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{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-23T15:09:07","documenter_version":"1.1.2"}}
{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-23T16:00:43","documenter_version":"1.1.2"}}
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16 changes: 8 additions & 8 deletions previews/PR243/benchmarks/lotkavolterra/index.html
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verbose = false,
)

plot(wp, color=[2 2 2 4 4 4 5 5 5], xticks = 10.0 .^ (-16:1:5))</code></pre><p><img src="../figures/lotkavolterra_7_1.svg" alt/></p><h2 id="Conclusion"><a class="docs-heading-anchor" href="#Conclusion">Conclusion</a><a id="Conclusion-1"></a><a class="docs-heading-anchor-permalink" href="#Conclusion" title="Permalink"></a></h2><ul><li><strong>Use the EK1!</strong> It seems to be strictly better than the EK0 here. Though note that by using ParameterizedFunctions.jl, the Jacobian of the vector field is available analytically.</li><li>Orders behave as in classic solvers: Use low order for low accuracy, medium order for medium accuracy, high order for high accuracy.</li><li>Most likely, the default choice of <code>diffusionmodel=DynamicDiffusion</code> and <code>initialization=TaylorModeInit</code> are fine.</li></ul><h2 id="Appendix"><a class="docs-heading-anchor" href="#Appendix">Appendix</a><a id="Appendix-1"></a><a class="docs-heading-anchor-permalink" href="#Appendix" title="Permalink"></a></h2><p>Computer information:</p><pre><code class="language-julia hljs">using InteractiveUtils
plot(wp, color=[2 2 2 4 4 4 5 5 5], xticks = 10.0 .^ (-16:1:5))</code></pre><p><img src="../figures/lotkavolterra_7_1.svg" alt/></p><h2 id="Conclusion"><a class="docs-heading-anchor" href="#Conclusion">Conclusion</a><a id="Conclusion-1"></a><a class="docs-heading-anchor-permalink" href="#Conclusion" title="Permalink"></a></h2><ul><li>For such a low-dimensional problem the EK0 and EK1 have a very similar runtime. Though note that by using ParameterizedFunctions.jl, the Jacobian of the vector field is available analytically.</li><li>Orders behave as in classic solvers: Use low order for low accuracy, medium order for medium accuracy, high order for high accuracy.</li><li>Most likely, the default choice of <code>diffusionmodel=DynamicDiffusion</code> and <code>initialization=TaylorModeInit</code> are fine.</li></ul><h2 id="Appendix"><a class="docs-heading-anchor" href="#Appendix">Appendix</a><a id="Appendix-1"></a><a class="docs-heading-anchor-permalink" href="#Appendix" title="Permalink"></a></h2><p>Computer information:</p><pre><code class="language-julia hljs">using InteractiveUtils
InteractiveUtils.versioninfo()</code></pre><pre><code class="nohighlight hljs">Julia Version 1.9.3
Commit bed2cd540a1 (2023-08-24 14:43 UTC)
Build Info:
Expand Down Expand Up @@ -199,7 +199,7 @@
[65888b18] ParameterizedFunctions v5.16.0
[91a5bcdd] Plots v1.39.0
[bf3e78b0] ProbNumDiffEq v0.12.1 `~/.julia/dev/ProbNumDiffEq`
