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.
  Formula: CH3CH2CH2OO
  FullName: Primary peroxy radical from C3H8
  Is_Gas: true
  MW_g: 75.10
  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 ...

  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 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 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:

  • Formula

  • FullName

  • MW_g

  • Either Is_Gas or Is_Aerosol

For more information about species properties, please see View GEOS-Chem species properties in the Supplemental Guides section.