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diff --git a/t/old/t.jl b/t/old/t.jl new file mode 100644 index 0000000..6a06777 --- /dev/null +++ b/t/old/t.jl @@ -0,0 +1,755 @@ +# molecular dynamics 2d. + +# usage: +# at the end of this script, under the header "DEMOS", +# you'll see some functions which implement demos from GN chapter 9. +# simply load the script in your development environment +# (I strongly recommend not using jupiter) +# and in the console/REPL run +# demo_0() +# etc. + +# demos 0,1,3 can optionally make an animated gif +# if you call it with the optional argument demo_3(gif=1) + +# lmk if this script is giving you grief or if you find any bugs +# kian@brown.edu + +using Statistics +using StatsPlots + +mutable struct ParticleSystem + N::Int64# number of particles + L::Float64# square box side length + T₀::Float64# initial temperature + t::Float64# system time + dt::Float64# time step + state::Vector{Float64}# state space array + steps::Int64# number of steps + sampleInterval::Int64# interval for sampling data + timeData::Vector{Float64}# array of sampled time points + energyData::Vector{Float64}# array of sampled energy values + tempData::Vector{Float64}# array of sampled temperature values + tempAccumulator::Float64# temperature accumulator + squareTempAccumulator::Float64# T^2 accumulator + virialAccumulator::Float64# virial accumulator + xData::Vector{Vector{Float64}} # array of sampled position data + vData::Vector{Vector{Float64}} # array of sampled velocity data + forceType::String# force +end + +function ParticleSystem(N::Int64 = 64, L::Float64 = 10.0, T₀::Float64 = 1.0) + t = 0.0 + dt = 0.001 + state = zeros(4N) # state space array, [x1,y1,x2,y2,...,vx1,vy1,...] + steps = 0 + timeData = Float64[] + energyData = Float64[] + sampleInterval = 100 + tempData = Float64[] + tempAccumulator = 0.0 + squareTempAccumulator = 0.0 + virialAccumulator = 0.0 + xData = Vector{Float64}[] + vData = Vector{Float64}[] + forceType = "lennardJones" + + return ParticleSystem( + N, + L, + T₀, + t, + dt, + state, + steps, + sampleInterval, + timeData, + energyData, + tempData, + tempAccumulator, + squareTempAccumulator, + virialAccumulator, + xData, + vData, + forceType, + ) +end + +# some useful "views" of the state array +# (read the performance tips chapter of the julia manual) +@views positions(state) = state[1:Int64(length(state) / 2)] +@views velocities(state) = state[(Int64(length(state) / 2)+1):end] +@views xcomponent(vector) = vector[1:2:end] +@views ycomponent(vector) = vector[2:2:end] +@views particle(n, vector) = [vector[2n-1], vector[2n]] + +# INITIALIZATION +################################################################################ + +function set_random_positions!(sys::ParticleSystem) + println("\tposition configuration: random") + positions(sys.state) .= rand(2 * sys.N) .* sys.L + cool!(sys) +end + +function set_square_lattice_positions!(sys::ParticleSystem) + println("\tposition configuration: square lattice") + + n = Int64(floor(sqrt(sys.N))) # num lattice points per axis + latticeSpacing = sys.L / n + + if sys.N != n^2 + println("\t\toops... your chosen N=$(sys.N) is not a square number") + println("\t\t-> resetting N to $(n^2).") + sys.N = n^2 + sys.state = zeros(4 * sys.N) + end + + for i in 0:(n-1) + for j in 0:(n-1) + sys.state[2*(i*n+j)+1] = (i + 0.5) * latticeSpacing + sys.state[2*(i*n+j)+2] = (j + 0.5) * latticeSpacing + end + end +end + +function set_triangular_lattice_positions!(sys::ParticleSystem) +end + +function add_position_jitter!(sys::ParticleSystem, jitter::Float64 = 0.5) + println("\tadding a wee bit of random jitter to particle positions...") + + for i ∈ 1:length(positions(sys.state)) + sys.state[i] += rand() - jitter + end +end + +function set_random_velocities!