51_JMAX
Input_Opt%ND51b_JMIN
Input_Opt%ND51b_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 GMAO 4° x 5° grid: 1 46
  • For GMAO 2° x 2.5° grid: 1 91
10 Input_Opt%ND51_LMIN
Input_Opt%ND51_LMAX
Input_Opt%ND51b_LMIN
Input_Opt%ND51b_LMAX
The indices which determine the vertical extent of the 3D region of the globe.

--Bob Yantosca (talk) 17:43, 17 November 2016 (UTC)

ND63 Menu

NOTE: The binary punch file format is slated to be removed from the next version of GEOS-Chem (i.e., v11-02).

01: %%% ND63 MENU %%%       :
02: Turn on ND63 diagnostic : F
03: Inst 3-D timeser. file  : paranox_ts.YYYYMMDD.bpch
04: Tracers to include      : 1
05: Frequency [min]         : 120
06: IMIN, IMAX of region    :  70  30
07: JMIN, JMAX of region    :  23  46
Line What gets defined Description
1 nothing Header line
2 Input_Opt%DO_ND63 Set this to T to turn on the ND63 ship timeseries diagnostic.
3 Input_Opt%ND63_FILE 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.
4 Input_Opt%ND63_TRACERS Specify the ND63 diagnostic quantities that you wish to save to disk. Separate each number with a space.
5 Input_Opt%ND63_FREQ The frequency in minutes at which the ND63 ship diagnostics will be written to disk.
6 Input_Opt%ND63_IMIN
Input_Opt%ND63_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 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.

7 Input_Opt%ND63_JMIN
Input_Opt%ND63_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 GMAO 4° x 5° grid: 1 46
  • For GMAO 2° x 2.5° grid: 1 91

--Bob Yantosca (talk) 17:21, 17 November 2016 (UTC)

Prod and Loss Menu

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% PROD & LOSS MENU %%%:
02: Turn on P/L (ND65) diag?: T
03: # of levels for ND65    : 72
04: Save O3 P/L (ND20)?     : F
Line What gets defined Description
1 nothing Header line
2 Input_Opt%DO_SAVE_PL 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.
3 Input_Opt%ND65 Specify the number of levels to save for the chemical family production & loss diagnostic.
  • 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.
4 Input_Opt%DO_SAVE_O3 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).

Benchmark Menu

NOTE: The binary punch file format is slated to be removed from the next version of GEOS-Chem (i.e., v11-02).

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% BENCHMARK MENU %%%  :
02: Save benchmark output?  : T
03: File w/ initial Ox      : Ox.mass.initial
04: File w/ final Ox        : Ox.mass.final
Line What gets defined Description
1 nothing Header line
2 Input_Opt%LSTDRUN 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.
3 Input_Opt%STDRUN_INIT_FILE Specify name of file (binary punch format) that will contain initial tracer mass.
4 Input_Opt%STDRUN_FINAL_FILE Specify name of file (binary punch format) that will contain final tracer mass.

--Bob Yantosca (talk) 20:59, 16 November 2016 (UTC)

Nested Grid Menu

NOTE: This menu controls options for the various GEOS-Chem nested grid simulations. This is an optional menu and may be omitted from input.geos if you are not concerned with these simulations.

For more information, please see:

