SciML / DiffEqNoiseProcess.jl

A library of noise processes for stochastic systems like stochastic differential equations (SDEs) and other systems that are present in scientific machine learning (SciML)
https://docs.sciml.ai/DiffEqNoiseProcess/stable/
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Small documentation issue (actionable) #188

Closed damianodegaspari closed 6 months ago

damianodegaspari commented 7 months ago

First of all let me quickly say that I am new to Julia, new to GitHub, new to programming in general. If I'm showing inappropriate/inefficient/incorrect behaviour and/or actions please let me know. Among other considerations, I'm asking this as a question because of the following

  1. You may not get a response here for packages with a very narrow audience. In that case, you may want to consider opening an issue on Github (or Gitlab, etc) for the package repository, just to ask a question. Most packages are OK with this.

in Tamas_Papp's post Please read: make it easier to help you" on Julia Discourse.

I was going through the DiffEqNoiseProcess.jl documentation and stumbled upon the following problem.

Trying to execute the blocks of code in the Direct Simulation of the Noise Process section, I get (from a fresh start of Julia):

julia> using DifferentialEquations

julia> μ = 1.0
1.0

julia> σ = 2.0
2.0

julia> W = GeometricBrownianMotionProcess(μ, σ, 0.0, 1.0, 1.0)
t: 1-element Vector{Float64}:
 0.0
u: 1-element Vector{Float64}:
 1.0

julia> prob = NoiseProblem(W, (0.0, 1.0))
NoiseProblem with WType Float64 and tType Float64. In-place: false
timespan: (0.0, 1.0)

julia> sol = solve(prob; dt = 0.1)
t: 11-element Vector{Float64}:
 0.0
 0.1
 0.2
 0.30000000000000004
 0.4
 0.5
 0.6
 0.7
 0.7999999999999999
 0.8999999999999999
 0.9999999999999999
u: 11-element Vector{Float64}:
 1.0
 0.45358738849107394
 0.17952397022691163
 0.13843702026586097
 0.15892086024998012
 0.12726817194665152
 0.05589566907491762
 0.04653757976133095
 0.02799639432864082
 0.02190658557517465
 0.010375593646497911

julia> enprob = EnsembleProblem(prob)
EnsembleProblem with problem NoiseProblem

julia> sol = solve(enprob; dt = 0.1, num_monte = 100)
ERROR: UndefKeywordError: keyword argument `trajectories` not assigned
Stacktrace:
 [1] __solve(prob::EnsembleProblem{NoiseProblem{NoiseProcess{Float64, 1, Float64, Float64, Float64, Vector{Float64}, DiffEqNoiseProcess.GeometricBrownianMotion{Float64, Float64}, DiffEqNoiseProcess.var"#34#35"{DiffEqNoiseProcess.GeometricBrownianMotion{Float64, Float64}}, false, ResettableStacks.ResettableStack{Tuple{Float64, Float64, Float64}, false}, ResettableStacks.ResettableStack{Tuple{Float64, Float64, Float64}, false}, RSWM{Float64}, Nothing, RandomNumbers.Xorshifts.Xoroshiro128Plus}, Tuple{Float64, Float64}, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}}, typeof(SciMLBase.DEFAULT_PROB_FUNC), typeof(SciMLBase.DEFAULT_OUTPUT_FUNC), typeof(SciMLBase.DEFAULT_REDUCTION), Nothing}, alg::Nothing; kwargs::Base.Pairs{Symbol, Real, Tuple{Symbol, Symbol}, NamedTuple{(:dt, :num_monte), Tuple{Float64, Int64}}})
   @ SciMLBase ~/.julia/packages/SciMLBase/2HZ5m/src/ensemble/basic_ensemble_solve.jl:100
 [2] solve(::EnsembleProblem{NoiseProblem{NoiseProcess{Float64, 1, Float64, Float64, Float64, Vector{Float64}, DiffEqNoiseProcess.GeometricBrownianMotion{Float64, Float64}, DiffEqNoiseProcess.var"#34#35"{DiffEqNoiseProcess.GeometricBrownianMotion{Float64, Float64}}, false, ResettableStacks.ResettableStack{Tuple{Float64, Float64, Float64}, false}, ResettableStacks.ResettableStack{Tuple{Float64, Float64, Float64}, false}, RSWM{Float64}, Nothing, RandomNumbers.Xorshifts.Xoroshiro128Plus}, Tuple{Float64, Float64}, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}}, typeof(SciMLBase.DEFAULT_PROB_FUNC), typeof(SciMLBase.DEFAULT_OUTPUT_FUNC), typeof(SciMLBase.DEFAULT_REDUCTION), Nothing}; kwargs::Base.Pairs{Symbol, Real, Tuple{Symbol, Symbol}, NamedTuple{(:dt, :num_monte), Tuple{Float64, Int64}}})
   @ DiffEqBase ~/.julia/packages/DiffEqBase/eTCPy/src/solve.jl:1075
 [3] top-level scope
   @ REPL[9]:1

