Merge pull request #222 from OceanBioME/jsw/fix-hard-coded-number-types

Automatically change parameter and return float types

Project.toml

@@ -1,7 +1,7 @@
 name = "OceanBioME"
 uuid = "a49af516-9db8-4be4-be45-1dad61c5a376"
 authors = ["Jago Strong-Wright <[email protected]> and contributors"]
-version = "0.13.2"
+version = "0.13.3"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

docs/src/model_components/individuals/slatissima.md

@@ -14,7 +14,7 @@ using OceanBioME
 kelp_bgc = SugarKelp()
 
 # output
-SugarKelp{FT} biogeochemistry (Broch & Slagstad, 2012) tracking the `N`itrogen and `C`arbon in a frond of `A`rea
+SugarKelp{Float64} biogeochemistry (Broch & Slagstad, 2012) tracking the `N`itrogen and `C`arbon in a frond of `A`rea
 ```
 which can be put into `BiogeochemicalParticles`, or you can directly manifest particles:
 ```jldoctest
@@ -24,7 +24,7 @@ grid = RectilinearGrid(size = (1, 1, 1), extent = (1, 1, 1));
 particles = SugarKelpParticles(10; grid)
 
 # output
-10 BiogeochemicalParticles with SugarKelp{FT} biogeochemistry:
+10 BiogeochemicalParticles with SugarKelp{Float64} biogeochemistry:
 ├── fields: (:A, :N, :C)
 └── coupled tracers: (:NO₃, :NH₄, :DIC, :O₂, :DOC, :DON, :bPOC, :bPON)
 

src/Light/2band.jl

@@ -74,7 +74,7 @@ struct TwoBandPhotosyntheticallyActiveRadiation{FT, F, SPAR}
 end
 
 """
-    TwoBandPhotosyntheticallyActiveRadiation(; grid, 
+    TwoBandPhotosyntheticallyActiveRadiation(; grid::AbstractGrid{FT}, 
                                                water_red_attenuation::FT = 0.225, # 1/m
                                                water_blue_attenuation::FT = 0.0232, # 1/m
                                                chlorophyll_red_attenuation::FT = 0.037, # 1/(m * (mgChl/m³) ^ eʳ)
@@ -94,7 +94,7 @@ Keyword Arguments
    which should be `f(x, y, t)` where `x` and `y` are the native coordinates (i.e. meters for rectilinear grids
    and latitude/longitude as appropriate)
 """
-function TwoBandPhotosyntheticallyActiveRadiation(; grid, 
+function TwoBandPhotosyntheticallyActiveRadiation(; grid::AbstractGrid{FT}, 
                                                     water_red_attenuation::FT = 0.225, # 1/m
                                                     water_blue_attenuation::FT = 0.0232, # 1/m
                                                     chlorophyll_red_attenuation::FT = 0.037, # 1/(m * (mgChl/m³) ^ eʳ)

src/Light/Light.jl

@@ -13,7 +13,7 @@ using KernelAbstractions, Oceananigans.Units
 using Oceananigans.Architectures: device, architecture, on_architecture
 using Oceananigans.Utils: launch!
 using Oceananigans: Center, Face, fields
-using Oceananigans.Grids: node, znodes, znode
+using Oceananigans.Grids: node, znodes, znode, AbstractGrid
 using Oceananigans.Fields: CenterField, TracerFields, location
 using Oceananigans.BoundaryConditions: fill_halo_regions!, 
                                        ValueBoundaryCondition, 

src/Light/compute_euphotic_depth.jl

@@ -1,11 +1,11 @@
 using Oceananigans.Fields: ConstantField, ZeroField
 
-@kernel function _compute_euphotic_depth!(euphotic_depth, PAR, grid, cutoff)
+@kernel function _compute_euphotic_depth!(euphotic_depth, PAR, grid::AbstractGrid{FT}, cutoff) where FT
     i, j = @index(Global, NTuple)
 
     surface_PAR = @inbounds (PAR[i, j, grid.Nz] + PAR[i, j, grid.Nz + 1])/2
 
-    @inbounds euphotic_depth[i, j, 1] = -Inf
+    @inbounds euphotic_depth[i, j, 1] = convert(FT, -Inf)
 
     for k in grid.Nz-1:-1:1
         PARₖ = @inbounds PAR[i, j, k]

src/Light/multi_band.jl

@@ -37,7 +37,7 @@ struct MultiBandPhotosyntheticallyActiveRadiation{T, F, FN, K, E, C, SPAR, SPARD
 end
 
