Merge pull request #215 from OceanBioME/jsw/fix-data-assimilation-exa…

…mple Fixs data assimilation example
OceanBioME · Oct 2, 2024 · daebb41 · daebb41 · jagoosw · Oct 2, 2024
2 parents 3c287d6 + f8436e0
commit daebb41
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Showing 2 changed files with 11 additions and 5 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "OceanBioME"
 uuid = "a49af516-9db8-4be4-be45-1dad61c5a376"
 authors = ["Jago Strong-Wright <[email protected]> and contributors"]
-version = "0.11.1"
+version = "0.11.2"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

diff --git a/examples/data_assimilation.jl b/examples/data_assimilation.jl
@@ -24,6 +24,8 @@ using Distributions
 using EnsembleKalmanProcesses
 using EnsembleKalmanProcesses.ParameterDistributions
 
+using Oceananigans.Fields: FunctionField
+
 const year = years = 365day
 
 rng_seed = 41
@@ -34,22 +36,26 @@ rng = Random.MersenneTwister(rng_seed)
 @inline PAR⁰(t) = 60 * (1 - cos((t + 15days) * 2π / year)) * (1 / (1 + 0.2 * exp(-((mod(t, year) - 200days) / 50days)^2))) + 2
 
 z = -10 # nominal depth of the box for the PAR profile
-@inline PAR(t) = PAR⁰(t) * exp(0.2z) # Modify the PAR based on the nominal depth and exponential decay 
+@inline PAR_func(t) = PAR⁰(t) * exp(0.2z) # Modify the PAR based on the nominal depth and exponential decay 
 
 function run_box_simulation(initial_photosynthetic_slope,
                             base_maximum_growth,
                             nutrient_half_saturation,
                             phyto_base_mortality_rate,
                             j)
+    grid = BoxModelGrid()
+    clock = Clock(; time = zero(grid))
 
-    biogeochemistry = NutrientPhytoplanktonZooplanktonDetritus(; grid = BoxModelGrid(),
+    PAR = FunctionField{Center, Center, Center}(PAR_func, grid; clock)
+
+    biogeochemistry = NutrientPhytoplanktonZooplanktonDetritus(; grid,
                                                                  initial_photosynthetic_slope,
                                                                  base_maximum_growth,
                                                                  nutrient_half_saturation,
                                                                  phyto_base_mortality_rate,
-                                                                 light_attenuation_model = nothing)
+                                                                 light_attenuation_model = PrescribedPhotosyntheticallyActiveRadiation(PAR))
 
-    model = BoxModel(; biogeochemistry, forcing = (; PAR))
+    model = BoxModel(; biogeochemistry, clock)
 
     set!(model, N = 10.0, P = 0.1, Z = 0.01)