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Adding progress bars, on the fly plotting/saving and density matrix …
…Observables (#17) * Added progress bars, on the fly plotting/saving and possibility to pass reduced density matrices as Observables * Bug fixes and documentation typos * Corrected a bug where the progress bar wouldn't flush in julia notebooks * Corrected bug of the progressbar * exported new features and readded time logging when progressbar is false * changed default tmp saving directory to be inside the run directory * added Documenter compatibility back * corrected bugs on onthefly
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| Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" | ||
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| [compat] | ||
| Documenter = "1.8" | ||
| Documenter = "1.8" | ||
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| mutable struct ProgressBar | ||
| numsteps::Int | ||
| ETA::Bool | ||
| times::Vector{<:Float64} | ||
| Dmax::Int | ||
| length::UInt | ||
| end | ||
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| """ | ||
| ProgressBar(numsteps::Int; ETA=false, last=10) | ||
| An iterable returning values from 1 to `numsteps`. Displays a progress bar for the for loop where it has been called. | ||
| If ETA is true then displays an estimation of the remaining time calculated based on the time spent computing the last `last` values. | ||
| The progress bar can be activated or deactivated by setting the `progressbar` keyword argument in `runsim` to true or false.""" | ||
| ProgressBar(numsteps::Int; ETA=false, last=10) = ProgressBar(numsteps, ETA, fill(0., (ETA ? last : 1)+1), 0, displaysize(stdout)[2] > 54 ? min(displaysize(stdout)[2]-54, 50) : error("Error : Terminal window too narrow")) | ||
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| function Base.iterate(bar::ProgressBar, state=1) | ||
| Ntimes = length(bar.times)-1 | ||
| if state > bar.numsteps | ||
| println() | ||
| return nothing | ||
| elseif state == 1 | ||
| printstyled("\nCompiling..."; color=:red, bold=true) | ||
| bar.times = fill(time(), Ntimes+1) | ||
| else | ||
| tnow = time() | ||
| dtelapsed = tnow - bar.times[1] | ||
| dtETA = (tnow - bar.times[2+state%Ntimes])*(bar.numsteps - state)/min(state-1, Ntimes) | ||
| dtiter = tnow - bar.times[2+(state-1)%Ntimes] | ||
| bar.times[2+state%Ntimes] = tnow | ||
| elapsedstr = Dates.format(Time(0)+Second(floor(Int, dtelapsed)), dtelapsed>3600 ? "HH:MM:SS" : "MM:SS") | ||
| ETAstr = Dates.format(Time(0)+Second(floor(Int, dtETA)), dtETA>3600 ? "HH:MM:SS" : "MM:SS") | ||
| iterstr = Dates.format(Time(0)+Millisecond(floor(Int, 1000*dtiter)), dtiter>60 ? "MM:SS.sss" : "SS.sss") | ||
| print("\r") | ||
| printstyled("$(round(100*state/bar.numsteps, digits=1))% "; color = :green, bold=true) | ||
| print("┣"*"#"^(round(Int, state/bar.numsteps*bar.length))*" "^(bar.length-round(Int, state/bar.numsteps*bar.length))*"┫") | ||
| printstyled(" $state/$(bar.numsteps) [$(elapsedstr)s"*(bar.ETA ? "; ETA:$(ETAstr)s" : "")*"; $(iterstr)s/it"*(bar.Dmax > 0 ? "; Dmax=$(bar.Dmax)" : "")*"]"; color = :green, bold=true) | ||
| end | ||
| return (state, state+1) | ||
| end | ||
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| """ | ||
| onthefly(;plot_obs=nothing::Union{<:Observable, Nothing}, save_obs=Vector{Observable}(undef, 0)::Union{<:Observable, Vector{<:Observable}}, savedir="auto", step=10::Int, func=identity<:Function, compare=nothing::Union{Tuple{Vector{Float64}, Vector{Float64}}, Nothing}, clear=identity<:Function) | ||
| Helper function returning a dictionnary containing the necessary arguments for on the fly plotting or saving in the `runsim` function. | ||
| # Arguments | ||
| * `plot_obs` : Observable to plot | ||
| * `save_obs` : List of Observable(s) to save | ||
| * `savedir` : Used to specify the path where temporary files are stored, default is `"auto"` which saves in a "tmp" folder in the run folder (generally located at "~/MPSDynamics/<unid>/tmp/"). | ||
| * `step` : Number of time steps every which the function plots or saves the data | ||
| * `func` : Function to apply to the result of measurement of plot_obs (for example `real` or `abs` to make a complex result possible to plot) | ||
