Fixed graphics

analysis/mean_squared_displacement.jl

@@ -9,7 +9,7 @@ using ProgressMeter: ProgressMeter
 
 using ReCo: ReCo
 
-includet("../graphics/common_CairoMakie.jl")
+includet("../src/Visualization/common_CairoMakie.jl")
 
 # IMPORTANT: Disable the periodic boundary conditions
 # The arguments types have to match for the function to be overwritten!
@@ -35,10 +35,11 @@ function msd_simulation(
     half_box_len::Float64,
     T::Float64,
     snapshot_at::Float64,
-    parent_dir::String,
+    parent_dir::String;
     comment::String="",
+    seed::Int64=42,
 )
-    Random.seed!(42)
+    Random.seed!(seed)
 
     dir = ReCo.init_sim(;
         n_particles=1,
@@ -76,7 +77,7 @@ function mean_squared_displacement(;
         parent_dir = main_parent_dir * "/$v₀"
 
         Threads.@threads for sim_ind in 1:n_simulations
-            dir = msd_simulation(v₀, half_box_len, T, 0.5, parent_dir, "$sim_ind")
+            dir = msd_simulation(v₀, half_box_len, T, 0.5, parent_dir; comment="$sim_ind")
 
             sim_dirs[sim_ind, v₀_ind] = dir
 
@@ -172,10 +173,8 @@ function run_msd_analysis()
 end
 
 function plot_random_walk(; T::Float64, v₀::Float64, seed::Int64)
-    Random.seed!(seed)
-
     half_box_len = max_possible_displacement(T, v₀)
-    dir = msd_simulation(v₀, half_box_len, T, 8.0, "random_walk_$(Dates.now())")
+    dir = msd_simulation(v₀, half_box_len, T, 8.0, "random_walk_$(Dates.now())"; seed=seed)
 
     ts = Float64[]
     cs = SVector{2,Float64}[]
@@ -209,12 +208,14 @@ function plot_random_walk(; T::Float64, v₀::Float64, seed::Int64)
 
     end_point_plot = scatter!(ax, cs[end]; markersize=marker_size, color=:red)
 
-    expected_mean_squared_displacement_plot = poly!(
+    expected_mean_squared_displacement_plot = arc!(
         ax,
-        Circle(Point2(0.0, 0.0), expected_mean_displacement);
-        strokecolor=:orange,
-        strokewidth=1,
-        color=RGBAf(0.0, 0.0, 0.0, 0.0),
+        Point2(0.0, 0.0),
+        expected_mean_displacement,
+        0,
+        2 * π;
+        color=:orange,
+        linewidth=1,
     )
 
     Legend(

analysis/radial_distribution_function/radial_distribution_function.jl

@@ -9,7 +9,7 @@ using Random: Random
 
 using ReCo: ReCo
 
-includet("../../graphics/common_CairoMakie.jl")
+includet("../../src/Visualization/common_CairoMakie.jl")
 
 function radial_distribution_simulation(;
     n_particles::Int64, v₀s::NTuple{N,Float64}, T::Float64, packing_ratio::Float64