From 9e1d396715f4e615b63336bdcd6c214de101ddf2 Mon Sep 17 00:00:00 2001
From: Alexis Renchon <a.renchon@gmail.com>
Date: Wed, 14 Aug 2024 11:26:06 -0700
Subject: [PATCH] WIP

---
 experiments/long_runs/land.jl           |  4 ++--
 src/diagnostics/define_diagnostics.jl   | 14 +++++++-------
 src/diagnostics/land_compute_methods.jl |  1 -
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/experiments/long_runs/land.jl b/experiments/long_runs/land.jl
index bb29528f13..db477ea678 100644
--- a/experiments/long_runs/land.jl
+++ b/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 = :long,
+        output_vars = :short,
     )
 
     diagnostic_handler =
@@ -645,7 +645,7 @@ setup_and_solve_problem(; greet = true);
 # read in diagnostics and make some plots!
 #### ClimaAnalysis ####
 simdir = ClimaAnalysis.SimDir(outdir)
-short_names_2D = ["gpp", "ct", "slw", "si"]
+short_names_2D = ["gpp", "ct", "swc"] # , "si"] 
 times = 0.0:(60.0 * 60.0 * 12):(60.0 * 60.0 * 24 * 7)
 for t in times
     for short_name in short_names_2D
diff --git a/src/diagnostics/define_diagnostics.jl b/src/diagnostics/define_diagnostics.jl
index be1379de47..252c2b455b 100644
--- a/src/diagnostics/define_diagnostics.jl
+++ b/src/diagnostics/define_diagnostics.jl
@@ -203,7 +203,7 @@ function define_diagnostics!(land_model)
         short_name = "ra",
         long_name = "Autotrophic Respiration",
         standard_name = "autotrophic_respiration",
-        units = "kg C m^-2 s^-1", 
+        units = "kg C m^-2 s^-1",
         comments = "The canopy autotrophic respiration, the sum of leaves, stems and roots respiration.",
         compute! = (out, Y, p, t) ->
             compute_autotrophic_respiration!(out, Y, p, t, land_model),
@@ -238,8 +238,8 @@ function define_diagnostics!(land_model)
         short_name = "crae",
         long_name = "Canopy Aerodynamic Resistance",
         standard_name = "canopy_aerodynamic_resistance",
-        units = "s m^-1", 
-        comments = "The canopy aerodynamic resistance. Aerodynamic resistance (r_a) is a measure of how much the air near the Earth's surface resists the movement of water vapor and heat from the surface into the air.", 
+        units = "s m^-1",
+        comments = "The canopy aerodynamic resistance. Aerodynamic resistance (r_a) is a measure of how much the air near the Earth's surface resists the movement of water vapor and heat from the surface into the air.",
         compute! = (out, Y, p, t) ->
             compute_canopy_aerodynamic_resistance!(out, Y, p, t, land_model),
     )
@@ -284,7 +284,7 @@ function define_diagnostics!(land_model)
         long_name = "Cross Section",
         standard_name = "cross_section",
         units = "m s^-1",
-        comments = "Flux of water volume per m^2 of plant per second, multiplied by the area index (plant area/ground area).", 
+        comments = "Flux of water volume per m^2 of plant per second, multiplied by the area index (plant area/ground area).",
         compute! = (out, Y, p, t) ->
             compute_cross_section!(out, Y, p, t, land_model),
     )
@@ -295,7 +295,7 @@ function define_diagnostics!(land_model)
         long_name = "Root Cross Section",
         standard_name = "Cross Section",
         units = "m s^-1",
-        comments = "Flux of water volume per m^2 of root per second, multiplied by the area index (root area/ground area).", 
+        comments = "Flux of water volume per m^2 of root per second, multiplied by the area index (root area/ground area).",
         compute! = (out, Y, p, t) ->
             compute_cross_section_roots!(out, Y, p, t, land_model),
     )
@@ -563,7 +563,7 @@ function define_diagnostics!(land_model)
         short_name = "rain",
         long_name = "Rainfall",
         standard_name = "rainfall",
-        units = "m s^-1", 
+        units = "m s^-1",
         comments = "Precipitation of liquid water volume (m^3 of water per m^2 of ground per second).",
         compute! = (out, Y, p, t) ->
             compute_rainfall!(out, Y, p, t, land_model),
@@ -820,7 +820,7 @@ function define_diagnostics!(land_model)
         short_name = "sie",
         long_name = "Soil Internal Energy",
         standard_name = "soil_internal_energy",
-        units = "W m^-2", 
+        units = "W m^-2",
         comments = "The energy per volume of soil.",
         compute! = (out, Y, p, t) ->
             compute_soil_internal_energy!(out, Y, p, t, land_model),
diff --git a/src/diagnostics/land_compute_methods.jl b/src/diagnostics/land_compute_methods.jl
index 6138d3545d..1063b213ef 100644
--- a/src/diagnostics/land_compute_methods.jl
+++ b/src/diagnostics/land_compute_methods.jl
@@ -1,7 +1,6 @@
 """
     @land_compute name model compute
 
-
 Macro generating a function to compute a land diagnostic,
 needed in the ClimaDiagnostics framework.