Merge pull request #106 from jbisits/jib-oceananigansupdate

Changes with Oceananigans.jl 0.95
jbisits · Jan 7, 2025 · 3ecbc4f · 3ecbc4f
2 parents 09cde61 + 975eed1
commit 3ecbc4f
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Showing 6 changed files with 12 additions and 10 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "StaircaseShenanigans"
 uuid = "c2bb06a8-94f3-4279-b990-30bf3ab8ba6f"
 authors = ["Josef Bisits <[email protected]>"]
-version = "0.6.1"
+version = "0.6.2"
 
 [deps]
 GibbsSeaWater = "9a22fb26-0b63-4589-b28e-8f9d0b5c3d05"

diff --git a/src/StaircaseShenanigans.jl b/src/StaircaseShenanigans.jl
@@ -2,8 +2,7 @@ module StaircaseShenanigans
 
 using Oceananigans, Reexport, Printf
 using Oceananigans: seawater_density
-using Oceananigans.BoundaryConditions: update_boundary_condition!
-using Oceananigans.Operators: ℑzᵃᵃᶠ
+using Oceananigans.BuoyancyFormulations: buoyancy_frequency
 using Oceananigans.Fields: condition_operand
 import Oceananigans.BackgroundField
 using SeawaterPolynomials.TEOS10

diff --git a/src/single_interfaces_initial_conditions.jl b/src/single_interfaces_initial_conditions.jl
@@ -23,7 +23,7 @@ function STSingleInterfaceInitialConditions(model, depth_of_interface, salinity,
                                             interface_smoothing = NoSmoothing,
                                             background_state = NoBackground)
 
-    eos = model.buoyancy.model.equation_of_state
+    eos = model.buoyancy.formulation.equation_of_state
 
     R_ρ = compute_R_ρ(salinity, temperature, depth_of_interface, eos)
 

diff --git a/src/staircase_initial_conditions.jl b/src/staircase_initial_conditions.jl
@@ -18,7 +18,7 @@ struct STStaircaseInitialConditions{T} <: AbstractStaircaseInitialConditions
 end
 function STStaircaseInitialConditions(model, number_of_interfaces, depth_of_interfaces, salinity, temperature)
 
-    eos = model.buoyancy.model.equation_of_state
+    eos = model.buoyancy.formulation.equation_of_state
 
     R_ρ = compute_R_ρ(salinity, temperature, depth_of_interfaces, eos)
 

diff --git a/src/staircase_simulation.jl b/src/staircase_simulation.jl
@@ -77,7 +77,7 @@ function output_directory(sdns::StaircaseDNS, stop_time::Number, output_path)
     ic_type = typeof(sdns.initial_conditions)
     ic_string = ic_type <: STStaircaseInitialConditions ? "staircase" : "single_interface"
 
-    eos_string = is_linear_eos(sdns.model.buoyancy.model.equation_of_state.seawater_polynomial)
+    eos_string = is_linear_eos(sdns.model.buoyancy.formulation.equation_of_state.seawater_polynomial)
 
     stop_time_min = stop_time / 60 ≥ 1 ? string(round(Int, stop_time / 60)) :
                                          string(round(stop_time / 60; digits = 2))
@@ -220,11 +220,14 @@ function save_computed_output!(simulation, sdns, save_schedule, save_file, outpu
     T = typeof(ics.background_state) <: NoBackground ? model.tracers.T : Field(model.background_fields.tracers.T + model.tracers.T)
 
     σ = seawater_density(model, temperature = T, salinity = S, geopotential_height = reference_gp_height)
+    N² = buoyancy_frequency(model)
 
-    computed_outputs = Dict("σ" => σ)
+    computed_outputs = Dict("σ" => σ, "N²" => N²)
     oa = Dict(
         "σ" => Dict("longname" => "Seawater potential density calculated using equation of state in model.",
-                    "units" => "kgm⁻³")
+                    "units" => "kgm⁻³"),
+        "N²" => Dict("longname" => "Buoyancy frequency.",
+                    "units" => "s⁻¹")
         )
 
     if !(typeof(ics.background_state) <: NoBackground)

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -28,8 +28,8 @@ using Test
         include("R_sub_rho.jl")
         ΔS, ΔΘ = diff(salinity[1:2]), diff(temperature[1:2])
         Sₘ, Θₘ = (sum(salinity[1:2]) / 2), (sum(temperature[1:2]) / 2)
-        β = haline_contraction(Θₘ, Sₘ, 0, model.buoyancy.model.equation_of_state)
-        α = -thermal_expansion(Θₘ, Sₘ, 0, model.buoyancy.model.equation_of_state)
+        β = haline_contraction(Θₘ, Sₘ, 0, model.buoyancy.formulation.equation_of_state)
+        α = -thermal_expansion(Θₘ, Sₘ, 0, model.buoyancy.formulation.equation_of_state)
 
         @test all(step_ics.R_ρ .≈ (β * ΔS) / (α * ΔΘ))
         @test (interface_ics.R_ρ ≈ vec((β * ΔS) / (α * ΔΘ))[1])