View source for The input.geos file

__FORCETOC__
'''''[[GEOS-Chem configuration files|Previous]] | [[The HEMCO_Config.rc file|Next]] | [[Getting Started with GEOS-Chem]]'''''
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#*<span style="color:blue">'''Editing <tt>input.geos</tt>'''</span>
#*[[The HEMCO_Config.rc file|Editing <tt>HEMCO_Config.rc</tt>]]
#*[[The HEMCO_Diagn.rc file|Editing <tt>HEMCO_Diagn.rc</tt>]]
#*[[HISTORY.rc and other configuration files|Editing <tt>HISTORY.rc</tt> and other configuration files]]
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#[[GEOS-Chem_overview#Further_reading|Further reading]]


The <tt>input.geos</tt> configuration file contains settings for most GEOS-Chem options (excluding [[The HEMCO User's Guide|emissions]] and [[Guide to GEOS-Chem History diagnostics|History diagnostics]])

== Overview ==

'''NOTE: The <tt>input.geos</tt> file has been migrated to <tt>geoschem_config.yml</tt> in GEOS-Chem 14.0.0 and later versions.'''

An <tt>input.geos</tt> file ships with each GEOS-Chem run directory. We invite you to [[Creating GEOS-Chem run directories|create the run directory]] for the simulation(s) that you are interested in and view the corresponding <tt>input.geos</tt> file.  You will note that the <tt>input.geos</tt> 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 <tt>input.geos</tt> will be stored as fields of the <tt>Input_Opt</tt> derived-type object.

== Currently-used menus in input.geos ==

=== Simulation ===
 
Line numbers are not part of the <tt>input.geos</tt> file, but have been included for reference.

 01: %%% SIMULATION MENU %%% :
 02: Start YYYYMMDD, hhmmss  : 20190701 000000
 03: End   YYYYMMDD, hhmmss  : 20190801 000000
 04: Run directory           : ./
 05: Root data directory     :  <span style="color:red">/path/to/data/</span>
 06: Met field               : MERRA2
 07: Simulation name         : fullchem
 08: Species database file   : ./species_database.yml
 09: Turn on debug printout? : F
 10: Use GC classic timers?  : F

Note: <span style="color:red"><tt>/path/to/data/</tt></span> indicates the path to the root data folder on your system.  If you don't know where this is, ask your IT staff.

{| border=1 cellspacing=0 cellpadding=5 

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|1
|nothing
|Header line 
|

|-valign="top"
|2
|<tt>Input_Opt%NYMDb</tt><br><tt>Input_Opt%NHMSb</tt>
|The starting date and time of the GEOS-Chem simulation. The date must be in <tt>YYYYMMDD</tt> format (4-digit year, month, and day). The time must be in <tt>hhmmss</tt> 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. 
|

|-valign="top"
|3
|<tt>Input_Opt%NYMDe</tt><br><tt>Input_Opt%NHMSe</tt>
|Specify the ending date (<tt>YYYYMMDD</tt> format) and time (<tt>hhmmss</tt> format) of the GEOS-Chem simulation.
|

|-valign="top"
|4
|<tt>Input_Opt%RUN_DIR</tt>
|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. <tt>./</tt>).
|

|-valign="top"
|5
|<tt>Input_Opt%DATA_DIR</tt>
|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 <tt>Input_Opt%DATA_DIR</tt>. The met fields are also stored in subdirectories of <tt>Input_Opt%DATA_DIR</tt>.

For more information, please see [[Downloading GEOS-Chem data directories]].
|

|-valign="top"
|6
|<tt>Input_Opt%MetField</tt>
|Specify the meteorology fields for your simulation. Current options are [[GEOS-FP]] or [[MERRA-2]].
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top"
|7
|<tt>Input_Opt%SimulationName</tt>
|Specify the name of the simulation.  Please see our ''[[Guide to GEOS-Chem simulations]]'' for detailed information about each simulation.  Allowable values (case-insensitive) are:

 Full-chemistry    Specialry
 simulations       simulations
 --------------    ---------------
  fullchem         aerosol
  custom           CH4 (and tagCH4)
                   CO2 
                   Hg (and tagHg)
                   POPs
                   tagCO
                   tagO3
                   TransportTracers 
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top"
|8
|<tt>Input_Opt%SpcDatabaseFile</tt>
|Specify the path to the YAML file containing the GEOS-Chem species database.  The species database file is placed in the GEOS-Chem run directory, so you should not have to modify this line. 
|<span style="color:darkgreen">'''Added in 12.9.0'''</span>

|-valign="top"
|9
|<tt>Input_Opt%LPRT</tt>
|Specify if additional debug information should be printed out to the log file.  This was formerly toggled by the ND70 diagnostic. 
|<span style="color:darkgreen">'''Added in 12.9.0'''</span>

|-valign="top"
|10
|<tt>Input_Opt%UseTimers</tt>
|Specify if GEOS-Chem timing information should be printed out.  Was formerly toggled by the Makefile option <tt>TIMERS=1</tt>. 
|<span style="color:darkgreen">'''Added in 12.9.0'''</span>

|}

=== Grid ===

<span style="color:darkgreen">'''''NOTE: The Grid Menu was introduced in [[GEOS-Chem 12#12.4.0|GEOS-Chem 12.4.0]]. This menu is not read by GCHP or when running GEOS-Chem in an ESM.'''''</span>

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 

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|<tt>State_Grid%GridRes</tt>
|The horizontal grid resolution for your simulation. Current supported options are [[GEOS-Chem_horizontal_grids#GMAO_4_x_5_grid|4.0x5.0]], [[GEOS-Chem_horizontal_grids#GMAO_2_x_2.5_grid|2.0x2.5]], [[GEOS-Chem_horizontal_grids#GMAO_0.5_x_0.625_grid|0.5x0.625]], and [[GEOS-Chem_horizontal_grids#GMAO_0.25_x_0.3125_grid|0.25x0.3215]].

GEOS-Chem will split this string and store values in <tt>State_Grid%DX</tt> and <tt>State_Grid%DY</tt>.
|<span style="color:darkgreen">'''Added in 12.4.0'''</span>

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|3
|<tt>State_Grid%XMin<br>State_Grid%XMax</tt>
|The minimum and maximum longitudes in decimal degrees that define your domain. For global simulations, this should be set to <tt>-180.0 180.0</tt>.

The number of grid boxes in the X dimension are computed from these bounds using:
:<tt>State_Grid%NX = ( State_Grid%XMax - State_Grid%XMin ) / State_Grid%DX )</tt>.
|<span style="color:darkgreen">'''Added in 12.4.0'''</span>

|-valign="top"
|4
|<tt>State_Grid%YMin<br>State_Grid%YMax</tt>
|The minimum and maximum latitude in decimal degrees that define your domain. For global simulations, this should be set to <tt>-90.0 90.0</tt>.

