Update Oceananigans compat

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.12'
         os:
           - ubuntu-latest
         arch:
@@ -47,7 +47,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.12'
         os:
           - ubuntu-latest
         arch:
@@ -72,7 +72,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.12'
         os:
           - ubuntu-latest
         arch:
@@ -97,7 +97,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.12'
         os:
           - ubuntu-latest
         arch:
@@ -122,7 +122,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.12'
         os:
           - ubuntu-latest
         arch:
@@ -147,7 +147,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.12'
         os:
           - ubuntu-latest
         arch:
@@ -172,7 +172,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.12'
         os:
           - ubuntu-latest
         arch:
@@ -197,7 +197,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.12'
         os:
           - ubuntu-latest
         arch:
@@ -222,7 +222,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.12'
         os:
           - ubuntu-latest
         arch:
@@ -247,7 +247,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.12'
         os:
           - ubuntu-latest
         arch:
@@ -272,7 +272,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.12'
         os:
           - ubuntu-latest
         arch:

.github/workflows/documentation.yml

@@ -19,7 +19,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@v2
         with:
-          version: '1.10'
+          version: '1.12'
       - name: Install dependencies
         run: julia --color=yes --project -e 'using Pkg; Pkg.instantiate()'
       - name: Build and deploy

Project.toml

@@ -1,7 +1,7 @@
 name = "Oceanostics"
 uuid = "d0ccf422-c8fb-49b5-a76d-74acdde946ac"
+version = "0.16.5"
 authors = ["tomchor <[email protected]>"]
-version = "0.16.4"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
@@ -11,7 +11,7 @@ SeawaterPolynomials = "d496a93d-167e-4197-9f49-d3af4ff8fe40"
 
 [compat]
 DocStringExtensions = "0.9"
-Oceananigans = "^0.100.3"
+Oceananigans = "0.101"
 SeawaterPolynomials = "0.3"
 julia = "1.9"
 

src/KineticEnergyEquation.jl

@@ -87,11 +87,11 @@ KineticEnergy(model; kwargs...) = KineticEnergy(model, model.velocities...; kwar
                                         velocities,
                                         tracers,
                                         auxiliary_fields,
-                                        diffusivity_fields,
+                                        closure_fields,
                                         pHY′,
                                         clock,
                                         forcings)
-    common_args = (buoyancy, background_fields, velocities, tracers, auxiliary_fields, diffusivity_fields, pHY′, clock)
+    common_args = (buoyancy, background_fields, velocities, tracers, auxiliary_fields, closure_fields, pHY′, clock)
     u∂ₜu = ℑxᶜᵃᵃ(i, j, k, grid, ψf, velocities.u, u_velocity_tendency, advection, coriolis, stokes_drift, closure, u_immersed_bc, common_args..., forcings.u)
     v∂ₜv = ℑyᵃᶜᵃ(i, j, k, grid, ψf, velocities.v, v_velocity_tendency, advection, coriolis, stokes_drift, closure, v_immersed_bc, common_args..., forcings.v)
     w∂ₜw = ℑzᵃᵃᶜ(i, j, k, grid, ψf, velocities.w, w_velocity_tendency, advection, coriolis, stokes_drift, closure, w_immersed_bc, common_args..., forcings.w)
@@ -138,7 +138,7 @@ function KineticEnergyTendency(model::NonhydrostaticModel; location = (Center, C
                     model.velocities,
                     model.tracers,
                     model.auxiliary_fields,
-                    model.diffusivity_fields,
+                    model.closure_fields,
                     model.pressures.pHY′,
                     model.clock,
                     model.forcing,)
@@ -191,14 +191,14 @@ end
 
 #+++ KineticEnergyStress
 @inline function uᵢ∂ⱼ_τᵢⱼᶜᶜᶜ(i, j, k, grid, closure,
-                                            diffusivity_fields,
+                                            closure_fields,
                                             clock,
                                             model_fields,
                                             buoyancy)
 
