Configuring a run directoryΒΆ


Another useful resource for instructions on configuring HEMCO run directories is our YouTube tutorial.

Navigate to your new run directory, and examine the contents:

$ cd /scratch/rundirs/hemco_4x5_merra2
$ ls
build/           HEMCO_Diagn.rc        HEMCO_sa_Spec.rc  README
CodeDir@         HEMCO_sa_Config.rc    HEMCO_sa_Time.rc  rundir.version
HEMCO_Config.rc  HEMCO_sa_Grid.4x5.rc  OutputDir/*

The following files can be modified to set up your HEMCO standalone simulation.


Main configuration file for the HEMCO standalone simulation. This file points to the other configuration files used to set up your simulation (e.g. HEMCO_sa_Grid.4x5, HEMCO_sa_Time.rc). This file typically references a HEMCO_Config.rc file using >>>include HEMCO_Config.rc which contains the emissions settings. Settings in HEMCO_sa_Config.rc will always override any settings in the included HEMCO_Config.rc.


Contains emissions settings. This file is typically obtained from another model (e.g. GEOS-Chem).


Specifies which fields to save out to the HEMCO diagnostics file saved in OutputDir by default. The frequency to save out diagnostics is controlled by the DiagnFreq setting in HEMCO_Config_sa.rc


Defines the grid specification. Sample files are provided for 4.0 x 5.0, 2.0 x 2.5, 0.5 x 0.625, and 0.25 x 0.3125 global grids in HEMCO/run/ and are automatically copied to the run directory based on options chosen when running If you choose to run with a custom grid or over a regional domain, you will need to modify this file manually.


Defines the species to include in the HEMCO standalone simulation. By default, the species in a GEOS-Chem full-chemistry simulation are defined. To include other species, you can modify this file by providing the species name, molecular weight, and other properties.


Defines the start and end times of the HEMCO standalone simulation as well as the emissions timestep (s).

Sample run script for submitting a HEMCO standalone simulation via SLURM.