build based on d660156

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-26T17:53:50","documenter_version":"1.4.1"}}
+{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-27T01:55:38","documenter_version":"1.4.1"}}

dev/assets/Manifest.toml

@@ -2255,9 +2255,9 @@ version = "1.6.3"
 
 [[deps.OrdinaryDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "a4af6d00e3f0682b21d734fccf934566f60be767"
+git-tree-sha1 = "75b0d2bf28d0df92931919004a5be5304c38cca2"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.80.0"
+version = "6.80.1"
 
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -2407,9 +2407,9 @@ version = "0.2.0"
 
 [[deps.PrettyTables]]
 deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"]
-git-tree-sha1 = "88b895d13d53b5577fd53379d913b9ab9ac82660"
+git-tree-sha1 = "66b20dd35966a748321d3b2537c4584cf40387c7"
 uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
-version = "2.3.1"
+version = "2.3.2"
 
 [[deps.Primes]]
 deps = ["IntegerMathUtils"]

dev/getting_started/find_root/index.html

@@ -66,4 +66,4 @@
 u: 2-element Vector{Float64}:
  -2.129924444096732e-29
  -2.398137151871876e-28</code></pre><h3 id="Step-5:-Analyze-the-Solution"><a class="docs-heading-anchor" href="#Step-5:-Analyze-the-Solution">Step 5: Analyze the Solution</a><a id="Step-5:-Analyze-the-Solution-1"></a><a class="docs-heading-anchor-permalink" href="#Step-5:-Analyze-the-Solution" title="Permalink"></a></h3><p>Now let&#39;s check out the solution. First of all, what kind of thing is the <code>sol</code>? We can see that by asking for its type:</p><pre><code class="language-julia hljs">typeof(sol)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">SciMLBase.NonlinearSolution{Float64, 1, Vector{Float64}, Vector{Float64}, SciMLBase.NonlinearProblem{Vector{Float64}, true, ModelingToolkit.MTKParameters{Tuple{Vector{Float64}}, Tuple{}, Tuple{}, Tuple{}, Tuple{}, Nothing, Nothing}, SciMLBase.NonlinearFunction{true, SciMLBase.FullSpecialize, ModelingToolkit.var&quot;#f#529&quot;{RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋arg1, :ˍ₋arg2), ModelingToolkit.var&quot;#_RGF_ModTag&quot;, ModelingToolkit.var&quot;#_RGF_ModTag&quot;, (0x0bec91c5, 0x7102a3b4, 0x25790b05, 0xeedeb041, 0xb28da2c7), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :ˍ₋arg1, :ˍ₋arg2), ModelingToolkit.var&quot;#_RGF_ModTag&quot;, ModelingToolkit.var&quot;#_RGF_ModTag&quot;, (0x85b9a698, 0x76e4b08e, 0x07ba5224, 0xe2c014ba, 0x43cce4c2), Nothing}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, ModelingToolkit.var&quot;#generated_observed#532&quot;{ModelingToolkit.NonlinearSystem, Dict{Any, Any}}, Nothing, ModelingToolkit.NonlinearSystem, Nothing}, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}, SciMLBase.StandardNonlinearProblem}, NonlinearSolve.GeneralizedFirstOrderAlgorithm{nothing, :NewtonRaphson, NonlinearSolve.NoLineSearch, Missing, NonlinearSolve.NewtonDescent{Nothing, typeof(NonlinearSolve.DEFAULT_PRECS)}, Nothing