added instant reminerlaisation and tests

OceanBioME · Jan 2, 2025 · 30db3ce · 30db3ce
1 parent f18ea41
commit 30db3ce
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Showing 8 changed files with 109 additions and 189 deletions.
diff --git a/src/Models/Models.jl b/src/Models/Models.jl
@@ -1,6 +1,6 @@
 module Models
 
-export Sediments
+export InstantRemineralisationSediment
 
 export NPZD, 
        NutrientPhytoplanktonZooplanktonDetritus, 

diff --git a/src/Models/Sediments/instant_remineralization.jl b/src/Models/Sediments/instant_remineralization.jl
@@ -47,18 +47,18 @@ sediment_model = InstantRemineralisation(grid)
 ```
 """
 InstantRemineralisationSediment(grid;
-                                sinking_tracers = :D, 
+                                sinking_tracers = (:P, :D), 
                                 remineralisation_reciever = :N,
                                 burial_efficiency_constant1 = 0.013,
                                 burial_efficiency_constant2 = 0.53,
-                                burial_efficiency_half_saturation = 7.0,
+                                burial_efficiency_half_saturation = 7.0 / 6.56,
                                 kwargs...) =
     BiogeochemicalSediment(grid, 
                            InstantRemineralisation(burial_efficiency_constant1, 
                                                    burial_efficiency_constant2, 
                                                    burial_efficiency_half_saturation,
                                                    tracernames(sinking_tracers),
-                                                   remineralisation_reciever), 
+                                                   remineralisation_reciever);
                            kwargs...)
 
 @inline required_sediment_fields(::InstantRemineralisation) = (:storage, )
@@ -71,27 +71,23 @@ InstantRemineralisationSediment(grid;
     b = s.burial_efficiency_constant2
     k = s.burial_efficiency_half_saturation
 
-    total_sinking_flux = sum(args)
+    flux = @inbounds sum(args[2:end])
 
-    carbon_flux = total_sinking_flux * 6.56
-
-    burial_efficiency = a + b * (carbon_flux / (k + carbon_flux)) ^ 2
-
-    return burial_efficiency * total_sinking_flux
+    burial_efficiency = a + b * (flux / (k + flux)) ^ 2
+
+    return burial_efficiency * flux
 end
 
 @inline function remineralisation(s::InstantRemineralisation, x, y, t, args...)
     a = s.burial_efficiency_constant1
     b = s.burial_efficiency_constant2
     k = s.burial_efficiency_half_saturation
 
-    total_sinking_flux = sum(args)
-
-    carbon_flux = total_sinking_flux * 6.56
+    flux = @inbounds sum(args[2:end])
 
-    burial_efficiency = a + b * (carbon_flux / (k + carbon_flux)) ^ 2
+    burial_efficiency = a + b * (flux / (k + flux)) ^ 2
 
-    return (1 - burial_efficiency) * total_sinking_flux
+    return (1 - burial_efficiency) * flux
 end
 
 function add_remineralisation_methods!(remineralisation_reciever; fname = remineralisation)

diff --git a/src/OceanBioME.jl b/src/OceanBioME.jl
@@ -6,6 +6,7 @@ module OceanBioME
 
 # Biogeochemistry models and useful things
 export Biogeochemistry, LOBSTER, PISCES, NutrientPhytoplanktonZooplanktonDetritus, NPZD, redfield
+export InstantRemineralisationSediment
 export DepthDependantSinkingSpeed, PrescribedLatitude, ModelLatitude, PISCESModel
 
 # Macroalgae models

diff --git a/src/Sediments/Sediments.jl b/src/Sediments/Sediments.jl
@@ -32,11 +32,15 @@ end
 @inline sinking_fluxs(s::BiogeochemicalSediment) = sinking_fluxs(s.biogeochemistry)
 @inline coupled_tracers(s::BiogeochemicalSediment) = coupled_tracers(s.biogeochemistry)
 
+abstract type AbstractSedimentBiogeochemistry end
+abstract type AbstractContinuousFormSedimentBiogeochemistry <: AbstractSedimentBiogeochemistry end
+
+const ACFSBGC = AbstractContinuousFormSedimentBiogeochemistry
+
 include("timesteppers.jl")
 include("bottom_indices.jl")
 include("tracked_fields.jl")
 include("update_state.jl")
-include("sediment_biogeochemistries.jl")
 include("compute_tendencies.jl")
 include("tracer_coupling.jl")
 

diff --git a/src/Sediments/compute_tendencies.jl b/src/Sediments/compute_tendencies.jl
@@ -3,7 +3,9 @@ using Oceananigans.Fields: Center
 using Oceananigans.Grids: xnode, ynode
 
 function compute_sediment_tendencies!(model)
-    fields = prognostic_fields(model)
+    field_names = required_sediment_fields(model)
+
+    sediment_fields = model.fields
     tracked_fields = model.tracked_fields
 
     grid = model.grid
@@ -15,10 +17,10 @@ function compute_sediment_tendencies!(model)
 
     arch = architecture(grid)
 
-    for (field_name, field) in pairs(fields)
+    for field_name in field_names
         G = Gⁿ[field_name]
 
-        args = (Val(field_name), biogeochemistry, fields, tracked_fields, clock)
+        args = (Val(field_name), biogeochemistry, sediment_fields, tracked_fields, clock)
 
         launch!(arch, grid, :xy, compute_sediment_tendency!, G, grid, args)
     end

diff --git a/src/Sediments/sediment_biogeochemistries.jl b/src/Sediments/sediment_biogeochemistries.jl
diff --git a/src/Sediments/update_state.jl b/src/Sediments/update_state.jl
@@ -9,7 +9,7 @@ function update_biogeochemical_state!(model, sediment_model::BiogeochemicalSedim
     update_tracked_fields!(sediment_model, model)
 
     if isfinite(Δt)
-        time_step!(sediment_model, Δt)
+        time_step!(sediment_model, Δt;)
     end
 
     return nothing