Add 1D advection-diffusion

Project.toml

@@ -4,7 +4,7 @@ license = "MIT"
 authors = ["Navid C. Constantinou <[email protected]>", "Gregory L. Wagner <[email protected]>"]
 documentation = "https://fourierflows.github.io/PassiveTracerFlowsDocumentation/dev/"
 repository = "https://github.com/FourierFlows/PassiveTracerFlows.jl"
-version = "0.6.1"
+version = "0.7.0"
 
 [deps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
@@ -19,8 +19,8 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
 CUDA = "^1.3, ^2, ^3"
-DocStringExtensions = "^0.8"
-FourierFlows = "^0.6.17, ^0.7, 0.8, 0.9"
+DocStringExtensions = "0.8, 0.9"
+FourierFlows = "0.9.2"
 GeophysicalFlows = "0.14"
 JLD2 = "^0.1, ^0.2, ^0.3, ^0.4"
 Reexport = "^0.2, ^1"

README.md

@@ -49,6 +49,6 @@ See `examples/` for example scripts.
 
 The code is citable via [zenodo](https://zenodo.org). Please cite as:
 
-> Navid C. Constantinou. and Gregory L. Wagner (2022). FourierFlows/PassiveTracerFlows.jl: PassiveTracerFlows v0.6.1 (Version v0.6.1). Zenodo.  [https://doi.org/10.5281/zenodo.2535983](https://doi.org/10.5281/zenodo.2535983)
+> Navid C. Constantinou, Josef Bisits, and Gregory L. Wagner (2022). FourierFlows/PassiveTracerFlows.jl: PassiveTracerFlows v0.7.0 (Version v0.7.0). Zenodo. [https://doi.org/10.5281/zenodo.2535983](https://doi.org/10.5281/zenodo.2535983)
 
 [FourierFlows.jl]: https://github.com/FourierFlows/FourierFlows.jl

docs/make.jl

@@ -17,6 +17,7 @@ const EXAMPLES_DIR = joinpath(@__DIR__, "..", "examples")
 const OUTPUT_DIR   = joinpath(@__DIR__, "src/literated")
 
 examples = [
+    "onedim_gaussiandiffusion.jl",
     "cellularflow.jl",
     "turbulent_advection-diffusion.jl"
 ]
@@ -56,6 +57,7 @@ makedocs(
            "Home" => "index.md",
            "Examples" => Any[
              "TracerAdvectionDiffusion" => Any[
+               "literated/onedim_gaussiandiffusion.md",
                "literated/cellularflow.md",
                "literated/turbulent_advection-diffusion.md",
                ]

examples/cellularflow.jl

@@ -45,6 +45,8 @@ nothing # hide
 # ## Set up cellular flow
 # We create a two-dimensional grid to construct the cellular flow. Our cellular flow is derived
 # from a streamfunction ``ψ(x, y) = ψ₀ \cos(x) \cos(y)`` as ``(u, v) = (-∂_y ψ, ∂_x ψ)``.
+# The cellular flow is then passed into the `TwoDAdvectingFlow` constructor with `steadyflow = true`
+# to indicate that the flow is not time dependent.
 grid = TwoDGrid(n, L)
 
 ψ₀ = 0.2
@@ -54,13 +56,13 @@ mx, my = 1, 1
 
 uvel(x, y) =  ψ₀ * my * cos(mx * x) * sin(my * y)
 vvel(x, y) = -ψ₀ * mx * sin(mx * x) * cos(my * y)
+advecting_flow = TwoDAdvectingFlow(; u = uvel, v = vvel, steadyflow = true)
 nothing # hide
 
 
 # ## Problem setup
 # We initialize a `Problem` by providing a set of keyword arguments.
-prob = TracerAdvectionDiffusion.Problem(dev; nx=n, Lx=L, κ=κ, steadyflow=true, u=uvel, v=vvel,
-                                          dt=dt, stepper=stepper)
+prob = TracerAdvectionDiffusion.Problem(dev, advecting_flow; nx=n, Lx=L, κ, dt, stepper)
 nothing # hide
 
