Merge pull request #68 from jbisits/jib-patches

Specify `NamedTuple` type in struct +`show` fixes

Project.toml

@@ -1,7 +1,7 @@
 name = "StaircaseShenanigans"
 uuid = "c2bb06a8-94f3-4279-b990-30bf3ab8ba6f"
 authors = ["Josef Bisits <[email protected]>"]
-version = "0.4.2"
+version = "0.4.3"
 
 [deps]
 GibbsSeaWater = "9a22fb26-0b63-4589-b28e-8f9d0b5c3d05"

examples/single_interface_periodic.jl

@@ -11,7 +11,7 @@ model_setup = (;architecture, diffusivities, domain_extent, resolution, eos)
 depth_of_interface = -0.5
 salinity = [34.58, 34.70]
 temperature = [-1.5, 0.5]
-interface_ics = PeriodoicSingleInterfaceICs(eos, depth_of_interface, salinity, temperature, BackgroundTanh())
+interface_ics = PeriodoicSingleInterfaceICs(eos, depth_of_interface, salinity, temperature, BackgroundTanh(tanh_background, 100, NamedTuple()))
 tracer_noise = TracerNoise(1e-6, 1e-6)
 
 ## setup model

src/StaircaseShenanigans.jl

@@ -22,6 +22,7 @@ import SeawaterPolynomials.SecondOrderSeawaterPolynomials: RoquetSeawaterPolynom
 abstract type AbstractStaircaseModel end
 abstract type AbstractInitialConditions end
 abstract type AbstractNoise end
+abstract type BackgroundFunction end
 
 export StaircaseDNS, PeriodicStaircaseDNS, DNSModel, SDNS_simulation_setup
 

src/staircase_initial_conditions.jl

@@ -42,7 +42,7 @@ function STSingleInterfaceInitialConditions(eos::BoussinesqEquationOfState, dept
 
 end
 const SingleInterfaceICs = STSingleInterfaceInitialConditions # alias
-
+Base.summary(ics::SingleInterfaceICs) = "Single S-T interface at z = $(ics.depth_of_interface)"
 """
     struct PeriodicSTSingleInterfaceInitialConditions
 Sets a `BackgroundField` according to `background_State` and uses a triply periodic domain
@@ -68,6 +68,7 @@ function PeriodicSTSingleInterfaceInitialConditions(eos::BoussinesqEquationOfSta
 
 end
 const PeriodoicSingleInterfaceICs = PeriodicSTSingleInterfaceInitialConditions # alias
+Base.summary(ics::PeriodoicSingleInterfaceICs) = "Single S-T interface at z = $(ics.depth_of_interface) on triply periodic domain with $(summary(ics.background_state)) state"
 
 "Container for initial conditions that have well mixed layers seperated by sharp step interfaces."
 struct STStaircaseInitialConditions{T} <: AbstractStaircaseInitialConditions
@@ -92,6 +93,8 @@ function STStaircaseInitialConditions(model, number_of_interfaces, depth_of_inte
 
 end
 const StaircaseICs = STStaircaseInitialConditions # alias
+Base.summary(ics::StaircaseICs) = "Multiple S-T interfaces at z = $(ics.depth_of_interfaces)"
+
 """
     function compute_R_ρ(salinity, temperature, depth_of_interfaces, eos)
 Compute the density ratio, ``R_{\rho}``, at a diffusive interface with a non-linear equation of state
@@ -154,7 +157,7 @@ function Base.show(io::IO, sics::AbstractStaircaseInitialConditions)
         println(io, "┣━━━━ salinity_values: $(sics.salinity_values)")
         println(io, "┣━ temperature_values: $(sics.temperature_values)")
         println(io, "┣━━━━━━━━━━━━━━━━ R_ρ: $(round.(sics.R_ρ; digits = 2))")
-        println(io, "┗━━━ background_state: $(typeof(sics.background_state))")
+        println(io, "┗━━━ background_state: $(summary(sics.background_state))")
     elseif sics isa STSingleInterfaceInitialConditions
         println(io, "STSingleInterfaceInitialConditions")
         println(io, "┣━ depth_of_interface: $(sics.depth_of_interface)")
@@ -171,10 +174,10 @@ function Base.show(io::IO, sics::AbstractStaircaseInitialConditions)
         print(io,   "┗━━━━━━━━━━━━━━━━━━ R_ρ: $(round.(sics.R_ρ; digits = 2))")
     elseif sics isa SmoothSTStaircaseInitialConditions
         println(io, "STStaircaseInitialConditions")
-        println(io, "┣━━━━ number_of_interfaces: $(sics.number_of_interfaces)")
-        println(io, "┣━━━━━ depth_of_interfaces: $(sics.depth_of_interfaces)")
-        println(io, "┣━━━━ salinity_values: $(sics.salinity_values)")
-        println(io, "┣━ temperature_values: $(sics.temperature_values)")
-        print(io,   "┗━ smoothing_funciton: $(sics.smoothing_funciton)")
+        println(io, "┣━ number_of_interfaces: $(sics.number_of_interfaces)")
+        println(io, "┣━━ depth_of_interfaces: $(sics.depth_of_interfaces)")
+        println(io, "┣━━━━━━ salinity_values: $(sics.salinity_values)")
+        println(io, "┣━━━ temperature_values: $(sics.temperature_values)")
+        print(io,   "┗━━━ smoothing_funciton: $(sics.smoothing_funciton)")
     end
 end

