View source for Other tools for visualizing and analyzing GEOS-Chem output

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#[[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>


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 ===

<span style="color:red">'''''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.'''''</span>

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:

*[http://acmg.seas.harvard.edu/gamap/ GAMAP web page]
*[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]
*GEOS-Chem wiki: [[GAMAP tips and tricks]]

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:50, 10 January 2019 (UTC)

=== R-language software tools ===

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

<blockquote>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 http://www.cuhk.edu.hk/sci/essc/tgabi/tools.html]</blockquote>

=== 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:

#[http://meteora.ucsd.edu/~pierce/ncview_home_page.html ncview]: A useful tool for quickly examining the contents of a netCDF file.
#[https://www.giss.nasa.gov/tools/panoply/download/ Panoply]: Viewer for netCDF, HDF and, GRIB data
#*[https://www.youtube.com/watch?v=dTvxE5zcY08 Making a lat-lon plot with Panoply]
#[https://www.unidata.ucar.edu/software/netcdf/software.html List of software for displaying netCDF data]

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 ===

[http://wiki.seas.harvard.edu/geos-chem/index.php/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].

=== FlexAOD ===

[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 Â«opticalÂ» 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. [http://www.libradtran.org/ libRadtran])

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