Add SoilCanopyModel diagnostics

This PR finalizes the addition of SoilCanopyModel diagnostics.
It also adds a macro to generate land compute functions,
And an optional argument for period averaging for default diagnostics.

Co-authored-by: AlexisRenchon <a.renchon@gmail.com>
Co-authored-by: SBozzolo <gbozzola@caltech.edu>
Co-authored-by: kmdeck <kdeck@caltech.edu>
Co-authored-by: braghiere <renato.braghiere@gmail.com>

docs/src/diagnostics/make_diagnostic_table.jl

@@ -16,7 +16,14 @@ for d in values(CL.Diagnostics.ALL_DIAGNOSTICS)
     push!(comments, d.comments)
     push!(standard_names, d.standard_name)
 end
-data = hcat(short_names, long_names, units, comments, standard_names)
+i = sortperm(short_names) # indices of short_names sorted alphabetically
+data = hcat(
+    short_names[i],
+    long_names[i],
+    units[i],
+    comments[i],
+    standard_names[i],
+)
 pretty_table(
     data;
     autowrap = true,

experiments/long_runs/land.jl

@@ -601,7 +601,7 @@ function setup_prob(t0, tf, Δt; outdir = outdir, nelements = (101, 15))
         land,
         t0;
         output_writer = nc_writer,
-        output_vars = :short,
+        output_vars = :long,
     )
 
     diagnostic_handler =

src/diagnostics/default_diagnostics.jl

@@ -62,7 +62,7 @@ function default_diagnostics(land_model::BucketModel, t_start; output_writer)
         "wsoil",
         "wsfc",
         "ssfc",
-    ] # TO DO: would it be helpful to return this list?
+    ]
 
     default_outputs =
         hourly_averages(bucket_diagnostics...; output_writer, t_start)
@@ -75,6 +75,7 @@ function default_diagnostics(
     t_start;
     output_writer,
     output_vars = :long,
+    average_period = :hourly,
 )
 
     define_diagnostics!(land_model)
@@ -96,7 +97,7 @@ function default_diagnostics(
             "gs",
             "mt",
             "trans",
-            "rain", # do we want?
+            "rain",
             "an",
             "gpp",
             "rd",
@@ -118,8 +119,17 @@ function default_diagnostics(
         soilcanopy_diagnostics = ["gpp", "ct", "ai", "slw", "si"]
     end
 
-    default_outputs =
-        hourly_averages(soilcanopy_diagnostics...; output_writer, t_start)
+    if average_period == :hourly
+        default_outputs =
+            hourly_averages(soilcanopy_diagnostics...; output_writer, t_start)
+    elseif average_period == :daily
+        default_outputs =
+            daily_averages(soilcanopy_diagnostics...; output_writer, t_start)
+    elseif average_period == :monthly # !! this is currently 30 days, not exact month
+        default_outputs =
+            monthly_averages(soilcanopy_diagnostics...; output_writer, t_start)
+    end
+
     return [default_outputs...]
 end