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On this page we describe the input files that ship with the various GEOS-Chem run directories. For a list of files created by GEOS-Chem, please see our [[GEOS-Chem Output Files|''GEOS-Chem Output Files'' wiki page]].
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__FORCETOC__
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'''''[[Creating GEOS-Chem run directories|Previous]] | [[The input.geos file|Next]] | [[Getting Started with GEOS-Chem]]'''''
 +
#[[Minimum system requirements for GEOS-Chem|Minimum system requirements (and software installation)]]
 +
#[[Configuring your computational environment]]
 +
#[[Downloading GEOS-Chem source code|Downloading source code]]
 +
#[[Downloading GEOS-Chem data directories|Downloading data directories]]
 +
#[[Creating GEOS-Chem run directories|Creating run directories]]
 +
#<span style="color:blue">'''Configuring runs'''</span>
 +
#*[[The input.geos file|Editing <tt>input.geos</tt>]]
 +
#*[[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]]
 +
#[[Compiling GEOS-Chem|Compiling]]
 +
#[[Running GEOS-Chem|Running]]
 +
#[[GEOS-Chem output files|Output files]]
 +
#[[Python tools for use with GEOS-Chem]]
 +
#[[GEOS-Chem_coding_and_debugging|Coding and debugging]]
 +
#[[GEOS-Chem_overview#Further_reading|Further reading]]
  
''NOTE: This page describes the input files that you need for [[GEOS-Chem v11-02]].  If you are still using [[GEOS-Chem v11-01]], please see our [[GEOS-Chem input files for v11-01]] wiki page.''
 
  
== Overview ==
+
== List of GEOS-Chem configuration files ==
  
This page describes the input files that are read by GEOS-Chem.  These files will reside in the various GEOS-Chem run directories. Each run directory is customized for a unique combination of [[Species in GEOS-Chem|simulation]], [[GEOS-Chem horizontal grids|horizontal resolution]], and [[Overview of GMAO met data products|met field type]], and contains the various input files with which you select options for your GEOS-Chem simulation.  
+
This page describes the configuration files that are read by GEOS-Chem.  Several configuration files are automaticaly added to a GEOS-Chem run directory when it is created. Other configuration files are located in the source code or in the GEOS-Chem data directories. The configuration files contain "out-of-the-box" default settings for each type of GEOS-Chem simulation.  But you can edit these files to customize your GEOS-Chem simulation with different options.
  
You can generate GEOS-Chem run directories from the GEOS-Chem Unit Tester.  Please see our [[Creating GEOS-Chem run directories|our ''Creating GEOS-Chem run directories'' wiki page]] for detailed instructions.  We recommend that you create a different run directory for each of your GEOS-Chem simulations to avoid overwriting output with subsequent model runs.
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=== User-editable configuration files ===
  
Note that run directories compatible with previous versions of GEOS-Chem will not work with [[GEOS-Chem v11-01]|v11-01]].
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These configuration files that specify user inputs are located in each GEOS-Chem run directory.
  
=== List of GEOS-Chem input files ===
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You can edit any of the default settings in these files to change the options that will be used in your GEOS-Chem simulation.
 
+
Below is a table listing GEOS-Chem input files that reside in the run directory.
+
  
 
{| border=1 cellspacing=0 cellpadding=5  
 
{| border=1 cellspacing=0 cellpadding=5  
 
|-valign="top" bgcolor="#CCCCCC"
 
|-valign="top" bgcolor="#CCCCCC"
!colspan="2"|GEOS-Chem user input files
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!width="175px"|File
 +
!width="525px"|Description
 +
!width="275px"|Also see
  
 
|-valign="top"
 
|-valign="top"
|width="200px"|<tt>input.geos</tt>
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|[[The input.geos file|<tt>input.geos</tt>]]
|width="800px"|File containing all GEOS-Chem user options. In this file, you may specify the following options:
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|File containing all GEOS-Chem user options, such as:
 
*Start & end time of the simulation
 
*Start & end time of the simulation
*Names of the input and output files
+
*[[FlexGrid|Grid definitions]]
*Which [[List of diagnostics for v11-01|diagnostics]] to save to disk
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*Which processes (e.g. chemistry, transport, dry deposition, etc.) to turn on,
*Which processes (e.g. chemistry, transport, dry deposition, etc.) to turn on, etc.
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*etc.
 +
|'''NOTE: <tt>input.geos</tt> has been migrated to a YAML format configuration file named [https://geos-chem.readthedocs.io/en/latest/gcc-guide/03-config/geoschem-config.html <tt>geoschem_config.yml</tt>] in GEOS-Chem 14.0.0 and later versions.'''
  
 
|-valign="top"
 
|-valign="top"
|<tt>HEMCO_Config.rc</tt>
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|[https://geos-chem.readthedocs.io/en/latest/gcc-guide/03-config/geoschem-config.html <tt>geoschem_config.yml</tt>]
|Specifies emission inventories that you want to include in GEOS-Chem via the [[HEMCO|HEMCO emissions component]].
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|Main GEOS-Chem configuration file (replacing <tt>input.geos</tt>) in [[GEOS-Chem 14.0.0]] and later versions
 +
|[https://geos-chem.readthedocs.io <tt>geos-chem.readthedocs.io</tt>]
  
 
|-valign="top"
 
|-valign="top"
|<tt>HEMCO_Diagn.rc</tt>
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|[https://geos-chem.readthedocs.io/en/latest/gcc-guide/03-config/hemco-config.html <tt>HEMCO_Config.rc</tt>]
|Specifies diagnostic archival options for emissions and related quantities computed by [[HEMCO|HEMCO emissions component]].
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|Specifies emission inventories (as well as other data sources) that you want to read into in GEOS-Chem via the [https://hemco.readthedocs.io Harmonized Emisions Component (HEMCO)].
*For more information, please see [[The HEMCO User's Guide#Diagnostics|The ''Diagnostics'' section of ''The HEMCO User's Guide'']].
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|[https://hemco.readthedocs.io <tt>hemco.readthedocs.io</tt>]
  
