remove PlantHydraulicsModel

CliMA · Jun 2, 2024 · 2c6f8c7 · 2c6f8c7
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diff --git a/docs/src/APIs/canopy/PlantHydraulics.md b/docs/src/APIs/canopy/PlantHydraulics.md
@@ -6,7 +6,6 @@ CurrentModule = ClimaLand.PlantHydraulics
 ## Models
 
 ```@docs
-ClimaLand.PlantHydraulics.PlantHydraulicsModel
 ClimaLand.PlantHydraulics.BigLeafHydraulicsModel
 ```
 

diff --git a/docs/tutorials/integrated/soil_canopy_tutorial.jl b/docs/tutorials/integrated/soil_canopy_tutorial.jl
@@ -68,12 +68,8 @@ f_root_to_shoot = FT(3.5)
 SAI = FT(0.00242)
 maxLAI = FT(4.2)
 plant_ν = FT(2.46e-4)
-n_stem = Int64(1)
-n_leaf = Int64(1)
 h_stem = FT(9)
 h_leaf = FT(9.5)
-compartment_midpoints = [h_stem / 2, h_stem + h_leaf / 2]
-compartment_surfaces = [zmax, h_stem, h_stem + h_leaf]
 land_domain = Column(; zlim = (zmin, zmax), nelements = nelements);
 
 # - We will be using prescribed atmospheric and radiative drivers from the

diff --git a/docs/tutorials/standalone/Canopy/canopy_tutorial.jl b/docs/tutorials/standalone/Canopy/canopy_tutorial.jl
@@ -84,12 +84,8 @@ f_root_to_shoot = FT(3.5)
 SAI = FT(0.00242)
 maxLAI = FT(4.2)
 plant_ν = FT(2.46e-4) # kg/m^2
-n_stem = Int64(1)
-n_leaf = Int64(1)
 h_stem = FT(9)
 h_leaf = FT(9.5)
-compartment_midpoints = [h_stem / 2, h_stem + h_leaf / 2]
-compartment_surfaces = [zmax, h_stem, h_stem + h_leaf]
 land_domain = Point(; z_sfc = FT(0.0))
 
 # - We will be using prescribed atmospheric and radiative drivers from the
@@ -233,12 +229,10 @@ plant_hydraulics_ps = PlantHydraulics.PlantHydraulicsParameters(;
 
 # Define the remaining variables required for the plant hydraulics model.
 
-plant_hydraulics = PlantHydraulics.PlantHydraulicsModel{FT}(;
+plant_hydraulics = PlantHydraulics.BigLeafHydraulicsModel{FT}(;
     parameters = plant_hydraulics_ps,
-    n_stem = n_stem,
-    n_leaf = n_leaf,
-    compartment_surfaces = compartment_surfaces,
-    compartment_midpoints = compartment_midpoints,
+    h_stem = h_stem,
+    h_leaf = h_leaf,
 );
 
 # Now, instantiate the canopy model, using the atmospheric and radiative

diff --git a/experiments/integrated/fluxnet/US-Ha1/US-Ha1_simulation.jl b/experiments/integrated/fluxnet/US-Ha1/US-Ha1_simulation.jl
@@ -9,8 +9,6 @@ dz_bottom = FT(1.5)
 dz_top = FT(0.025)
 
 # Stem and leaf compartments and their heights:
-n_stem = Int64(1)
-n_leaf = Int64(1)
 h_leaf = FT(12) # m
 h_stem = FT(14) # m
 

diff --git a/experiments/integrated/fluxnet/US-MOz/US-MOz_simulation.jl b/experiments/integrated/fluxnet/US-MOz/US-MOz_simulation.jl
@@ -9,8 +9,6 @@ dz_bottom = FT(1.5)
 dz_top = FT(0.025)
 
