Skip to content

Commit

Permalink
deploy: e7f4253
Browse files Browse the repository at this point in the history
  • Loading branch information
martinjrobins committed Dec 9, 2024
1 parent 743247f commit 57f48cf
Show file tree
Hide file tree
Showing 14 changed files with 1,529 additions and 12 deletions.
4 changes: 2 additions & 2 deletions primer/electrical_circuits.html
Original file line number Diff line number Diff line change
Expand Up @@ -285,7 +285,7 @@ <h1 id="example-electrical-circuits"><a class="header" href="#example-electrical
<i class="fa fa-angle-left"></i>
</a>

<a rel="next prefetch" href="../specify/specifying_the_problem.html" class="mobile-nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
<a rel="next prefetch" href="../primer/pdes.html" class="mobile-nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
<i class="fa fa-angle-right"></i>
</a>

Expand All @@ -299,7 +299,7 @@ <h1 id="example-electrical-circuits"><a class="header" href="#example-electrical
<i class="fa fa-angle-left"></i>
</a>

<a rel="next prefetch" href="../specify/specifying_the_problem.html" class="nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
<a rel="next prefetch" href="../primer/pdes.html" class="nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
<i class="fa fa-angle-right"></i>
</a>
</nav>
Expand Down
4 changes: 2 additions & 2 deletions primer/first_order_odes.html
Original file line number Diff line number Diff line change
Expand Up @@ -160,8 +160,8 @@ <h1 id="explicit-first-order-odes"><a class="header" href="#explicit-first-order
<p>\[
\frac{dc}{dt} = k c
\]</p>
<p>where \(k\) is a constant that describes the growth rate of the cells. This is a first order ODE, because it involves only the first derivative of the state variable \(c\) with respect to time. We can write down a general form for a first order ODE as:</p>
<p>We can also use the same form to solve a coupled set of equations, say we had <em>two</em> populations of cells in the same dish that grow with different rates. We could define the state of the system as the concentrations of the two cell populations, and assign these states to variables \(c_1\) and \(c_2\). We could then write down both equations as:</p>
<p>where \(k\) is a constant that describes the growth rate of the cells. This is a first order ODE, because it involves only the first derivative of the state variable \(c\) with respect to time.</p>
<p>We can also solve a coupled set of equations, say we had <em>two</em> populations of cells in the same dish that grow with different rates. We could define the state of the system as the concentrations of the two cell populations, and assign these states to variables \(c_1\) and \(c_2\). We could then write down both equations as:</p>
<p>\[
\begin{align*}
\frac{dc_1}{dt} &amp;= k_1 c_1 \\
Expand Down
407 changes: 407 additions & 0 deletions primer/heat_equation.html

Large diffs are not rendered by default.

4 changes: 4 additions & 0 deletions primer/images/battery-simulation.html

Large diffs are not rendered by default.

4 changes: 4 additions & 0 deletions primer/images/heat-equation.html

Large diffs are not rendered by default.

226 changes: 226 additions & 0 deletions primer/pdes.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,226 @@
<!DOCTYPE HTML>
<html lang="en" class="light sidebar-visible" dir="ltr">
<head>
<!-- Book generated using mdBook -->
<meta charset="UTF-8">
<title>PDEs - DiffSol</title>


<!-- Custom HTML head -->
<script src="https://cdn.plot.ly/plotly-2.35.2.min.js" charset="utf-8"></script>

<meta name="description" content="">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="theme-color" content="#ffffff">

<link rel="icon" href="../favicon.svg">
<link rel="shortcut icon" href="../favicon.png">
<link rel="stylesheet" href="../css/variables.css">
<link rel="stylesheet" href="../css/general.css">
<link rel="stylesheet" href="../css/chrome.css">
<link rel="stylesheet" href="../css/print.css" media="print">

<!-- Fonts -->
<link rel="stylesheet" href="../FontAwesome/css/font-awesome.css">
<link rel="stylesheet" href="../fonts/fonts.css">

<!-- Highlight.js Stylesheets -->
<link rel="stylesheet" href="../highlight.css">
<link rel="stylesheet" href="../tomorrow-night.css">
<link rel="stylesheet" href="../ayu-highlight.css">

