Difference between revisions of "The input.geos file"

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On this page, we describe the settings and switches that are found <tt>input.geos</tt> file.
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== Overview ==
 
== Overview ==
  

Revision as of 15:10, 10 December 2019

On this page, we describe the settings and switches that are found input.geos file.

Overview

Most user-defined input switches and settings which customize GEOS-Chem options (other than emissions and diagnostic output settings) are defined in the input.geos configuration 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.

Currently-used menus in input.geos

Simulation

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: Root data directory     : /path/to/data/
06: Met field               : geosfp
07: Simulation name         : standard

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 Added/Removed?
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%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 Downloading GEOS-Chem data directories.

6 Input_Opt%MetField Specify the meteorology fields for your simulation. Current options are GEOS-FP or MERRA-2. Added in 12.6.0
7 Input_Opt%SimulationName Specify the name of the simulation. Allowable values (case-insensitive) are:
  1. aciduptake
  2. aerosol
  3. apm
  4. benchmark
  5. CH4
  6. CO2
  7. complexSOA
  8. complexSOA_SVPOA
  9. HEMCO
  10. Hg
  11. marinePOA
  12. POPs
  13. RRTMG
  14. standard
  15. TransportTracers
  16. tropchem
  17. tagCO
  18. tagCH4
  19. tagHg
  20. tagO3
  21. TOMAS12
  22. TOMAS15
  23. TOMAS30
  24. TOMAS40
 Added in 12.6.0

--Melissa Sulprizio (talk) 14:31, 28 June 2019 (UTC)
--Bob Yantosca (talk) 18:29, 9 December 2019 (UTC)

Grid

NOTE: The Grid Menu was introduced in GEOS-Chem 12.4.0. This menu is not read by GCHP or when running GEOS-Chem in an ESM.

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

01: %%% GRID MENU %%%       :
02: Grid resolution         : 4.0x5.0
03: Longitude min/max       : -180.0 180.0
04: Latitude  min/max       : -90.0   90.0
05:  Half-sized polar boxes?: T
06: Number of levels        : 72
07: Nested grid simulation? : F
08:  Buffer zone (N S E W ) :  0  0  0  0
Line What gets defined Description Added/Removed?
1 nothing Header line
2 State_Grid%GridRes The horizontal grid resolution for your simulation. Current supported options are 4.0x5.0, 2.0x2.5, 0.5x0.625, and 0.25x0.3215.

GEOS-Chem will split this string and store values in State_Grid%DX and State_Grid%DY.

Added in 12.4.0
3 State_Grid%XMin
State_Grid%XMax 		The minimum and maximum longitudes in decimal degrees that define your domain. For global simulations, this should be set to -180.0 180.0.

The number of grid boxes in the X dimension are computed from these bounds using:

State_Grid%NX = ( State_Grid%XMax - State_Grid%XMin ) / State_Grid%DX ).
 Added in 12.4.0
4 State_Grid%YMin
State_Grid%YMax 		The minimum and maximum latitude in decimal degrees that define your domain. For global simulations, this should be set to -90.0 90.0.

The number of grid boxes in the Y dimension are computed from these bounds using:

State_Grid%NY = ( State_Grid%YMax - State_Grid%YMin ) / State_Grid%DY ).
 Added in 12.4.0
5 State_Grid%HalfPolar Set this to T to use half-sized polar grid boxes. This should always be set to T when using GMAO met fields (i.e. GEOS-FP, MERRA-2). Added in 12.4.0
6 State_Grid%NZ The number of vertical levels. Current supported options are 47 and 72. Added in 12.4.0
7 State_Grid%NestedGrid Set this to T when running a nested grid simulation or to F otherwise. Added in 12.4.0
8 State_Grid%NorthBuffer
State_Grid%SouthBuffer
State_Grid%EastBuffer
State_Grid%WestBuffer 		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 are 3 3 3 3. Added in 12.4.0

--Melissa Sulprizio (talk) 17:57, 11 July 2019 (UTC)
--Bob Yantosca (talk) 20:02, 9 December 2019 (UTC)

Timestep

NOTE: In GEOS-Chem 12, we have changed the units of all timesteps from minutes to seconds. We made this change in order to be able to interface GEOS-Chem with the NASA the GEOS-DAS Earth System Model more efficiently.

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

01: %%% TIMESTEP MENU %%%   :
02: Tran/conv timestep [sec]: 600
03: Chem/emis timestep [sec]: 1200
Line What gets defined Description Added/Removed?
1 nothing Header line
2 Input_Opt%TS_DYN
Input_Opt%TS_CONV 		The dynamic (aka "Heartbeat") timestep in seconds. This is the timestep at which transport, PBL mixing, cloud convection, and wet deposition occur.

