Two dimensional turbulence example
In this example, we initialize a random velocity field and observe its turbulent decay in a two-dimensional domain. This example demonstrates:
- How to run a model with no tracers and no buoyancy model.
- How to use computed
Field
s to generate output.
Install dependencies
First let's make sure we have all required packages installed.
using Pkg
pkg"add Oceananigans, CairoMakie"
Model setup
We instantiate the model with an isotropic diffusivity. We use a grid with 128² points, a fifth-order advection scheme, third-order Runge-Kutta time-stepping, and a small isotropic viscosity. Note that we assign Flat
to the z
direction.
using Oceananigans
grid = RectilinearGrid(size=(128, 128), extent=(2π, 2π), topology=(Periodic, Periodic, Flat))
model = NonhydrostaticModel(; grid,
timestepper = :RungeKutta3,
advection = UpwindBiasedFifthOrder(),
closure = ScalarDiffusivity(ν=1e-5))
NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
├── grid: 128×128×1 RectilinearGrid{Float64, Periodic, Periodic, Flat} on CPU with 3×3×0 halo
├── timestepper: RungeKutta3TimeStepper
├── advection scheme: Upwind Biased reconstruction order 5
├── tracers: ()
├── closure: ScalarDiffusivity{ExplicitTimeDiscretization}(ν=1.0e-5)
├── buoyancy: Nothing
└── coriolis: Nothing
Random initial conditions
Our initial condition randomizes model.velocities.u
and model.velocities.v
. We ensure that both have zero mean for aesthetic reasons.
using Statistics
u, v, w = model.velocities
uᵢ = rand(size(u)...)
vᵢ = rand(size(v)...)
uᵢ .-= mean(uᵢ)
vᵢ .-= mean(vᵢ)
set!(model, u=uᵢ, v=vᵢ)
Setting up a simulation
We set-up a simulation that stops at 50 time units, with an initial time-step of 0.1, and with adaptive time-stepping and progress printing.
simulation = Simulation(model, Δt=0.2, stop_time=50)
Simulation of NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
├── Next time step: 200 ms
├── Elapsed wall time: 0 seconds
├── Wall time per iteration: NaN days
├── Stop time: 50 seconds
├── Stop iteration : Inf
├── Wall time limit: Inf
├── Callbacks: OrderedDict with 4 entries:
│ ├── stop_time_exceeded => Callback of stop_time_exceeded on IterationInterval(1)
│ ├── stop_iteration_exceeded => Callback of stop_iteration_exceeded on IterationInterval(1)
│ ├── wall_time_limit_exceeded => Callback of wall_time_limit_exceeded on IterationInterval(1)
│ └── nan_checker => Callback of NaNChecker for u on IterationInterval(100)
├── Output writers: OrderedDict with no entries
└── Diagnostics: OrderedDict with no entries
The TimeStepWizard
helps ensure stable time-stepping with a Courant-Freidrichs-Lewy (CFL) number of 0.7.
wizard = TimeStepWizard(cfl=0.7, max_change=1.1, max_Δt=0.5)
simulation.callbacks[:wizard] = Callback(wizard, IterationInterval(10))
Callback of TimeStepWizard(cfl=0.7, max_Δt=0.5, min_Δt=0.0) on IterationInterval(10)
Logging simulation progress
We set up a callback that logs the simulation iteration and time every 100 iterations.
using Printf
function progress_message(sim)
max_abs_u = maximum(abs, sim.model.velocities.u)
walltime = prettytime(sim.run_wall_time)
return @info @sprintf("Iteration: %04d, time: %1.3f, Δt: %.2e, max(|u|) = %.1e, wall time: %s\n",
iteration(sim), time(sim), sim.Δt, max_abs_u, walltime)
end
add_callback!(simulation, progress_message, IterationInterval(100))
Output
We set up an output writer for the simulation that saves vorticity and speed every 20 iterations.
Computing vorticity and speed
To make our equations prettier, we unpack u
, v
, and w
from the NamedTuple
model.velocities:
u, v, w = model.velocities
NamedTuple with 3 Fields on 128×128×1 RectilinearGrid{Float64, Periodic, Periodic, Flat} on CPU with 3×3×0 halo:
├── u: 128×128×1 Field{Face, Center, Center} on RectilinearGrid on CPU
├── v: 128×128×1 Field{Center, Face, Center} on RectilinearGrid on CPU
└── w: 128×128×1 Field{Center, Center, Face} on RectilinearGrid on CPU
Next we create two Field
s that calculate (i) vorticity that measures the rate at which the fluid rotates and is defined as
\[ω = ∂_x v - ∂_y u \, ,\]
ω = ∂x(v) - ∂y(u)
BinaryOperation at (Face, Face, Center)
├── grid: 128×128×1 RectilinearGrid{Float64, Periodic, Periodic, Flat} on CPU with 3×3×0 halo
└── tree:
- at (Face, Face, Center)
├── ∂xᶠᶠᶜ at (Face, Face, Center) via identity
│ └── 128×128×1 Field{Center, Face, Center} on RectilinearGrid on CPU
└── ∂yᶠᶠᶜ at (Face, Face, Center) via identity
└── 128×128×1 Field{Face, Center, Center} on RectilinearGrid on CPU
We also calculate (ii) the speed of the flow,
\[s = \sqrt{u^2 + v^2} \, .\]
s = sqrt(u^2 + v^2)
UnaryOperation at (Face, Center, Center)
├── grid: 128×128×1 RectilinearGrid{Float64, Periodic, Periodic, Flat} on CPU with 3×3×0 halo
└── tree:
sqrt at (Face, Center, Center) via identity
└── + at (Face, Center, Center)
├── ^ at (Face, Center, Center)
│ ├── 128×128×1 Field{Face, Center, Center} on RectilinearGrid on CPU
│ └── 2
└── ^ at (Center, Face, Center)
├── 128×128×1 Field{Center, Face, Center} on RectilinearGrid on CPU
└── 2
We pass these operations to an output writer below to calculate and output them during the simulation.