 
|-valign="top"
 
|-valign="top"
|<tt>HISTORY.rc</tt>
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|[https://geos-chem.readthedocs.io/en/latest/gcc-guide/03-config/hemco-diagn.html <tt>HEMCO_Diagn.rc</tt>]
|Specifies which GEOS-Chem diagnostics will be archived to netCDF output (for both GEOS-Chem "Classic" and GCHP modes)
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|Specifies diagnostic archival options for emissions and related quantities computed by the [https://hemco.readthedocs.io Harmonized Emisions Component (HEMCO)].
*For more information, please [[List of diagnostics archived to netCDF format|our ''List of diagnostics archived to netCDF format'' wiki page]].
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|[https://hemco.readthedocs.io <tt>hemco.readthedocs.io</tt>]
  
 
|-valign="top"
 
|-valign="top"
|<tt>Planeflight.dat</tt>
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|[https://geos-chem.readthedocs.io/en/latest/gcc-guide/03-config/history.html <tt>HISTORY.rc</tt>]
|Specifies flight tracks for which you want to save out specific tracers, chemical species, or met field quantities.
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|Specifies which GEOS-Chem diagnostics will be archived to netCDF output (for both GEOS-Chem "Classic" and GCHP modes)
 +
|[[Guide to GEOS-Chem History diagnostics]]
  
|-valign="top" bgcolor="#CCCCCC"
 
!colspan="2"|GEOS-Chem photolysis mechanism files<br>These are only found in the run directories for the various full-chemistry and aerosol-only simulations.
 
 
|-valign="top"
 
|<tt>FJX_spec.dat</tt>
 
|Contains cross-section and quantum yields for [[FAST-JX_v7.0_photolysis_mechanism|FAST-JX photolysis]] species.
 
 
|-valign="top"
 
|<tt>FJX_j2j.dat</tt>
 
|Links "GEOS-Chem species" to "FAST-JX" species. FAST-JX photolysis species are defined in the data file <tt>FJX_spec.dat</tt>, GEOS-Chem species in <tt>globchem.spc</tt>. See [[FAST-JX_v7.0_photolysis_mechanism#FJX_j2j.dat|this post]] for more information.
 
 
|-valign="top"
 
|<tt>jv_spec_mie.dat</tt>
 
|Contains aerosol optical properties at 5 wavelengths.
 
 
|-valign="top"
 
|<tt>dust.dat</tt>
 
|Contains aerosol optical properties for dust at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
 
 
|-valign="top"
 
|<tt>org.dat</tt>
 
|Contains aerosol optical properties for organic carbon at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
 
 
|-valign="top"
 
|<tt>so4.dat</tt>
 
|Contains aerosol optical properties for sulfate at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
 
 
|-valign="top"
 
|<tt>soot.dat</tt>
 
|Contains aerosol optical properties for black carbon at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
 
 
|-valign="top"
 
|<tt>ssa.dat</tt>
 
|Contains aerosol optical properties for accumulation mode sea salt aerosol at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
 
 
|-valign="top"
 
|<tt>ssc.dat</tt>
 
|Contains aerosol optical properties for coarse mode sea salt aerosol at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
 
 
|}
 
|}
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:04, 16 November 2016 (UTC)
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=== Photolysis and chemistry mechanism configuration files ===
 
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=== Chemical mechanism files ship with the GEOS-Chem source code ===
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+
For your reference, we store the master KPP equation files for [[GEOS-Chem v11-02]] (<tt>globchem.def</tt>, <tt>globchem.eqn</tt>, and <tt>globchem.spc</tt>) in the various subfolders of the GEOS-Chem source code directory, i.e.
+
 
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*<tt>KPP/Standard</tt>
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*<tt>KPP/Tropchem</tt>
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*<tt>KPP/SOA_SVPOA</tt>
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If you need to add new species or reactions, you can modify these <tt>globchem.*</tt> files and then rebuild the KPP code.  It is recommended that you place any custom modifications to the GEOS-Chem chemistry mechanisms into this folder:
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*<tt>KPP/Custom</tt>
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+
You can ask the [[GEOS-Chem Support Team]] for assistance with this.
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+
In the very near future, we hope to build KPP fresh each time when GEOS-Chem is compiled.  This will make it much easier to change the existing chemical mechanisms.
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:52, 21 March 2018 (UTC)
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== The input.geos file ==
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GEOS-Chem combines all the input options and switches into a single input file, input.geos. All user-defined input switches and settings which customize GEOS-Chem output options are now defined within this file.
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+
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.
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Most of the information listed in <tt>input.geos</tt> will be stored as fields of the <tt>Input_Opt</tt> derived-type object.
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=== Simulation Menu ===
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+
Line numbers are not part of the <tt>input.geos</tt> file, but have been included for reference.
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+
01: %%% SIMULATION MENU %%% :
+
02: Start YYYYMMDD, hhmmss  : 20130701 000000
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03: End  YYYYMMDD, hhmmss  : 20130801 000000
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04: Run directory          : ./
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05: Input restart file      : GEOSChem_restart.YYYYMMDDhhmm.nc
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06: Root data directory    : <span style="color:red">/path/to/data/</span>
+
07:  => GEOS-FP subdir      : GEOS_FP/YYYY/MM/
+
08:  => MERRA2  subdir      : MERRA2/YYYY/MM/
+
09: Global offsets I0, J0  : 0 0
+
 
+
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
+
 
+
|-valign="top"
+
!bgcolor="#CCCCCC" width="50px"|Line
+
!bgcolor="#CCCCCC" width="250px"|What gets defined
+
!bgcolor="#CCCCCC" width="700px"|Description
+
 
