Merge branch 'main' into jsw/bump-oceananigans-0.90

Project.toml

@@ -13,7 +13,7 @@ StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
 
 [compat]
 Adapt = "3"
-Documenter = "0.27"
+Documenter = "1"
 JLD2 = "0.4"
 KernelAbstractions = "0.9"
 Oceananigans = "0.90"

docs/make.jl

@@ -59,10 +59,10 @@ model_parameters = (LOBSTER(; grid = BoxModelGrid()),
                     GasExchange(; gas = :CO₂).condition.func,
                     GasExchange(; gas = :O₂).condition.func)
 
-gas_exchange_gas(::Val{G}) where G = G
+exchanged_gas(::Val{G}) where G = G
 
 model_name(model) = if Base.typename(typeof(model)).wrapper == GasExchange
-                        "$(gas_exchange_gas(model.gas)) air-sea exchange"
+                        "$(exchanged_gas(model.gas)) air-sea exchange"
                     else
                         Base.typename(typeof(model)).wrapper
                     end

docs/src/model_components/biogeochemical/LOBSTER.md

@@ -12,17 +12,11 @@ julia> using OceanBioME, Oceananigans
 julia> grid = RectilinearGrid(size=(3, 3, 30), extent=(10, 10, 200));
 
 julia> bgc_model = LOBSTER(; grid, carbonates = true)
-Lodyc-DAMTP Ocean Biogeochemical Simulation Tools for Ecosystem and Resources (LOBSTER) model (Float64) 
- Optional components:
-    ├── Carbonates ✅ 
-    ├── Oxygen ❌ 
-    └── Variable Redfield Ratio ❌
- Sinking Velocities:
-    ├── sPOM: 0.0 to -3.47e-5 m/s 
-    └── bPOM: 0.0 to -0.0023148148148148147 m/s 
+LOBSTER{Float64} with carbonates ✅, oxygen ❌, variable Redfield ratio ❌and (:sPOM, :bPOM) sinking 
  Light attenuation: Two-band light attenuation model (Float64)
  Sediment: Nothing
  Particles: Nothing
+ Modifiers: Nothing
 ```
 
 ## Model equations

src/Light/2band.jl

@@ -109,8 +109,7 @@ function TwoBandPhotosyntheticallyActiveRadiation(; grid,
 
     field = CenterField(grid; boundary_conditions = 
                             regularize_field_boundary_conditions(
-                            FieldBoundaryConditions(top = ValueBoundaryCondition(surface_PAR)),
-                            grid, :PAR))
+                                FieldBoundaryConditions(top = ValueBoundaryCondition(surface_PAR)), grid, :PAR))
 
     return TwoBandPhotosyntheticallyActiveRadiation(water_red_attenuation,
                                                     water_blue_attenuation,

src/Models/AdvectedPopulations/LOBSTER/LOBSTER.jl

@@ -246,17 +246,11 @@ julia> using Oceananigans
 julia> grid = RectilinearGrid(size=(3, 3, 30), extent=(10, 10, 200));
 
 julia> model = LOBSTER(; grid)
-Lodyc-DAMTP Ocean Biogeochemical Simulation Tools for Ecosystem and Resources (LOBSTER) model (Float64) 
- Optional components:
-    ├── Carbonates ❌ 
-    ├── Oxygen ❌ 
-    └── Variable Redfield Ratio ❌
- Sinking Velocities:
-    ├── sPOM: 0.0 to -3.47e-5 m/s 
-    └── bPOM: 0.0 to -0.0023148148148148147 m/s 
+LOBSTER{Float64} with carbonates ❌, oxygen ❌, variable Redfield ratio ❌and (:sPOM, :bPOM) sinking 
  Light attenuation: Two-band light attenuation model (Float64)
  Sediment: Nothing
  Particles: Nothing
+ Modifiers: Nothing
 ```
 """
 function LOBSTER(; grid,
@@ -353,7 +347,13 @@ function LOBSTER(; grid,
 
     if scale_negatives
         scaler = ScaleNegativeTracers(underlying_biogeochemistry, grid)
-        modifiers = isnothing(modifiers) ? scaler : (modifiers..., scaler)
+        if isnothing(modifiers)
+            modifiers = scaler
+        elseif modifiers isa Tuple
+            modifiers = (modifiers..., scaler)
+        else
+            modifiers = (modifiers, scaler)
+        end
     end
 
     return Biogeochemistry(underlying_biogeochemistry;
@@ -432,14 +432,14 @@ adapt_structure(to, lobster::LOBSTER) =
             adapt(to, lobster.optionals),
             adapt(to, lobster.sinking_velocities))
 
-summary(::LOBSTER{FT, B, W}) where {FT, B, W} = string("Lodyc-DAMTP Ocean Biogeochemical Simulation Tools for Ecosystem and Resources (LOBSTER) model ($FT)")
+summary(::LOBSTER{FT, Val{B}, NamedTuple{K, V}}) where {FT, B, K, V} = string("LOBSTER{$FT} with carbonates $(B[1] ? :✅ : :❌), oxygen $(B[2] ? :✅ : :❌), variable Redfield ratio $(B[3] ? :✅ : :❌)and $K sinking")
 
