From ba2c6d00741055897d3d941e9c1f5a73e14ee49b Mon Sep 17 00:00:00 2001 From: Avik Pal Date: Mon, 19 Feb 2024 22:36:24 -0500 Subject: [PATCH 01/12] Start migrating to NonlinearSolve --- Project.toml | 6 +-- src/DiffEqCallbacks.jl | 2 +- src/manifold.jl | 108 ++++++++++++++++++++++------------------- 3 files changed, 61 insertions(+), 55 deletions(-) diff --git a/Project.toml b/Project.toml index e924a1db..cc480073 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "DiffEqCallbacks" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" authors = ["Chris Rackauckas "] -version = "2.37.0" +version = "3.0.0" [deps] DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" @@ -10,7 +10,7 @@ ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a" -NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" +NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a" RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" @@ -30,7 +30,6 @@ ForwardDiff = "0.10.19" Functors = "0.4" LinearAlgebra = "1.10" Markdown = "1.10" -NLsolve = "4.5" ODEProblemLibrary = "0.1.5" OrdinaryDiffEq = "6.68" Parameters = "0.12" @@ -62,4 +61,3 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [targets] test = ["Aqua", "DataInterpolations", "OrdinaryDiffEq", "ODEProblemLibrary", "Test", "QuadGK", "SciMLSensitivity", "StaticArrays", "Tracker", "Zygote"] - diff --git a/src/DiffEqCallbacks.jl b/src/DiffEqCallbacks.jl index 748839ae..09328c58 100644 --- a/src/DiffEqCallbacks.jl +++ b/src/DiffEqCallbacks.jl @@ -1,7 +1,7 @@ module DiffEqCallbacks using DiffEqBase, RecursiveArrayTools, DataStructures, RecipesBase, LinearAlgebra, - StaticArraysCore, NLsolve, ForwardDiff, Functors + StaticArraysCore, NonlinearSolve, ForwardDiff, Functors import Base.Iterators diff --git a/src/manifold.jl b/src/manifold.jl index 81e1507e..5f831e49 100644 --- a/src/manifold.jl +++ b/src/manifold.jl @@ -1,13 +1,13 @@ -Base.@pure function determine_chunksize(u, alg::DiffEqBase.DEAlgorithm) - determine_chunksize(u, get_chunksize(alg)) -end -Base.@pure function determine_chunksize(u, CS) - if CS != 0 - return CS - else - return ForwardDiff.pickchunksize(length(u)) - end -end +# Base.@pure function determine_chunksize(u, alg::DiffEqBase.DEAlgorithm) +# determine_chunksize(u, get_chunksize(alg)) +# end +# Base.@pure function determine_chunksize(u, CS) +# if CS != 0 +# return CS +# else +# return ForwardDiff.pickchunksize(length(u)) +# end +# end struct NLSOLVEJL_SETUP{CS, AD} end Base.@pure function NLSOLVEJL_SETUP(; chunk_size = 0, autodiff = true) @@ -21,13 +21,16 @@ function (p::NLSOLVEJL_SETUP{CS, AD})(::Type{Val{:init}}, f, u0_prototype) where end # wrapper for non-autonomous functions -mutable struct NonAutonomousFunction{F, autonomous} +mutable struct NonAutonomousFunction{iip, F, autonomous, T} f::F - t::Any - p::Any + t::T end -(p::NonAutonomousFunction{F, true})(res, u) where {F} = p.f(res, u, p.p) -(p::NonAutonomousFunction{F, false})(res, u) where {F} = p.f(res, u, p.p, p.t) +(f::NonAutonomousFunction{true, F, true})(res, u, p) where {F} = f.f(res, u, p) +(f::NonAutonomousFunction{true, F, false})(res, u, p) where {F} = f.f(res, u, p, p.t) +(f::NonAutonomousFunction{false, F, true})(u, p) where {F} = f.f(u, p) +(f::NonAutonomousFunction{false, F, false})(u, p) where {F} = f.f(u, p, p.t) + +SciMLBase.isinplace(::NonAutonomousFunction{iip}) where {iip} = iip """ ```julia @@ -81,50 +84,55 @@ Ernst Hairer, Christian Lubich, Gerhard Wanner. Geometric Numerical Integration: Structure-Preserving Algorithms for Ordinary Differential Equations. Berlin ; New York :Springer, 2002. """ -mutable struct ManifoldProjection{autonomous, F, NL, O} +mutable struct ManifoldProjection{iip, autonomous, F, NL, NO} g::F nl_rhs::Any - nlsolve::NL - nlopts::O - - function ManifoldProjection{autonomous}(g, nlsolve, nlopts) where {autonomous} - # replace residual function if it is time-dependent - # since NLsolve only accepts functions with two arguments - _g = NonAutonomousFunction{typeof(g), autonomous}(g, 0, 0) - new{autonomous, typeof(_g), typeof(nlsolve), typeof(nlopts)}(_g, _g, nlsolve, - nlopts) + nlsolver::NL + nlopts::NO + + # TODO: Caching for NonlinearSolve solvers + function ManifoldProjection{iip, autonomous}(g, nlsolve, nlopts) where {iip, autonomous} + replace residual function if it is time-dependent + _g = NonAutonomousFunction{iip, typeof(g), autonomous}(g, 0) + return new{iip, autonomous, typeof(_g), typeof(nlsolve), typeof(nlopts)}(_g, _g, + nlsolve, nlopts) end end -# Now make `affect!` for this: -function (p::ManifoldProjection{autonomous, NL})(integrator) where {autonomous, NL} - # update current time if residual function is time-dependent - if !autonomous - p.g.t = integrator.t +# # Now make `affect!` for this: +# function (p::ManifoldProjection{autonomous, NL})(integrator) where {autonomous, NL} +# # update current time if residual function is time-dependent +# if !autonomous +# p.g.t = integrator.t +# end +# p.g.p = integrator.p + +# integrator.u .= p.nlsolve(p.nl_rhs, integrator.u; p.nlopts...) +# end + +# function Manifold_initialize(cb, u::Number, t, integrator) +# cb.affect!.nl_rhs = cb.affect!.nlsolve(Val{:init}, cb.affect!.g, [u]) +# u_modified!(integrator, false) +# end + +# function Manifold_initialize(cb, u, t, integrator) +# cb.affect!.nl_rhs = cb.affect!.nlsolve(Val{:init}, cb.affect!.g, u) +# u_modified!(integrator, false) +# end + +function ManifoldProjection(g; nlsolve = nothing, save = true, isinplace = Val(true), + autonomous = nothing, nlopts = (;)) + if autonomous === nothing + if SciMLBase._unwrap_val(isinplace) + autonomous = maximum(SciMLBase.numargs(g)) == 3 + else + autonomous = maximum(SciMLBase.numargs(g)) == 2 + end end - p.g.p = integrator.p - - integrator.u .= p.nlsolve(p.nl_rhs, integrator.u; p.nlopts...) -end - -function Manifold_initialize(cb, u::Number, t, integrator) - cb.affect!.nl_rhs = cb.affect!.nlsolve(Val{:init}, cb.affect!.g, [u]) - u_modified!(integrator, false) -end - -function Manifold_initialize(cb, u, t, integrator) - cb.affect!.nl_rhs = cb.affect!.nlsolve(Val{:init}, cb.affect!.g, u) - u_modified!(integrator, false) -end - -function ManifoldProjection(g; nlsolve = NLSOLVEJL_SETUP(), save = true, - autonomous = maximum(SciMLBase.numargs(g)) == 3, - nlopts = Dict{Symbol, Any}()) affect! = ManifoldProjection{autonomous}(g, nlsolve, nlopts) condition = (u, t, integrator) -> true save_positions = (false, save) - DiscreteCallback(condition, affect!; - initialize = Manifold_initialize, + return DiscreteCallback(condition, affect!; initialize = Manifold_initialize, save_positions = save_positions) end From 2f56a5fad0f54672074845f782fe3d24a6907999 Mon Sep 17 00:00:00 2001 From: Avik Pal Date: Tue, 20 Feb 2024 11:45:39 -0500 Subject: [PATCH 02/12] Progress on replacing NLsolve with NonlinearSolve --- src/domain.jl | 13 ++--- src/manifold.jl | 128 +++++++++++++++++++++++++---------------- test/manifold_tests.jl | 10 ++-- 3 files changed, 90 insertions(+), 61 deletions(-) diff --git a/src/domain.jl b/src/domain.jl index 3df35e42..b4d7909d 100644 --- a/src/domain.jl +++ b/src/domain.jl @@ -213,7 +213,7 @@ end """ ```julia -GeneralDomain(g, u = nothing; nlsolve = NLSOLVEJL_SETUP(), save = true, +GeneralDomain(g, u = nothing; nlsolve = NewtonRaphson(), save = true, abstol = nothing, scalefactor = nothing, autonomous = maximum(SciMLBase.numargs(g)) == 3, nlopts = Dict(:ftol => 10 * eps())) @@ -242,7 +242,7 @@ preferred. ## Keyword Arguments - - `nlsolve`: A nonlinear solver as defined [in the nlsolve format](https://docs.sciml.ai/DiffEqDocs/stable/features/linear_nonlinear/) + - `nlsolve`: A nonlinear solver as defined in the [NonlinearSolve.jl format](https://docs.sciml.ai/NonlinearSolve/stable/basics/solve/) which is passed to a `ManifoldProjection`. - `save`: Whether to do the standard saving (applied after the callback). - `abstol`: Tolerance up to, which residuals are accepted. Element-wise tolerances @@ -252,8 +252,8 @@ preferred. specified, time steps are halved. - `autonomous`: Whether `g` is an autonomous function of the form `g(resid, u, p)`. - `nlopts`: Optional arguments to nonlinear solver of a `ManifoldProjection` which - can be any of the [NLsolve keywords](https://github.com/JuliaNLSolvers/NLsolve.jl#fine-tunings). - The default value of `ftol = 10*eps()` ensures that convergence is only declared + can be any of the [NonlinearSolve.jl keywords](https://docs.sciml.ai/NonlinearSolve/stable/basics/solve/). + The default value of `abstol = 10 * eps()` ensures that convergence is only declared if the infinite norm of residuals is very small and hence the state vector is very close to the domain. @@ -263,10 +263,9 @@ Shampine, Lawrence F., Skip Thompson, Jacek Kierzenka and G. D. Byrne. Non-negative solutions of ODEs. Applied Mathematics and Computation 170 (2005): 556-569. """ -function GeneralDomain(g, u = nothing; nlsolve = NLSOLVEJL_SETUP(), save = true, +function GeneralDomain(g, u = nothing; nlsolve = NewtonRaphson(), save = true, abstol = nothing, scalefactor = nothing, - autonomous = maximum(SciMLBase.numargs(g)) == 3, - nlopts = Dict(:ftol => 10 * eps())) + autonomous = maximum(SciMLBase.numargs(g)) == 3, nlopts = (; abstol = 10 * eps())) if u isa Nothing affect! = GeneralDomainAffect{autonomous}(g, abstol, scalefactor, nothing, nothing) else diff --git a/src/manifold.jl b/src/manifold.jl index 5f831e49..290d9415 100644 --- a/src/manifold.jl +++ b/src/manifold.jl @@ -9,38 +9,40 @@ # end # end -struct NLSOLVEJL_SETUP{CS, AD} end -Base.