The number of grid boxes in the Y dimension are computed from these bounds using:
:<tt>State_Grid%NY = ( State_Grid%YMax - State_Grid%YMin ) / State_Grid%DY )</tt>.
|<span style="color:darkgreen">'''Added in 12.4.0'''</span>

|-valign="top"
|5
|<tt>State_Grid%HalfPolar</tt>
|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]]).
|<span style="color:darkgreen">'''Added in 12.4.0'''</span>

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|6
|<tt>State_Grid%NZ</tt>
|The number of vertical levels. Current supported options are [[GEOS-Chem_vertical_grids#47-layer_reduced_vertical_grid|47]] and [[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72]].
|<span style="color:darkgreen">'''Added in 12.4.0'''</span>

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|7
|<tt>State_Grid%NestedGrid</tt>
|Set this to T when running a nested grid simulation or to F otherwise.
|<span style="color:darkgreen">'''Added in 12.4.0'''</span>

|-valign="top"
|8
|<tt>State_Grid%NorthBuffer<br>State_Grid%SouthBuffer<br>State_Grid%EastBuffer<br>State_Grid%WestBuffer</tt>
|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 <tt>tpcore_bc_mod.F</tt> for more information. Recommended values are <tt>3 3 3 3</tt>.
|<span style="color:darkgreen">'''Added in 12.4.0'''</span>

|}

=== Timestep ===

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

 01: %%% TIMESTEP MENU %%%   :
 02: Tran/conv timestep [sec]: 600
 03: Chem/emis timestep [sec]: 1200

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|<tt>Input_Opt%TS_DYN</tt><br><tt>Input_Opt%TS_CONV</tt>
|The dynamic (aka "Heartbeat") timestep in seconds.  This is the timestep at which [[Advection scheme TPCORE|transport]], [[Boundary layer mixing|PBL mixing]], [[Cloud convection|cloud convection]], and [[Wet deposition|wet deposition]] occur.

Recommended values:
*300 sec (=5 min) for:
**0.25&deg; x 0.3125&deg; GEOS-FP nested-grid simulations
**0.5&deg; x 0.625&deg; MERRA-2 nested-grid simulations
*600 sec (=10 min) for:
**2&deg; x 2.5&deg; global simulations: 600 sec (=10 min)
**4&deg; x 5&deg; global simulations: 600 sec (=10 min)
|<span style="color:darkgreen">'''Added in 12.0.0'''</span>

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|3
|<tt>Input_Opt%TS_CHEM</tt><br><tt>Input_Opt%TS_EMIS</tt>
|The chemistry timestep in seconds.  This is the timestep at which [[Dry deposition|dry deposition]], emissions, and chemistry occur.

Recommended values:
*600 sec (=10 min) for:
**0.25&deg; x 0.3125&deg; GEOS-FP nested-grid simulations
**0.5&deg; x 0.625&deg; MERRA-2 nested-grid simulations
*1200 sec (=20 min) for:
**2&deg; x 2.5&deg; global simulations: 600 sec (=10 min)
**4&deg; x 5&deg; global simulations: 600 sec (=10 min)
|<span style="color:darkgreen">'''Added in 12.0.0'''</span>

|-valign="top"
|colspan="4"|<span style="color:red">'''''CAVEAT: Running GEOS-Chem with [[Centralized_chemistry_time_step#Optimal_Configuration|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 [[Speeding_up_GEOS-Chem|our ''Speeding up GEOS-Chem'' wiki page]].

|}

=== Advected Species ===

Line numbers are not part of the <tt>input.geos</tt> 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 ...

{| border=1 cellspacing=0 cellpadding=5 
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|<tt>Input_Opt%SIM_TYPE</tt>
|The type of GEOS-Chem simulation that you wish to perform. The choices are:

#[[Rn-Pb-Be simulation]]
#UNUSED
#One of the [[GEOS-Chem_chemistry_mechanisms#NOx-Ox-hydrocarbon-aerosol_chemistry_and_variants|NOx-Ox-Hydrocarbon-aerosol (aka "full chemistry") simulations]]
#UNUSED
#UNUSED
#[[Tagged O3 simulation]]
#[[Tagged CO simulation]]
#C2H6 simulation
#[[CH4 simulation]]
#[[Aerosol-only simulation]]
#[[Mercury|Mercury simulation]]
#[[CO2 simulation]]
#UNUSED
#[[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.
|<span style="color:red">'''Removed in in 12.6.0'''</span>

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|3
|nothing
|Header line
|<span style="color:red">'''Removed in in 12.6.0'''</span>

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|4 -
|<tt>Input_Opt%AdvectSpc_Name</tt>
|A list of the advected species names.  Place only one species name on each line. These entries are used to populate the [[GEOS-Chem_species_database|species database]].
|

|}

=== Transport ===

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
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|<tt>Input_Opt%LTRAN</tt>
|Set this to T to turn on TPCORE transport, or set to F to turn off TPCORE transport.
|

|-valign="top"
|3
|<tt>Input_Opt%LFILL</tt>
|Set this to T to cause TPCORE to fill negative values with zeroes.
|

|-valign="top"
|4
|<tt>Input_Opt%TPCORE_IORD</tt><br><tt>Input_Opt%TPCORE_JORD</tt><br><tt>Input_Opt%TPCORE_KORD</tt>
|These settings determine how TPCORE performs transport in the E/W, N/S, and vertical directions.
*Recommended values are 3, 3, 7. 
|

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:01, 9 December 2019 (UTC)

=== Convection ===

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
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|<tt>Input_Opt%LCONV</tt>
|Set this to T to turn on cloud convection.
|

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|3
|<tt>Input_Opt%LTURB</tt>
|Set this to T to turn on PBL mixing.
|

|-valign="top"
|4
|<tt>Input_Opt%LNLPBL</tt>
|The options are as follows:
*To use the [[Boundary_layer_mixing#VDIFF|non-local PBL mixing scheme (aka VDIFF)]], then set this to T.
*To use the [[Boundary_layer_mixing#TURBDAY|full mixing in the PBL (aka TURBDAY)]], then set this to F.

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

<span style="color:red">'''''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 simulation|CH4]] or [[CO2 simulation|CO2]] specialty simulations, we recommend to use the full TURBDAY mixing by setting this <tt>Input_Opt%LNLPBL</tt> switch to <tt>F</tt>.  For more information please see these wiki posts below.'''''</span>

*[[Boundary_layer_mixing#Mass_is_not_conserved_when_using_non-local_PBL_mixing|Mass is not conserved when using non-local PBL mixing (on our ''Boundary layer mixing'' page)]]
*[[Flexible_precision_in_GEOS-Chem#Mass_conservation|Mass conservation (on our ''Flexible precision in GEOS-Chem'' page]]
|

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:03, 9 December 2019 (UTC)

=== Emissions (12.9.0 and later) ===

 01: %%% EMISSIONS MENU %%%  :
 02: HEMCO Input file        : HEMCO_Config.rc
 03: Switches for UCX        :---
 04:  => Use CH4 emissions?  : F
 05:  => Set init. strat. H2O: T

