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Diffstat (limited to 't')
5098 files changed, 0 insertions, 2037 deletions
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plot( - q, y, - seriestype = :scatter, label = "Masses @ t = $t", - # xlims = (-1, N + 1), - ylims = (-1, 1), - markerstrokewidth = 0, - ) - - # plot the middle one as red - plot!( - [q[Int(N / 2)]], [0], - seriestype = :scatter, label = "Large mass @ t = $t", - color = :red, - markerstrokewidth = 0, markersize = 10, - ) - - return plot!() -end - -# update the state -function update_state!(q, p, dt) - new_q = copy(q) - new_p = copy(p) - - # update the small masses state - for i in 2:N-1 - dx_right = q[i+1] - q[i] - dx_left = q[i] - q[i-1] - - new_q[i] += dt * p[i] / m - new_p[i] += dt * (K * dx_right - K * dx_left) - end - - # handle the ends, since our 1D system is cyclic - # case where i = 1, first particle - dx_right = q[2] - q[1] - distance_from_L = L - q[N] - dy_left = q[1] - distance_from_L - new_q[1] += dt * p[1] / m - new_p[1] += dt * (K * dx_right - K * dy_left) - - # case where i = N, last particle - distance_from_0 = q[1] - dx_right = L + q[1] - q[N] - dx_left = q[N] - q[N-1] - new_q[N] += dt * p[N] / m - new_p[N] += dt * (K * dx_right - K * dx_left) - - - # update the large mass in middle (different mass, difference case) - middle_index = Int(N / 2) - dx_right = q[middle_index+1] - q[middle_index] - dx_left = q[middle_index] - q[middle_index-1] - new_q[middle_index] += dt * p[middle_index] / M - new_p[Int(N / 2)] += dt * (K * dx_right - K * dx_left) - - # update the state - for i in 1:N - q[i] = new_q[i] - p[i] = new_p[i] - end -end - -display(plot_positions(q, 0)) - -function progress_system(q, p, dt, t_final) - t = 0 - while t < t_final - update_state!(q, p, dt) - t += dt - end -end - -progress_system(q, p, dt, t_final) - -println("Final state:") -println(q) -println(p) - -display(plot_positions(q, t_final)) diff --git a/t/old/animate-positions-.1stringa.mp4 b/t/old/animate-positions-.1stringa.mp4 Binary files differdeleted file mode 100644 index 0964313..0000000 --- a/t/old/animate-positions-.1stringa.mp4 +++ /dev/null diff --git 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diff --git a/t/old/animate-positions-t.mp4 b/t/old/animate-positions-t.mp4 Binary files differdeleted file mode 100644 index a4a34e0..0000000 --- a/t/old/animate-positions-t.mp4 +++ /dev/null diff --git a/t/old/disp.jl b/t/old/disp.jl deleted file mode 100644 index 18e0a1b..0000000 --- a/t/old/disp.jl +++ /dev/null @@ -1,272 +0,0 @@ -M = 10 -m = 1 # mass of particles - -function calculate_force( - left_pos, - middle_pos, - right_pos, - K, - alpha = 0.0, - beta = 1000.0, -) - linear_force = K * (left_pos + right_pos - 2 * middle_pos) - quadratic_force = alpha * (left_pos - middle_pos)^2 + alpha * (right_pos - middle_pos)^2 - cubic_force = beta * (left_pos - middle_pos)^3 + beta * (right_pos - middle_pos)^3 - - return linear_force + quadratic_force + cubic_force -end - -function tendency!(du, u, p, t) - # unpack the params - N, K, m = p - - # get the positions and momenta - qs = u[1:2:end] - ps = u[2:2:end] - - # go over the points in the lattice and update the state - for i in 1:N-1 - mass = m - if i == Int(N / 2) - mass = M - end - - left_index = max(1, i - 1) - right_index = min(N, i + 1) - - du[i*2-1] = ps[i] / mass - force = calculate_force(qs[left_index], qs[i], qs[right_index], K) - du[i*2] = force / mass - end - - # make last point same as first - du[N*2-1] = du[1] = 0 # set to 0 - du[N*2] = du[2] = 0 - - - if t % 100000 == 0 - println("TIME UPDATE: ", t) - end - - # if ps[Int(N / 2)] / M >= 1 - # println("(in sim!) Time: ", t, " Vel: ", ps[Int(N / 2)] / M) - # # println("Other Positions: ", qs) - # println("Other Velocities: ", ps, "\n") - # end -end - -function get_initial_state( - N, - initial_displacement = 2, - initial_velocity = 0, -) - state = zeros(2 * N) - - middle_index = 2 * Int(N / 2) - 1 # middle mass - state[middle_index] = initial_displacement - state[middle_index+1] = initial_velocity * M - return state -end - -using DifferentialEquations -function run_simulation( - N, - K, - m, - final_time, - initial_displacement = 2, - initial_velocity = 0, -) - println("Running simulation with N = $N, K = $K, m = $m, final_time = $final_time, initial_displacement = $initial_displacement, initial_velocity = $initial_velocity\n") - s_0 = get_initial_state(N, initial_displacement, initial_velocity) - - calculate_energy(s_0) - - # pack the params - p = N, K, m - t_span = (0.0, final_time) - prob = ODEProblem(tendency!, s_0, t_span, p) - sol = solve(prob, Tsit5(), reltol = 1e-5, abstol = 1e-5, maxiters = 1e10) # control simulation - - calculate_energy(sol.u[end]) - - println("Done Running Sim!