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Iron proof of concept (scalar module) #352

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7 changes: 7 additions & 0 deletions src/Models/AdvectedPopulations/PISCES/common.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -64,3 +64,10 @@ end

return min(1, max(0, 0.4 * (min_1 - O₂) / (min_2 + O₂)))
end

@inline function anoxia_factor(O₂ₘᵢₙ₁, O₂ₘᵢₙ₂, O₂)
min_1 = O₂ₘᵢₙ₁
min_2 = O₂ₘᵢₙ₂

return min(1, max(0, 0.4 * (min_1 - O₂) / (min_2 + O₂)))
end
139 changes: 120 additions & 19 deletions src/Models/AdvectedPopulations/PISCES/dissolved_organic_matter/dissolved_organic_carbon.jl
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Expand Up @@ -53,26 +53,58 @@ required_biogeochemical_tracers(::DissolvedOrganicCarbon) = tuple(:DOC)
- dissolved_breakdown - aggregation_to_particles)
end

@inline function degradation(dom::DissolvedOrganicCarbon, i, j, k, grid, bgc, clock, fields, auxiliary_fields)
@inline function degradation(dom::DissolvedOrganicCarbon, T, DOC, Bact, LBact)
Bact_ref = dom.reference_bacteria_concentration
b = dom.temperature_sensitivity
λ = dom.remineralisation_rate

f = b^T

return λ * f * LBact * Bact / Bact_ref * DOC # differes from Aumont 2015 since the dimensions don't make sense
end

@inline function degradation(dom::DissolvedOrganicCarbon, i, j, k, grid, bgc, clock, fields, auxiliary_fields)
T = @inbounds fields.T[i, j, k]
DOC = @inbounds fields.DOC[i, j, k]

f = b^T

Bact = bacteria_concentration(bgc.zooplankton, i, j, k, grid, bgc, clock, fields, auxiliary_fields)

LBact = bacteria_activity(bgc.zooplankton, i, j, k, grid, bgc, clock, fields, auxiliary_fields)

return λ * f * LBact * Bact / Bact_ref * DOC # differs from Aumont 2015 since the dimensions don't make sense
return degradation(dom, T, DOC, Bact, LBact)
end

@inline function aggregation(dom::DissolvedOrganicCarbon, i, j, k, grid, bgc, clock, fields, auxiliary_fields)
@inline function aggregation(a₁,
a₂,
a₃,
a₄,
a₅,
z,
zₘₓₗ,
background_shear,
mixed_layer_shear,
DOC,
POC,
GOC)

shear = ifelse(z < zₘₓₗ, background_shear, mixed_layer_shear)

Φ₁ = shear * (a₁ * DOC + a₂ * POC) * DOC
Φ₂ = shear * (a₃ * GOC) * DOC
Φ₃ = (a₄ * POC + a₅ * DOC) * DOC

return Φ₁ + Φ₂ + Φ₃, Φ₁, Φ₂, Φ₃
end

@inline function aggregation(dom::DissolvedOrganicCarbon, z, zₘₓₗ, background_shear, mixed_layer_shear, DOC, POC, GOC)
a₁, a₂, a₃, a₄, a₅ = dom.aggregation_parameters

return aggregation(a₁, a₂, a₃, a₄, a₅,
z, zₘₓₗ, background_shear, mixed_layer_shear,
DOC, POC, GOC)
end

@inline function aggregation(dom::DissolvedOrganicCarbon, i, j, k, grid, bgc, clock, fields, auxiliary_fields)
background_shear = bgc.background_shear
mixed_layer_shear = bgc.mixed_layer_shear

Expand All @@ -84,31 +116,100 @@ end
POC = @inbounds fields.POC[i, j, k]
GOC = @inbounds fields.GOC[i, j, k]

shear = ifelse(z < zₘₓₗ, background_shear, mixed_layer_shear)

Φ₁ = shear * (a₁ * DOC + a₂ * POC) * DOC
Φ₂ = shear * (a₃ * GOC) * DOC
Φ₃ = (a₄ * POC + a₅ * DOC) * DOC

return Φ₁ + Φ₂ + Φ₃, Φ₁, Φ₂, Φ₃
return aggregation(dom, z, zₘₓₗ, background_shear, mixed_layer_shear, DOC, POC, GOC)
end

@inline function aggregation_of_colloidal_iron(dom::DissolvedOrganicCarbon, i, j, k, grid, bgc, clock, fields, auxiliary_fields)
_, Φ₁, Φ₂, Φ₃ = aggregation(dom, i, j, k, grid, bgc, clock, fields, auxiliary_fields)

Fe = @inbounds fields.Fe[i, j, k]
DOC = @inbounds fields.DOC[i, j, k]
@inline function aggregation_of_colloidal_iron(a₁,
a₂,
a₃,
a₄,
a₅,
background_shear,
mixed_layer_shear,
z,
zₘₓₗ,
Fe,
Fe′,
DOC,
POC,
GOC)

_, Φ₁, Φ₂, Φ₃ = aggregation(a₁,
a₂,
a₃,
a₄,
a₅,
z,
zₘₓₗ,
background_shear,
mixed_layer_shear,
DOC,
POC,
GOC)