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
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!bgcolor="#CCCCCC" width="250px"|What gets defined
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|-valign="top"
|1
|nothing
|Header Line
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|-valign="top"
|2
|<tt>Input_Opt%HcoConfigFile</tt>
|The name of the HEMCO configuration file. The emission inventories that your simulation will use are set in this file.
|

|-valign="top"
|3
|nothing
|Header Line
|

|-valign="top"
|4
|<tt>Input_Opt%LCH4EMIS</tt>
|Set this T to use online methane emissions in the full-chemistry mechanism.
|

|-valign="top"
|5
|<tt>Input_Opt%LSETH2O</tt>
|Set this to T to initialize stratospheric H2O mixing ratios based on meteorology data for the first timestep, overriding any restart file values.
|

|}

=== Aerosols ===

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
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!bgcolor="#CCCCCC" width="250px"|What gets defined
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|-valign="top"
|2
|<tt>Input_Opt%LSULF</tt>
|Set this to T to turn on chemistry for sulfate aerosols (DMS, SO2, SO4, MSA, NH3, NH4, NIT).
|

|-valign="top"
|3
|<tt>Input_Opt%LMETALCATSO2</tt>
|Set this to T to turn on metal-catalyzed oxidation of SO2.  This option is turned on by default.
|

|-valign="top"
|4
|<tt>Input_Opt%LCARB</tt>
|Set this to T to turn on chemistry for carbonaceous aerosols (BCPI, BCPO, OCPI, OCPO).
|

|-valign="top"
|5
|<tt>Input_Opt%LBRC</tt>
|Set this to T to turn on brown carbon aerosols.
|

|-valign="top"
|6
|<tt>Input_Opt%LSOA</tt>
|Set this to T to turn on the complex SOA chemistry option.  (Default is to use the simple SOA option).
|

|-valign="top"
|7
|<tt>Input_Opt%LSVPOA</tt>
|Set this to T to use the semivolatile POA option.
|

|-valign="top"
|8
|<tt>Input_Opt%LOMOC</tt>
|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.
|

|-valign="top"
|9
|<tt>Input_Opt%LDUST</tt>
|Set this to T to turn on removal for mineral dust aerosol species (DST1, DST2, DST3, DST4)
|

|-valign="top"
|10
|<tt>Input_Opt%LDSTUP</tt>
|Set this to T to turn on [[Mineral_dust_aerosols#Surface_chemistry_on_dust|acid uptake on dust aerosols]].
|

|-valign="top"
|11
|<tt>Input_Opt%LSSALT</tt>
|Set this to T to turn on chemistry for sea salt aerosols (SALA, SALC).
|

|-valign="top"
|12
|<tt>Input_Opt%SALA_REDGE_um</tt>
|The bin edges (in microns) that denote accumulation mode sea salt species.
*Recommended setting: 0.01 to 0.5 microns.
|

|-valign="top"
|13
|<tt>Input_Opt%SALC_REDGE_um</tt>
|The bin edges (in microns) that denote coarse mode sea salt tracer in microns.
*Recommended setting: 0.5 to 8 microns. 
|

|-valign="top"
|14
|<tt>Input_Opt%LMPOA</tt>
|Set this to T top turn on [[Aerosol_emissions#Online_emission_of_marine_primary_organic_aerosol_.28POA.29|marine organic aerosols]].
|

|-valign="top"
|22
|<tt>Input_Opt%LBCAE</tt>
|Set this to T to enhance black carbon (BC) absorption due to coating.
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top"
|23
|<tt>Input_Opt%BCAE_1</tt>
|Specify the enhancement for hydrophilic BC.
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top"
|24
|<tt>Input_Opt%BCAE_2</tt>
|Specify the enhancement for hydrophobic BC.
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top"
|25
|<tt>Input_Opt%hvAerNIT</tt>
|Set this to T to turn on photolysis of nitrate aerosol (it is off by default)
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top"
|26
|<tt>Input_Opt%hvAerNIT_JNITs</tt>
|Define scale factor for JHNO3 photolyizing NITs aerosol
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top"
|27
|<tt>Input_Opt%hvAerNIT_JNIT</tt>
|Define scale factor for JHNO3 photolyizing NIT aerosol
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top"
|28
|<tt>Input_Opt%JNITChanA</tt>
|Define fraction for JNITs/NIT channel A (H2O2) for NITs photolysis
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top"
|29
|<tt>Input_Opt%JNITChanB</tt>
|Define fraction for JNITs/NIT channel B (NO2) for NITs photolysis
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top
!colspan="4" bgcolor="#CCFFFF"|The following lines contain settings specific to the [[UCX chemistry mechanism]].<br>You can turn all of these options off if your simulation does not use the UCX mechanism (e.g "tropchem", "complexSOA").

|-valign="top"
|15
|<tt>Input_Opt%LGRAVSTRAT</tt>
|Set this to T to apply gravitational settling to stratospheric solid particulate aerosols (SPA, trapezoidal scheme) and stratospheric liquid aerosols (SLA, corrected Stokes' Law).
|

|-valign="top"
|16
|<tt>Input_Opt%LSOLIDPSC</tt>
|Set this to T to use solid polar stratospheric clouds (PSCs).
|

|-valign="top"
|17
|<tt>Input_Opt%LHOMNUCNAT</tt>
|Set this to T to allow NAT to form homogeneously from freezing of HNO3.
|

|-valign="top"
|18
|<tt>Input_Opt%T_NAT_SUPERCOOL</tt>
|The degrees Kelvin of cooling required for homogeneous NAT nucleation.
|

|-valign="top"
|19
|<tt>Input_Opt%P_ICE_SUPERSAT</tt>
|The supersaturation factor required for ice nucleation. 
*Recommended values: 1.2 for coarse grids; 1.5 for fine grids.
|

|-valign="top"
|20
|<tt>Input_Opt%LPSCCHEM</tt>
|Set this to T to allow heterogeneous chemistry on stratospheric aerosols. 
|

|-valign="top"
|21
|<tt>Input_Opt%LSTRATOD</tt>
|Set this to T to include online stratospheric aerosols in extinction calculations for photolysis.
|

|}

=== Deposition ===

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line 
|

|-valign="top"
|2
|<tt>Input_Opt%LDRYD</tt>
|Set this to T to turn on [[Dry deposition|dry deposition]], or F to turn off dry deposition.
|

|-valign="top"
|3
|<tt>Input_Opt%LWETD</tt>
|Set this to T to turn on [[Wet deposition|wet deposition]], or F to turn off wet deposition.
|

|-valign="top"
|4
|<tt>Input_Opt%CO2_EFFECT</tt>
|Set this to T to turn on the [[Dry_deposition#Simple_parameterization_for_CO2_dependence_of_stomatal_resistance|simple parameterization for CO2 dependence on stomatal resistance]].
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top"
|5
|<tt>Input_Opt%CO2_LEVEL</tt>
|Specify the CO2 level (in ppb) for the [[Dry_deposition#Simple_parameterization_for_CO2_dependence_of_stomatal_resistance|simple parameterization for CO2 dependence on stomatal resistance]]
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top"
|6
|<tt>Input_Opt%LWETD</tt>
|Specify the reference CO2 level (ppb) for the [[Dry_deposition#Simple_parameterization_for_CO2_dependence_of_stomatal_resistance|simple parameterization for CO2 dependence on stomatal resistance]]
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|-valign="top"
|7
|<tt>Input_Opt%RA_Alt_Above_Sfc</tt>
|Specify the altitude above the surface (in m) for the [[GEOS-Chem_chemistry_mechanisms#Correcting_ozone_from_the_height_of_the_lowest_model_level_to_10m|diagnostic that corrects O3 and HNO3 from the surface to a user-defined altitude (e.g. the ConcAboveSfc collection)]]
|<span style="color:darkgreen">'''Added in 12.6.0'''</span>