+
|-valign="top"
+
|1
+
|nothing
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|Header line
+
 
+
|-valign="top"
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|2
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|<tt>Input_Opt%NYMDb</tt><br><tt>Input_Opt%NHMSb</tt>
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|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"
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|3
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|<tt>Input_Opt%NYMDe</tt><br><tt>Input_Opt%NHMSe</tt>
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|Specify the ending date (<tt>YYYYMMDD</tt> format) and time (<tt>hhmmss</tt> format) of the GEOS-Chem simulation.
+
 
+
|-valign="top"
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|4
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|<tt>Input_Opt%RUN_DIR</tt>
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|The name of the GEOS-Chem run directory (e.g. where the executable file and input files reside).
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*NOTE: This can usually be set to the current directory (i.e. <tt>./</tt>).
+
 
+
|-valign="top"
+
|5
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|<tt>Input_Opt%IN_RST_FILE</tt>
+
|The name of GEOS-Chem input restart file, which contains the instantaneous concentrations of the advected species specified in the [[#Advected Species Menu|Advected Species Menu]]. This file is used to initialize the species concentrations at the start of your simulation.
+
 
+
You can change the name of the restart file to match the file that you have. If you just specify the file name, GEOS-Chem will look for the restart file in the run directory. You may also specify an entire directory path. Also, you may include the following tokens in the file name:
+
 
+
*<tt>YYYY</tt>: Replaced by 4-digit year (e.g. 2013)
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*<tt>MM</tt>: Replaced by 2-digit month (01-12)
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*<tt>DD</tt>: Replaced by 2-digit day (01-31)
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*<tt>hh</tt>: Replaced by 2-digit hour (0-23)
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*<tt>mm</tt>: Replaced by 2-digit minutes (0-59)
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*<tt>ss</tt>: Replaced by 2-digit seconds (0-59)
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NOTE: Using <tt>YYYYMMDDhhmm</tt> in the restart file names allow for test simulations of less than one hour to be performed.
+
 
+
|-valign="top"
+
|6
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|<tt>Input_Opt%DATA_DIR</tt>
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|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 [[Setting up the ExtData directory|our ''Setting up the ExtData directory'' wiki page]].
+
 
+
|-valign="top"
+
|7
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|<tt>Input_Opt%GEOS_FP_DIR</tt>
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|The directory path where GEOS-FP met fields are stored. You may include the <tt>YYYY</tt> and <tt>MM</tt> tokens as described above.
+
 
+
|-valign="top"
+
|8
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|<tt>Input_Opt%MERRA2_DIR</tt>
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|The directory path where MERRA-2 met fields are stored. You may include the <tt>YYYY</tt> and <tt>MM</tt> tokens as described above.
+
 
+
|-valign="top"
+
|9
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|<tt>Input_Opt%NESTED_I0</tt><br><tt>Input_Opt%NESTED_J0</tt>
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|Nested grid offsets.  For a global run, I0 and J0 must both be set to zero. However, for nested grid runs, we must set I0 and J0 to the appropriate offsets. See [[Setting up GEOS-Chem nested grid simulations|our ''Setting up GEOS-Chem nested grid simulations'' wiki page]] for more information.
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:44, 19 March 2018 (UTC)
+
 
+
=== Timestep menu ===
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+
''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.''
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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
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03: Chem/emis timestep [sec]: 1200
+
 
+
{| border=1 cellspacing=0 cellpadding=5
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|-valign="top"
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!bgcolor="#CCCCCC" width="50px"|Line
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!bgcolor="#CCCCCC" width="250px"|What gets defined
+
!bgcolor="#CCCCCC" width="700px"|Description
+
 
+
|-valign="top"
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|1
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|nothing
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|Header line
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|-valign="top"
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|2
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|<tt>Input_Opt%TS_DYN</tt><br><tt>Input_Opt%TS_CONV</tt>
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|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.
+
 
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Recommended values:
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*300 sec (=5 min) for:
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**0.25&deg; x 0.3125&deg; GEOS-FP nested-grid simulations
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**0.5&deg; x 0.625&deg; MERRA-2 nested-grid simulations
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*600 sec (=10 min) for:
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**2&deg; x 2.5&deg; global simulations: 600 sec (=10 min)
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**4&deg; x 5&deg; global simulations: 600 sec (=10 min)
+
 
+
|-valign="top"
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|3
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|<tt>Input_Opt%TS_CHEM</tt><br><tt>Input_Opt%TS_EMIS</tt>
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|The chemistry timestep in seconds.  This is the timestep at which [[Dry deposition|dry deposition]], emissions, and chemistry occur.
+
 
+
Recommended values:
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*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
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*1200 sec (=20 min) for:
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**2&deg; x 2.5&deg; global simulations: 600 sec (=10 min)
+
**4&deg; x 5&deg; global simulations: 600 sec (=10 min)
+
 
+
|-valign="top"
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|colspan="3"|<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]].
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:20, 20 March 2018 (UTC)
+
 
+
=== Advected Species Menu ===
+
 
+
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
+
|-valign="top"
+
!bgcolor="#CCCCCC" width="50px"|Line
+
!bgcolor="#CCCCCC" width="250px"|What gets defined
+
!bgcolor="#CCCCCC" width="700px"|Description
+
 
+
|-valign="top"
+
|1
+
|nothing
+
|Header line
+
 
+
|-valign="top"
+
|2
+
|<tt>Input_Opt%SIM_TYPE</tt>
+
|The type of GEOS-Chem simulation that you wish to perform. The choices are:
+
 
+
#[[Rn-Pb-Be simulation]]
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#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.
+
 
+
|-valign="top"
+
|3
+
|nothing
+
|Header line
+
 
+
|-valign="top"
+
|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]].
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:51, 19 March 2018 (UTC)
+
 
