Difference between revisions of "GEOS-Chem configuration files"

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__FORCETOC__
 
__FORCETOC__
 
'''''[[Creating GEOS-Chem run directories|Previous]] | [[The input.geos file|Next]] | [[Getting Started with GEOS-Chem]]'''''
 
'''''[[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]]
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#[[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 source code|Downloading source code]]
 
#[[Downloading GEOS-Chem data directories|Downloading data directories]]
 
#[[Downloading GEOS-Chem data directories|Downloading data directories]]
 
#[[Creating GEOS-Chem run directories|Creating run directories]]
 
#[[Creating GEOS-Chem run directories|Creating run directories]]
 
#<span style="color:blue">'''Configuring runs'''</span>
 
#<span style="color:blue">'''Configuring runs'''</span>
#*<tt>input.geos</tt>
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#*[[The input.geos file|Editing <tt>input.geos</tt>]]
#*<tt>HEMCO_Config.rc</tt>
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#*[[The HEMCO_Config.rc file|Editing <tt>HEMCO_Config.rc</tt>]]
#*<tt>HEMCO_Diagn.rc</tt>
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#*[[The HEMCO_Diagn.rc file|Editing <tt>HEMCO_Diagn.rc</tt>]]
#*<tt>HISTORY.rc</tt> and other configuration files
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#*[[HISTORY.rc and other configuration files|Editing <tt>HISTORY.rc</tt> and other configuration files]]
#*Other configuration files
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#[[Compiling GEOS-Chem|Compiling]]
 
#[[Compiling GEOS-Chem|Compiling]]
 
#[[Running GEOS-Chem|Running]]
 
#[[Running GEOS-Chem|Running]]
 
#[[GEOS-Chem output files|Output files]]
 
#[[GEOS-Chem output files|Output files]]
#[[Guide_to_visualization_and_analysis_tools_for_GEOS-Chem|Visualizing and processing output]]
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#[[Python tools for use with GEOS-Chem]]
 
#[[GEOS-Chem_coding_and_debugging|Coding and debugging]]
 
#[[GEOS-Chem_coding_and_debugging|Coding and debugging]]
 
#[[GEOS-Chem_overview#Further_reading|Further reading]]
 
#[[GEOS-Chem_overview#Further_reading|Further reading]]
  
  
== Overview ==
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== List of GEOS-Chem configuration files ==
  
This page describes the configuration files that are read by GEOS-Chem.  Configuration files are automaticaly added to a GEOS-Chem run directory when it is created. 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.
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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.
  
=== List of GEOS-Chem configuration files ===
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=== User-editable configuration files ===
  
Below is a table listing GEOS-Chem input files that reside in the run directory.
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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.
  
 
{| 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
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*[[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
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|[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.
+
 
+
*<tt>KPP/Standard</tt>
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*<tt>KPP/Tropchem</tt>
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*<tt>KPP/SOA_SVPOA</tt>
+
 
+
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:
+
 
+
*<tt>KPP/Custom</tt>
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+
You can ask the [[GEOS-Chem Support Team]] for assistance with this.
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:52, 21 March 2018 (UTC)
+
 
+
== 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 [[Overview_of_History_diagnostics#Sample_HISTORY.rc_diagnostic_input_file|the ''Sample HISTORY.rc diagnostic input file'' wiki chapter]].
+
 
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:11, 23 July 2019 (UTC)
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+
== The Planeflight.dat file==
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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.
+
 
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== The ObsPack input file ==
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+
Please see our [[ObsPack diagnostic|our ''ObsPack diagnostic'' wiki page]] for more information about the format of ObsPack diagnostic input files.
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+
== Input files for the photolysis mechanism ==
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+
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.
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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)
+
  
== Additional input files for GCHP ==
+
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>].
  
If you are using [[GCHP_Main_Page|GEOS-Chem with the high-performance computing option (aka GCHP)]], you will require a few additional input files beyond those described above.  Please see [[GCHP_Run_Configuration_Files|our ''GCHP Run Configuration Files'' wiki page]] for more information.
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=== GEOS-Chem species database ===
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:19, 11 January 2019 (UTC)
+
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>]
  
  
 
----
 
----
 
'''''[[Creating GEOS-Chem run directories|Previous]] | [[The input.geos file|Next]] | [[Getting Started with GEOS-Chem]]'''''
 
'''''[[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