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% NESTED GRID MENU %%%:
02: Save TPCORE BC's        : F
03: Input BCs at 2x2.5?     : F
04: Over North America?     : F
05: TPCORE NA BC directory  : BC_4x5_NA/
06: Over Europe?            : F
07: TPCORE EU BC directory  : BC_4x5_EU/
08: Over China?             : F
09: TPCORE CH BC directory  : BC_4x5_CH/
10: Over Asia?              : F
11: TPCORE AS BC directory  : BC_4x5_AS/
12: Over Custom Region?     : F
13: TPCORE BC directory     : BC_4x5/
14: BC timestep [min]       : 180
15: LL box of BC region     :   9  26
16: UR box of BC region     :  29  41
17: I0_W, J0_W, I0_E, J0_E  :   3   3   3   3
Line What gets defined Description
1 nothing Header line
2 Input_Opt%LWINDO Set this 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°).
3 Input_Opt%LWINDO2x25 Set this to T if you are using boundary conditions archived from a 2° x 2.5° GEOS-Chem simulation, or F otherwise.
4 Input_Opt%LWINDO_NA Set this to T if you wish to perform a GEOS-Chem nested grid simulation over the North American nested domain.
5 Input_Opt%TPBC_DIR_NA The directory path containing boundary conditions for your North American nested-grid simulation.
6 Input_Opt%LWINDO_EU Set this to T if you wish to perform a GEOS-Chem nested grid simulation over the European nested domain.
7 Input_Opt%TPBC_DIR_EU The directory path containing boundary conditions for your European nested-grid simulation.
8 Input_Opt%LWINDO_CH Set this to T if you wish to perform a GEOS-Chem nested grid simulation over the China/SE Asia nested domain.
9 Input_Opt%TPBC_DIR_CH Which is the directory path containing boundary conditions for your China/SE Asia nested-grid simulation.
10 Input_Opt%LWINDO_AS Set this T if you wish to perform a GEOS-Chem nested grid simulation over the MERRA-2 extended Asia region.
11 Input_Opt%TPBC_DIR_AS The directory path containing boundary conditions for your SE Asia nested-grid simulation.
12 Input_Opt%LWINDO_CU Set this to T if you wish to perform a GEOS-Chem nested grid simulation a domain that you have customized yourself.
13 Input_Opt%TPBC_DIR_CU which is the directory path containing the boundary conditions for your custom-domain nested-grid simulation.
14 Input_Opt%NESTED_TS 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).
15 Input_Opt%NESTED_I1
Input_Opt%NESTED_J1
These are the longitude and latitude indices of the grid box at the LOWER LEFT CORNER of the window region in which boundary conditions are being saved.
16 Input_Opt%NESTED_I2
Input_Opt%NESTED_J2
These are the the longitude and latitude indices of the grid box at the UPPER RIGHT CORNER of the window region in which boundary conditions are being saved.
17 Input_Opt%NESTED_I0W
Input_Opt%NESTED_J0W
Input_Opt%NESTED_I0E
Input_Opt%NESTED_J0E
These are the nested grid longitude and latitude offsets (in # of boxes) of the which are used to define an inner window region 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:

  • Input_Opt%NESTED_I0W=3 and Input_Opt%NESTED_J0W=3.
  • Input_Opt%NESTED_I0E=3 and Input_Opt%NESTED_J0E=3.
    • But for some grids (e.g. SE Asia) you may want to use Input_Opt%NESTED_I0E=2 and Input_Opt%NESTED_J0E=2.

For more information, please contact the Nested Model Working Group.

--Bob Yantosca (talk) 21:37, 16 November 2016 (UTC)

Unix Commands Menu

This menu specifies various Unix characters. It is by now mostly obsolete. We recommend that you do not edit this.

%%% UNIX CMDS MENU %%%  :
Background symbol       : &
Redirect symbol         :  >
Unix remove command     : rm -f
Unix pathname separator : /
Unix wildcard character : *
Unix unzip command      : gzip -dc
Zip file suffix         : .gz

--Bob Yantosca (talk) 21:38, 16 November 2016 (UTC)

Passive Species Menu

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% PASSIVE SPECIES MENU %%%:
02: Number of passive spec. : 2
03: Passive species #1      : PASV1 1.0 -1 1.0e-7
04: Passive species #2      : PASV2 50.0 3600.0 1.0e-12
Line What gets defined Description
1 nothing Header line
2 nPassive The number of passive species that you want to include.
3-4 SpcName
SpcMW
SpcTau
SpcInitConc
For each passive species, you must provide the following information (separated by spaces):
  • Species name
  • Species molecular weight (g/mol)
  • Atmospheric lifetime (s)
    • Specify 0 or negative value for no loss
  • Default initial atmospheric concentration (v/v)
    • This value will only be used if the species is not found in the restart file.

There must be a matching entry in the advected species menu for every passive species defined in the passive species menu. If the two menus aren't consistent, you will get a species database error. For more information, see this wiki post on adding passive species.

--Melissa Sulprizio (talk) 20:58, 21 March 2017 (UTC)

CH4 simulation menu

This menu controls options for the tagged CH4 simulation only. This is an optional menu and may be omitted from input.geos if you are not concerned with this simulation. For more information, please see our CH4 simulation wiki page.

