From c45e5ec77b57ebae09866f3098c935ce0125e21e Mon Sep 17 00:00:00 2001
From: AlexisRenchon <a.renchon@gmail.com>
Date: Mon, 19 Aug 2024 15:17:48 -0700
Subject: [PATCH] All CO2 fluxes in mol CO2 m-2 s-1

There was some inconsistencies, as well as some bug in the code,
because of sometimes expressing CO2 fluxes in gC m-2 s-1,
and sometimes in mol CO2 m-2 s-1.
In this PR, we express all CO2 fluxes in mol CO2 m-2 s-1.
Note: the parameter "f1" (:mol_CO2_to_kg_C_factor) from
AutotrophicRespirationParameters has been removed,
and the parameter "f2" (:relative_contribution_factor)
renamed to "f". This change is also happening in ClimaParams.jl

Co-authored-by: AlexisRenchon <a.renchon@gmail.com>
Co-authored-by: kmdeck <kdeck@caltech.edu>
---
 ext/CreateParametersExt.jl                          |  3 +--
 .../Vegetation/autotrophic_respiration.jl           | 13 ++++++-------
 .../Vegetation/canopy_parameterizations.jl          |  8 +++-----
 3 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/ext/CreateParametersExt.jl b/ext/CreateParametersExt.jl
index 514495916b..e501cabc35 100644
--- a/ext/CreateParametersExt.jl
+++ b/ext/CreateParametersExt.jl
@@ -96,8 +96,7 @@ function AutotrophicRespirationParameters(
         :live_stem_wood_coeff => :ηsl,
         :specific_leaf_density => :σl,
         :root_leaf_nitrogen_ratio => :μr,
-        :mol_CO2_to_kg_C_factor => :f1,
-        :relative_contribution_factor => :f2,
+        :relative_contribution_factor => :f,
         :stem_leaf_nitrogen_ratio => :μs,
     )
     parameters = CP.get_parameter_values(toml_dict, name_map, "Land")
diff --git a/src/standalone/Vegetation/autotrophic_respiration.jl b/src/standalone/Vegetation/autotrophic_respiration.jl
index 78d73bb616..a56c585dcf 100644
--- a/src/standalone/Vegetation/autotrophic_respiration.jl
+++ b/src/standalone/Vegetation/autotrophic_respiration.jl
@@ -22,10 +22,8 @@ Base.@kwdef struct AutotrophicRespirationParameters{FT <: AbstractFloat}
     μr::FT
     "Ratio stem nitrogen to top leaf nitrogen (-), typical value 0.1"
     μs::FT
-    "Factor to convert from mol CO2 to kg C"
-    f1::FT
     "Factor of relative contribution or Rgrowth (-)"
-    f2::FT
+    f::FT
 end
 
 Base.eltype(::AutotrophicRespirationParameters{FT}) where {FT} = FT
@@ -73,7 +71,7 @@ ClimaLand.auxiliary_domain_names(::AutotrophicRespirationModel) = (:surface,)
                                   h,
                                  )
 
-Computes the autotrophic respiration as the sum of the plant maintenance
+Computes the autotrophic respiration (mol co2 m^-2 s^-1) as the sum of the plant maintenance
 and growth respirations, according to the JULES model.
 
 Clark, D. B., et al. "The Joint UK Land Environment Simulator (JULES), model description–Part 2: carbon fluxes and vegetation dynamics." Geoscientific Model Development 4.3 (2011): 701-722.
@@ -92,13 +90,14 @@ function compute_autrophic_respiration(
     h,
 )
 
-    (; ne, ηsl, σl, μr, μs, f1, f2) = model.parameters
+    (; ne, ηsl, σl, μr, μs, f) = model.parameters
     Nl, Nr, Ns =
         nitrogen_content(ne, Vcmax25, LAI, SAI, RAI, ηsl, h, σl, μr, μs)
-    Rpm = plant_respiration_maintenance(Rd, β, Nl, Nr, Ns, f1)
-    Rg = plant_respiration_growth(f2, An, Rpm)
+    Rpm = plant_respiration_maintenance(Rd, β, Nl, Nr, Ns)
+    Rg = plant_respiration_growth(f, An, Rpm)
     Ra = Rpm + Rg
     return Ra * (1 - exp(-K * LAI * Ω)) / (K * Ω) # adjust to canopy level
 end
 
 Base.broadcastable(model::AutotrophicRespirationModel) = tuple(model) # this is so that @. does not broadcast on Ref(canopy.autotrophic_respiration)
+
diff --git a/src/standalone/Vegetation/canopy_parameterizations.jl b/src/standalone/Vegetation/canopy_parameterizations.jl
index 6522c50d2f..75e8c0b84b 100644
--- a/src/standalone/Vegetation/canopy_parameterizations.jl
+++ b/src/standalone/Vegetation/canopy_parameterizations.jl
@@ -1007,7 +1007,6 @@ end
         Nl::FT, # Nitrogen content of leafs
         Nr::FT, # Nitrogen content of roots
         Ns::FT, # Nitrogen content of stems
-        f::FT # Factor to convert from mol CO2 to kg C
         ) where {FT}
 
 Computes plant maintenance respiration as a function of dark respiration (Rd),
@@ -1020,10 +1019,9 @@ function plant_respiration_maintenance(
     Nl::FT, # Nitrogen content of leafs
     Nr::FT, # Nitrogen content of roots
     Ns::FT, # Nitrogen content of stems
-    f1::FT, # Factor to convert from mol CO2 to kg C
 ) where {FT}
     # When LAI is zero, Nl = 0
-    Rpm = f1 * Rd * (β + (Nr + Ns) / max(Nl, eps(FT)))
+    Rpm = Rd * (β + (Nr + Ns) / max(Nl, eps(FT)))
     return Rpm
 end
 
@@ -1037,7 +1035,7 @@ end
 Computes plant growth respiration as a function of net photosynthesis (An),
 plant maintenance respiration (Rpm), and a relative contribution factor, f.
 """
-function plant_respiration_growth(f2::FT, An::FT, Rpm::FT) where {FT}
-    Rg = f2 * (An - Rpm)
+function plant_respiration_growth(f::FT, An::FT, Rpm::FT) where {FT}
+    Rg = f * (An - Rpm)
     return Rg
 end