Difference between revisions of "Other tools for visualizing and analyzing GEOS-Chem output"

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__FORCETOC__
 
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'''''[[Python tools for use with GEOS-Chem|Previous]] | [[Guide to visualization and analysis tools for GEOS-Chem|Next]] | [[Guide to visualization and analysis tools for GEOS-Chem|Visualization & Analysis Home]] | [[Getting_Started_with_GEOS-Chem|User Manual Home]] | [[Main_Page|GEOS-Chem Main Page]]'''''
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'''''[[Python tools for use with GEOS-Chem|Previous]] | [[Visualization and analysis examples|Next]] | [[Getting Started with GEOS-Chem]]'''''
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#[[Minimum system requirements for GEOS-Chem|Minimum system requirements]]
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#[[Installing required software]]
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#[[Configuring your computational environment]]
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#[[Downloading GEOS-Chem source code|Downloading source code]]
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#[[Downloading GEOS-Chem data directories|Downloading data directories]]
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#[[Creating GEOS-Chem run directories|Creating run directories]]
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#[[GEOS-Chem input files|Configuring runs]]
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#[[Compiling GEOS-Chem|Compiling]]
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#[[Running GEOS-Chem|Running]]
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#[[GEOS-Chem output files|Output files]]
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#[[Guide to visualization and analysis tools for GEOS-Chem|Visualizing and processing output]]
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#*[[Python tools for use with GEOS-Chem|Python tools]]
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#*<span style="color:blue">'''Other tools'''</span>
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#*[[Visualization and analysis examples|Examples]]
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#[[GEOS-Chem_coding_and_debugging|Coding and debugging]]
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#[[GEOS-Chem_overview#Further_reading|Further reading]]
  
#[[Python tools for use with GEOS-Chem|Python tools for visualizing and analyzing GEOS-Chem output]]
 
#<span style="color:blue">'''Other tools for visualizing and analyzing GEOS-Chem output'''</span>
 
  
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== Visualization tools ==
  
 
On this page, we provide information about non-Python-based tools for visualizing and analyzing GEOS-Chem output.
 
On this page, we provide information about non-Python-based tools for visualizing and analyzing GEOS-Chem output.
 
== Visualization tools ==
 
  
 
=== GAMAP and other IDL-based software tools ===
 
=== GAMAP and other IDL-based software tools ===
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*[http://acmg.seas.harvard.edu/gamap/doc/index.html GAMAP online manual]
 
*[http://acmg.seas.harvard.edu/gamap/doc/index.html GAMAP online manual]
 
*[http://acmg.seas.harvard.edu/gamap/doc/Chapter_5.html Documentation for individual GAMAP routines]
 
*[http://acmg.seas.harvard.edu/gamap/doc/Chapter_5.html Documentation for individual GAMAP routines]
*GEOS-Chem wiki: [[GAMAP tips and tricks]]
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*[[GAMAP tips and tricks]]
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If you use the GEOS-Chem planeflight diagnostic, we have a GAMAP-based package for creating input files for GEOS-Chem from aircraft mission "nav" files in NOAA format:
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*[http://acmg.seas.harvard.edu/geos/doc/flight/ Planeflight Diagnostic Setup Code]  
  
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:50, 10 January 2019 (UTC)
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:50, 10 January 2019 (UTC)
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You can use these software packages for offline analysis or post-processing of GEOS-Chem data.
 
You can use these software packages for offline analysis or post-processing of GEOS-Chem data.
  
    DSMACC: The Dynamically Simple Model of Atmospheric Chemical Complexity is designed to be a simple box model which can easily change its chemical scheme and can be used both for free running and constrained simulations. We are using DSMACC to test new GEOS-Chem chemical mechanisms. DSMACC is based out of the Institute for Climate and Atmospheric Science at the School of Earth and Environment of the University of Leeds.
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=== DSMACC ===
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[[DSMACC_chemical_box_model|The Dynamically Simple Model of Atmospheric Chemical Complexity (DSMACC)]] is designed to be a simple box model which can easily change its chemical scheme and can be used both for free running and constrained simulations. We are using DSMACC to test new GEOS-Chem chemical mechanisms. DSMACC is based out of the [http://www.see.leeds.ac.uk/research/icas/index.html Institute for Climate and Atmospheric Science] at the [http://www.see.leeds.ac.uk/research/icas/index.htm School of Earth and Environment] of the [http://www.leeds.ac.uk/ University of Leeds].
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=== FlexAOD ===
  
    FlexAOD: A GEOS-Chem post-processing tool for Aerosol Optical Properties calculations. The standard on-line AOD diagnostic of GEOS-Chem chemistry-transport model may pose limits to full exploitation of the information content of aerosol observations in combination with model simulations. FlexAOD is aimed at filling this gap. The development of the code stems from the on-line AOD diagnostic of GEOS-Chem: aerosol optical properties are calculated for 6 «optical» aerosol species (inorganic ions (sulfate + nitrate + ammonium), organic carbon, blank carbon, sea salts, and soil dust) assumed as externally mixed.
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[http://pumpkin.aquila.infn.it/flexaod/ FlexAOD] is a GEOS-Chem post-processing tool for Aerosol Optical Properties calculations. The standard on-line AOD diagnostic of GEOS-Chem chemistry-transport model may pose limits to full exploitation of the information content of aerosol observations in combination with model simulations. FlexAOD is aimed at filling this gap. The development of the code stems from the on-line AOD diagnostic of GEOS-Chem: aerosol optical properties are calculated for 6 «optical» aerosol species (inorganic ions (sulfate + nitrate + ammonium), organic carbon, blank carbon, sea salts, and soil dust) assumed as externally mixed.
  
