Clean up broken comment examples

.gitignore

@@ -3,6 +3,7 @@
 *.jl.cov
 *.jl.mem
 *package-lock.json
+*package.json
 *Manifest.toml
 /docs/build/
 /docs/src/generated/
@@ -16,3 +17,4 @@
 
 # Mac OS
 *.DS_Store
+docs/make.jl

docs/make.jl

@@ -45,9 +45,10 @@ examples = [
 
 # Convert scripts to executable markdown files
 output = "generated"
+outputdir = joinpath(@__DIR__, "src", output)
+rm(outputdir; recursive = true)
 for e ∈ examples
     inputfile = joinpath(@__DIR__, "..", "examples", e.name * ".jl")
-    outputdir = joinpath(@__DIR__, "src", output)
     if e.run
         # With code execution blocks
         Literate.markdown(inputfile, outputdir)
@@ -60,7 +61,7 @@ for e ∈ examples
             inputfile,
             outputdir;
             preprocess = content ->
-                "# *Note: Output is not generated for this example to save resources on GitHub.*\n\n" *
+                "# *Note: Output is not generated for this example (to save resources on GitHub).*\n\n" *
                 content,
             postprocess = content -> replace(content, r"@example.*" => "julia"),
         )

examples/Actuator2D.jl

@@ -15,13 +15,13 @@ using GLMakie #!md
 using IncompressibleNavierStokes
 
 # Output directory
-output = "output/Actuator2D"
+outdir = joinpath(@__DIR__, "output", "Actuator2D")
 
 # A 2D grid is a Cartesian product of two vectors
 n = 40
 x = LinRange(0.0, 10.0, 5n + 1)
 y = LinRange(-2.0, 2.0, 2n + 1)
-plotgrid(x, y)
+plotgrid(x, y; figure = (; size = (600, 300)))
 
 # Boundary conditions
 boundary_conditions = (
@@ -65,13 +65,13 @@ state, outputs = solve_unsteady(;
     method = RKMethods.RK44P2(),
     Δt = 0.05,
     processors = (
-        rtp = realtimeplotter(; setup, plot = fieldplot, nupdate = 1),
+        rtp = realtimeplotter(; setup, size = (600, 300), nupdate = 1),
         ## ehist = realtimeplotter(; setup, plot = energy_history_plot, nupdate = 1),
         ## espec = realtimeplotter(; setup, plot = energy_spectrum_plot, nupdate = 1),
-        ## anim = animator(; setup, path = "$output/vorticity.mkv", nupdate = 20),
-        ## vtk = vtk_writer(; setup, nupdate = 10, dir = "$output", filename = "solution"),
+        ## anim = animator(; setup, path = "$outdir/vorticity.mkv", nupdate = 20),
+        ## vtk = vtk_writer(; setup, nupdate = 10, dir = "$outdir", filename = "solution"),
         ## field = fieldsaver(; setup, nupdate = 10),
-        log = timelogger(; nupdate = 1),
+        log = timelogger(; nupdate = 24),
     ),
 );
 
@@ -80,7 +80,7 @@ state, outputs = solve_unsteady(;
 # We may visualize or export the computed fields `(u, p)`.
 
 # Export to VTK
-save_vtk(setup, state.u, state.t, "$output/solution")
+save_vtk(setup, state.u, state.t, "$outdir/solution")
 
 # We create a box to visualize the actuator.
 box = (
@@ -89,16 +89,16 @@ box = (
 )
 
 # Plot pressure
-fig = fieldplot(state; setup, fieldname = :pressure)
+fig = fieldplot(state; setup, size = (600, 300), fieldname = :pressure)
 lines!(box...; color = :red)
 fig
 
 # Plot velocity
-fig = fieldplot(state; setup, fieldname = :velocitynorm)
+fig = fieldplot(state; setup, size = (600, 300), fieldname = :velocitynorm)
 lines!(box...; color = :red)
 fig
 