\n\n") - return sol -end - -using Plots -function animate_positions( - states, - time_steps, - time_min = 0, - time_max = 30, - red_threshold = 2, - shift = true, -) - println("Animating positions") - anim = @animate for i in 1:length(time_steps) - t = time_steps[i] - if t < time_min - continue - end - if t > time_max - break - end - positions = states[i][1:2:end] - v_middle = states[i][Int(length(states[1]) / 2)] / M - p_middle = states[i][Int(length(states[1]) / 2)-1] - y_lims = shift ? (-3 + p_middle, 3 + p_middle) : (-3, 3) - # plot(positions, label = "t = $(round(t, digits = 3)), v_middle=$(round(v_middle, digits=3))", marker = :circle, xlabel = "Mass Number", ylabel = "Displacement", ylim = (-3, 3)) - if v_middle >= red_threshold - plot(positions, label = "t = $(round(t, digits = 7)), v_middle=$(round(v_middle, digits=7))", marker = :circle, xlabel = "Mass Number", ylabel = "Displacement", ylim = y_lims, - color = :red, legend = :topright, - ) - else - plot(positions, label = "t = $(round(t, digits = 7)), v_middle=$(round(v_middle, digits=7))", marker = :circle, xlabel = "Mass Number", ylabel = "Displacement", ylim = y_lims, - color = :blue, legend = :topright, - ) - end - end - mp4(anim, "t/animate-positions.mp4", fps = 30) - println("Done animating positions") -end - -function plot_starting_and_final_positions( - states, - time_steps, -) - # plot the positions - middle_index = Int(length(states[1]) / 2) - 1 - pos_init = [x - states[1][middle_index] for x in states[1][1:2:end]] - pos_final = [x - states[end][middle_index] for x in states[end][1:2:end]] - p1 = plot(pos_init, label = "Initial", marker = :circle, xlabel = "Mass Number", ylabel = "Displacement", title = "Positions Over Time") - plot!(p1, pos_final, label = "Final", marker = :circle) - - # plot the vels - vels_init = [x / M for x in states[1][2:2:end]] - vels_final = [x / M for x in states[end][2:2:end]] - p2 = plot(states[1][2:2:end], label = "Initial", marker = :circle, xlabel = "Mass Number", ylabel = "Velocity", title = "Velocities Over Time") - plot!(p2, states[end][2:2:end], label = "Final t = $(time_steps[end])", marker = :circle) - - # save the plots - savefig(p1, "t/initial-final-positions.png") - savefig(p2, "t/initial-final-velocities.png") -end - -function analyize_vels( - states, - time_steps, - threshold = 1.975, -) - println("Analyzing velocities:\n") - output = [] - for i in 1:length(states) - v = states[i][Int(length(states[i]) / 2)] / M - if v >= threshold - 10e-6 - push!(output, i) - println("Time: ", time_steps[i], " Vel: ", v) - end - end - - data = [] - for i in 1:length(states) - push!(data, states[i][Int(length(states[i]) / 2)]) - end - p = plot(data, label = "Velocity Over Time", xlabel = "Time", ylabel = "Velocity") - savefig(p, "t/velocity-over-time.png") - - println("\nDone!\n\n") - return output -end - -function analyize_pos( - states, - time_steps, - threshold = 1.975, -) - println("Analyzing positions:\n") - output = [] - for i in 1:length(states) - if states[i][Int(length(states[i]) / 2)-1] >= threshold - push!(output, i) - println("Time: ", time_steps[i], " Position: ", states[i][Int(length(states[i]) / 2)]) - end - end - - # plot the first 10 seconds of Velocity - data = [] - for i in 1:length(states) - if time_steps[i] > 10 - break - end - push!(data, states[i][Int(length(states[i]) / 2)] - 1) - end - p = plot(data, label = "Position Over Time", xlabel = "Time", ylabel = "Position") - savefig(p, "t/pos-over-time.png") - - println("\nDone!\n\n") - return output -end - -function calculate_energy(state) - # calculate the kinetic energy - kinetic_energy = 0 - vels = state[2:2:end] - for i in 1:N - mass = i == Int(N / 2) - 1 ? M : m - # calculate the kinetic energy - kinetic_energy += 0.5 * vels[i] * vels[i] / mass - end - - # calcaute the potential energy - potential_energy = 0 - pos = state[1:2:end] - for i in 1:N-1 - left_index = max(1, i - 1) - right_index = min(N, i + 1) - potential_energy += 0.5 * K * (pos[left_index] - pos[i])^2 - potential_energy += 0.5 * K * (pos[right_index] - pos[i])^2 - end - - # print the energy - println("Kinetic Energy: ", kinetic_energy) - println("Potential Energy: ", potential_energy) - println("Total Energy: ", kinetic_energy + potential_energy, "\n") -end - -function plot_middle_mass_phase_space(states) - # get the index of the middle mass - middle_index = Int(length(states[1]) / 2) - 1 - # build an array of the pos and vel over time - pos = [] - vel = [] - for i in 1:length(states) - push!(pos, states[i][middle_index]) - push!(vel, states[i][middle_index+1]) - end - - # plot the phase space - p = plot(pos, vel, xlabel = "Position", ylabel = "Momentum", title = "Phase Space of Middle Mass in FPU", label = "Beta = 10, K = 1, N = 64, M = $M") - - # save the plot - savefig(p, "t/phase-space.png") -end - - -# Run the simulation -N = 64 # number of masses -K = 1 # spring constant -final_time = 1000 # seconds -plot_data = [] - -my_vel = 100 - -sol = run_simulation(N, K, m, final_time, 0, my_vel) - -println("final time: ", sol.t[end]) -# s = sol.u[1:2:end] -# analyize_vels(sol.u, sol.t, my_vel) -# analyize_pos(sol.u, sol.t, 1.4) -plot_starting_and_final_positions(sol.u, sol.t) -# animate_positions(sol.u, sol.t, 0, 100, my_vel) # expect 80913.35854226245 for k=10?? rip -plot_middle_mass_phase_space(sol.u) diff --git a/t/old/initial-final-positions.png b/t/old/initial-final-positions.png Binary files differdeleted file mode 100644 index e76793d..0000000 --- a/t/old/initial-final-positions.png +++ /dev/null diff --git a/t/old/initial-final-velocities.png