 # Stem and leaf compartments and their heights:
-n_stem = Int64(1)
-n_leaf = Int64(1)
 h_stem = FT(9) # m
 h_leaf = FT(9.5) # m
 

diff --git a/experiments/integrated/fluxnet/US-NR1/US-NR1_simulation.jl b/experiments/integrated/fluxnet/US-NR1/US-NR1_simulation.jl
@@ -9,8 +9,6 @@ dz_bottom = FT(1.25)
 dz_top = FT(0.05)
 
 # Stem and leaf compartments and their heights:
-n_stem = Int64(1)
-n_leaf = Int64(1)
 h_leaf = FT(6.5) # m
 h_stem = FT(7.5) # m
 

diff --git a/experiments/integrated/fluxnet/US-Var/US-Var_simulation.jl b/experiments/integrated/fluxnet/US-Var/US-Var_simulation.jl
@@ -9,8 +9,6 @@ dz_bottom = FT(1.0)
 dz_top = FT(0.05)
 
 # Stem and leaf compartments and their heights:
-n_stem = Int64(0)
-n_leaf = Int64(1)
 h_leaf = FT(0.7) # m
 h_stem = FT(0) # m
 

diff --git a/experiments/integrated/fluxnet/fluxnet_domain.jl b/experiments/integrated/fluxnet/fluxnet_domain.jl
@@ -8,9 +8,6 @@ nelements = 20
 zmin = FT(-10)
 zmax = FT(0)
 h_canopy = h_stem + h_leaf
-compartment_midpoints =
-    n_stem > 0 ? [h_stem / 2, h_stem + h_leaf / 2] : [h_leaf / 2]
-compartment_surfaces = n_stem > 0 ? [zmax, h_stem, h_canopy] : [zmax, h_leaf]
 
 land_domain = Column(;
     zlim = (zmin, zmax),

diff --git a/experiments/integrated/fluxnet/ozark_pft.jl b/experiments/integrated/fluxnet/ozark_pft.jl
@@ -168,7 +168,7 @@ canopy_component_types = (;
     radiative_transfer = Canopy.TwoStreamModel{FT},
     photosynthesis = Canopy.FarquharModel{FT},
     conductance = Canopy.MedlynConductanceModel{FT},
-    hydraulics = Canopy.PlantHydraulicsModel{FT},
+    hydraulics = Canopy.BigLeafHydraulicsModel{FT},
     energy = Canopy.BigLeafEnergyModel{FT},
 )
 # Individual Component arguments
@@ -211,10 +211,8 @@ plant_hydraulics_ps = PlantHydraulics.PlantHydraulicsParameters(;
 )
 plant_hydraulics_args = (
     parameters = plant_hydraulics_ps,
-    n_stem = n_stem,
-    n_leaf = n_leaf,
-    compartment_midpoints = compartment_midpoints,
-    compartment_surfaces = compartment_surfaces,
+    h_stem = h_stem,
+    h_leaf = h_leaf,
 )
 
 energy_args = (parameters = Canopy.BigLeafEnergyParameters{FT}(ac_canopy),)
@@ -276,12 +274,12 @@ Y.soil.ρe_int =
 Y.soilco2.C .= FT(0.000412) # set to atmospheric co2, mol co2 per mol air
 ψ_stem_0 = FT(-1e5 / 9800) # pressure in the leaf divided by rho_liquid*gravitational acceleration [m] 
 ψ_leaf_0 = FT(-2e5 / 9800)
-ψ_comps = n_stem > 0 ? [ψ_stem_0, ψ_leaf_0] : ψ_leaf_0
+ψ_comps = h_stem > 0 ? [ψ_stem_0, ψ_leaf_0] : ψ_leaf_0
 
 S_l_ini =
     inverse_water_retention_curve.(retention_model, ψ_comps, plant_ν, plant_S_s)
 