(sys::ParticleSystem) + println("\tvelocity configuration: random") + + velocities(sys.state) .= rand(2 * sys.N) .- 0.5 + zero_total_momentum!(sys) + velocities(sys.state) .*= sqrt(sys.T₀ / temperature(sys)) +end + +function zero_total_momentum!(sys::ParticleSystem) + xcomponent(velocities(sys.state)) .-= + mean(xcomponent(velocities(sys.state))) + ycomponent(velocities(sys.state)) .-= + mean(ycomponent(velocities(sys.state))) +end + + +# FORCES / POTENTIALS +################################################################################ + +function force(sys::ParticleSystem) + if sys.forceType == "lennardJones" + force, virial = lennard_jones_force(sys) + elseif sys.forceType == "powerLaw" + force, virial = power_law_force(sys) + end + + sys.virialAccumulator += virial + + return force +end + +# the minimum image approximation +# (periodic boundary conditions) +function minimum_image(xij::Float64, L::Float64) + if xij > (L / 2) + xij -= L + elseif xij < -(L / 2) + xij += L + end + return xij +end + +function lennard_jones_force(sys::ParticleSystem) + x = xcomponent(positions(sys.state)) + y = ycomponent(positions(sys.state)) + virial = 0.0 + force = zeros(2 * sys.N) + + Threads.@threads for i ∈ 1:(sys.N-1) + for j ∈ (i+1):sys.N + dx = minimum_image(x[i] - x[j], sys.L) + dy = minimum_image(y[i] - y[j], sys.L) + + r2inv = 1.0 / (dx^2 + dy^2) + f = 48.0 * r2inv^7 - 24.0 * r2inv^4 + fx = dx * f + fy = dy * f + + force[2*i-1] += fx + force[2*i] += fy + force[2*j-1] -= fx + force[2*j] -= fy + + virial += fx * dx + fy * dy + end + end + + return force, 0.5 * virial +end + +function lennard_jones_potential(sys::ParticleSystem) + x = xcomponent(positions(sys.state)) + y = ycomponent(positions(sys.state)) + U = 0.0 + + Threads.@threads for i in 1:(sys.N-1) + for j in (i+1):sys.N + dx = minimum_image(x[i] - x[j], sys.L) + dy = minimum_image(y[i] - y[j], sys.L) + + r2inv = 1.0 / (dx^2 + dy^2) + U += r2inv^6 - r2inv^3 + end + end + return 4.0 * U +end + +function power_law_force(sys::ParticleSystem) +end + +function power_law_potential(sys::ParticleSystem) +end + +# TIME EVOLUTION +################################################################################ + +function keep_particles_in_box!(sys::ParticleSystem) + for i in 1:(2*sys.N) + if positions(sys.state)[i] > sys.L + positions(sys.state)[i] -= sys.L + elseif positions(sys.state)[i] < 0.0 + positions(sys.state)[i] += sys.L + end + end + + # # another way of doing this: use the ternary operator + # for i in 1:(2 * sys.N) + # positions(sys.state)[i] < 0.0 ? + # positions(sys.state)[i] % sys.L + sys.L : + # positions(sys.state)[i] % sys.L + # end +end + +function verlet_step!(sys::ParticleSystem) + # compute acceleration at current time + acceleration = force(sys) + + # compute positions at t + dt + positions(sys.state) .+= + velocities(sys.state) .* sys.dt .+ + 0.5 .* acceleration .* (sys.dt)^2 + + # enforce boundary conditions + # (basically check if any particles left the box and put them back) + # see function implementation for deets + keep_particles_in_box!(sys) + + # compute velocities at t + dt + velocities(sys.state) .+= + 0.5 * sys.dt .* (acceleration + force(sys)) +end + +function evolve!(sys::ParticleSystem, runtime::Float64 = 10.0) + numsteps = Int64(abs(runtime / sys.dt) + 1) + + print_evolution_message(runtime, numsteps) + + @time for step in 1:numsteps + verlet_step!(sys) + zero_total_momentum!(sys) + + if (step % sys.sampleInterval == 1) + push!(sys.timeData, sys.t) + push!(sys.energyData, energy(sys)) + push!(sys.xData, positions(sys.state)) + push!