    In its present version, FlexAOD allows the user to:
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In its present version, FlexAOD allows the user to:
        Calculate AOD at several wavelngths without repeating the GEOS-Chem simulation
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*Calculate AOD at several wavelngths without repeating the GEOS-Chem simulation
        Calculate additional aerosol optical properties (e.g. single scattering albedo, backscattering coefficient, asymmetry factor, etc.)
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*Calculate additional aerosol optical properties (e.g. single scattering albedo, backscattering coefficient, asymmetry factor, etc.)
        Extract aerosol concentrations and optical profiles at selected locations and times
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*Extract aerosol concentrations and optical profiles at selected locations and times
        Prepare aerosol input to Radiative Transfer Model (e.g. libRadtran)
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*Prepare aerosol input to Radiative Transfer Model (e.g. [http://www.libradtran.org/ libRadtran])
  
  
 
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'''''[[Python tools for visualizing and analyzing GEOS-Chem output|Previous]] | [[Guide to visualization and analysis tools for GEOS-Chem|Next]] | [[Guide to visualization and analysis tools for GEOS-Chem|Visualization & Analysis Home]] | [[Getting_Started_with_GEOS-Chem|User Manual Home]] | [[Main_Page|GEOS-Chem Main Page]]'''''
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'''''[[Python tools for use with GEOS-Chem|Previous]] | [[Visualization and analysis examples|Next]] | [[Getting Started with GEOS-Chem]]'''''

Latest revision as of 21:09, 20 November 2020

Previous | Next | Getting Started with GEOS-Chem

  1. Minimum system requirements
  2. Installing required software
  3. Configuring your computational environment
  4. Downloading source code
  5. Downloading data directories
  6. Creating run directories
  7. Configuring runs
  8. Compiling
  9. Running
  10. Output files
  11. Visualizing and processing output
  12. Coding and debugging
  13. Further reading


Visualization tools

On this page, we provide information about non-Python-based tools for visualizing and analyzing GEOS-Chem output.

GAMAP and other IDL-based software tools

NOTE: IDL, which is proprietary software, can be very expensive. For this reason, the GEOS-Chem Support Team and other GEOS-Chem developers are currently developing several open-source software packages (mostly based on Python) for GEOS-Chem data analysis and visualization. Please see our Python tools for use with GEOS-Chem wiki page.

The traditional GEOS-Chem visualization software is GAMAP. This package was customized to GEOS-Chem and is still heavily used today. GAMAP requires the Interactive Data Language (a proprietary package). For more information about GAMAP, please see:

If you use the GEOS-Chem planeflight diagnostic, we have a GAMAP-based package for creating input files for GEOS-Chem from aircraft mission "nav" files in NOAA format:

--Bob Yantosca (talk) 22:50, 10 January 2019 (UTC)

R-language software tools

Amos Tai <amostai@cuhk.edu.hk> wrote (Dec 2017):

Over the years, I have written many functions in R to analyze/visualize atmospheric and geophysical data including GEOS-Chem inputs/outputs, e.g., regridding, plotting fields/vectors, spatial interpolation, temporal and regressional statistics, etc. I have also developed a tutorial, “R for Atmospheric Scientists”, via which one can easily learn the essence of using R for atmospheric and geophysical analyses. More recently, we have developed a Terrestrial Ecosystem Model in R (TEMIR). All of these materials can be found here: http://www.cuhk.edu.hk/sci/essc/tgabi/tools.html

File viewers

Here is a list of some third-party tools that will let you immediately visualize data in netCDF and other common file formats:

  1. ncview: A useful tool for quickly examining the contents of a netCDF file.
  2. Panoply: Viewer for netCDF, HDF and, GRIB data
  3. List of software for displaying netCDF data

--Bob Yantosca (talk) 16:47, 14 June 2019 (UTC)

Analysis tools

You can use these software packages for offline analysis or post-processing of GEOS-Chem data.

DSMACC

The Dynamically Simple Model of Atmospheric Chemical Complexity (DSMACC) is designed to be a simple box model which can easily change its chemical scheme and can be used both for free running and constrained simulations. We are using DSMACC to test new GEOS-Chem chemical mechanisms. DSMACC is based out of the Institute for Climate and Atmospheric Science at the School of Earth and Environment of the University of Leeds.

FlexAOD

FlexAOD is a GEOS-Chem post-processing tool for Aerosol Optical Properties calculations. The standard on-line AOD diagnostic of GEOS-Chem chemistry-transport model may pose limits to full exploitation of the information content of aerosol observations in combination with model simulations. FlexAOD is aimed at filling this gap. The development of the code stems from the on-line AOD diagnostic of GEOS-Chem: aerosol optical properties are calculated for 6 «optical» aerosol species (inorganic ions (sulfate + nitrate + ammonium), organic carbon, blank carbon, sea salts, and soil dust) assumed as externally mixed.

In its present version, FlexAOD allows the user to:

  • Calculate AOD at several wavelngths without repeating the GEOS-Chem simulation
  • Calculate additional aerosol optical properties (e.g. single scattering albedo, backscattering coefficient, asymmetry factor, etc.)
  • Extract aerosol concentrations and optical profiles at selected locations and times
  • Prepare aerosol input to Radiative Transfer Model (e.g. libRadtran)



Previous | Next | Getting Started with GEOS-Chem