+
=== Transport Menu ===
+
 
+
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"
+
!bgcolor="#CCCCCC" width="50px"|Line
+
!bgcolor="#CCCCCC" width="250px"|What gets defined
+
!bgcolor="#CCCCCC" width="700px"|Description
+
 
+
|-valign="top"
+
|1
+
|nothing
+
|Header line
+
 
+
|-valign="top"
+
|2
+
|<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]]) 15:54, 30 January 2017 (UTC)
+
 
+
=== Convection Menu ===
+
 
+
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"
+
!bgcolor="#CCCCCC" width="50px"|Line
+
!bgcolor="#CCCCCC" width="250px"|What gets defined
+
!bgcolor="#CCCCCC" width="700px"|Description
+
 
+
|-valign="top"
+
|1
+
|nothing
+
|Header line
+
 
+
|-valign="top"
+
|2
+
|<tt>Input_Opt%LCONV</tt>
+
|Set this to T to turn on cloud convection.
+
 
+
|-valign="top"
+
|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>. '''''</span>
+
 
+
<span style="color:red">'''''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]]) 21:15, 19 March 2018 (UTC)
+
 
+
=== Emissions Menu ===
+
 
+
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="700px"|Description
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-valign="top
+
!colspan="3" 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
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-valign="top"
+
|13
+
|<tt>Input_Opt%LN2OEMIS</tt>
+
|Set this to T to fix surface mixing ratios of N2O.
+
 
+
|-valign="top"
+
|14
+
|nothing
+
|Header line
+
 
+
|-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.
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:18, 19 March 2018 (UTC)
+
 
+
=== Aerosol Menu ===
+
 
+
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
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top"
+
!bgcolor="#CCCCCC" width="50px"|Line
+
!bgcolor="#CCCCCC" width="250px"|What gets defined
+
!bgcolor="#CCCCCC" width="700px"|Description
+
 
+
|-valign="top"
+
|1
+
|nothing
+
|Header line
+
 
+
|-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.
+
 
+
|-valign="top"
+
|23
+
|<tt>Input_Opt%LBCAE_1</tt>
+
|Specify the enhancement for hydrophilic BC.
+
 
+
|-valign="top"
+
|24
+
|<tt>Input_Opt%LBCAE_2</tt>
+
|Specify the enhancement for hydrophobic BC.
+
 
+
|-valign="top
+
!colspan="3" 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.
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:58, 21 March 2018 (UTC)
+
 
+
=== Deposition Menu ===
+
 
+
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
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top"
+
!bgcolor="#CCCCCC" width="50px"|Line
+
!bgcolor="#CCCCCC" width="250px"|What gets defined
+
!bgcolor="#CCCCCC" width="700px"|Description
+
 
+
|-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.
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:35, 19 March 2018 (UTC)
+
 
+
=== Chemistry Menu ===
+
 
+
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="700px"|Description
+
 
+
|-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]]) 16:25, 20 March 2018 (UTC)
+
 
+
=== Output Menu ===
+
 
+
''NOTE: This menu is used by GEOS-Chem in "Classic" mode, but not by [[GCHP]].''
+
 
+
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="700px"|Description
+
 
+
|-valign="top"
+
|1
+
|nothing
+
|Header line
+
 
+
|-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!
+
 
+
|-valign="top"
+
|3
+
|Schedule diagnostic output for FEBRUARY
+
 
+
|-valign="top"
+
|4
+
|Schedule diagnostic output for MARCH
+
 
+
|-valign="top"
+
|5
+
|Schedule diagnostic output for APRIL
+
 
+
|-valign="top"
+
|6
+
|Schedule diagnostic output for MAY
+
 
+
|-valign="top"
+
|7
+
|Schedule diagnostic output for JUNE
+
 
+
|-valign="top"
+
|8
+
|Schedule diagnostic output for JULY
+
 
+
|-valign="top"
+
|9
+
|Schedule diagnostic output for AUGUST
+
 
+
|-valign="top"
+
|10
+
|Schedule diagnostic output for SEPTEMBER
+
 
+
|-valign="top"
+
|11
+
|Schedule diagnostic output for OCTOBER
+
 
+
|-valign="top"
+
|12
+
|Schedule diagnostic output for NOVEMBER
+
 
+
|-valign="top"
+
|13
+
|Schedule diagnostic output for DECEMBER
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:13, 16 November 2016 (UTC)
+
 
+
=== GAMAP Menu ===
+
 
+
''NOTE: This menu is used by GEOS-Chem in "Classic" mode, but not by [[GCHP]].''
+
 
+
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="700px"|Description
+
 
+
|-valign="top"
+
|1
+
|nothing
+
|Header line
+
 
+
|-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.
+
 
+
|-valign="top"
+
|3
+
||<tt>Input_Opt%GAMAP_TRACERINFO</tt>
+
|Path name of the <tt>tracerinfo.dat</tt> file for GAMAP. GEOS-Chem will create this file, which will be customized to the particular simulation that is being done.  This may be either a relative path name or an absolute path name.
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:44, 17 November 2016 (UTC)
+
 
+
=== Diagnostic Menu ===
+
 
+
''NOTE: This menu is used by GEOS-Chem in "Classic" mode, but not by [[GCHP]].''
+
 
+
''ALSO NOTE: In [[GEOS-Chem 12]], you can also [[List of diagnostics archived to netCDF format|save diagnostic output to netCDF format]].''
+
 
+
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]].
+
 
+
%%% 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
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:30, 11 January 2019 (UTC)
+
 
+
=== Planeflight Menu ===
+
 
+
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="700px"|Description
+
 
+
|-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]]) 16:25, 11 January 2019 (UTC)
+
 