(sys.vData, velocities(sys.state)) + + T = temperature(sys) + push!(sys.tempData, T) + sys.tempAccumulator += T + sys.squareTempAccumulator += T^2 + end + + sys.t += sys.dt + sys.steps += 1 + end + println("done.") +end + +function reverse_time!(sys) + sys.dt *= -1 + println("\ntime reversed! dt = $(sys.dt)") +end + +function cool!(sys::ParticleSystem, cooltime::Float64 = 1.0) + numsteps = Int64(cooltime / sys.dt) + for step in 1:numsteps + verlet_step!(sys) + velocities(sys.state) .*= (1.0 - sys.dt) + end + reset_statistics!(sys) +end + +# MEASUREMENTS +################################################################################ + +function kinetic_energy(sys::ParticleSystem) + return 0.5 * sum(velocities(sys.state) .* velocities(sys.state)) +end + +function potential_energy(sys::ParticleSystem) + return lennard_jones_potential(sys) +end + +function temperature(sys::ParticleSystem) + return kinetic_energy(sys) / sys.N +end + +function energy(sys::ParticleSystem) + return potential_energy(sys) + kinetic_energy(sys) +end + +# STATISTICS +################################################################################ + +function reset_statistics!(sys::ParticleSystem) + sys.steps = 0 + sys.tempAccumulator = 0.0 + sys.squareTempAccumulator = 0.0 + sys.virialAccumulator = 0.0 + sys.xData = [] + sys.vData = [] +end + +function mean_temperature(sys::ParticleSystem) + return sys.tempAccumulator / sys.steps +end + +function mean_square_temperature(sys::ParticleSystem) + return sys.squareTempAccumulator / sys.steps +end + +function mean_pressure(sys::ParticleSystem) + # factor of half because force is calculated twice each step + meanVirial = 0.5 * sys.virialAccumulator / sys.steps + return 1.0 + 0.5 * meanVirial / (sys.N * mean_temperature(sys)) +end + +function heat_capacity(sys::ParticleSystem) + meanTemperature = mean_temperature(sys) + meanSquareTemperature = mean_square_temperature(sys) + σ2 = meanSquareTemperature - meanTemperature^2 + denom = 1.0 - σ2 * sys.N / meanTemperature^2 + return sys.N / denom +end + +function mean_energy(sys::ParticleSystem) + return mean(sys.energyData) +end + +function std_energy(sys::ParticleSystem) + return std(sys.energyData) +end + +# MATH / ADDITIONAL FUNCTIONS +################################################################################ + +function dot(v1::Vector{Float64}, v2::Vector{Float64}) + return sum(v1 .* v2) +end + +# GRAPHS +################################################################################ + +function initialize_plot() + plot( + size = (800, 800), + titlefontsize = 12, + guidefontsize = 12, + ) +end + +function plot_positions_t(sys::ParticleSystem, t::Int64) + initialize_plot() + for n ∈ 1:sys.N + scatter!( + [sys.xData[t][2n-1]], + [sys.xData[t][2n]], + markersize = 4.0, + markercolor = n, + markerstrokewidth = 0.4, + grid = true, + framestyle = :box, + legend = false, + ) + end +end + +function animate(sys::ParticleSystem, interval::Int64 = 1) + println("\ngenerating gif...") + + scatter!() + animation = @animate for t in 1:length(sys.xData) + scatter() + for n ∈ 1:sys.N + scatter!( + [sys.xData[t][2n-1]], + [sys.xData[t][2n]], + #markersize = 4.0, + markercolor = n, + #markerstrokewidth = 0.4, + grid = true, + framestyle = :box, + legend = false, + ) + end + xlims!(0, sys.L) + ylims!(0, sys.L) + xlabel!("x") + ylabel!("y") + end every interval + + gif(animation, "./animation.gif") + println("done.") +end + +function plot_positions(sys::ParticleSystem) + initialize_plot() + for n ∈ 1:sys.N + scatter!( + [xcomponent(positions(sys.state))[n]], + [ycomponent(positions(sys.state))[n]], + markersize = 4.0, + markercolor = n, + markerstrokewidth = 0.4, + grid = true, + framestyle = :box, + legend = false, + ) + end + xlims!