Fixed generating particles in run_sim

analysis/pair_correlation.jl

@@ -5,14 +5,16 @@ end
 if splitdir(pwd())[2] != "ReCo"
     error("You have to be in the main directeory ReCo!")
 else
-    include("src/ReCo.jl")
-    includet("src/analysis/pair_correlation_function.jl")
+    include("src/analysis/pair_correlation_function.jl")
 end
 
 ##
 
+using JLD2
+
 using CairoMakie
 CairoMakie.activate!()
+set_theme!(theme_black())
 
 ##
 

src/Particle.jl

@@ -10,7 +10,7 @@ mutable struct Particle
     φ::Float64 # Angle
 
     function Particle(; id::Int64, c::Vector{Float64}, φ::Float64)
-        return new(id, c, copy(c), φ)
+        return new(id, c, zeros(2), φ)
     end
 end
 

src/PreVector.jl

@@ -1,3 +1,5 @@
+import Base: push!, iterate
+
 mutable struct PreVector{T}
     last_ind::UInt64
     v::Vector{T}

src/analysis/pair_correlation_function.jl

@@ -1,3 +1,9 @@
+using CairoMakie, LaTeXStrings
+using StaticArrays
+using LoopVectorization: @tturbo
+
+using ReCo: minimum_image
+
 function plot_g(radius, g, variables)
     fig = Figure()
     ax = Axis(

src/animation.jl

@@ -4,6 +4,8 @@ using LaTeXStrings: @L_str
 function animate(dir::String; framerate=0)
     println("Generating animation...")
 
+    set_theme!(theme_black())
+
     fig = Figure(; resolution=(1080, 1080))
     ax = Axis(
         fig[1, 1];

src/run.jl

@@ -1,5 +1,6 @@
 using Random: Random
 using JSON3: JSON3
+using JLD2: JLD2
 
 function run_sim(
     dir::String;
@@ -33,6 +34,12 @@ function run_sim(
 
     n_bundle_snapshots = min(n_snapshots, n_bundle_snapshots)
 
+    status = JSON3.read(read("$dir/status.json", String))
+    n_bundles = status.n_bundles
+
+    bundles_dir = "$dir/bundles"
+    bundle = JLD2.load_object("$bundles_dir/bundle_$n_bundles.jld2")
+
     args = (
         v=sim_consts.v,
         skin_r=skin_r,
@@ -49,17 +56,13 @@ function run_sim(
         N=sim_consts.N,
         l=sim_consts.l,
         particle_diameter=sim_consts.particle_diameter,
-        particles=generate_particles(
-            sim_consts.grid_n, sim_consts.grid_box_width, sim_consts.l
-        ),
+        particles=generate_particles(bundle, sim_consts.N),
         verlet_list=[PreVector{Int64}(sim_consts.N - 1) for i in 1:(sim_consts.N - 1)],
         n_bundle_snapshots=n_bundle_snapshots,
         bundle=Bundle(sim_consts.N, n_bundle_snapshots),
     )
 
-    status = JSON3.read(read("$dir/status.json", String))
     T0::Float64 = status.T
-
     T = T0 + duration
 
     start_datetime = now()
@@ -82,10 +85,7 @@ function run_sim(
         start_datetime,
     )
 
-    n_bundles::Int64 = status.n_bundles
     next_bundle = n_bundles + 1
-    bundles_dir = "$dir/bundles"
-    mkpath(bundles_dir)
 
     if n_bundle_snapshots > 0
         save_data = true

src/setup.jl

@@ -1,13 +1,14 @@
 using Distributions: Uniform
 using Dates: now
 using JSON3: JSON3
+using ReCo: Bundle, Particle
 
 function initial_particle_grid_pos(i, j; grid_box_width, l)
     term = -0.5 * grid_box_width - l
     return [k * grid_box_width + term for k in (i, j)]
 end
 
-function generate_particles(grid_n, grid_box_width, l)
+function generate_particles(grid_n::Int64, grid_box_width::Float64, l::Float64)
     particles = Vector{Particle}(undef, grid_n^2)
 
     id = 1
@@ -27,6 +28,16 @@ function generate_particles(grid_n, grid_box_width, l)
     return particles
 end
 
+function generate_particles(bundle::Bundle, N::Int64)
+    particles = Vector{Particle}(undef, N)
+
+    for id in 1:N
+        particles[id] = Particle(; id=id, c=bundle.c[id, end], φ=bundle.φ[id, end])
+    end
+
+    return particles
+end
+
 function init_sim(;
     N::Int64, v::Float64, δt::Float64=1e-5, packing_ratio::Float64=0.5, comment::String=""
 )