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PlantHydraulics.jl

Plant hydraulics package using numerical methods.

Installation

using Pkg;
Pkg.add("PlantHydraulics");

About

PlantHydraulics.jl provides numerical hydraulic models that can be used to simulate the flow and pressure profiles in plants. In the model, hydraulic system is a combination of hydraulic organs, which are Root, Stem, and Leaf. And as a result, the functions to simulate flow and pressure profiles can be used at organ level and system level. For example, for the simplest case, one can simulate the pressure profile within a xylem segment; and for the most complex case, one can simulate the flow and pressure profiles in a tree with multiple roots, trunk, multiple canopy layers (a stem and a leaf per layer).

Although PlantHydraulics.jl is meant to server as a fundamental dependency package of the CliMA Land, it can also be used as a standalone package and thus to use with other vegetation modeling other than CliMA Land. Below, we will show some examples of how to use PlantHydraulics.jl at organ and plant level.

Organ Level Simulations

Root, Stem, and Leaf organs differ in the following:

  • Root has a rhizosphere component before the xylem
  • Leaf has an extraxylary component after the xylem
  • Stem and Root have a height change to account for gravity
  • Stem and Root capacitance is along the flow path
  • Leaf capacitance is at the end of the flow path (along with extraxylary component)

For example in a Leaf, to simulate the flow and pressure profiles, what you need to do are

using ClimaCache
using PlantHydraulics
FT = Float64;

leaf = ClimaCache.Leaf{FT}();
stem = ClimaCache.Stem{FT}();
root = ClimaCache.Root{FT}();
soil = ClimaCache.SoilLayer{FT}();
PlantHydraulics.xylem_flow_profile!(leaf, FT(1));
PlantHydraulics.xylem_flow_profile!(stem, FT(1));
PlantHydraulics.xylem_flow_profile!(root, FT(1));
PlantHydraulics.xylem_pressure_profile!(leaf);
PlantHydraulics.xylem_pressure_profile!(stem);
PlantHydraulics.xylem_pressure_profile!(root, soil);

Note the second parameter FT(1) is the time step in second to use with non-steady state mode. If the flow mode is steady state, FT(1) will not be used; otherwise, water source/sink term will be applied based on the state of the capacitance tissue. As there is a rhizosphere component in the Root, which uses soil moisture retension curve to compute soil water potential, we need to pass soil information to the xylem_pressure_profile! function when updating soil pressure profile.

Plant Level Simulation

While one can always customize the hydraulic system using functions xylem_flow_profile! and xylem_pressure_profile!, we provide shortcut functions to soil-plant-air continuum where soil layers, plant, and air layers are aligned. For example, a spac of a tree (MonoMLTreeSPAC).

spac = ClimaCache.MonoMLTreeSPAC{FT}();
PlantHydraulics.xylem_flow_profile!(spac, FT(1));
PlantHydraulics.xylem_pressure_profile!(spac);

Similarly, one can use MonoMLGrassSPAC, MonoMLPalmSPAC, and MonoElementSPAC (Mono means mono species spac, ML means multiple root and canopy layers, Grass with no trunk and branch, Palm with no branch, and Element means the spac consists of one soil layer, root, stem, and leaf element each). Currently, the predefined SPAC only supports the four listed above. If you need more customized SPACs, you will need to combine the fundamental functions xylem_flow_profile! and xylem_pressure_profile! appropriately. Be carefuly to not forget to synchronize the flow rates with stomtal conductance (this is done automactically for predefined SPACs).