 # and define some shortcuts

examples/onedim_gaussiandiffusion.jl

@@ -0,0 +1,130 @@
+# # Advection-diffusion of tracer in one dimension
+#
+# This is an example demonstrating the advection-diffusion of a passive tracer in 
+# one dimension. 
+#
+# ## Install dependencies
+#
+# First let's make sure we have all the required packages installed
+
+# ```julia
+# using Pkg
+# pkg.add(["PassiveTracerFlows", "Printf", "Plots", "JLD2"])
+# ```
+#
+# ## Let's begin
+# First load packages needed to run this example.
+using PassiveTracerFlows, Plots, Printf, JLD2, LinearAlgebra
+
+# ## Choosing a device: CPU or GPU
+
+dev = CPU()     # Device (CPU/GPU)
+nothing # hide
+
+
+# ## Numerical parameters and time-stepping parameters
+
+      n = 128            # 2D resolution = n²
+stepper = "RK4"          # timestepper
+     dt = 0.02           # timestep
+ nsteps = 5000           # total number of time-steps
+nothing # hide
+
+
+# ## Physical parameters
+
+L = 2π       # domain size
+κ = 0.01     # diffusivity
+nothing # hide
+
+# ## Flow
+# We set a constant background flow and pass this to `OneDAdvectingFlow` with `steadyflow = true` to indicate the flow is not time dependent.
+u(x) = 0.05
+advecting_flow = OneDAdvectingFlow(; u, steadyflow = true)
+
+# ## Problem setup
+# We initialize a `Problem` by providing a set of keyword arguments.
+prob = TracerAdvectionDiffusion.Problem(dev, advecting_flow; nx=n, Lx=L, κ, dt, stepper)
+nothing # hide
+
+# and define some shortcuts
+sol, clock, vars, params, grid = prob.sol, prob.clock, prob.vars, prob.params, prob.grid
+x = grid.x
+
+# ## Initial condition
+# We advect-diffuse a concentration field that has an initial concentration set to Gaussian.
+gaussian(x, σ) = exp(-x^2 / 2σ^2)
+
+amplitude, spread = 1, 0.15
+c₀ = [amplitude * gaussian(x[i], spread) for i in 1:grid.nx]
+
+TracerAdvectionDiffusion.set_c!(prob, c₀)
+nothing #hide
+
+# ## Saving output
+# We create the saved output using the `Output` function from `FourierFlows.jl` then
+# save the concentration field using the `get_concentration` function every 50 timesteps.
+function get_concentration(prob)
+  ldiv!(prob.vars.c, prob.grid.rfftplan, deepcopy(prob.sol))
+
+  return prob.vars.c
+end
+
+output = Output(prob, "advection-diffusion1D.jld2",
+                (:concentration, get_concentration))
+
+# By calling `saveproblem(output)` we save information that we will use for plotting later on.
+saveproblem(output)
+
+# ## Stepping the problem forward
+# Now we step the problem forward and save output every 50 timesteps.
+
+save_frequency = 50 # frequency at which output is saved
+
+startwalltime = time()
+while clock.step <= nsteps
+  if clock.step % save_frequency == 0
+    saveoutput(output)
+    log = @sprintf("Output saved, step: %04d, t: %.2f, walltime: %.2f min",
+                   clock.step, clock.t, (time()-startwalltime) / 60)
+
+    println(log)
+  end
+
+  stepforward!(prob)
+end
+
+# ## Visualising the output
+# We load the `.jld2` file and create a timeseries of the concentration field
+file = jldopen(output.path)
+
+iterations = parse.(Int, keys(file["snapshots/t"]))
+
+t = [file["snapshots/t/$i"] for i ∈ iterations]
+c = [file["snapshots/concentration/$i"] for i ∈ iterations]
+nothing # hide
+
+# Set up the plotting arguments and look at the initial concentration.
+x, Lx  = file["grid/x"], file["grid/Lx"]
+
+plot_args = (xlabel = "x",
+             ylabel = "c",
+             framestyle = :box,
+             xlims = (-Lx/2, Lx/2),
+             ylims = (0, maximum(c[1])),
+             legend = :false,
+             color = :balance)
+
+p = plot(x, Array(c[1]);
+         title = "concentration, t = " * @sprintf("%.2f", t[1]),
+         plot_args...)
+nothing # hide
+
+# Now, we create a movie of the tracer concentration being advected and  diffused.
+
+anim = @animate for i ∈ 1:length(t)
+  p[1][:title] = "concentration, t = " * @sprintf("%.2f", t[i])
+  p[1][1][:y] = Array(c[i])
+end
+
+mp4(anim, "1D_advection-diffusion.mp4", fps = 12)