Optional but recommended software packages

GCPy

GCPy is our recommended python companion software to GEOS-Chem.

While GCPy is not a general-purpose plotting package, it does contain many useful functions for creating zonal mean and horizontal plots from GEOS-Chem output. It also contains scripts to generate plots and tables from GEOS-Chem benchmark simulations.

Best way to install: From PyPi (see gcpy.readthedocs.io)

gdb and cgdb

The GNU debugger (gdb) and its graphical interface (cgdb) are very useful tools for tracking down the source of GEOS-Chem errors, such as segmentation faults, out-of-bounds errors, etc.

Best way to install: With Spack.

ncview

The ncview program is a netCDF file viewer. While it does not produce publication-quality output, ncview can let you easily examine the contents of a netCDF data file (such as those which are input and output by GEOS-Chem). Ncview is very useful for debugging and development.

nco

The netCDF operators (nco) are powerful command-line tools for editing and manipulating data in netCDF format.

Best way to install: With Spack.

cdo

The Climate Data Operators (cdo) are powerful command-line utilities for editing and manipulating data in netCDF format.

Best way to install: With Spack.

KPP

The Kinetic PreProcessor (KPP) translates a chemical mechanism specification from user-configurable input files to Fortran-90 source code. You will need to use KPP if you plan on updating any of the chemical mechanisms that ship with GEOS-Chem.

Best way to install: Clone from github.com/KineticPreProcessor/KPP and build the the KPP executable from source.

flex and bison

Flex is the Fast Lexical Analyzer, and bison is a general purpose parser-generator. KPP uses both flex and bison to parse chemical mechanism definition files. Depending on your setup, these packages might have already been installed for you.

Best way to install: With Spack.