using Dates: Dates using Distributions: Uniform using JLD2: JLD2 using StaticArrays: SVector const DEFAULT_PACKING_FRACTION = 0.5 const DEFAULT_δt = 1e-5 const DEFAULT_SKIN_TO_INTERACTION_RADIUS_RATIO = 3.0 const DEFAULT_EXPORTS_DIR = "exports" const DEFAULT_PARENT_DIR = "" const DEFAULT_COMMENT = "" const DEFAULT_PARTICLE_RADIUS = 0.5 const DEFAULT_Dₜ = 1.0 const DEFAULT_μₜ = 1.0 const DEFAULT_ϵ = 100.0 const DEFAULT_HALF_BOX_LEN = 0.0 function initial_particle_grid_pos( i::Int64, j::Int64, grid_box_width::Float64, half_box_len::Float64 ) term = -0.5 * grid_box_width - half_box_len return SVector(i * grid_box_width + term, j * grid_box_width + term) end function gen_particles(grid_n::Int64, grid_box_width::Float64, half_box_len::Float64) particles = Vector{Particle}(undef, grid_n^2) id = 1 for i in 1:grid_n for j in 1:grid_n particles[id] = Particle( id, initial_particle_grid_pos(i, j, grid_box_width, half_box_len), rand(Uniform(-π, π)), ) id += 1 end end return particles end function gen_particles(bundle::Bundle, n_particles::Int64) particles = Vector{Particle}(undef, n_particles) @simd for id in 1:n_particles particles[id] = Particle(id, bundle.c[id, end], bundle.φ[id, end]) end return particles end function gen_sim_consts( n_particles::Int64, v₀::Float64; δt::Float64=DEFAULT_δt, packing_fraction::Float64=DEFAULT_PACKING_FRACTION, skin_to_interaction_radius_ratio::Float64=DEFAULT_SKIN_TO_INTERACTION_RADIUS_RATIO, half_box_len::Float64=0.0, ) @assert n_particles > 0 @assert v₀ >= 0 @assert δt in 1e-7:1e-7:1e-4 @assert packing_fraction > 0 μₜ = DEFAULT_μₜ Dₜ = DEFAULT_Dₜ particle_radius = DEFAULT_PARTICLE_RADIUS Dᵣ = 3 * Dₜ / ((2 * particle_radius)^2) σ = 2 * particle_radius * 2^(-1 / 6) ϵ = DEFAULT_ϵ interaction_radius = 2^(1 / 6) * σ skin_radius = skin_to_interaction_radius_ratio * interaction_radius buffer = 3 max_approach_after_one_integration_step = buffer * (2 * v₀ * δt) @assert skin_radius >= interaction_radius + max_approach_after_one_integration_step if v₀ != 0.0 n_steps_before_verlet_list_update = floor( Int64, (skin_radius - interaction_radius) / max_approach_after_one_integration_step, ) else n_steps_before_verlet_list_update = 1000 end grid_n = round(Int64, ceil(sqrt(n_particles))) n_particles = grid_n^2 if half_box_len == 0.0 half_box_len = sqrt(n_particles * π / packing_fraction) * σ * 2^(-11 / 6) elseif packing_fraction != DEFAULT_PACKING_FRACTION error("You can not specify half_box_len and packing_fraction at the same time!") else @assert half_box_len > 0.0 end grid_box_width = 2 * half_box_len / grid_n return SimConsts( # Input n_particles, v₀, δt, packing_fraction, # Internal μₜ, Dₜ, particle_radius, Dᵣ, σ, ϵ, interaction_radius, skin_radius, n_steps_before_verlet_list_update, grid_n, half_box_len, grid_box_width, ) end function init_sim_with_sim_consts( sim_consts::SimConsts; exports_dir::String=DEFAULT_EXPORTS_DIR, parent_dir::String=DEFAULT_PARENT_DIR, comment::String=DEFAULT_COMMENT, ) particles = gen_particles( sim_consts.grid_n, sim_consts.grid_box_width, sim_consts.half_box_len ) bundle = Bundle(sim_consts.n_particles, 1) save_snapshot!(bundle, 1, 0.0, particles) sim_dir = exports_dir if length(parent_dir) > 0 sim_dir *= "/$parent_dir" end start_datetime = Dates.now() sim_dir *= "/$(start_datetime)_N=$(sim_consts.n_particles)_v=$(sim_consts.v₀)_R$(rand(1000:9999))" if length(comment) > 0 sim_dir *= "_$comment" end mkpath(sim_dir) task = @async JLD2.save_object("$sim_dir/sim_consts.jld2", sim_consts) save_bundle(sim_dir, bundle, 1, 0.0) runs_dir = "$sim_dir/runs" mkpath(runs_dir) wait(task) return sim_dir end """ init_sim(n_particles::Int64, v₀::Float64; ) Initialize a simulation and return the relative path of the simulation directory. Return `nothing`. # Arguments - `n_particles::Int64`: Number of particles. - `v₀::Float64`: Self-propulsion velocity. Only values in the interval [0.0, 80.0] are tested. - `δt::Float64=$DEFAULT_δt`: Integration time step. - `packing_fraction::Float64=$DEFAULT_PACKING_FRACTION`: Packing fraction. - `skin_to_interaction_radius_ratio::Float64=$DEFAULT_SKIN_TO_INTERACTION_RADIUS_RATIO`: Ratio of skin radius to interaction radius. - `exports_dir::String="$DEFAULT_EXPORTS_DIR"`: Path to exports directory relative to the directory `ReCo.jl`. - `parent_dir::String="$DEFAULT_PARENT_DIR"`: Directory relative to `exports_dir` where the simulation directory is placed. - `comment::String="$DEFAULT_COMMENT"`: Comment to append to the simulation directory name. - `half_box_len::Float64=$DEFAULT_HALF_BOX_LEN` Half box length. The default of 0.0 means that the half box length will be calculated from the packing fraction. Otherwise, the provided half box length will be used. It is not possible to provide a half box length and a packing fraction at the same time. """ function init_sim(; n_particles::Int64, v₀::Float64, δt::Float64=DEFAULT_δt, packing_fraction::Float64=DEFAULT_PACKING_FRACTION, skin_to_interaction_radius_ratio::Float64=DEFAULT_SKIN_TO_INTERACTION_RADIUS_RATIO, exports_dir::String=DEFAULT_EXPORTS_DIR, parent_dir::String=DEFAULT_PARENT_DIR, comment::String=DEFAULT_COMMENT, half_box_len::Float64=DEFAULT_HALF_BOX_LEN, ) sim_consts = gen_sim_consts( n_particles, v₀; δt=δt, packing_fraction=packing_fraction, skin_to_interaction_radius_ratio=skin_to_interaction_radius_ratio, half_box_len, ) return init_sim_with_sim_consts( sim_consts; exports_dir=exports_dir, parent_dir=parent_dir, comment=comment ) end