|}

=== Chemistry ===

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|

|-valign="top"
|2
|<tt>Input_Opt%LCHEM</tt>
|Set this to T to turn on chemistry, or F to turn off chemistry.
|
|-valign="top"
|3
|<tt>Input_Opt%LSCHEM</tt>
|Set this to T to turn on linearized stratospheric chemistry, or F to turn off stratospheric chemistry.
*''NOTE: If the [[UCX chemistry mechanism]] is used (see line 5), then linearized chemistry is applied in the mesosphere.''
|

|-valign="top"
|4
|<tt>Input_Opt%LLINOZ</tt>
|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.''
|
|-valign="top"
|5
|<tt>Input_Opt%LUCX</tt>
|Set this to T to use the [[UCX chemistry mechanism]].  Otherwise online chemistry will only be applied in the troposphere. 
|

|-valign="top"
|6
|<tt>Input_Opt%LCH4CHEM</tt>
|Set this to T to use online methane chemistry.
|

|-valign="top"
|7
|<tt>Input_Opt%LACTIVEH2O</tt>
|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).''
|

|-valign="top"
|8
|nothing
|Separator line
|

|-valign="top"
|9
|<tt>Input_Opt%USE_ONLINE_O3</tt>
|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.''
|

|-valign="top"
|10
|<tt>Input_Opt%USE_O3_FROM_MET</tt>
|''Set this to T to use ozone columns from the met fields (e.g. TO3).''
|

|-valign="top"
|11
|<tt>Input_Opt%USE_TOMS_O3</tt>
|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.''
|

|-valign="top"
|12
|<tt>Input_Opt%GAMMA_HO2</tt>
|The recommended setting is 0.2.
|

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:47, 9 December 2019 (UTC)

=== Photolysis ===

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

 01: %%% PHOTOLYSIS MENU %%% :
 02: FAST-JX directory       : /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2020-02/

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|

|-valign="top"
|2
|<tt>Input_Opt%FAST_JX_DIR</tt>
|Specify the directory containing input files (e.g. cross-sections, scattering weights, etc.) for the FAST-JX photolysis mechanism.  We have made this a configurable setting in order to preserve backwards compatibility with older GEOS-Chem versions.
|

|}

=== Planeflight diagnostic ===

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|

|-valign="top"
|2
|<tt>Input_Opt%DO_PF</tt>
|Set this to T to turn on the planeflight diagnostic (aka ND40).
|

|-valign="top"
|3
|<tt>Input_Opt%PF_IFILE</tt>
|Specify the name of the input file (usually called <tt>Planeflight.dat.YYYYMMDD</tt>) for the plane flight diagnostic. This file is [[GEOS-Chem_Input_Files#The_Planeflight.dat_file|described below]]. You may use date & time tokens <tt>YYYY, MM, DD, hh, mm, ss</tt> 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 <tt>Planeflight.dat.YYYYMMDD</tt> file for each YYYYMMDD date. Then it will save out various quantities along the flight track(s) defined within the <tt>Planeflight.dat.YYYYMMDD</tt> file.
|

|-valign="top"
|4
|<tt>Input_Opt%PF_OFILE</tt>
|Specify the name of the output file (usually called <tt>plane.log.YYYYMMDD</tt>) for the plane flight diagnostic. You may use date & time tokens <tt>YYYY, MM, DD, hh, mm, ss</tt> and GEOS-Chem will replace these with the appropriate values.
|

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:05, 9 December 2019 (UTC)

=== ObsPack diagnostic ===

Line numbers are not part of the <tt>input.geos</tt> 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?

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed

|-valign="top"
|1
|nothing
|Header line
|

|-valign="top"
|2
|<tt>Input_Opt%Do_ObsPack</tt>
|Set this to T to turn on the ObsPack diagnostic.  ObsPack is turned off by default.
|Added in [[GEOS-Chem 12#12.2.0|12.2.0]]

|-valign="top"
|3
|<tt>Input_Opt%ObsPack_Quiet</tt>
|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 [[GEOS-Chem 12#12.2.0|12.2.0]]

|-valign="top"
|4
|<tt>Input_Opt%ObsPack_InputFile</tt>
|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 <tt>YYYY, MM, DD, hh, mm, ss</tt> 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 [[ObsPack diagnostic|our ''ObsPack diagnostic'' wiki page]].
|Added in [[GEOS-Chem 12#12.2.0|12.2.0]]

|-valign="top"
|5
|<tt>Input_Opt%ObsPack_OutputFile</tt>
|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 <tt>YYYY, MM, DD, hh, mm, ss</tt> 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 [[ObsPack diagnostic|our ''ObsPack diagnostic'' wiki page]].
|Added in [[GEOS-Chem 12#12.2.0|12.2.0]]

|-valign="top"
|6
|<tt>Input_Opt%ObsPack_SpcName</tt>
|List the names of GEOS-Chem species that you wish to archive using the ObsPack diagnostic.  You can list individual species names (e.g <tt>NO CO O3, ...</tt>) or use the <tt>?ADV?</tt> wildcard if you wish to archive all advected species.
|Added in [[GEOS-Chem 12#12.2.0|12.2.0]];<br>Wildcard in [[GEOS-Chem 13.3.0|13.3.0]]

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:34, 28 September 2021 (UTC)

=== ND51 and ND51b diagnostics ===

<span style="color:red">'''''The ND51 and ND51b satellite timeseries diagnostics will be preserved for the time being.  But in [[GEOS-Chem 12#12.7.0|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.'''''</span>

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|

|-valign="top"
|2
|<tt>Input_Opt%DO_ND51</tt><br><tt>Input_Opt%DO_ND51b</tt>
|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.
|

|-valign="top"
|3
|<tt>Input_Opt%ND51_FILE<br>Input_Opt%ND51b_FILE</tt>
|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.
|

|-valign="top"
|4
|nothing
|OBSOLETE
|

|-valign="top"
|5
|<tt>Input_Opt%ND51_TRACERS</tt><br><tt>Input_Opt%ND51b_TRACERS</tt>
|The [[List_of_diagnostics_for_v11-01#ND51_and_ND51b:_Satellite_timeseries|ND51 and/or ND51b diagnostic quantities]] to save to disk. Separate each number with a space. 
|

|-valign="top"
|6
|<tt>Input_Opt%ND51_HR_WRITE</tt><br><tt>Input_Opt%ND51b_HR_WRITE</tt>
|The time of day (in GMT hours) at which the ND51 timeseries file will be written to disk. Recommended value: 0 GMT each day. 
|

|-valign="top"
|7
|<tt>Input_Opt%ND51_HR_1</tt><br><tt>Input_Opt%ND51_HR2</tt><br><tt>Input_Opt%ND51b_HR_1</tt><br><tt>Input_Opt%ND51b_HR2</tt>
|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.
|

|-valign="top"
|8
|<tt>Input_Opt%ND51_IMIN</tt><br><tt>Input_Opt%ND51_IMAX</tt><br><tt>Input_Opt%ND51b_IMIN</tt><br><tt>Input_Opt%ND51b_IMAX</tt>
|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&deg; x 5&deg; grid: 1 72
*For GMAO 2&deg; x 2.5&deg; grid: 1 144