@pure function NLSOLVEJL_SETUP(; chunk_size = 0, autodiff = true) - NLSOLVEJL_SETUP{chunk_size, autodiff}() -end -(::NLSOLVEJL_SETUP)(f, u0; kwargs...) = (res = NLsolve.nlsolve(f, u0; kwargs...); res.zero) -function (p::NLSOLVEJL_SETUP{CS, AD})(::Type{Val{:init}}, f, u0_prototype) where {CS, AD} - AD ? autodiff = :forward : autodiff = :central - OnceDifferentiable(f, u0_prototype, u0_prototype, autodiff, - ForwardDiff.Chunk(determine_chunksize(u0_prototype, CS))) -end +# struct NLSOLVEJL_SETUP{CS, AD} end +# Base.@pure function NLSOLVEJL_SETUP(; chunk_size = 0, autodiff = true) +# NLSOLVEJL_SETUP{chunk_size, autodiff}() +# end +# (::NLSOLVEJL_SETUP)(f, u0; kwargs...) = (res = NLsolve.nlsolve(f, u0; kwargs...); res.zero) +# function (p::NLSOLVEJL_SETUP{CS, AD})(::Type{Val{:init}}, f, u0_prototype) where {CS, AD} +# AD ? autodiff = :forward : autodiff = :central +# OnceDifferentiable(f, u0_prototype, u0_prototype, autodiff, +# ForwardDiff.Chunk(determine_chunksize(u0_prototype, CS))) +# end # wrapper for non-autonomous functions -mutable struct NonAutonomousFunction{iip, F, autonomous, T} +mutable struct NonAutonomousFunction{iip, F, autonomous} f::F - t::T + t::Any end + (f::NonAutonomousFunction{true, F, true})(res, u, p) where {F} = f.f(res, u, p) (f::NonAutonomousFunction{true, F, false})(res, u, p) where {F} = f.f(res, u, p, p.t) + (f::NonAutonomousFunction{false, F, true})(u, p) where {F} = f.f(u, p) (f::NonAutonomousFunction{false, F, false})(u, p) where {F} = f.f(u, p, p.t) SciMLBase.isinplace(::NonAutonomousFunction{iip}) where {iip} = iip """ -```julia -ManifoldProjection(g; nlsolve = NLSOLVEJL_SETUP(), save = true) -``` + ManifoldProjection(g; nlsolve = missing, save = true, nlls = Val(true), + isinplace = Val(true), autonomous = nothing, nlopts = (;), + resid_prototype = nothing) In many cases, you may want to declare a manifold on which a solution lives. Mathematically, a manifold `M` is defined by a function `g` as the set of points -where `g(u)=0`. An embedded manifold can be a lower dimensional object which -constrains the solution. For example, `g(u)=E(u)-C` where `E` is the energy +where `g(u) = 0`. An embedded manifold can be a lower dimensional object which +constrains the solution. For example, `g(u) = E(u) - C` where `E` is the energy of the system in state `u`, meaning that the energy must be constant (energy preservation). Thus by defining the manifold the solution should live on, you can retain desired properties of the solution. @@ -62,10 +64,12 @@ properties. ## Keyword Arguments - - `nlsolve`: A nonlinear solver as defined [in the nlsolve format](https://docs.sciml.ai/DiffEqDocs/stable/features/linear_nonlinear/) + - `nlsolve`: A nonlinear solver as defined in the + [NonlinearSolve.jl format](https://docs.sciml.ai/NonlinearSolve/stable/basics/solve/) - `save`: Whether to do the standard saving (applied after the callback) - `autonomous`: Whether `g` is an autonomous function of the form `g(resid, u)`. - - `nlopts`: Optional arguments to nonlinear solver which can be any of the [NLsolve keywords](https://github.com/JuliaNLSolvers/NLsolve.jl#fine-tunings). + - `nlopts`: Optional arguments to nonlinear solver which can be any of the + [NonlinearSolve.jl keywords](https://docs.sciml.ai/NonlinearSolve/stable/basics/solve/). ### Saveat Warning @@ -84,56 +88,80 @@ Ernst Hairer, Christian Lubich, Gerhard Wanner. Geometric Numerical Integration: Structure-Preserving Algorithms for Ordinary Differential Equations. Berlin ; New York :Springer, 2002. """ -mutable struct ManifoldProjection{iip, autonomous, F, NL, NO} +mutable struct ManifoldProjection{iip, nlls, autonomous, F, NL, NO, R} g::F - nl_rhs::Any - nlsolver::NL + nlcache::Any + nlsolve::NL nlopts::NO + resid_prototype::R - # TODO: Caching for NonlinearSolve solvers - function ManifoldProjection{iip, autonomous}(g, nlsolve, nlopts) where {iip, autonomous} - replace residual function if it is time-dependent + function ManifoldProjection{iip, nlls, autonomous}( + g, nlsolve, nlopts, resid_prototype) where {iip, nlls, autonomous} + # replace residual function if it is time-dependent _g = NonAutonomousFunction{iip, typeof(g), autonomous}(g, 0) - return new{iip, autonomous, typeof(_g), typeof(nlsolve), typeof(nlopts)}(_g, _g, - nlsolve, nlopts) + return new{iip, nlls, autonomous, typeof(_g), typeof(nlsolve), + typeof(nlopts), typeof(resid_prototype)}( + _g, nothing, nlsolve, nlopts, resid_prototype) end end -# # Now make `affect!` for this: -# function (p::ManifoldProjection{autonomous, NL})(integrator) where {autonomous, NL} -# # update current time if residual function is time-dependent -# if !autonomous -# p.g.t = integrator.t -# end -# p.g.p = integrator.p +# Now make `affect!` for this: +function (p::ManifoldProjection{iip, nlls, autonomous, NL})(integrator) where {iip, nlls, + autonomous, NL} + # update current time if residual function is time-dependent + if !autonomous + p.g.t = integrator.t + end -# integrator.u .= p.nlsolve(p.nl_rhs, integrator.u; p.nlopts...) -# end + # solve the nonlinear problem + reinit!(p.nlcache, integrator.u; p = integrator.p) + sol = solve!(p.nlcache) -# function Manifold_initialize(cb, u::Number, t, integrator) -# cb.affect!.nl_rhs = cb.affect!.nlsolve(Val{:init}, cb.affect!.g, [u]) -# u_modified!(integrator, false) -# end + if !SciMLBase.successful_retcode(sol) && (nlls && sol.retcode != ReturnCode.Stalled) + SciMLBase.terminate!(integrator, sol.retcode) + return + end -# function Manifold_initialize(cb, u, t, integrator) -# cb.affect!.nl_rhs = cb.affect!.nlsolve(Val{:init}, cb.affect!.g, u) -# u_modified!(integrator, false) -# end + copyto!(integrator.u, sol.u) +end + +function Manifold_initialize(cb, u, t, integrator) + return Manifold_initialize(cb.affect!, u, t, integrator) +end +function Manifold_initialize( + affect!::ManifoldProjection{iip, nlls}, u, t, integrator) where {iip, nlls} + nlfunc = NonlinearFunction{iip}(affect!.g; affect!.resid_prototype) + nlprob = if nlls + NonlinearLeastSquaresProblem(nlfunc, u, integrator.p) + else + NonlinearProblem(nlfunc, u, integrator.p) + end + affect!.nlcache = init(nlprob, affect!.nlsolve; affect!.nlopts...) + u_modified!(integrator, false) +end -function ManifoldProjection(g; nlsolve = nothing, save = true, isinplace = Val(true), - autonomous = nothing, nlopts = (;)) +# Since this is applied to every point, we can reasonably assume that the solution is close +# to the initial guess, so we would want to use NewtonRaphson / RobustMultiNewton instead of +# the default one. +function ManifoldProjection(g; nlsolve = missing, save = true, nlls = Val(true), + isinplace = Val(true), autonomous = nothing, nlopts = (;), + resid_prototype = nothing) + # `nothing` is a valid solver, so this need to be `missing` + _nlls = SciMLBase._unwrap_val(nlls) + _nlsolve = nlsolve === missing ? (_nlls ? GaussNewton() : NewtonRaphson()) : nlsolve + iip = SciMLBase._unwrap_val(isinplace) if autonomous === nothing - if SciMLBase._unwrap_val(isinplace) + if iip autonomous = maximum(SciMLBase.numargs(g)) == 3 else autonomous = maximum(SciMLBase.numargs(g)) == 2 end end - affect! = ManifoldProjection{autonomous}(g, nlsolve, nlopts) + affect! = ManifoldProjection{iip, _nlls, autonomous}( + g, _nlsolve, nlopts, resid_prototype) condition = (u, t, integrator) -> true - save_positions = (false, save) return DiscreteCallback(condition, affect!; initialize = Manifold_initialize, - save_positions = save_positions) + save_positions = (false, save)) end export ManifoldProjection diff --git a/test/manifold_tests.jl b/test/manifold_tests.jl index d6092e8f..4f9a0953 100644 --- a/test/manifold_tests.jl +++ b/test/manifold_tests.jl @@ -10,19 +10,21 @@ prob = ODEProblem(f, u0, (0.0, 100.0)) function g(resid, u, p) resid[1] = u[2]^2 + u[1]^2 - 2 resid[2] = u[3]^2 + u[4]^2 - 2 - resid[3] = 0 - resid[4] = 0 end g_t(resid, u, p, t) = g(resid, u, p) -isautonomous(p::ManifoldProjection{autonomous, NL}) where {autonomous, NL} = autonomous +function isautonomous(::ManifoldProjection{ + iip, nlls, autonomous, NL}) where {iip, nlls, autonomous, NL} + return autonomous +end sol = solve(prob, Vern7()) @test !(sol[end][1]^2 + sol[end][2]^2 ≈ 2) # autodiff=true -cb = ManifoldProjection(g) +@inferred ManifoldProjection(g; autonomous = Val(true), resid_prototype = zeros(2)) +cb = ManifoldProjection(g; resid_prototype = zeros(2)) @test isautonomous(cb.affect!) solve(prob, Vern7(), callback = cb) @time sol = solve(prob, Vern7(), callback = cb) From c16671b45cb5d462dda8053439e7134bc6327579 Mon Sep 17 00:00:00 2001 From: Avik Pal Date: Tue, 20 Feb 2024 13:36:33 -0500 Subject: [PATCH 03/12] Finish ManifoldProjection --- Project.toml | 5 +- src/manifold.jl | 108 ++++++++++++++++++----------------------- test/manifold_tests.jl | 37 ++++++++++---- 3 files changed, 77 insertions(+), 73 deletions(-) diff --git a/Project.toml b/Project.toml index cc480073..bf595272 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "DiffEqCallbacks" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" authors = ["Chris Rackauckas "] -version = "3.0.0" +version = "2.38.0" # Make it 3.0.0 before releasing. This is needed to allow resolver to work for test dependencies [deps] DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" @@ -49,6 +49,7 @@ julia = "1.10" [extras] Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595" DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" +NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" ODEProblemLibrary = "fdc4e326-1af4-4b90-96e7-779fcce2daa5" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" @@ -60,4 +61,4 @@ Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [targets] -test = ["Aqua", "DataInterpolations", "OrdinaryDiffEq", "ODEProblemLibrary", "Test", "QuadGK", "SciMLSensitivity", "StaticArrays", "Tracker", "Zygote"] +test = ["Aqua", "DataInterpolations", "OrdinaryDiffEq", "ODEProblemLibrary", "Test", "QuadGK", "SciMLSensitivity", "StaticArrays", "Tracker", "Zygote", "NonlinearSolve"] diff --git a/src/manifold.jl b/src/manifold.jl index 290d9415..ad9d714d 100644 --- a/src/manifold.jl +++ b/src/manifold.jl @@ -1,25 +1,3 @@ -# Base.