-    u∂ⱼ_τ₁ⱼ = ℑxᶜᵃᵃ(i, j, k, grid, ψf, model_fields.u, ∂ⱼ_τ₁ⱼ, closure, diffusivity_fields, clock, model_fields, buoyancy)
-    v∂ⱼ_τ₂ⱼ = ℑyᵃᶜᵃ(i, j, k, grid, ψf, model_fields.v, ∂ⱼ_τ₂ⱼ, closure, diffusivity_fields, clock, model_fields, buoyancy)
-    w∂ⱼ_τ₃ⱼ = ℑzᵃᵃᶜ(i, j, k, grid, ψf, model_fields.w, ∂ⱼ_τ₃ⱼ, closure, diffusivity_fields, clock, model_fields, buoyancy)
+    u∂ⱼ_τ₁ⱼ = ℑxᶜᵃᵃ(i, j, k, grid, ψf, model_fields.u, ∂ⱼ_τ₁ⱼ, closure, closure_fields, clock, model_fields, buoyancy)
+    v∂ⱼ_τ₂ⱼ = ℑyᵃᶜᵃ(i, j, k, grid, ψf, model_fields.v, ∂ⱼ_τ₂ⱼ, closure, closure_fields, clock, model_fields, buoyancy)
+    w∂ⱼ_τ₃ⱼ = ℑzᵃᵃᶜ(i, j, k, grid, ψf, model_fields.w, ∂ⱼ_τ₃ⱼ, closure, closure_fields, clock, model_fields, buoyancy)
 
     return u∂ⱼ_τ₁ⱼ+ v∂ⱼ_τ₂ⱼ + w∂ⱼ_τ₃ⱼ
 end
@@ -240,7 +240,7 @@ function KineticEnergyStress(model; location = (Center, Center, Center))
         model_fields = (; model_fields..., w=ZeroField())
     end
     dependencies = (model.closure,
-                    model.diffusivity_fields,
+                    model.closure_fields,
                     model.clock,
                     fields(model),
                     model.buoyancy)
@@ -434,18 +434,18 @@ Axᶠᶜᶠ_δwᶠᶜᶠ_F₃₁ᶠᶜᶠ(i, j, k, grid, closure, K_fields, clo,
 Ayᶜᶠᶠ_δwᶜᶠᶠ_F₃₂ᶜᶠᶠ(i, j, k, grid, closure, K_fields, clo, fields, b) = -Ayᶜᶠᶠ(i, j, k, grid) * δyᵃᶠᵃ(i, j, k, grid, fields.w) * viscous_flux_wy(i, j, k, grid, closure, K_fields, clo, fields, b)
 Azᶜᶜᶜ_δwᶜᶜᶜ_F₃₃ᶜᶜᶜ(i, j, k, grid, closure, K_fields, clo, fields, b) = -Azᶜᶜᶜ(i, j, k, grid) * δzᵃᵃᶜ(i, j, k, grid, fields.w) * viscous_flux_wz(i, j, k, grid, closure, K_fields, clo, fields, b)
 
-@inline viscous_dissipation_rate_ccc(i, j, k, grid, diffusivity_fields, fields, p) =
-    (Axᶜᶜᶜ_δuᶜᶜᶜ_F₁₁ᶜᶜᶜ(i, j, k, grid,         p.closure, diffusivity_fields, p.clock, fields, p.buoyancy) + # C, C, C
-     ℑxyᶜᶜᵃ(i, j, k, grid, Ayᶠᶠᶜ_δuᶠᶠᶜ_F₁₂ᶠᶠᶜ, p.closure, diffusivity_fields, p.clock, fields, p.buoyancy) + # F, F, C  → C, C, C
-     ℑxzᶜᵃᶜ(i, j, k, grid, Azᶠᶜᶠ_δuᶠᶜᶠ_F₁₃ᶠᶜᶠ, p.closure, diffusivity_fields, p.clock, fields, p.buoyancy) + # F, C, F  → C, C, C
+@inline viscous_dissipation_rate_ccc(i, j, k, grid, closure_fields, fields, p) =
+    (Axᶜᶜᶜ_δuᶜᶜᶜ_F₁₁ᶜᶜᶜ(i, j, k, grid,         p.closure, closure_fields, p.clock, fields, p.buoyancy) + # C, C, C
+     ℑxyᶜᶜᵃ(i, j, k, grid, Ayᶠᶠᶜ_δuᶠᶠᶜ_F₁₂ᶠᶠᶜ, p.closure, closure_fields, p.clock, fields, p.buoyancy) + # F, F, C  → C, C, C
+     ℑxzᶜᵃᶜ(i, j, k, grid, Azᶠᶜᶠ_δuᶠᶜᶠ_F₁₃ᶠᶜᶠ, p.closure, closure_fields, p.clock, fields, p.buoyancy) + # F, C, F  → C, C, C
 
