doc: Move 2D example to Literate.jl

examples/2d.jl

@@ -0,0 +1,87 @@
+# # Example: 2D Simulation
+#
+# ## Set up Julia environment
+
+import Pkg
+Pkg.activate(mktempdir())
+
+Pkg.add("CairoMakie")
+Pkg.add("CSV")
+Pkg.add("NPZ")
+Pkg.add("PencilFFTs")
+Pkg.develop(path = joinpath(@__DIR__, ".."))  # Load version of UltraDark in this repo
+
+using UltraDark
+using Test
+using NPZ
+using CairoMakie
+using CSV
+
+Threads.nthreads()
+
+# ## Define initial conditions
+#
+# Define a 2D grid.
+
+resol = 128
+len = 10.0
+
+grids = Grids((len, len, len / resol), (resol, resol, 1));
+
+# Add some solitons to the grid.  Strictly speaking, these aren't solitons in 2D, but they'll do for demonstration purposes.
+
+mass = 10
+position_1 = [-len / 5, -len / 5, 0]
+position_2 = [-len / 5, +len / 5, 0]
+velocity = [1, 0, 0]
+phase_1 = 0
+phase_2 = π
+t0 = 0
+
+UltraDark.Initialise.add_fdm_soliton!(grids, mass, position_1, velocity, phase_1, t0)
+UltraDark.Initialise.add_fdm_soliton!(grids, mass, position_2, velocity, phase_2, t0)
+
+# ## Set options
+
+output_dir = joinpath(mktempdir(), "output", "2D")
+
+output_times = 0:0.1:5
+output_config = OutputConfig(output_dir, output_times);
+
+options = Config.SimulationConfig();
+
+# ## Run simulation
+
+@time simulate!(grids, options, output_config)
+
+# ## Plot output
+
+summary = CSV.File(joinpath(output_config.directory, "summary.csv"));
+
+# rho_init = npzread("$(output_config.directory)/rho_1.npy");
+rho_last = npzread("$(output_config.directory)/rho_$(length(output_times)).npy");
+δ_lims = extrema(rho_last .- 1)
+
+fig_anim = Figure()
+ax_anim = Axis(fig_anim[1, 1], aspect = DataAspect())
+
+hidedecorations!(ax_anim)
+
+cb_density = Colorbar(fig_anim[1, 2], limits = δ_lims, label = L"$\rho/\rho_{\text{crit}}$")
+
+frame = Observable(1)
+
+rho = lift(i -> npzread(joinpath(output_config.directory, "rho_$(i).npy"))[:, :, 1], frame)
+δ = @lift($rho .- 1)
+
+contourf!(
+    ax_anim,
+    grids.x[:, 1, 1],
+    grids.y[1, :, 1],
+    δ,
+    levels = range(δ_lims[1], δ_lims[2], 10),
+)
+
+Record(fig_anim, 1:length(output_times); framerate = 5) do f
+    frame[] = f
+end