Each GEOS-Chem Classic run directory that you create will contain the files and folders listed below. The GEOS-Chem and HEMCO
configuration files <cfg>
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 <compile>
the GEOS-Chem source code.
build_info/
This folder is created when you compile GEOS-Chem
<compile>
. 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 dry-run
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 <cfg>
).
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 <cfg>
).
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 <cfg>
).
HISTORY.rc
Configuration file for GEOS-Chem History diagnostics (see Configure your simulation <cfg>
).
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 <restart-files>
will be created.
Restarts/GEOSChem.Restart.YYYYMMDD_hhmmzz.nc4
Restart file <restart-files>
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 cfg-spec-db
file will be discussed in more detail in a following section.