Also, note you can wrap around the date line.
|

|-valign="top"
|9
|<tt>Input_Opt%ND51_JMIN</tt><br><tt>Input_Opt%ND51_JMAX</tt><br><tt>Input_Opt%ND51b_JMIN</tt><br><tt>Input_Opt%ND51b_JMAX</tt>
|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&deg; x 5&deg; grid: 1 46
*For GMAO 2&deg; x 2.5&deg; grid: 1 91
|

|-valign="top"
|10
|<tt>Input_Opt%ND51_LMIN</tt><br><tt>Input_Opt%ND51_LMAX</tt><br><tt>Input_Opt%ND51b_LMIN</tt><br><tt>Input_Opt%ND51b_LMAX</tt>
|The indices which determine the vertical extent of the 3D region of the globe.
|

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:08, 9 December 2019 (UTC)

=== Passive Species Menu ===

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|

|-valign="top"
|2-3
|<tt>SpcName<br>SpcMW<br>SpcTau<br>SpcInitConc</tt>
|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 [[GEOS-Chem 12#12.2.0|12.2.0]]

|}

There must be a matching entry in the [[#Advected_Species_Menu|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 [[HEMCO_examples#Passive_species|this wiki post on adding passive species]].

'''''NOTE:''''' In [[GEOS-Chem 12#12.2.0|GEOS-Chem 12.2.0]] the line <code>Number of passive spec. : 2</code> (stored in <tt>Input_Opt%NPASSIVE</tt>) was removed. This value is now determined when the input.geos file is read.

--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 01:30, 26 February 2019 (UTC)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>input.geos</tt> if you are not concerned with this simulation.  For more information, please see [[CH4 simulation|our ''CH4 simulation'' wiki page]].

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|

|-valign="top"
|2
|<tt>Input_Opt%LCH4BUD</tt>
|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.''
|

|-valign="top"
|3
|<tt>Input_Opt%LGAO</tt>
|Set this to F to turn off CH4 emissions from gas and oil.
|

|-valign="top"
|4
|<tt>Input_Opt%LCOL</tt>
|Set this to F to turn off CH4 emissions from coal.
|

|-valign="top"
|5
|<tt>Input_Opt%LLIV</tt>
|Set this to F to turn off CH4 emissions from livestock.
|

|-valign="top"
|6
|<tt>Input_Opt%LWAST</tt>
|Set this to F to turn off CH4 emissions from waste.
|

|-valign="top"
|7
|<tt>Input_Opt%LBFCH4</tt>
|Set this to F to turn off CH4 emissions from biofuels.
|

|-valign="top"
|8
|<tt>Input_Opt%LRICE</tt>
|Set this to F to turn off CH4 emissions from rice fields.
|

|-valign="top"
|9
|<tt>Input_Opt%LOTANT</tt>
|Set this to F to turn off other CH4 anthropogenic emissions.
|

|-valign="top"
|10
|<tt>Input_Opt%LBMCH4</tt>
|Set this to F to turn off CH4 emissions from biomass burning.
|

|-valign="top"
|11
|<tt>Input_Opt%LWETL</tt>
|Set this to F to turn off CH4 emissions from wetlands.
|

|-valign="top"
|12
|<tt>Input_Opt%LSOABS</tt>
|Set this to F to turn off CH4 absorption by soils.
|

|-valign="top"
|13
|<tt>Input_Opt%LOTNAT</tt>
|Set this F to turn off other CH4 natural emissions.
|

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>input.geos</tt> if you are not concerned with these simulations. For more information, please see:

* [[CO2 simulation|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'', <u>Geoscientific Model Development</u>, '''3''', 689-716, 2010.

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|

|-valign="top"
|2
|<tt>Input_Opt%LFOSSIL</tt>
|Set this to T to use fossil-fuel emissions of CO2 as computed by [[HEMCO]].
|

|-valign="top"
|3
|<tt>Input_Opt%LOCEAN</tt>
|Set this to T to use ocean exchange of CO2 as as computed by [[HEMCO]].
|

|-valign="top"
|4
|<tt>Input_Opt%LBIODIURNAL</tt>
|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].
|

|-valign="top"
|5
|<tt>Input_Opt%LBIONETCLIM</tt>
|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. 
|

|-valign="top"
|6
|<tt>Input_Opt%LSHIP</tt>
|Set this to T to use on ship emissions of CO2 as computed by [[HEMCO]].
|

|-valign="top"
|7
|<tt>Input_Opt%LPLANE</tt>
|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. 
|

|-valign="top"
|8
|<tt>Input_Opt%LCHEMCO2</tt>
|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. 
|

|-valign="top"
|9
|nothing
|Header line
|

|-valign="top"
|10
|<tt>Input_Opt%LFFBKGRD</tt>
|Set this to T to save CO2 background.
|

|-valign="top"
|11
|<tt>Input_Opt%LBIOSPHTAG</tt> 
|Set this to T to tag biosphere regions (28), ocean regions (11) and the Rest of the World (ROW) as specified in the <tt>Regions_land.dat</tt> and <tt>Regions_ocean.dat</tt> files.

*''NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.''
|

|-valign="top"
|12
|<tt>Input_Opt%LFOSSILTAG</tt>
|Set this to T to tag fossil fuel regions (28) as specified in the <tt>Regions_land.dat</tt> 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.''
|

|-valign="top"
|13
|<tt>Input_Opt%LSHIPTAG</tt>
|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.''
|

|-valign="top"
|14
|<tt>Input_Opt%LPLANETAG</tt>
|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.''
|

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:20, 9 December 2019 (UTC)

=== POPs simulation ===

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

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|

|-valign="top"
|2
|<tt>Input_Opt%POP_TYPE</tt>
|Current options are PHE (phenanthrene), PYR (pyrene), or BAP (benzo[a]pyrene).
|

|-valign="top"
|3
|<tt>Input_Opt%CHEM_PROCESS</tt>
|Set this to T to use POPs chemistry.
|

|-valign="top"
|4
|<tt>Input_Opt%POP_XMW</tt>
|The molecular weight of the POPs species in kg/mol.

