From 2046e89ef360e70163c209cf91ad6454f44a084f Mon Sep 17 00:00:00 2001
From: Alexis Renchon <a.renchon@gmail.com>
Date: Mon, 5 Aug 2024 14:51:50 -0700
Subject: [PATCH] WIP

---
 docs/src/diagnostics/make_diagnostic_table.jl | 8 +++++++-
 src/diagnostics/define_diagnostics.jl         | 6 +++---
 src/diagnostics/land_compute_methods.jl       | 9 +++++----
 3 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/docs/src/diagnostics/make_diagnostic_table.jl b/docs/src/diagnostics/make_diagnostic_table.jl
index 2fd993fd8f..4839efd307 100644
--- a/docs/src/diagnostics/make_diagnostic_table.jl
+++ b/docs/src/diagnostics/make_diagnostic_table.jl
@@ -17,7 +17,13 @@ for d in values(CL.Diagnostics.ALL_DIAGNOSTICS)
     push!(standard_names, d.standard_name)
 end
 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])
+data = hcat(
+    short_names[i],
+    long_names[i],
+    units[i],
+    comments[i],
+    standard_names[i],
+)
 pretty_table(
     data;
     autowrap = true,
diff --git a/src/diagnostics/define_diagnostics.jl b/src/diagnostics/define_diagnostics.jl
index 3ed936f258..6264f77468 100644
--- a/src/diagnostics/define_diagnostics.jl
+++ b/src/diagnostics/define_diagnostics.jl
@@ -199,7 +199,7 @@ function define_diagnostics!(land_model)
         short_name = "infil",
         long_name = "Infiltration",
         standard_name = "infiltration",
-        units = "m s^-1", 
+        units = "m s^-1",
         comments = "The flux of liquid water into the soil.",
         compute! = (out, Y, p, t) ->
             compute_infiltration!(out, Y, p, t, land_model),
@@ -221,7 +221,7 @@ function define_diagnostics!(land_model)
         short_name = "scms",
         long_name = "Soil CO2 Microbial Source",
         standard_name = "soil_co2_microbial_source",
-        units = "kg CO2 m^-2 s^-1", 
+        units = "kg CO2 m^-2 s^-1",
         comments = "The production of CO2 by microbes in the soil. Vary by layers of soil depth.",
         compute! = (out, Y, p, t) ->
             compute_soilco2_source_microbe!(out, Y, p, t, land_model),
@@ -254,7 +254,7 @@ function define_diagnostics!(land_model)
         short_name = "trans",
         long_name = "Canopy Transpiration",
         standard_name = "canopy_transpiration",
-        units = "m s^-1", 
+        units = "m s^-1",
         comments = "The water evaporated from the canopy due to leaf transpiration.",
         compute! = (out, Y, p, t) ->
             compute_canopy_transpiration!(out, Y, p, t, land_model),
diff --git a/src/diagnostics/land_compute_methods.jl b/src/diagnostics/land_compute_methods.jl
index 1501925d26..c7cca5e112 100644
--- a/src/diagnostics/land_compute_methods.jl
+++ b/src/diagnostics/land_compute_methods.jl
@@ -38,7 +38,7 @@ end
 
 ### BucketModel ###
 
-# variables stored in p
+# variables stored in p (diagnostics variables stored in the cache)
 @land_compute "aerodynamic_resistance" BucketModel p.bucket.turbulent_fluxes.r_ae
 @land_compute "albedo" BucketModel p.bucket.α_sfc
 @land_compute "latent_heat_flux" BucketModel p.bucket.turbulent_fluxes.lhf
@@ -49,7 +49,7 @@ end
 @land_compute "surface_temperature" BucketModel p.bucket.T_sfc
 @land_compute "vapor_flux" BucketModel p.bucket.turbulent_fluxes.vapor_flux
 
-# variables stored in Y
+# variables stored in Y (prognostic or state variables)
 @land_compute "snow_water_equivalent" BucketModel Y.bucket.σS
 @land_compute "soil_temperature" BucketModel Y.bucket.T
 @land_compute "subsurface_water_storage" BucketModel Y.bucket.W
@@ -57,7 +57,7 @@ end
 
 ### SoilCanopyModel ###
 
-# variables stored in p
+# variables stored in p (diagnostics variables stored in the cache)
 
 ## Canopy Module ##
 
@@ -139,7 +139,8 @@ end
 @land_compute "soilco2_diffusivity" SoilCanopyModel p.soilco2.D
 @land_compute "soilco2_source_microbe" SoilCanopyModel p.soilco2.Sm
 
-# variables stored in Y
+# variables stored in Y (prognostic or state variables)
+
 @land_compute "canopy_temperature" SoilCanopyModel Y.canopy.energy.T
 @land_compute "soil_ice" SoilCanopyModel top_center_to_surface(Y.soil.θ_i)
 @land_compute "soilco2" SoilCanopyModel Y.soilco2.C