diff --git a/.gitignore b/.gitignore index b067edd..a19d79c 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ /Manifest.toml +/.vscode \ No newline at end of file diff --git a/Project.toml b/Project.toml index ccc5adb..bd5a5f1 100644 --- a/Project.toml +++ b/Project.toml @@ -1,14 +1,11 @@ name = "MechGlueDiffEqBase" uuid = "2532746b-52b5-4539-9431-8bb183ab067f" authors = ["hustf and contributors"] -version = "0.1.31" +version = "0.1.32" [deps] DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" -MechGluePlots = "03a24088-0a82-4850-846f-2cad5d056ae1" -MechanicalUnits = "e6be9192-89dc-11e9-36e6-5dbcb28f419e" -RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" +RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" Unitfu = "5ee08b94-2369-4f4a-b8c7-99333ba35fb0" [compat] @@ -16,6 +13,7 @@ julia = "1" [extras] Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +MechanicalUnits = "e6be9192-89dc-11e9-36e6-5dbcb28f419e" [targets] test = ["Test"] diff --git a/README.md b/README.md index f9dd613..fea7233 100644 --- a/README.md +++ b/README.md @@ -1 +1,15 @@ # MechGlueDiffEqBase +Glue code for making [DiffEqBase](https://github.com/SciML/DiffEqBase.jl) work with units. + +It also includes glue code for [RecursiveArrayTools](https://github.com/SciML/RecursiveArrayTools.jl), which enables type-stable solution of equations with mixed units. + +This defines how to calculate the vector norm when the vector is given in units compatible with [Unitfu.jl](https://github.com/hustf/Unitfu.jl), from registy [M8](https://github.com/hustf/M8). The differential equation algorithms expects the norm to be unitless, as can be seen in e.g. step size estimators: + +err_scaled = **error** / (**abstol** + norm(u) * **reltol**) + +where **bold** indicates unitful objects. + +The functions are adaptions of corresponding code from [DiffEqBase](https://github.com/SciML/DiffEqBase.jl/blob/6bb8830711e729ef513f2b1beb95853e4a691375/src/init.jl). + + + diff --git a/src/MechGlueDiffEqBase.jl b/src/MechGlueDiffEqBase.jl index 3bf44e4..1837263 100644 --- a/src/MechGlueDiffEqBase.jl +++ b/src/MechGlueDiffEqBase.jl @@ -1,139 +1,37 @@ module MechGlueDiffEqBase -import Unitfu: AbstractQuantity, Quantity, ustrip -import DiffEqBase: value, ODE_DEFAULT_NORM, UNITLESS_ABS2 +import Unitfu: AbstractQuantity, Quantity, ustrip, norm +import DiffEqBase: value, ODE_DEFAULT_NORM, UNITLESS_ABS2, zero +import DiffEqBase: calculate_residuals, @muladd +using RecursiveArrayTools export value, ODE_DEFAULT_NORM, UNITLESS_ABS2, Unitfu, AbstractQuantity, Quantity +export norm, ArrayPartition - -import RecipesBase -import RecipesBase.@recipe -import SciMLBase -import SciMLBase: AbstractTimeseriesSolution, RecipesBase -import SciMLBase: AbstractDiscreteProblem, AbstractRODESolution, SensitivityInterpolation -import SciMLBase: getsyms, interpret_vars, cleansyms -import SciMLBase: diffeq_to_arrays, issymbollike, getindepsym_defaultt -import SciMLBase: DEFAULT_PLOT_FUNC - - +# This is identical to what DiffEqBase defines for Unitful function value(x::Type{AbstractQuantity{T,D,U}}) where {T,D,U} T end -function value(x::AbstractQuantity) - x.val -end +# This is different from what DiffEqBase defines for Unitful +value(::Type{<:AbstractQuantity{T,D,U}}) where {T,D,U<:Core.TypeofBottom} = Base.undef_ref_str +value(x::Q) where {Q<:AbstractQuantity} = ustrip(x) + + +# This is identical to what DiffEqBase defines for