You will only need to edit
species_database.yml if you are
adding new species to a GEOS-Chem simulation.
The GEOS-Chem Species Database is a YAML file that contains a listing of metadata for each
species used by GEOS-Chem. The Species Database is included in your
run directory as file
species_database.yml, a snippet of which
is shown below.
# GEOS-Chem Species Database # Core species only (neglecting microphysics) # NOTE: Anchors must be defined before any variables that reference them. A3O2: Formula: CH3CH2CH2OO FullName: Primary peroxy radical from C3H8 Is_Gas: true MW_g: 75.10 ACET: DD_F0: 1.0 DD_Hstar: 1.0e+5 Formula: CH3C(O)CH3 FullName: Acetone Henry_CR: 5500.0 Henry_K0: 2.74e+1 Is_Advected: true Is_DryDep: true Is_Gas: true Is_Photolysis: true MW_g: 58.09 ... etc ... AERI: DD_DvzAerSnow: 0.03 DD_DvzMinVal: [0.01, 0.01] DD_F0: 0.0 DD_Hstar: 0.0 Formula: I FullName: Iodine on aerosol Is_Advected: true Is_Aerosol: true Is_DryDep: true Is_WetDep: true MW_g: 126.90 WD_AerScavEff: 1.0 WD_KcScaleFac: [1.0, 0.5, 1.0] WD_RainoutEff: [1.0, 0.0, 1.0] WD_RainoutEff_Luo: [0.4, 0.0, 1.0] ... etc ...
Species NO (nitrogen oxide) must be listed in
'NO':. This will avoid
YAML readers mis-intepreting this as
Each species name begins in the first column of the file, followed by
the species name follows an indented block of species properties in
Property: Value format.
Some properties listed above are only applicable to gas-phase species, and others to aerosol species. But at the very least, each species should have the following properties defined:
For more information about species properties, please see View GEOS-Chem species properties in the Supplemental Guides section.