*NOTE: This should be superseded by the molecular weight field from the [[GEOS-Chem species database]].
|

|-valign="top"
|5
|<tt>Input_Opt%POP_KOA</tt>
|The POP octanol-water partition coefficient.
|

|-valign="top"
|6
|<tt>Input_Opt%POP_KBC</tt>
|The POP black carbon-air partition coefficient.
|

|-valign="top"
|7
|<tt>Input_Opt%POP_K_POPG_OH</tt>
|The POP reaction rate constant for reaction of gas phase POP with hydroxyl radical in cm3/molec/s.
|

|-valign="top"
|8
|<tt>Input_Opt%POP_K_POPP_O3A</tt>
|The POP reaction rate constant for reaction of particle phase POP with ozone in s-1. 
|

|-valign="top"
|9
|<tt>Input_Opt%POP_K_POPP_O3B</tt>
|The POP reaction rate constant for reaction of particle phase POP with ozone in molec/cm3.
|

|-valign="top"
|10
|<tt>Input_Opt%POP_HSTAR</tt>
|The Henry's Law constant for the POPs species.

*''NOTE: This should be superseded by the Henry's law constant field from the [[GEOS-Chem species database]].''
|

|-valign="top"
|11
|<tt>Input_Opt%POP_DEL_H</tt>
|The enthalpy of air-water exchange in J/mol.
|

|-valign="top"
|12
|<tt>Input_Opt%POP_DEL_Hw</tt>
|The enthalpy of phase transfer from gas phase to particle phase.
|

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <tt>input.geos</tt> if you are not concerned with this simulation.

For more information, please see:

*[[Mercury|Mercury simulation]]
*[[Global Terrestrial Mercury Model]]

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|

|-valign="top"
|2
|<tt>Input_Opt%ANTHRO_Hg_YEAR</tt>
|Baseline year of the anthropogenic mercury emissions that are used in the tagged mercury simulation.  Current options are either 2006 or 2050.
|

|-valign="top"
|3
|<tt>Input_Opt%Hg_SCENARIO</tt>
|Future emissions are based on the four IPCC SRES scenarios. Current options are PRESENT, A1B, A2, B1, or B2.
|

|-valign="top"
|4
|<tt>Input_Opt%USE_CHECKS</tt>
|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.
|

|-valign="top"
|5
|<tt>Input_Opt%LDYNOCEAN.</tt>
|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.
|

|-valign="top"
|6
|<tt>Input_Opt%LPREINDHG</tt>
|Set to T if you want to run a preindustrial simulation (turn off anthropogenic emissions), to F otherwise.
|

|-valign="top"
|8
|<tt>Input_Opt%LGTMM</tt>
|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.''
|

|-valign="top"
|8
|<tt>Input_Opt%GTMM_RST_FILE</tt>
|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.''
|

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:24, 9 December 2019 (UTC)

=== Radiation (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 <tt>input.geos</tt> if you are not concerned with this simulation.  For more information, please see [[Coupling GEOS-Chem with RRTMG|our ''Coupling GEOS-chem with RRTMG'' wiki page]].

Line numbers are not part of the <tt>input.geos</tt> 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]

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|

|-valign="top"
|2
|<tt>WVSELECT</tt>
|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_v7.0_photolysis_mechanism|Fast-JX photolysis mechanism]], regardless of whether the [[Coupling_GEOS-Chem_with_RRTMG|RRTMG radiative transfer model]] is used. 
|

|-valign="top"
|3
|<tt>Input_Opt%LRAD</tt>
|Set this to T to turn on online radiative transfer using RRTMG, or F to turn off RRTMG.
|

|-valign="top"
|4
|<tt>Input_Opt%LLWRAD</tt>
|Set this to T to turn on longwave radiation calculation.
|

|-valign="top"
|5
|<tt>Input_Opt%LSWRAD</tt>
|Set this to T to turn on shortwave radiation calculation.
|

|-valign="top"
|6
|<tt>Input_Opt%LSYKRAD(1)</tt>
|Set this to T to turn turn on calculation for clear-sky fluxes. This option will perform radiative calculations without clouds.
|

|-valign="top"
|7
|<tt>Input_Opt%LSYKRAD(2)</tt>
|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.
|

|-valign="top"
|8
|<tt>Input_Opt%TS_RAD</tt>
|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.).
|

|-valign="top"
|9
|<tt>LSPECRADMENU</tt>
|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 [[GEOS-Chem 12#12.2.1|12.2.1]]

|-valign="top"
|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 [[GEOS-Chem 12#12.2.1|12.2.1]]
|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:28, 9 December 2019 (UTC)

== Deprecated menus in input.geos ==

Recent updates to GEOS-Chem have made several menus of <tt>input.geos</tt> obsolete.  Some of these menus (especially the diagnostic menus below) will only be read if you compile GEOS-Chem with the binary punch diagnostics turned on (i.e. with compile option <tt>BPCH_DIAG=y</tt>). We will list these menus here for further reference.

=== Emissions (prior to 12.9.0) ===

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header Line
|

|-valign="top"
|2
|<tt>Input_Opt%LEMIS</tt>
|Set this to T to turn on emissions or F to turn off emissions.
|<span style="color:red">'''Removed in 12.9.0'''</span>


|-valign="top"
|3
|<tt>Input_Opt%HcoConfigFile</tt>
|The name of the HEMCO configuration file. The emission inventories that your simulation will use are set in this file.
|

|-valign="top"
|4
|<tt>Input_Opt%LFIX_PBL_BrO</tt>
|Set this to T to set Bro concentrations in the PBL equal to 1 ppt during the day.
|<span style="color:red">'''Removed in 12.9.0'''</span>

|-valign="top
!colspan="4" bgcolor="#CCFFFF"|The following lines contain settings specific to the [[UCX chemistry mechanism]].<br>You can turn all of these options off if your simulation does not use the UCX mechanism (e.g "tropchem", "complexSOA").

|-valign="top"
|5
|nothing
|Header line.  
|

|-valign="top"
|6
|<tt>Input_Opt%LCH4EMIS</tt>
|Set this T to use online methane emissions.
|

|-valign="top"
|7
|nothing
|Header line
|<span style="color:red">'''Removed in 12.9.0'''</span>

|-valign="top"
|8
|<tt>Input_Opt%LCH4SBC</tt>
|Set this T to fix surface mixing ratio of methane.
|

|-valign="top"
|9
|<tt>Input_Opt%LOCSEMIS</tt>
|Set this to T to fix surface mixing ratios of OCS.
|<span style="color:red">'''Removed in 12.9.0'''</span>

|-valign="top"
|10
|<tt>Input_Opt%LCFCEMIS</tt>
|Set this to T to fix surface mixing ratios of CFCs, HCFCs, and halons to match WMO projections under the Montreal Protocol.
|<span style="color:red">'''Removed in 12.9.0'''</span>

|-valign="top"
|11
|<tt>Input_Opt%LCLEMIS</tt>
|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.
|<span style="color:red">'''Removed in 12.9.0'''</span>

|-valign="top"
|12
|<tt>Input_Opt%LBREMIS</tt>
|Set this to T to fix surface mixing ratios of bromine species. Not recommended if other bromine emissions are enabled.
|<span style="color:red">'''Removed in 12.9.0'''</span>

|-valign="top"
|13
|<tt>Input_Opt%LN2OEMIS</tt>
|Set this to T to fix surface mixing ratios of N2O.
|<span style="color:red">'''Removed in 12.9.0'''</span>

|-valign="top"
|14
|nothing
|Header line
|<span style="color:red">'''Removed in 12.9.0'''</span>


|-valign="top"
|15
|<tt>Input_Opt%LSETH2O</tt>
|Set this to T to initialize stratospheric H2O mixing ratios based on meteorology data for the first timestep, overriding any restart file values.
|

|-valign="top"
|16
|<tt>Input_Opt%CFCYEAR</tt>
|Specify the starting year for CFC emissions.
|<span style="color:red">'''Removed in 12.9.0'''</span>

|}

=== GAMAP ===

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

 01: %%% GAMAP MENU %%%      :
 02: diaginfo.dat path       : diaginfo.dat
 03: tracerinfo.dat path     : tracerinfo.dat

