Note
You will only need to edit :file:`species_database.yml` if you are adding new species to a GEOS-Chem simulation.
The :ref:`GEOS-Chem Species Database <spcguide>` 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 :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 ...
Important
Species NO (nitrogen oxide) must be listed in
:file:`species_database.yml` as 'NO':
. This will avoid
YAML readers mis-intepreting this as no
(meaning
false
).
Each species name begins in the first column of the file, followed by
a :
. Underneath
the species name follows an indented block of :ref:`species properties
<spcguide>` 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:
Formula
FullName
MW_g
- Either
Is_Gas
orIs_Aerosol
For more information about species properties, please see :ref:`spcguide` in the Supplemental Guides section.