Moved to JLD2 because to preserve floats

Project.toml

@@ -19,7 +19,6 @@ LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LoopVectorization = "bdcacae8-1622-11e9-2a5c-532679323890"
 Luxor = "ae8d54c2-7ccd-5906-9d76-62fc9837b5bc"
-OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 ProfileView = "c46f51b8-102a-5cf2-8d2c-8597cb0e0da7"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

src/Animation.jl

@@ -5,13 +5,12 @@ export animate
 using GLMakie
 using ColorSchemes: cyclic_mrybm_35_75_c68_n256_s25
 using LaTeXStrings: @L_str
-using JSON3: JSON3
 using JLD2: JLD2
 using ProgressMeter: @showprogress
 
-using ..ReCo: ReCo, Bundle
+using ..ReCo: ReCo
 
-function animate_bundle!(args, sim_consts)
+function animate_bundle!(args, sim_consts::ReCo.SimConsts)
     bundle_t = args.bundle.t
     bundle_c = args.bundle.c
     bundle_φ = args.bundle.φ
@@ -136,7 +135,7 @@ end
 
 function animate_with_sim_consts(
     dir::String,
-    sim_consts,
+    sim_consts::ReCo.SimConsts,
     framerate::Int64,
     show_center_of_mass::Bool,
     show_interaction_circle::Bool,
@@ -205,7 +204,7 @@ function animate_with_sim_consts(
         bundle_paths = sort_bundle_paths(bundle_paths)
 
         @showprogress 1 for (n_bundle, bundle_path) in enumerate(bundle_paths)
-            bundle::Bundle = JLD2.load_object(bundle_path)
+            bundle::ReCo.Bundle = JLD2.load_object(bundle_path)
 
             args = (;
                 # Input
@@ -248,7 +247,7 @@ function animate(
 )
     println("Generating animation...")
 
-    sim_consts = JSON3.read(read("$dir/sim_consts.json", String))
+    sim_consts::ReCo.SimConsts = JLD2.load_object("$dir/sim_consts.jld2")
 
     animate_with_sim_consts(
         dir,

src/Benchmark.jl

@@ -1,7 +1,7 @@
 module Benchmark
 
 using Statistics: mean
-using Dates: now
+using Dates: Dates
 using BenchmarkTools: @benchmark
 using JSON3: JSON3
 
@@ -34,7 +34,7 @@ function run_benchmarks(
                 "duration" => duration,
                 "n_bundle_snapshots" => n_bundle_snapshots,
                 "comment" => comment,
-                "datetime" => now(),
+                "datetime" => Dates.now(),
                 "mean_time/ns" => mean(benchmark.times),
                 "allocs" => benchmark.allocs,
                 "memory" => benchmark.memory,

src/ReCo.jl

@@ -3,15 +3,13 @@ module ReCo
 export init_sim, run_sim, run_rl, animate, LocalCOMEnv
 
 using StaticArrays: SVector
-using OrderedCollections: OrderedDict
 using JLD2: JLD2
-using JSON3: JSON3
 using Distributions: Uniform, Normal
 using ProgressMeter: @showprogress
 using CellListMap: Box, CellList, map_pairwise!, UpdateCellList!
 
 using Random: Random
-using Dates: Dates, now
+using Dates: Dates
 
 include("Error.jl")
 using .Error

src/data.jl

@@ -1,3 +1,40 @@
+struct SimConsts
+    n_particles::Int64
+    v₀::Float64
+    δt::Float64
+    packing_ratio::Float64
+    μ::Float64
+    Dₜ::Float64
+    particle_radius::Float64
+    Dᵣ::Float64
+    σ::Float64
+    ϵ::Float64
+    interaction_r::Float64
+    skin_r::Float64
+    n_steps_before_verlet_list_update::Int64
+    grid_n::Int64
+    half_box_len::Float64
+    grid_box_width::Float64
+end
+
+struct RunParams
+    duration::Float64
+    snapshot_at::Float64
+    seed::Int64
+    n_bundle_snapshots::Int64
+    integration_steps::Int64
+    n_steps_before_snapshot::Int64
+    n_snapshots::Int64
+    T::Float64
+    T0::Float64
+    start_datetime::Dates.DateTime
+end
+
+struct SimState
+    n_bundles::Int64
+    T::Float64
+end
+
 struct Bundle
     t::Vector{Float64}
     c::Matrix{SVector{2,Float64}}
@@ -30,35 +67,13 @@ function save_snapshot!(
     return nothing
 end
 
-function save_bundle(dir::String, bundle::Bundle, n::Int64, T::Float64)
+function save_bundle(dir::String, bundle::Bundle, n_bundle::Int64, T::Float64)
     bundles_dir = "$dir/bundles"
     mkpath(bundles_dir)
 