+
=== ObsPack Menu ===
+
 
+
''NOTE: The [[ObsPack diagnostic]] may be used in [[GEOS-Chem 12#12.2.0|GEOS-Chem 12.2.0]] and later versions.''
+
 
+
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?  : T
+
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="700px"|Description
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-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 new 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]].
+
 
+
|-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]].
+
 
+
|-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.
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:25, 11 January 2019 (UTC)
+
 
+
=== ND48 Menu ===
+
 
+
''NOTE: The ND48 diagnostic is still available in [[GEOS-Chem 12]].  It will eventually be superseded by the [[ObsPack diagnostic]], which may be used in [[GEOS-Chem 12#12.2.0|GEOS-Chem 12.2.0]] and later versions.''
+
 
+
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="700px"|Description
+
 
+
|-valign="top"
+
|1
+
|nothing
+
|Header line
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-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).
+
 
+
|-valign="top"
+
|5
+
|<tt>Input_Opt%ND48_N_STA</tt>
+
|The number of ND48 stations at which timeseries data will be saved to disk.
+
 
+
|-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)
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:50, 20 March 2018 (UTC)
+
 
+
=== ND49 Menu ===
+
 
+
''NOTE: The ND49 diagnostic is still available in [[GEOS-Chem 12]] for the time being.  Learn how you can [[List_of_diagnostics_archived_to_netCDF_format#ND49_instantaneous_timeseries_diagnostic|generate the same type of instantaneous output as ND49 in netCDF format]].''
+
 
+
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="700px"|Description
+
 
+
|-valign="top"
+
|1
+
|nothing
+
|Header line
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-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!
+
 
+
|-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.
+
 
+
|-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
+
 
+
|-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.
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:48, 20 March 2018 (UTC)
+
 
+
=== ND50 Menu ===
+
 
+
''NOTE: The ND50 diagnostic is still available in [[GEOS-Chem 12]] for the time being.  Learn how you can [[List_of_diagnostics_archived_to_netCDF_format#ND50 24-hr average timeseries diagnostic|generate the same type of instantaneous output as ND50 in netCDF format]].''
+
 
+
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="700px"|Description
+
 
+
 
+
|-valign="top"
+
|1
+
|nothing
+
|Header line
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-valign="top"
+
|4
+
|nothing
+
|OBSOLETE
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-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
+
 
+
|-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.
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:50, 20 March 2018 (UTC)
+
 
+
=== ND51 and ND51b Menus ===
+
 
+
''NOTE: The ND51 and ND51b bpch diagnostics are still available in [[GEOS-Chem 12]].  It will likely be replaced by equivalent netCDF diagnostics in a future version.''
+
 
+
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="700px"|Description
+
 
+
|-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]]) 16:50, 20 March 2018 (UTC)
+
 
+
=== ND63 Menu ===
+
 
+
''NOTE: The ND63 is still available in [[GEOS-Chem 12]].  It will likely be replaced by equivalent netCDF diagnostic output in a future version.''
+
 
+
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="700px"|Description
+
 
+
|-valign="top
+
|1
+
|nothing
+
|Header line
+
 
+
|-valign="top"
+
|2
+
|<tt>Input_Opt%DO_ND63</tt>
+
|Set this to T to turn on the ND63 ship timeseries diagnostic.
+
 
+
|-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.
+
|-valign="top"
+
 
+
|-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.
+
 
+
|-valign="top"
+
|5
+
|<tt>Input_Opt%ND63_FREQ</tt>
+
|The frequency in seconds at which the ND63 ship diagnostics will be written to disk.
+
 
+
|-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.
+
 
+
|-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
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:49, 20 March 2018 (UTC)
+
 
+
=== Prod and Loss Menu ===
+
 
+
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="700px"|Description
+
 
+
|-valign="top
+
|1
+
|nothing
+
|Header line
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-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).
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:51, 20 March 2018 (UTC)
+
 
+
=== Benchmark Menu ===
+
 
+
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="700px"|Description
+
 
+
|-valign="top"
+
|1
+
|nothing
+
|Header line
+
 
+
|-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].
+
 
+
|-valign="top"
+
|3
+
|<tt>Input_Opt%STDRUN_INIT_FILE</tt>
+
|Specify name of file (binary punch format) that will contain initial tracer mass.
+
 
+
|-valign="top"
+
|4
+
|<tt>Input_Opt%STDRUN_FINAL_FILE</tt>
+
|Specify name of file (binary punch format) that will contain final tracer mass.
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:59, 16 November 2016 (UTC)
+
 
+
=== Nested Grid Menu ===
+
 
+
NOTE: This menu controls options for the various GEOS-Chem nested grid simulations. This is an optional menu and may be omitted from <tt>input.geos</tt> if you are not concerned with these simulations.
+
 
+
For more information, please see:
+
 
+
* [[GEOS-Chem_nested_grid_simulations|Nested-grid simulations]]
+
* [[Setting up GEOS-Chem nested grid simulations]]
+
* [[Available met data for nested grid 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="700px"|Description
+
 
+
|-valign="top"
+
|1
+
|nothing
+
|Header line
+
 
+
|-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;).
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-valign="top"
+
|5
+
|<tt>Input_Opt%TPBC_DIR_NA</tt>
+
|The directory path containing boundary conditions for your North American nested-grid simulation.
+
 
+
|-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.
+
 
+
|-valign="top"
+
|7
+
|<tt>Input_Opt%TPBC_DIR_EU</tt>
+
|The directory path containing boundary conditions for your European nested-grid simulation.
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-valign="top"
+
|11
+
|<tt>Input_Opt%TPBC_DIR_AS</tt>
+
|The directory path containing boundary conditions for your SE Asia nested-grid simulation.
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-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).
+
 
