From d52d6851ebf66aaad0ed06ee6bd8a4194abd9f03 Mon Sep 17 00:00:00 2001
From: kmdeck <kdeck@caltech.edu>
Date: Wed, 11 Sep 2024 08:00:07 -0700
Subject: [PATCH] review comments

---
 experiments/long_runs/land_region.jl | 22 +++++++++++++++-------
 src/shared_utilities/Domains.jl      |  6 ++++--
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/experiments/long_runs/land_region.jl b/experiments/long_runs/land_region.jl
index ed6bde2d38..7dfe7962fa 100644
--- a/experiments/long_runs/land_region.jl
+++ b/experiments/long_runs/land_region.jl
@@ -1,6 +1,6 @@
 # # Global run of land model
 
-# The code sets up and runs the soil/canopy model for 6 hours on a spherical domain,
+# The code sets up and runs the soil/canopy model for 6 hours on a small region of the globe in Southern California,
 # using ERA5 data. In this simulation, we have
 # turned lateral flow off because horizontal boundary conditions and the
 # land/sea mask are not yet supported by ClimaCore.
@@ -56,7 +56,7 @@ diagnostics_outdir = joinpath(root_path, "regional_diagnostics")
 outdir =
     ClimaUtilities.OutputPathGenerator.generate_output_path(diagnostics_outdir)
 
-function setup_prob(t0, tf, Δt; outdir = outdir, nelements = (2, 2, 15))
+function setup_prob(t0, tf, Δt; outdir = outdir, nelements = (10, 10, 15))
 
     earth_param_set = LP.LandParameters(FT)
     radius = FT(6378.1e3)
@@ -371,8 +371,16 @@ function setup_prob(t0, tf, Δt; outdir = outdir, nelements = (2, 2, 15))
     # Conductance Model
     g1 = FT(141) # Wang et al: 141 sqrt(Pa) for Medlyn model; Natan used 300.
 
-    #Photosynthesis model
-    Vcmax25 = FT(9e-5) # from Yujie's paper 4.5e-5 , Natan used 9e-5
+    clm_artifact_path = ClimaLand.Artifacts.clm_data_folder_path(; context)
+    # vcmax is read in units of umol CO2/m^2/s and then converted to mol CO2/m^2/s
+    Vcmax25 = SpaceVaryingInput(
+        joinpath(clm_artifact_path, "vegetation_properties_map.nc"),
+        "vcmx25",
+        surface_space;
+        regridder_type,
+        regridder_kwargs = (; extrapolation_bc,),
+        file_reader_kwargs = (; preprocess_func = (data) -> data / 1_000_000,),
+    )
 
     # Plant Hydraulics and general plant parameters
     SAI = FT(0.0) # m2/m2
@@ -608,7 +616,7 @@ function setup_prob(t0, tf, Δt; outdir = outdir, nelements = (2, 2, 15))
         ref_time;
         output_writer = nc_writer,
         output_vars = :short,
-        average_period = :daily,
+        average_period = :monthly,
     )
 
     diagnostic_handler =
@@ -623,9 +631,9 @@ end
 function setup_and_solve_problem(; greet = false)
 
     t0 = 0.0
-    tf = 60 * 60.0 * 24 * 2
+    tf = 60 * 60.0 * 24 * 334
     Δt = 900.0
-    nelements = (2, 2, 15)
+    nelements = (10, 10, 15)
     if greet
         @info "Run: Regional Soil-Canopy Model"
         @info "Resolution: $nelements"
diff --git a/src/shared_utilities/Domains.jl b/src/shared_utilities/Domains.jl
index 779b946386..9cc109afeb 100644
--- a/src/shared_utilities/Domains.jl
+++ b/src/shared_utilities/Domains.jl
@@ -267,8 +267,10 @@ function Plane(;
         @assert periodic == (false, false)
         radius_earth = FT(radius_earth)
         long, lat = longlat
-        dxlim = xlim # long
-        dylim = ylim # lat
+        dxlim = xlim # long bounds
+        dylim = ylim # lat bounds
+        # Now make x refer to lat, and y refer to long,
+        # for compatibility with ClimaCore
         xlim =
             (lat - dylim[1] / (2radius_earth), lat + dylim[2] / (2radius_earth))
         ylim = (