Recommended values:

  • 300 sec (=5 min) for:
    • 0.25° x 0.3125° GEOS-FP nested-grid simulations
    • 0.5° x 0.625° MERRA-2 nested-grid simulations
  • 600 sec (=10 min) for:
    • 2° x 2.5° global simulations: 600 sec (=10 min)
    • 4° x 5° global simulations: 600 sec (=10 min)
 Added in 12.0.0
3 Input_Opt%TS_CHEM
Input_Opt%TS_EMIS 		The chemistry timestep in seconds. This is the timestep at which dry deposition, emissions, and chemistry occur.

Recommended values:

  • 600 sec (=10 min) for:
    • 0.25° x 0.3125° GEOS-FP nested-grid simulations
    • 0.5° x 0.625° MERRA-2 nested-grid simulations
  • 1200 sec (=20 min) for:
    • 2° x 2.5° global simulations: 600 sec (=10 min)
    • 4° x 5° global simulations: 600 sec (=10 min)
 Added in 12.0.0
CAVEAT: Running GEOS-Chem with the recommended timesteps from Philip et al. (2016)] has been shown to increase run times by approximately a factor of 2. For tips on improving run time, please see our Speeding up GEOS-Chem wiki page.

--Bob Yantosca (talk) 20:48, 9 December 2019 (UTC)

Advected Species

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: Species Entries ------->: Name
04: Species #1              : NO
05: Species #2              : O3
06: Species #3              : PAN
07: Species #4              : CO
... etc not shown here ...
Line What gets defined Description Added/Removed?
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. UNUSED
  3. One of the NOx-Ox-Hydrocarbon-aerosol (aka "full chemistry") simulations
  4. UNUSED
  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. UNUSED
  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.

Removed in 12.6.0
3 nothing Header line Removed in 12.6.0


4 - 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) 20:49, 9 December 2019 (UTC)

Transport

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
Line What gets defined Description Added/Removed?
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.

--Bob Yantosca (talk) 20:01, 9 December 2019 (UTC)

Convection

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
Line What gets defined Description Added/Removed?
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.

--Bob Yantosca (talk) 20:03, 9 December 2019 (UTC)

Emissions

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: HEMCO Input file        : HEMCO_Config.rc
04:  => 1ppt MBL BRO Sim.?  : F
05: Switches for UCX        :---
06:  => Use CH4 emissions?  : F
07:  => Turn on surface BCs :---
08:     => CH4?             : T
19:     => OCS?             : T
10:     => CFCs?            : T
11:     => Cl species?      : T
12:     => Br species?      : F
13:     => N2O?             : T
14:  => Set initial glob MRs:---
15:     => strat. H2O?      : T
16:  => CFC emission year   : 0
Line What gets defined Description Added/Removed?
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%HcoConfigFile The name of the HEMCO configuration file. The emission inventories that your simulation will use are set in this file.
4 Input_Opt%LFIX_PBL_BrO Set this to T to set Bro concentrations in the PBL equal to 1 ppt during the day.
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 (e.g "tropchem", "complexSOA").
5 nothing Header line.
6 Input_Opt%LCH4EMIS Set this T to use online methane emissions.
7 nothing Header line
8 Input_Opt%LCH4SBC Set this T to fix surface mixing ratio of methane.
9 Input_Opt%LOCSEMIS Set this to T to fix surface mixing ratios of OCS.
10 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.
11 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.
12 Input_Opt%LBREMIS Set this to T to fix surface mixing ratios of bromine species. Not recommended if other bromine emissions are enabled.
13 Input_Opt%LN2OEMIS Set this to T to fix surface mixing ratios of N2O.
14 nothing Header line
15 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.
16 Input_Opt%CFCYEAR Specify the starting year for CFC emissions.

--Bob Yantosca (talk) 20:05, 9 December 2019 (UTC)

