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]