Fe′ = free_iron(bgc.iron, i, j, k, grid, bgc, clock, fields, auxiliary_fields)
ligand_iron = Fe - Fe′
colloidal_iron = 0.5 * ligand_iron

CgFe1 = (Φ₁ + Φ₃) * colloidal_iron / (DOC + eps(0.0))
CgFe2 = Φ₂ * colloidal_iron / (DOC + eps(0.0))

return CgFe1 + CgFe2, CgFe1, CgFe2
end

@inline function aggregation_of_colloidal_iron(dom::DissolvedOrganicCarbon,
background_shear,
mixed_layer_shear,
z,
zₘₓₗ,
Fe,
Fe′,
DOC,
POC,
GOC)

a₁, a₂, a₃, a₄, a₅ = dom.aggregation_parameters

return aggregation_of_colloidal_iron(a₁, a₂, a₃, a₄, a₅,
background_shear,
mixed_layer_shear,
z,
zₘₓₗ,
Fe,
Fe′,
DOC,
POC,
GOC)
end

@inline function aggregation_of_colloidal_iron(dom::DissolvedOrganicCarbon, i, j, k, grid, bgc, clock, fields, auxiliary_fields)

background_shear = bgc.background_shear
mixed_layer_shear = bgc.mixed_layer_shear

z = znode(i, j, k, grid, Center(), Center(), Center())

zₘₓₗ = @inbounds auxiliary_fields.zₘₓₗ[i, j, k]


Fe = @inbounds fields.Fe[i, j, k]
Fe′ = free_iron(bgc.iron, i, j, k, grid, bgc, clock, fields, auxiliary_fields)

DOC = @inbounds fields.DOC[i, j, k]
POC = @inbounds fields.POC[i, j, k]
GOC = @inbounds fields.GOC[i, j, k]


return aggregation_of_colloidal_iron(dom,
background_shear,
mixed_layer_shear,
z,
zₘₓₗ,
Fe,
Fe′,
DOC,
POC,
GOC)
end

@inline function oxic_remineralisation(dom::DissolvedOrganicCarbon, i, j, k, grid, bgc, clock, fields, auxiliary_fields)
O₂ = @inbounds fields.O₂[i, j, k]

Expand Down
38 changes: 29 additions & 9 deletions src/Models/AdvectedPopulations/PISCES/iron/iron.jl
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Original file line number Diff line number Diff line change
@@ -1,39 +1,59 @@
module Iron

export SimpleIron
export SimpleIron, IronTendencyArgs

using Oceananigans.Units
using Oceananigans.Grids: znode, Center

using OceanBioME.Models.PISCESModel: PISCES
using OceanBioME.Models.PISCESModel: PISCES, anoxia_factor

using OceanBioME.Models.PISCESModel.DissolvedOrganicMatter:
aggregation_of_colloidal_iron, degradation

using OceanBioME.Models.PISCESModel.ParticulateOrganicMatter:
iron_scavenging, iron_scavenging_rate, bacterial_iron_uptake
iron_scavenging, iron_scavenging_rate, bacterial_iron_uptake,
specific_degradation_rate, edible_flux_rate, edible_iron_flux_rate

using OceanBioME.Models.PISCESModel.Phytoplankton: uptake

using OceanBioME.Models.PISCESModel.Zooplankton:
non_assimilated_iron, upper_trophic_dissolved_iron
non_assimilated_iron, upper_trophic_dissolved_iron,
bacteria_concentration, bacteria_activity

import Oceananigans.Biogeochemistry: required_biogeochemical_tracers
import OceanBioME.Models.PISCESModel: free_iron

include("simple_iron.jl")

@inline function free_iron(::SimpleIron, i, j, k, grid, bgc, clock, fields, auxiliary_fields)
DOC = @inbounds fields.DOC[i, j, k]
Fe = @inbounds fields.Fe[i, j, k]
@inline function ligand_concentration(iron::SimpleIron, DOC)
Lₜᵐᵃˣ = iron.maximum_ligand_concentration
Lₜ = iron.dissolved_ligand_ratio * DOC - Lₜᵐᵃˣ

return max(Lₜᵐᵃˣ, Lₜ)
end

T = @inbounds fields.T[i, j, k]
@inline function ligand_aggregation(iron::SimpleIron, Fe, DOC, T, scavenging_rate)
Lₜ = ligand_concentration(iron, DOC)
Fe′ = free_iron(iron, Fe, DOC, T)
ΔFe = max(zero(Fe), Fe - Lₜ)

return iron.excess_scavenging_enhancement * scavenging_rate * ΔFe * Fe′
end

# maybe some of these numbers should be parameters
@inline function free_iron(::SimpleIron, Fe, DOC, T)
ligands = max(0.6, 0.09 * (DOC + 40) - 3)
K = exp(16.27 - 1565.7 / max(T + 273.15, 5))
Δ = 1 + K * ligands - K * Fe

return (-Δ + √(Δ^2 + 4K * Fe)) / 2K
end

@inline function free_iron(iron::SimpleIron, i, j, k, grid, bgc, clock, fields, auxiliary_fields)
DOC = @inbounds fields.DOC[i, j, k]
Fe = @inbounds fields.Fe[i, j, k]
T = @inbounds fields.T[i, j, k]

return free_iron(iron, Fe, DOC, T)
end

end # module
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