Aerosols

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

01: %%% AEROSOL MENU %%%    :
02: Online SULFATE AEROSOLS : T
03:  => Metal cat. SO2 ox.? : T
04: Online CARBON  AEROSOLS : T
05:  => Use Brown Carbon?   : F
06: Online COMPLEX SOA      : T
07:  => Semivolatile POA?   : F
08: Spatial & seasonal OM/OC: F
09: Online DUST    AEROSOLS : T
10:  => Acidic uptake ?     : F
11: Online SEASALT AEROSOLS : T
12:  => SALA radius bin [um]: 0.01 0.5
13:  => SALC radius bin [um]: 0.5  8.0
14:  => MARINE ORG AEROSOLS : 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
22: Enhance BC Absorption?  : T
23:  => hydrophilic BC      : 1.5
24:  => hydrophobic BC      : 1.0
25: Photolyse nitrate aer.? : F
26:  => NITs Jscale (JHNO3) : 0.0
27:  => NIT  Jscale (JHNO3) : 0.0
28:  => % channel A (HONO)  : 66.667
29:  => % channel B (NO2)   : 33.333
Line What gets defined Description Added/Removed?
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 Input_Opt%LMETALCATSO2 Set this to T to turn on metal-catalyzed oxidation of SO2. This option is turned on by default.
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 the complex SOA chemistry option. (Default is to use the simple SOA option).
7 Input_Opt%LSVPOA Set this to T to use the semivolatile POA option.
8 Input_Opt%LOMOC Set this to T to make the ratios of Organic Matter to Organic Carbon (OM:OC) for SOA species vary by lon/lat location and season. The default is to set these to a single global parameter.
9 Input_Opt%LDUST Set this to T to turn on removal for mineral dust aerosol species (DST1, DST2, DST3, DST4)
10 Input_Opt%LDSTUP Set this to T to turn on acid uptake on dust aerosols.
11 Input_Opt%LSSALT Set this to T to turn on chemistry for sea salt aerosols (SALA, SALC).
12 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.
13 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.
14 Input_Opt%LMPOA Set this to T top turn on marine organic aerosols.
22 Input_Opt%LBCAE Set this to T to enhance black carbon (BC) absorption due to coating. Added in 12.6.0
23 Input_Opt%LBCAE_1 Specify the enhancement for hydrophilic BC. Added in 12.6.0
24 Input_Opt%LBCAE_2 Specify the enhancement for hydrophobic BC. Added in 12.6.0
25 Input_Opt%hvAerNIT Set this to T to turn on photolysis of nitrate aerosol (it is off by default) Added in 12.6.0
26 Input_Opt%hvAerNIT_JNITs Define scale factor for JHNO3 photolyizing NITs aerosol Added in 12.6.0
27 Input_Opt%hvAerNIT_JNIT Define scale factor for JHNO3 photolyizing NIT aerosol Added in 12.6.0
28 Input_Opt%JNITChanA Define fraction for JNITs/NIT channel A (H2O2) for NITs photolysis Added in 12.6.0
29 Input_Opt%JNITChanB Define fraction for JNITs/NIT channel B (NO2) for NITs photolysis Added in 12.6.0
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 (e.g "tropchem", "complexSOA").
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) 20:31, 9 December 2019 (UTC)

Deposition

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
04: Turn on CO2 Effect?     : F
05: CO2 level               : 600.0
06: Reference CO2 level     : 380.0
07: Diag alt above sfc [m]  : 10
Line What gets defined Description Added/Removed?
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.
4 Input_Opt%CO2_EFFECT Set this to T to turn on the simple parameterization for CO2 dependence on stomatal resistance. Added in 12.6.0
5 Input_Opt%CO2_LEVEL Specify the CO2 level (in ppb) for the simple parameterization for CO2 dependence on stomatal resistance Added in 12.6.0
6 Input_Opt%LWETD Specify the reference CO2 level (ppb) for the simple parameterization for CO2 dependence on stomatal resistance Added in 12.6.0
7 Input_Opt%RA_Alt_Above_Sfc Specify the altitude above the surface (in m) for the diagnostic that corrects O3 and HNO3 from the surface to a user-defined altitude (e.g. the ConcAboveSfc collection) Added in 12.6.0

--Bob Yantosca (talk) 20:45, 9 December 2019 (UTC)

Chemistry

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: Overhead O3 for FAST-JX :---
09:  => Online O3 from model: T
10:  => O3 from met fields  : T
11:  => TOMS/SBUV O3        : F
12: Gamma HO2               : 0.2
Line What gets defined Description Added/Removed?
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.
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 nothing Separator line
9 Input_Opt%USE_ONLINE_O3 Set this to T to use online O3 from GEOS-Chem in the extinction calculations for FAST-JX photolysis.
  • NOTE: This is the recommended option.
10 Input_Opt%USE_O3_FROM_MET Set this to T to use ozone columns from the met fields (e.g. TO3).
11 Input_Opt%USE_TOMS_O3 Set this to T to use online O3 from the TOMS/SBUV archive.
  • 'NOTE: We recommend that you set this to F for simulations with GEOS-FP and MERRA-2 meteorology.
12 Input_Opt%GAMMA_HO2 The recommended setting is 0.2.

