Difference between revisions of "GEOS-Chem configuration files"

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(The HEMCO_Config.rc file)
(The HEMCO_Diagn.rc file)
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:52, 21 March 2018 (UTC)
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:52, 21 March 2018 (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'']]
 
#''[[Guide to HEMCO emissions diagnostics]]''
 
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:53, 23 July 2019 (UTC)
 
  
 
== The HISTORY.rc file ==
 
== The HISTORY.rc file ==

Revision as of 15:32, 10 December 2019

Previous | Next | Getting Started with GEOS-Chem

  1. Minimum system requirements
  2. Downloading source code
  3. Downloading data directories
  4. Creating run directories
  5. Configuring runs
    • The input.geos configuration file
    • The HEMCO_Config.rc configuration file
    • The HEMCO_Diagn.rc configuration file
    • The HISTORY.rc configuration file
    • Other configuration files
  6. Compiling
  7. Running
  8. Output files
  9. Visualizing and processing output
  10. Coding and debugging
  11. 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

Below is a table listing GEOS-Chem input files that reside in the run directory.

GEOS-Chem user input files
input.geos File containing all GEOS-Chem user options. In this file, you may specify the following options:
  • Start & end time of the simulation
  • Names of the input and output files
  • Which diagnostics to save to disk
  • Which processes (e.g. chemistry, transport, dry deposition, etc.) to turn on, etc.
HEMCO_Config.rc Specifies emission inventories that you want to include in GEOS-Chem via the HEMCO emissions component.
HEMCO_Diagn.rc Specifies diagnostic archival options for emissions and related quantities computed by HEMCO emissions component.
HISTORY.rc Specifies which GEOS-Chem diagnostics will be archived to netCDF output (for both GEOS-Chem "Classic" and GCHP modes)
Planeflight.dat Specifies flight tracks for which you want to save out specific tracers, chemical species, or met field quantities.
GEOS-Chem photolysis mechanism files
These are only found in the run directories for the various full-chemistry and aerosol-only simulations.
FJX_spec.dat Contains cross-section and quantum yields for FAST-JX photolysis species.
FJX_j2j.dat Links "GEOS-Chem species" to "FAST-JX" species. FAST-JX photolysis species are defined in the data file FJX_spec.dat, GEOS-Chem species in globchem.spc. See this post for more information.
jv_spec_mie.dat Contains aerosol optical properties at 5 wavelengths.
dust.dat Contains aerosol optical properties for dust at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
org.dat Contains aerosol optical properties for organic carbon at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
so4.dat Contains aerosol optical properties for sulfate at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
soot.dat Contains aerosol optical properties for black carbon at multiple wavelengths for use in Fast-JX and the RRTMG radiatiaive transfer model (if enabled).
ssa.dat 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).
ssc.dat 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).

--Bob Yantosca (talk) 17:04, 16 November 2016 (UTC)

Chemical mechanism files ship with the GEOS-Chem source code

For your reference, we store the master KPP equation files for GEOS-Chem v11-02 (globchem.def, globchem.eqn, and globchem.spc) in the various subfolders of the GEOS-Chem source code directory, i.e.

  • KPP/Standard
  • KPP/Tropchem
  • KPP/SOA_SVPOA

If you need to add new species or reactions, you can modify these globchem.* 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:

  • KPP/Custom

You can ask the GEOS-Chem Support Team for assistance with this.

--Bob Yantosca (talk) 18:52, 21 March 2018 (UTC)

The HISTORY.rc file

The HISTORY.rc 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 the Sample HISTORY.rc diagnostic input file wiki chapter.

--Bob Yantosca (talk) 16:11, 23 July 2019 (UTC)

The Planeflight.dat file

The Planeflight.dat.YYYYMMDD 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 our Planeflight diagnostic wiki page for more information.

The ObsPack input file

Please see our our ObsPack diagnostic wiki page for more information about the format of ObsPack diagnostic input files.

Input files for the photolysis mechanism

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.

For more information, please see our Input files for FAST-JX v7.0 wiki post.

--Bob Yantosca (talk) 20:26, 17 November 2016 (UTC)

Additional input files for GCHP

If you are using GEOS-Chem with the high-performance computing option (aka GCHP), you will require a few additional input files beyond those described above. Please see our GCHP Run Configuration Files wiki page for more information.

--Bob Yantosca (talk) 17:19, 11 January 2019 (UTC)



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