b/t/old/initial-final-velocities.png Binary files differdeleted file mode 100644 index b7cc859..0000000 --- a/t/old/initial-final-velocities.png +++ /dev/null diff --git a/t/old/modes-beta15.png b/t/old/modes-beta15.png Binary files differdeleted file mode 100644 index dbb632d..0000000 --- a/t/old/modes-beta15.png +++ /dev/null diff --git a/t/old/phase-space-.5vel.png b/t/old/phase-space-.5vel.png Binary files differdeleted file mode 100644 index 100cd2e..0000000 --- a/t/old/phase-space-.5vel.png +++ /dev/null diff --git a/t/old/phase-space-chos.png b/t/old/phase-space-chos.png Binary files differdeleted file mode 100644 index cbbbf09..0000000 --- a/t/old/phase-space-chos.png +++ /dev/null diff --git a/t/old/phase-space-stable.png b/t/old/phase-space-stable.png Binary files differdeleted file mode 100644 index 2ffa7c6..0000000 --- a/t/old/phase-space-stable.png +++ /dev/null diff --git a/t/old/phase-space.01strings.png b/t/old/phase-space.01strings.png Binary files differdeleted file mode 100644 index 5e78901..0000000 --- a/t/old/phase-space.01strings.png +++ /dev/null diff --git a/t/old/phase-space.png b/t/old/phase-space.png Binary files differdeleted file mode 100644 index 48e5368..0000000 --- a/t/old/phase-space.png +++ /dev/null diff --git a/t/old/plot_data.png b/t/old/plot_data.png Binary files differdeleted file mode 100644 index d052983..0000000 --- a/t/old/plot_data.png +++ /dev/null diff --git a/t/old/plz.gif b/t/old/plz.gif Binary files differdeleted file mode 100644 index febf678..0000000 --- a/t/old/plz.gif +++ /dev/null diff --git a/t/old/plz.mp4 b/t/old/plz.mp4 Binary files differdeleted file mode 100644 index 6a0d7b4..0000000 --- a/t/old/plz.mp4 +++ /dev/null diff --git a/t/old/pos-over-time.png b/t/old/pos-over-time.png Binary files differdeleted file mode 100644 index e3a732d..0000000 --- a/t/old/pos-over-time.png +++ /dev/null diff --git a/t/old/r.jl b/t/old/r.jl deleted file mode 100644 index 516ab09..0000000 --- a/t/old/r.jl +++ /dev/null @@ -1,134 +0,0 @@ -function dynamics!( - state, - prev_state, - params, - states, - plot_data, -) - # Unpack the parameters - N, K, beta, A, dt, num_steps = params - - for j in 1:num_steps - next_state = zeros(N) - - # update the left particle (set to rest) - state[1] = 0 - - # update the right particle (set to rest) - state[N] = 0 - - # update the middle particles - for i in 2:N-1 - a = 2 * state[i] - prev_state[i] - b = dt * dt * K * (state[i+1] - 2 * state[i] + state[i-1]) - c = dt * dt * beta * ((state[i+1] - state[i])^3 + (state[i-1] - state[i])^3) - - this_mass = 1 - if i == Int(N / 2) - # time = i * dt - # push!(plot_data, (state[i])) - this_mass = 1 - end - next_state[i] = (a + b + c) / this_mass - end - - # push!(states, next_state) - - # update the previous state - for i in 1:N - prev_state[i] = state[i] - end - # update the current state - for i in 1:N - state[i] = next_state[i] - end - - # if the middle mass is close to 2, print the time and position - if state[Int(N / 2)] > 1.995 - println("Time: ", j * dt, " Positions: ", state[Int(N / 2)]) - println("Other Positions: ", state, "\n") - push!(states, (j * dt, state)) - end - - if (j * dt % 100000) == 0 - println("TIME UPDATE: ", j * dt) - end - end -end - -function get_initial_state( - N, - modes, - beta, - A, -) - state = zeros(N) - # amp = A * sqrt(2 / (N - 1)) - # for i in 2:N-1 - # state[i] = amp * sin((modes * π * (i - 1)) / (N - 1)) - # end - # set the middle to be the largest - state[Int(N / 2)] = 2 - return state -end - -function run_simulation( - N, - modes, - beta, - A, - dt, - num_steps, - plot_data, -) - states = [] - state = get_initial_state(N, 1, beta, A) - prev_state = zeros(N) - for i in 1:N - prev_state[i] = state[i] - end - params = (N, modes, beta, A, dt, num_steps) - dynamics!(state, prev_state, params, states, plot_data) - return states -end - -# Run the simulation -N = 10 # number of masses -beta = 0 # cubic string spring -K = 100 # spring constant -A = 10 # amplitude -modes = 3 # number of modes to plot -final_time = 10000000 # seconds -dt = 0.001 # seconds -num_steps = Int(final_time / dt) -params = (N, K, beta, A, dt, num_steps) -plot_data = [] -s = run_simulation(N, K, beta, A, dt, num_steps, plot_data) -println("\nStates of interest:", s) - -# plot the inital positions and the final positions -# using Plots -# plot(get_initial_state(N, 1, beta, A), label = "Initial", marker = :circle, xlabel = "Mass Number", ylabel = "Displacement", title = "First Three Modes") -# plot!(s[end], label = "Final", marker = :circle) - -# plot the middle of the lattice over time -# time_steps = [i * dt for i in 1:num_steps] -# plot(time_steps, plot_data, label = "Middle Mass Over Time", xlabel = "Time", ylabel = "Displacement") -# savefig("t/plot_data.png") - -# print the points close to the origional displacement -# output = [] -# for i in 1:length(plot_data) -# if plot_data[i] > 1.975 -# push!