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.
-
archiveRun.sh
¶
This script can be used to create an archive of the run directory. Run this script with:
$ ./archiveRun.sh directory-name
Where
directory-name
is the name of the archive folder. This can be either a relative path or an absolute path.
-
build/
¶
This is a blank directory where you can direct CMake to configure and build the GEOS-Chem source code.
-
build_info/
¶
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.
-
cleanRunDir.sh
¶
Typing
$ ./cleanRunDir.sh
will remove log files and diagnostic output files left over from a previous GEOS-Chem simulation.
-
CodeDir
¶
Symbolic link to the top-level source code folder (i.e. the
GCClassic
superproject folder).
-
CreateRunDirLogs/rundir_vars.txt
¶
Log file containing environment variable settings used in run directory creation. Running the
init_rd.sh
script on this file will create a duplicate run directory.
-
download_data.py
¶
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.
-
download_data.yml
¶
Configuration file for
download_data.py
.
-
geoschem_config.yml
¶
The main GEOS-Chem configuration file (see Configure your simulation).
-
getRunInfo
¶
This file is now deprecated and will be removed in a future version.
-
HEMCO_Config.rc
¶
The main HEMCO configuration file (see Configure your simulation).
-
HEMCO_Config.rc.gmao_metfields
¶
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_Config.rc.gcap2_metfields
¶
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.
-
HEMCO_Diagn.rc
¶
Configuration file for HEMCO diagnostics (see Configure your simulation).
-
HISTORY.rc
¶
Configuration file for GEOS-Chem History diagnostics (see Configure your simulation).
-
metrics.py
¶
This Python script can be used to print the OH metrics for a full-chemistry simulation. Typing:
$ ./metrics.py
will generate output such as:
============================================================================== GEOS-Chem FULL-CHEMISTRY SIMULATION METRICS 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
-
OutputDir/
¶
Blank directory where GEOS-Chem diagnostic output files will be created.
-
README.md
¶
README file (in Markdown format) with containing links to information about GEOS-Chem.
-
Restarts/
¶
Directory where GEOS-Chem restart files will be created.
-
Restarts/GEOSChem.Restart.YYYYMMDD_hhmmzz.nc4
¶
Restart file containing initial conditions for the GEOS-Chem simulation.
Attention
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.
-
runScriptSamples
¶
Symbolic link to the folder in the GEOS-Chem “Science Codebase”” repository that contains sample scripts for running GEOS-Chem.
-
species_database.yml
¶
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.