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% CH4 MENU %%%        :
02: Compute CH4 budget?     : F
03: Use Gas & Oil emis?     : T
04: Use Coal Mine emis?     : T
05: Use Livestock emis?     : T
06: Use Waste emis?         : T
07: Use Biofuel emis?       : T
07: Use Rice emis?          : T
08: Use Ot. Anthro emis?    : T
09: Use Biomass emis?       : T
10: Use Wetlands emis?      : T
11: Use Soil Absorption?    : T
12: Use Ot. Natural?        : T
Line What gets defined Description
1 nothing Header line
2 Input_Opt%LCH4BUD Set this to T to calculate a monthly budget for CH4.
  • NOTE: The CH4 budget is not working well, we recommend setting leaving this set to F.
3 Input_Opt%LGAO Set this to F to turn off CH4 emissions from gas and oil.
4 Input_Opt%LCOL Set this to F to turn off CH4 emissions from coal.
5 Input_Opt%LLIV Set this to F to turn off CH4 emissions from livestock.
6 Input_Opt%LWAST Set this to F to turn off CH4 emissions from waste.
7 Input_Opt%LBFCH4 Set this to F to turn off CH4 emissions from biofuels.
8 Input_Opt%LRICE Set this to F to turn off CH4 emissions from rice fields.
9 Input_Opt%LOTANT Set this to F to turn off other CH4 anthropogenic emissions.
10 Input_Opt%LBMCH4 Set this to F to turn off CH4 emissions from biomass burning.
11 Input_Opt%LWETL Set this to F to turn off CH4 emissions from wetlands.
12 Input_Opt%LSOABS Set this to F to turn off CH4 absorption by soils.
13 Input_Opt%LOTNAT Set this F to turn off other CH4 natural emissions.

--Bob Yantosca (talk) 15:55, 17 November 2016 (UTC)

CO2 Simulation Menu

This menu only controls options for the CO2 and tagged CO2 simulations. This is an optional menu and may be omitted from input.geos if you are not concerned with these simulations. For more information, please see:

  • Our CO2 simulation wiki page.
  • A more detailed account of all settings can be found in:
    • Nassar, R., D.B.A. Jones, P. Suntharalingam, J.M. Chen, R.J. Andres, K.J. Wecht, R.M. Yantosca, S.S. Kulawik, K.W. Bowman, J.R. Worden, T. Machida, and H. Matsueda, Modeling CO2 with improved emission inventories and CO2 production from the oxidation of other carbon species, Geoscientific Model Development, 3, 689-716, 2010.

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% CO2 SIM MENU %%%    :
02: Fossil Fuel Emissions   : T
03: Ocean Exchange          : T
04: Balanced Biosphere Exch : T
05: Net Terrestrial Exch    : T
06: Ship emissions          : T
07: Aviation emissions 3-D  : T
08: 3-D Chemical Oxid Source: T
09: Tagged CO2 runs         :---
10:  Save Fossil in Bckgrnd: F
11:  Tag Bio/Ocean CO2 reg : F
12:  Tag Land FF CO2 reg   : F
13:  Tag Global Ship CO2   : F
14:  Tag Global Plane CO2  : F
Line What gets defined Description
1 nothing Header line
2 Input_Opt%LFOSSIL Set this to T to use fossil-fuel emissions of CO2 as computed by HEMCO.
3 Input_Opt%LOCEAN Set this to T to use ocean exchange of CO2 as as computed by HEMCO.
4 Input_Opt%LBIODIURNAL Set this to T to turn on the CASA model 3-hourly Net Ecosystem Production (balanced – no net annual flux) [Potter et al., 1993; Olsen and Randerson, 2004].
5 Input_Opt%LBIONETCLIM Set this to T to turn on Net Terrestrial Exchange (climatology) of -5.29 PgC/yr [Baker et al., 2006] adjusted for biomass/biofuel burning.
6 Input_Opt%LSHIP Set this to T to use on ship emissions of CO2 as computed by HEMCO.
7 Input_Opt%LPLANE Set this to T to turn on the 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.
8 Input_Opt%LCHEMCO2 Set this to T to turn on the 3D CO2 chemical source from oxidation of CO, CH4 and NMHCs based on Suntharalingam et al. [2005], with appropriate surface emission corrections.
9 nothing Header line
10 Input_Opt%LFFBKGRD Set this to T to save CO2 background.
11 Input_Opt%LBIOSPHTAG Set this to T to tag biosphere regions (28), ocean regions (11) and the Rest of the World (ROW) as specified in the Regions_land.dat and Regions_ocean.dat files.
  • NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.
12 Input_Opt%LFOSSILTAG Set this to T to tag fossil fuel regions (28) as specified in the Regions_land.dat file and ROW.
  • NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.
13 Input_Opt%LSHIPTAG Set this to T to tag global ship emissions as a single tracer.
  • NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.
14 Input_Opt%LPLANETAG Set this to T to Tag global aviation emissions as a single tracer.
  • NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.

