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Documenter.jl committed Nov 3, 2024
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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-10-31T21:37:22","documenter_version":"1.7.0"}}
{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-03T23:26:16","documenter_version":"1.7.0"}}
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4 changes: 2 additions & 2 deletions dev/advection/index.html
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@parameters x
domain = DomainInfo(constIC(0.0, t ∈ Interval(0, 1.0)), constBC(1.0, x ∈ Interval(0, 1.0)))</code></pre><p>Now we convert add advection to each of the state variables. We&#39;re also adding a constant wind (<a href="../api/#EarthSciMLBase.ConstantWind-Tuple{Any, Vararg{Any}}"><code>ConstantWind</code></a>) in the x-direction, with a speed of 1.0.</p><pre><code class="language-julia hljs">sys_advection = couple(ExampleSys(), domain, ConstantWind(t, 1.0), Advection())
sys_mtk = convert(PDESystem, sys_advection)</code></pre><p class="math-container">\[ \begin{align}
\frac{\mathrm{d}}{\mathrm{d}t} \mathtt{ExampleSys.y}\left( t, x \right) &amp;= \mathtt{ExampleSys.p} - \mathtt{MeanWind.v\_x}\left( t, x \right) \frac{\mathrm{d}}{\mathrm{d}x} \mathtt{ExampleSys.y}\left( t, x \right) \\
\mathtt{MeanWind.v\_x}\left( t, x \right) &amp;= \mathtt{ConstantWind.v\_1}\left( t, x \right) \\
\frac{\mathrm{d}}{\mathrm{d}t} \mathtt{ExampleSys.y}\left( t, x \right) &amp;= \mathtt{ExampleSys.p} - \mathtt{MeanWind.v\_x}\left( t, x \right) \frac{\mathrm{d}}{\mathrm{d}x} \mathtt{ExampleSys.y}\left( t, x \right) \\
\mathtt{ConstantWind.v\_1}\left( t, x \right) &amp;= \mathtt{ConstantWind.c\_v1}
\end{align}
\]</p><p>Finally, we can discretize the system and solve it:</p><pre><code class="language-julia hljs">using MethodOfLines, DifferentialEquations, Plots
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anim = @animate for k in 1:length(discrete_t)
plot(discrete_x, soly[k, 1:end], title=&quot;t=\$(discrete_t[k])&quot;, ylim=(0,2.5), lab=:none)
end
gif(anim, fps = 8)</code></pre><img src="09a42f74.gif" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../icbc/">« Initial and Boundary Conditions</a><a class="docs-footer-nextpage" href="../coord_transforms/">Coordinate Transforms »</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 1.7.0 on <span class="colophon-date" title="Thursday 31 October 2024 21:37">Thursday 31 October 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
gif(anim, fps = 8)</code></pre><img src="e2bfbca2.gif" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../icbc/">« Initial and Boundary Conditions</a><a class="docs-footer-nextpage" href="../coord_transforms/">Coordinate Transforms »</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 1.7.0 on <span class="colophon-date" title="Sunday 3 November 2024 23:26">Sunday 3 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
66 changes: 34 additions & 32 deletions dev/api/index.html
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4 changes: 2 additions & 2 deletions dev/composition/index.html
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))
end</code></pre><p>Finally, we can compose the model components together to create our complete model. To do so, we just initialize each model component and add the components together using the <a href="../api/#EarthSciMLBase.couple-Tuple"><code>couple</code></a> function. We can use the <code>convert</code> function to convert the composed model to a <a href="https://mtk.sciml.ai/dev/">ModelingToolkit</a> <code>ODESystem</code> so we can see what the combined equations look like.</p><pre><code class="language-julia hljs">model = couple(Photolysis(), Chemistry(), Emissions())
convert(ODESystem, model)</code></pre><p class="math-container">\[ \begin{align}
\frac{\mathrm{d} \mathtt{Chemistry.NO2}\left( t \right)}{\mathrm{d}t} &amp;= \mathtt{Chemistry.Emissions\_NO2}\left( t \right) - \mathtt{Chemistry.jNO2}\left( t \right) \mathtt{Chemistry.NO2}\left( t \right) \\
\mathtt{Chemistry.jNO2}\left( t \right) &amp;= \mathtt{Photolysis.j\_NO2}\left( t \right) \\
\mathtt{Chemistry.Emissions\_NO2}\left( t \right) &amp;= \mathtt{Emissions.NO2}\left( t \right) \\
\mathtt{Photolysis.j\_NO2}\left( t \right) &amp;= max\left( \sin\left( \frac{1}{86400} t \right), 0 \right) \\
\frac{\mathrm{d} \mathtt{Chemistry.NO2}\left( t \right)}{\mathrm{d}t} &amp;= \mathtt{Chemistry.Emissions\_NO2}\left( t \right) - \mathtt{Chemistry.jNO2}\left( t \right) \mathtt{Chemistry.NO2}\left( t \right) \\
\mathtt{Emissions.NO2}\left( t \right) &amp;= \mathtt{Emissions.emis}
\end{align}
\]</p><p>Finally, we can use the <a href="../api/#EarthSciMLBase.graph-Tuple{CoupledSystem}"><code>graph</code></a> function to visualize the model components and their connections.</p><pre><code class="language-julia hljs">using MetaGraphsNext
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f, ax, p = graphplot(g; ilabels=labels(g))
hidedecorations!(ax); hidespines!(ax); ax.aspect = DataAspect()

f</code></pre><img src="61e920a3.png" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../operator_compose/">Operator Composition »</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 1.7.0 on <span class="colophon-date" title="Thursday 31 October 2024 21:37">Thursday 31 October 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
f</code></pre><img src="61e920a3.png" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../operator_compose/">Operator Composition »</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 1.7.0 on <span class="colophon-date" title="Sunday 3 November 2024 23:26">Sunday 3 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 changes: 1 addition & 1 deletion dev/coord_transforms/index.html
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\end{array}
\right]
\end{equation}
\]</p><p>You can see an example of how this is implemented in the source code for the <a href="../advection/#Advection"><code>Advection</code></a> model component.</p><p>Additional transformation functions may be defined in other packages. We recommend that the names of these functions start with <code>partialderivatives_</code> to make it clear that they are intended to be used in this context.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../advection/">« Advection</a><a class="docs-footer-nextpage" href="../operator/">Operators »</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 1.7.0 on <span class="colophon-date" title="Thursday 31 October 2024 21:37">Thursday 31 October 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
\]</p><p>You can see an example of how this is implemented in the source code for the <a href="../advection/#Advection"><code>Advection</code></a> model component.</p><p>Additional transformation functions may be defined in other packages. We recommend that the names of these functions start with <code>partialderivatives_</code> to make it clear that they are intended to be used in this context.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../advection/">« Advection</a><a class="docs-footer-nextpage" href="../operator/">Operators »</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 1.7.0 on <span class="colophon-date" title="Sunday 3 November 2024 23:26">Sunday 3 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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