-     ℑxyᶜᶜᵃ(i, j, k, grid, Axᶠᶠᶜ_δvᶠᶠᶜ_F₂₁ᶠᶠᶜ, p.closure, diffusivity_fields, p.clock, fields, p.buoyancy) + # F, F, C  → C, C, C
-     Ayᶜᶜᶜ_δvᶜᶜᶜ_F₂₂ᶜᶜᶜ(i, j, k, grid,         p.closure, diffusivity_fields, p.clock, fields, p.buoyancy) + # C, C, C
-     ℑyzᵃᶜᶜ(i, j, k, grid, Azᶜᶠᶠ_δvᶜᶠᶠ_F₂₃ᶜᶠᶠ, p.closure, diffusivity_fields, p.clock, fields, p.buoyancy) + # C, F, F  → C, C, C
+     ℑxyᶜᶜᵃ(i, j, k, grid, Axᶠᶠᶜ_δvᶠᶠᶜ_F₂₁ᶠᶠᶜ, p.closure, closure_fields, p.clock, fields, p.buoyancy) + # F, F, C  → C, C, C
+     Ayᶜᶜᶜ_δvᶜᶜᶜ_F₂₂ᶜᶜᶜ(i, j, k, grid,         p.closure, closure_fields, p.clock, fields, p.buoyancy) + # C, C, C
+     ℑyzᵃᶜᶜ(i, j, k, grid, Azᶜᶠᶠ_δvᶜᶠᶠ_F₂₃ᶜᶠᶠ, p.closure, closure_fields, p.clock, fields, p.buoyancy) + # C, F, F  → C, C, C
 
-     ℑxzᶜᵃᶜ(i, j, k, grid, Axᶠᶜᶠ_δwᶠᶜᶠ_F₃₁ᶠᶜᶠ, p.closure, diffusivity_fields, p.clock, fields, p.buoyancy) + # F, C, F  → C, C, C
-     ℑyzᵃᶜᶜ(i, j, k, grid, Ayᶜᶠᶠ_δwᶜᶠᶠ_F₃₂ᶜᶠᶠ, p.closure, diffusivity_fields, p.clock, fields, p.buoyancy) + # C, F, F  → C, C, C
-     Azᶜᶜᶜ_δwᶜᶜᶜ_F₃₃ᶜᶜᶜ(i, j, k, grid,         p.closure, diffusivity_fields, p.clock, fields, p.buoyancy)   # C, C, C
+     ℑxzᶜᵃᶜ(i, j, k, grid, Axᶠᶜᶠ_δwᶠᶜᶠ_F₃₁ᶠᶜᶠ, p.closure, closure_fields, p.clock, fields, p.buoyancy) + # F, C, F  → C, C, C
+     ℑyzᵃᶜᶜ(i, j, k, grid, Ayᶜᶠᶠ_δwᶜᶠᶠ_F₃₂ᶜᶠᶠ, p.closure, closure_fields, p.clock, fields, p.buoyancy) + # C, F, F  → C, C, C
+     Azᶜᶜᶜ_δwᶜᶜᶜ_F₃₃ᶜᶜᶜ(i, j, k, grid,         p.closure, closure_fields, p.clock, fields, p.buoyancy)   # C, C, C
      ) / Vᶜᶜᶜ(i, j, k, grid) # This division by volume, coupled with the call to A*δuᵢ above, ensures a derivative operation
 
 const KineticEnergyDissipationRate = CustomKFO{<:typeof(viscous_dissipation_rate_ccc)}
@@ -484,7 +484,7 @@ function DissipationRate(model; U=ZeroField(), V=ZeroField(), W=ZeroField(),
                   model.buoyancy)
 
     return KernelFunctionOperation{Center, Center, Center}(viscous_dissipation_rate_ccc, model.grid,
-                                                           model.diffusivity_fields, model_fields, parameters)
+                                                           model.closure_fields, model_fields, parameters)
 end
 #---
 
@@ -499,7 +499,7 @@ end
     Σˣᶻ² = ℑxzᶜᵃᶜ(i, j, k, grid, fψ_plus_gφ², ∂zᶠᶜᶠ, u, ∂xᶠᶜᶠ, w) / 4
     Σʸᶻ² = ℑyzᵃᶜᶜ(i, j, k, grid, fψ_plus_gφ², ∂zᶜᶠᶠ, v, ∂yᶜᶠᶠ, w) / 4
 