Unitful @inline function ODE_DEFAULT_NORM(u::AbstractArray{<:AbstractQuantity,N},t) where {N} + # Support adaptive errors should be errorless for exponentiation sqrt(sum(x->ODE_DEFAULT_NORM(x[1],x[2]),zip((value(x) for x in u),Iterators.repeated(t))) / length(u)) end +# This is identical to what DiffEqBase defines for Unitful @inline function ODE_DEFAULT_NORM(u::Array{<:AbstractQuantity,N},t) where {N} sqrt(sum(x->ODE_DEFAULT_NORM(x[1],x[2]),zip((value(x) for x in u),Iterators.repeated(t))) / length(u)) end -@inline function ODE_DEFAULT_NORM(u::AbstractQuantity,t) - abs(value(u)) + +# This is identical to what DiffEqBase defines for Unitful + +@inline function ODE_DEFAULT_NORM(u::AbstractQuantity, t) + abs(ustrip(u)) end +# This is slightly different from what DiffEqBase defines for Unitful @inline function UNITLESS_ABS2(x::AbstractQuantity) - real(abs2(x)/oneunit(x)*oneunit(x)) + real(abs2(x) / (oneunit(x)^2)) end - -# This recipe is copied from SciMLBase, and only the signature is adopted -# for use with unitful solutions. It can perhaps be deleted now, and the link to RecipesBase be deleted. -@recipe function f(sol::AbstractTimeseriesSolution{T, N, A}; - plot_analytic=false, - denseplot = (sol.dense || - typeof(sol.prob) <: AbstractDiscreteProblem) && - !(typeof(sol) <: AbstractRODESolution) && - !(hasfield(typeof(sol),:interp) && - typeof(sol.interp) <: SensitivityInterpolation), - plotdensity = min(Int(1e5),sol.tslocation==0 ? - (typeof(sol.prob) <: AbstractDiscreteProblem ? - max(1000,100*length(sol)) : - max(1000,10*length(sol))) : - 1000*sol.tslocation), - tspan = nothing, axis_safety = 0.1, - vars=nothing) where {T<:Quantity, N, A<:Array{<:Quantity}} - syms = getsyms(sol) - int_vars = interpret_vars(vars,sol,syms) - strs = cleansyms(syms) - - tscale = get(plotattributes, :xscale, :identity) - plot_vecs,labels = diffeq_to_arrays(sol,plot_analytic,denseplot, - plotdensity,tspan,axis_safety, - vars,int_vars,tscale,strs) - - tdir = sign(sol.t[end]-sol.t[1]) - xflip --> tdir < 0 - seriestype --> :path - - # Special case labels when vars = (:x,:y,:z) or (:x) or [:x,:y] ... - if typeof(vars) <: Tuple && (issymbollike(vars[1]) && issymbollike(vars[2])) - xguide --> issymbollike(int_vars[1][2]) ? Symbol(int_vars[1][2]) : strs[int_vars[1][2]] - yguide --> issymbollike(int_vars[1][3]) ? Symbol(int_vars[1][3]) : strs[int_vars[1][3]] - if length(vars) > 2 - zguide --> issymbollike(int_vars[1][4]) ? Symbol(int_vars[1][4]) : strs[int_vars[1][4]] - end - end - - if (!any(issymbollike,getindex.(int_vars,1)) && getindex.(int_vars,1) == zeros(length(int_vars))) || - (!any(issymbollike,getindex.(int_vars,2)) && getindex.(int_vars,2) == zeros(length(int_vars))) || - all(t->Symbol(t)==getindepsym_defaultt(sol),getindex.(int_vars,1)) || all(t->Symbol(t)==getindepsym_defaultt(sol),getindex.(int_vars,2)) - xguide --> "$(getindepsym_defaultt(sol))" - end - if length(int_vars[1]) >= 3 && ((!any(issymbollike,getindex.(int_vars,3)) && getindex.(int_vars,3) == zeros(length(int_vars))) || - all(t->Symbol(t)==getindepsym_defaultt(sol),getindex.(int_vars,3))) - yguide --> "$(getindepsym_defaultt(sol))" - end - if length(int_vars[1]) >= 4 && ((!any(issymbollike,getindex.(int_vars,4)) && getindex.(int_vars,4) == zeros(length(int_vars))) || - all(t->Symbol(t)==getindepsym_defaultt(sol),getindex.(int_vars,4))) - zguide --> "$(getindepsym_defaultt(sol))" - end - - if (!any(issymbollike,getindex.