-for i in 1:(n_stem + n_leaf)
+for i in 1:(h_stem < 0 + 1)
     Y.canopy.hydraulics.ϑ_l.:($i) .=
         augmented_liquid_fraction.(plant_ν, S_l_ini[i])
 end

diff --git a/experiments/integrated/fluxnet/run_fluxnet.jl b/experiments/integrated/fluxnet/run_fluxnet.jl
@@ -130,7 +130,7 @@ canopy_component_types = (;
     radiative_transfer = Canopy.TwoStreamModel{FT},
     photosynthesis = Canopy.FarquharModel{FT},
     conductance = Canopy.MedlynConductanceModel{FT},
-    hydraulics = Canopy.PlantHydraulicsModel{FT},
+    hydraulics = Canopy.BigLeafHydraulicsModel{FT},
     energy = Canopy.BigLeafEnergyModel{FT},
 )
 # Individual Component arguments
@@ -171,10 +171,8 @@ plant_hydraulics_ps = PlantHydraulics.PlantHydraulicsParameters(;
 )
 plant_hydraulics_args = (
     parameters = plant_hydraulics_ps,
-    n_stem = n_stem,
-    n_leaf = n_leaf,
-    compartment_midpoints = compartment_midpoints,
-    compartment_surfaces = compartment_surfaces,
+    h_stem = h_stem,
+    h_leaf = h_leaf,
 )
 
 energy_args = (parameters = Canopy.BigLeafEnergyParameters{FT}(ac_canopy),)
@@ -236,12 +234,12 @@ Y.soil.ρe_int =
 Y.soilco2.C .= FT(0.000412) # set to atmospheric co2, mol co2 per mol air
 ψ_stem_0 = FT(-1e5 / 9800) # pressure in the leaf divided by rho_liquid*gravitational acceleration [m] 
 ψ_leaf_0 = FT(-2e5 / 9800)
-ψ_comps = n_stem > 0 ? [ψ_stem_0, ψ_leaf_0] : ψ_leaf_0
+ψ_comps = h_stem > 0 ? [ψ_stem_0, ψ_leaf_0] : ψ_leaf_0
 
 S_l_ini =
     inverse_water_retention_curve.(retention_model, ψ_comps, plant_ν, plant_S_s)
 
-for i in 1:(n_stem + n_leaf)
+for i in 1:(h_stem > 0 + 1)
     Y.canopy.hydraulics.ϑ_l.:($i) .=
         augmented_liquid_fraction.(plant_ν, S_l_ini[i])
 end

diff --git a/experiments/integrated/performance/conservation/ozark_conservation_setup.jl b/experiments/integrated/performance/conservation/ozark_conservation_setup.jl
@@ -6,8 +6,6 @@ dz_bottom = FT(1.5)
 dz_top = FT(0.025)
 
 # Stem and leaf compartments and their heights:
-n_stem = Int64(1)
-n_leaf = Int64(1)
 h_stem = FT(9) # m
 h_leaf = FT(9.5) # m
 
@@ -112,7 +110,7 @@ canopy_component_types = (;
     radiative_transfer = Canopy.TwoStreamModel{FT},
     photosynthesis = Canopy.FarquharModel{FT},
     conductance = Canopy.MedlynConductanceModel{FT},
-    hydraulics = Canopy.PlantHydraulicsModel{FT},
+    hydraulics = Canopy.BigLeafHydraulicsModel{FT},
     energy = Canopy.BigLeafEnergyModel{FT},
 )
 # Individual Component arguments
@@ -155,10 +153,8 @@ plant_hydraulics_ps = PlantHydraulics.PlantHydraulicsParameters(;
 )
 plant_hydraulics_args = (
     parameters = plant_hydraulics_ps,
-    n_stem = n_stem,
-    n_leaf = n_leaf,
-    compartment_midpoints = compartment_midpoints,
-    compartment_surfaces = compartment_surfaces,
+    h_stem = h_stem,
+    h_leaf = h_leaf,
 )
 