, Nothing, Nothing}, Nothing, Nothing, NonlinearSolve.ImmutableNLStats, NonlinearSolve.NonlinearSolveTrace{false, false, NonlinearSolve.TraceMinimal, Nothing, SciMLBase.NonlinearProblem{Vector{Float64}, true, ModelingToolkit.MTKParameters{Tuple{Vector{Float64}}, Tuple{}, Tuple{}, Tuple{}, Tuple{}, Nothing, Nothing}, SciMLBase.NonlinearFunction{true, SciMLBase.FullSpecialize, ModelingToolkit.var&quot;#f#529&quot;{RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋arg1, :ˍ₋arg2), ModelingToolkit.var&quot;#_RGF_ModTag&quot;, ModelingToolkit.var&quot;#_RGF_ModTag&quot;, (0x0bec91c5, 0x7102a3b4, 0x25790b05, 0xeedeb041, 0xb28da2c7), Nothing}, RuntimeGeneratedFunctions.RuntimeGeneratedFunction{(:ˍ₋out, :ˍ₋arg1, :ˍ₋arg2), ModelingToolkit.var&quot;#_RGF_ModTag&quot;, ModelingToolkit.var&quot;#_RGF_ModTag&quot;, (0x85b9a698, 0x76e4b08e, 0x07ba5224, 0xe2c014ba, 0x43cce4c2), Nothing}}, LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, ModelingToolkit.var&quot;#generated_observed#532&quot;{ModelingToolkit.NonlinearSystem, Dict{Any, Any}}, Nothing, ModelingToolkit.NonlinearSystem, Nothing}, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}, SciMLBase.StandardNonlinearProblem}}}</code></pre><p>From this, we can see that it is an <code>NonlinearSolution</code>. We can see the documentation for how to use the <code>NonlinearSolution</code> by checking the <a href="https://docs.sciml.ai/NonlinearSolve/stable/basics/nonlinear_solution/">NonlinearSolve.jl solution type page.</a> For example, the solution is stored as <code>.u</code>. What is the solution to our nonlinear system, and what is the final residual value? We can check it as follows:</p><pre><code class="language-julia hljs"># Analyze the solution
-@show sol[[x,y,z]], sol.resid</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">([-2.129924444096732e-29, -5.537803554651503e-28, -2.398137151871876e-28], [-5.32481111024183e-27, 6.395032404991669e-28])</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../fit_simulation/">« Fit a simulation to a dataset</a><a class="docs-footer-nextpage" href="../../comparisons/python/">Getting Started with Julia&#39;s SciML for the Python User »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Sunday 26 May 2024 17:53">Sunday 26 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+@show sol[[x,y,z]], sol.resid</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">([-2.129924444096732e-29, -5.537803554651503e-28, -2.398137151871876e-28], [-5.32481111024183e-27, 6.395032404991669e-28])</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../fit_simulation/">« Fit a simulation to a dataset</a><a class="docs-footer-nextpage" href="../../comparisons/python/">Getting Started with Julia&#39;s SciML for the Python User »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Monday 27 May 2024 01:55">Monday 27 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/getting_started/first_optimization/index.html