--Bob Yantosca (talk) 22:41, 16 November 2016 (UTC)

POPs simulation menu

This menu controls options for the persistent organic pollutants (POPs) simulation only. This is an optional menu and may be omitted from input.geos if you are not concerned with this simulation. For more information, please see our POPs simulation wiki page.

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% POPS MENU %%%       :
02: POP type [PHE,PYR,BAP]  : PHE
03: Chemistry processing on?: T
04: POP_XMW                 : 178.23d-3
05: POP_KOA                 : 4.37d7
06: POP_KBC                 : 1.0d10
07: POP_K_POPG_OH           : 2.7d-11
08: POP_K_POPG_O3A          : 0d0
09: POP_K_POPG_O3B          : 2.15d15
10: POP_HSTAR               : 1.74d-3
11: POP_DEL_H               : -74d3
12: POP_DEL_Hw              : 47d0
Line What gets defined Description
1 nothing Header line
2 Input_Opt%POP_TYPE Current options are PHE (phenanthrene), PYR (pyrene), or BAP (benzo[a]pyrene).
3 Input_Opt%CHEM_PROCESS Set this to T to use POPs chemistry.
4 Input_Opt%POP_XMW The molecular weight of the POPs species in kg/mol.
5 Input_Opt%POP_KOA The POP octanol-water partition coefficient.
6 Input_Opt%POP_KBC The POP black carbon-air partition coefficient.
7 Input_Opt%POP_K_POPG_OH The POP reaction rate constant for reaction of gas phase POP with hydroxyl radical in cm3/molec/s.
8 Input_Opt%POP_K_POPP_O3A The POP reaction rate constant for reaction of particle phase POP with ozone in s-1.
9 Input_Opt%POP_K_POPP_O3B The POP reaction rate constant for reaction of particle phase POP with ozone in molec/cm3.
10 Input_Opt%POP_HSTAR The Henry's Law constant for the POPs species.
11 Input_Opt%POP_DEL_H The enthalpy of air-water exchange in J/mol.
12 Input_Opt%POP_DEL_Hw The enthalpy of phase transfer from gas phase to particle phase.

--Bob Yantosca (talk) 15:50, 17 November 2016 (UTC)

Mercury Simulation Menu

NOTE: The Global Terrestrial Mercury Model is broken in v11-01. We need to convert the GTMM restart file from bpch to netCDF. The work is ongoing.

This menu only controls options for the mercury simulation (with or without the Global Terrestrial Mercury Model). This is an optional menu and may be omitted from input.geos if you are not concerned with this simulation.

For more information, please see:

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% MERCURY MENU %%%    :
02: Use anthro Hg emiss for : 2006
03: Use future emissions?   : PRESENT
04: Error check tag/tot Hg? : F
05: Use dynamic ocean Hg?   : T
06: Preindustrial sim?      : F
07: Use GTMM soil model?    : F
08: GTMM Hg rst file (bpch) : GTM.totHg.YYYYMMDDhh
09: Use Arctic river Hg?    : T
10: Tie HgII(aq) red to UVB?: T
Line What gets defined Description
1 nothing Header line
2 Input_Opt%ANTHRO_Hg_YEAR Baseline year of the anthropogenic mercury emissions that are used in the tagged mercury simulation. Current options are either 2006 or 2050.
3 Input_Opt%Hg_SCENARIO Future emissions are based on the four IPCC SRES scenarios. Current options are PRESENT, A1B, A2, B1, or B2.
4 Input_Opt%USE_CHECKS Set this 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.
5 Input_Opt%LDYNOCEAN. Set this 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.
6 Input_Opt%LPREINDHG Set to T if you want to run a preindustrial simulation (turn off anthropogenic emissions), to F otherwise.
8 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.
8 Input_Opt%GTMM_RST_FILE 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.
  • NOTE: The GTMM restart file will have to be converted from bpch to netCDF format.