| * `compare` : Tuple `(times, data)` of previous results to compare against the plot_obs results, | ||
| * `clear` : Function used to clear the output before each attempt to plot, helpful for working in Jupyter notebooks where clear=IJulia.clear_output allows to reduce the size of the cell output | ||
| # Examples | ||
| For example in the [Spin-Boson model example](@ref "The Spin Boson Model"), adding the following argument to the `runsim` function allows to save | ||
| the "sz" observable `ob1` in the directory "~/MPSDynamics/<unid>/tmp/" and plot its real part during the simulation: | ||
| ```julia | ||
| runsim(..., onthefly=onthefly(plot_obs=ob1, save_obs=[ob1], savedir="auto", step=10, func=real)) | ||
| ``` | ||
| To merge the temporary files in one usable file, one can then use [`MPSDynamics.mergetmp`](@ref). | ||
| """ | ||
| function onthefly(;plot_obs=nothing::Union{<:Observable, Nothing}, save_obs=Vector{Observable}(undef, 0)::Union{<:Observable, Vector{<:Observable}}, savedir="auto", step=10::Int, func=identity::Function, compare=nothing::Union{Tuple{Vector{Float64}, Vector{Float64}}, Nothing}, clear=nothing) | ||
| if isnothing(plot_obs) && isempty(save_obs) | ||
| error("Must provide an observable to plot/save") | ||
| end | ||
| # !isempty(save_obs) && (isdir(savedir) || mkdir(savedir)) | ||
| plt = isnothing(plot_obs) ? nothing : plot(title="Intermediate Results", xlabel="t", ylabel=plot_obs.name) | ||
| !isnothing(compare) && plot!(compare) | ||
| println("On the fly mode activated") | ||
| return Dict(:plot_obs => isnothing(plot_obs) ? nothing : plot_obs.name, :save_obs => [ob.name for ob in save_obs], :savedir => savedir, :step => step, :func => func, :clear => clear, :compare => compare, :plot => plt) | ||
| end | ||
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| """ | ||
| ontheflyplot(onthefly, tstep, times, data) | ||
| Plots data according to the arguments of the `onthefly` dictionnary.""" | ||
| function ontheflyplot(onthefly, tstep, times, data) | ||
| tstep < onthefly[:step]+2 && plot!(onthefly[:plot], [], []) | ||
| N = ndims(data[onthefly[:plot_obs]]) | ||
| N == 1 ? slicefunc(arr, N, i) = arr[i] : slicefunc = selectdim | ||
| append!(onthefly[:plot].series_list[end], times[tstep-onthefly[:step]+1:tstep+1], map(onthefly[:func], (slicefunc(data[onthefly[:plot_obs]], N, i) for i in (tstep-onthefly[:step]+1):(tstep+1)))) | ||
| !isnothing(onthefly[:clear]) && onthefly[:clear](true) | ||
| sleep(0.05);display(onthefly[:plot]) | ||
| end | ||
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| """ | ||
| ontheflysave(onthefly, tstep, times, data) | ||
| Saves data according to the arguments of the `onthefly` dictionnary.""" | ||
| function ontheflysave(onthefly, tstep, times, data) | ||
| jldopen(onthefly[:savedir]*"tmp$(tstep÷onthefly[:step]).jld", "w") do file | ||
| write(file, "times", times[tstep-onthefly[:step]+1:tstep+1]) | ||
| for name in onthefly[:save_obs] | ||
| write(file, name, data[name][tstep-onthefly[:step]+1:tstep+1]) | ||
| end | ||
| end | ||
| end | ||
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| """ | ||
| mergetmp(tmpdir; fields=[], overwrite=true) | ||
| Merges the temporary files created by the `ontheflysave` function at the directory `tmpdir` and returns a dictionnary containing the resulting data. | ||
| By default all fields are present but one can select the fields of interest with a list of names in `fields`.""" | ||
| function mergetmp(tmpdir; fields=[], overwrite=true) | ||
| tmpdir[end] != '/' && (tmpdir *= '/') | ||
| !isdir(tmpdir) && error("Choose a valid directory") | ||
| files = [walkdir(tmpdir)...][1][3] | ||
| files = filter(x->!isnothing(match(r"tmp(\d+).jld", x)), files) | ||
| files = sort(files, by=(x -> parse(Int, match(r"(\d+)", x).captures[1]))) | ||
| isempty(fields) && (fields = keys(JLD.load(tmpdir*files[1]))) | ||
| merged_data = Dict(ob => [] for ob in fields) | ||
| i = 1 | ||
| for file in files | ||
| for ob in fields | ||
| append!(merged_data[ob], JLD.load(tmpdir*file, ob)) | ||
| end | ||
| i += 1 | ||
| end | ||
| if overwrite | ||
| for file in files | ||
| rm(tmpdir*file) | ||
| end | ||
| JLD.save(tmpdir*files[end], Iterators.flatten(merged_data)...) | ||
| end | ||
| return merged_data | ||
| end |