 """
-    MultiBandPhotosyntheticallyActiveRadiation(; grid, 
+    MultiBandPhotosyntheticallyActiveRadiation(; grid::AbstractGrid{FT}, 
                                                  bands = ((400, 500), (500, 600), (600, 700)), #nm
                                                  base_bands = MOREL_λ,
                                                  base_water_attenuation_coefficient = MOREL_kʷ,
@@ -65,15 +65,15 @@ Keyword Arguments
    and latitude/longitude as appropriate)
 
 """
-function MultiBandPhotosyntheticallyActiveRadiation(; grid, 
+function MultiBandPhotosyntheticallyActiveRadiation(; grid::AbstractGrid{FT}, 
                                                       bands = ((400, 500), (500, 600), (600, 700)), #nm
                                                       base_bands = MOREL_λ,
                                                       base_water_attenuation_coefficient = MOREL_kʷ,
                                                       base_chlorophyll_exponent = MOREL_e,
                                                       base_chlorophyll_attenuation_coefficient = MOREL_χ,
                                                       field_names = ntuple(n->par_symbol(n), Val(length(bands))),
                                                       surface_PAR = default_surface_PAR,
-                                                      surface_PAR_division = fill(1 / length(bands), length(bands)))
+                                                      surface_PAR_division = fill(1 / length(bands), length(bands))) where FT
     Nbands = length(bands)
 
     kʷ = zeros(eltype(grid), Nbands)
@@ -108,9 +108,9 @@ function MultiBandPhotosyntheticallyActiveRadiation(; grid,
     return MultiBandPhotosyntheticallyActiveRadiation(total_PAR,
                                                       fields, 
                                                       tuple(field_names...), 
-                                                      kʷ, 
-                                                      e, 
-                                                      χ, 
+                                                      convert.(FT, kʷ), 
+                                                      convert.(FT, e), 
+                                                      convert.(FT, χ), 
                                                       surface_PAR, 
                                                       surface_PAR_division)
 end

src/Models/AdvectedPopulations/LOBSTER/LOBSTER.jl

@@ -45,6 +45,7 @@ export LOBSTER
 
 using Oceananigans.Units
 using Oceananigans.Fields: Field, TracerFields, CenterField, ZeroField
+using Oceananigans.Grids: AbstractGrid
 
 using OceanBioME.Light: TwoBandPhotosyntheticallyActiveRadiation, default_surface_PAR
 using OceanBioME: setup_velocity_fields, show_sinking_velocities, Biogeochemistry, ScaleNegativeTracers
@@ -169,7 +170,7 @@ struct LOBSTER{FT, B, W} <: AbstractContinuousFormBiogeochemistry
 end
 