(0, sys.L) + ylims!(0, sys.L) + xlabel!("x") + ylabel!("y") + title!("positions at t=$(round(sys.t, digits=4))") +end + +function plot_trajectories(sys::ParticleSystem, particles::Vector{Int64} = [1]) + initialize_plot() + for n ∈ 1:sys.N + scatter!( + [xcomponent(positions(sys.state))[n]], + [ycomponent(positions(sys.state))[n]], + markersize = 4.0, + markercolor = n, + markerstrokewidth = 0.4, + grid = true, + framestyle = :box, + legend = false, + ) + end + + for n in collect(particles) + xdata = [sys.xData[i][2n-1] for i in 1:length(sys.xData)] + ydata = [sys.xData[i][2n] for i in 1:length(sys.xData)] + + # plot trajectory line for nth particle + scatter!( + xdata, + ydata, + color = n, + #markerstrokewidth = 0, + markerstrokecolor = n, + markersize = 0.7, + markeralpha = 0.5, + label = false, + widen = false, + ) + + # plot initial position for nth particle + scatter!( + [sys.xData[1][2n-1]], + [sys.xData[1][2n]], + markersize = 4.0, + markercolor = n, + markerstrokewidth = 0.4, + markeralpha = 0.3, + #label = "pcl. $n @t=t₀", + widen = false, + ) + + # plot final position for nth particle + scatter!( + [sys.xData[end][2n-1]], + [sys.xData[end][2n]], + markersize = 4.0, + markercolor = n, + markerstrokewidth = 0.4, + markeralpha = 1.0, + #label = "pcl $n @t=t", + widen = false, + ) + end + title!("positions & trajectories at time t=$(round(sys.t, digits=2))") + plot!() +end + +function plot_temperature(sys::ParticleSystem) + initialize_plot() + plot!( + sys.timeData, + sys.tempData, + #widen = true, + ) + ylims!( + mean(sys.tempData) - std(sys.tempData) * 20, + mean(sys.tempData) + std(sys.tempData) * 20, + ) + xlabel!("t") + ylabel!("T(t)") + title!("temperature vs time") + +end + +function plot_energy(sys::ParticleSystem, ylimit::Float64 = 1.0) + initialize_plot() + plot!( + sys.timeData, + sys.energyData, + #widen = true, + ) + ylims!( + #ylimit * (mean(sys.energyData) - 1), + #ylimit * (mean(sys.energyData) + 1) + mean(sys.energyData) - std(sys.energyData) * 10, + mean(sys.energyData) + std(sys.energyData) * 10, + ) + xlabel!("t") + ylabel!("E(t)") + title!("energy vs time") +end + +function plot_speed_distribution(sys::ParticleSystem, numSamples::Int64 = 5) + initialize_plot() + + numDataPoints = Int64(length(sys.vData)) + interval = Int64(floor(numDataPoints / numSamples)) + + samples = collect(1:interval:numDataPoints) + for s in samples + speed = sqrt.( + xcomponent(sys.vData[s]) .^ 2 .* + ycomponent(sys.vData[s]) .^ 2 + ) + density!( + sys.vData[s], + normalize = :pdf, + label = "t = $(round(sys.timeData[s], digits=2))", + ) + end + xlabel!("speed") + title!("speed distribution") +end + +# CONSOLE PRINT DATA +################################################################################ + +function print_hello() + println("\nmolecular dynamics!") + println("number of threads: ", Threads.nthreads()) +end + +function print_bonjour() + println("\nbonjour") +end + +function print_system_parameters(sys::ParticleSystem) + println("\nsystem parameters:") + println("\tN = $(sys.N) (number of particles)") + println("\tL = $(sys.L) (side length of square box)") + println("\tDT = $(sys.dt) (time step)") +end + +function print_system_data(sys::ParticleSystem) + println("\nsystem data at time t=$(round(sys.t, digits=4))") + + if sys.steps == 0 + println("\ttemperature: $(temperature(sys))") + println("\tenergy: $(energy(sys))") + else + println("\tsteps evolved: $(sys.steps)") + println("\ttemperature: $(temperature(sys))") + println("\tenergy: $(energy(sys))") + println("\tmean energy: $(mean_energy(sys))") + println("\tstd energy: $(std_energy(sys))") + println("\theat capacity: $(heat_capacity(sys))") + println("\tPV/NkT: $(mean_pressure(sys))") + end +end + +function print_evolution_message(runtime, numsteps) + println("\nevolving...") +end + +# DEMOS +################################################################################ + + +# DEMO 0: APPROACH TO EQUILIBRIUM +function demo_0(; gif = 0) + println("\nDEMO 0: APPROACH TO EQUILIBRIUM") + println("----------------------------------------") + + sys = ParticleSystem(64, 120.0, 1.0) + print_system_parameters(sys) + + set_square_lattice_positions!