@pure function determine_chunksize(u, alg::DiffEqBase.DEAlgorithm) -# determine_chunksize(u, get_chunksize(alg)) -# end -# Base.@pure function determine_chunksize(u, CS) -# if CS != 0 -# return CS -# else -# return ForwardDiff.pickchunksize(length(u)) -# end -# end - -# struct NLSOLVEJL_SETUP{CS, AD} end -# Base.@pure function NLSOLVEJL_SETUP(; chunk_size = 0, autodiff = true) -# NLSOLVEJL_SETUP{chunk_size, autodiff}() -# end -# (::NLSOLVEJL_SETUP)(f, u0; kwargs...) = (res = NLsolve.nlsolve(f, u0; kwargs...); res.zero) -# function (p::NLSOLVEJL_SETUP{CS, AD})(::Type{Val{:init}}, f, u0_prototype) where {CS, AD} -# AD ? autodiff = :forward : autodiff = :central -# OnceDifferentiable(f, u0_prototype, u0_prototype, autodiff, -# ForwardDiff.Chunk(determine_chunksize(u0_prototype, CS))) -# end - # wrapper for non-autonomous functions mutable struct NonAutonomousFunction{iip, F, autonomous} f::F @@ -27,25 +5,24 @@ mutable struct NonAutonomousFunction{iip, F, autonomous} end (f::NonAutonomousFunction{true, F, true})(res, u, p) where {F} = f.f(res, u, p) -(f::NonAutonomousFunction{true, F, false})(res, u, p) where {F} = f.f(res, u, p, p.t) +(f::NonAutonomousFunction{true, F, false})(res, u, p) where {F} = f.f(res, u, p, f.t) (f::NonAutonomousFunction{false, F, true})(u, p) where {F} = f.f(u, p) -(f::NonAutonomousFunction{false, F, false})(u, p) where {F} = f.f(u, p, p.t) +(f::NonAutonomousFunction{false, F, false})(u, p) where {F} = f.f(u, p, f.t) SciMLBase.isinplace(::NonAutonomousFunction{iip}) where {iip} = iip """ ManifoldProjection(g; nlsolve = missing, save = true, nlls = Val(true), - isinplace = Val(true), autonomous = nothing, nlopts = (;), - resid_prototype = nothing) + isinplace = Val(true), autonomous = nothing, resid_prototype = nothing, + kwargs...) -In many cases, you may want to declare a manifold on which a solution lives. -Mathematically, a manifold `M` is defined by a function `g` as the set of points -where `g(u) = 0`. An embedded manifold can be a lower dimensional object which -constrains the solution. For example, `g(u) = E(u) - C` where `E` is the energy -of the system in state `u`, meaning that the energy must be constant (energy -preservation). Thus by defining the manifold the solution should live on, you -can retain desired properties of the solution. +In many cases, you may want to declare a manifold on which a solution lives. Mathematically, +a manifold `M` is defined by a function `g` as the set of points where `g(u) = 0`. An +embedded manifold can be a lower dimensional object which constrains the solution. For +example, `g(u) = E(u) - C` where `E` is the energy of the system in state `u`, meaning that +the energy must be constant (energy preservation). Thus by defining the manifold the +solution should live on, you can retain desired properties of the solution. `ManifoldProjection` projects the solution of the differential equation to the chosen manifold `g`, conserving a property while conserving the order. It is a consequence of @@ -57,30 +34,41 @@ properties. ## Arguments - - `g`: The residual function for the manifold. This is an inplace function of form - `g(resid, u)` or `g(resid, u, p, t)` which writes to the residual `resid` the - difference from the manifold components. Here, it is assumed that `resid` is of - the same shape as `u`. + - `g`: The residual function for the manifold. + + * This is an inplace function of form `g(resid, u, p)` or `g(resid, u, p, t)` which + writes to the residual `resid` the difference from the manifold components. Here, it + is assumed that `resid` is of the same shape as `u`. + * If `isinplace = Val(false)`, then `g` should be a function of the form `g(u, p)` or + `g(u, p, t)` which returns the residual. ## Keyword Arguments - `nlsolve`: A nonlinear solver as defined in the [NonlinearSolve.jl format](https://docs.sciml.ai/NonlinearSolve/stable/basics/solve/) - `save`: Whether to do the standard saving (applied after the callback) - - `autonomous`: Whether `g` is an autonomous function of the form `g(resid, u)`. - - `nlopts`: Optional arguments to nonlinear solver which can be any of the - [NonlinearSolve.jl keywords](https://docs.sciml.ai/NonlinearSolve/stable/basics/solve/). + - `nlls`: If the problem is a nonlinear least squares problem. `nlls = Val(false)` + generates a `NonlinearProblem` which is typically faster than + `NonlinearLeastSquaresProblem`, but is only applicable if the residual size is same as + the state size. + - `autonomous`: Whether `g` is an autonomous function of the form `g(resid, u, p)` or + `g(u, p)`. Specify it as `Val(::Bool)` to ensure this function call is type stable. + - `residual_prototype`: This needs to be specified if `nlls = Val(true)` and + `inplace = Val(true)` are specified together, else it is taken to be same as `u`. + - `kwargs`: All other keyword arguments are passed to + [NonlinearSolve.jl](https://docs.sciml.ai/NonlinearSolve/stable/basics/solve/). ### Saveat Warning -Note that the `ManifoldProjection` callback modifies the endpoints of the integration intervals -and thus breaks assumptions of internal interpolations. Because of this, the values for given by -saveat will not be order-matching. However, the interpolation error can be proportional to the -change by the projection, so if the projection is making small changes then one is still safe. -However, if there are large changes from each projection, you should consider only saving at -stopping/projection times. To do this, set `tstops` to the same values as `saveat`. There is a -performance hit by doing so because now the integrator is forced to stop at every saving point, -but this is guerenteed to match the order of the integrator even with the ManifoldProjection. +Note that the `ManifoldProjection` callback modifies the endpoints of the integration +intervals and thus breaks assumptions of internal interpolations. Because of this, the +values for given by saveat will not be order-matching. However, the interpolation error can +be proportional to the change by the projection, so if the projection is making small +changes then one is still safe. However, if there are large changes from each projection, +you should consider only saving at stopping/projection times. To do this, set `tstops` to +the same values as `saveat`. There is a performance hit by doing so because now the +integrator is forced to stop at every saving point, but this is guerenteed to match the +order of the integrator even with the ManifoldProjection. ## References @@ -88,20 +76,20 @@ Ernst Hairer, Christian Lubich, Gerhard Wanner. Geometric Numerical Integration: Structure-Preserving Algorithms for Ordinary Differential Equations. Berlin ; New York :Springer, 2002. """ -mutable struct ManifoldProjection{iip, nlls, autonomous, F, NL, NO, R} +mutable struct ManifoldProjection{iip, nlls, autonomous, F, NL, R, K} g::F nlcache::Any nlsolve::NL - nlopts::NO resid_prototype::R + kwargs::K function ManifoldProjection{iip, nlls, autonomous}( - g, nlsolve, nlopts, resid_prototype) where {iip, nlls, autonomous} + g, nlsolve, resid_prototype, kwargs) where {iip, nlls, autonomous} # replace residual function if it is time-dependent _g = NonAutonomousFunction{iip, typeof(g), autonomous}(g, 0) return new{iip, nlls, autonomous, typeof(_g), typeof(nlsolve), - typeof(nlopts), typeof(resid_prototype)}( - _g, nothing, nlsolve, nlopts, resid_prototype) + typeof(resid_prototype), typeof(kwargs)}( + _g, nothing, nlsolve, resid_prototype, kwargs) end end @@ -109,15 +97,13 @@ end function (p::ManifoldProjection{iip, nlls, autonomous, NL})(integrator) where {iip, nlls, autonomous, NL} # update current time if residual function is time-dependent - if !autonomous - p.g.t = integrator.t - end + !autonomous && (p.g.t = integrator.t) # solve the nonlinear problem reinit!(p.nlcache, integrator.u; p = integrator.p) sol = solve!(p.nlcache) - if !SciMLBase.successful_retcode(sol) && (nlls && sol.retcode != ReturnCode.Stalled) + if !SciMLBase.successful_retcode(sol) SciMLBase.terminate!(integrator, sol.retcode) return end @@ -136,7 +122,7 @@ function Manifold_initialize( else NonlinearProblem(nlfunc, u, integrator.p) end - affect!.nlcache = init(nlprob, affect!.nlsolve; affect!.nlopts...) + affect!.nlcache = init(nlprob, affect!.nlsolve; affect!.kwargs...) u_modified!