 # Plot vorticity
-fig = fieldplot(state; setup, fieldname = :vorticity)
+fig = fieldplot(state; setup, size = (600, 300), fieldname = :vorticity)
 lines!(box...; color = :red)
 fig

examples/Actuator3D.jl

@@ -15,7 +15,7 @@ using GLMakie #!md
 using IncompressibleNavierStokes
 
 # Output directory
-output = "output/Actuator3D"
+outdir = joinpath(@__DIR__, "output", "Actuator3D")
 
 # Floating point type
 T = Float64
@@ -89,8 +89,8 @@ ustart = create_initial_conditions(setup, (dim, x, y, z) -> dim() == 1 ? one(x)
             ## plot = energy_spectrum_plot,
             nupdate = 1,
         ),
-        ## anim = animator(; setup, path = "$output/vorticity.mkv", nupdate = 20),
-        ## vtk = vtk_writer(; setup, nupdate = 10, dir = "$output", filename = "solution"),
+        ## anim = animator(; setup, path = "$outdir/vorticity.mkv", nupdate = 20),
+        ## vtk = vtk_writer(; setup, nupdate = 10, dir = "$outdir", filename = "solution"),
         ## field = fieldsaver(; setup, nupdate = 10),
         log = timelogger(; nupdate = 1),
     ),
@@ -104,4 +104,4 @@ ustart = create_initial_conditions(setup, (dim, x, y, z) -> dim() == 1 ? one(x)
 outputs.rtp
 
 # Export to VTK
-save_vtk(setup, u, t, "$output/solution")
+save_vtk(setup, u, t, "$outdir/solution")

examples/BackwardFacingStep2D.jl

@@ -16,7 +16,7 @@ using GLMakie #!md
 using IncompressibleNavierStokes
 
 # Output directory
-output = "output/BackwardFacingStep2D"
+outdir = joinpath(@__DIR__, "output", "BackwardFacingStep2D")
 
 # Floating point type
 T = Float64
@@ -47,7 +47,7 @@ boundary_conditions = (
 # the walls.
 x = LinRange(T(0), T(10), 301)
 y = cosine_grid(-T(0.5), T(0.5), 51)
-plotgrid(x, y)
+plotgrid(x, y; figure = (; size = (600, 150)))
 
 # Build setup and assemble operators
 setup = Setup(x, y; Re, boundary_conditions, ArrayType);
@@ -71,12 +71,14 @@ state, outputs = solve_unsteady(;
             plot = fieldplot,
             ## plot = energy_history_plot,
             ## plot = energy_spectrum_plot,
+            docolorbar = false,
+            size = (600, 150),
             nupdate = 1,
         ),
-        ## anim = animator(; setup, path = "$output/vorticity.mkv", nupdate = 20),
-        ## vtk = vtk_writer(; setup, nupdate = 10, dir = output, filename = "solution"),
+        ## anim = animator(; setup, path = "$outdir/vorticity.mkv", nupdate = 20),
+        ## vtk = vtk_writer(; setup, nupdate = 10, dir = outdir, filename = "solution"),
         ## field = fieldsaver(; setup, nupdate = 10),
-        log = timelogger(; nupdate = 1),
+        log = timelogger(; nupdate = 500),
     ),
 );
 
@@ -85,13 +87,13 @@ state, outputs = solve_unsteady(;
 # We may visualize or export the computed fields
 
 # Export to VTK
-save_vtk(setup, state.u, state.t, "$output/solution")
+save_vtk(setup, state.u, state.t, "$outdir/solution")
 
 # Plot pressure
-fieldplot(state; setup, fieldname = :pressure)
+fieldplot(state; setup, size = (600, 150), fieldname = :pressure)
 
 # Plot velocity
-fieldplot(state; setup, fieldname = :velocitynorm)
+fieldplot(state; setup, size = (600, 150), fieldname = :velocitynorm)
 
 # Plot vorticity
-fieldplot(state; setup, fieldname = :vorticity)
+fieldplot(state; setup, size = (600, 150), fieldname = :vorticity)

examples/BackwardFacingStep3D.jl

@@ -16,10 +16,10 @@ using GLMakie #!md
 using IncompressibleNavierStokes
 
 # Output directory
-output = "output/BackwardFacingStep3D"
+outdir = joinpath(@__DIR__, "output", "BackwardFacingStep3D")
 
