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@Espeer5
Espeer5 committed May 15, 2024
1 parent 1fca4e1 commit a99ae93
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7 changes: 2 additions & 5 deletions docs/tutorials/integrated/soil_canopy_tutorial.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -270,11 +270,8 @@ plant_hydraulics_ps = PlantHydraulics.PlantHydraulicsParameters(;
retention_model = retention_model,
)

plant_hydraulics_args = (
parameters = plant_hydraulics_ps,
h_stem = h_stem,
h_leaf = h_leaf,
);
plant_hydraulics_args =
(parameters = plant_hydraulics_ps, h_stem = h_stem, h_leaf = h_leaf);

# We may now collect all of the canopy component argument tuples into one
# arguments tuple for the canopy component models.
Expand Down
18 changes: 11 additions & 7 deletions src/integrated/soil_canopy_model.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -336,14 +336,16 @@ function make_update_boundary_fluxes(
ClimaCore.Fields.coordinate_field(
land.soil.domain.space.subsurface,
).z
(; h_stem, h_leaf, conductivity_model) = land.canopy.hydraulics.parameters
(label, midpoint) = h_stem > 0 ? (:stem, h_stem / 2) : (:leaf, h_leaf / 2)
(; h_stem, h_leaf, conductivity_model) =
land.canopy.hydraulics.parameters
(label, midpoint) =
h_stem > 0 ? (:stem, h_stem / 2) : (:leaf, h_leaf / 2)

area_index = p.canopy.hydraulics.area_index

above_ground_area_index = getproperty(area_index, label)

@. p.root_extraction =
@. p.root_extraction =
PlantHydraulics.flux(
z,
midpoint,
Expand All @@ -357,14 +359,13 @@ function make_update_boundary_fluxes(
conductivity_model,
p.canopy.hydraulics.ψ.:1,
),
) *
(land.canopy.hydraulics.parameters.root_distribution(z))
) * (land.canopy.hydraulics.parameters.root_distribution(z))
@. p.root_energy_extraction =
p.root_extraction * ClimaLand.Soil.volumetric_internal_energy_liq(
p.soil.T,
land.soil.parameters,
)

# Radiation
lsm_radiant_energy_fluxes!(
p,
Expand Down Expand Up @@ -553,7 +554,10 @@ roots and soil at each soil layer.
function PlantHydraulics.root_water_flux_per_ground_area!(
fa::ClimaCore.Fields.Field,
s::PrognosticSoil,
model::Union{Canopy.PlantHydraulics.PlantHydraulicsModel{FT}, Canopy.PlantHydraulics.BigLeafHydraulicsModel{FT}},
model::Union{
Canopy.PlantHydraulics.PlantHydraulicsModel{FT},
Canopy.PlantHydraulics.BigLeafHydraulicsModel{FT},
},
Y::ClimaCore.Fields.FieldVector,
p::NamedTuple,
t,
Expand Down
154 changes: 66 additions & 88 deletions src/standalone/Vegetation/PlantHydraulics.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -86,44 +86,6 @@ function PrescribedSiteAreaIndex{FT}(
PrescribedSiteAreaIndex{FT, typeof(LAIfunction)}(LAIfunction, SAI, RAI)
end

"""
lai_consistency_check(
model::PlantHydraulicsModel{FT},
) where {FT}
Carries out consistency checks using the area indices supplied and the number of
stem elements being modeled.
Note that it is possible to have a plant with no stem compartments
but with leaf compartments, and that a plant must have leaf compartments
(even if LAI = 0).
Specifically, this checks that:
1. n_leaf > 0
2. if LAI is nonzero or SAI is nonzero, RAI must be nonzero.
3. if SAI > 0, n_stem must be > 0 for consistency. If SAI == 0, n_stem must
be zero.
"""
function lai_consistency_check(
model::PlantHydraulicsModel{FT},
area_index::NamedTuple{(:root, :stem, :leaf), Tuple{FT, FT, FT}},
) where {FT}
n_stem = model.n_stem
n_leaf = model.n_leaf
@assert n_leaf > 0
if area_index.leaf > eps(FT) || area_index.stem > eps(FT)
@assert area_index.root > eps(FT)
end
# If there SAI is zero, there should be no stem compartment
if area_index.stem < eps(FT)
@assert n_stem == FT(0)
else
# if SAI is > 0, n_stem should be > 0 for consistency
@assert n_stem > 0
end

end


"""
PlantHydraulicsParameters
Expand Down Expand Up @@ -306,45 +268,42 @@ ClimaLand.auxiliary_domain_names(::PlantHydraulicsModel) =