(output, i) -# println("Time: ", i * dt, " Position: ", plot_data[i]) -# end -# end - - -# animate the s array of positions -# anim = @animate for i in 1:length(s) -# plot(s[i], label = "t = $(round(i * dt, digits = 3))", marker = :circle, xlabel = "Mass Number", ylabel = "Displacement", ylim = (-3, 3)) -# end -# mp4(anim, "t/plz.mp4", fps = 30) -# println("Output: ", output) diff --git a/t/old/semi-old b/t/old/semi-old deleted file mode 100644 index e69de29..0000000 --- a/t/old/semi-old +++ /dev/null diff --git a/t/old/t.jl b/t/old/t.jl deleted file mode 100644 index 6a06777..0000000 --- a/t/old/t.jl +++ /dev/null @@ -1,755 +0,0 @@ -# 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() diff --git a/t/old/velocity-over-time.png b/t/old/velocity-over-time.png Binary files differdeleted file mode 100644 index 3cab01f..0000000 --- a/t/old/velocity-over-time.png +++ /dev/null diff --git a/t/plz.jl b/t/plz.jl deleted file mode 100644 index 962398a..0000000 --- a/t/plz.jl +++ /dev/null @@ -1,767 +0,0 @@ -function calculate_force( - left_pos, - middle_pos, - right_pos, - K, - alpha = 0.0, - beta = 0.0, -) - linear_force = K * (left_pos + right_pos - 2 * middle_pos) - quadratic_force = alpha * (left_pos - middle_pos)^2 + alpha * (right_pos - middle_pos)^2 - cubic_force = beta * (left_pos - middle_pos)^3 + beta * (right_pos - middle_pos)^3 - - return linear_force + quadratic_force + cubic_force -end - -function tendency!(du, u, params, t) - # unpack the params - N, modes, beta, A, dt, num_steps = params - - # get the positions and momenta - qs = u[1:2:end] - ps = u[2:2:end] - - num_masses = length(qs) - - # go over the points in the lattice and update the state - for i in 2:num_masses-1 - # left_index = max(1, i - 1) - # right_index = min(N, i + 1) - - du[i*2-1] = ps[i] - force = calculate_force(qs[i-1], qs[i], qs[i+1], 1, 0, beta) - du[i*2] = force - end - - # make last point same as first at rest - du[num_masses*2-1] = du[1] = 0 # set to 0 - du[num_masses*2] = du[2] = 0 - - # if ps[Int(N / 2)] / M >= 1 - # println("(in sim!) Time: ", t, " Vel: ", ps[Int(N / 2)] / M) - # # println("Other Positions: ", qs) - # println("Other Velocities: ", ps, "\n") - # end -end - -function get_initial_state( - N, - modes, - beta, - A, -) - state = zeros(N + 2) - amp = A * sqrt(2 / (N + 1)) - for i in 2:N+1 - state[i] = amp * sin((modes * π * (i - 1)) / (N + 1)) - end - return state -end - -using DifferentialEquations -function run_simulation( - N, - modes, - beta, - A, - dt, - num_steps, -) - println("Running simulation with params: N=$N, modes=$modes, beta=$beta, A=$A, dt=$dt, num_steps=$num_steps") - # states = [] - state = get_initial_state(N, 1, beta, A) - # prev_state = zeros(N) - # for i in 1:N - # prev_state[i] = state[i] - # end - params = (N, modes, beta, A, dt, num_steps) - # dynamics!(state, prev_state, params, states) - - # state above is position, need to add in momentum - s_0 = zeros(2 * (N + 2)) - for i in 1:length(state) - s_0[i*2-1] = state[i] - end - final_time = num_steps * dt - t_span = (0.0, final_time) - prob = ODEProblem(tendency!, s_0, t_span, params) - sol = solve(prob, Tsit5(), reltol = 1e-8, abstol = 1e-8, maxiters = 1e10) # control simulation - - return sol -end - -function get_pos_from_state(state) - return state[1:2:end] -end - -# Run the simulation -# N = 32 # number of masses -# beta = 2.3 # cubic string spring -# A = 10 # amplitude -# modes = 3 # number of modes to plot -# final_time = 100000 # seconds -# dt = 0.05 # seconds -# num_steps = Int(final_time / dt) -# params = (N, modes, beta, A, dt, num_steps) -# println("Running simulation with params: ", params) -# sol = run_simulation(N, modes, beta, A, dt, num_steps) -# states = sol.u -# timesteps = sol.t -# println("Final state: ", states[end]) - -# plot the inital positions and the final positions -using Plots -# init_pos = get_initial_state(N, 1, beta, A) -# final_pos = get_pos_from_state(states[end]) -# println("Initial: ", init_pos) -# println("Final: ", final_pos) -# plot(init_pos, label = "Initial", marker = :circle, xlabel = "Mass Number", ylabel = "Displacement", title = "First Three Modes") -# plot!(final_pos, label = "Final", marker = :circle) -# println("Saving initial-final-beta15.png") -# savefig("t/initial-final-beta-$beta.png") - -function animate_states(states, timesteps, from = 1, to = 1000) - println("\nAnimating states") - # animate the s array of positions - # find the timestep that maps to the state index - i_start = 1 - i_end = length(timesteps) - for i in 1:length(timesteps) - if timesteps[i] <= from - i_start = i - continue - end - if timesteps[i] >= to - i_end = i - break - end - end - - anim = @animate for i in i_start:i_end - s = get_pos_from_state(states[i]) - t = timesteps[i] - plot(s, label = "t = $t", marker = :circle, xlabel = "Mass Number", ylabel = "Displacement", ylim = (-3, 3)) - end - - mp4(anim, "t/animated-fpu.mp4", fps = 30) - println("Done animating, wrote to animated-fpu.mp4\n") -end -# animate_states(states, timesteps, 149500, 150000) - -function caluclate_energies_for_mode(states, mode) - N = length(states[1]) / 2 - 2 - - total = [] - kinetic = [] - potential = [] - - for i in 1:length(states) - total_energy = 0 - kinetic_energy = 0 - potential_energy = 0 - - # find a_k for this mode - poses = get_pos_from_state(states[i]) - a_k = 0 - for j in 1:length(poses) - a_k += poses[j] * sin((mode * (j - 1) * π) / (N + 1)) - end - amp = sqrt(2 / (N + 1)) - a_k *= amp - - # get the potenital energy - omega_k = 2 * sin((mode * π) / (2 * (N + 1))) - p = 0.5 * omega_k^2 * a_k^2 - - # find the kinetic energy - v_k = 0 - vels = states[i][2:2:end] - for j in 1:length(vels) - v_k += vels[j] * sin((mode * (j - 1) * π) / (N + 1)) - end - v_k *= amp - k = 0.5 * v_k^2 - - - total_energy += k + p - kinetic_energy += k - potential_energy += p - push!