filename = "two_dimensional_turbulence"
simulation.output_writers[:fields] = JLD2OutputWriter(model, (; ω, s),
schedule = TimeInterval(0.6),
filename = filename * ".jld2",
overwrite_existing = true)
JLD2OutputWriter scheduled on TimeInterval(600 ms):
├── filepath: ./two_dimensional_turbulence.jld2
├── 2 outputs: (ω, s)
├── array type: Array{Float64}
├── including: [:grid, :coriolis, :buoyancy, :closure]
├── file_splitting: NoFileSplitting
└── file size: 27.1 KiB
Running the simulation
Pretty much just
run!(simulation)
[ Info: Initializing simulation...
[ Info: Iteration: 0000, time: 0.000, Δt: 1.00e-01, max(|u|) = 7.2e-01, wall time: 0 seconds
[ Info: ... simulation initialization complete (12.373 seconds)
[ Info: Executing initial time step...
[ Info: ... initial time step complete (9.186 seconds).
[ Info: Iteration: 0100, time: 6.669, Δt: 7.29e-02, max(|u|) = 3.3e-01, wall time: 24.852 seconds
[ Info: Iteration: 0200, time: 13.615, Δt: 8.29e-02, max(|u|) = 3.0e-01, wall time: 29.956 seconds
[ Info: Iteration: 0300, time: 21.174, Δt: 8.47e-02, max(|u|) = 3.0e-01, wall time: 32.585 seconds
[ Info: Iteration: 0400, time: 28.800, Δt: 8.22e-02, max(|u|) = 3.2e-01, wall time: 36.181 seconds
[ Info: Iteration: 0500, time: 35.854, Δt: 7.37e-02, max(|u|) = 2.7e-01, wall time: 38.831 seconds
[ Info: Iteration: 0600, time: 43.150, Δt: 7.91e-02, max(|u|) = 2.6e-01, wall time: 40.681 seconds
[ Info: Simulation is stopping after running for 42.881 seconds.
[ Info: Simulation time 50 seconds equals or exceeds stop time 50 seconds.
Visualizing the results
We load the output.
ω_timeseries = FieldTimeSeries(filename * ".jld2", "ω")
s_timeseries = FieldTimeSeries(filename * ".jld2", "s")
times = ω_timeseries.times
85-element Vector{Float64}:
0.0
0.6
1.2
1.7999999999999998
2.4
3.0000000000000004
3.6
4.200000000000001
4.8
5.3999999999999995
5.999999999999999
6.599999999999999
7.199999999999998
7.799999999999998
8.399999999999999
8.999999999999998
9.599999999999998
10.199999999999998
10.799999999999997
11.399999999999997
11.999999999999996
12.599999999999996
13.199999999999996
13.799999999999995
14.399999999999995
14.999999999999995
15.599999999999996
15.6
16.2
16.8
17.400000000000002
18.000000000000004
18.60000000000001
19.2
19.8
20.400000000000002
21.000000000000004
21.600000000000005
22.200000000000006
22.800000000000008
23.40000000000001
24.00000000000001
24.600000000000012
25.200000000000014
25.800000000000015
26.400000000000016
27.000000000000018
27.60000000000002
28.20000000000002
28.800000000000022
29.400000000000023
30.000000000000025
30.600000000000026
31.200000000000028
31.80000000000003
32.40000000000003
33.00000000000003
33.60000000000003
34.20000000000003
34.80000000000003
35.400000000000034
36.000000000000036
36.60000000000004
37.20000000000004
37.80000000000005
38.4
39.0
39.6
40.2
40.800000000000004
41.400000000000006
42.00000000000001
42.60000000000001
43.20000000000001
43.80000000000001
44.40000000000001
45.000000000000014
45.600000000000016
46.20000000000002
46.80000000000002
47.40000000000002
48.00000000000003
48.6
49.2
49.80000000000001
Construct the $x, y, z$ grid for plotting purposes,
xω, yω, zω = nodes(ω_timeseries)
xs, ys, zs = nodes(s_timeseries)
and animate the vorticity and fluid speed.
using CairoMakie
set_theme!(Theme(fontsize = 24))
fig = Figure(size = (800, 500))
axis_kwargs = (xlabel = "x",
ylabel = "y",
limits = ((0, 2π), (0, 2π)),
aspect = AxisAspect(1))
ax_ω = Axis(fig[2, 1]; title = "Vorticity", axis_kwargs...)
ax_s = Axis(fig[2, 2]; title = "Speed", axis_kwargs...)
We use Makie's Observable
to animate the data. To dive into how Observable
s work we refer to Makie.jl's Documentation.
n = Observable(1)
Observable(1)
Now let's plot the vorticity and speed.
ω = @lift interior(ω_timeseries[$n], :, :, 1)
s = @lift interior(s_timeseries[$n], :, :, 1)
heatmap!(ax_ω, xω, yω, ω; colormap = :balance, colorrange = (-2, 2))
heatmap!(ax_s, xs, ys, s; colormap = :speed, colorrange = (0, 0.2))
title = @lift "t = " * string(round(times[$n], digits=2))
Label(fig[1, 1:2], title, fontsize=24, tellwidth=false)
fig
Finally, we record a movie.
frames = 1:length(times)
@info "Making a neat animation of vorticity and speed..."
record(fig, filename * ".mp4", frames, framerate=24) do i
n[] = i
end
[ Info: Making a neat animation of vorticity and speed...
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