 # Canopy component args

diff --git a/experiments/integrated/performance/profile_allocations.jl b/experiments/integrated/performance/profile_allocations.jl
@@ -86,14 +86,10 @@ dz_bottom = FT(2.0)
 dz_top = FT(0.2)
 soil_depth = FT(5)
 z_sfc = FT(0)
-n_stem = Int64(1)
-n_leaf = Int64(1)
 h_stem = FT(9) # m
 h_leaf = FT(9.5) # m
 
 h_canopy = h_stem + h_leaf
-compartment_midpoints = [h_stem / 2, h_stem + h_leaf / 2]
-compartment_surfaces = [z_sfc, h_stem, h_canopy]
 
 land_domain = ClimaLand.Domains.SphericalShell(;
     radius = FT(6.3781e6),
@@ -258,7 +254,7 @@ canopy_component_types = (;
     radiative_transfer = Canopy.TwoStreamModel{FT},
     photosynthesis = Canopy.FarquharModel{FT},
     conductance = Canopy.MedlynConductanceModel{FT},
-    hydraulics = Canopy.PlantHydraulicsModel{FT},
+    hydraulics = Canopy.BigLeafHydraulicsModel{FT},
     energy = Canopy.BigLeafEnergyModel{FT},
 )
 # Individual Component arguments
@@ -289,10 +285,8 @@ plant_hydraulics_ps = PlantHydraulics.PlantHydraulicsParameters(;
 )
 plant_hydraulics_args = (
     parameters = plant_hydraulics_ps,
-    n_stem = n_stem,
-    n_leaf = n_leaf,
-    compartment_midpoints = compartment_midpoints,
-    compartment_surfaces = compartment_surfaces,
+    h_stem = h_stem,
+    h_leaf = h_leaf,
 )
 
 # Canopy component args

diff --git a/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-Ha1/US-Ha1_simulation.jl b/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-Ha1/US-Ha1_simulation.jl
@@ -4,8 +4,6 @@ export harvard_default_args
 	function harvard_default_args(;
 		dz_bottom = FT(1.5),
 		dz_top = FT(0.025),
-		n_stem = Int64(1),
-		n_leaf = Int64(1),
 		h_leaf = FT(12), # m
 		h_stem = FT(14), # m
 		t0 = Float64(120 * 3600 * 24),
@@ -15,8 +13,6 @@ export harvard_default_args
 		return (
 			dz_bottom = dz_bottom,
 			dz_top = dz_top,
-			n_stem = n_stem,
-			n_leaf = n_leaf,
 			h_stem = h_stem,
 			h_leaf = h_leaf,
 			t0 = t0,
@@ -30,8 +26,6 @@ Named Tuple containing default simulation parameter for the Harvard site.
 function harvard_default_args(;
     dz_bottom = FT(1.5),
     dz_top = FT(0.025),
-    n_stem = Int64(1),
-    n_leaf = Int64(1),
     h_leaf = FT(12), # m
     h_stem = FT(14), # m
     t0 = Float64(120 * 3600 * 24),
@@ -41,8 +35,6 @@ function harvard_default_args(;
     return (
         dz_bottom = dz_bottom,
         dz_top = dz_top,
-        n_stem = n_stem,
-        n_leaf = n_leaf,
         h_stem = h_stem,
         h_leaf = h_leaf,
         t0 = t0,

diff --git a/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-MOz/US-MOz_simulation.jl b/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-MOz/US-MOz_simulation.jl
@@ -4,8 +4,6 @@ export ozark_default_args
 	function ozark_default_args(;
 		dz_bottom = FT(1.5),
 		dz_top = FT(0.025),
-		n_stem = Int64(1),
-		n_leaf = Int64(1),
 		h_stem = FT(9),
 		h_leaf = FT(9.5),
 		t0 = Float64(120 * 3600 * 24),
@@ -15,8 +13,6 @@ export ozark_default_args
 		return (
 			dz_bottom = dz_bottom,
 			dz_top = dz_top,
-			n_stem = n_stem,
-			n_leaf = n_leaf,
 			h_stem = h_stem,
 			h_leaf = h_leaf,
 			t0 = t0,
@@ -30,8 +26,6 @@ Named Tuple containing default simulation parameter for the Ozark site.
 function ozark_default_args(;
     dz_bottom = FT(1.5),
     dz_top = FT(0.025),
-    n_stem = Int64(1),
-    n_leaf = Int64(1),
     h_stem = FT(9),
     h_leaf = FT(9.5),
     t0 = Float64(120 * 3600 * 24),
@@ -41,8 +35,6 @@ function ozark_default_args(;
     return (
         dz_bottom = dz_bottom,
         dz_top = dz_top,
-        n_stem = n_stem,
-        n_leaf = n_leaf,
         h_stem = h_stem,
         h_leaf = h_leaf,
         t0 = t0,