+
|-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.
+
 
+
|-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.
+
 
+
|-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]].
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:37, 16 November 2016 (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: Number of passive spec. : 2
+
03: Passive species #1      : PASV1 1.0 -1 1.0e-7
+
04: Passive species #2      : PASV2 50.0 3600.0 1.0e-12
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-valign="top"
+
!bgcolor="#CCCCCC" width="50px"|Line
+
!bgcolor="#CCCCCC" width="250px"|What gets defined
+
!bgcolor="#CCCCCC" width="700px"|Description
+
 
+
|-valign="top"
+
|1
+
|nothing
+
|Header line
+
 
+
|-valign="top"
+
|2
+
|<tt>nPassive</tt>
+
|The number of passive species that you want to include.
+
 
+
|-valign="top"
+
|3-4
+
|<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.
+
 
+
|}
+
 
+
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]].
+
 
+
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 20:58, 21 March 2017 (UTC)
+
 
+
=== CH4 simulation menu ===
+
 
+
This menu controls options for the tagged CH4 simulation only. This is an optional menu and may be omitted from <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="700px"|Description
+
 
+
|-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]]) 15:55, 17 November 2016 (UTC)
+
 
+
=== CO2 Simulation Menu ===
+
 
+
This menu only controls options for the CO2 and tagged CO2 simulations. This is an optional menu and may be omitted from <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="700px"|Description
+
 
+
|-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]]) 22:41, 16 November 2016 (UTC)
+
 
+
=== POPs simulation menu ===
+
 
+
This menu controls options for the persistent organic pollutants (POPs) simulation only. This is an optional menu and may be omitted from <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="700px"|Description
+
 
+
|-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]]) 15:50, 17 November 2016 (UTC)
+
 
+
=== Mercury Simulation Menu ===
+
 
+
<span style="color:darkorange">'''''NOTE: The Global Terrestrial Mercury Model is broken in [[GEOS-Chem v11-01|v11-01]].  We need to convert the GTMM restart file from bpch to netCDF.  The work is ongoing.'''''</span>
+
 
+
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="700px"|Description
+
 
+
|-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.
+
 
+
|-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]]) 15:47, 17 November 2016 (UTC)
+
 
+
=== Radiation Menu ===
+
 
+
This menu controls options for GEOS-Chem simulations coupled to the RRTMG radiative transfer model.  This is an optional menu and may be omitted from <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="700px"|Description
+
 
+
|-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.
+
 
+
|-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)
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:45, 20 March 2018 (UTC)
+
 
+
== The HEMCO_Config.rc file ==
+
 
+
=== Overview ===
+
 
+
In [[GEOS-Chem v10-01]] and later versions, emissions are read, regridded, and calculated by the [[HEMCO|HEMCO emissions component]]. The emission settings are specified in the HEMCO Configuration file (<tt>HEMCO_Config.rc</tt>).
+
 
+
For more information about the <tt>HEMCO_Config.rc</tt> file, please see:
+
 
+
*[[The HEMCO User's Guide]]
+
*[[HEMCO examples]]
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 23:25, 16 November 2016 (UTC)
+
 
+
=== Enabling and disabling emissions ===
+
 
+
The <tt>HEMCO_Config.rc</tt> file for each GEOS-Chem simulation contains a set of switches that allow you to quickly toggle individual emissions inventories on or off. 
+
 
+
Each time you [[Creating GEOS-Chem run directories|create a GEOS-Chem run directory from the Unit Tester]], a new <tt>HEMCO_Config.rc</tt> file with default emissions settings will be created in the run directory.  These default settings are located near the top of the <tt>HEMCO_Config.rc</tt> file.
+
 
+
For example, the default emissions settings for the "Standard" full-chemistry simulation are:
+
 
+
# ExtNr ExtName          on/off  Species
+
0      Base              : on    *
+
    --> HEMCO_RESTART    :      true
+
    --> AEIC              :      true
+
    --> BIOFUEL          :      true
+
    --> BOND              :      true
+
    --> BRAVO            :      true
+
    --> CAC              :      true
+
    --> XIAO              :      true
+
    --> EDGAR            :      true
+
    --> HTAP              :      false
+
    --> EMEP              :      true
+
    --> EMEP_SHIP        :      true
+
    --> GEIA              :      true
+
    --> LIANG_BROMOCARB  :      true
+
    --> NEI2005          :      false
+
    --> NEI2011          :      true
+
    --> RETRO            :      true
+
    --> SHIP              :      true
+
    --> NEI2011_SHIP      :      false
+
    --> MIX              :      true
+
    --> STREETS          :      false
+
    --> VOLCANO          :      true
+
    --> RCP_3PD          :      false
+
    --> RCP_45            :      false
+
    --> RCP_60            :      false
+
    --> RCP_85            :      false
+
    --> QFED2            :      false
+
# -----------------------------------------------------------------------------
+
100    Custom            : off  -
+
101    SeaFlux          : on    DMS/ACET
+
102    ParaNOx          : on    NO/NO2/O3/HNO3
+
    --> LUT data format  :      nc
+
    --> LUT source dir    :      $ROOT/PARANOX/v2015-02
+
103    LightNOx          : on    NO
+
    --> OTD-LIS factors  :      true
+
    --> CDF table        :      $ROOT/LIGHTNOX/v2014-07/light_dist.ott2010.dat
+
104    SoilNOx          : on    NO
+
    --> Use fertilizer NOx:      true
+
105    DustDead          : on    DST1/DST2/DST3/DST4
+
106    DustGinoux        : off  DST1/DST2/DST3/DST4
+
115    DustAlk          : off  DSTAL1/DSTAL2/DSTAL3/DSTAL4
+
107    SeaSalt          : on    SALA/SALC/Br2
+
    --> SALA lower radius :      0.01
+
    --> SALA upper radius :      0.5
+
    --> SALC lower radius :      0.5
+
    --> SALC upper radius :      8.0
+
    --> Emit Br2          :      true 
+
    --> Br2 scaling      :      1.0
+
116    MarinePOA        : off  MOPO/MOPI
+
108    MEGAN            : on    ISOP/ACET/PRPE/C2H4/ALD2
+
    --> Isoprene scaling  :      1.0
+
    --> CO2 inhibition    :      true
+
    --> CO2 conc (ppmv)  :      390.0
+
109    MEGAN_Mono        : on    CO/OCPI/MONX
+
110    MEGAN_SOA        : on    MTPA/MTPO/LIMO/SESQ
+
111    GFED              : on    NO/CO/ALK4/ACET/MEK/ALD2/PRPE/C3H8/CH2O/C2H6/SO2/NH3/BCPO/BCPI/OCPO/OCPI/POG1/POG2/NAP
+
    --> GFED3            :      false
+
    --> GFED4            :      true
+
    --> GFED_daily        :      false
+
    --> GFED_3hourly      :      false
+
    --> Scaling_CO        :      1.05
+
    --> Scaling_POG1      :      1.27
+
    --> Scaling_POG2      :      1.27
+
    --> Scaling_NAP      :      2.75e-4
+
    --> hydrophilic BC    :      0.2
+
    --> hydrophilic OC    :      0.5
+
    --> fraction POG1    :      0.49
+
114    FINN              : off  NO/CO/ALK4/ACET/MEK/ALD2/PRPE/C3H8/CH2O/C2H6/SO2/NH3/BCPI/BCPO/OCPI/OCPO/GLYC/HAC
+
    --> FINN_daily        :      false
+
    --> Scaling_CO        :      1.0
+
    --> hydrophilic BC    :      0.2
+
    --> hydrophilic OC    :      0.5
+
 
