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.