small changes

Project.toml

@@ -4,6 +4,8 @@ ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 ProfileView = "c46f51b8-102a-5cf2-8d2c-8597cb0e0da7"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"

src/Particle.jl

@@ -39,21 +39,23 @@ function minimum_image_coordinate(value::Float64; l::Float64)
 end
 
 function minimum_image(v::SVector{2,Float64}; l::Float64)
-    return minimum_image_coordinate.(v; l=l)
+    return SVector(minimum_image_coordinate(v[1]; l=l), minimum_image_coordinate(v[2]; l=l))
 end
 
 function are_overlapping(p1::Particle, p2::Particle, overlapping_r²::Float64, l::Float64)
-    r⃗₁₂ = SVector{2}(p2.c) - SVector{2}(p1.c) # 1 -> 2
+    r⃗₁₂ = SVector(p2.c[1] - p1.c[1], p2.c[2] - p1.c[2]) # 1 -> 2
 
     r⃗₁₂ = minimum_image(r⃗₁₂; l=l)
 
     distance² = r⃗₁₂[1]^2 + r⃗₁₂[2]^2
 
-    return (distance² < overlapping_r², r⃗₁₂, distance²)
+    overlapping = distance² < overlapping_r²
+
+    return (; overlapping, r⃗₁₂, distance²)
 end
 
 function update!(p::Particle)
     @simd for i in 1:2
         p.c[i] = p.tmp_c[i]
     end
-end
+end

src/PreVector.jl

@@ -24,4 +24,4 @@ function iterate(pv::PreVector{T}, state=1) where {T}
     else
         return (pv.v[state], state + 1)
     end
-end
+end

src/ReCo.jl

@@ -20,4 +20,4 @@ includet("setup.jl")
 includet("simulation.jl")
 includet("data.jl")
 includet("animation.jl")
-includet("run.jl")
+includet("run.jl")

src/animation.jl

@@ -33,7 +33,7 @@ function animate(sol::Solution, args, name_part::String; framerate::Int64=10)
             skin_colors = Observable(Vector{RGBAf}(undef, args.N))
         end
 
-        @showprogress 0.5 for frame in 1:(args.n_frames)
+        @showprogress 0.6 for frame in 1:(args.n_frames)
             @simd for i in 1:(args.N)
                 circles[][i] = Circle(
                     Point2(sol.center[i, frame]), args.particle_diameter / 2

src/data.jl

@@ -4,7 +4,9 @@ struct Solution
     φ::Matrix{Float64}
 
     function Solution(N::Int64, n_frames::Int64)
-        return new(zeros(n_frames), [zeros(2) for i in 1:N, j in 1:n_frames], zeros((N, n_frames)))
+        return new(
+            zeros(n_frames), [zeros(2) for i in 1:N, j in 1:n_frames], zeros((N, n_frames))
+        )
     end
 end
 
@@ -17,7 +19,7 @@ function save_frame!(sol, frame, t, particles)
         p_id = p.id
 
         pre_pos = sol.center[p_id, frame]
-        
+
         @simd for i in 1:2
             pre_pos[i] = p.c[i]
         end

src/pair_correlation_function.jl

@@ -10,7 +10,7 @@ function pair_correlation(frame=0, dr=0.1)
     )
 
     n_r = 100
-    rs = range(0, args.l; length=n_r)
+    radius = range(0, args.l; length=n_r)
     N_g = zeros((args.N, n_r))
 
     if frame == 0
@@ -18,7 +18,7 @@ function pair_correlation(frame=0, dr=0.1)
     end
 
     for r_ind in 1:n_r
-        r = rs[r_ind]
+        r = radius[r_ind]
 
         for i in 1:(args.N)
             for j in 1:(args.N)
@@ -43,7 +43,7 @@ function pair_correlation(frame=0, dr=0.1)
     g = zeros(n_r)
 
     for r_ind in 1:n_r
-        r = rs[r_ind]
+        r = radius[r_ind]
         tmp_g = 0.0
 
         for i in 1:(args.N)
@@ -54,14 +54,14 @@ function pair_correlation(frame=0, dr=0.1)
         g[r_ind] = tmp_g
     end
 
-    return plot_g(rs, g)
+    return plot_g(radius, g)
 end
 
-function plot_g(rs, g)
+function plot_g(radius, g)
     fig = Figure(; resolution=(1080, 1080))
     ax = Axis(fig[1, 1]; xlabel=L"r", ylabel=L"g(r)")
 
-    scatterlines!(ax, rs, g)
+    scatterlines!(ax, radius, g)
 
-    return (fig, rs, g)
+    return (; fig, radius, g)
-end
+end

src/run.jl

@@ -5,7 +5,7 @@ function run(;
     δt::Float64=2e-5,
     save_at::Float64=0.1,
     framerate::Int64=0,
-    save_data::Bool=false,
+    save_data::Bool=true,
     n_steps_before_verlet_list_update::Int64=100,
     debug::Bool=false,
 )
@@ -56,15 +56,15 @@ function run(;
         args, δt, T, n_steps_before_verlet_list_update, n_steps_before_save
     )
 
-    name_part = "$(end_time)_T=$(T)_N=$(N)_v=$(v)_dt=$(δt)"
+    name_part = "$(end_time)_T=$(T)_N=$(N)_v=$(v)"
 
     if save_data
-        save_data_jld(sol, args, name_part)
+        save_data_jld(name_part, sol, args, n_steps_before_verlet_list_update)
     end
 
     if framerate > 0
         animate(sol, args, name_part; framerate=framerate)
     end
 
-    return (sol=sol, args=args, name_part=name_part)
+    return (; sol, args, name_part)
 end

src/simulation.jl

@@ -10,7 +10,7 @@ function update_verlet_list!(args)
             p1 = args.particles[i]
             p2 = args.particles[j]
 
-            overlapping, r⃗₁₂, distance² = are_overlapping(p1, p2, args.skin_r², args.l)
+            overlapping = are_overlapping(p1, p2, args.skin_r², args.l).overlapping
 
             if overlapping
                 push!(args.verlet_list[i], j)
@@ -79,7 +79,7 @@ function simulate(
     start_time = now()
     println("Started simulation at $start_time.")
 
-    @showprogress 0.2 for (integration_step, t) in enumerate(0:δt:T)
+    @showprogress 0.6 for (integration_step, t) in enumerate(0:δt:T)
         if integration_step % n_steps_before_save == 0
             frame = save_frame!(sol, frame, t, args.particles)
         end
@@ -95,5 +95,5 @@ function simulate(
     elapsed_time = canonicalize(CompoundPeriod(end_time - start_time))
     println("Done simulation at $end_time and took $elapsed_time.")
 
-    return (sol, end_time)
+    return (; sol, end_time)
 end