(total, total_energy) - push!(kinetic, kinetic_energy) - push!(potential, potential_energy) - end - return total, kinetic, potential -end - -function calculate_total_energy_by_state(states, timesteps) - total = [] - kinetic = [] - potential = [] - for i in 1:length(states) - vels = states[i][2:2:end] - k = 0.5 * sum(vels .^ 2) - - poses = get_pos_from_state(states[i]) - p = 0 - for j in 2:length(poses) - p += beta * (poses[j] - poses[j-1])^2 - end - - push!(total, k + p) - push!(kinetic, k) - push!(potential, p) - end - - # plot all three over time on the same plot - plot(timesteps, total, label = "Total Energy", xlabel = "Time", ylabel = "Energy", title = "Total Energy Over Time") - plot!(timesteps, kinetic, label = "Kinetic Energy") - plot!(timesteps, potential, label = "Potential Energy") - - return total, kinetic, potential -end - -function print_energies_for_modes(states, max_mode = 3, index = 1) - # get the sum of total energy over all mode - total = 0 - kinetic = 0 - potential = 0 - for i in 1:max_mode - t, k, p = caluclate_energies_for_mode(states, i) - total += t[index] - kinetic += k[index] - potential += p[index] - end - println("Total Energy: ", total) - println("Kinetic Energy: ", kinetic) - println("Potential Energy: ", potential) -end - -function plot_phase_space(states, mass_number, intersecting_mass = 4) - # get the positions and momenta - qs = [] - ps = [] - - for i in 2:length(states) - # only store if the other mass is crossing 0 - if (states[i-1][intersecting_mass*2-1] < 0 && states[i][intersecting_mass*2-1] > 0) || (states[i-1][intersecting_mass*2-1] > 0 && states[i][intersecting_mass*2-1] < 0) - s = states[i] - q = s[mass_number*2-1] - p = s[mass_number*2] - push!(qs, q) - push!(ps, p) - end - end - - s = scatter( - qs, - ps, - label = "Mass $mass_number", - xlabel = "Displacement", - ylabel = "Momentum", - title = "Phase Space for Masses when Mass $intersecting_mass crosses 0", - legend = :topleft, - marker = :circle, - markersize = 2, - xlim = (-1.5, 1.5), - ylim = (-1.5, 1.5), - ) - - # savefig(s, "t/phase-space-mass$mass_number-beta15.png") - - return s -end - -function analyze_energies_of_n_modes(modes::Array{Int}, states, timesteps, beta) - println("Analyzing energies of modes: ", modes) - - total_by_mode = Dict() - kinetic_by_mode = Dict() - potential_by_mode = Dict() - for j in modes - t, k, p = caluclate_energies_for_mode(states, j) - - total_by_mode[j] = t - kinetic_by_mode[j] = k - potential_by_mode[j] = p - end - - total_energy = [] - kinetic_energy = [] - potential_energy = [] - for i in 1:length(states) - total = 0 - kinetic = 0 - potential = 0 - - for j in modes - total += total_by_mode[j][i] - kinetic += kinetic_by_mode[j][i] - potential += potential_by_mode[j][i] - end - - push!(total_energy, total) - push!(kinetic_energy, kinetic) - push!(potential_energy, potential) - end - - # plot all three over time on the same plot - plot(timesteps, total_energy, label = "Total Energy", xlabel = "Time", ylabel = "Energy", title = "Total Energy Over Time") - plot!(timesteps, kinetic_energy, label = "Kinetic Energy") - plot!(timesteps, potential_energy, label = "Potential Energy") - savefig("t/procs/energies-modes-sum-beta-$beta.png") - println("Saved energies-modes-sum-beta-$beta.png. Summary Below:\n") - - # plot the energies for each mode over time - plt = plot(title = "Energy Over Time for Modes $(join(modes, ", "))", xlabel = "Time", ylabel = "Energy") - for mode in modes - plot!(plt, timesteps, total_by_mode[mode], label = "Mode $mode") - # plot!(plt, timesteps, kinetic_by_mode[mode], label = "Mode $mode Kinetic") - # plot!(plt, timesteps, potential_by_mode[mode], label = "Mode $mode Potential") - end - savefig(plt, "t/procs/energies-modes-separate-beta-$beta.png") - - # print the energies - println("Total Energy Initial: ", total_energy[1]) - println("Total Energy Final: ", total_energy[end]) - println("Kinetic Energy Initial: ", kinetic_energy[1]) - println("Kinetic Energy Final: ", kinetic_energy[end]) - println("Potential Energy Initial: ", potential_energy[1]) - println("Potential Energy Final: ", potential_energy[end], "\n") - - println("Done analyzing energies of modes: ", modes, "\n") - - return total_energy, kinetic_energy, potential_energy, total_by_mode, kinetic_by_mode, potential_by_mode -end - -function animate_masses_phase_space(states, mass_numbers, intersecting_mass = 4) - println("\nAnimating phase space for mass $mass_numbers when mass $intersecting_mass crosses 0") - # animate the s array of positions - # find the timestep that maps to the state index - anim = @animate for i in mass_numbers - s = plot_phase_space(states, i, intersecting_mass) - s - end - - mp4(anim, "t/animated-phase-space-masses-beta-$beta.mp4", fps = 24) -end - -function plot_mode_phase_space(states, mode_num, intersecting_mode, beta) - println("\nPlotting phase space for mode $mode_num") - - # convert the state to a mode - a_modes = [] - vel_modes = [] - a_inter_modes = [] - vel_inter_modes = [] - - N = length(states[1]) / 2 - 2 - - for i in 1:length(states) - a_mode = 0 - vel_mode = 0 - a_inter_mode = 0 - vel_inter_mode = 0 - - positions = states[i][1:2:end] - velocities = states[i][2:2:end] - for j in 2:length(positions)-1 - a_mode += positions[j] * sin((mode_num * (j - 1) * π) / (N + 1)) - vel_mode += velocities[j] * sin((mode_num * (j - 1) * π) / (N + 1)) - a_inter_mode += positions[j] * sin((intersecting_mode * (j - 1) * π) / (N + 1)) - vel_inter_mode += velocities[j] * sin((intersecting_mode * (j - 1) * π) / (N + 1)) - end - - amp = sqrt(2 / (N + 1)) - a_mode *= amp - vel_mode *= amp - a_inter_mode *= amp - vel_inter_mode *= amp - - if i == 1 - push!(a_inter_modes, a_inter_mode) - push!(vel_inter_modes, vel_inter_mode) - continue - end - - if ((a_inter_modes[end] < 0 && a_inter_mode > 0) || (a_inter_modes[end] > 0 && a_inter_mode < 0)) - push!(a_modes, a_mode) - push!(vel_modes, vel_mode) - end - push!(a_inter_modes, a_inter_mode) - push!(vel_inter_modes, vel_inter_mode) - end - - - # plot the phase space - scatter(a_modes, vel_modes, label = "Beta = $beta", xlabel = "Displacement", ylabel = "Momentum", - title = "Phase Space for Mode $mode_num when a_$intersecting_mode crosses 0", - xlim = (-10, 10), - ylim = (-1, 1), - color = :red, - legend = :topright, - ) - # savefig("t/frames/phase-space-mode-$mode_num-beta-$beta.png") - println("Saved phase-space-mode-$mode_num-beta-$beta.png") -end - -function animate_phase_space_plots_over_beta(betas, t_max, desired_mode, intersecting_mode) - N = 32 # number of masses - A = 10 # amplitude - modes = 3 # number of modes to plot - final_time = t_max # seconds - dt = 0.05 # seconds - num_steps = Int(final_time / dt) - - results = [] - for b in betas - s = run_simulation(N, modes, b, A, dt, num_steps) - states = s.u - timesteps = s.t - - push!(results, states) - - println("Simualted beta: ", b, " to t=", timesteps[end]) - end - - anim = @animate for i in 1:length(betas) - plot_mode_phase_space(results[i], desired_mode, intersecting_mode, betas[i]) - end - - mp4(anim, "t/animated-phase-space-modes-over-beta.mp4", fps = 15) -end - -# animate_phase_space_plots_over_beta(collect(0:0.025:4), 25000, 1, 3) - -# analyze_energies_of_n_modes([1, 3, 5, 7, 9, 11], timesteps) - -# animate_masses_phase_space(states, collect(2:N+1), 17) - -# plot_mode_phase_space(states, 1, 3) - -function estimate_lynapov_exponent(t_max, beta, jitter = 0.001) - println("Estimating Lynapov Exponent for beta: ", beta) - - N = 32 # number of masses - A = 10 # amplitude - modes = 3 # number of modes to plot - println("t_msx: ", t_max) - final_time = t_max # seconds - dt = 0.05 # seconds - num_steps = Int(final_time / dt) - - t_span = (0.0, final_time) - params = (N, modes, beta, A, dt, num_steps) - - # run a simulation with normal parameters - is = get_initial_state(N, 1, beta, A) - # plot iniital state - plot(is, label = "Initial State", marker = :circle, xlabel = "Mass Number", ylabel = "Displacement", title = "Initial Positions of Masses", markersize = 4) - is_0 = zeros(2 * (N + 2)) - for i in 1:length(is) - is_0[i*2-1] = is[i] - end - prob_s = ODEProblem(tendency!, is_0, t_span, params) - # solve so that the timestep is exactly set to dt - s = solve(prob_s, SSPRK33(), dt = dt) - states_control = s.u - timesteps = s.t - - - # run a simulation with a small perturbation - # dynamics!(state, prev_state, params, states) - # state above is position, need to add in momentum - is2 = get_initial_state(N, 1, beta, A) .* (1 - jitter) # perturb the initial state - # is2 = get_initial_state(N, 1, beta, A) .- jitter # perturb the initial state - plot!(is2, label = "Perturbed Initial State", marker = :cross, xlabel = "Mass Number", ylabel = "Displacement", title = "Perturbed Initial Positions of Masses", msw = 2) - savefig("t/new/inits-jitter.png") - s_0 = zeros(2 * (N + 2)) - for i in 1:length(is2) - s_0[i*2-1] = is2[i] - end - - # add random jitter to the initial state - # middle_index = Int(N / 2) * 2 - # s_0[middle_index] -= jitter # subtract a little from momenetum of middle particle - - final_time = num_steps * dt - t_span = (0.0, final_time) - prob = ODEProblem(tendency!, s_0, t_span, params) - sol = solve(prob, SSPRK33(), dt = dt) # perturbed simulation - state_perturbed = sol.u - time_perturbed = sol.t - - # println(time_perturbed .- timesteps, "\n") - - println("Finished simulations") - println("Control len: ", length(states_control), " Perturbed len: ", length(state_perturbed), " Time len: ", length(time_perturbed)) - - - # # print the difference in the two initial states - # println("Initial State Difference (pertrubed - control): ", state_perturbed[1] .- states_control[1]) - # println("Final State Difference (pertrubed - control): ", state_perturbed[end] .