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Notes

|-valign="top"
|1
|nothing
|Header line
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|2
|<tt>Input_Opt%GAMAP_DIAGINFO</tt>
|Path name of the <tt>diaginfo.dat</tt> file for [http://acmg.seas.harvard.edu/gamap/ 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.
|<span style="color:red">'''Deprecated in 12.7.0'''</span>
|}

=== Output ===

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Status

|-valign="top"
|1
|nothing
|Header line
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|2
|rowspan="12"|<tt>Input_Opt%NJDAY</tt>
|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!
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|3
|Schedule diagnostic output for FEBRUARY
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|4
|Schedule diagnostic output for MARCH
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|5
|Schedule diagnostic output for APRIL
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|6
|Schedule diagnostic output for MAY
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|7
|Schedule diagnostic output for JUNE
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|8
|Schedule diagnostic output for JULY
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|9
|Schedule diagnostic output for AUGUST
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|10
|Schedule diagnostic output for SEPTEMBER
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|11
|Schedule diagnostic output for OCTOBER
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|12
|Schedule diagnostic output for NOVEMBER
|<span style="color:red">'''Deprecated in 12.7.0'''</span>

|-valign="top"
|13
|Schedule diagnostic output for DECEMBER
|<span style="color:red">'''Deprecated in 12.7.0'''</span>
|}

=== Diagnostics (binary punch format) ===

<span style="color:red">'''This menu is now deprecated in 12.7.0 and later versions.'''</span>

This menu lets you specify which GEOS_Chem diagnostic quantities will be archived to disk as binary punch (aka bpch) format.  For a complete list of diagnostic settings, please see [[List of diagnostics archived to bpch format|our ''List of diagnostics archived to bpch format'' wiki page]].

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

 %%% 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

== Menus recently removed from input.geos ==

The following menus were removed from recent GEOS-Chem 12.Y.Z versions:

=== Benchmark ===

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Status

|-valign="top"
|1
|nothing
|Header line
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|2
|<tt>Input_Opt%LSTDRUN</tt>
|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 [http://acmg.seas.harvard.edu/gamap/doc/by_category/Benchmarking.html 1-month benchmark simulation plotting routines].
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|3
|<tt>Input_Opt%STDRUN_INIT_FILE</tt>
|Specify name of file (binary punch format) that will contain initial tracer mass.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|4
|<tt>Input_Opt%STDRUN_FINAL_FILE</tt>
|Specify name of file (binary punch format) that will contain final tracer mass.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|}

=== ND48 diagnostic ===

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

 01: %%% ND48 MENU %%%       :
 02: Turn on ND48 stations   : F
 03: Station Timeseries file : stations.YYYYMMDD
 04: Frequency [sec]         : 3600
 05: Number of stations      : 1
 06: Station #1 (I,J,Lmax,N) : 133 29 15 2

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Status

|-valign="top"
|1
|nothing
|Header line
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|2
|<tt>Input_Opt%DO_ND48</tt>
|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. 
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|3
|<tt>Input_Opt%ND48_FILE</tt>
|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.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|4
|<tt>Input_Opt%ND48_FREQ</tt>
|The frequency in seconds at which data will be archived by the ND48 station timeseries diagnostic. Recommended values: 3600 sec (= 1 hour) or 7200 sec (=2 hours).
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|5
|<tt>Input_Opt%ND48_N_STA</tt>
|The number of ND48 stations at which timeseries data will be saved to disk.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|6
|<tt>Input_Opt%ND48_IARR</tt><br><tt>Input_Opt%ND48_JARR</tt><br><tt>Input_Opt%ND48_LARR</tt><br><tt>Input_Opt%ND48_NARR</tt>
|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)
|<span style="color:red">'''Removed in 12.7.0'''</span>

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:12, 9 December 2019 (UTC)

=== ND49 diagnostic ===

Line numbers are not part of the <tt>input.geos</tt> 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 [sec]         : 7200
 06: IMIN, IMAX of region    :  70  30
 07: JMIN, JMAX of region    :  23  46
 08: LMIN, LMAX of region    :   1   1

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|2
|<tt>Input_Opt%DO_ND49</tt>
|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.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|3
|<tt>Input_Opt%ND49_FILE</tt>
|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.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|4
|<tt>Input_Opt%ND49_TRACERS</tt>
|The [[List_of_diagnostics_for_v11-01#ND49:_instantaneous_timeseries|ND49 diagnostic quantities]] that you wish to save to disk. Separate each number with a space. 
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|5
|<tt>Input_Opt%ND49_FREQ</tt>
|The frequency (in minutes) at which ND49 will save data for a 3D region of the globe data to disk. Recommended value: 7200 min (= 2 hours) or 10800 min (= 3 hours). You may save data at a higher temporal resolution (e.g. every hour) but this will create HUGE data files! 
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|6
|<tt>Input_Opt%ND49_IMIN</tt><br><tt>Input_Opt%ND49_IMAX</tt>
|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&deg; x 5&deg; grid: 1 72 
*For GMAO 2&deg; x 2.5&deg; 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.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|7
|<tt>Input_Opt%ND49_JMIN</tt><br><tt>Input_Opt%ND49_JMAX</tt>
|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&deg; x 5&deg; grid: 1 46
*For GMAO 2&deg; x 2.5&deg; grid: 1 91
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|8
|<tt>Input_Opt%ND51_LMIN</tt><br><tt>Input_Opt%ND51_LMAX</tt>
|The indices which determine the vertical extent of the 3D region of the globe.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:54, 9 December 2019 (UTC)

=== ND50 diagnostic ===

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|2
|<tt>Input_Opt%DO_ND50</tt>
|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.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|3
|<tt>Input_Opt%ND50_FILE</tt>
|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.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|4
|nothing
|OBSOLETE
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|5
|<tt>Input_Opt%ND50_TRACERS</tt>
|The [[List_of_diagnostics_for_v11-01#ND50:_instantaneous_timeseries|ND50 diagnostic quantities]] that you wish to save to disk. Separate each number with a space. 
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|6
|<tt>Input_Opt%ND50_IMIN</tt><br><tt>Input_Opt%ND50_IMAX</tt>
|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&deg; x 5&deg; grid: 1 72 
*For GMAO 2&deg; x 2.5&deg; grid: 1 144 

