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 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 to read data from disk.

config_for_offline_emissions/

Contains sample HEMCO_Config.rc files, organized by horizontal resolution and meteorological input, that enable individual HEMCO extensions (e.g. DustL23M) for the purpose of generating standalone offline emissions output. Copy the sample file that matches your resolution/meteorology combination over HEMCO_Config.rc, or merge the relevant extension settings into your existing HEMCO_Config.rc, to reproduce these emissions.

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, 0.25 x 0.3125, and 0.125 x 0.15625 global grids) are stored in the HEMCO/run/ folder. These 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.