-    ν = _νᶜᶜᶜ(i, j, k, grid, p.closure, p.diffusivity_fields, p.clock)
+    ν = _νᶜᶜᶜ(i, j, k, grid, p.closure, p.closure_fields, p.clock, p.model_fields)
 
     return 2ν * (Σˣˣ² + Σʸʸ² + Σᶻᶻ² + 2 * (Σˣʸ² + Σˣᶻ² + Σʸᶻ²))
 end
@@ -531,17 +531,17 @@ KernelFunctionOperation at (Center, Center, Center)
 └── arguments: ("Field", "Field", "Field", "NamedTuple")
 ```
 """
-function KineticEnergyIsotropicDissipationRate(u, v, w, closure, diffusivity_fields, clock; location = (Center, Center, Center))
+function KineticEnergyIsotropicDissipationRate(u, v, w, closure, closure_fields, model_fields, clock; location = (Center, Center, Center))
     validate_location(location, "KineticEnergyIsotropicDissipationRate")
     validate_dissipative_closure(closure)
 
-    parameters = (; closure, diffusivity_fields, clock)
+    parameters = (; closure, closure_fields, clock, model_fields)
     return KernelFunctionOperation{Center, Center, Center}(isotropic_viscous_dissipation_rate_ccc, u.grid,
                                                            u, v, w, parameters)
 end
 
 @inline KineticEnergyIsotropicDissipationRate(model; location = (Center, Center, Center)) =
-    KineticEnergyIsotropicDissipationRate(model.velocities..., model.closure, model.diffusivity_fields, model.clock; location = location)
+    KineticEnergyIsotropicDissipationRate(model.velocities..., model.closure, model.closure_fields, fields(model), model.clock; location = location)
 #---
 
 end # module 

src/ProgressMessengers/cfl.jl

@@ -41,7 +41,7 @@ tuple_to_op(::Nothing) = nothing
 tuple_to_op(ν_tuple::Tuple) = sum(ν_tuple)
 
 @inline function (maxν::MaxViscosity)(simulation)
-    ν = tuple_to_op(viscosity(simulation.model.closure, simulation.model.diffusivity_fields))
+    ν = tuple_to_op(viscosity(simulation.model.closure, simulation.model.closure_fields))
     ν_max = maximum(abs, ν)
     message = @sprintf("%.2g", ν_max)
     maxν.with_prefix && (message = "νₘₐₓ = " * message)

src/TracerEquation.jl

@@ -11,9 +11,9 @@ export Advection, Diffusion, ImmersedDiffusion, TotalDiffusion, Forcing,
        TracerAdvection, TracerDiffusion, TracerImmersedDiffusion, TracerTotalDiffusion, TracerForcing
 
 # Inline function for total diffusion
-@inline total_∇_dot_qᶜ(i, j, k, grid, c, c_immersed_bc, closure, diffusivity_fields, val_tracer_index, clock, model_fields, buoyancy) =
-    ∇_dot_qᶜ(i, j, k, grid, closure, diffusivity_fields, val_tracer_index, c, clock, model_fields, buoyancy) +
-    immersed_∇_dot_qᶜ(i, j, k, grid, c, c_immersed_bc, closure, diffusivity_fields, val_tracer_index, clock, model_fields, buoyancy)
+@inline total_∇_dot_qᶜ(i, j, k, grid, c, c_immersed_bc, closure, closure_fields, val_tracer_index, clock, model_fields, buoyancy) =
+    ∇_dot_qᶜ(i, j, k, grid, closure, closure_fields, val_tracer_index, c, clock, model_fields, buoyancy) +
+    immersed_∇_dot_qᶜ(i, j, k, grid, c, c_immersed_bc, closure, closure_fields, val_tracer_index, clock, model_fields, buoyancy)
 
 # Type aliases for major functions
 const Advection = CustomKFO{<:typeof(div_Uc)}
@@ -93,15 +93,15 @@ KernelFunctionOperation at (Center, Center, Center)
 └── arguments: ("Nothing", "Nothing", "Val", "Field", "Clock", "NamedTuple", "Nothing")
 ```
 """
-function Diffusion(model, val_tracer_index, c, closure, diffusivity_fields, clock, model_fields, buoyancy; location = (Center, Center, Center))
+function Diffusion(model, val_tracer_index, c, closure, closure_fields, clock, model_fields, buoyancy; location = (Center, Center, Center))
     validate_location(location, "Diffusion", (Center, Center, Center))
-    return KernelFunctionOperation{Center, Center, Center}(∇_dot_qᶜ, model.grid, closure, diffusivity_fields, val_tracer_index, c, clock, model_fields, buoyancy)
+    return KernelFunctionOperation{Center, Center, Center}(∇_dot_qᶜ, model.grid, closure, closure_fields, val_tracer_index, c, clock, model_fields, buoyancy)
 end
 
