build based on d32f34f

previews/PR161/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.7","generation_timestamp":"2025-01-07T08:48:14","documenter_version":"1.8.0"}}
+{"documenter":{"julia_version":"1.10.7","generation_timestamp":"2025-01-08T09:55:37","documenter_version":"1.8.0"}}

previews/PR161/examples/gMAM_Maierstein/index.html

@@ -98,14 +98,14 @@
     markersize=10) for i in eachindex(fp)]
 
 lines!(ax2, reduce(hcat, tr), linewidth=1, color=(:black, 0.2))
-fig</code></pre><img src="7c7b3202.png" alt="Example block output"/><h2 id="Basins-of-attraction"><a class="docs-heading-anchor" href="#Basins-of-attraction">Basins of attraction</a><a id="Basins-of-attraction-1"></a><a class="docs-heading-anchor-permalink" href="#Basins-of-attraction" title="Permalink"></a></h2><p>Basins of attraction are the regions in the state space that lead to a particular attractor. We can find the basins of attraction using the function <code>basins</code>.</p><pre><code class="language-julia hljs">using Attractors
+fig</code></pre><img src="3445424a.png" alt="Example block output"/><h2 id="Basins-of-attraction"><a class="docs-heading-anchor" href="#Basins-of-attraction">Basins of attraction</a><a id="Basins-of-attraction-1"></a><a class="docs-heading-anchor-permalink" href="#Basins-of-attraction" title="Permalink"></a></h2><p>Basins of attraction are the regions in the state space that lead to a particular attractor. We can find the basins of attraction using the function <code>basins</code>.</p><pre><code class="language-julia hljs">using Attractors
 
 ba = basins(sys, [0.0, 0], [0.0, 1], [1.0, 0], intervals_to_box([-2, -2], [2, 2]), bstep=[0.01, 0.01], ϵ_mapper=0.001, Ttr=100)
 Ur, Vr, atr, M = ba
 heatmap(Ur, Vr, M)</code></pre><img src="a4971797.png" alt="Example block output"/><p>The basin boundaries can be quickly extracted using the function <code>basin_boundaries</code>.</p><pre><code class="language-julia hljs">bb = basinboundary(ba)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">2×401 Matrix{Float64}:
  -2.0  -1.99  -1.98  -1.97  -1.96  …  1.95  1.96  1.97  1.98  1.99  2.0
   0.0   0.0    0.0    0.0    0.0      0.0   0.0   0.0   0.0   0.0   0.0</code></pre><h2 id="Transitions"><a class="docs-heading-anchor" href="#Transitions">Transitions</a><a id="Transitions-1"></a><a class="docs-heading-anchor-permalink" href="#Transitions" title="Permalink"></a></h2><p>We can quickly find a path which computes a transition from one attractor to another using the function `transition.</p><pre><code class="language-julia hljs">paths_ends = (fp[stab][1], fp[stab][2])
-path, time, succes = transition(sys, paths_ends...);</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">(2-dimensional StateSpaceSet{Float64} with 91365 points, [0.0, 0.0030239108736880727, 0.005446804757570316, 0.00817256037693784, 0.01098125424289292, 0.014141034842092386, 0.017695788016191785, 0.02169488533705361, 0.026193869823023165, 0.03125522736973892  …  999.9478772489692, 999.9538707591029, 999.9598339821588, 999.9660581381002, 999.9724283199939, 999.9789251523881, 999.9854185139233, 999.992322511214, 999.9990162747773, 1000.0], false)</code></pre><pre><code class="language-julia hljs">fig = Figure(size=(600, 400), fontsize=13)
+path, time, succes = transition(sys, paths_ends...);</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">(2-dimensional StateSpaceSet{Float64} with 551 points, [238.20926082669612, 238.23221525455347, 238.2527904662481, 238.27423821251404, 238.29446451557146, 238.31538352646183, 238.33674275957824, 238.35431546537419, 238.37138499572015, 238.3858743301118  …  243.97076447287097, 243.9833578224427, 243.99593873108245, 244.00866609581266, 244.0222788645876, 244.03585335059796, 244.0506564190937, 244.0655172362733, 244.0819422037472, 244.0819422037472], true)</code></pre><pre><code class="language-julia hljs">fig = Figure(size=(600, 400), fontsize=13)
 ax = Axis(fig[1, 1], xlabel=&quot;u&quot;, ylabel=&quot;v&quot;, aspect=1.4,
     xgridcolor=:transparent, ygridcolor=:transparent,
     ylabelrotation=0)
@@ -125,7 +125,7 @@
 fig
 