 """
-    LOBSTER(; grid,
+    LOBSTER(; grid::AbstractGrid{FT},
               phytoplankton_preference::FT = 0.5,
               maximum_grazing_rate::FT = 9.26e-6, # 1/s
               grazing_half_saturation::FT = 1.0, # mmol N/m³
@@ -254,7 +255,7 @@ LOBSTER{Float64} with carbonates ❌, oxygen ❌, variable Redfield ratio ❌ an
  Modifiers: Nothing
 ```
 """
-function LOBSTER(; grid,
+function LOBSTER(; grid::AbstractGrid{FT},
                    phytoplankton_preference::FT = 0.5,
                    maximum_grazing_rate::FT = 9.26e-6, # 1/s
                    grazing_half_saturation::FT = 1.0, # mmol N/m³
@@ -457,9 +458,9 @@ const VariableRedfieldLobster = Union{LOBSTER{<:Any, <:Val{(false, false, true)}
 
 @inline redfield(::Val{:P}, bgc::LOBSTER) = (1 + bgc.organic_carbon_calcate_ratio) * bgc.phytoplankton_redfield
 @inline redfield(::Val{:Z}, bgc::LOBSTER) = bgc.phytoplankton_redfield
-@inline redfield(::Union{Val{:NO₃}, Val{:NH₄}, Val{:Alk}, Val{:O₂}}, bgc::LOBSTER) = 0
+@inline redfield(::Union{Val{:NO₃}, Val{:NH₄}, Val{:Alk}, Val{:O₂}}, bgc::LOBSTER{FT}) where FT = convert(FT, 0)
 @inline redfield(::Union{Val{:sPOM}, Val{:bPOM}, Val{:DOM}}, bgc::LOBSTER) = bgc.organic_redfield
-@inline redfield(::Union{Val{:sPOC}, Val{:bPOC}, Val{:DOC}, Val{:DIC}}, bgc::LOBSTER) = 1
+@inline redfield(::Union{Val{:sPOC}, Val{:bPOC}, Val{:DOC}, Val{:DIC}}, bgc::LOBSTER{FT}) where FT = convert(FT, 1)
 
 @inline redfield(i, j, k, ::Val{:sPON}, bgc::VariableRedfieldLobster, tracers) = @inbounds tracers.sPOC[i, j, k] / tracers.sPON[i, j, k]
 @inline redfield(i, j, k, ::Val{:bPON}, bgc::VariableRedfieldLobster, tracers) = @inbounds tracers.bPOC[i, j, k] / tracers.bPON[i, j, k]

src/Models/AdvectedPopulations/NPZD.jl

@@ -21,6 +21,7 @@ using Oceananigans.Biogeochemistry: AbstractContinuousFormBiogeochemistry
 
 using Oceananigans.Units
 using Oceananigans.Fields: ZeroField
+using Oceananigans.Grids: AbstractGrid
 
 using OceanBioME.Light: TwoBandPhotosyntheticallyActiveRadiation, default_surface_PAR
 using OceanBioME: setup_velocity_fields, show_sinking_velocities
@@ -93,7 +94,7 @@ struct NutrientPhytoplanktonZooplanktonDetritus{FT, W} <: AbstractContinuousForm
 end
 
 """
-    NutrientPhytoplanktonZooplanktonDetritus(; grid,
+    NutrientPhytoplanktonZooplanktonDetritus(; grid::AbstractGrid{FT},
                                                initial_photosynthetic_slope::FT = 0.1953 / day, # 1/(W/m²)/s
                                                base_maximum_growth::FT = 0.6989 / day, # 1/s
                                                nutrient_half_saturation::FT = 2.3868, # mmol N/m³
@@ -154,7 +155,7 @@ NutrientPhytoplanktonZooplanktonDetritus{Float64} model, with (:P, :D) sinking
  Modifiers: Nothing
 ```
 """
-function NutrientPhytoplanktonZooplanktonDetritus(; grid,
+function NutrientPhytoplanktonZooplanktonDetritus(; grid::AbstractGrid{FT},
                                                     initial_photosynthetic_slope::FT = 0.1953 / day, # 1/(W/m²)/s
                                                     base_maximum_growth::FT = 0.6989 / day, # 1/s
                                                     nutrient_half_saturation::FT = 2.3868, # mmol N/m³
@@ -316,8 +317,8 @@ adapt_structure(to, npzd::NPZD) =
                                              adapt(to, npzd.sinking_velocities))
 
 @inline redfield(i, j, k, val_tracer_name, bgc::NPZD, tracers) = redfield(val_tracer_name, bgc)
-@inline redfield(::Union{Val{:N}}, bgc::NPZD) = 0
-@inline redfield(::Union{Val{:P}, Val{:Z}, Val{:D}}, bgc::NPZD) = 6.56
+@inline redfield(::Union{Val{:N}}, bgc::NPZD{FT}) where FT = convert(FT, 0)
+@inline redfield(::Union{Val{:P}, Val{:Z}, Val{:D}}, bgc::NPZD{FT}) where FT = convert(FT, 6.56)
 
 @inline nitrogen_flux(i, j, k, grid, advection, bgc::NPZD, tracers) = sinking_flux(i, j, k, grid, advection, Val(:D), bgc, tracers) +
                                                                       sinking_flux(i, j, k, grid, advection, Val(:P), bgc, tracers)
@@ -329,6 +330,6 @@ adapt_structure(to, npzd::NPZD) =
 @inline conserved_tracers(::NPZD) = (:N, :P, :Z, :D)
 @inline sinking_tracers(bgc::NPZD) = keys(bgc.sinking_velocities)
 
-@inline chlorophyll(bgc::NPZD, model) = 1.31 * model.tracers.P
+@inline chlorophyll(bgc::NPZD{FT}, model) where FT = convert(FT, 1.31) * model.tracers.P
 
 end # module

src/Models/AdvectedPopulations/PISCES/PISCES.jl

@@ -36,7 +36,7 @@ using OceanBioME.Models.CarbonChemistryModel: CarbonChemistry
 
 using Oceananigans.Biogeochemistry: AbstractBiogeochemistry
 using Oceananigans.Fields: set!
-using Oceananigans.Grids: φnodes, RectilinearGrid
+using Oceananigans.Grids: φnodes, RectilinearGrid, AbstractGrid
 
 import OceanBioME: redfield, conserved_tracers, maximum_sinking_velocity, chlorophyll
 