- states_control[end]) - - # plot the difference in the two states over time - differences = [] - for i in 1:length(state_perturbed) - # calculate mode 1 difference - a_k = 0 - amp = sqrt(2 / (N + 1)) - for j in 1:N - diff = abs(state_perturbed[i][j*2-1] - states_control[i][j*2-1]) - a_k += diff * sin((1 * (j - 1) * π) / (N + 1)) - end - a_k *= amp - push!(differences, a_k) - end - plot(time_perturbed, differences, label = "Difference in States", xlabel = "Time", ylabel = "Difference", title = "Absolute Difference in States Over Time", lw = 1.5, color = :blue) - savefig("t/frames/difference-in-states-beta-$beta.png") - # perform a linear regression on the log of the differences - # cut the data set into everythign after t=500 - # find the index where t = 500 - # index = 1 - # for i in 1:length(time_perturbed) - # if time_perturbed[i] >= 500 - # index = i - # break - # end - # end - # differences = differences[index:end] - # time_perturbed = time_perturbed[index:end] - ln_differeces = log.(differences) - (a, b) = linear_regression(time_perturbed, ln_differeces) - a = round(a, digits = 4) - b = round(b, digits = 4) - plot(time_perturbed, differences, label = "ln(difference in mode1)", xlabel = "Time", ylabel = "Difference", title = "Absolute Difference in States Over Time", msw = 0.0, yscale = :ln, color = :blue, lw = 1.5) - plot!(time_perturbed, exp.(a * time_perturbed .+ b), label = "exp($a*t + $b)", lw = 2, color = :red, linestyle = :dash) - savefig("t/frames/difference-in-states-beta-$beta-log.png") - - println("Saved difference-in-states-beta-$beta.png and difference-in-states-beta-$beta-log.png\n") - println("Lynapov Exponent: ", a) - - # check that solve doesn't explode - # animate_states(state_perturbed, time_perturbed, 0, 1) - return a -end - -# linear regression of the log of the difference -function linear_regression(x, y) - n = length(x) - x̄ = sum(x) / n - ȳ = sum(y) / n - a = sum((x .- x̄) .* (y .- ȳ)) / sum((x .- x̄) .^ 2) - b = ȳ - a * x̄ - return (a, b) -end - -function analyze_equiparition(t_max, beta) - # run a simulation with normal parameters - N = 32 # number of masses - A = 10 # amplitude - modes = 3 # number of modes to plot - final_time = t_max # seconds - dt = 0.05 # seconds - num_steps = Int(final_time / dt) - - t_span = (0.0, final_time) - params = (N, modes, beta, A, dt, num_steps) - s = run_simulation(N, modes, beta, A, dt, num_steps) - - states = s.u - timesteps = s.t - - analyze_energies_of_n_modes([1, 3, 5, 7], states, timesteps, beta) -end - -# my_beta = 0.3 -# estimate_lynapov_exponent(10000, my_beta, 0.001) -# analyze_equiparition(10000, my_beta) - -# function plot_betas_versus_lynapov_exponent(betas, t_max, jitter = 0.001) -# lynapovs = [] -# for b in betas -# lynapov = estimate_lynapov_exponent(t_max, b, jitter) -# push!(lynapovs, lynapov) -# end - -# plot(betas, lynapovs, label = "Lynapov Exponent", xlabel = "Beta", ylabel = "Lynapov Exponent", title = "Lynapov Exponent Over Beta") -# savefig("t/lynapov-over-beta.png") -# end - -function plot_probability_distrubtion_of_mode(energy_of_mode, total_energy, timesteps, beta) - # get the probability distribution of the mode - prob = [] - for i in 1:length(timesteps) - push!(prob, energy_of_mode[i] / total_energy[1]) # energy is conserved - end - - plot(timesteps, prob, label = "Probability of Mode 1", xlabel = "Time", ylabel = "Probability", title = "Probability of Mode 1 Over Time with beta=$beta", ylim = (0, 1)) - savefig("t/probability-mode1-beta-$beta.png") -end - -function analyze_probability_distribution_of_mode(t_max, beta) - # run a simulation with normal parameters - N = 32 # number of masses - A = 10 # amplitude - modes = 3 # number of modes to plot - final_time = t_max # seconds - dt = 0.05 # seconds - num_steps = Int(final_time / dt) - - t_span = (0.0, final_time) - params = (N, modes, beta, A, dt, num_steps) - s = run_simulation(N, modes, beta, A, dt, num_steps) - - states = s.u - timesteps = s.t - - # get the energies of the mode - total_energy, kinetic_energy, potential_energy, total_by_mode, kinetic_by_mode, potential_by_mode = analyze_energies_of_n_modes([1, 3, 5, 7, 9, 11, 13], states, timesteps, beta) - - # get the probability distribution of the mode - # plot_probability_distrubtion_of_mode(total_by_mode[1], total_energy, timesteps, beta) - - # print the time when the probability gets lower than .5 - for i in 1:length(timesteps) - if (total_by_mode[1][i] / total_energy[1]) < 0.6 - println("TIME when probability of mode 1 is less than 0.6 for beta=$beta: ", timesteps[i]) - return timesteps[i] - end - end - - return -1 -end - -# estimate_lynapov_exponent(1000, 0.3, 0.001) - -function plot_pos_at_time_t(t, beta) - # run a simulation with normal parameters - N = 32 # number of masses - A = 10 # amplitude - modes = 3 # number of modes to plot - final_time = t # seconds - dt = 0.05 # seconds - num_steps = Int(final_time / dt) - - t_span = (0.0, final_time) - params = (N, modes, beta, A, dt, num_steps) - s = run_simulation(N, modes, beta, A, dt, num_steps) - - states = s.u - timesteps = s.t - positions = s.u[end][1:2:end] - inital_positions = s.u[1][1:2:end] - - plot(positions, label = "Positions at t=$t", xlabel = "Mass Number", ylabel = "Displacement", title = "Positions of Masses at t=$t, beta=$beta", lw = 2, marker = :circle) - plot!