Also, note you can wrap around the date line.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|7
|<tt>Input_Opt%ND50_JMIN</tt><br><tt>Input_Opt%ND50_JMAX</tt>
|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&deg; x 5&deg; grid: 1 46
*For GMAO 2&deg; x 2.5&deg; grid: 1 91
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|8
|<tt>Input_Opt%ND50_LMIN</tt><br><tt>Input_Opt%ND50_LMAX</tt>
|The indices which determine the vertical extent of the 3D region of the globe.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:50, 20 March 2018 (UTC)

=== ND63 diagnostic ===

 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 [sec]         : 7200
 06: IMIN, IMAX of region    :  70  30
 07: JMIN, JMAX of region    :  23  46

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top
|1
|nothing
|Header line
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|2
|<tt>Input_Opt%DO_ND63</tt>
|Set this to T to turn on the ND63 ship timeseries diagnostic.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|3
|<tt>Input_Opt%ND63_FILE</tt>
|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.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|4
|<tt>Input_Opt%ND63_TRACERS</tt>
|Specify the [[List_of_diagnostics_for_v11-01#ND63:_Ship_emission_diagnostics|ND63 diagnostic quantities]] that you wish to save to disk.  Separate each number with a space.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|5
|<tt>Input_Opt%ND63_FREQ</tt>
|The frequency in seconds at which the ND63 ship diagnostics will be written to disk.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|6
|<tt>Input_Opt%ND63_IMIN<br>Input_Opt%ND63_IMAX</tt>
|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&deg; x 5&deg; grid: 1 72 
*For GMAO 2&deg; x 2.5&deg; grid: 1 144 

Also, note you can wrap around the date line.
|<span style="color:red">'''Removed in 12.7.0'''</span>

|-valign="top"
|7
|<tt>Input_Opt%ND63_JMIN<br>Input_Opt%ND63_JMAX</tt>
|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&deg; x 5&deg; grid: 1 46
*For GMAO 2&deg; x 2.5&deg; grid: 1 91
|<span style="color:red">'''Removed in 12.7.0'''</span>
|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:58, 9 December 2019 (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 <tt>input.geos</tt> if you are not concerned with these simulations.

Line numbers are not part of the <tt>input.geos</tt> 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 [sec]       : 10800
 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

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top"
|1
|nothing
|Header line
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|2
|<tt>Input_Opt%LWINDO</tt>
|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&deg; x 2.5&deg;).
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|3
|<tt>Input_Opt%LWINDO2x25</tt>
|Set this to T if you are using boundary conditions archived from a 2&deg; x 2.5&deg; GEOS-Chem simulation, or F otherwise.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|4
|<tt>Input_Opt%LWINDO_NA</tt>
|Set this to T if you wish to perform a GEOS-Chem nested grid simulation over the North American nested domain.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|5
|<tt>Input_Opt%TPBC_DIR_NA</tt>
|The directory path containing boundary conditions for your North American nested-grid simulation.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|6
|<tt>Input_Opt%LWINDO_EU</tt>
|Set this to T if you wish to perform a GEOS-Chem nested grid simulation over the European nested domain.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|7
|<tt>Input_Opt%TPBC_DIR_EU</tt>
|The directory path containing boundary conditions for your European nested-grid simulation.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|8
|<tt>Input_Opt%LWINDO_CH</tt>
|Set this to T if you wish to perform a GEOS-Chem nested grid simulation over the China/SE Asia nested domain.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|9
|<tt>Input_Opt%TPBC_DIR_CH</tt>
|Which is the directory path containing boundary conditions for your China/SE Asia nested-grid simulation.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|10
|<tt>Input_Opt%LWINDO_AS</tt>
|Set this T if you wish to perform a GEOS-Chem nested grid simulation over the MERRA-2 extended Asia region.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|11
|<tt>Input_Opt%TPBC_DIR_AS</tt>
|The directory path containing boundary conditions for your SE Asia nested-grid simulation.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|12
|<tt>Input_Opt%LWINDO_CU</tt>
|Set this to T if you wish to perform a GEOS-Chem nested grid simulation a domain that you have customized yourself.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|13
|<tt>Input_Opt%TPBC_DIR_CU</tt>
|which is the directory path containing the boundary conditions for your custom-domain nested-grid simulation.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|14
|<tt>Input_Opt%NESTED_TS</tt>
|Specify the frequency in seconds at which the 2&deg; x 2.5&deg; or 4&deg; x 5&deg; boundary conditions will be saved to disk. Recommended value: 10800 sec (= 3 hours).
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|15
|<tt>Input_Opt%NESTED_I1</tt><br><tt>Input_Opt%NESTED_J1</tt>
|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.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|16
|<tt>Input_Opt%NESTED_I2</tt><br><tt>Input_Opt%NESTED_J2</tt>
|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.
|<span style="color:red">'''Removed in 12.4.0'''</span>

|-valign="top"
|17
|<tt>Input_Opt%NESTED_I0W</tt><br><tt>Input_Opt%NESTED_J0W</tt><br><tt>Input_Opt%NESTED_I0E</tt><br><tt>Input_Opt%NESTED_J0E</tt>
|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 <tt>tpcore_bc_mod.F</tt> for more information. 

Recommended values: 
*<tt>Input_Opt%NESTED_I0W=3</tt> and <tt>Input_Opt%NESTED_J0W=3</tt>. 
*<tt>Input_Opt%NESTED_I0E=3</tt> and <tt>Input_Opt%NESTED_J0E=3</tt>.
**But for some grids (e.g. SE Asia) you may want to use <tt>Input_Opt%NESTED_I0E=2</tt> and <tt>Input_Opt%NESTED_J0E=2</tt>.

For more information, please contact the [[Nested Model Working Group]].
|<span style="color:red">'''Removed in 12.4.0'''</span>

|}

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:14, 9 December 2019 (UTC)

=== Prod and Loss diagnostic (binary punch format) ===

Line numbers are not part of the <tt>input.geos</tt> 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

{| border=1 cellspacing=0 cellpadding=5 

|-valign="top"
!bgcolor="#CCCCCC" width="50px"|Line
!bgcolor="#CCCCCC" width="250px"|What gets defined
!bgcolor="#CCCCCC" width="600px"|Description
!bgcolor="#CCCCCC" width="150px"|Added/Removed?

|-valign="top
|1
|nothing
|Header line
|<span style="color:red">'''Removed in in 13.0.0'''</span>

|-valign="top"
|2
|<tt>Input_Opt%DO_SAVE_PL</tt>
|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.
|<span style="color:red">'''Removed in in 13.0.0'''</span>

|-valign="top"
|3
|<tt>Input_Opt%ND65</tt>
|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.
|<span style="color:red">'''Removed in in 13.0.0'''</span>

|-valign="top"
|4
|<tt>Input_Opt%DO_SAVE_O3</tt>
|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). 
|<span style="color:red">'''Removed in in 13.0.0'''</span>

|}


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