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{"documenter":{"julia_version":"1.10.1","generation_timestamp":"2024-02-26T22:44:54","documenter_version":"1.2.1"}}
{"documenter":{"julia_version":"1.10.1","generation_timestamp":"2024-02-27T18:23:22","documenter_version":"1.2.1"}}
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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Misc Features · Decapodes.jl</title><meta name="title" content="Misc Features · Decapodes.jl"/><meta property="og:title" content="Misc Features · Decapodes.jl"/><meta property="twitter:title" content="Misc Features · Decapodes.jl"/><meta name="description" content="Documentation for Decapodes.jl."/><meta property="og:description" content="Documentation for Decapodes.jl."/><meta property="twitter:description" content="Documentation for Decapodes.jl."/><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../search_index.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script><script src="../assets/analytics.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">Decapodes.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="../">Decapodes.jl</a></li><li><a class="tocitem" href="../overview/">Overview</a></li><li><a class="tocitem" href="../cism/">CISM v2.1</a></li><li><a class="tocitem" href="../klausmeier/">Klausmeier</a></li><li><a class="tocitem" href="../equations/">Equations</a></li><li><a class="tocitem" href="../ascii/">ASCII Operators</a></li><li class="is-active"><a class="tocitem" href>Misc Features</a></li><li><a class="tocitem" href="../poiseuille/">Pipe Flow</a></li><li><a class="tocitem" href="../ice_dynamics/">Glacial Flow</a></li><li><a class="tocitem" href="../grigoriev/">Grigoriev Ice Cap</a></li><li><a class="tocitem" href="../budyko_sellers_halfar/">Budyko-Sellers-Halfar</a></li><li><a class="tocitem" href="../api/">Library Reference</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Misc Features</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Misc Features</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/AlgebraicJulia/Decapodes.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/AlgebraicJulia/Decapodes.jl/blob/main/docs/src/bc_debug.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Simulation-Setup"><a class="docs-heading-anchor" href="#Simulation-Setup">Simulation Setup</a><a id="Simulation-Setup-1"></a><a class="docs-heading-anchor-permalink" href="#Simulation-Setup" title="Permalink"></a></h1><p>This tutorial showcases some of the other features included in the Decapodes.jl package. Currently, these features are the treatment of boundary conditions and the simulation debugger interface. To begin, we set up the same advection-diffusion problem presented in the Overview section. As before, we define the Diffusion, Advection, and Superposition components, and now include a BC (Bounday Condition) component. Decapodes.jl interprets any <code>Hom</code> which begins with a <code>∂</code> as a boundary condition. These boundary conditions recieve special treatment at the scheduling step. Below we show the graphical rendering of this boundary condition diagram, which we will use to impose a Dirichlet condition on the time derivative of concentration at the mesh boundary.</p><pre><code class="language-julia hljs">using Catlab
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Misc Features · Decapodes.jl</title><meta name="title" content="Misc Features · Decapodes.jl"/><meta property="og:title" content="Misc Features · Decapodes.jl"/><meta property="twitter:title" content="Misc Features · Decapodes.jl"/><meta name="description" content="Documentation for Decapodes.jl."/><meta property="og:description" content="Documentation for Decapodes.jl."/><meta property="twitter:description" content="Documentation for Decapodes.jl."/><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../search_index.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script><script src="../assets/analytics.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">Decapodes.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="../">Decapodes.jl</a></li><li><a class="tocitem" href="../overview/">Overview</a></li><li><a class="tocitem" href="../cism/">CISM v2.1</a></li><li><a class="tocitem" href="../klausmeier/">Klausmeier</a></li><li><a class="tocitem" href="../equations/">Equations</a></li><li><a class="tocitem" href="../ascii/">ASCII Operators</a></li><li class="is-active"><a class="tocitem" href>Misc Features</a></li><li><a class="tocitem" href="../poiseuille/">Pipe Flow</a></li><li><a class="tocitem" href="../ice_dynamics/">Glacial Flow</a></li><li><a class="tocitem" href="../grigoriev/">Grigoriev Ice Cap</a></li><li><a class="tocitem" href="../budyko_sellers_halfar/">Budyko-Sellers-Halfar</a></li><li><a class="tocitem" href="../canon/">Canonical Models</a></li><li><a class="tocitem" href="../api/">Library Reference</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Misc Features</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Misc Features</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/AlgebraicJulia/Decapodes.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/AlgebraicJulia/Decapodes.jl/blob/main/docs/src/bc_debug.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Simulation-Setup"><a class="docs-heading-anchor" href="#Simulation-Setup">Simulation Setup</a><a id="Simulation-Setup-1"></a><a class="docs-heading-anchor-permalink" href="#Simulation-Setup" title="Permalink"></a></h1><p>This tutorial showcases some of the other features included in the Decapodes.jl package. Currently, these features are the treatment of boundary conditions and the simulation debugger interface. To begin, we set up the same advection-diffusion problem presented in the Overview section. As before, we define the Diffusion, Advection, and Superposition components, and now include a BC (Bounday Condition) component. Decapodes.jl interprets any <code>Hom</code> which begins with a <code>∂</code> as a boundary condition. These boundary conditions recieve special treatment at the scheduling step. Below we show the graphical rendering of this boundary condition diagram, which we will use to impose a Dirichlet condition on the time derivative of concentration at the mesh boundary.</p><pre><code class="language-julia hljs">using Catlab
using Catlab.Graphics
using DiagrammaticEquations
using DiagrammaticEquations.Deca
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# Animation
record(fig, &quot;diff_adv_right.gif&quot;, range(0.0, 100.0; length=150); framerate = 30) do t
pmsh.color = sol(t).C
end</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">&quot;diff_adv_right.gif&quot;</code></pre><p><img src="../diff_adv_right.gif" alt/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../ascii/">« ASCII Operators</a><a class="docs-footer-nextpage" href="../poiseuille/">Pipe Flow »</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 1.2.1 on <span class="colophon-date" title="Monday 26 February 2024 22:44">Monday 26 February 2024</span>. Using Julia version 1.10.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
end</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">&quot;diff_adv_right.gif&quot;</code></pre><p><img src="../diff_adv_right.gif" alt/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../ascii/">« ASCII Operators</a><a class="docs-footer-nextpage" href="../poiseuille/">Pipe Flow »</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 1.2.1 on <span class="colophon-date" title="Tuesday 27 February 2024 18:23">Tuesday 27 February 2024</span>. Using Julia version 1.10.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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