[0bca4576] SciMLBase v2.4.2
[0bca4576] SciMLBase v2.4.3
[505e40e9] SciPyDiffEq v0.2.1
[90137ffa] StaticArrays v1.6.5
[c3572dad] Sundials v4.20.0
Expand All @@ -214,7 +214,7 @@
[4fba245c] ArrayInterface v7.4.11
[30b0a656] ArrayInterfaceCore v0.1.29
[6e4b80f9] BenchmarkTools v1.3.2
[e2ed5e7c] Bijections v0.1.5
[e2ed5e7c] Bijections v0.1.6
[d1d4a3ce] BitFlags v0.1.7
[62783981] BitTwiddlingConvenienceFunctions v0.1.5
⌅ [fa961155] CEnum v0.4.2
Expand Down Expand Up @@ -300,7 +300,7 @@
[d25df0c9] Inflate v0.1.4
[842dd82b] InlineStrings v1.4.0
[18e54dd8] IntegerMathUtils v0.1.2
[8197267c] IntervalSets v0.7.7
[8197267c] IntervalSets v0.7.8
[41ab1584] InvertedIndices v1.3.0
[92d709cd] IrrationalConstants v0.2.2
[c8e1da08] IterTools v1.8.0
Expand All @@ -322,7 +322,7 @@
[50d2b5c4] Lazy v0.15.1
[1d6d02ad] LeftChildRightSiblingTrees v0.2.0
[d3d80556] LineSearches v7.2.0
[7ed4a6bd] LinearSolve v2.11.0
[7ed4a6bd] LinearSolve v2.11.1
[2ab3a3ac] LogExpFunctions v0.3.26
[e6f89c97] LoggingExtras v1.0.3
[bdcacae8] LoopVectorization v0.12.165
Expand All @@ -343,7 +343,7 @@
[2774e3e8] NLsolve v4.5.1
[77ba4419] NaNMath v1.0.2
⌅ [356022a1] NamedDims v0.2.50
[8913a72c] NonlinearSolve v2.3.0
[8913a72c] NonlinearSolve v2.4.0
[54ca160b] ODEInterface v0.5.0
[09606e27] ODEInterfaceDiffEq v3.13.3
[6fd5a793] Octavian v0.3.27
Expand Down Expand Up @@ -396,7 +396,7 @@
[fdea26ae] SIMD v3.4.5
[94e857df] SIMDTypes v0.1.0
[476501e8] SLEEFPirates v0.6.39
[0bca4576] SciMLBase v2.4.2
[0bca4576] SciMLBase v2.4.3
[e9a6253c] SciMLNLSolve v0.1.9
[c0aeaf25] SciMLOperators v0.3.6
[505e40e9] SciPyDiffEq v0.2.1
Expand Down Expand Up @@ -600,4 +600,4 @@
[3f19e933] p7zip_jll v17.4.0+0
Info Packages marked with ⌃ and ⌅ have new versions available, but those wi
th ⌅ are restricted by compatibility constraints from upgrading. To see why
use `status --outdated -m`</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../multi-language-wrappers/">« Multi-Language Wrapper Benchmark</a><a class="docs-footer-nextpage" href="../vanderpol/">Stiff ODE: Van der Pol »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Monday 23 October 2023 15:08">Monday 23 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
use `status --outdated -m`</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../multi-language-wrappers/">« Multi-Language Wrapper Benchmark</a><a class="docs-footer-nextpage" href="../vanderpol/">Stiff ODE: Van der Pol »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Monday 23 October 2023 16:00">Monday 23 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
33 changes: 21 additions & 12 deletions previews/PR243/benchmarks/multi-language-wrappers/index.html
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Expand Up @@ -13,7 +13,7 @@
size = (1000, 400),
)</code></pre><pre><code class="language-julia hljs"># Constants used throughout this benchmark
const DENSE = false # used to decide if we smooth or not
const SAVE_EVERYSTEP = false;</code></pre><pre><code class="language-julia hljs">_COLORS = Dict(