<!-- Custom theme stylesheets -->

<!-- MathJax -->
<script async src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>

<!-- Provide site root to javascript -->
<script>
var path_to_root = "../";
var default_theme = window.matchMedia("(prefers-color-scheme: dark)").matches ? "navy" : "light";
</script>
<!-- Start loading toc.js asap -->
<script src="../toc.js"></script>
</head>
<body>
<div id="body-container">
<!-- Work around some values being stored in localStorage wrapped in quotes -->
<script>
try {
var theme = localStorage.getItem('mdbook-theme');
var sidebar = localStorage.getItem('mdbook-sidebar');

if (theme.startsWith('"') && theme.endsWith('"')) {
localStorage.setItem('mdbook-theme', theme.slice(1, theme.length - 1));
}

if (sidebar.startsWith('"') && sidebar.endsWith('"')) {
localStorage.setItem('mdbook-sidebar', sidebar.slice(1, sidebar.length - 1));
}
} catch (e) { }
</script>

<!-- Set the theme before any content is loaded, prevents flash -->
<script>
var theme;
try { theme = localStorage.getItem('mdbook-theme'); } catch(e) { }
if (theme === null || theme === undefined) { theme = default_theme; }
const html = document.documentElement;
html.classList.remove('light')
html.classList.add(theme);
html.classList.add("js");
</script>

<input type="checkbox" id="sidebar-toggle-anchor" class="hidden">

<!-- Hide / unhide sidebar before it is displayed -->
<script>
var sidebar = null;
var sidebar_toggle = document.getElementById("sidebar-toggle-anchor");
if (document.body.clientWidth >= 1080) {
try { sidebar = localStorage.getItem('mdbook-sidebar'); } catch(e) { }
sidebar = sidebar || 'visible';
} else {
sidebar = 'hidden';
}
sidebar_toggle.checked = sidebar === 'visible';
html.classList.remove('sidebar-visible');
html.classList.add("sidebar-" + sidebar);
</script>

<nav id="sidebar" class="sidebar" aria-label="Table of contents">
<!-- populated by js -->
<mdbook-sidebar-scrollbox class="sidebar-scrollbox"></mdbook-sidebar-scrollbox>
<noscript>
<iframe class="sidebar-iframe-outer" src="../toc.html"></iframe>
</noscript>
<div id="sidebar-resize-handle" class="sidebar-resize-handle">
<div class="sidebar-resize-indicator"></div>
</div>
</nav>

<div id="page-wrapper" class="page-wrapper">

<div class="page">
<div id="menu-bar-hover-placeholder"></div>
<div id="menu-bar" class="menu-bar sticky">
<div class="left-buttons">
<label id="sidebar-toggle" class="icon-button" for="sidebar-toggle-anchor" title="Toggle Table of Contents" aria-label="Toggle Table of Contents" aria-controls="sidebar">
<i class="fa fa-bars"></i>
</label>
<button id="theme-toggle" class="icon-button" type="button" title="Change theme" aria-label="Change theme" aria-haspopup="true" aria-expanded="false" aria-controls="theme-list">
<i class="fa fa-paint-brush"></i>
</button>
<ul id="theme-list" class="theme-popup" aria-label="Themes" role="menu">
<li role="none"><button role="menuitem" class="theme" id="light">Light</button></li>
<li role="none"><button role="menuitem" class="theme" id="rust">Rust</button></li>
<li role="none"><button role="menuitem" class="theme" id="coal">Coal</button></li>
<li role="none"><button role="menuitem" class="theme" id="navy">Navy</button></li>
<li role="none"><button role="menuitem" class="theme" id="ayu">Ayu</button></li>
</ul>
<button id="search-toggle" class="icon-button" type="button" title="Search. (Shortkey: s)" aria-label="Toggle Searchbar" aria-expanded="false" aria-keyshortcuts="S" aria-controls="searchbar">
<i class="fa fa-search"></i>
</button>
</div>

<h1 class="menu-title">DiffSol</h1>

<div class="right-buttons">
<a href="../print.html" title="Print this book" aria-label="Print this book">
<i id="print-button" class="fa fa-print"></i>
</a>