I was also reading the section Ensemble Simulations in the documentation of the DifferentialEquation.jl package. With that knowledge I tried to run the following:

julia> sol = solve(enprob; dt = 0.1, trajectories = 100)
EnsembleSolution Solution of length 100 with uType:
NoiseProcess{Float64, 1, Float64, Float64, Float64, Vector{Float64}, DiffEqNoiseProcess.GeometricBrownianMotion{Float64, Float64}, DiffEqNoiseProcess.var"#34#35"{DiffEqNoiseProcess.GeometricBrownianMotion{Float64, Float64}}, false, ResettableStacks.ResettableStack{Tuple{Float64, Float64, Float64}, false}, ResettableStacks.ResettableStack{Tuple{Float64, Float64, Float64}, false}, RSWM{Float64}, Nothing, RandomNumbers.Xorshifts.Xoroshiro128Plus}

which seemed to work.

Additional outputs that are asked about in the GitHub section about opening a bug:

julia> using Pkg; Pkg.status()
Status `~/.julia/environments/v1.9/Project.toml`
  [0c46a032] DifferentialEquations v7.12.0
  [c3e4b0f8] Pluto v0.19.37
julia> using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)
Status `~/.julia/environments/v1.9/Manifest.toml`
  [47edcb42] ADTypes v0.2.6
⌅ [79e6a3ab] Adapt v3.7.2
  [ec485272] ArnoldiMethod v0.2.0
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  [6e4b80f9] BenchmarkTools v1.4.0
  [d1d4a3ce] BitFlags v0.1.8
  [62783981] BitTwiddlingConvenienceFunctions v0.1.5
⌃ [764a87c0] BoundaryValueDiffEq v5.6.0
  [fa961155] CEnum v0.5.0
  [2a0fbf3d] CPUSummary v0.2.4
  [49dc2e85] Calculus v0.5.1
  [fb6a15b2] CloseOpenIntervals v0.1.12
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  [944b1d66] CodecZlib v0.7.3
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  [bbf7d656] CommonSubexpressions v0.3.0
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  [e2d170a0] DataValueInterfaces v1.0.0
⌃ [bcd4f6db] DelayDiffEq v5.45.1
⌃ [2b5f629d] DiffEqBase v6.145.6
  [459566f4] DiffEqCallbacks v2.36.1
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⌅ [1dea7af3] OrdinaryDiffEq v6.66.0
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⌅ [fb77eaff] Sundials_jll v5.2.1+0
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  [7b1f6079] FileWatching
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
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  [b27032c2] LibCURL v0.6.3
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  [8e850ede] nghttp2_jll v1.48.0+0
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Info Packages marked with ⌃ and ⌅ have new versions available, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
julia> versioninfo()
Julia Version 1.9.2
Commit e4ee485e90 (2023-07-05 09:39 UTC)
Platform Info:
  OS: Linux (x86_64-redhat-linux)
  CPU: 12 × AMD Ryzen 5 PRO 4650U with Radeon Graphics
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, znver2)
  Threads: 1 on 12 virtual cores

Moreover, on that same page, one can read the following sentence: " For some noise process W, you can get its ith timepoint like W[i] and the associated time W.t[i]. If the NoiseProcess has a bridging distribution defined, it can be interpolated to arbitrary time points using W(t) " In my experiments this is true AFTER I define a NoiseProblem and solve it, whereas it is not true if I try to do it immediately after, e.g.

W = GeometricBrownianMotionProcess(μ, σ, 0.0, 1.0, 1.0)

This confused me at first, so I would rephrase that sentence. However, it is also very much possible that I was confused because I just started with all of this and still learning basic things.

Finally, I noticed that there are some "missing docstrings". I don't want to blame anybody, but I assume at some points those will be filled in. When that happens, I would suggest to also review and improve the already existing ones. Two small improvements I would make:

I hope that I didn't go too long, either in not splitting this into two separate questions of in the effort of providing all the details I could think of.

ChrisRackauckas commented 6 months ago

It was a bit hard to find out what the actual question is in here, but I think it's addressed in https://github.com/SciML/DiffEqNoiseProcess.jl/pull/196

I didn't understand what Z0 is, and I could not find that information anywhere else.

This is an extra Brownian, used in SDE adpativity.

one discovers that the aforementioned function allows one to use a complex brownian motion only when reading the docstring of DiffEqNoiseProcess.RealWienerProcess. I would add the comment made there for the function in my bullet point above.

Which comment?