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Fixs data assimilation example #215

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merged 5 commits into from
Oct 2, 2024
Merged

Fixs data assimilation example #215

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23acff2
Update data_assimilation.jl
jagoosw Sep 20, 2024
bfaed62
Update data_assimilation.jl
jagoosw Sep 20, 2024
8afa9ad
Update data_assimilation.jl
jagoosw Sep 24, 2024
8c7bef7
oops
jagoosw Sep 30, 2024
f8436e0
Bump patch
jagoosw Oct 1, 2024
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2 changes: 1 addition & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
@@ -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"
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14 changes: 10 additions & 4 deletions examples/data_assimilation.jl
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Expand Up @@ -24,6 +24,8 @@ using Distributions
using EnsembleKalmanProcesses
using EnsembleKalmanProcesses.ParameterDistributions

using Oceananigans.Fields: FunctionField

const year = years = 365day

rng_seed = 41
Expand All @@ -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)

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