(int_vars,2)) && getindex.(int_vars,2) == zeros(length(int_vars))) || - all(t->Symbol(t)==getindepsym_defaultt(sol),getindex.(int_vars,2)) - if tspan === nothing - if tdir > 0 - xlims --> (sol.t[1],sol.t[end]) - else - xlims --> (sol.t[end],sol.t[1]) - end - else - xlims --> (tspan[1],tspan[end]) - end - else - mins = minimum(sol[int_vars[1][2],:]) - maxs = maximum(sol[int_vars[1][2],:]) - for iv in int_vars - mins = min(mins,minimum(sol[iv[2],:])) - maxs = max(maxs,maximum(sol[iv[2],:])) - end - xlims --> ((1-sign(mins)*axis_safety)*mins,(1+sign(maxs)*axis_safety)*maxs) - end - - # Analytical solutions do not save enough information to have a good idea - # of the axis ahead of time - # Only set axis for animations - if sol.tslocation != 0 && !(typeof(sol) <: AbstractAnalyticalSolution) - if all(getindex.(int_vars,1) .== DEFAULT_PLOT_FUNC) - mins = minimum(sol[int_vars[1][3],:]) - maxs = maximum(sol[int_vars[1][3],:]) - for iv in int_vars - mins = min(mins,minimum(sol[iv[3],:])) - maxs = max(maxs,maximum(sol[iv[3],:])) - end - ylims --> ((1-sign(mins)*axis_safety)*mins,(1+sign(maxs)*axis_safety)*maxs) - - if length(int_vars[1]) >= 4 - mins = minimum(sol[int_vars[1][4],:]) - maxs = maximum(sol[int_vars[1][4],:]) - for iv in int_vars - mins = min(mins,minimum(sol[iv[4],:])) - maxs = max(mins,maximum(sol[iv[4],:])) - end - zlims --> ((1-sign(mins)*axis_safety)*mins,(1+sign(maxs)*axis_safety)*maxs) - end - end - end - - label --> reshape(labels,1,length(labels)) - println("----------------------------------MechGlueDiffEqBase") - (plot_vecs...,) -end - end diff --git a/test/Manifest.toml b/test/Manifest.toml deleted file mode 100644 index 577307b..0000000 --- a/test/Manifest.toml +++ /dev/null @@ -1,1361 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -[[AbstractAlgebra]] -deps = ["InteractiveUtils", "LinearAlgebra", "Markdown", "Random", "RandomExtensions", "SparseArrays", "Test"] -git-tree-sha1 = "919d4d78d4fc415ed989e21dc74aef981052a22d" -uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" -version = "0.15.1" - -[[AbstractTrees]] -git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" -uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.3.4" - 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-[[xkbcommon_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6" -uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "0.9.1+5" diff --git a/test/Project.toml b/test/Project.toml deleted file mode 100644 index 8f72e54..0000000 --- a/test/Project.toml +++ /dev/null @@ -1,6 +0,0 @@ -[deps] -DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -MechGlueDiffEqBase = "2532746b-52b5-4539-9431-8bb183ab067f" -MechGluePlots = "03a24088-0a82-4850-846f-2cad5d056ae1" -Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" diff --git a/test/runtests.jl b/test/runtests.jl index e65b87b..15635c5 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,41 +1,4 @@ -using MechGlueDiffEqBase -using MechGluePlots -import MechanicalUnits: @import_expand, Quantity, Time, Force, ∙ -import Unitfu.AbstractQuantity -import DifferentialEquations -import DifferentialEquations: SciMLBase, solve, ODEProblem, Tsit5 -import SciMLBase -import SciMLBase: AbstractTimeseriesSolution, RecipesBase -import SciMLBase: AbstractDiscreteProblem, AbstractRODESolution, SensitivityInterpolation using Test -import Plots.plot - -@import_expand(N, s, m) -@testset "ODE" begin - f = (y, p, t) -> 