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/           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/        runHEMCO.sh*

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.4x5.rc, 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 file.

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.4x5.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 createRunDir.sh. 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 simulation are defined. To include other species, you can modify this file by providing the species name, molecular weight, and other properties.

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.