--Bob Yantosca (talk) 15:47, 17 November 2016 (UTC)

Radiation Menu

This menu controls options for GEOS-Chem simulations coupled to the RRTMG radiative transfer model. This is an optional menu and may be omitted from input.geos if you are not concerned with this simulation. For more information, please see our Coupling GEOS-chem with RRTMG wiki page.

Line numbers are not part of the input.geos file, but have been included for reference.

01: %%% RADIATION MENU %%%  :
02: AOD Wavelength (nm)     : 550
03: Turn on RRTMG?          : F
04: Calculate LW fluxes?    : F
05: Calculate SW fluxes?    : F
06: Clear-sky flux?         : F
07: All-sky flux?           : F
08: Radiation Timestep [min]: 180
09: Species fluxes          : 0 0 0 0 0 0 0 0 0 1 0
10:  ---[O3,ME,SU,NI,AM,BC,OA,SS,DU,PM,ST]
Line What gets defined Description
1 nothing Header line
2 WVSELECT 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.
3 Input_Opt%LRAD Set this to T to turn on online radiative transfer using RRTMG, or F to turn off RRTMG.
4 Input_Opt%LLWRAD Set this to T to turn on longwave radiation calculation.
5 Input_Opt%LSWRAD Set this to T to turn on shortwave radiation calculation.
6 Input_Opt%LSYKRAD(1) Set this to T to turn turn on calculation for clear-sky fluxes. This option will perform radiative calculations without clouds.
7 Input_Opt%LSYKRAD(2) Set this 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.
8 Input_Opt%TS_RAD Radiation timestep 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.).
9 LSPECRADMENU 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.
  • NOTE: 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.
10 nothing 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:
  • O3 (Ozone)
  • ME (Methane)
  • SU (Sulfate)
  • NI (Nitrate)
  • AM (Ammonium)
  • BC (Black carbon)
  • OA (Organic aerosol)
  • SS (Sea salt)
  • DU (Mineral dust)
  • PM (All particulate matter)
  • ST (Stratospheric aerosol, UCX simulation only)

--Bob Yantosca (talk) 20:09, 16 November 2016 (UTC)

The HEMCO_Config.rc file

Overview

In GEOS-Chem v10-01 and later versions, emissions are read, regridded, and calculated by the HEMCO emissions component. The emission settings are specified in the HEMCO Configuration file (HEMCO_Config.rc).

For more information about the HEMCO_Config.rc file, please see:

--Bob Yantosca (talk) 23:25, 16 November 2016 (UTC)

Enabling and disabling emissions

The HEMCO_Config.rc file for each GEOS-Chem simulation contains a set of switches that allow you to quickly toggle individual emissions inventories on or off.

Each time you create a GEOS-Chem run directory from the Unit Tester, a new HEMCO_Config.rc file with default emissions settings will be created in the run directory. These default settings are located near the top of the HEMCO_Config.rc file.

For example, the default emissions settings for the "Standard" full-chemistry simulation are:

# ExtNr ExtName           on/off  Species
0       Base              : on    *
    --> HEMCO_RESTART     :       true
    --> AEIC              :       true
    --> BIOFUEL           :       true
    --> BOND              :       true
    --> BRAVO             :       true
    --> CAC               :       true
    --> XIAO              :       true
    --> EDGAR             :       true
    --> HTAP              :       false
    --> EMEP              :       true
    --> EMEP_SHIP         :       true
    --> GEIA              :       true
    --> LIANG_BROMOCARB   :       true
    --> NEI2005           :       false
    --> NEI2011           :       true
    --> RETRO             :       true 
    --> SHIP              :       true
    --> NEI2011_SHIP      :       false
    --> MIX               :       true
    --> STREETS           :       false
    --> VOLCANO           :       true
    --> RCP_3PD           :       false 
    --> RCP_45            :       false
    --> RCP_60            :       false
    --> RCP_85            :       false
    --> QFED2             :       false
# -----------------------------------------------------------------------------
100     Custom            : off   - 
101     SeaFlux           : on    DMS/ACET
102     ParaNOx           : on    NO/NO2/O3/HNO3
    --> LUT data format   :       nc
    --> LUT source dir    :       $ROOT/PARANOX/v2015-02
103     LightNOx          : on    NO
    --> OTD-LIS factors   :       true
    --> CDF table         :       $ROOT/LIGHTNOX/v2014-07/light_dist.ott2010.dat
104     SoilNOx           : on    NO 
    --> Use fertilizer NOx:       true
105     DustDead          : on    DST1/DST2/DST3/DST4 
106     DustGinoux        : off   DST1/DST2/DST3/DST4
115     DustAlk           : off   DSTAL1/DSTAL2/DSTAL3/DSTAL4
107     SeaSalt           : on    SALA/SALC/Br2
    --> SALA lower radius :       0.01 
    --> SALA upper radius :       0.5
    --> SALC lower radius :       0.5
    --> SALC upper radius :       8.0
    --> Emit Br2          :       true  
    --> Br2 scaling       :       1.0 
116     MarinePOA         : off   MOPO/MOPI 
108     MEGAN             : on    ISOP/ACET/PRPE/C2H4/ALD2
    --> Isoprene scaling  :       1.0 
    --> CO2 inhibition    :       true
    --> CO2 conc (ppmv)   :       390.0
109     MEGAN_Mono        : on    CO/OCPI/MONX
110     MEGAN_SOA         : on    MTPA/MTPO/LIMO/SESQ
111     GFED              : on    NO/CO/ALK4/ACET/MEK/ALD2/PRPE/C3H8/CH2O/C2H6/SO2/NH3/BCPO/BCPI/OCPO/OCPI/POG1/POG2/NAP
    --> GFED3             :       false 
    --> GFED4             :       true
    --> GFED_daily        :       false
    --> GFED_3hourly      :       false
    --> Scaling_CO        :       1.05
    --> Scaling_POG1      :       1.27
    --> Scaling_POG2      :       1.27
    --> Scaling_NAP       :       2.75e-4
    --> hydrophilic BC    :       0.2
    --> hydrophilic OC    :       0.5
    --> fraction POG1     :       0.49
114     FINN              : off   NO/CO/ALK4/ACET/MEK/ALD2/PRPE/C3H8/CH2O/C2H6/SO2/NH3/BCPI/BCPO/OCPI/OCPO/GLYC/HAC
    --> FINN_daily        :       false
    --> Scaling_CO        :       1.0
    --> hydrophilic BC    :       0.2
    --> hydrophilic OC    :       0.5 

If you would like to turn off NEI2011, simply change the true in this line:

     --> NEI2011           :       true

to false:

     --> NEI2011           :       false

And if you also wanted to turn off the MEGAN biogenic emissions, simply change the on in this line:

108     MEGAN             : on    ISOP/ACET/PRPE/C2H4/ALD2

to off:

108     MEGAN             : off    ISOP/ACET/PRPE/C2H4/ALD2

etc.

--Bob Yantosca (talk) 23:08, 16 November 2016 (UTC)

The Planeflight.dat file

NOTE: Some of the quantities in the plane flight diagnostic were disabled when SMVGEAR was replaced with the new FlexChem solver package.

Sometimes it is necessary to compare GEOS-Chem output against aircraft observations. The plane flight following diagnostic (a.k.a. ND40 diagnostic) allows you to save out GEOS-Chem diagnostic quantities for grid boxes corresponding to aircraft flight tracks. This prevents you from having to save out huge 3-D punch files with lots of species.

The Planeflight.dat.YYYYMMDD files allow you to specify the diagnostic quantities (tracers, reaction rates, met fields, or chemical species) that you want to print out for a specific longitude, latitude, altitude, and time. A sample Planeflight.dat.YYYYMMDD file is given below. Of course if you have lots of flight track data points, your file will be much longer.

In GEOS-Chem v7-03-06 and higher versions, the plane flight following diagnostic has been modified to be consistent with the method of saving out plane flight data used in the ICARTT mission. If the plane flight following diagnostic is switched on, then it will look for a new Planeflight.dat.YYYYMMDD file each day. If a Planeflight.dat.YYYYMMDD file is found for a given day, then GEOS-Chem will save out diagnostic quantities along the flight track(s) specified within the file.