 # Floating point type
-T = Float64
+T = Float32
 
 # Array type
 ArrayType = Array
@@ -29,7 +29,7 @@ ArrayType = Array
 ## using Metal; ArrayType = MtlArray
 
 # Reynolds number
-Re = T(3000)
+Re = T(1000)
 
 # A 3D grid is a Cartesian product of three vectors
 x = LinRange(T(0), T(10), 129)
@@ -75,10 +75,10 @@ state, outputs = solve_unsteady(;
             ## plot = energy_spectrum_plot,
             nupdate = 1,
         ),
-        ## anim = animator(; setup, path = "$output/vorticity.mkv", nupdate = 20),
-        ## vtk = vtk_writer(; setup, nupdate = 10, dir = output, filename = "solution"),
+        ## anim = animator(; setup, path = "$outdir/vorticity.mkv", nupdate = 20),
+        ## vtk = vtk_writer(; setup, nupdate = 10, dir = outdir, filename = "solution"),
         ## field = fieldsaver(; setup, nupdate = 10),
-        log = timelogger(; nupdate = 1),
+        log = timelogger(; nupdate = 100),
     ),
 )
 
@@ -87,7 +87,7 @@ state, outputs = solve_unsteady(;
 # We may visualize or export the computed fields
 
 # Export to VTK
-save_vtk(setup, state.u, state.t, "$output/solution")
+save_vtk(setup, state.u, state.t, "$outdir/solution")
 
 # Plot pressure
 fieldplot(state; setup, fieldname = :pressure)

examples/DecayingTurbulence2D.jl

@@ -11,7 +11,7 @@ using GLMakie #!md
 using IncompressibleNavierStokes
 
 # Output directory
-output = "output/DecayingTurbulence2D"
+outdir = joinpath(@__DIR__, "output", "DecayingTurbulence2D")
 
 # Floating point precision
 T = Float64
@@ -52,8 +52,8 @@ state, outputs = solve_unsteady(;
             displayfig = false,
         ),
         espec = realtimeplotter(; setup, plot = energy_spectrum_plot, nupdate = 10),
-        ## anim = animator(; setup, path = "$output/solution.mkv", nupdate = 20),
-        ## vtk = vtk_writer(; setup, nupdate = 10, dir = output, filename = "solution"),
+        ## anim = animator(; setup, path = "$outdir/solution.mkv", nupdate = 20),
+        ## vtk = vtk_writer(; setup, nupdate = 10, dir = outdir, filename = "solution"),
         ## field = fieldsaver(; setup, nupdate = 10),
         log = timelogger(; nupdate = 100),
     ),
@@ -70,7 +70,7 @@ outputs.ehist
 outputs.espec
 
 # Export to VTK
-save_vtk(setup, state.u, state.t, "$output/solution")
+save_vtk(setup, state.u, state.t, "$outdir/solution")
 
 # Plot field
 fieldplot(state; setup)

examples/DecayingTurbulence3D.jl

@@ -11,7 +11,7 @@ using GLMakie #!md
 using IncompressibleNavierStokes
 
 # Output directory
-output = "output/DecayingTurbulence3D"
+outdir = joinpath(@__DIR__, "output", "DecayingTurbulence3D")
 
 # Floating point precision
 T = Float64
@@ -59,8 +59,8 @@ ustart = random_field(setup; psolver);
             displayfig = false,
         ),
         espec = realtimeplotter(; setup, plot = energy_spectrum_plot, nupdate = 10),
-        ## anim = animator(; setup, path = "$output/solution.mkv", nupdate = 20),
-        ## vtk = vtk_writer(; setup, nupdate = 10, dir = output, filename = "solution"),
+        ## anim = animator(; setup, path = "$outdir/solution.mkv", nupdate = 20),
+        ## vtk = vtk_writer(; setup, nupdate = 10, dir = outdir, filename = "solution"),
         ## field = fieldsaver(; setup, nupdate = 10),
         log = timelogger(; nupdate = 100),
     ),
@@ -77,4 +77,4 @@ outputs.ehist
 outputs.espec
 
