Better modularity and export

Project.toml

@@ -11,4 +11,3 @@ ProfileView = "c46f51b8-102a-5cf2-8d2c-8597cb0e0da7"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
-Traceur = "37b6cedf-1f77-55f8-9503-c64b63398394"

src/ReCo.jl

@@ -21,4 +21,5 @@ includet("setup.jl")
 includet("simulation.jl")
 includet("data.jl")
 includet("animation.jl")
+includet("postprocess.jl")
 includet("run.jl")

src/animation.jl

@@ -1,4 +1,4 @@
-function animate(sol::Solution, args, filename::String; framerate::Int64=10)
+function animate(directory::String, sol::Solution, variables)
     println("Generating animation...")
 
     set_theme!(theme_black())
@@ -6,7 +6,7 @@ function animate(sol::Solution, args, filename::String; framerate::Int64=10)
     fig = Figure(; resolution=(1080, 1080))
     ax = Axis(
         fig[1, 1];
-        limits=(-args.l, args.l, -args.l, args.l),
+        limits=(-variables.l, variables.l, -variables.l, variables.l),
         aspect=AxisAspect(1),
         xlabel=L"x",
         ylabel=L"y",
@@ -16,37 +16,39 @@ function animate(sol::Solution, args, filename::String; framerate::Int64=10)
 
     Colorbar(fig[1, 2]; limits=(0, 2), colormap=color_scheme, label=L"\frac{\varphi}{\pi}")
 
-    animation_path = "exports/$filename.mkv"
+    animation_path = "$directory/animation.mkv"
 
-    record(fig, animation_path; framerate=framerate) do io
+    record(fig, animation_path; framerate=variables.framerate) do io
-        circles = Observable(Vector{Circle}(undef, args.N))
+        circles = Observable(Vector{Circle}(undef, variables.N))
-        colors = Observable(Vector{RGBAf}(undef, args.N))
+        colors = Observable(Vector{RGBAf}(undef, variables.N))
 
-        if args.debug
+        if variables.debug
-            segments_x = Observable(zeros(2 * args.N))
+            segments_x = Observable(zeros(2 * variables.N))
-            segments_y = Observable(zeros(2 * args.N))
+            segments_y = Observable(zeros(2 * variables.N))
 
-            interaction_circles = Observable(Vector{Circle}(undef, args.N))
+            interaction_circles = Observable(Vector{Circle}(undef, variables.N))
-            skin_circles = Observable(Vector{Circle}(undef, args.N))
+            skin_circles = Observable(Vector{Circle}(undef, variables.N))
 
-            interaction_colors = Observable(Vector{RGBAf}(undef, args.N))
+            interaction_colors = Observable(Vector{RGBAf}(undef, variables.N))
-            skin_colors = Observable(Vector{RGBAf}(undef, args.N))
+            skin_colors = Observable(Vector{RGBAf}(undef, variables.N))
         end
 
-        @showprogress 0.6 for frame in 1:(args.n_frames)
+        @showprogress 0.6 for frame in 1:(variables.n_frames)
-            @simd for i in 1:(args.N)
+            @simd for i in 1:(variables.N)
                 circles[][i] = Circle(
-                    Point2(sol.center[i, frame]), args.particle_diameter / 2
+                    Point2(sol.center[i, frame]), variables.particle_diameter / 2
                 )
 
                 color = get(color_scheme, rem2pi(sol.φ[i, frame] / (2 * π), RoundDown))
                 colors[][i] = RGBAf(color)
 
-                if args.debug
+                if variables.debug
                     interaction_circles[][i] = Circle(
-                        Point2(sol.center[i, frame]), args.interaction_r
+                        Point2(sol.center[i, frame]), variables.interaction_r
+                    )
+                    skin_circles[][i] = Circle(
+                        Point2(sol.center[i, frame]), variables.skin_r
                     )
-                    skin_circles[][i] = Circle(Point2(sol.center[i, frame]), args.skin_r)
 
                     interaction_colors[][i] = RGBAf(color, 0.12)
                     skin_colors[][i] = RGBAf(color, 0.06)
@@ -54,8 +56,8 @@ function animate(sol::Solution, args, filename::String; framerate::Int64=10)
             end
 
             if frame > 1
-                if args.debug
+                if variables.debug
-                    @simd for i in 1:(args.N)
+                    @simd for i in 1:(variables.N)
                         segments_x[][2 * i - 1] = sol.center[i, frame - 1][1]
                         segments_x[][2 * i] = sol.center[i, frame][1]
 
@@ -70,18 +72,18 @@ function animate(sol::Solution, args, filename::String; framerate::Int64=10)
             else # First frame
                 poly!(ax, circles; color=colors)
 