src/staircase_model.jl

@@ -10,9 +10,9 @@ struct StaircaseDNS{NHM <: NonhydrostaticModel,
 end
 function Base.show(io::IO, sdns::StaircaseDNS)
     println(io, "StaircaseDirectNumericalSimulation")
-    println(io, "┣━━━━━━━━━━━━━━━━ model: $(summary(sdns.model))")
-    println(io, "┣━━━ initial_conditions: $(typeof(sdns.initial_conditions))")
-    print(io,   "┗━━━━━━━━ initial_noise: $(typeof(sdns.initial_noise))")
+    println(io, "┣━━━━━━━━━━━━━━ model: $(summary(sdns.model))")
+    println(io, "┣━ initial_conditions: $(summary(sdns.initial_conditions))")
+    print(io,   "┗━━━━━━ initial_noise: $(summary(sdns.initial_noise))")
 end
 """
     function StaircaseDNS(model, initial_conditions; initial_noise = nothing)

src/staircase_noise.jl

@@ -1,3 +1,6 @@
+Base.iterate(noise::AbstractNoise, state = 1) =
+    state > length(fieldnames(noise)) ? nothing : (getfield(noise, state), state + 1)
+
 """
     struct VelocityNoise{T}
 Container for the magnitudes of normally distributed noise added to velocity fields.
@@ -20,20 +23,22 @@ struct TracerNoise{T} <: AbstractNoise
     "Noise magnitude for `T` tracer field"
     T_magnitude :: T
 end
-Base.iterate(noise::AbstractNoise, state = 1) =
-    state > length(fieldnames(noise)) ? nothing : (getfield(noise, state), state + 1)
+"Convenience for all noise at same magnitude `c`, default behaviour is 1e-4"
+TracerNoise(c::Float64=1e-4) = TracerNoise(c, c)
+Base.summary(noise::TracerNoise) = "Random noise magnitude in S and T fields $(noise.S_magnitude) and $(noise.T_magnitude) respectively"
 
 function Base.show(io::IO, noise::AbstractNoise)
     if noise isa VelocityNoise
         println(io, "VelocityNoise")
-        println(io, "┣━━ u_noise_magnitude: $(noise.u_magnitude)")
-        println(io, "┣━━ v_noise_magnitude: $(noise.v_magnitude)")
-        print(io,   "┗━━ w_noise_magnitude: $(noise.w_magnitude)")
+        println(io, "┣━ u_noise_magnitude: $(noise.u_magnitude)")
+        println(io, "┣━ v_noise_magnitude: $(noise.v_magnitude)")
+        print(io,   "┗━ w_noise_magnitude: $(noise.w_magnitude)")
     elseif noise isa TracerNoise
         println(io, "TracerNoise")
-        println(io, "┣━━ S_noise_magnitude: $(noise.S_magnitude)")
-        print(io,   "┗━━ T_noise_magnitude: $(noise.T_magnitude)")
+        println(io, "┣━ S_noise_magnitude: $(noise.S_magnitude)")
+        print(io,   "┗━ T_noise_magnitude: $(noise.T_magnitude)")
     end
 end
 "Convenience for all noise at same magnitude `c`, default behaviour is 1e-4"
 VelocityNoise(c::Float64=1e-4) = VelocityNoise(c, c, c)
+Base.summary(noise::VelocityNoise) = "Random noise magnitude in u, v and w fields $(noise.u_magnitude), $(noise.v_magnitude), and $(noise.w_magnitude) respectively"