const SAVE_EVERYSTEP = false;</code></pre><pre><code class="language-julia hljs">COLORS = Dict(
&quot;Julia&quot; =&gt; :LightGreen,
&quot;Julia (static)&quot; =&gt; :DarkGreen,
&quot;Hairer&quot; =&gt; :Red,
Expand All @@ -22,9 +22,14 @@
&quot;deSolve&quot; =&gt; :Blue,
&quot;Sundials&quot; =&gt; :Purple,
&quot;liblsoda&quot; =&gt; :Purple,
&quot;ProbNumDiffEq&quot; =&gt; :Darkgray,
&quot;ProbNumDiffEq: EK0&quot; =&gt; :Gray30,
&quot;ProbNumDiffEq: EK1&quot; =&gt; :Gray60,
)
tocolor(n) = _COLORS[split(n, &#39;:&#39;)[1]];</code></pre><pre><code class="language-julia hljs">deprecated_filter(log_args) = !contains(log_args.message, &quot;deprecated&quot;)
tocolor(n) = if split(n, &#39;(&#39;)[1] in keys(COLORS)
COLORS[split(n, &#39;(&#39;)[1]]
else
COLORS[split(n, &#39;:&#39;)[1]]
end</code></pre><pre><code class="nohighlight hljs">tocolor (generic function with 1 method)</code></pre><pre><code class="language-julia hljs">deprecated_filter(log_args) = !contains(log_args.message, &quot;deprecated&quot;)
filtered_logger = ActiveFilteredLogger(deprecated_filter, global_logger());</code></pre><h2 id="Non-Stiff-Problem-1:-Lotka-Volterra"><a class="docs-heading-anchor" href="#Non-Stiff-Problem-1:-Lotka-Volterra">Non-Stiff Problem 1: Lotka-Volterra</a><a id="Non-Stiff-Problem-1:-Lotka-Volterra-1"></a><a class="docs-heading-anchor-permalink" href="#Non-Stiff-Problem-1:-Lotka-Volterra" title="Permalink"></a></h2><pre><code class="language-julia hljs">f = @ode_def LotkaVolterra begin
dx = a*x - b*x*y
dy = -c*y + d*x*y
Expand All @@ -50,10 +55,12 @@
&quot;deSolve: lsoda&quot; =&gt; Dict(:alg=&gt;deSolveDiffEq.lsoda())
&quot;deSolve: ode45&quot; =&gt; Dict(:alg=&gt;deSolveDiffEq.ode45())
&quot;Sundials: Adams&quot; =&gt; Dict(:alg=&gt;Sundials.CVODE_Adams())
&quot;ProbNumDiffEq: EK0(2)&quot; =&gt; Dict(:alg=&gt;EK0(order=2, smooth=DENSE))
&quot;ProbNumDiffEq: EK0(3)&quot; =&gt; Dict(:alg=&gt;EK0(order=3, smooth=DENSE))
&quot;ProbNumDiffEq: EK0(5)&quot; =&gt; Dict(:alg=&gt;EK0(order=5, smooth=DENSE))
&quot;ProbNumDiffEq: EK0(8)&quot; =&gt; Dict(:alg=&gt;EK0(order=8, smooth=DENSE))
&quot;ProbNumDiffEq: EK1(3)&quot; =&gt; Dict(:alg=&gt;EK1(order=3, smooth=DENSE))
&quot;ProbNumDiffEq: EK1(5)&quot; =&gt; Dict(:alg=&gt;EK1(order=5, smooth=DENSE))
&quot;ProbNumDiffEq: EK1(8)&quot; =&gt; Dict(:alg=&gt;EK1(order=8, smooth=DENSE))
]

labels = first.(_setups)
Expand Down Expand Up @@ -108,10 +115,12 @@
&quot;deSolve: lsoda&quot; =&gt; Dict(:alg=&gt;deSolveDiffEq.lsoda())
&quot;deSolve: ode45&quot; =&gt; Dict(:alg=&gt;deSolveDiffEq.ode45())
&quot;Sundials: Adams&quot; =&gt; Dict(:alg=&gt;CVODE_Adams())
&quot;ProbNumDiffEq: EK0(2)&quot; =&gt; Dict(:alg=&gt;EK0(order=2, smooth=DENSE))
&quot;ProbNumDiffEq: EK0(3)&quot; =&gt; Dict(:alg=&gt;EK0(order=3, smooth=DENSE))
&quot;ProbNumDiffEq: EK0(5)&quot; =&gt; Dict(:alg=&gt;EK0(order=5, smooth=DENSE))
&quot;ProbNumDiffEq: EK0(8)&quot; =&gt; Dict(:alg=&gt;EK0(order=8, smooth=DENSE))
&quot;ProbNumDiffEq: EK1(3)&quot; =&gt; Dict(:alg=&gt;EK1(order=3, smooth=DENSE))
