activate! GLMakie

src/Animation.jl

@@ -115,24 +115,6 @@ function animate_bundle!(args, sim_consts::ReCo.SimConsts)
     return nothing
 end
 
-function sort_bundle_paths(bundle_paths::Vector{String})
-    n_bundles = length(bundle_paths)
-
-    bundle_nums = Vector{Int64}(undef, n_bundles)
-
-    extension_length = 5 # == length(".jld2")
-
-    for i in 1:n_bundles
-        bundle_path = bundle_paths[i]
-        bundle_num_string = bundle_path[(findfirst("bundle_", bundle_path).stop + 1):(end - extension_length)]
-        bundle_nums[i] = parse(Int64, bundle_num_string)
-    end
-
-    sort_perm = sortperm(bundle_nums)
-
-    return bundle_paths[sort_perm]
-end
-
 function animate_with_sim_consts(
     dir::String,
     sim_consts::ReCo.SimConsts,
@@ -142,6 +124,7 @@ function animate_with_sim_consts(
     show_skin_circle::Bool,
     show_frame_diff::Bool,
 )
+    GLMakie.activate!()
     set_theme!(theme_black())
 
     fig = Figure(; resolution=(1080, 1080))
@@ -199,9 +182,7 @@ function animate_with_sim_consts(
             segments_y = Observable(zeros(2 * n_particles))
         end
 
-        bundle_paths = readdir("$dir/bundles"; join=true, sort=false)
+        bundle_paths = ReCo.sorted_bundle_paths(dir)
-
-        bundle_paths = sort_bundle_paths(bundle_paths)
 
         @showprogress 1 for (n_bundle, bundle_path) in enumerate(bundle_paths)
             bundle::ReCo.Bundle = JLD2.load_object(bundle_path)

src/ReCo.jl

@@ -6,7 +6,7 @@ using StaticArrays: SVector
 using JLD2: JLD2
 using Distributions: Uniform, Normal
 using ProgressMeter: @showprogress
-using CellListMap: Box, CellList, map_pairwise!, UpdateCellList!
+using CellListMap: CellListMap
 
 using Random: Random
 using Dates: Dates

src/data.jl

@@ -76,4 +76,24 @@ function save_bundle(dir::String, bundle::Bundle, n_bundle::Int64, T::Float64)
     JLD2.save_object("$dir/sim_state.jld2", SimState(n_bundle, round(T; digits=3)))
 
     return nothing
+end
+
+function sorted_bundle_paths(dir::String)
+    bundle_paths = readdir("$dir/bundles"; join=true, sort=false)
+
+    n_bundles = length(bundle_paths)
+
+    bundle_nums = Vector{Int64}(undef, n_bundles)
+
+    extension_length = 5 # == length(".jld2")
+
+    for i in 1:n_bundles
+        bundle_path = bundle_paths[i]
+        bundle_num_string = bundle_path[(findfirst("bundle_", bundle_path).stop + 1):(end - extension_length)]
+        bundle_nums[i] = parse(Int64, bundle_num_string)
+    end
+
+    sort_perm = sortperm(bundle_nums)
+
+    return bundle_paths[sort_perm]
 end

src/run.jl

@@ -2,6 +2,10 @@ function empty_hook(args...)
     return nothing
 end
 
+function gen_cell_list_box(half_box_len::Float64, skin_r::Float64)
+    return CellListMap.Box(SVector(2 * half_box_len, 2 * half_box_len), skin_r)
+end
+
 function run_sim(
     dir::String;
     duration::Float64,
@@ -97,10 +101,7 @@ function run_sim(
         ],
         n_bundle_snapshots=n_bundle_snapshots,
         bundle=Bundle(sim_consts.n_particles, n_bundle_snapshots),
-        box=Box(
+        box=gen_cell_list_box(sim_consts.half_box_len, sim_consts.skin_r),
-            SVector(2 * sim_consts.half_box_len, 2 * sim_consts.half_box_len),
-            sim_consts.skin_r,
-        ),
     )
 
     simulate!(

src/simulation.jl

@@ -21,9 +21,9 @@ function update_verlet_lists!(args, cl)
         args.particles_c[i] = args.particles[i].c
     end
 
-    cl = UpdateCellList!(args.particles_c, args.box, cl; parallel=false)
+    cl = CellListMap.UpdateCellList!(args.particles_c, args.box, cl; parallel=false)
 
-    map_pairwise!(
+    CellListMap.map_pairwise!(
         (x, y, i, j, d2, output) -> push_to_verlet_list!(args.verlet_lists, i, j),
         nothing,
         args.box,
@@ -102,6 +102,10 @@ function gen_run_additional_hooks(env_helper::RL.EnvHelper, integration_step::In
            (integration_step == 1)
 end
 
+function gen_cell_list(particles_c::Vector{SVector{2,Float64}}, box::CellListMap.Box)
+    return CellListMap.CellList(particles_c, box; parallel=false)
+end
+
 function simulate!(
     args,
     T0::Float64,
@@ -117,7 +121,7 @@ function simulate!(
 
     task::Union{Task,Nothing} = nothing
 
-    cl = CellList(args.particles_c, args.box; parallel=false)
+    cl = gen_cell_list(args.particles_c, args.box)
     cl = update_verlet_lists!(args, cl)
 
     first_integration_step = true