 # Export to VTK
-save_vtk(setup, u, t, "$output/solution")
+save_vtk(setup, u, t, "$outdir/solution")

examples/LidDrivenCavity2D.jl

@@ -17,7 +17,7 @@ using GLMakie #!md
 using IncompressibleNavierStokes
 
 # Case name for saving results
-output = "output/LidDrivenCavity2D"
+outdir = joinpath(@__DIR__, "output", "LidDrivenCavity2D")
 
 # The code allows for using different floating point number types, including single
 # precision (`Float32`) and double precision (`Float64`). On the CPU, the speed
@@ -90,8 +90,8 @@ processors = (
     ## rtp = realtimeplotter(; setup, plot = fieldplot, nupdate = 50),
     ## ehist = realtimeplotter(; setup, plot = energy_history_plot, nupdate = 10),
     ## espec = realtimeplotter(; setup, plot = energy_spectrum_plot, nupdate = 10),
-    ## anim = animator(; setup, path = "$output/solution.mkv", nupdate = 20),
-    ## vtk = vtk_writer(; setup, nupdate = 100, dir = output, filename = "solution"),
+    ## anim = animator(; setup, path = "$outdir/solution.mkv", nupdate = 20),
+    ## vtk = vtk_writer(; setup, nupdate = 100, dir = outdir, filename = "solution"),
     ## field = fieldsaver(; setup, nupdate = 10),
     log = timelogger(; nupdate = 1000),
 );
@@ -105,10 +105,10 @@ state, outputs = solve_unsteady(; setup, ustart, tlims, Δt = T(1e-3), processor
 #
 # We may visualize or export the computed fields
 
-# Export fields to VTK. The file `output/solution.vti` may be opened for
+# Export fields to VTK. The file `outdir/solution.vti` may be opened for
 # visualization in [ParaView](https://www.paraview.org/). This is particularly
 # useful for inspecting results from 3D simulations.
-save_vtk(setup, state.u, state.t, "$output/solution")
+save_vtk(setup, state.u, state.t, "$outdir/solution")
 
 # Plot pressure
 fieldplot(state; setup, fieldname = :pressure)
@@ -127,7 +127,7 @@ fieldplot(state; setup, fieldname = :vorticity)
 ## outputs.rtp
 ## outputs.ehist
 ## outputs.espec
-## outputs.anim 
+## outputs.anim
 ## outputs.vtk
 ## outputs.field
 outputs.log

examples/LidDrivenCavity3D.jl

@@ -9,7 +9,7 @@ using GLMakie #!md
 using IncompressibleNavierStokes
 
 # Case name for saving results
-output = "output/LidDrivenCavity3D"
+outdir = joinpath(@__DIR__, "output", "LidDrivenCavity3D")
 
 # Floating point type
 T = Float64
@@ -61,19 +61,19 @@ ustart = create_initial_conditions(setup, (dim, x, y, z) -> zero(x))
         ## rtp = realtimeplotter(; setup, plot = fieldplot, nupdate = 50),
         ehist = realtimeplotter(; setup, plot = energy_history_plot, nupdate = 10),
         ## espec = realtimeplotter(; setup, plot = energy_spectrum_plot, nupdate = 10),
-        ## anim = animator(; setup, path = "$output/solution.mkv", nupdate = 20),
-        # vtk = vtk_writer(; setup, nupdate = 100, dir = output, filename = "solution"),
+        ## anim = animator(; setup, path = "$outdir/solution.mkv", nupdate = 20),
+        ## vtk = vtk_writer(; setup, nupdate = 100, dir = outdir, filename = "solution"),
         ## field = fieldsaver(; setup, nupdate = 10),
         log = timelogger(; nupdate = 20),
     ),
 );
 
 # ## Post-process
 #
-# We may visualize or export the computed fields `(V, p)`
+# We may visualize or export the computed fields
 
 # Export to VTK
-save_vtk(setup, u, t, "$output/solution")
+save_vtk(setup, u, t, "$outdir/solution")
 
 # Energy history
 outputs.ehist