&quot;ProbNumDiffEq: EK1(5)&quot; =&gt; Dict(:alg=&gt;EK1(order=5, smooth=DENSE))
&quot;ProbNumDiffEq: EK1(8)&quot; =&gt; Dict(:alg=&gt;EK1(order=8, smooth=DENSE))
]

labels = first.(_setups)
Expand Down Expand Up @@ -290,7 +299,7 @@
[65888b18] ParameterizedFunctions v5.16.0
[91a5bcdd] Plots v1.39.0
[bf3e78b0] ProbNumDiffEq v0.12.1 `~/.julia/dev/ProbNumDiffEq`
[0bca4576] SciMLBase v2.4.2
[0bca4576] SciMLBase v2.4.3
[505e40e9] SciPyDiffEq v0.2.1
[90137ffa] StaticArrays v1.6.5
[c3572dad] Sundials v4.20.0
Expand All @@ -305,7 +314,7 @@
[4fba245c] ArrayInterface v7.4.11
[30b0a656] ArrayInterfaceCore v0.1.29
[6e4b80f9] BenchmarkTools v1.3.2
[e2ed5e7c] Bijections v0.1.5
[e2ed5e7c] Bijections v0.1.6
[d1d4a3ce] BitFlags v0.1.7
[62783981] BitTwiddlingConvenienceFunctions v0.1.5
⌅ [fa961155] CEnum v0.4.2
Expand Down Expand Up @@ -391,7 +400,7 @@
[d25df0c9] Inflate v0.1.4
[842dd82b] InlineStrings v1.4.0
[18e54dd8] IntegerMathUtils v0.1.2
[8197267c] IntervalSets v0.7.7
[8197267c] IntervalSets v0.7.8
[41ab1584] InvertedIndices v1.3.0
[92d709cd] IrrationalConstants v0.2.2
[c8e1da08] IterTools v1.8.0
Expand All @@ -413,7 +422,7 @@
[50d2b5c4] Lazy v0.15.1
[1d6d02ad] LeftChildRightSiblingTrees v0.2.0
[d3d80556] LineSearches v7.2.0
[7ed4a6bd] LinearSolve v2.11.0
[7ed4a6bd] LinearSolve v2.11.1
[2ab3a3ac] LogExpFunctions v0.3.26
[e6f89c97] LoggingExtras v1.0.3
[bdcacae8] LoopVectorization v0.12.165
Expand All @@ -434,7 +443,7 @@
[2774e3e8] NLsolve v4.5.1
[77ba4419] NaNMath v1.0.2
⌅ [356022a1] NamedDims v0.2.50
[8913a72c] NonlinearSolve v2.3.0
[8913a72c] NonlinearSolve v2.4.0
[54ca160b] ODEInterface v0.5.0
[09606e27] ODEInterfaceDiffEq v3.13.3
[6fd5a793] Octavian v0.3.27
Expand Down Expand Up @@ -487,7 +496,7 @@
[fdea26ae] SIMD v3.4.5
[94e857df] SIMDTypes v0.1.0
[476501e8] SLEEFPirates v0.6.39
[0bca4576] SciMLBase v2.4.2
[0bca4576] SciMLBase v2.4.3
[e9a6253c] SciMLNLSolve v0.1.9
[c0aeaf25] SciMLOperators v0.3.6
[505e40e9] SciPyDiffEq v0.2.1
Expand Down Expand Up @@ -691,4 +700,4 @@
[3f19e933] p7zip_jll v17.4.0+0
Info Packages marked with ⌃ and ⌅ have new versions available, but those wi
th ⌅ are restricted by compatibility constraints from upgrading. To see why
use `status --outdated -m`</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../diffusions/">« Diffusion models and calibration</a><a class="docs-footer-nextpage" href="../lotkavolterra/">Non-stiff ODE: Lotka-Volterra »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Monday 23 October 2023 15:09">Monday 23 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
use `status --outdated -m`</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../diffusions/">« Diffusion models and calibration</a><a class="docs-footer-nextpage" href="../lotkavolterra/">Non-stiff ODE: Lotka-Volterra »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Monday 23 October 2023 16:00">Monday 23 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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