@@ -29,4 +29,4 @@
 u: 2-element Vector{Float64}:
  1.0
  1.0</code></pre><h3 id="Step-4:-Analyze-the-Solution"><a class="docs-heading-anchor" href="#Step-4:-Analyze-the-Solution">Step 4: Analyze the Solution</a><a id="Step-4:-Analyze-the-Solution-1"></a><a class="docs-heading-anchor-permalink" href="#Step-4:-Analyze-the-Solution" title="Permalink"></a></h3><p>Now let&#39;s check out the solution. First of all, what kind of thing is the <code>sol</code>? We can see that by asking for its type:</p><pre><code class="language-julia hljs">typeof(sol)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">SciMLBase.OptimizationSolution{Float64, 1, Vector{Float64}, OptimizationBase.OptimizationCache{SciMLBase.OptimizationFunction{true, ADTypes.AutoForwardDiff{nothing, Nothing}, typeof(Main.L), OptimizationForwardDiffExt.var&quot;#38#56&quot;{ForwardDiff.GradientConfig{ForwardDiff.Tag{OptimizationForwardDiffExt.var&quot;#37#55&quot;{SciMLBase.OptimizationFunction{true, ADTypes.AutoForwardDiff{nothing, Nothing}, typeof(Main.L), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, OptimizationBase.ReInitCache{Vector{Float64}, Vector{Float64}}}, Float64}, Float64, 2, Vector{ForwardDiff.Dual{ForwardDiff.Tag{OptimizationForwardDiffExt.var&quot;#37#55&quot;{SciMLBase.OptimizationFunction{true, ADTypes.AutoForwardDiff{nothing, Nothing}, typeof(Main.L), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, OptimizationBase.ReInitCache{Vector{Float64}, Vector{Float64}}}, Float64}, Float64, 2}}}, OptimizationForwardDiffExt.var&quot;#37#55&quot;{SciMLBase.OptimizationFunction{true, ADTypes.AutoForwardDiff{nothing, Nothing}, typeof(Main.L), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, OptimizationBase.ReInitCache{Vector{Float64}, Vector{Float64}}}}, OptimizationForwardDiffExt.var&quot;#41#59&quot;{ForwardDiff.HessianConfig{ForwardDiff.Tag{OptimizationForwardDiffExt.var&quot;#37#55&quot;{SciMLBase.OptimizationFunction{true, ADTypes.AutoForwardDiff{nothing, Nothing}, typeof(Main.L), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, OptimizationBase.ReInitCache{Vector{Float64}, Vector{Float64}}}, Float64}, Float64, 2, Vector{ForwardDiff.Dual{ForwardDiff.Tag{OptimizationForwardDiffExt.var&quot;#37#55&quot;{SciMLBase.OptimizationFunction{true, ADTypes.AutoForwardDiff{nothing, Nothing}, typeof(Main.L), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, OptimizationBase.ReInitCache{Vector{Float64}, Vector{Float64}}}, Float64}, ForwardDiff.Dual{ForwardDiff.Tag{OptimizationForwardDiffExt.var&quot;#37#55&quot;{SciMLBase.OptimizationFunction{true, ADTypes.AutoForwardDiff{nothing, Nothing}, typeof(Main.L), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, OptimizationBase.ReInitCache{Vector{Float64}, Vector{Float64}}}, Float64}, Float64, 2}, 2}}, Vector{ForwardDiff.Dual{ForwardDiff.Tag{OptimizationForwardDiffExt.var&quot;#37#55&quot;{SciMLBase.OptimizationFunction{true, ADTypes.AutoForwardDiff{nothing, Nothing}, typeof(Main.L), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, OptimizationBase.ReInitCache{Vector{Float64}, Vector{Float64}}}, Float64}, Float64, 2}}}, OptimizationForwardDiffExt.var&quot;#37#55&quot;{SciMLBase.OptimizationFunction{true, ADTypes.AutoForwardDiff{nothing, Nothing}, typeof(Main.L), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, OptimizationBase.ReInitCache{Vector{Float64}, Vector{Float64}}}}, OptimizationForwardDiffExt.var&quot;#44#62&quot;, Nothing, OptimizationForwardDiffExt.var&quot;#48#66&quot;{SciMLBase.OptimizationFunction{true, ADTypes.AutoForwardDiff{nothing, Nothing}, typeof(Main.L), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, OptimizationBase.ReInitCache{Vector{Float64}, Vector{Float64}}}, Nothing, Nothing, OptimizationForwardDiffExt.var&quot;#53#71&quot;{SciMLBase.OptimizationFunction{true, ADTypes.AutoForwardDiff{nothing, Nothing}, typeof(Main.L), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, OptimizationBase.ReInitCache{Vector{Float64}, Vector{Float64}}}, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED_NO_TIME), Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, OptimizationBase.ReInitCache{Vector{Float64}, Vector{Float64}}, Vector{Float64}, Vector{Float64}, Nothing, Nothing, Nothing, NLopt.Algorithm, Base.Iterators.Cycle{Tuple{OptimizationBase.NullData}}, Bool, OptimizationBase.NullCallback}, NLopt.Algorithm, Float64, NLopt.Opt, SciMLBase.OptimizationStats}</code></pre><p>From this, we can see that it is an <code>OptimizationSolution</code>. We can see the documentation for how to use the <code>OptimizationSolution</code> by checking the <a href="https://docs.sciml.ai/Optimization/stable/API/optimization_solution/">Optimization.jl solution type page</a>. For example, the solution is stored as <code>.u</code>. What is the solution to our optimization, and what is the final loss value? We can check it as follows:</p><pre><code class="language-julia hljs"># Analyze the solution
-@show sol.u, L(sol.u, p)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">([1.0, 1.0], 0.0)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../first_simulation/">« Build and run your first simulation with Julia&#39;s SciML</a><a class="docs-footer-nextpage" href="../fit_simulation/">Fit a simulation to a dataset »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Sunday 26 May 2024 17:53">Sunday 26 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+@show sol.u, L(sol.u, p)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">([1.0, 1.0], 0.0)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../first_simulation/">« Build and run your first simulation with Julia&#39;s SciML</a><a class="docs-footer-nextpage" href="../fit_simulation/">Fit a simulation to a dataset »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Monday 27 May 2024 01:55">Monday 27 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>