 lines!(ax, path, color=:black)
-fig</code></pre><img src="e98d9a06.png" alt="Example block output"/><p>If we want to compute many: <code>transitions</code> is the function to use.</p><pre><code class="language-julia hljs">tt = transitions(sys, paths_ends..., 3; tmax=1e3);</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Transition path ensemble of 3 samples
+fig</code></pre><img src="eef77caf.png" alt="Example block output"/><p>If we want to compute many: <code>transitions</code> is the function to use.</p><pre><code class="language-julia hljs">tt = transitions(sys, paths_ends..., 3; tmax=1e3);</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Transition path ensemble of 3 samples
            - sampling success rate:  1.0
            - mean residence time:    97.8
            - mean transition time:   4.65
@@ -195,4 +195,4 @@
 
 lines!(ax, init, linewidth=3, color=:black, linestyle=:dash)
 lines!(ax, MLP, linewidth=3, color=:orange)
-fig</code></pre><img src="75107219.png" alt="Example block output"/><hr/><p>Author: Orjan Ameye (orjan.ameye@hotmail.com) Date: 13 Feb 2024</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../tutorial/">« Tutorial</a><a class="docs-footer-nextpage" href="../sgMAM_KPO/">sgMAM for the Kerr Parametric Oscillator »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Tuesday 7 January 2025 08:48">Tuesday 7 January 2025</span>. Using Julia version 1.10.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+fig</code></pre><img src="75107219.png" alt="Example block output"/><hr/><p>Author: Orjan Ameye (orjan.ameye@hotmail.com) Date: 13 Feb 2024</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../tutorial/">« Tutorial</a><a class="docs-footer-nextpage" href="../sgMAM_KPO/">sgMAM for the Kerr Parametric Oscillator »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Wednesday 8 January 2025 09:55">Wednesday 8 January 2025</span>. Using Julia version 1.10.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR161/examples/sgMAM_KPO/index.html

@@ -72,10 +72,10 @@
   0.0213246  -0.100612
   0.0206353  -0.100001
   0.0208     -0.0991</code></pre><p>The function returns the optimal path <code>x_min</code>, the minmal action <code>S_min</code>, the Lagrange multipliers <code>lambda</code> associated with the optimal path, the optimal generalised momentum <code>p</code>, and the time derivative of the optimal path <code>xdot</code>. We can plot the initial trajectory and the optimal path:</p><pre><code class="language-julia hljs">fig, ax, _ = lines(x_initial[1, :], x_initial[2, :]; label=&quot;init&quot;, linewidth=3, color=:black)
-lines!(x_min[1, :], x_min[2, :]; label=&quot;MLP&quot;, linewidth=3, color=:red)
+lines!(x_min[:, 1], x_min[:, 2]; label=&quot;MLP&quot;, linewidth=3, color=:red)
 streamplot!(ax, stream, (-0.08, 0.08), (-0.15, 0.15);
     gridsize=(20, 20), arrow_size=10, stepsize=0.001,
     colormap=[:gray, :gray]
 )
 axislegend(ax)
-fig</code></pre><img src="34f50c09.png" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../gMAM_Maierstein/">« Anlyses of the Maier-Stein system</a><a class="docs-footer-nextpage" href="../duffing_TPT/">Transition Path Theory using finite element method »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Tuesday 7 January 2025 08:48">Tuesday 7 January 2025</span>. Using Julia version 1.10.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+fig</code></pre><img src="6fff253a.png" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../gMAM_Maierstein/">« Anlyses of the Maier-Stein system</a><a class="docs-footer-nextpage" href="../duffing_TPT/">Transition Path Theory using finite element method »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Wednesday 8 January 2025 09:55">Wednesday 8 January 2025</span>. Using Julia version 1.10.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>