From 07245f92cafbe75c6938d134bba4243b62e9be39 Mon Sep 17 00:00:00 2001
From: Alexis Renchon <a.renchon@gmail.com>
Date: Wed, 7 Aug 2024 13:08:56 -0700
Subject: [PATCH] WIP

---
 .../Vegetation/solar_induced_fluorescence.jl  | 58 +++++++++++++------
 1 file changed, 41 insertions(+), 17 deletions(-)

diff --git a/src/standalone/Vegetation/solar_induced_fluorescence.jl b/src/standalone/Vegetation/solar_induced_fluorescence.jl
index 40379aff88..f780952ec8 100644
--- a/src/standalone/Vegetation/solar_induced_fluorescence.jl
+++ b/src/standalone/Vegetation/solar_induced_fluorescence.jl
@@ -9,25 +9,49 @@ The required parameters for the SIF parameterisation
 Lee et al, 2015. Global Change Biology 21, 3469-3477, doi:10.1111/gcb.12948.
 $(DocStringExtensions.FIELDS)
 """
-@kwdef struct SIFParameters{FT <: AbstractFloat}
+Base.@kwdef struct SIFParameters{FT <: AbstractFloat}
     "The rate coefficient for florescence, unitless"
-    kf::FT = FT(0.05)
+    kf::FT
     "Parameter used to compute the rate coefficient for heat loss in dark-adapted conditions, Tol et al. 2014, unitless"
-    kd_p1::FT = FT(0.03)
+    kd_p1::FT
     "Parameter used to compute the rate coefficient for heat loss in dark-adapted conditions, Tol et al. 2014, unitless"
-    kd_p2::FT = FT(0.0273)
+    kd_p2::FT
     "Parameter used to compute the rate coefficient for heat loss in dark-adapted conditions, Tol et al. 2014, unitless"
-    min_kd::FT = FT(0.087)
+    min_kd::FT
     "Parameter used to compute the rate coefficient for heat loss in light-adapted conditions, Lee et al 2013 (unitless)"
-    kn_p1::FT = FT(6.2473)
+    kn_p1::FT
     "Parameter used to compute the rate coefficient for heat loss in light-adapted conditions, Lee et al 2013 (unitless)"
-    kn_p2::FT = FT(0.5944)
+    kn_p2::FT
     "Rate coefficient for photochemical quenching"
-    kp::FT = FT(4.0)
+    kp::FT
     "Slope of line relating leaf-level fluorescence to spectrometer-observed fluorescence as a function of Vcmax 25. Lee et al 2015."
-    kappa_p1::FT = FT(0.045)
+    kappa_p1::FT
     "Intercept of line relating leaf-level fluorescence to spectrometer-observed fluorescence as a function of Vcmax 25.  Lee et al 2015."
-    kappa_p2::FT = FT(7.85)
+    kappa_p2::FT
+end
+
+function SIFParameters{FT}(;
+    kf = FT(0.05),
+    kd_p1 = FT(0.03),
+    kd_p2 = FT(0.0273),
+    min_kd = FT(0.087),
+    kn_p1 = FT(6.2473),
+    kn_p2 = FT(0.5944),
+    kp = FT(4.0),
+    kappa_p1 = FT(0.045),
+    kappa_p2 = FT(7.85),
+    ) where {FT}
+    return SIFParameters{FT}(
+                         kf,
+                         kd_p1,
+                         kd_p2,
+                         min_kd,
+                         kn_p1,
+                         kn_p2,
+                         kp,
+                         kappa_p1,
+                         kappa_p2,
+                        )
 end
 
 Base.eltype(::SIFParameters{FT}) where {FT} = FT
@@ -51,14 +75,14 @@ ClimaLand.auxiliary_domain_names(::Lee2015SIFModel) = (:surface,)
 # call function below inside photosynthesis.jl p
 
 function compute_SIF_at_a_point(
-    APAR,
-    Tc,
-    Vcmax25,
-    R,
-    T_freeze,
+    APAR::FT,
+    Tc::FT,
+    Vcmax25::FT,
+    R::FT,
+    T_freeze::FT,
     photosynthesis_parameters,
     sif_parameters,
-)
+) where {FT}
     (; ΔHJmax, To, θj, ϕ) = photosynthesis_parameters
     Jmax = max_electron_transport(Vcmax25, ΔHJmax, Tc, To, R)
     J = electron_transport(APAR, Jmax, θj, ϕ)
@@ -70,7 +94,7 @@ function compute_SIF_at_a_point(
     ϕp0 = kp / (kf + kp + kn)
     ϕp = J / Jmax * ϕp0
     ϕf = kf / (kf + kd + kn) * (1 - ϕp)
-    κ = kappa_p1 * Vcmax25 * FT(1000000.0) + kappa_p2 # formula expects Vcmax25 in μmol/m^2/s
+    κ = kappa_p1 * Vcmax25 * FT(1e6) + kappa_p2 # formula expects Vcmax25 in μmol/m^2/s
     F = APAR * ϕf
     SIF_755 = F / κ