Line numbers are not part of the Planeflight.dat file, but are provided for reference.

01: Planeflight.dat
02: Bob Yantosca
03: 26 Apr 2004
04: -------------------------------------------------------------------------------
05: 9 < -- # of variables to be output (list them below, one per line)
06: -------------------------------------------------------------------------------
07: TRA_004
08: O3
09: GMAO_TEMP
10: GMAO_ABSH
11: GMAO_SURF
12: AODB_SULF
13: AODC_BLKC
14: -------------------------------------------------------------------------------
15: Now give the times and locations of the flight
16: -------------------------------------------------------------------------------
17: Point Type  DD-MM-YYYY HH:MM   LAT    LON    PRESS
18:     1 P3B04 01-01-2003 00:00   42.00  290.00 500.00
19:     2 DC801 01-01-2003 00:00   42.00  290.00 500.00
20:     3 P3B04 01-01-2003 01:00   41.00  290.00 500.00
21:     4 DC801 01-01-2003 01:00   42.00  289.00 500.00
22:     5 P3B04 01-01-2003 02:00   40.00  290.00 500.00
23: 99999 END   0- 0- 0    0 :0    0.00   0.00   0.00
Line bgcolor="#CCCCCC" width="950px"Description
1-4 Header lines with comments
5 Number of diagnostic quantities to print out.
6 Separator line
7-13 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.)
TRA_nnn
Advected tracer (where nnn is the tracer number from input.geos)
O3, OH, NO, etc.
Chemical species (use the same names as in the globchem.dat mechanism file)
GMAO_TEMP
Temperature from the met fields
GMAO_ABSH
Absolute humidity derived from the met fields
GMAO_SURF
Aerosol surface area
GMAO_PSFC
Surface pressure
GMAO_UWND
Zonal winds
GMAO_VWND
Meridional winds
GMAO_IIEV
GEOS-Chem grid box index, longitude
GMAO_JJEV
GEOS-Chem grid box index, latitude
GMAO_LLEV
GEOS-Chem grid box index, altitude
GMAO_ICEnn
SEAICEnn fields (i.e. the fraction of each grid box that has nn% to nn+10% of sea ice coverage)
  • NOTE: You can only use this option for MERRA and GEOS-5.7.x met fields.
AODB_SULF
Sulfate optical depth—column from surface up to location of aircraft
AODB_BLKC
Black carbon optical depth—column from surface up to location of aircraft
AODB_ORGC
Organic carbon optical depth—column from surface up to location of aircraft
AODB_ORGC
Organic carbon optical depth—column from surface up to location of aircraft
AODB_ORGC
Organic carbon optical depth—column from surface up to location of aircraft
AODB_SALC
Coarse mode sea salt optical depth—column from surface up to location of aircraft
AODC_SULF
Sulfate optical depth—tropospheric column
AODC_BLKC
Black carbon optical depth—tropospheric column
AODC_ORGC
Organic carbon optical depth—tropospheric column
AODC_SALA
Accumulation mode sea salt optical depth—tropospheric column
AODC_SALC
Coarse mode sea salt optical depth—tropospheric column

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.

14-16 Separator Lines
17 Comment line which shows you where to line up each column field of the flight track points.
18-22 Here we list quantities which define each flight track point. Make sure that each field lines up with the guides in the line above.
Point
Flight track data point number (used internally for reference)
Type
A short string that denotes the aircraft type and flight number.
Date
List the day, month, and year (GMT date) for each flight track point.
HH
MM: List the hour and minute (GMT time) for each flight track point.
Lat
List the latitude (-90 to 90 degrees) for each flight track point.
Lon 
List the longitude (-180 to 180 degrees) for each flight track point.
Press
List the pressure in hPa for each flight track point.

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.

26 Ending line

--Bob Yantosca (talk) 20:19, 17 November 2016 (UTC)

Input files for the photolysis mechanism

GEOS-Chem v10-01 and later versions use the FAST-JX v7.0 photolysis mechanism. Several input files for the FAST-JX photolysis mechanism ship with the GEOS-Chem run directories. You should only have to modify these files if you wish to change the chemical mechanism or photolysis mechanism.

For more information, please see our Input files for FAST-JX v7.0 wiki post.

--Bob Yantosca (talk) 20:26, 17 November 2016 (UTC)