add diagnostics

.buildkite/longruns_gpu/pipeline.yml

@@ -30,10 +30,10 @@ steps:
       - label: ":seedling: Soil-Canopy"
         command:
           - julia --color=yes --project=.buildkite experiments/long_runs/land.jl
-        artifact_paths: "$$JOB_NAME/output_active/*"
+        artifact_paths: "$$JOB_NAME/*png"
         agents:
           slurm_gpus: 1
           slurm_time: 12:00:00
         env:
           CLIMACOMMS_DEVICE: "CUDA"
-          JOB_NAME: "soil_canopy"
+          JOB_NAME: "land_longrun_gpu"

experiments/long_runs/land.jl

@@ -55,7 +55,6 @@ root_path = "land_longrun_$(device_suffix)"
 diagnostics_outdir = joinpath(root_path, "global_diagnostics")
 outdir =
     ClimaUtilities.OutputPathGenerator.generate_output_path(diagnostics_outdir)
-!ispath(outdir) && mkpath(outdir)
 
 function setup_prob(t0, tf, Δt; outdir = outdir, nelements = (101, 15))
 
@@ -650,7 +649,7 @@ setup_and_solve_problem(; greet = true)
 # read in diagnostics and make some plots!
 #### ClimaAnalysis ####
 simdir = ClimaAnalysis.SimDir(outdir)
-short_names_2D = ["gpp"] #["ai", "rn", "ct", "lhf", "shf", "vflux", "gpp"]
+short_names_2D = ["gpp", "ct", "ai", "slw", "si"] #["ai", "rn", "ct", "lhf", "shf", "vflux", "gpp"]
 # short_names_3D = ["tsoil", "si", "slw"]
 times = 0.0:(60.0 * 60.0 * 1):(60.0 * 60.0 * 24)
 for t in times

src/diagnostics/Diagnostics.jl

@@ -6,6 +6,8 @@ using ..Bucket: BucketModel
 
 import ..SoilCanopyModel
 
+import ..Domains: top_center_to_surface
+
 import ClimaDiagnostics:
     DiagnosticVariable, ScheduledDiagnostic, average_pre_output_hook!
 

src/diagnostics/default_diagnostics.jl

@@ -81,10 +81,12 @@ function default_diagnostics(
 
     if output_vars == :long
         soilcanopy_diagnostics = [
-            "rn",
-            "lhf",
-            "rae",
-            "shf",
+            "rn_canopy",
+            "rn_soil",
+            "lhf_soil",
+            "lhf_canopy",
+            "shf_canopy",
+            "shf_soil",
             "vflux",
             "tsoil",
             "slw",
@@ -113,7 +115,7 @@ function default_diagnostics(
             "soilco2",
         ]
     elseif output_vars == :short
-        soilcanopy_diagnostics = ["gpp"]
+        soilcanopy_diagnostics = ["gpp", "ct", "ai", "slw", "si"]
     end
 
     default_outputs =

src/diagnostics/define_diagnostics.jl

@@ -588,7 +588,7 @@ function define_diagnostics!(land_model)
         long_name = "Area Index",
         standard_name = "area_index",
         units = "",
-        comments = "The area index.", #?? of steam, leaves, roots?
+        comments = "The area index of leaves.",
         compute! = (out, Y, p, t) ->
             compute_area_index!(out, Y, p, t, land_model),
     )
@@ -627,7 +627,7 @@ function define_diagnostics!(land_model)
         short_name = "ct",
         long_name = "Canopy Temperature",
         standard_name = "canopy_temperature",
-        units = "",
+        units = "K",
         comments = "Canopy temperature.", #?? of steam, leaves, roots?
         compute! = (out, Y, p, t) ->
             compute_canopy_temperature!(out, Y, p, t, land_model),
@@ -638,7 +638,7 @@ function define_diagnostics!(land_model)
         long_name = "Soil Ice",
         standard_name = "soil_ice",
         units = "m^3 m^-3",
-        comments = "soil ice.", #?? of steam, leaves, roots?
+        comments = "soil ice.", 
         compute! = (out, Y, p, t) ->
             compute_soil_ice!(out, Y, p, t, land_model),
     )

src/diagnostics/soilcanopy_compute_methods.jl

@@ -60,17 +60,17 @@ end
 
 function compute_soil_temperature!(out, Y, p, t, land_model::SoilCanopyModel)
     if isnothing(out)
-        return copy(p.drivers.T) # or is it p.soil.T?
+        return copy(p.soil.T) # or is it p.soil.T?
     else
-        out .= p.drivers.T
+        out .= p.soil.T
     end
 end
 
-function compute_soil_water_liquid(out, Y, p, t, land_model::SoilCanopyModel)
+function compute_soil_water_liquid!(out, Y, p, t, land_model::SoilCanopyModel)
     if isnothing(out)
-        return copy(p.soil.θ_l) # or is it in Y.soil?
+        return copy(top_center_to_surface(p.soil.θ_l)) # or is it in Y.soil?
     else
-        out .= p.soil.θ_l
+        out .= top_center_to_surface(p.soil.θ_l)
     end
 end
 
@@ -512,11 +512,11 @@ function compute_cross_section_roots(out, Y, p, t, land_model::SoilCanopyModel)
     end
 end
 
-function compute_area_index(out, Y, p, t, land_model::SoilCanopyModel)
+function compute_area_index!(out, Y, p, t, land_model::SoilCanopyModel)
     if isnothing(out)
-        return copy(p.canopy.hydraulics.area_index)
+        return copy(p.canopy.hydraulics.area_index.leaf)
     else
-        p.canopy.hydraulics.area_index
+        out .= p.canopy.hydraulics.area_index.leaf
     end
 end
 
@@ -562,18 +562,18 @@ function compute_canopy_aerodynamic_resistance(
     end
 end
 
-function compute_canopy_temperature(out, Y, p, t, land_model::SoilCanopyModel)
+function compute_canopy_temperature!(out, Y, p, t, land_model::SoilCanopyModel)
     if isnothing(out)
         return copy(Y.canopy.energy.T)
     else
-        Y.canopy.energy.T
+        out .= Y.canopy.energy.T
     end
 end
 
-function compute_soil_ice(out, Y, p, t, land_model::SoilCanopyModel)
+function compute_soil_ice!(out, Y, p, t, land_model::SoilCanopyModel)
     if isnothing(out)
-        return copy(Y.soil.θ_i)
+        return copy(top_center_to_surface(Y.soil.θ_i))
     else
-        Y.soil.θ_i
+        out .= top_center_to_surface(Y.soil.θ_i)
     end
 end