-                if args.debug
+                if variables.debug
                     poly!(ax, interaction_circles; color=interaction_colors)
                     poly!(ax, skin_circles; color=skin_colors)
                 end
 
-                println("Started recording!")
+                println("Recording started!")
             end
 
             notify(circles)
             notify(colors)
 
-            if args.debug
+            if variables.debug
                 notify(interaction_circles)
                 notify(interaction_colors)
 

src/data.jl

@@ -30,22 +30,20 @@ function save_frame!(sol, frame, t, particles)
     return frame
 end
 
-function save_data_jld(sol, args, filename)
+function save_data_jld(directory::String; kwargs...)
-    println("Saving data...")
+    path = "$directory/data.jld2"
-
+    JLD2.jldsave(path; kwargs...)
-    path = "exports/$filename.jld2"
-    JLD2.jldsave(path; sol, args, filename)
 
     println("Data saved to $path.")
 
     return nothing
 end
 
-function save_JSON(filename::String, kwargs...)
+function save_variables(directory::String; kwargs...)
-    path = "exports/$filename.json"
+    path = "$directory/variables.json"
 
     open(path, "w") do io
-        JSON3.pretty(io, kwargs)
+        JSON3.pretty(io, kwargs...)
     end
 
     println("Variables saved to $path.")

src/postprocess.jl

@@ -0,0 +1,21 @@
+function postprocess(sol, variables, save_data)
+    if !isdir("exports")
+        mkdir("exports")
+    end
+
+    directory = "exports/$(variables.end_time)_T=$(variables.T)_N=$(variables.N)_v=$(variables.v)"
+
+    mkdir(directory)
+
+    if save_data
+        save_data_jld(directory; sol=sol, variables=variables)
+
+        save_variables(directory; variables=variables)
+    end
+
+    if variables.framerate > 0
+        animate(directory, sol, variables)
+    end
+
+    return nothing
+end

src/run.jl

@@ -32,6 +32,8 @@ function run(;
     integration_steps = floor(Int64, T / δt) + 1
     n_steps_before_save = round(Int64, save_at / δt)
 
+    n_frames = floor(Int64, integration_steps / n_steps_before_save) + 1
+
     args = (
         v=v,
         c₁=4 * ϵ * 6 * σ^6 * δt * μ,
@@ -49,7 +51,7 @@ function run(;
         skin_r=skin_r,
         skin_r²=skin_r^2,
         verlet_list=[PreVector(Int64, N - 1) for i in 1:(N - 1)],
-        n_frames=floor(Int64, integration_steps / n_steps_before_save) + 1,
+        n_frames=n_frames,
         debug=debug,
     )
 
@@ -57,18 +59,20 @@ function run(;
         args, δt, T, n_steps_before_verlet_list_update, n_steps_before_save
     )
 
-    filename = "$(end_time)_T=$(T)_N=$(N)_v=$(v)"
+    args = nothing
 
-    save_variables_to_JSON = false
+    variables = (;
-
+        # Input
-    additional_variables = (;
+        N,
         T,
+        v,
         δt,
         save_at,
         framerate,
         n_steps_before_verlet_list_update,
         packing_ratio,
         debug,
+        # Calculated
         μ,
         D₀,
         particle_diameter,
@@ -82,24 +86,12 @@ function run(;
         skin_r,
         integration_steps,
         n_steps_before_save,
+        n_frames,
+        # Output
         end_time,
     )
 
-    if save_data
+    postprocess(sol, variables, save_data)
-        save_data_jld(filename, sol, args, additional_variables)
 
-        save_variables_to_JSON = true
+    return (; sol, variables)
-    end
-
-    if framerate > 0
-        animate(sol, args, filename; framerate=framerate)
-
-        save_variables_to_JSON = true
-    end
-
-    if save_variables_to_JSON
-        save_JSON(filename, args, additional_variables)
-    end
-
-    return (; sol, args, filename)
 end

src/setup.jl

@@ -1,7 +1,7 @@
 function initial_particle_grid_pos(i, j; grid_box_width, l)
     dim1_pos(x) = (x - 0.5) * grid_box_width - l
 
-    return dim1_pos.(SVector(i, j))
+    return SVector(dim1_pos(i), dim1_pos(j))
 end
 
 function generate_particles(grid_n, grid_box_width, l)

src/simulation.jl

@@ -93,7 +93,7 @@ function simulate(
 
     end_time = now()
     elapsed_time = canonicalize(CompoundPeriod(end_time - start_time))
-    println("Done simulation at $end_time and took $elapsed_time.")
+    println("Simulation done at $end_time and took $elapsed_time.")
 
     return (; sol, end_time)
 end