diff --git a/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-NR1/US-NR1_simulation.jl b/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-NR1/US-NR1_simulation.jl
@@ -4,8 +4,6 @@ export niwotridge_default_args
 	function niwotridge_default_args(;
 		dz_bottom = FT(1.25),
 		dz_top = FT(0.05),
-		n_stem = Int64(1),
-		n_leaf = Int64(1),
 		h_leaf = FT(6.5), # m,
 		h_stem = FT(7.5), # m,
 		t0 = Float64(120 * 3600 * 24), # start mid year to avoid snow,
@@ -15,8 +13,6 @@ export niwotridge_default_args
 		return (
 			dz_bottom = dz_bottom,
 			dz_top = dz_top,
-			n_stem = n_stem,
-			n_leaf = n_leaf,
 			h_stem = h_stem,
 			h_leaf = h_leaf,
 			t0 = t0,
@@ -30,8 +26,6 @@ Named Tuple containing default simulation parameter for the Niwot Ridge site.
 function niwotridge_default_args(;
     dz_bottom = FT(1.25),
     dz_top = FT(0.05),
-    n_stem = Int64(1),
-    n_leaf = Int64(1),
     h_leaf = FT(6.5), # m,
     h_stem = FT(7.5), # m,
     t0 = Float64(120 * 3600 * 24), # start mid year to avoid snow,
@@ -41,8 +35,6 @@ function niwotridge_default_args(;
     return (
         dz_bottom = dz_bottom,
         dz_top = dz_top,
-        n_stem = n_stem,
-        n_leaf = n_leaf,
         h_stem = h_stem,
         h_leaf = h_leaf,
         t0 = t0,

diff --git a/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-Var/US-Var_simulation.jl b/lib/ClimaLandSimulations/src/Fluxnet/fluxnet_sites/US-Var/US-Var_simulation.jl
@@ -4,8 +4,6 @@ export vairaranch_default_args
 	function vairaranch_default_args(;
 		dz_bottom = FT(1.0),
 		dz_top = FT(0.05),
-		n_stem = Int64(0),
-		n_leaf = Int64(1),
 		h_leaf = FT(0.7), # m,
 		h_stem = FT(0), # m,
 		t0 = Float64(21 * 3600 * 24), # start day 21 of the year,
@@ -15,8 +13,6 @@ export vairaranch_default_args
 		return (
 			dz_bottom = dz_bottom,
 			dz_top = dz_top,
-			n_stem = n_stem,
-			n_leaf = n_leaf,
 			h_stem = h_stem,
 			h_leaf = h_leaf,
 			t0 = t0,
@@ -30,8 +26,6 @@ Named Tuple containing default simulation parameter for the Vaira Ranch site.
 function vairaranch_default_args(;
     dz_bottom = FT(1.0),
     dz_top = FT(0.05),
-    n_stem = Int64(0),
-    n_leaf = Int64(1),
     h_leaf = FT(0.7), # m,
     h_stem = FT(0), # m,
     t0 = Float64(21 * 3600 * 24), # start day 21 of the year,
@@ -41,8 +35,6 @@ function vairaranch_default_args(;
     return (
         dz_bottom = dz_bottom,
         dz_top = dz_top,
-        n_stem = n_stem,
-        n_leaf = n_leaf,
         h_stem = h_stem,
         h_leaf = h_leaf,
         t0 = t0,