src/staircase_restoring.jl

@@ -1,5 +1,3 @@
-abstract type BackgroundFunction end
-
 Oceananigans.BackgroundField(bf::BackgroundFunction) =
     BackgroundField(bf.func, parameters = bf.parameters)
 """
@@ -12,16 +10,10 @@ mutable struct BackgroundTanh{F, T} <: BackgroundFunction
     "Scale the steepness of the `tanh` change"
          scale :: T
     "Parameters for the tanh background field"
-    parameters :: Any
+    parameters :: NamedTuple
 end
 BackgroundTanh() = BackgroundTanh(tanh_background, 100, NamedTuple())
 BackgroundTanh(scale) = BackgroundTanh(tanh_background, scale, NamedTuple())
-function Base.show(io, bt::BackgroundTanh)
-    println(io, "BackgroundTanh")
-    println(io, "┣━━━ function: $(bt.func)")
-    println(io, "┣━━━━━━ scale: $(bt.scale)")
-      print(io, "┗━ parameters: $(bt.parameters)")
-end
 """
     mutable struct BackgroundLinear{F, P}
 Container for a linear background field.
@@ -30,14 +22,25 @@ mutable struct BackgroundLinear{F} <: BackgroundFunction
     "Linear function"
           func :: F
     "Parameters for the tanh background field"
-    parameters :: Any
+    parameters :: NamedTuple
 end
 BackgroundLinear() = BackgroundLinear(linear_background, NamedTuple())
-function Base.show(io, bl::BackgroundLinear)
-    println(io, "BackgroundLinear")
-    println(io, "┣━━━ function: $(bl.func)")
-      print(io, "┗━ parameters: $(bl.parameters)")
+
+function Base.show(io::IO, bf::BackgroundFunction)
+    if bf isa BackgroundTanh
+        println(io, "BackgroundTanh")
+        println(io, "┣━━━ function: $(bf.func)")
+        println(io, "┣━━━━━━ scale: $(bf.scale)")
+          print(io, "┗━ parameters: $(bf.parameters)")
+    elseif bf isa BackgroundLinear
+        println(io, "BackgroundLinear")
+        println(io, "┣━━━ function: $(bf.func)")
+          print(io, "┗━ parameters: $(bf.parameters)")
+    end
 end
+Base.summary(bt::BackgroundTanh) = "$(bt.func)"
+Base.summary(bl::BackgroundLinear) = "$(bl.func)"
+
 """
     function S_and_T_background_fields(initial_conditions)
 Set background fields for the `S` and `T` tracer fields where the domain is triply periodic.
@@ -53,9 +56,9 @@ function S_and_T_background_fields(ics::PeriodicSTSingleInterfaceInitialConditio
 end
 "Sets a background state that is hyperbolic tangent. There is also a method to save an
 `Array` of this backgorund state to output."
-tanh_background(x, y, z, t, p) = p.Cₗ - 0.5 * p.ΔC * (1  + tanh(p.D * (z - p.z_interface) / p.Lz))
+@inline tanh_background(x, y, z, t, p) = p.Cₗ - 0.5 * p.ΔC * (1  + tanh(p.D * (z - p.z_interface) / p.Lz))
 tanh_background(z, ΔC, Cₗ, Lz, z_interface, D) = Cₗ - 0.5 * ΔC * (1  + tanh(D * (z - z_interface) / Lz))
-linear_background(x, y, z, t, p) = p.Cᵤ - p.ΔC * z / p.Lz
+@inline linear_background(x, y, z, t, p) = p.Cᵤ - p.ΔC * z / p.Lz
 linear_background(z, ΔC, Cᵤ, Lz) = Cᵤ - ΔC * z / Lz
 
 function get_parameters!(ics::PeriodicSTSingleInterfaceInitialConditions, tracer::Symbol, Lz)
@@ -132,6 +135,7 @@ function save_background_state!(simulation, model, initial_conditions::Periodoic
 
     return nothing
 end
+
 # The following functions are to be used as `BoundaryConditions` so that tracers can
 # re-enter the domain with the initial gradient added effectively allowing the gradient to
 # be maintained. Another option is to add background tracer fields and only evolve the anomaly