(integrator, false) end @@ -144,8 +130,8 @@ end # to the initial guess, so we would want to use NewtonRaphson / RobustMultiNewton instead of # the default one. function ManifoldProjection(g; nlsolve = missing, save = true, nlls = Val(true), - isinplace = Val(true), autonomous = nothing, nlopts = (;), - resid_prototype = nothing) + isinplace = Val(true), autonomous = nothing, resid_prototype = nothing, + kwargs...) # `nothing` is a valid solver, so this need to be `missing` _nlls = SciMLBase._unwrap_val(nlls) _nlsolve = nlsolve === missing ? (_nlls ? GaussNewton() : NewtonRaphson()) : nlsolve @@ -158,7 +144,7 @@ function ManifoldProjection(g; nlsolve = missing, save = true, nlls = Val(true), end end affect! = ManifoldProjection{iip, _nlls, autonomous}( - g, _nlsolve, nlopts, resid_prototype) + g, _nlsolve, resid_prototype, kwargs) condition = (u, t, integrator) -> true return DiscreteCallback(condition, affect!; initialize = Manifold_initialize, save_positions = (false, save)) diff --git a/test/manifold_tests.jl b/test/manifold_tests.jl index 4f9a0953..865b3b13 100644 --- a/test/manifold_tests.jl +++ b/test/manifold_tests.jl @@ -1,4 +1,4 @@ -using OrdinaryDiffEq, Test, DiffEqBase, DiffEqCallbacks, RecursiveArrayTools +using OrdinaryDiffEq, Test, DiffEqBase, DiffEqCallbacks, RecursiveArrayTools, NonlinearSolve u0 = ones(2, 2) f = function (du, u, p, t) @@ -23,29 +23,29 @@ sol = solve(prob, Vern7()) @test !(sol[end][1]^2 + sol[end][2]^2 ≈ 2) # autodiff=true -@inferred ManifoldProjection(g; autonomous = Val(true), resid_prototype = zeros(2)) +@inferred ManifoldProjection(g; autonomous = Val(false), resid_prototype = zeros(2)) cb = ManifoldProjection(g; resid_prototype = zeros(2)) @test isautonomous(cb.affect!) solve(prob, Vern7(), callback = cb) @time sol = solve(prob, Vern7(), callback = cb) @test sol[end][1]^2 + sol[end][2]^2 ≈ 2 -cb_t = ManifoldProjection(g_t) +cb_t = ManifoldProjection(g_t; resid_prototype = zeros(2)) @test !isautonomous(cb_t.affect!) solve(prob, Vern7(), callback = cb_t) @time sol_t = solve(prob, Vern7(), callback = cb_t) @test sol_t.u == sol.u && sol_t.t == sol.t # autodiff=false -cb_false = ManifoldProjection(g, - nlsolve = DiffEqCallbacks.NLSOLVEJL_SETUP(autodiff = false)) +cb_false = ManifoldProjection( + g; nlsolve = GaussNewton(; autodiff = AutoFiniteDiff()), resid_prototype = zeros(2)) @test isautonomous(cb_false.affect!) solve(prob, Vern7(), callback = cb_false) sol = solve(prob, Vern7(), callback = cb_false) @test sol[end][1]^2 + sol[end][2]^2 ≈ 2 cb_t_false = ManifoldProjection(g_t, - nlsolve = DiffEqCallbacks.NLSOLVEJL_SETUP(autodiff = false)) + nlsolve = GaussNewton(; autodiff = AutoFiniteDiff()), resid_prototype = zeros(2)) @test !isautonomous(cb_t_false.affect!) solve(prob, Vern7(), callback = cb_t_false) sol_t = solve(prob, Vern7(), callback = cb_t_false) @@ -61,10 +61,27 @@ sol = solve(prob, Vern7(), callback = cb) sol = solve(prob, Vern7(), callback = cb_t) @test sol[end][1]^2 + sol[end][2]^2 ≈ 2 -# does not work since Calculus.jl (on which NLsolve.jl depends) -# implements only Jacobians of vectors sol = solve(prob, Vern7(), callback = cb_false) -sol[end][1]^2 + sol[end][2]^2 ≈ 2 +@test sol[end][1]^2 + sol[end][2]^2 ≈ 2 sol = solve(prob, Vern7(), callback = cb_t_false) -sol[end][1]^2 + sol[end][2]^2 ≈ 2 +@test sol[end][1]^2 + sol[end][2]^2 ≈ 2 + +# Test termination if cannot project to manifold +function g_unsat(resid, u, p) + resid[1] = u[2]^2 + u[1]^2 - 1000 + resid[2] = u[2]^2 + u[1]^2 - 20 +end + +cb_unsat = ManifoldProjection(g_unsat; resid_prototype = zeros(2)) +sol = solve(prob, Vern7(), callback = cb_unsat) +@test !SciMLBase.successful_retcode(sol) +@test last(sol.t) != 100.0 + +# Tests for OOP Manifold Projection +function g_oop(u, p) + return [u[2]^2 + u[1]^2 - 2 + u[3]^2 + u[4]^2 - 2] +end + +g_t(resid, u, p, t) = g(resid, u, p) From 48736d01d766799933ab31499ea96df7846192ad Mon Sep 17 00:00:00 2001 From: Avik Pal Date: Tue, 20 Feb 2024 13:42:07 -0500 Subject: [PATCH 04/12] Check in Manifest file --- Manifest.toml | 1541 ++++++++++++++++++++++++++++++++++++++++ Project.toml | 3 +- test/manifold_tests.jl | 49 +- 3 files changed, 1591 insertions(+), 2 deletions(-) create mode 100644 Manifest.toml diff --git a/Manifest.toml b/Manifest.toml new file mode 100644 index 00000000..a89c4d6a --- /dev/null +++ b/Manifest.toml @@ -0,0 +1,1541 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.10.1" +manifest_format = "2.0" +project_hash = 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+weakdeps = ["Random", "Test"] + + [deps.TranscodingStreams.extensions] + TestExt = ["Test", "Random"] + +[[deps.TriangularSolve]] +deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] +git-tree-sha1 = "fadebab77bf3ae041f77346dd1c290173da5a443" +uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" +version = "0.1.20" + +[[deps.Tricks]] +git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" +uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" +version = "0.1.8" + +[[deps.TruncatedStacktraces]] +deps = ["InteractiveUtils", "MacroTools", "Preferences"] +git-tree-sha1 = "ea3e54c2bdde39062abf5a9758a23735558705e1" +uuid = "781d530d-4396-4725-bb49-402e4bee1e77" +version = "1.4.0" + +[[deps.UUIDs]] +deps = ["Random", "SHA"] +uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" + +[[deps.UnPack]] +git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" +uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" +version = "1.0.2" + +[[deps.Unicode]] +uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" + +[[deps.UnsafeAtomics]] +git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" +uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" +version = "0.2.1" + +[[deps.UnsafeAtomicsLLVM]] +deps = ["LLVM", "UnsafeAtomics"] +git-tree-sha1 = "323e3d0acf5e78a56dfae7bd8928c989b4f3083e" +uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" +version = "0.1.3" + +[[deps.VectorizationBase]] +deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] +git-tree-sha1 = "7209df901e6ed7489fe9b7aa3e46fb788e15db85" +uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" +version = "0.21.65" + +[[deps.VertexSafeGraphs]] +deps = ["Graphs"] +git-tree-sha1 = "8351f8d73d7e880bfc042a8b6922684ebeafb35c" +uuid = "19fa3120-7c27-5ec5-8db8-b0b0aa330d6f" +version = "0.2.0" + +[[deps.Zlib_jll]] +deps = ["Libdl"] +uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.13+1" + +[[deps.Zygote]] +deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] +git-tree-sha1 = "4ddb4470e47b0094c93055a3bcae799165cc68f1" +uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" +version = "0.6.69" + + [deps.Zygote.extensions] + ZygoteColorsExt = "Colors" + ZygoteDistancesExt = "Distances" + ZygoteTrackerExt = "Tracker" + + [deps.Zygote.weakdeps] + Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" + Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + +[[deps.ZygoteRules]] +deps = ["ChainRulesCore", "MacroTools"] +git-tree-sha1 = "27798139afc0a2afa7b1824c206d5e87ea587a00" +uuid = "700de1a5-db45-46bc-99cf-38207098b444" +version = "0.2.5" + +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.8.0+1" + +[[deps.nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.52.0+1" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+2" diff --git a/Project.toml b/Project.toml index bf595272..5ef7eef1 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "DiffEqCallbacks" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" authors = ["Chris Rackauckas "] -version = "2.38.0" # Make it 3.0.0 before releasing. This is needed to allow resolver to work for test dependencies +version = "3.0.0" [deps] DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" @@ -15,6 +15,7 @@ Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a" RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" +SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1" # Remove before merging StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" [weakdeps] diff --git a/test/manifold_tests.jl b/test/manifold_tests.jl index 865b3b13..6fe160db 100644 --- a/test/manifold_tests.jl +++ b/test/manifold_tests.jl @@ -84,4 +84,51 @@ function g_oop(u, p) u[3]^2 + u[4]^2 - 2] end -g_t(resid, u, p, t) = g(resid, u, p) +g_oop_t(u, p, t) = g_oop(u, p) + +prob = ODEProblem(f, u0, (0.0, 100.0)) + +# autodiff=true +@inferred ManifoldProjection(g_oop; autonomous = Val(false), isinplace = Val(false)) +cb = ManifoldProjection(g_oop; isinplace = Val(false)) +@test isautonomous(cb.affect!) +solve(prob, Vern7(), callback = cb) +@time sol = solve(prob, Vern7(), callback = cb) +@test sol[end][1]^2 + sol[end][2]^2 ≈ 2 + +cb_t = ManifoldProjection(g_oop_t; isinplace = Val(false)) +@test !isautonomous(cb_t.affect!) +solve(prob, Vern7(), callback = cb_t) +@time sol_t = solve(prob, Vern7(), callback = cb_t) +@test sol_t.u == sol.u && sol_t.t == sol.t + +# autodiff=false +cb_false = ManifoldProjection( + g_oop; nlsolve = GaussNewton(; autodiff = AutoFiniteDiff()), isinplace = Val(false)) +@test isautonomous(cb_false.affect!) +solve(prob, Vern7(), callback = cb_false) +sol = solve(prob, Vern7(), callback = cb_false) +@test sol[end][1]^2 + sol[end][2]^2 ≈ 2 + +cb_t_false = ManifoldProjection(g_oop_t, + nlsolve = GaussNewton(; autodiff = AutoFiniteDiff()), isinplace = Val(false)) +@test !isautonomous(cb_t_false.affect!) +solve(prob, Vern7(), callback = cb_t_false) +sol_t = solve(prob, Vern7(), callback = cb_t_false) +@test sol_t.u == sol.u && sol_t.t == sol.t + +# test array partitions +u₀ = ArrayPartition(ones(2), ones(2)) +prob = ODEProblem(f, u₀, (0.0, 100.0)) + +sol = solve(prob, Vern7(), callback = cb) +@test sol[end][1]^2 + sol[end][2]^2 ≈ 2 + +sol = solve(prob, Vern7(), callback = cb_t) +@test sol[end][1]^2 + sol[end][2]^2 ≈ 2 + +sol = solve(prob, Vern7(), callback = cb_false) +@test sol[end][1]^2 + sol[end][2]^2 ≈ 2 + +sol = solve(prob, Vern7(), callback = cb_t_false) +@test sol[end][1]^2 + sol[end][2]^2 ≈ 2 From 6c269859b8228e951cd7e47a979c83c69ad5cbed Mon Sep 17 00:00:00 2001 From: Avik Pal Date: Tue, 20 Feb 2024 13:45:28 -0500 Subject: [PATCH 05/12] Test with v2 --- Manifest.toml | 532 ++------------------------------------------------ Project.toml | 3 +- 2 files changed, 22 insertions(+), 513 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index a89c4d6a..452022d1 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,24 +2,13 @@ julia_version = "1.10.1" manifest_format = "2.0" -project_hash = "fda666f65901bef90bd561df2c0aa1aa8ce7a7a1" +project_hash = "ff8ab445d2203081161a6e655c54e210003036ff" [[deps.ADTypes]] git-tree-sha1 = "41c37aa88889c171f1300ceac1313c06e891d245" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" version = "0.2.6" -[[deps.AbstractFFTs]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" -uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.5.0" -weakdeps = ["ChainRulesCore", "Test"] - - [deps.AbstractFFTs.extensions] - AbstractFFTsChainRulesCoreExt = "ChainRulesCore" - AbstractFFTsTestExt = "Test" - [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] git-tree-sha1 = "0fb305e0253fd4e833d486914367a2ee2c2e78d0" @@ -75,89 +64,27 @@ weakdeps = ["SparseArrays"] [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -[[deps.Atomix]] -deps = ["UnsafeAtomics"] -git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" -uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" -version = "0.1.0" - [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -[[deps.BenchmarkTools]] -deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "f1f03a9fa24271160ed7e73051fba3c1a759b53f" -uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.4.0" - [[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b" uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" version = "0.1.5" -[[deps.Bzip2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" -uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+1" - -[[deps.CEnum]] -git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" -uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" -version = "0.5.0" - [[deps.CPUSummary]] deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] git-tree-sha1 = "601f7e7b3d36f18790e2caf83a882d88e9b71ff1" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" version = "0.2.4" -[[deps.Calculus]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" -uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" -version = "0.5.1" - -[[deps.Cassette]] -git-tree-sha1 = "0970356c3bb9113309c74c27c87083cf9c73880a" -uuid = "7057c7e9-c182-5462-911a-8362d720325c" -version = "0.3.13" - -[[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "4e42872be98fa3343c4f8458cbda8c5c6a6fa97c" -uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.63.0" - -[[deps.ChainRulesCore]] -deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "892b245fdec1c511906671b6a5e1bafa38a727c1" -uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.22.0" -weakdeps = ["SparseArrays"] - - [deps.ChainRulesCore.extensions] - ChainRulesCoreSparseArraysExt = "SparseArrays" - [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" version = "0.1.12" -[[deps.CodecBzip2]] -deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"] -git-tree-sha1 = "9b1ca1aa6ce3f71b3d1840c538a8210a043625eb" -uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" -version = "0.8.2" - -[[deps.CodecZlib]] -deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73" -uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.4" - [[deps.CommonSolve]] git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" @@ -259,22 +186,6 @@ version = "6.147.0" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" -[[deps.DiffEqCallbacks]] -deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NonlinearSolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "SciMLSensitivity", "StaticArraysCore"] -path = "/mnt/research/manifolds/DiffEqCallbacks.jl" -uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "3.0.0" - -[[deps.DiffEqNoiseProcess]] -deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "3d440ee25f48e5c7b08af71f2997daca45bf6856" -uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.20.1" -weakdeps = ["ReverseDiff"] - - [deps.DiffEqNoiseProcess.extensions] - DiffEqNoiseProcessReverseDiffExt = "ReverseDiff" - [[deps.DiffResults]] deps = ["StaticArraysCore"] git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" @@ -287,37 +198,10 @@ git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" version = "1.15.1" -[[deps.Distances]] -deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" -uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.11" -weakdeps = ["ChainRulesCore", "SparseArrays"] - - [deps.Distances.extensions] - DistancesChainRulesCoreExt = "ChainRulesCore" - DistancesSparseArraysExt = "SparseArrays" - [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" -[[deps.Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "7c302d7a5fec5214eb8a5a4c466dcf7a51fcf169" -uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.107" - - [deps.Distributions.extensions] - DistributionsChainRulesCoreExt = "ChainRulesCore" - DistributionsDensityInterfaceExt = "DensityInterface" - DistributionsTestExt = "Test" - - [deps.Distributions.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" - Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" - [[deps.DocStringExtensions]] deps = ["LibGit2"] git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" @@ -329,33 +213,11 @@ deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" -[[deps.DualNumbers]] -deps = ["Calculus", "NaNMath", "SpecialFunctions"] -git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" -uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" -version = "0.6.8" - -[[deps.EllipsisNotation]] -deps = ["StaticArrayInterface"] -git-tree-sha1 = "3507300d4343e8e4ad080ad24e335274c2e297a9" -uuid = "da5c29d0-fa7d-589e-88eb-ea29b0a81949" -version = "1.8.0" - [[deps.EnumX]] git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" -[[deps.Enzyme]] -deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Preferences", "Printf", "Random"] -git-tree-sha1 = "090a6f1996d357329bea66f0b1c7621b64d70bb0" -uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.11.16" -weakdeps = ["SpecialFunctions"] - - [deps.Enzyme.extensions] - EnzymeSpecialFunctionsExt = "SpecialFunctions" - [[deps.EnzymeCore]] git-tree-sha1 = "59c44d8fbc651c0395d8a6eda64b05ce316f58b4" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" @@ -365,18 +227,6 @@ weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] AdaptExt = "Adapt" -[[deps.Enzyme_jll]] -deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "32d418c804279c60dd38ac7868126696f3205a4f" -uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.102+0" - -[[deps.ExponentialUtilities]] -deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] -git-tree-sha1 = "8e18940a5ba7f4ddb41fe2b79b6acaac50880a86" -uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" -version = "1.26.1" - [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" @@ -407,13 +257,17 @@ deps = ["LinearAlgebra", "Random"] git-tree-sha1 = "5b93957f6dcd33fc343044af3d48c215be2562f1" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" version = "1.9.3" -weakdeps = ["PDMats", "SparseArrays", "Statistics"] [deps.FillArrays.extensions] FillArraysPDMatsExt = "PDMats" FillArraysSparseArraysExt = "SparseArrays" FillArraysStatisticsExt = "Statistics" + [deps.FillArrays.weakdeps] + PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" + [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] git-tree-sha1 = "73d1214fec245096717847c62d389a5d2ac86504" @@ -440,12 +294,6 @@ weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] ForwardDiffStaticArraysExt = "StaticArrays" -[[deps.FunctionProperties]] -deps = ["Cassette", "DiffRules"] -git-tree-sha1 = "663f3171531d52f9a68c089aa89de282001b3d5b" -uuid = "f62d2435-5019-4c03-9749-2d4c77af0cbc" -version = "0.1.0" - [[deps.FunctionWrappers]] git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" @@ -467,30 +315,12 @@ version = "0.4.7" deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" -[[deps.GPUArrays]] -deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "47e4686ec18a9620850bad110b79966132f14283" -uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "10.0.2" - [[deps.GPUArraysCore]] deps = ["Adapt"] git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" version = "0.1.6" -[[deps.GPUCompiler]] -deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "a846f297ce9d09ccba02ead0cae70690e072a119" -uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.25.0" - -[[deps.GenericSchur]] -deps = ["LinearAlgebra", "Printf"] -git-tree-sha1 = "fb69b2a645fa69ba5f474af09221b9308b160ce6" -uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e" -version = "0.5.3" - [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] git-tree-sha1 = "899050ace26649433ef1af25bc17a815b3db52b7" @@ -503,18 +333,6 @@ git-tree-sha1 = "eb8fed28f4994600e29beef49744639d985a04b2" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" version = "0.1.16" -[[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" -uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.23" - -[[deps.IRTools]] -deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "5d8c5713f38f7bc029e26627b687710ba406d0dd" -uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.12" - [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" @@ -551,62 +369,18 @@ git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" version = "1.5.0" -[[deps.JSON]] -deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" -uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.4" - -[[deps.JumpProcesses]] -deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "UnPack"] -git-tree-sha1 = "c451feb97251965a9fe40bacd62551a72cc5902c" -uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.10.1" -weakdeps = ["FastBroadcast"] - - [deps.JumpProcesses.extensions] - JumpProcessFastBroadcastExt = "FastBroadcast" - [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] git-tree-sha1 = "01bb1d420d959b9f668e252a5732444a61ff25de" uuid = "ef3ab10e-7fda-4108-b977-705223b18434" version = "0.5.0" -[[deps.KernelAbstractions]] -deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "4e0cb2f5aad44dcfdc91088e85dee4ecb22c791c" -uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.16" -weakdeps = ["EnzymeCore"] - - [deps.KernelAbstractions.extensions] - EnzymeExt = "EnzymeCore" - [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] git-tree-sha1 = "8a6837ec02fe5fb3def1abc907bb802ef11a0729" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" version = "0.9.5" -[[deps.LLVM]] -deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] -git-tree-sha1 = "9e70165cca7459d25406367f0c55e517a9a7bfe7" -uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.5.0" - - [deps.LLVM.extensions] - BFloat16sExt = "BFloat16s" - - [deps.LLVM.weakdeps] - BFloat16s = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" - -[[deps.LLVMExtra_jll]] -deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "114e3a48f13d4c18ddd7fd6a00107b4b96f60f9c" -uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.28+0" - [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277" @@ -633,12 +407,6 @@ weakdeps = ["StaticArrays"] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" -[[deps.LevyArea]] -deps = ["LinearAlgebra", "Random", "SpecialFunctions"] -git-tree-sha1 = "56513a09b8e0ae6485f34401ea9e2f31357958ec" -uuid = "2d8b4e74-eb68-11e8-0fb9-d5eb67b50637" -version = "1.0.0" - [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" @@ -735,12 +503,16 @@ deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensio git-tree-sha1 = "0f5648fbae0d015e3abe5867bca2b362f67a5894" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" version = "0.12.166" -weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [deps.LoopVectorization.extensions] ForwardDiffExt = ["ChainRulesCore", "ForwardDiff"] SpecialFunctionsExt = "SpecialFunctions" + [deps.LoopVectorization.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl"] git-tree-sha1 = "72dc3cf284559eb8f53aa593fe62cb33f83ed0c0" @@ -762,12 +534,6 @@ version = "0.1.8" deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -[[deps.MathOptInterface]] -deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"] -git-tree-sha1 = "569a003f93d7c64068d3afaab908d21f67a22cd5" -uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" -version = "1.25.3" - [[deps.MatrixFactorizations]] deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] git-tree-sha1 = "78f6e33434939b0ac9ba1df81e6d005ee85a7396" @@ -785,12 +551,6 @@ deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" version = "2.28.2+1" -[[deps.Missings]] -deps = ["DataAPI"] -git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" -uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.1.0" - [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -803,42 +563,12 @@ git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab" uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221" version = "0.2.4" -[[deps.MutableArithmetics]] -deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "302fd161eb1c439e4115b51ae456da4e9984f130" -uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.4.1" - [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" version = "7.8.3" -[[deps.NLsolve]] -deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] -git-tree-sha1 = "019f12e9a1a7880459d0173c182e6a99365d7ac1" -uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" -version = "4.5.1" - -[[deps.NNlib]] -deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "877f15c331337d54cf24c797d5bcb2e48ce21221" -uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.12" - - [deps.NNlib.extensions] - NNlibAMDGPUExt = "AMDGPU" - NNlibCUDACUDNNExt = ["CUDA", "cuDNN"] - NNlibCUDAExt = "CUDA" - NNlibEnzymeCoreExt = "EnzymeCore" - - [deps.NNlib.weakdeps] - AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" - CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" - cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" - [[deps.NaNMath]] deps = ["OpenLibm_jll"] git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" @@ -883,12 +613,6 @@ version = "3.7.0" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" -[[deps.ObjectFile]] -deps = ["Reexport", "StructIO"] -git-tree-sha1 = "195e0a19842f678dd3473ceafbe9d82dfacc583c" -uuid = "d8793406-e978-5875-9003-1fc021f44a92" -version = "0.4.1" - [[deps.OffsetArrays]] git-tree-sha1 = "6a731f2b5c03157418a20c12195eb4b74c8f8621" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" @@ -914,35 +638,11 @@ git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.5+0" -[[deps.Optim]] -deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "MathOptInterface", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "d024bfb56144d947d4fafcd9cb5cafbe3410b133" -uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.9.2" - -[[deps.Optimisers]] -deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "264b061c1903bc0fe9be77cb9050ebacff66bb63" -uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.3.2" - [[deps.OrderedCollections]] git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.6.3" -[[deps.OrdinaryDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "ed171bfea6156d6458007b19790a22f4754bd501" -uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.71.0" - -[[deps.PDMats]] -deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" -uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.31" - [[deps.PackageExtensionCompat]] git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930" @@ -955,23 +655,11 @@ git-tree-sha1 = "34c0e9ad262e5f7fc75b10a9952ca7692cfc5fbe" uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" version = "0.12.3" -[[deps.Parsers]] -deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" -uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.8.1" - [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" version = "1.10.0" -[[deps.PoissonRandom]] -deps = ["Random"] -git-tree-sha1 = "a0f1159c33f846aa77c3f30ebbc69795e5327152" -uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" -version = "0.4.4" - [[deps.Polyester]] deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] git-tree-sha1 = "fca25670784a1ae44546bcb17288218310af2778" @@ -984,22 +672,18 @@ git-tree-sha1 = "240d7170f5ffdb285f9427b92333c3463bf65bf6" uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" version = "0.2.1" -[[deps.PositiveFactorizations]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" -uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" -version = "0.2.4" - [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterface", "ForwardDiff"] git-tree-sha1 = "b6665214f2d0739f2d09a17474dd443b9139784a" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" version = "0.4.20" -weakdeps = ["ReverseDiff"] [deps.PreallocationTools.extensions] PreallocationToolsReverseDiffExt = "ReverseDiff" + [deps.PreallocationTools.weakdeps] + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + [[deps.PrecompileTools]] deps = ["Preferences"] git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" @@ -1016,16 +700,6 @@ version = "1.4.1" deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -[[deps.Profile]] -deps = ["Printf"] -uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" - -[[deps.QuadGK]] -deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "9b23c31e76e333e6fb4c1595ae6afa74966a729e" -uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.9.4" - [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" @@ -1034,24 +708,6 @@ uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -[[deps.Random123]] -deps = ["Random", "RandomNumbers"] -git-tree-sha1 = "c860e84651f58ce240dd79e5d9e055d55234c35a" -uuid = "74087812-796a-5b5d-8853-05524746bad3" -version = "1.6.2" - -[[deps.RandomNumbers]] -deps = ["Random", "Requires"] -git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" -uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" -version = "1.5.3" - -[[deps.RealDot]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "9f0a1b71baaf7650f4fa8a1d168c7fb6ee41f0c9" -uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" -version = "0.1.0" - [[deps.RecipesBase]] deps = ["PrecompileTools"] git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff" @@ -1101,30 +757,6 @@ git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" uuid = "ae029012-a4dd-5104-9daa-d747884805df" version = "1.3.0" -[[deps.ResettableStacks]] -deps = ["StaticArrays"] -git-tree-sha1 = "256eeeec186fa7f26f2801732774ccf277f05db9" -uuid = "ae5879a3-cd67-5da8-be7f-38c6eb64a37b" -version = "1.1.1" - -[[deps.ReverseDiff]] -deps = ["ChainRulesCore", "DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] -git-tree-sha1 = "d1235bdd57a93bd7504225b792b867e9a7df38d5" -uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -version = "1.15.1" - -[[deps.Rmath]] -deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" -uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.1" - -[[deps.Rmath_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" -uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.0+0" - [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] git-tree-sha1 = "6aacc5eefe8415f47b3e34214c1d79d2674a0ba2" @@ -1177,20 +809,6 @@ git-tree-sha1 = "51ae235ff058a64815e0a2c34b1db7578a06813d" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" version = "0.3.7" -[[deps.SciMLSensitivity]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "EllipsisNotation", "Enzyme", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEq", "Parameters", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLOperators", "SparseDiffTools", "StaticArrays", "StaticArraysCore", "Statistics", "StochasticDiffEq", "Tracker", "TruncatedStacktraces", "Zygote"] -git-tree-sha1 = "2f679801847d6e23b4bdb0aacfbea7f4c2c76fd0" -repo-rev = "ap/diffeqcallbacks" -repo-url = "https://github.com/SciML/SciMLSensitivity.jl.git" -uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.56.0" - -[[deps.Scratch]] -deps = ["Dates"] -git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" -uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.2.1" - [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1226,20 +844,9 @@ git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" version = "0.9.4" -[[deps.SimpleUnPack]] -git-tree-sha1 = "58e6353e72cde29b90a69527e56df1b5c3d8c437" -uuid = "ce78b400-467f-4804-87d8-8f486da07d0a" -version = "1.1.0" - [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -[[deps.SortingAlgorithms]] -deps = ["DataStructures"] -git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085" -uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.2.1" - [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" @@ -1265,12 +872,6 @@ version = "2.17.0" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" -[[deps.SparseInverseSubset]] -deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "52962839426b75b3021296f7df242e40ecfc0852" -uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" -version = "0.1.2" - [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] git-tree-sha1 = "342cf4b449c299d8d1ceaf00b7a49f4fbc7940e7" @@ -1282,11 +883,13 @@ deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_j git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" version = "2.3.1" -weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" + [deps.SpecialFunctions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + [[deps.Static]] deps = ["IfElse"] git-tree-sha1 = "d2fdac9ff3906e27f7a618d47b676941baa6c80c" @@ -1309,12 +912,15 @@ deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] git-tree-sha1 = "7b0e9c14c624e435076d19aea1e5cbdec2b9ca37" uuid = "90137ffa-7385-5640-81b9-e52037218182" version = "1.9.2" -weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] StaticArraysChainRulesCoreExt = "ChainRulesCore" StaticArraysStatisticsExt = "Statistics" + [deps.StaticArrays.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" + [[deps.StaticArraysCore]] git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" @@ -1325,56 +931,12 @@ deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" version = "1.10.0" -[[deps.StatsAPI]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" -uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.7.0" - -[[deps.StatsBase]] -deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "1d77abd07f617c4868c33d4f5b9e1dbb2643c9cf" -uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.2" - -[[deps.StatsFuns]] -deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" -uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.1" - - [deps.StatsFuns.extensions] - StatsFunsChainRulesCoreExt = "ChainRulesCore" - StatsFunsInverseFunctionsExt = "InverseFunctions" - - [deps.StatsFuns.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - -[[deps.StochasticDiffEq]] -deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "f5eb6f4794a2a56d6b9d3dcdb9d6cb217a2ac660" -uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.65.0" - [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] git-tree-sha1 = "d6415f66f3d89c615929af907fdc6a3e17af0d8c" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" version = "0.5.2" -[[deps.StructArrays]] -deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "1b0b1205a56dc288b71b1961d48e351520702e24" -uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.17" - -[[deps.StructIO]] -deps = ["Test"] -git-tree-sha1 = "010dc73c7146869c042b49adcdb6bf528c12e859" -uuid = "53d494c1-5632-5724-8f4c-31dff12d585f" -version = "0.3.0" - [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" @@ -1427,25 +989,6 @@ git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" version = "0.5.23" -[[deps.Tracker]] -deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "5c942be30a85ac75d14e9e527b55504031e1bbd3" -uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.31" -weakdeps = ["PDMats"] - - [deps.Tracker.extensions] - TrackerPDMatsExt = "PDMats" - -[[deps.TranscodingStreams]] -git-tree-sha1 = "54194d92959d8ebaa8e26227dbe3cdefcdcd594f" -uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.10.3" -weakdeps = ["Random", "Test"] - - [deps.TranscodingStreams.extensions] - TestExt = ["Test", "Random"] - [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] git-tree-sha1 = "fadebab77bf3ae041f77346dd1c290173da5a443" @@ -1475,17 +1018,6 @@ version = "1.0.2" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -[[deps.UnsafeAtomics]] -git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" -uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" -version = "0.2.1" - -[[deps.UnsafeAtomicsLLVM]] -deps = ["LLVM", "UnsafeAtomics"] -git-tree-sha1 = "323e3d0acf5e78a56dfae7bd8928c989b4f3083e" -uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" -version = "0.1.3" - [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] git-tree-sha1 = "7209df901e6ed7489fe9b7aa3e46fb788e15db85" @@ -1503,28 +1035,6 @@ deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" version = "1.2.13+1" -[[deps.Zygote]] -deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "4ddb4470e47b0094c93055a3bcae799165cc68f1" -uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.69" - - [deps.Zygote.extensions] - ZygoteColorsExt = "Colors" - ZygoteDistancesExt = "Distances" - ZygoteTrackerExt = "Tracker" - - [deps.Zygote.weakdeps] - Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" - Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - -[[deps.ZygoteRules]] -deps = ["ChainRulesCore", "MacroTools"] -git-tree-sha1 = "27798139afc0a2afa7b1824c206d5e87ea587a00" -uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.5" - [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" diff --git a/Project.toml b/Project.toml index 5ef7eef1..515c9578 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "DiffEqCallbacks" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" authors = ["Chris Rackauckas "] -version = "3.0.0" +version = "2.38.0" # Make this 3.0.0 before tagging [deps] DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" @@ -15,7 +15,6 @@ Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a" RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1" # Remove before merging StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" [weakdeps] From 88c3ddc2d300b8e4ceb62545eaa30d175c76b1f4 Mon Sep 17 00:00:00 2001 From: Avik Pal Date: Tue, 20 Feb 2024 14:01:39 -0500 Subject: [PATCH 06/12] Document the changes in GeneralDomain --- Project.toml | 3 ++- src/domain.jl | 37 +++++++++++++++++-------------------- 2 files changed, 19 insertions(+), 21 deletions(-) diff --git a/Project.toml b/Project.toml index 515c9578..cdefe9a9 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "DiffEqCallbacks" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" authors = ["Chris Rackauckas "] -version = "2.38.0" # Make this 3.0.0 before tagging +version = "2.38.0" [deps] DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" @@ -30,6 +30,7 @@ ForwardDiff = "0.10.19" Functors = "0.4" LinearAlgebra = "1.10" Markdown = "1.10" +NonlinearSolve = "3.6" ODEProblemLibrary = "0.1.5" OrdinaryDiffEq = "6.68" Parameters = "0.12" diff --git a/src/domain.jl b/src/domain.jl index b4d7909d..daa4c381 100644 --- a/src/domain.jl +++ b/src/domain.jl @@ -212,12 +212,10 @@ end # callback definitions """ -```julia -GeneralDomain(g, u = nothing; nlsolve = NewtonRaphson(), save = true, - abstol = nothing, scalefactor = nothing, - autonomous = maximum(SciMLBase.numargs(g)) == 3, - nlopts = Dict(:ftol => 10 * eps())) -``` + GeneralDomain( + g, u = nothing; save = true, abstol = nothing, scalefactor = nothing, + autonomous = maximum(SciMLBase.numargs(g)) == 3, nlsolve_kwargs = (; + abstol = 10 * eps()), kwargs...) A `GeneralDomain` callback in DiffEqCallbacks.jl generalizes the concept of a `PositiveDomain` callback to arbitrary domains. Domains are specified by @@ -242,8 +240,6 @@ preferred. ## Keyword Arguments - - `nlsolve`: A nonlinear solver as defined in the [NonlinearSolve.jl format](https://docs.sciml.ai/NonlinearSolve/stable/basics/solve/) - which is passed to a `ManifoldProjection`. - `save`: Whether to do the standard saving (applied after the callback). - `abstol`: Tolerance up to, which residuals are accepted. Element-wise tolerances are allowed. If it is not specified, every application of the callback uses the @@ -251,11 +247,10 @@ preferred. - `scalefactor`: Factor by which an unaccepted time step is reduced. If it is not specified, time steps are halved. - `autonomous`: Whether `g` is an autonomous function of the form `g(resid, u, p)`. - - `nlopts`: Optional arguments to nonlinear solver of a `ManifoldProjection` which - can be any of the [NonlinearSolve.jl keywords](https://docs.sciml.ai/NonlinearSolve/stable/basics/solve/). - The default value of `abstol = 10 * eps()` ensures that convergence is only declared - if the infinite norm of residuals is very small and hence the state vector is very - close to the domain. + If it is not specified, it is determined automatically. + - `kwargs`: All other keyword arguments are passed to `ManifoldProjection`. + - `nlsolve_kwargs`: All keyword arguments are passed to the nonlinear solver in + `ManifoldProjection`. The default is `(; abstol = 10 * eps())`. ## References @@ -263,19 +258,21 @@ Shampine, Lawrence F., Skip Thompson, Jacek Kierzenka and G. D. Byrne. Non-negative solutions of ODEs. Applied Mathematics and Computation 170 (2005): 556-569. """ -function GeneralDomain(g, u = nothing; nlsolve = NewtonRaphson(), save = true, - abstol = nothing, scalefactor = nothing, - autonomous = maximum(SciMLBase.numargs(g)) == 3, nlopts = (; abstol = 10 * eps())) +function GeneralDomain( + g, u = nothing; save = true, abstol = nothing, scalefactor = nothing, + autonomous = maximum(SciMLBase.numargs(g)) == 3, nlsolve_kwargs = (; + abstol = 10 * eps()), kwargs...) + _autonomous = SciMLBase._unwrap_val(autonomous) if u isa Nothing - affect! = GeneralDomainAffect{autonomous}(g, abstol, scalefactor, nothing, nothing) + affect! = GeneralDomainAffect{_autonomous}(g, abstol, scalefactor, nothing, nothing) else - affect! = GeneralDomainAffect{autonomous}(g, abstol, scalefactor, deepcopy(u), + affect! = GeneralDomainAffect{_autonomous}(g, abstol, scalefactor, deepcopy(u), deepcopy(u)) end condition = (u, t, integrator) -> true CallbackSet( - ManifoldProjection(g; nlsolve = nlsolve, save = false, - autonomous = autonomous, nlopts = nlopts), + ManifoldProjection( + g; save = false, autonomous, isinplace = Val(true), kwargs..., nlsolve_kwargs...), DiscreteCallback(condition, affect!; save_positions = (false, save))) end From 233c3445eb61a429ef842239571109d6faa583e1 Mon Sep 17 00:00:00 2001 From: Avik Pal Date: Tue, 20 Feb 2024 18:21:03 -0500 Subject: [PATCH 07/12] Fix mistake in type construction --- src/manifold.jl | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/manifold.jl b/src/manifold.jl index ad9d714d..7559c3c3 100644 --- a/src/manifold.jl +++ b/src/manifold.jl @@ -94,7 +94,8 @@ mutable struct ManifoldProjection{iip, nlls, autonomous, F, NL, R, K} end # Now make `affect!` for this: -function (p::ManifoldProjection{iip, nlls, autonomous, NL})(integrator) where {iip, nlls, +function (p::ManifoldProjection{ + iip, nlls, autonomous, NL})(integrator) where {iip, nlls, autonomous, NL} # update current time if residual function is time-dependent !autonomous && (p.g.t = integrator.t) @@ -143,7 +144,7 @@ function ManifoldProjection(g; nlsolve = missing, save = true, nlls = Val(true), autonomous = maximum(SciMLBase.numargs(g)) == 2 end end - affect! = ManifoldProjection{iip, _nlls, autonomous}( + affect! = ManifoldProjection{iip, _nlls, SciMLBase._unwrap_val(autonomous)}( g, _nlsolve, resid_prototype, kwargs) condition = (u, t, integrator) -> true return DiscreteCallback(condition, affect!; initialize = Manifold_initialize, From 0339962f9053a2a2dbb6c9a3e814e14fea693c9d Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Wed, 21 Feb 2024 04:17:18 -0500 Subject: [PATCH 08/12] Delete Manifest.toml --- Manifest.toml | 1051 ------------------------------------------------- 1 file changed, 1051 deletions(-) delete mode 100644 Manifest.toml diff --git a/Manifest.toml b/Manifest.toml deleted file mode 100644 index 452022d1..00000000 --- a/Manifest.toml +++ /dev/null @@ -1,1051 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.1" -manifest_format = "2.0" -project_hash = "ff8ab445d2203081161a6e655c54e210003036ff" - -[[deps.ADTypes]] -git-tree-sha1 = "41c37aa88889c171f1300ceac1313c06e891d245" -uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.2.6" - 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-[[deps.nghttp2_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.52.0+1" - -[[deps.p7zip_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+2" From ecb8897daca58c012ba9468e69ce3be349777c75 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Wed, 21 Feb 2024 04:20:20 -0500 Subject: [PATCH 09/12] Update Project.toml --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index cdefe9a9..47cf724f 100644 --- a/Project.toml +++ b/Project.toml @@ -36,7 +36,7 @@ OrdinaryDiffEq = "6.68" Parameters = "0.12" QuadGK = "2.4" RecipesBase = "1.1" -RecursiveArrayTools = "2.38, 3" +RecursiveArrayTools = "3" SciMLBase = "2.9" SciMLSensitivity = "7.49" StaticArrays = "1.8" From b99538f05ad4823aad715c691b86b49481079af0 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Wed, 21 Feb 2024 04:21:55 -0500 Subject: [PATCH 10/12] Update Project.toml --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 47cf724f..e1fb487a 100644 --- a/Project.toml +++ b/Project.toml @@ -36,7 +36,7 @@ OrdinaryDiffEq = "6.68" Parameters = "0.12" QuadGK = "2.4" RecipesBase = "1.1" -RecursiveArrayTools = "3" +RecursiveArrayTools = "3.8" SciMLBase = "2.9" SciMLSensitivity = "7.49" StaticArrays = "1.8" From eb73790c3449df19aa55ac5f255db9a9d5c31ca0 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Wed, 21 Feb 2024 04:36:06 -0500 Subject: [PATCH 11/12] Update Project.toml --- Project.toml | 16 ++++++++-------- src/domain.jl | 2 +- src/saving.jl | 2 +- test/saving_tests.jl | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/Project.toml b/Project.toml index e1fb487a..6492a0ac 100644 --- a/Project.toml +++ b/Project.toml @@ -23,10 +23,10 @@ Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" [compat] Aqua = "0.8" -DataInterpolations = "4" +DataInterpolations = "4.6" DataStructures = "0.18.13" -DiffEqBase = "6.141" -ForwardDiff = "0.10.19" +DiffEqBase = "6.146" +ForwardDiff = "0.10.36" Functors = "0.4" LinearAlgebra = "1.10" Markdown = "1.10" @@ -35,16 +35,16 @@ ODEProblemLibrary = "0.1.5" OrdinaryDiffEq = "6.68" Parameters = "0.12" QuadGK = "2.4" -RecipesBase = "1.1" -RecursiveArrayTools = "3.8" -SciMLBase = "2.9" +RecipesBase = "1.3.4" +RecursiveArrayTools = "3.9" +SciMLBase = "2.26" SciMLSensitivity = "7.49" StaticArrays = "1.8" StaticArraysCore = "1.4" Sundials = "4.19.2" Test = "1" -Tracker = "0.2.15" -Zygote = "0.6.61" +Tracker = "0.2.26" +Zygote = "0.6.69" julia = "1.10" [extras] diff --git a/src/domain.jl b/src/domain.jl index daa4c381..d9879886 100644 --- a/src/domain.jl +++ b/src/domain.jl @@ -94,7 +94,7 @@ function affect!(integrator, f::AbstractDomainAffect{T, S, uType}) where {T, S, if dtcache == dt if integrator.opts.verbose @warn("Could not restrict values to domain. Iteration was canceled since ", - "proposed time step dt = ", dt," could not be reduced.") + "proposed time step dt = ", dt, " could not be reduced.") end break end diff --git a/src/saving.jl b/src/saving.jl index 1cd8a0ae..423c0cde 100644 --- a/src/saving.jl +++ b/src/saving.jl @@ -233,7 +233,7 @@ function linearize_period(t₀, t₁, u₀, u₁, integ, ilsc, caches, u_mask, # Sanity check that we don't accidentally infinitely recurse if t₁ - t₀ < dtmin @debug("Linearization failure", - t₁, t₀, string(u₀), string(u₁), string(u_mask),dtmin) + t₁, t₀, string(u₀), string(u₁), string(u_mask), dtmin) throw(ArgumentError("Linearization failed, fell below linearization subdivision threshold")) end diff --git a/test/saving_tests.jl b/test/saving_tests.jl index 2a7d2e61..f8a9d1d0 100644 --- a/test/saving_tests.jl +++ b/test/saving_tests.jl @@ -198,7 +198,7 @@ if VERSION >= v"1.9" # stack atol = abstol^(2.0^(-deriv_idx)), rtol = reltol^(2.0^(-deriv_idx))) if !check - @error("Check failed", solver,deriv_idx) + @error("Check failed", solver, deriv_idx) display(abs.(u_linear_upsampled .- u_interp_upsampled)) end @test check From 090a7cbb3c477fb6a8bb4fea01bb3844224894c8 Mon Sep 17 00:00:00 2001 From: Avik Pal Date: Wed, 21 Feb 2024 16:12:06 -0500 Subject: [PATCH 12/12] Up Project --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 6492a0ac..78b7c16c 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "DiffEqCallbacks" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" authors = ["Chris Rackauckas "] -version = "2.38.0" +version = "3.0.0" [deps] DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"