-    JLD2.save_object("$bundles_dir/bundle_$n.jld2", bundle)
+    JLD2.save_object("$bundles_dir/bundle_$n_bundle.jld2", bundle)
 
-    set_sim_state(dir, n, T)
+    JLD2.save_object("$dir/sim_state.jld2", SimState(n_bundle, round(T; digits=3)))
-
-    return nothing
-end
-
-function set_sim_state(dir::String, n_bundles::Int64, T::Float64)
-    open("$dir/sim_state.json", "w") do f
-        JSON3.write(f, (n_bundles=n_bundles, T=round(T; digits=3)))
-    end
-
-    return nothing
-end
-
-function struct_to_ordered_dict(s)
-    return OrderedDict(key => getfield(s, key) for key in propertynames(s))
-end
-
-function write_struct_to_json(s, path_without_extension::String)
-    ordered_dict = struct_to_ordered_dict(s)
-
-    open("$path_without_extension.json", "w") do f
-        JSON3.write(f, ordered_dict)
-    end
 
     return nothing
 end

src/run.jl

@@ -18,7 +18,7 @@ function run_sim(
 
     Random.seed!(seed)
 
-    sim_consts = JSON3.read(read("$dir/sim_consts.json", String))
+    sim_consts::SimConsts = JLD2.load_object("$dir/sim_consts.jld2")
 
     integration_steps = floor(Int64, duration / sim_consts.δt) + 1
 
@@ -29,7 +29,7 @@ function run_sim(
 
     n_bundle_snapshots = min(n_snapshots, n_bundle_snapshots)
 
-    sim_state = JSON3.read(read("$dir/sim_state.json", String))
+    sim_state::SimState = JLD2.load_object("$dir/sim_state.jld2")
     n_bundles = sim_state.n_bundles
 
     T0::Float64 = sim_state.T
@@ -42,9 +42,9 @@ function run_sim(
     end
 
     @async begin
-        start_datetime = now()
+        start_datetime = Dates.now()
 
-        run_params = (;
+        run_params = RunParams(
             # Input
             duration,
             snapshot_at,
@@ -64,12 +64,12 @@ function run_sim(
         runs_dir = "$dir/runs"
 
         if save_data
-            write_struct_to_json(run_params, "$runs_dir/run_params_$next_bundle")
+            JLD2.save_object("$runs_dir/run_params_$next_bundle.jld2", run_params)
         end
     end
 
     bundles_dir = "$dir/bundles"
-    bundle = JLD2.load_object("$bundles_dir/bundle_$n_bundles.jld2")
+    bundle::Bundle = JLD2.load_object("$bundles_dir/bundle_$n_bundles.jld2")
 
     particles = gen_particles(bundle, sim_consts.n_particles)
 

src/setup.jl

@@ -90,7 +90,7 @@ function gen_sim_consts(
 
     grid_box_width = 2 * half_box_len / grid_n
 
-    return (;
+    return SimConsts(
         # Input
         n_particles,
         v₀,
@@ -113,7 +113,7 @@ function gen_sim_consts(
 end
 
 function init_sim_with_sim_consts(
-    sim_consts;
+    sim_consts::SimConsts;
     exports_dir::String=DEFAULT_EXPORTS_DIR,
     parent_dir::String=DEFAULT_PARENT_DIR,
     comment::String=DEFAULT_COMMENT,
@@ -130,7 +130,7 @@ function init_sim_with_sim_consts(
         dir *= "/$parent_dir"
     end
 
-    start_datetime = now()
+    start_datetime = Dates.now()
     dir *= "/$(start_datetime)_N=$(sim_consts.n_particles)_v=$(sim_consts.v₀)_#$(rand(1000:9999))"
 
     if length(comment) > 0
@@ -139,7 +139,7 @@ function init_sim_with_sim_consts(
 
     mkpath(dir)
 
-    task = @async write_struct_to_json(sim_consts, "$dir/sim_consts")
+    task = @async JLD2.save_object("$dir/sim_consts.jld2", sim_consts)
 
     save_bundle(dir, bundle, 1, 0.0)
 

src/simulation.jl

@@ -125,7 +125,7 @@ function simulate!(
     state_update_helper_hook! =
         state_update_hook! = update_table_and_actions_hook! = empty_hook
 
-    start_time = now()
+    start_time = Dates.now()
     println("Started simulation at $start_time.")
 
     @showprogress 0.6 for (integration_step, t) in enumerate(T0:(args.δt):T)
@@ -186,7 +186,7 @@ function simulate!(
         save_bundle(dir, bundle, n_bundles, T)
     end
 
-    end_time = now()
+    end_time = Dates.now()
     elapsed_time = Dates.canonicalize(Dates.CompoundPeriod(end_time - start_time))
     println("Simulation done at $end_time and took $elapsed_time.")