0.5y / 3.0s # The derivative, yeah - u0 = 1.5N - tspan = (0.0s, 1.0s) - prob = ODEProblem(f, u0, tspan) - solve(prob, Tsit5()) - sol = solve(prob) - @test sol.t isa Vector{<:Time} - @test sol.u isa Vector{<:Force} -end - -#@testset "Plot ODE quantity" begin - SciMLBase.RecipesBase.debug(true) - f1 = (y, p, t) -> -1.5y / 0.3s # The derivative, yeah - u0 = 1.5N - tspan = (0.0s, 1.0s) - prob = ODEProblem(f1, u0, tspan) - solve(prob, Tsit5()) - sol = solve(prob) - @test sol isa AbstractTimeseriesSolution{T, N, A} where {T, N, A} - @test sol isa AbstractTimeseriesSolution{T, N, A} where {T<:Quantity, N, A} - @test sol isa AbstractTimeseriesSolution{T, N, A} where {T<:Quantity, N, A<:Array{<:Quantity}} - # Here, we only test this part of the dispatch mechanism. - # This is intended to work with MechGluePlots also loaded. - # See other tests in MechGluecode. - plot(sol) -#end - +include("test_1.jl") +include("test_2.jl") +include("test_3.jl") \ No newline at end of file diff --git a/test/test_1.jl b/test/test_1.jl new file mode 100644 index 0000000..a81a002 --- /dev/null +++ b/test/test_1.jl @@ -0,0 +1,54 @@ +using Test +using MechGlueDiffEqBase +using MechanicalUnits: @import_expand, dimension, NoDims +@import_expand(N, s, m) +using DifferentialEquations +@testset "ODE" begin + f = (y, p, t) -> 0.5y / 3.0 # The derivative, yeah + u0 = 1.5 + @test zero(u0) == 0 * u0 + @test value(u0) == 1.5 + tspan = (0.0, 1.0) + prob = ODEProblem(f, u0, tspan) + integrator = DiffEqBase.__init(prob, Tsit5(), dt = 0.1) + # Internalnorm's range should be dimensionless + internalnorm = integrator.opts.internalnorm + @test dimension(internalnorm(u0, tspan[1])) == NoDims + sol = solve(prob, Tsit5(), dt=0.1) + @test sol(0.0) == u0 + @test sol(1.0) ≈ 1.7720406 + @time solve(prob, Tsit5()) # 23 alloc, 4797 KiB +end +@testset "ODE quantity" begin + f = (y, p, t) -> 0.5y / 3.0s # The derivative, yeah + u0 = 1.5N + @test zero(u0) == 0 * u0 + @test value(u0) == 1.5 + tspan = (0.0s, 1.0s) + prob = ODEProblem(f, u0, tspan) + integrator = DiffEqBase.__init(prob, Tsit5(), dt = 0.1s) + # Internalnorm's range should be dimensionless + internalnorm = integrator.opts.internalnorm + @test dimension(internalnorm(u0, tspan[1])) == NoDims + sol = solve(prob, Tsit5(), dt=0.1s) + @test sol(0.0s) == u0 + @test sol(1.0s) ≈ 1.7720406N + @time solve(prob, Tsit5()) # 29 alloc, 5641KiB +end + +@testset "ODE quantity algorithms" begin + f = (y, p, t) -> 0.5y / 3.0s # The derivative, yeah + u0 = 1.5N + @test zero(u0) == 0 * u0 + @test value(u0) == 1.5 + tspan = (0.0s, 1.0s) + prob = ODEProblem(f, u0, tspan) + integrator = DiffEqBase.__init(prob, Tsit5(), dt = 0.1s) + # Internalnorm's range should be dimensionless + internalnorm = integrator.opts.internalnorm + @test dimension(internalnorm(u0, tspan[1])) == NoDims + sol = solve(prob, Tsit5(), dt=0.1s) + @test sol(0.0s) == u0 + @test sol(1.0s) ≈ 1.7720406N + @time solve(prob, Tsit5()) # 29 alloc, 5641KiB +end \ No newline at end of file diff --git a/test/test_2.jl b/test/test_2.jl new file mode 100644 index 0000000..6782aa1 --- /dev/null +++ b/test/test_2.jl @@ -0,0 +1,71 @@ +# Adapted from 'Ordinary Differential Equations' test/units_tests.jl +using Test +using MechGlueDiffEqBase +using MechanicalUnits: @import_expand, dimension, NoDims, ∙ +using OrdinaryDiffEq +@import_expand(N, s, m, km, kg) + +#using OrdinaryDiffEq, Unitfu +algs = [Euler(),Midpoint(),Heun(),Ralston(),RK4(),SSPRK104(),SSPRK22(),SSPRK33(), + SSPRK43(),SSPRK432(),BS3(),BS5(),DP5(),DP8(),Feagin10(),Feagin12(), + Feagin14(),TanYam7(),Tsit5(),TsitPap8(),Vern6(),Vern7(),Vern8(),Vern9()] + + +@testset "Unitful time with unitless state" begin + u0 = 30.0 + tspan = (0.0, 10.0)s + prob1 = ODEProblem((du,u,t,p) -> (du[1] = -0.2∙s⁻¹ * u[1]), [u0], tspan) + prob2 = ODEProblem((u,t,p) -> (-0.2∙s⁻¹ * u[1]), u0, tspan) + prob3 = ODEProblem((u,t,p) -> [-0.2∙s⁻¹* u[1]], [u0],tspan) + for prob in [prob1, prob2, prob3] + @test solve(prob, Tsit5()).retcode === :Success + end +end + +@testset "Scalar units" begin + f(y,p,t) = 0.5*y / 3.0s + u0 = 1.0∙N + prob = ODEProblem(f,u0,(0.0,1.0)s) + + for alg in algs + @show alg + @test solve(prob,alg,dt=1∙s/10).retcode === :Success + end +end + +@testset "2D units" begin + f(dy,y,p,t) = (dy .= 0.5.*y ./ 3.0s) + u0 = [1.0 2.0 + 3.0 1.0]N + prob = ODEProblem(f,u0,(0.0, 1.0)s) + + for alg in algs + @show alg + sol = solve(prob,alg,dt=1∙s/10) + end + sol = solve(prob,ExplicitRK()) +end + + + + + + + +@testset "Without ArrayPartition - broken" begin + # coordinate: u = [position, momentum] + # parameters: p = [mass, force constanst] + function f_harmonic!(du,u,p,t) + du[1] = u[2]/p[1] + du[2] = -p[2]*u[1] + end + + mass = 1.0∙kg + k = 1.0∙N/m + p = [mass, k] + + u0 = [1.0m, 0.0∙kg∙m/s] # initial values (position, momentum) + tspan = (0.0∙s, 10.0∙s) + prob = ODEProblem(f_harmonic!, u0, tspan, p) + @test_broken solve(prob, Tsit5()).retcode == :Success +end \ No newline at end of file diff --git a/test/test_3.jl b/test/test_3.jl new file mode 100644 index 0000000..9305c04 --- /dev/null +++ b/test/test_3.jl @@ -0,0 +1,57 @@ +# Differential equations with mixed units using ArrayPartition +using Test +using MechGlueDiffEqBase +using MechanicalUnits: @import_expand, dimension, NoDims, ∙ +@import_expand(N, s, m, km, kg) +using Unitfu, DiffEqBase, OrdinaryDiffEq + +@testset "Initial checks ArrayPartition" begin + r0 = [1131.340, -2282.343, 6672.423]∙km + v0 = [-5.64305, 4.30333, 2.42879]∙km/s + Δt = 86400.0*365∙s + μ = 398600.4418∙km³/s² + rv0 = ArrayPartition(r0,v0) + + function f(dy, y, μ, t) + r = norm(y.x[1]) + dy.x[1] .= y.x[2] + dy.x[2] .= -μ .* y.x[1] / r^3 + end + prob = ODEProblem(f,rv0,(0.0, 1.0)s,μ) + + integrator = DiffEqBase.__init(prob, Tsit5(), dt = 0.1s) + # Internalnorm's range should be dimensionless + internalnorm = integrator.opts.internalnorm + @test dimension(internalnorm(rv0, 0.0s)) == NoDims + + sol = solve(prob, Tsit5(), dt=0.1s) + @test sol(0.0s) == rv0 + sol1 = sol(Δt) + expected = ArrayPartition([5.699838107777531e19, -1.1522704782345573e20, 3.372551297486921e20]km, [-2.987239096323713e17, 2.2791800330017168e17, 1.2826177222463973e17]km∙s⁻¹) + boolpart = sol1 .≈ expected + @test all(boolpart) +end + +@testset "With ArrayPartition" begin + r0 = [1131.340, -2282.343, 6672.423]∙km + v0 = [-5.64305, 4.30333, 2.42879]∙km/s + Δt = 86400.0*365∙s + μ = 398600.4418∙km³/s² + rv0 = ArrayPartition(r0,v0) + + function f(dy, y, μ, t) + r = norm(y.x[1]) + dy.x[1] .= y.x[2] + dy.x[2] .= -μ .* y.x[1] / r^3 + end + + prob = ODEProblem(f,rv0,(0.0, 1.0)s,μ) + for alg in [Tsit5(), AutoVern6(Rodas5(autodiff=false)), + AutoVern7(Rodas5(autodiff=false)), + AutoVern8(Rodas5(autodiff=false)), + AutoVern9(Rodas5(autodiff=false))] + println(alg, " ") + @test solve(prob,alg).retcode === :Success + end + print("\n") +end \ No newline at end of file