Run directory files and folders

Each GEOS-Chem Classic run directory that you create will contain the files and folders listed below. The GEOS-Chem and HEMCO configuration files in the run directory will be appropriate to the type of simulation that you have selected.

This script can be used to create an archive of the run directory. Run this script with:

$ ./ directory-name

Where directory-name is the name of the archive folder. This can be either a relative path or an absolute path.


This is a blank directory where you can direct CMake to configure and build the GEOS-Chem source code.


This folder is created when you compile GEOS-Chem. It contains information about the options that were passed to CMake during the configuration and build process.


$ ./

will remove log files and diagnostic output files left over from a previous GEOS-Chem simulation.


Symbolic link to the top-level source code folder (i.e. the GCClassic superproject folder).


Log file containing environment variable settings used in run directory creation. Running the script on this file will create a duplicate run directory.

Use this Python script to download data from one of the GEOS-Chem data portals to your disk space. See our Download data with a dry-run simulation chapter for more information.


Configuration file for


The main GEOS-Chem configuration file (see Configure your simulation).


This file is now deprecated and will be removed in a future version.


The main HEMCO configuration file (see Configure your simulation).


HEMCO configuration file snippet containing entries for reading the GMAO meteorological fields. This file will only be present if you are using GEOS-FP or MERRA-2 meteorology to drive your GEOS-Chem simulation.


HEMCO configuration file snippet containing entries for reading the GCAP2 meteorological fields. This file will only be present if you are using GCAP2 meteorology to drive your GEOS-Chem simulation.


Configuration file for HEMCO diagnostics (see Configure your simulation).


Configuration file for GEOS-Chem History diagnostics (see Configure your simulation).

This Python script can be used to print the OH metrics for a full-chemistry simulation. Typing:

$ ./

will generate output such as:


Simulation start : 2019-07-01 00:00:00z
Simulation end   : 2019-07-01 01:00:00z

Mass-weighted mean OH concentration    = 10.04682154969 x 10^5 molec cm-3

CH3CCl3 lifetime w/r/t tropospheric OH = 6.3189 years

CH4 lifetime w/r/t tropospheric OH     = 10.6590 years

Blank directory where GEOS-Chem diagnostic output files will be created.

README file (in Markdown format) with containing links to information about GEOS-Chem.


Directory where GEOS-Chem restart files will be created.


Restart file containing initial conditions for the GEOS-Chem simulation.


The restart file that is created when you generate a run directory should not be used to start a production simulation. We recommend that you “spin up” your simulation for at least 6 months to a year in order to remove the signature of the initial conditions.


Symbolic link to the folder in the GEOS-Chem “Science Codebase”” repository that contains sample scripts for running GEOS-Chem.


YAML file containing metadata (e.g. molecular weight, Henry’s law constants, wetdep and drydep parameters, etc.) for each species used in the various GEOS-Chem simulations. You should not have to edit this file unless you are adding new species to your GEOS-Chem simulation. The species_database.yml file will be discussed in more detail in a following section.