+
If you would like to turn off NEI2011, simply change the <span style="color:red">true</span> in this line:
+
 
+
      --> NEI2011          :      <span style="color:red">true</span>
+
 
+
to <span style="color:green">false</span>:
+
 
+
      --> NEI2011          :      <span style="color:green">false</span>
+
 
+
And if you also wanted to turn off the MEGAN biogenic emissions, simply change the <span style="color:red">on</span> in this line:
+
 
+
108    MEGAN            : <span style="color:red">on</span>    ISOP/ACET/PRPE/C2H4/ALD2
+
 
+
to <span style="color:green">off</span>:
+
 
+
108    MEGAN            : <span style="color:green">off</span>    ISOP/ACET/PRPE/C2H4/ALD2
+
 
+
etc.
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 23:08, 16 November 2016 (UTC)
+
 
+
== The HEMCO_Diagn.rc file ==
+
 
+
You can archive any type of emissions (or other quantity) computed by the [[HEMCO|HEMCO emissions component]] to netCDF-format diagnostic output.  The <tt>HEMCO_Diagn.rc</tt> file [[The_HEMCO_User's_Guide#Diagnostics_input_file|controls diagnostic output options]] for HEMCO.
+
 
+
Here is a snapshot of the <tt>HEMCO_Config.rc</tt> from the <tt>geosfp_4x5_benchmark</tt> run directory.
+
 
+
#------------------------------------------------------------------------------
+
#                  GEOS-Chem Global Chemical Transport Model                  !
+
#------------------------------------------------------------------------------
+
#BOP
+
#
+
# !MODULE: HEMCO_Diagn.rc
+
#
+
# !DESCRIPTION: Configuration file for netCDF diagnostic output from HEMCO.
+
#\\
+
#\\
+
# !REMARKS:
+
#  Customized for the benchmark simulation.
+
#  TO DO: Add long names, which are used for netCDF variable attributes.
+
#
+
# !REVISION HISTORY:
+
#  13 Feb 2018 - E. Lundgren - Initial version
+
#EOP
+
#------------------------------------------------------------------------------
+
#BOC
+
# Name            Spec  ExtNr  Cat Hier Dim OutUnit      LongName
+
+
###############################################################################
+
#####  ACET emissions (in bpch ND11, ND28, ND34, ND36, ND46)            #####
+
###############################################################################
+
EmisACET_Total    ACET  -1    -1  -1  3  molec/cm2/s 
+
EmisACET_Anthro    ACET  0      1  -1  3  atomsC/cm2/s
+
EmisACET_BioBurn  ACET  111    -1  -1  2  atomsC/cm2/s
+
EmisACET_Biofuel  ACET  0      2  -1  2  atomsC/cm2/s
+
EmisACET_Biogenic  ACET  108    -1  -1  2  atomsC/cm2/s
+
EmisACET_DirectBio ACET  108    -1  -1  2  atomsC/cm2/s ACET_from_direct_emissions
+
EmisACET_MethylBut ACET  108    -1  -1  2  atomsC/cm2/s ACET_from_methyl_butenol
+
EmisACET_Monoterp  ACET  108    -1  -1  2  atomsC/cm2/s ACET_from_monoterpenes
+
EmisACET_Ocean    ACET  101    -1  -1  2  atomsC/cm2/s ACET_from_ocean_source
+
+
###############################################################################
+
#####  ALD2 emissions (in bpch ND28, ND34, ND36, ND46. ALD2_Ocean        #####
+
#####  and is new)                                                        #####
+
###############################################################################
+
EmisALD2_Total    ALD2  -1    -1  -1  3  molec/cm2/s
+
EmisALD2_Anthro    ALD2  0      1  -1  3  atomsC/cm2/s
+
EmisALD2_BioBurn  ALD2  111    -1  -1  2  atomsC/cm2/s
+
EmisALD2_Biofuel  ALD2  0      2  -1  2  atomsC/cm2/s
+
EmisALD2_Biogenic  ALD2  108    -1  -1  2  atomsC/cm2/s
+
EmisALD2_Ocean    ALD2  101    -1  -1  2  atomsC/cm2/s
+
EmisALD2_Senesc    ALD2  0      4  -1  2  atomsC/cm2/s
+
 