"""
set_canopy_prescribed_field!(component::PlantHydraulics{FT},
p,
t,
) where {FT}
Sets the canopy prescribed fields pertaining to the PlantHydraulics
component (the area indices) with their values at time t.
"""
function ClimaLand.Canopy.set_canopy_prescribed_field!(
component::Union{PlantHydraulicsModel{FT}, BigLeafHydraulicsModel{FT}},
p,
t,
) where {FT}
(; LAIfunction, SAI, RAI) = component.parameters.ai_parameterization
evaluate!(p.canopy.hydraulics.area_index.leaf, LAIfunction, t)
@. p.canopy.hydraulics.area_index.stem = SAI
@. p.canopy.hydraulics.area_index.root = RAI
end
lai_consistency_check(
model::PlantHydraulicsModel{FT},
) where {FT}
Carries out consistency checks using the area indices supplied and the number of
stem elements being modeled.
"""
update_canopy_prescribed_field!(component::Union{PlantHydraulics{FT}, BigLeafHydraulicsModel{FT}},
p,
t,
) where {FT}
Note that it is possible to have a plant with no stem compartments
but with leaf compartments, and that a plant must have leaf compartments
(even if LAI = 0).
Updates the canopy prescribed fields pertaining to the PlantHydraulics
component (the LAI only in this case) with their values at time t.
Specifically, this checks that:
1. n_leaf > 0
2. if LAI is nonzero or SAI is nonzero, RAI must be nonzero.
3. if SAI > 0, n_stem must be > 0 for consistency. If SAI == 0, n_stem must
be zero.
"""
function ClimaLand.Canopy.update_canopy_prescribed_field!(
component::Union{PlantHydraulicsModel{FT}, BigLeafHydraulicsModel{FT}},
p,
t,
function lai_consistency_check(
model::PlantHydraulicsModel{FT},
area_index::NamedTuple{(:root, :stem, :leaf), Tuple{FT, FT, FT}},
) where {FT}
(; LAIfunction) = component.parameters.ai_parameterization
evaluate!(p.canopy.hydraulics.area_index.leaf, LAIfunction, t)
end
n_stem = model.n_stem
n_leaf = model.n_leaf
@assert n_leaf > 0
if area_index.leaf > eps(FT) || area_index.stem > eps(FT)
@assert area_index.root > eps(FT)
end
# If there SAI is zero, there should be no stem compartment
if area_index.stem < eps(FT)
@assert n_stem == FT(0)
else
# if SAI is > 0, n_stem should be > 0 for consistency
@assert n_stem > 0
end

end

"""
flux(
Expand Down Expand Up @@ -768,14 +727,7 @@ function BigLeafHydraulicsModel{FT}(;
args = (parameters, transpiration)
@assert h_stem >= 0
@assert h_leaf >= 0
return BigLeafHydraulicsModel{
FT,
typeof.(args)...,
}(
h_stem,
h_leaf,
args...,
)
return BigLeafHydraulicsModel{FT, typeof.(args)...}(h_stem, h_leaf, args...)
end

"""
Expand Down Expand Up @@ -803,7 +755,7 @@ auxiliary_vars(model::BigLeafHydraulicsModel) =
Defines the prognostic types for the BigLeafHydraulicsModel.
"""
ClimaLand.prognostic_types(model::BigLeafHydraulicsModel{FT}) where {FT} =
ClimaLand.prognostic_types(model::BigLeafHydraulicsModel{FT}) where {FT} =
(NTuple{2, FT},)
ClimaLand.prognostic_domain_names(::BigLeafHydraulicsModel) = (:surface,)