(inital_positions, label = "Initial Positions", lw = 2, marker = :circle) - savefig("t/new/positions-at-t-$t-beta-$beta.png") -end - -function get_breakdown_time(beta, t_find = 3600) - t = analyze_probability_distribution_of_mode(t_find, beta) - if t == -1 - println("Could not find time for beta: ", beta) - return -1 - end - return t -end - - -# plot_pos_at_time_t(1000, 10) -# plot_pos_at_time_t(1000, 0) - - - -# plot_betas_versus_lynapov_exponent(collect(0:1:50), 1000, 0.001) - -# analyze_probability_distribution_of_mode(100000, 2.0) - -# break_down_times = [] -# bs = collect(1:0.5:50) -# for b_s in bs -# t_find = 3600 -# t = analyze_probability_distribution_of_mode(t_find, b_s) -# if t == -1 -# println("Could not find time for beta: ", b_s) -# continue -# end -# push!(break_down_times, t) -# end -# # plot beta vs breakdown time -# plot(bs, break_down_times, label = "Breakdown Time", xlabel = "Beta", ylabel = "Time", title = "Breakdown Time Over Beta") -# savefig("t/breakdown-time-over-beta.png") - -# # plot the log of this -# one_over_breakdown_time = break_down_times .^ (-1) -# (a, b) = linear_regression(bs, one_over_breakdown_time) -# a = round(a, digits = 4) -# b = round(b, digits = 4) -# plot(bs, one_over_breakdown_time, label = "1 / (breakdown time)", xlabel = "Beta", ylabel = "1 / (breakdown time)", title = "Breakdown Time ^ -1 Over Beta", msw = 0.0, color = :blue, lw = 1.5) -# plot!(bs, a * bs .+ b, label = "1 / t = $a * beta + $b", lw = 2, color = :red, linestyle = :dash) -# savefig("t/ln-breakdown-time-over-beta.png") - -# println("Done!") -# # for a range of betas, find the breakdown time and the lynapov exponent -function tmp(betas) - break_down_times = [] - lynapovs = [] - t_find = 350000 - for b in betas - # if b < 0.5 - # t_find = 10000 - # end - t = get_breakdown_time(b, t_find) - if t == -1 - continue - end - t_find = round(Int, t) + 100 - - l = estimate_lynapov_exponent(t_find, b, 0.001) - if l == 0 - println("Lynapov for beta was zero: ", b) - continue - end - push!(break_down_times, t) - push!(lynapovs, l) - end - - # plot lynapov vs breakdown time - scatter(break_down_times, lynapovs, label = "Lynapov Exponent", xlabel = "Breakdown Time", ylabel = "Lynapov Exponent", title = "Lynapov Exponent Over Breakdown Time") - savefig("t/new/new-lynapov-over-breakdown-time.png") - - # plot this over log of lynapovs - ln_lynapovs = log.(lynapovs) - ln_break_down_times = log.(break_down_times) - (a, b) = linear_regression(ln_break_down_times, ln_lynapovs) - a = round(a, digits = 4) - b = round(b, digits = 4) - scatter(ln_break_down_times, ln_lynapovs, label = "ln(Lynapov Exponent)", xlabel = "ln(Breakdown Time)", ylabel = "ln(Lynapov Exponent)", title = "ln(Lynapov Exponent) Over ln(Breakdown Time)", msw = 0.0, color = :blue, lw = 1.5) - plot!(ln_break_down_times, a * ln_break_down_times .+ b, label = "ln(beta) = $a * ln(t) + $b", lw = 2, color = :red, linestyle = :dash) - savefig("t/new/new-ln-lynapov-over-breakdown-time.png") - - # only one log - (a, b) = linear_regression(lynapovs, ln_break_down_times) - a = round(a, digits = 4) - b = round(b, digits = 4) - scatter(lynapovs, ln_break_down_times, label = "ln(Breakdown Time)", xlabel = "Lynapov Exponent", ylabel = "ln(Breakdown Time)", title = "ln(Breakdown Time) Over Lynapov Exponent", msw = 0.0, color = :blue, lw = 1.5) - plot!(lynapovs, a * lynapovs .+ b, label = "ln(t) = $a * beta + $b", lw = 2, color = :red, linestyle = :dash) - savefig("t/new/new-new-ln-breakdown-time-over-lynapov.png") - - - - # plot the lynapoovs to the ^-1 - one_over_breakdown_time = break_down_times .^ (-1) - (a, b) = linear_regression(lynapovs, one_over_breakdown_time) - a = round(a, digits = 4) - b = round(b, digits = 4) - scatter(lynapovs, one_over_breakdown_time, label = "1 / (breakdown time)", xlabel = "Lynapov Exponent", ylabel = "1 / (breakdown time)", title = "1 / (breakdown time) Over Lynapov Exponent", msw = 0.0, color = :blue, lw = 1.5) - plot!(lynapovs, a * lynapovs .+ b, label = "1 / t = $a * beta + $b", lw = 2, color = :red, linestyle = :dash) - savefig("t/new/new-one-over-lynapov-over-breakdown-time.png") - - # plot the lynapov over betas - scatter(betas, lynapovs, label = "Lynapov Exponent", xlabel = "Beta", ylabel = "Lynapov Exponent", title = "Lynapov Exponent Over Beta") - savefig("t/new/new-lynapov-over-beta.png") -end - -tmp(collect(0.3:0.025:10)) - -# estimate_lynapov_exponent(500000, 0.3, 0.001) diff --git a/t/probability-mode1-beta-0.0.png b/t/probability-mode1-beta-0.0.png Binary files differdeleted file mode 100644 index 89030b4..0000000 --- a/t/probability-mode1-beta-0.0.png +++ /dev/null diff --git a/t/probability-mode1-beta-0.3-long.png b/t/probability-mode1-beta-0.3-long.png Binary files differdeleted file mode 100644 index 1c750fc..0000000 --- a/t/probability-mode1-beta-0.3-long.png +++ /dev/null diff --git a/t/probability-mode1-beta-0.3.png b/t/probability-mode1-beta-0.3.png Binary files differdeleted file mode 100644 index 3a00c9c..0000000 --- a/t/probability-mode1-beta-0.3.png +++ /dev/null diff --git 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