+
As you can see, you can archive not only the total emissions for a given species, but also the individual emission sectors.  This gives you much more flexibility over the GEOS-Chem bpch diagnostic output.
+
 
+
Once you have your <tt>HEMCO_Diagn.rc</tt> file customized for your given simulation, make sure that you have these settings in your <tt>HEMCO_Config.rc</tt> file:
+
 
+
DiagnFile:                  HEMCO_Diagn.rc
+
DiagnPrefix:                HEMCO_diagnostics
+
DiagnFreq:                  End
+
 
+
where:
+
*<tt>DiagnFile</tt> specifies the location of the <tt>HEMCO_Diagn.rc</tt> file.
+
*<tt>DiagnPrefix</tt> specifies the the prefix for all HEMCO-generated diagnostic files.
+
*<tt>DiagnFreq</tt> specifies [[The HEMCO User's Guide#Diagnostics output frequency|the diagnostic archival frequency]].
+
 
+
For more information about how to archive diagnostics from HEMCO, please see [[The HEMCO User's Guide#Diagnostics|The ''Diagnostics'' section of ''The HEMCO User's Guide'']].
+
 
+
== The HISTORY.rc file ==
+
 
+
The <tt>HISTORY.rc</tt> file allows you to specify which diagnostic quantities will be archived to netCDF diagnostics in both GEOS-Chem "Classic" and GEOS-Chem with the High-Performance Option (aka GCHP).
+
 
+
For a detailed description of this file, please see [[List_of_diagnostics_archived_to_netCDF_format#Overview|the '''Overview''' section of our ''List of diagnostics archived to netCDF format'' wiki page]].
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:41, 24 May 2018 (UTC)
+
 
+
== The Planeflight.dat file==
+
  
The <tt>Planeflight.dat.YYYYMMDD</tt> files allow you to specify the diagnostic quantities (species, reaction rates, met fields) that you want to print out for a specific longitude, latitude, altitude, and time. See [[Planeflight diagnostic|our ''Planeflight diagnostic'' wiki page]] for more information.
+
This content has been migrated to the [https://geos-chem.readthedocs.io/en/latest/gcc-guide/03-config/phot-chem.html '''Photolysis and chemistry configuration files''' chapter of <tt>geos-chem.readthedocs.io</tt>].
  
== Input files for the photolysis mechanism ==
+
=== GEOS-Chem species database ===
  
GEOS-Chem v10-01 and later versions use the [[FAST-JX v7.0 photolysis mechanism]]. Several input files for the FAST-JX photolysis mechanism ship with the GEOS-Chem run directories. You should only have to modify these files if you wish to change the chemical mechanism or photolysis mechanism.
+
This content has been moved to the [https://geos-chem.readthedocs.io/en/latest/gcc-guide/03-config/spec-db.html '''species_database.yml''' chapter of <tt>geos-chem.readthedocs.io</tt>]
  
For more information, please see [[FAST-JX_v7.0_photolysis_mechanism#Input_files_for_FAST-JX_v7.0|our ''Input files for FAST-JX v7.0'' wiki post]].
 
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:26, 17 November 2016 (UTC)
+
----
 +
'''''[[Creating GEOS-Chem run directories|Previous]] | [[The input.geos file|Next]] | [[Getting Started with GEOS-Chem]]'''''

Latest revision as of 20:09, 4 August 2022

Previous | Next | Getting Started with GEOS-Chem

  1. Minimum system requirements (and software installation)
  2. Configuring your computational environment
  3. Downloading source code
  4. Downloading data directories
  5. Creating run directories
  6. Configuring runs
  7. Compiling
  8. Running
  9. Output files
  10. Python tools for use with GEOS-Chem
  11. Coding and debugging
  12. Further reading


List of GEOS-Chem configuration files

This page describes the configuration files that are read by GEOS-Chem. Several configuration files are automaticaly added to a GEOS-Chem run directory when it is created. Other configuration files are located in the source code or in the GEOS-Chem data directories. The configuration files contain "out-of-the-box" default settings for each type of GEOS-Chem simulation. But you can edit these files to customize your GEOS-Chem simulation with different options.

User-editable configuration files

These configuration files that specify user inputs are located in each GEOS-Chem run directory.

You can edit any of the default settings in these files to change the options that will be used in your GEOS-Chem simulation.

File Description Also see
input.geos File containing all GEOS-Chem user options, such as:
  • Start & end time of the simulation
  • Grid definitions
  • Which processes (e.g. chemistry, transport, dry deposition, etc.) to turn on,
  • etc.
NOTE: input.geos has been migrated to a YAML format configuration file named geoschem_config.yml in GEOS-Chem 14.0.0 and later versions.
geoschem_config.yml Main GEOS-Chem configuration file (replacing input.geos) in GEOS-Chem 14.0.0 and later versions geos-chem.readthedocs.io
HEMCO_Config.rc Specifies emission inventories (as well as other data sources) that you want to read into in GEOS-Chem via the Harmonized Emisions Component (HEMCO). hemco.readthedocs.io
HEMCO_Diagn.rc Specifies diagnostic archival options for emissions and related quantities computed by the Harmonized Emisions Component (HEMCO). hemco.readthedocs.io
HISTORY.rc Specifies which GEOS-Chem diagnostics will be archived to netCDF output (for both GEOS-Chem "Classic" and GCHP modes) Guide to GEOS-Chem History diagnostics

Photolysis and chemistry mechanism configuration files

This content has been migrated to the Photolysis and chemistry configuration files chapter of geos-chem.readthedocs.io.

GEOS-Chem species database

This content has been moved to the species_database.yml chapter of geos-chem.readthedocs.io



Previous | Next | Getting Started with GEOS-Chem