Difference between revisions of "The input.geos file"

Revision as of 15:09, 10 December 2019

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.

--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

--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

--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 ...

--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

--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

--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

--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

--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

--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

--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

--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?

--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

--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

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

--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

--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

--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:

• Mercury simulation
• Global Terrestrial Mercury Model

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

--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]

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