@@ -174,7 +174,7 @@ include("adapts.jl")
 include("show_methods.jl")
 
 """
-    PISCES(; grid,
+    PISCES(; grid::AbstractGrid{FT},
              phytoplankton = MixedMondoNanoAndDiatoms(),
              zooplankton = MicroAndMesoZooplankton(),
              dissolved_organic_matter = DissolvedOrganicCarbon(),
@@ -285,41 +285,42 @@ the classes to a single `phytoplankton` if more classes are required (see
 was desired a way to specify arbitary tracers for arguments would be required.
 """
 function PISCES(; grid,
-                  phytoplankton = MixedMondoNanoAndDiatoms(),
-                  zooplankton = MicroAndMesoZooplankton(),
-                  dissolved_organic_matter = DissolvedOrganicCarbon(),
-                  particulate_organic_matter = TwoCompartementCarbonIronParticles(),
+                  FT = eltype(grid),
+                  phytoplankton = MixedMondoNanoAndDiatoms(FT),
+                  zooplankton = MicroAndMesoZooplankton(FT),
+                  dissolved_organic_matter = DissolvedOrganicCarbon(FT),
+                  particulate_organic_matter = TwoCompartementCarbonIronParticles(FT),
 
-                  nitrogen = NitrateAmmonia(),
-                  iron = SimpleIron(),
+                  nitrogen = NitrateAmmonia{FT}(),
+                  iron = SimpleIron{FT}(),
                   silicate = Silicate(),
-                  oxygen = Oxygen(),
+                  oxygen = Oxygen{FT}(),
                   phosphate = Phosphate(),
 
                   inorganic_carbon = InorganicCarbon(),
 
                   # from Aumount 2005 rather than 2015 since it doesn't work the other way around
-                  first_anoxia_thresehold = 6.0,
-                  second_anoxia_thresehold = 1.0,
+                  first_anoxia_thresehold = convert(FT, 6.0),
+                  second_anoxia_thresehold = convert(FT, 1.0),
 
-                  nitrogen_redfield_ratio = 16/122,
-                  phosphate_redfield_ratio = 1/122,
+                  nitrogen_redfield_ratio = convert(FT, 16/122),
+                  phosphate_redfield_ratio = convert(FT, 1/122),
 
-                  mixed_layer_shear = 1.0,
-                  background_shear = 0.01, 
+                  mixed_layer_shear = convert(FT, 1.0),
+                  background_shear = convert(FT, 0.01), 
 
-                  latitude = PrescribedLatitude(45),
+                  latitude = PrescribedLatitude{FT}(45),
                   day_length = CBMDayLength(),
 
                   mixed_layer_depth = Field{Center, Center, Nothing}(grid),
                   euphotic_depth = Field{Center, Center, Nothing}(grid),
 
-                  silicate_climatology = ConstantField(7.5),
+                  silicate_climatology = ConstantField(convert(FT, 7.5)),
 
                   mean_mixed_layer_vertical_diffusivity = Field{Center, Center, Nothing}(grid),
                   mean_mixed_layer_light = Field{Center, Center, Nothing}(grid),
 
-                  carbon_chemistry = CarbonChemistry(),
+                  carbon_chemistry = CarbonChemistry(FT),
                   calcite_saturation = CenterField(grid),
 
                   surface_photosynthetically_active_radiation = default_surface_PAR,
@@ -328,9 +329,9 @@ function PISCES(; grid,
                     MultiBandPhotosyntheticallyActiveRadiation(; grid, 
                                                                  surface_PAR = surface_photosynthetically_active_radiation),
 
-                  sinking_speeds = (POC = 2/day, 
+                  sinking_speeds = (POC = convert(FT, 2/day), 
                                     # might be more efficient to just precompute this
-                                    GOC = Field(KernelFunctionOperation{Center, Center, Face}(DepthDependantSinkingSpeed(), 
+                                    GOC = Field(KernelFunctionOperation{Center, Center, Face}(DepthDependantSinkingSpeed{FT}(), 
                                                                                               grid, 
                                                                                               mixed_layer_depth, 
                                                                                               euphotic_depth))),
@@ -345,6 +346,8 @@ function PISCES(; grid,
 
     @warn "This implementation of PISCES is in early development and has not yet been validated against the operational version"
 
+    eltype(grid) == FT || @warn "The float type for parameters ($FT) does not match the grids float type ($(eltype(grid))). This will cause type instability."
+
     if !isnothing(sediment) && !open_bottom
         @warn "You have specified a sediment model but not `open_bottom` which will not work as the tracer will settle in the bottom cell"
     end