Expand All @@ -812,7 +764,7 @@ ClimaLand.prognostic_domain_names(::BigLeafHydraulicsModel) = (:surface,)
Defines the auxiliary types for the BigLeafHydraulicsModel.
"""
ClimaLand.auxiliarty_types(model::BigLeafHydraulicsModel{FT}) where {FT} = (
ClimaLand.auxiliary_types(model::BigLeafHydraulicsModel{FT}) where {FT} = (
FT,
NTuple{2, FT},
NTuple{2, FT},
Expand Down Expand Up @@ -841,7 +793,7 @@ To prevent dividing by zero, we change AI/(AI x dz)" to
"AI/max(AI x dz, eps(FT))"
"""
function make_compute_exp_tendency(
model::BigLeafHydraulicsmodel{FT},
model::BigLeafHydraulicsModel{FT},
canopy,
) where {FT}
function compute_exp_tendency!(dY, Y, p, t)
Expand All @@ -854,11 +806,12 @@ function make_compute_exp_tendency(
im1 = i - 1
ip1 = i + 1
compartment_type = labels[i]
dz = compartment_type == :stem ? model.h_stem : model.h_leaf - model.h_stem
dz =
compartment_type == :stem ? model.h_stem :
model.h_leaf - model.h_stem
# To prevent dividing by zero, change AI/(AI x dz)" to
# "AI/max(AI x dz, eps(FT))"
AIdz =
max.(getproperty(area_index, labels[i]) * (dz), eps(FT))
AIdz = max.(getproperty(area_index, labels[i]) * (dz), eps(FT))
if i == 1
@inbounds @. dY.canopy.hydraulics.ϑ_l.:($$i) =
1 / AIdz * (fa_roots - fa.:($$i))
Expand Down Expand Up @@ -897,7 +850,7 @@ function root_water_flux_per_ground_area!(
t,
) where {FT}
(; conductivity_model, root_distribution) = model.parameters
area_index = p.canopy.hydraulics,area_index
area_index = p.canopy.hydraulics, area_index
# We can index into a field of Tuple{FT} to extract a field of FT
# using the following notation: field.:index
ψ_base = p.canopy.hydraulics.ψ.:1
Expand All @@ -909,7 +862,9 @@ function root_water_flux_per_ground_area!(
@inbounds for i in 1:n_root_layers
above_ground_area_index = getproperty(area_index, labels[1])
compartment = labels[i]
midpoint = compartment == :stem ? model.h_stem / 2 : model.h_stem + (model.h_leaf / 2)
midpoint =
compartment == :stem ? model.h_stem / 2 :
model.h_stem + (model.h_leaf / 2)
if i != n_root_layers
@. fa +=
flux(
Expand Down Expand Up @@ -960,7 +915,7 @@ Specifically, this checks that:
be zero.
"""
function lai_consistency_check(
model::PlantHydraulicsModel{FT},
model::BigLeafHydraulicsModel{FT},
area_index::NamedTuple{(:root, :stem, :leaf), Tuple{FT, FT, FT}},
) where {FT}
if area_index.leaf > esp(FT) || area_index.stem > eso(FT)
Expand All @@ -975,4 +930,27 @@ function lai_consistency_check(
end
end

# SHARED METHODS FOR BigLeafHydraulics AND PlantHydraulics

"""
set_canopy_prescribed_field!(component::PlantHydraulics{FT},
p,
t,
) where {FT}
Sets the canopy prescribed fields pertaining to the PlantHydraulics
component (the area indices) with their values at time t.
"""
function ClimaLand.Canopy.set_canopy_prescribed_field!(
component::Union{PlantHydraulicsModel{FT}, BigLeafHydraulicsModel{FT}},
p,
t,
) where {FT}
(; LAIfunction, SAI, RAI) = component.parameters.ai_parameterization
evaluate!(p.canopy.hydraulics.area_index.leaf, LAIfunction, t)
@. p.canopy.hydraulics.area_index.stem = SAI
@. p.canopy.hydraulics.area_index.root = RAI
end

end

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