 function Diffusion(model, tracer_name; kwargs...)
     tracer_index = findfirst(x -> x == tracer_name, keys(model.tracers))
     @inbounds c = model.tracers[tracer_name]
-    return Diffusion(model, Val(tracer_index), c, model.closure, model.diffusivity_fields, model.clock, fields(model), model.buoyancy; kwargs...)
+    return Diffusion(model, Val(tracer_index), c, model.closure, model.closure_fields, model.clock, fields(model), model.buoyancy; kwargs...)
 end
 
 
@@ -129,16 +129,16 @@ KernelFunctionOperation at (Center, Center, Center)
 └── arguments: ("Field", "Nothing", "Nothing", "Nothing", "Val", "Clock", "NamedTuple")
 ```
 """
-function ImmersedDiffusion(model, c, c_immersed_bc, closure, diffusivity_fields, val_tracer_index, clock, model_fields; location = (Center, Center, Center))
+function ImmersedDiffusion(model, c, c_immersed_bc, closure, closure_fields, val_tracer_index, clock, model_fields; location = (Center, Center, Center))
     validate_location(location, "ImmersedDiffusion", (Center, Center, Center))
-    return KernelFunctionOperation{Center, Center, Center}(immersed_∇_dot_qᶜ, model.grid, c, c_immersed_bc, closure, diffusivity_fields, val_tracer_index, clock, model_fields)
+    return KernelFunctionOperation{Center, Center, Center}(immersed_∇_dot_qᶜ, model.grid, c, c_immersed_bc, closure, closure_fields, val_tracer_index, clock, model_fields)
 end
 
 function ImmersedDiffusion(model, tracer_name; kwargs...)
     tracer_index = findfirst(x -> x == tracer_name, keys(model.tracers))
     tracer = model.tracers[tracer_name]
     immersed_bc = tracer.boundary_conditions.immersed
-    return ImmersedDiffusion(model, tracer, immersed_bc, model.closure, model.diffusivity_fields, Val(tracer_index), model.clock, fields(model); kwargs...)
+    return ImmersedDiffusion(model, tracer, immersed_bc, model.closure, model.closure_fields, Val(tracer_index), model.clock, fields(model); kwargs...)
 end
 
 """
@@ -165,16 +165,16 @@ KernelFunctionOperation at (Center, Center, Center)
 └── arguments: ("Field", "Nothing", "Nothing", "Nothing", "Val", "Clock", "NamedTuple", "Nothing")
 ```
 """
-function TotalDiffusion(model, c, c_immersed_bc, closure, diffusivity_fields, val_tracer_index, clock, model_fields, buoyancy; location = (Center, Center, Center))
+function TotalDiffusion(model, c, c_immersed_bc, closure, closure_fields, val_tracer_index, clock, model_fields, buoyancy; location = (Center, Center, Center))
     validate_location(location, "TotalDiffusion", (Center, Center, Center))
-    return KernelFunctionOperation{Center, Center, Center}(total_∇_dot_qᶜ, model.grid, c, c_immersed_bc, closure, diffusivity_fields, val_tracer_index, clock, model_fields, buoyancy)
+    return KernelFunctionOperation{Center, Center, Center}(total_∇_dot_qᶜ, model.grid, c, c_immersed_bc, closure, closure_fields, val_tracer_index, clock, model_fields, buoyancy)
 end
 
 function TotalDiffusion(model, tracer_name; kwargs...)
     tracer_index = findfirst(x -> x == tracer_name, keys(model.tracers))
     tracer = model.tracers[tracer_index]
     immersed_bc = tracer.boundary_conditions.immersed
-    return TotalDiffusion(model, tracer, immersed_bc, model.closure, model.diffusivity_fields, Val(tracer_index), model.clock, fields(model), model.buoyancy; kwargs...)
+    return TotalDiffusion(model, tracer, immersed_bc, model.closure, model.closure_fields, Val(tracer_index), model.clock, fields(model), model.buoyancy; kwargs...)
 end
 #---