Biogeochemistry#

To accurately predict watershed ecohydrology, a carbon cycle model is needed to predict transpiration. By simulating a carbon cycle, we are able to predict the rate of photosynthesis as a function of space and time, and photosynthesis governs root water uptake. Currently only one big-leaf model is available, but ongoing work is wrapping a generalized Common/Colorado Land Model based on that developed within the ParFlow team, and another ongoing project is working on wrapping kernels from E3SM’s Land Model.

Biogeochemistry – Monolithic Version#

src/physics/ats/src/pks/biogeochemistry/bgc_simple/bgc_simple.hh

This PK solves for both above and belowground carbon cycle. It is a multi-leaf layer, big-leaf vegetation model coupled to a Century model for belowground carbon decomposition.

It leverages a PFT-based structure which allows multiple height-sorted PFTs to coexist on the same grid cells, with the shorter PFTs getting whatever light is left in the understory. The implementation is based on a standalone code by Chonggang Xu, and adapted for ATS. Outputs of this include transpiration, a critical sink for hydrology, as it solves photosynthesis based on water availability.

Note this is an “explicit PK,” or effectively a forward Euler timestep that is not written in ODE form.

Note this works on both the surface (vegetation) and subsurface (decomposition) meshes. It is required that the subsurface mesh is a “columnar” mesh, and that build_columns in the subsurface Mesh spec has been supplied.

“PK type” = “BGC simple”

pk-bgc-simple-spec

  • “initial timestep” [double] 1.0 Initial timestep size [s]

  • “number of carbon pools” [int] 7 Unclear whether this can actually change?

  • “soil carbon parameters” [soil-carbon-spec-list] List of soil carbon parameters by soil mesh partition region name.

  • “pft parameters” [pft-spec-list] List of PFT parameters by PFT name.

  • “latitude [degrees]” [double] 60 Latitude of the simulation in degrees. Used in radiation balance.

  • “wind speed reference height [m]” [double] 2.0 Reference height of the wind speed dataset.

  • “cryoturbation mixing coefficient [cm^2/yr]” [double] 5.0 Controls diffusion of carbon into the subsurface via cryoturbation.

  • “leaf biomass initial condition” [initial-conditions-spec] Sets the leaf biomass IC.

  • “domain name” [string] domain

  • “surface domain name” [string] surface

  • “transpiration key” [string] DOMAIN-transpiration The distributed transpiration flux [mol s^-1]

  • “shaded shortwave radiation key” [string] SURFACE_DOMAIN-shaded_shortwave_radiation Shortwave radiation that gets past the canopy and teo the bare ground for soil evaporation. [W m^-2]

  • “total leaf area index key” [string] SURFACE_DOMAIN-total_leaf_area_index Total LAI across all PFTs.

EVALUATORS:

  • “temperature” The soil temperature [K]

  • “pressure” soil mafic potential [Pa]

  • “surface-cell_volume” [m^2]

  • “surface-incoming shortwave radiation” [W m^-2]

  • “surface-air_temperature” [K]

  • “surface-vapor_pressure_air” [Pa]

  • “surface-wind_speed” [m s^-1]

  • “surface-co2_concentration” [ppm]