--Bob Yantosca (talk) 20:47, 9 December 2019 (UTC)

Planeflight diagnostic

The planeflight diagnostic will be preserved for the time being. But in GEOS-Chem 12.7.0 and later versions, you must compile GEOS-Chem with the BPCH_DIAG=y option if you wish to activate this diagnostic.

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 Added/Removed?
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.

--Bob Yantosca (talk) 21:05, 9 December 2019 (UTC)

ObsPack diagnostic

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

01: %%% OBSPACK MENU %%%:
02: Turn on ObsPack diag?   : F
03: Quiet logfile output    : F
04: ObsPack input file      : ./obspack_co2_1_OCO2MIP_2018-11-28.YYYYMMDD.nc
05: ObsPack output file     : GEOSChem.ObsPack.YYYYMMDD_hhmmz.nc4
06: ObsPack output species  : ?ADV?
Line What gets defined Description Added/Removed
1 nothing Header line
2 Input_Opt%Do_ObsPack Set this to T to turn on the ObsPack diagnostic. ObsPack is turned off by default. Added in 12.2.0
3 Input_Opt%ObsPack_Quiet Set this to T if you wish to suppress printing out information about which observations are being sampled on each timestep. This can be useful if you wish to reduce the amount of text that gets written to the log file. Added in 12.2.0
4 Input_Opt%ObsPack_InputFile Specify the input filename template for ObsPack. This file contains the coordinate information (longitude, latitude, altitude, and sampling strategy) that ObsPack will use in order to decide which grid boxes to sample on each timestep.

If the ObsPack diagnostic is turned on, then GEOS-Chem will look for a Added input file at the start of each new day. We recommend that you use date & time tokens YYYY, MM, DD, hh, mm, ss in the filename so that GEOS-Chem will replace these tokens with the appropriate values.

For more information about the input file format, please see our ObsPack diagnostic wiki page.

Added in 12.2.0
5 Input_Opt%ObsPack_OutputFile Specify the output filename template for ObsPack. This file contains data from GEOS-Chem sampled at each ObsPack location for the appropriate time range.

If the ObsPack diagnostic is turned on, then GEOS-Chem will create a new output file at the start of each new day. We recommend that you use date & time tokens YYYY, MM, DD, hh, mm, ss in the filename so that GEOS-Chem will replace these tokens with the appropriate values.

For more information about the input file format, please see our ObsPack diagnostic wiki page.

Added in 12.2.0
6 Input_Opt%ObsPack_SpcName List the names of GEOS-Chem species that you wish to archive using the ObsPack diagnostic. You can list individual species names (e.g NO CO O3, ...) or use the ?ADV? wildcard if you wish to archive all advected species. Added in 12.2.0

--Bob Yantosca (talk) 21:06, 9 December 2019 (UTC)

ND51 and ND51b diagnostics

The ND51 and ND51b satellite timeseries diagnostics will be preserved for the time being. But in GEOS-Chem 12.7.0 and later versions, you must compile GEOS-Chem with the BPCH_DIAG=y option if you wish to activate these diagnostics.

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 Added/Removed?
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) 21:08, 9 December 2019 (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: Passive species #1      : PASV1 1.0 -1 1.0e-7
03: Passive species #2      : PASV2 50.0 3600.0 1.0e-12
Line What gets defined Description Added/Removed?
1 nothing Header line
2-3 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.
  • OPTIONAL: Species long name
 Updated in 12.2.0

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.

NOTE: In GEOS-Chem 12.2.0 the line Number of passive spec. : 2 (stored in Input_Opt%NPASSIVE) was removed. This value is now determined when the input.geos file is read.

--Melissa Sulprizio (talk) 01:30, 26 February 2019 (UTC)
--Bob Yantosca (talk) 21:16, 9 December 2019 (UTC)

CH4 simulation

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 Added/Removed?
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) 21:17, 9 December 2019 (UTC)

CO2 simulation

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 Added/Removed?
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) 21:20, 9 December 2019 (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 Added/Removed?
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) 21:22, 9 December 2019 (UTC)

Hg simulation

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 Added/Removed?
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.
  • NOTE: The Global Terrestrial Mercury Model (GTMM) code has now become incompatible with the latest GEOS-Chem 12 version series. Please contact the Hg and POPs Working Group for assistance if you need to use the GTMM option.
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) 21:24, 9 December 2019 (UTC)

RRTMG

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 [sec]: 10800
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 Added/Removed?
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 seconds. 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 10800 sec = 3 hours (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.
 Removed in 12.2.1
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)
 Removed in 12.2.1

--Bob Yantosca (talk) 21:28, 9 December 2019 (UTC)

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