Configure a simulation

Note

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

Navigate to your new directory, and examine the contents:

$ cd /path/to/hemco/run/dir
$ ls
build/                         download_data.yml               HEMCO_sa_Grid.4x5.rc  Restarts/
cleanRunDir.sh*                HEMCO_Config.rc                 HEMCO_sa_Spec.rc      rundir.version
CodeDir@                       HEMCO_Config.rc.gmao_metfields  HEMCO_sa_Time.rc      runHEMCO.sh*
config_for_offline_emissions/  HEMCO_Diagn.rc                  OutputDir/
download_data.py*              HEMCO_sa_Config.rc              README

Run directory configuration files

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

HEMCO_sa_Config.rc

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.$RES.rc, HEMCO_sa_Time.rc, etc):.

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.

HEMCO_Config.rc

Contains emissions settings. HEMCO_Config.rc can be taken from a another model (such as GEOS-Chem), or can be built from a sample file.

For more information on editing HEMCO_Config.rc, please see the following chapters: The HEMCO configuration file, Basic examples, and More configuration examples.

Important

Make sure that the path to your data directory in the HEMCO_Config.rc file is correct. Otherwise, HEMCO standalone will not be able read data from disk.

HEMCO_Diagn.rc

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_sa_Config.rc.

For more information, please see the chapter entitled Configuration file for the Default collection.

HEMCO_sa_Grid.$RES.rc

Defines the grid specification for resolution $RES. Sample files for several horizontal resolutions (4.0 x 5.0, 2.0 x 2.5, 0.5 x 0.625, and 0.25 x 0.3125 global grids) are stored in the in HEMCO/run/ folder. These are are automatically copied to the run directory based on options chosen when running createRunDir.sh.

If you choose to run with a custom grid or over a regional domain, you will need to modify this file manually.

HEMCO_sa_Spec.rc

Defines the species to include in the HEMCO standalone simulation. By default, the species in a GEOS-Chem full-chemistry “standard” simulation are included.

You may easily generate a HEMCO_sa_Spec.rc corresponding to a different GEOS-Chem simulation with the GCPy example script make_hemco_sa_spec.py. For usage details, see the Generate a HEMCO_sa_Spec.rc for HEMCO Standalone documentation at gcpy.readthedocs.io.

HEMCO_sa_Time.rc

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

runHEMCO.sh

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