</div>
</div>

<div id="search-wrapper" class="hidden">
<form id="searchbar-outer" class="searchbar-outer">
<input type="search" id="searchbar" name="searchbar" placeholder="Search this book ..." aria-controls="searchresults-outer" aria-describedby="searchresults-header">
</form>
<div id="searchresults-outer" class="searchresults-outer hidden">
<div id="searchresults-header" class="searchresults-header"></div>
<ul id="searchresults">
</ul>
</div>
</div>

<!-- Apply ARIA attributes after the sidebar and the sidebar toggle button are added to the DOM -->
<script>
document.getElementById('sidebar-toggle').setAttribute('aria-expanded', sidebar === 'visible');
document.getElementById('sidebar').setAttribute('aria-hidden', sidebar !== 'visible');
Array.from(document.querySelectorAll('#sidebar a')).forEach(function(link) {
link.setAttribute('tabIndex', sidebar === 'visible' ? 0 : -1);
});
</script>

<div id="content" class="content">
<main>
<h1 id="partial-differential-equations-pdes"><a class="header" href="#partial-differential-equations-pdes">Partial Differential Equations (PDEs)</a></h1>
<p>DiffSol is an ODE solver, but it can also solve PDEs. The idea is to discretize the PDE in space and time, and then solve the resulting system of ODEs. This is called the method of lines.</p>
<p>Discretizing a PDE is a large topic, and there are many ways to do it. Common methods include finite difference, finite volume, finite element, and spectral methods. Finite difference methods are the simplest to understand and implement, so some of the examples in this book will demonstrate this method to give you a flavour of how to solve PDEs with DiffSol. However, in general we recommend that you use another package to discretise you PDE, and then import the resulting ODE system into DiffSol for solving.</p>
<h2 id="some-useful-packages"><a class="header" href="#some-useful-packages">Some useful packages</a></h2>
<p>There are many packages in the Python and Julia ecosystems that can help you discretise your PDE. Here are a few that we know of, but there are many more out there:</p>
<p>Python</p>
<ul>
<li><a href="https://fenicsproject.org/">FEniCS</a>: A finite element package. Uses the Unified Form Language (UFL) to specify PDEs.</li>
<li><a href="https://firedrakeproject.org/">FireDrake</a>: A finite element package, uses the same UFL as FEniCS.</li>
<li><a href="https://www.ctcms.nist.gov/fipy/">FiPy</a>: A finite volume package.</li>
<li><a href="https://scikit-fdiff.readthedocs.io/en/latest/">scikit-fdiff</a>: A finite difference package.</li>
</ul>
<p>Julia:</p>
<ul>
<li><a href="https://github.com/SciML/MethodOfLines.jl">MethodOfLines.jl</a>: A finite difference package.</li>
<li><a href="https://github.com/gridap/Gridap.jl">Gridap.jl</a>: A finite element package.</li>
</ul>

</main>

<nav class="nav-wrapper" aria-label="Page navigation">
<!-- Mobile navigation buttons -->
<a rel="prev" href="../primer/electrical_circuits.html" class="mobile-nav-chapters previous" title="Previous chapter" aria-label="Previous chapter" aria-keyshortcuts="Left">
<i class="fa fa-angle-left"></i>
</a>

<a rel="next prefetch" href="../primer/heat_equation.html" class="mobile-nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
<i class="fa fa-angle-right"></i>
</a>

<div style="clear: both"></div>
</nav>
</div>
</div>

<nav class="nav-wide-wrapper" aria-label="Page navigation">
<a rel="prev" href="../primer/electrical_circuits.html" class="nav-chapters previous" title="Previous chapter" aria-label="Previous chapter" aria-keyshortcuts="Left">
<i class="fa fa-angle-left"></i>
</a>

<a rel="next prefetch" href="../primer/heat_equation.html" class="nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
<i class="fa fa-angle-right"></i>
</a>
</nav>

</div>




<script>
window.playground_copyable = true;
</script>


<script src="../elasticlunr.min.js"></script>
<script src="../mark.min.js"></script>
<script src="../searcher.js"></script>

<script src="../clipboard.min.js"></script>
<script src="../highlight.js"></script>
<script src="../book.js"></script>

<!-- Custom JS scripts -->


</div>
</body>
</html>
Loading

0 comments on commit 57f48cf

Please sign in to comment.