(sys) + set_random_velocities!(sys) + print_system_data(sys) + p1 = plot_positions(sys) + + evolve!(sys, 20.0) + print_system_data(sys) + + p2 = plot_trajectories(sys, collect(1:64)) + p3 = plot_energy(sys) + p4 = plot_temperature(sys) + + # make gif + if gif == 1 + animate(sys, 1) + end + + plot( + p1, p2, p3, p4, + layout = grid(2, 2, heights = [0.7, 0.3]), + size = (1280, 720), + ) +end + +# DEMO 1: TIME REVERSAL TEST +function demo_1(; gif = 0) + println("\nDEMO 1: TIME REVERSAL TEST") + println("----------------------------------------") + + sys = ParticleSystem(64, 120.0, 1.0) + print_system_parameters(sys) + + set_square_lattice_positions!(sys) + set_random_velocities!(sys) + print_system_data(sys) + p1 = plot_positions(sys) + + evolve!(sys, 50.0) + #p2 = plot_trajectories(sys, collect(1:64)) + p2 = plot_positions(sys) + + reverse_time!(sys) + evolve!(sys, 50.0) + print_system_data(sys) + #p3 = plot_trajectories(sys, collect(1:64)) + p3 = plot_positions(sys) + + # make gif + if gif == 1 + animate(sys, 4) + end + + plot( + p1, p2, p3, + layout = (1, 3), + size = (1200, 400), + ) +end + +# DEMO 2: SPEED DISTRIBUTION +function demo_2() + println("\nDEMO 2: SPEED DISTRIBUTION") + println("----------------------------------------") + + sys = ParticleSystem[] + + # array for speed distribution plots + ps = Plots.Plot{Plots.GRBackend}[] + + # array for trajectory plots + pt = Plots.Plot{Plots.GRBackend}[] + + # initialize three systems with different initial conditions + # but same KE and PE, evolve, and save plots + for i ∈ 1:3 + push!(sys, ParticleSystem(64, 120.0, 1.0)) + + println("\nSYSTEM $i") + print_system_parameters(sys[i]) + + set_square_lattice_positions!(sys[i]) + add_position_jitter!(sys[i]) + set_random_velocities!(sys[i]) + print_system_data(sys[i]) + + evolve!(sys[i], 40.0) + print_system_data(sys[i]) + push!(ps, plot_speed_distribution(sys[i], 5)) + push!(pt, plot_trajectories(sys[i], collect(1:64))) + end + + + # plot speed distribution and trajectory plots + plot( + ps[1], ps[2], ps[3], + pt[1], pt[2], pt[3], + layout = (2, 3), + size = (1920, 1080), + ) +end + +# DEMO 3: MELTING TRANSITION +function demo_3(; gif = 0) + println("\nDEMO 3: MELTING TRANSITION") + println("----------------------------------------") + + # initialize system of particles on square lattice with zero velocity + sys = ParticleSystem(100, 10.0, 5.0) + set_square_lattice_positions!(sys) + print_system_data(sys) + p1 = plot_positions(sys) + + # evolve the system and watch them "crystallize" + # into a triangular lattice formation + evolve!(sys, 20.0) + print_system_data(sys) + p2 = plot_trajectories(sys, collect(1:100)) + + # now, increase the temperature of the system by giving the particles + # some velocity. evolve the system and plot the trajectories. + set_random_velocities!(sys) + evolve!(sys, 60.0) + print_system_data(sys) + p3 = plot_trajectories(sys, collect(1:100)) + + # some more plots + p4 = plot_energy(sys, 0.0) + p5 = plot_temperature(sys) + p6 = plot_speed_distribution(sys, 20) + + # make gif + if gif == 1 + animate(sys, 1) + end + + plot( + p1, p2, p3, p4, p5, p6, + layout = (2, 3), + size = (1280, 720), + ) +end + +demo_0() |