From a0a4f58146d88db8471eea650f9e5fc99eb217d9 Mon Sep 17 00:00:00 2001
From: "Katherine M. Deck" <kdeck@caltech.edu>
Date: Fri, 13 Sep 2024 11:03:44 -0700
Subject: [PATCH] lai clip

---
 experiments/long_runs/land.jl                | 2 +-
 experiments/long_runs/land_region.jl         | 4 ++--
 src/standalone/Vegetation/PlantHydraulics.jl | 6 +++++-
 test/shared_utilities/domains.jl             | 8 +++-----
 4 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/experiments/long_runs/land.jl b/experiments/long_runs/land.jl
index d044ff25dc..3ce5f6056f 100644
--- a/experiments/long_runs/land.jl
+++ b/experiments/long_runs/land.jl
@@ -68,7 +68,7 @@ function setup_prob(t0, tf, Δt; outdir = outdir, nelements = (101, 15))
         depth = depth,
         nelements = nelements,
         npolynomial = 1,
-        dz_tuple = FT.((10.0, 0.05)),# top layer should ideally be only a few cm!
+        dz_tuple = FT.((10.0, 0.05)),
     )
     surface_space = domain.space.surface
     subsurface_space = domain.space.subsurface
diff --git a/experiments/long_runs/land_region.jl b/experiments/long_runs/land_region.jl
index 92fa8afa87..ca80b58753 100644
--- a/experiments/long_runs/land_region.jl
+++ b/experiments/long_runs/land_region.jl
@@ -623,7 +623,7 @@ function setup_prob(t0, tf, Δt; outdir = outdir, nelements = (10, 10, 15))
         start_date;
         output_writer = nc_writer,
         output_vars = :short,
-        average_period = :monthly,
+        average_period = :daily,
     )
 
     diagnostic_handler =
@@ -638,7 +638,7 @@ end
 function setup_and_solve_problem(; greet = false)
 
     t0 = 0.0
-    tf = 60 * 60.0 * 24 * 365
+    tf = 60 * 60.0 * 24 * 30
     Δt = 900.0
     nelements = (10, 10, 15)
     if greet
diff --git a/src/standalone/Vegetation/PlantHydraulics.jl b/src/standalone/Vegetation/PlantHydraulics.jl
index 47ae13a88a..55552f648b 100644
--- a/src/standalone/Vegetation/PlantHydraulics.jl
+++ b/src/standalone/Vegetation/PlantHydraulics.jl
@@ -304,7 +304,9 @@ ClimaLand.auxiliary_types(model::PlantHydraulicsModel{FT}) where {FT} = (
 ClimaLand.auxiliary_domain_names(::PlantHydraulicsModel) =
     (:surface, :surface, :surface, :surface, :surface)
 
-
+function clip(x::FT, threshold::FT) where {FT}
+    x > threshold ? x : FT(0)
+end
 """
     set_canopy_prescribed_field!(component::PlantHydraulics{FT},
                                  p,
@@ -322,6 +324,8 @@ function ClimaLand.Canopy.set_canopy_prescribed_field!(
 ) where {FT}
     (; LAIfunction, SAI, RAI) = component.parameters.ai_parameterization
     evaluate!(p.canopy.hydraulics.area_index.leaf, LAIfunction, floor(t))
+    p.canopy.hydraulics.area_index.leaf .=
+        clip.(p.canopy.hydraulics.area_index.leaf, FT(0.05))
     @. p.canopy.hydraulics.area_index.stem = SAI
     @. p.canopy.hydraulics.area_index.root = RAI
 end
diff --git a/test/shared_utilities/domains.jl b/test/shared_utilities/domains.jl
index 1b44f5258b..b27f7e1c9c 100644
--- a/test/shared_utilities/domains.jl
+++ b/test/shared_utilities/domains.jl
@@ -43,7 +43,7 @@ FT = Float32
     face_space = obtain_face_space(shell.space.subsurface)
     z_face = ClimaCore.Fields.coordinate_field(face_space).z
     @test shell.fields.z_sfc == top_face_to_surface(z_face, shell.space.surface)
-    Δz_top, Δz_bottom, Δz = get_Δz(shell.fields.z)
+    Δz_top, Δz_bottom = get_Δz(shell.fields.z)
     @test shell.fields.Δz_top == Δz_top
     @test shell.fields.Δz_bottom == Δz_bottom
     @test shell.radius == radius
@@ -109,7 +109,7 @@ FT = Float32
     face_space = obtain_face_space(box.space.subsurface)
     z_face = ClimaCore.Fields.coordinate_field(face_space).z
     @test box.fields.z_sfc == top_face_to_surface(z_face, box.space.surface)
-    Δz_top, Δz_bottom, Δz = get_Δz(box.fields.z)
+    Δz_top, Δz_bottom = get_Δz(box.fields.z)
     @test box.fields.Δz_top == Δz_top
     @test box.fields.Δz_bottom == Δz_bottom
     box_coords = coordinates(box).subsurface
@@ -260,9 +260,7 @@ FT = Float32
     z_face = ClimaCore.Fields.coordinate_field(face_space).z
     @test z_column.fields.z_sfc ==
           top_face_to_surface(z_face, z_column.space.surface)
-    Δz_top, Δz_bottom, Δz = get_Δz(z_column.fields.z)
-    z = ClimaCore.Fields.coordinate_field(z_column.space.subsurface).z
-    @test z_column.fields.z == z
+    Δz_top, Δz_bottom = get_Δz(z_column.fields.z)
     @test z_column.fields.Δz_top == Δz_top
     @test z_column.fields.Δz_bottom == Δz_bottom
     column_coords = coordinates(z_column).subsurface