Difference between revisions of "GEOS-Chem configuration files"

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(List 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>
#*[[The input.geos file|<tt>input.geos</tt>]]
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#*[[The input.geos file|Editing <tt>input.geos</tt>]]
#*[[The HEMCO_Config.rc file|<tt>HEMCO_Config.rc</tt>]]
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#*[[The HEMCO_Config.rc file|Editing <tt>HEMCO_Config.rc</tt>]]
#*[[The HEMCO_Diagn.rc file|<tt>HEMCO_Diagn.rc</tt>]]
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#*[[The HEMCO_Diagn.rc file|Editing <tt>HEMCO_Diagn.rc</tt>]]
#*[[HISTORY.rc and other configuration files|<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]]
 
#[[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 ==
 
 
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.
 
  
 
== List of GEOS-Chem configuration files ==
 
== List of GEOS-Chem configuration files ==
  
Below is a table listing GEOS-Chem input files that reside in the run directory.
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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.
  
=== User inputs ===
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=== User-editable configuration files ===
  
Configuration files that specify user inputs are located in each GEOS-Chem 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.
 
You can edit any of the default settings in these files to change the options that will be used in your GEOS-Chem simulation.
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{| border=1 cellspacing=0 cellpadding=5  
 
{| border=1 cellspacing=0 cellpadding=5  
 
|-valign="top" bgcolor="#CCCCCC"
 
|-valign="top" bgcolor="#CCCCCC"
!width="150px"|File
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!width="175px"|File
!width="800px"|Description
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!width="525px"|Description
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!width="275px"|Also see
  
 
|-valign="top"
 
|-valign="top"
 
|[[The input.geos file|<tt>input.geos</tt>]]
 
|[[The input.geos file|<tt>input.geos</tt>]]
|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
 
*[[FlexGrid|Grid definitions]]
 
*[[FlexGrid|Grid definitions]]
*Which processes (e.g. chemistry, transport, dry deposition, etc.) to turn on, etc.
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*Which processes (e.g. chemistry, transport, dry deposition, etc.) to turn on,
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*etc.
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|'''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"
|[[The HEMCO_Config.rc file|<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"
|[[The HEMCO_Diagn.rc file|<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"
|[[HISTORY.rc and other configuration files|<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>]
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|Specifies diagnostic archival options for emissions and related quantities computed by the [https://hemco.readthedocs.io Harmonized Emisions Component (HEMCO)].
 +
|[https://hemco.readthedocs.io <tt>hemco.readthedocs.io</tt>]
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 +
|-valign="top"
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|[https://geos-chem.readthedocs.io/en/latest/gcc-guide/03-config/history.html <tt>HISTORY.rc</tt>]
 
|Specifies which GEOS-Chem diagnostics will be archived to netCDF output (for both GEOS-Chem "Classic" and GCHP modes)
 
|Specifies which GEOS-Chem diagnostics will be archived to netCDF output (for both GEOS-Chem "Classic" and GCHP modes)
*For more information, please see our ''[[Guide to GEOS-Chem History diagnostics]]''.
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|[[Guide to GEOS-Chem History diagnostics]]
  
 
|}
 
|}
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:40, 10 December 2019 (UTC)
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=== Photolysis and chemistry mechanism configuration files ===
 
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=== Photolysis mechanism ===
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These are found in the <tt>ExtData/CHEM_INPUTS/FAST_JX/</tt> directory structure.  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]] for details.
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You do not need to modify any of these files unless you are changing any of the photolysis properties in your chemistry mechanism.
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:54, 10 December 2019 (UTC)
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=== Chemical mechanism ===
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Configuration files for the predefined GEOS-Chem chemical mechanisms are located in the subfolders of the GEOS-Chem source code directory:
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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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You should not need to modify these unless you wish to change any of the default chemical mechanism settings.
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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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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>].
  
You can ask the [[GEOS-Chem Support Team]] for assistance with this.
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=== GEOS-Chem species database ===
  
Please also see [[FlexChem|our ''FlexChem'' wiki page]], which describes how to create and update GEOS-Chem mechanisms.
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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>]
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:19, 10 December 2019 (UTC)
 
  
 
----
 
----
 
'''''[[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