-show(io::IO, model::LOBSTER{FT, Val{B}, W}) where {FT, B, W}  = string(summary(model), " \n",
-                                                                       " Optional components:", "\n",
-                                                                       "    ├── Carbonates $(B[1] ? :✅ : :❌) \n",
-                                                                       "    ├── Oxygen $(B[2] ? :✅ : :❌) \n",
-                                                                       "    └── Variable Redfield Ratio $(B[3] ? :✅ : :❌)", "\n",
-                                                                       " Sinking Velocities:", "\n", show_sinking_velocities(model.sinking_velocities))
+show(io::IO, model::LOBSTER{FT, Val{B}, W}) where {FT, B, W}  = print(io, string("Lodyc-DAMTP Ocean Biogeochemical Simulation Tools for Ecosystem and Resources (LOBSTER) model \n",
+                                                                                 "├── Optional components:", "\n",
+                                                                                 "│   ├── Carbonates $(B[1] ? :✅ : :❌) \n",
+                                                                                 "│   ├── Oxygen $(B[2] ? :✅ : :❌) \n",
+                                                                                 "│   └── Variable Redfield Ratio $(B[3] ? :✅ : :❌)", "\n",
+                                                                                 "└── Sinking Velocities:", "\n", show_sinking_velocities(model.sinking_velocities)))
 
 @inline maximum_sinking_velocity(bgc::LOBSTER) = maximum(abs, bgc.sinking_velocities.bPOM.w)
 

src/Models/AdvectedPopulations/NPZD.jl

@@ -145,14 +145,11 @@ julia> using Oceananigans
 julia> grid = RectilinearGrid(size=(20, 30), extent=(200, 200), topology=(Bounded, Flat, Bounded));
 
 julia> model = NutrientPhytoplanktonZooplanktonDetritus(; grid)
-Nutrient Phytoplankton Zooplankton Detritus model (Float64) 
- Sinking Velocities:
-    ├── P: 0.0 to -2.9525462962962963e-6 m/s 
-    └── D: 0.0 to -3.181597222222222e-5 m/s 
+NutrientPhytoplanktonZooplanktonDetritus{Float64} model, with (:P, :D) sinking 
  Light attenuation: Two-band light attenuation model (Float64)
  Sediment: Nothing
  Particles: Nothing
-
+ Modifiers: Nothing
 ```
 """
 function NutrientPhytoplanktonZooplanktonDetritus(; grid,
@@ -297,9 +294,9 @@ function update_boxmodel_state!(model::BoxModel{<:Biogeochemistry{<:NPZD}, <:Any
     getproperty(model.values, :T) .= model.forcing.T(model.clock.time)
 end
 
-summary(::NPZD{FT, W}) where {FT, W} = string("Nutrient Phytoplankton Zooplankton Detritus model ($FT)")
-show(io::IO, model::NPZD) = string(summary(model), " \n",
-                                   " Sinking Velocities:", "\n", show_sinking_velocities(model.sinking_velocities))
+summary(::NPZD{FT, NamedTuple{K, V}}) where {FT, K, V} = string("NutrientPhytoplanktonZooplanktonDetritus{$FT} model, with $K sinking")
+show(io::IO, model::NPZD{FT}) where {FT} = print(io, string("NutrientPhytoplanktonZooplanktonDetritus{$FT} model \n",
+                                                            "└── Sinking Velocities:", "\n", show_sinking_velocities(model.sinking_velocities)))
 
 @inline maximum_sinking_velocity(bgc::NPZD) = maximum(abs, bgc.sinking_velocities.D.w)
 

src/OceanBioME.jl

@@ -163,10 +163,13 @@ conserved_tracers(model::Biogeochemistry) = conserved_tracers(model.underlying_b
 
 summary(bgc::Biogeochemistry) = string("Biogeochemical model based on $(summary(bgc.underlying_biogeochemistry))")
 show(io::IO, model::Biogeochemistry) =
-       print(io, show(model.underlying_biogeochemistry), " \n",
+       print(io, summary(model.underlying_biogeochemistry), " \n",
                 " Light attenuation: ", summary(model.light_attenuation), "\n",
                 " Sediment: ", summary(model.sediment), "\n",
-                " Particles: ", summary(model.particles))
+                " Particles: ", summary(model.particles), "\n",
+                " Modifiers: ", summary(model.modifiers))
+
+summary(modifiers::Tuple) = tuple([summary(modifier) for modifier in modifiers])
 
 include("Utils/Utils.jl")
 include("Boundaries/Boundaries.jl")

src/Utils/negative_tracers.jl

@@ -6,6 +6,7 @@ using Oceananigans.Architectures: device, architecture, arch_array
 using Oceananigans.Biogeochemistry: AbstractBiogeochemistry
 
 import Adapt: adapt_structure, adapt
+import Base: summary, show
 import Oceananigans.Biogeochemistry: update_tendencies!, update_biogeochemical_state!
 
 """
@@ -84,6 +85,10 @@ function ScaleNegativeTracers(bgc::AbstractBiogeochemistry, grid; warn = false)
     return ScaleNegativeTracers(tracers, scalefactors, warn)
 end
 
+summary(scaler::ScaleNegativeTracers) = string("Mass conserving negative scaling of $(scaler.tracers)")
+show(io::IO, scaler::ScaleNegativeTracers) = print(io, string(summary(scaler), "\n",
+                                                          "└── Scalefactors: $(scaler.scalefactors)"))
+
 function update_biogeochemical_state!(model, scale::ScaleNegativeTracers)
     workgroup, worksize = work_layout(model.grid, :xyz)