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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta http-equiv="x-ua-compatible" content="ie=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>Cookbook</title>
<link rel="stylesheet" href="/assets/css/readdy_documentation.css">
<link rel="canonical" href="https://readdy.github.io/cookbook.html">
<link href="https://fonts.googleapis.com/css?family=Inconsolata|Roboto+Mono|Lora|Lato|Source+Sans+Pro|Roboto+Slab|Merriweather" rel="stylesheet">
<link rel="stylesheet" href="https://readdy.github.io/libraries/perfect-scrollbar/css/perfect-scrollbar.min.css"/>
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.10.1/dist/katex.min.css" integrity="sha384-dbVIfZGuN1Yq7/1Ocstc1lUEm+AT+/rCkibIcC/OmWo5f0EA48Vf8CytHzGrSwbQ" crossorigin="anonymous">
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.10.1/dist/katex.min.js" integrity="sha384-2BKqo+exmr9su6dir+qCw08N2ZKRucY4PrGQPPWU1A7FtlCGjmEGFqXCv5nyM5Ij" crossorigin="anonymous"></script>
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.10.1/dist/contrib/auto-render.min.js"></script>
<script>
document.addEventListener("DOMContentLoaded", function() {
renderMathInElement(document.body, {
delimiters: [
{left: "$$", right: "$$", display: true},
{left: "$", right: "$", display: false},
{left: "\\[", right: "\\]", display: true},
{left: "\\(", right: "\\)", display: false},
]
});
});
</script>
<link rel="icon" type="image/png" href="/assets/icon_black_32px.png">
</head>
<body>
<div class="side-wrapper" id="unique-side-container">
<div class="side">
<div class="side-logo logo-readdy"><a href="https://readdy.github.io/index.html"></a></div>
<div style="margin-right: 1.5rem; text-align: center;">
<a href="https://readdy.github.io/index.html">ReaDDy - A particle-based<br>reaction-diffusion simulator</a>
</div>
<div class="side-searchbar-wrapper">
<form action="https://readdy.github.io/search.html" method="get">
<input type="text" id="search-box" name="query" placeholder="Search ...">
</form>
</div>
<nav class="side-nav">
<a class="side-nav-item" href="https://readdy.github.io/index.html">Home</a>
<a class="side-nav-item" href="https://readdy.github.io/installation.html">Install readdy</a>
<div class="nav-supergroup-delimiter">
<b>API</b>
</div>
<a class="side-nav-item" href="https://readdy.github.io/system.html">System configuration</a>
<a class="side-nav-item" href="https://readdy.github.io/simulation.html">Simulation</a>
<a class="side-nav-item" href="https://readdy.github.io/results.html">Post-processing</a>
<div class="nav-supergroup-delimiter">
<b>Examples</b>
</div>
<a class="side-nav-item" href="https://readdy.github.io/demonstration.html">Demonstration</a>
<a class="side-nav-item" href="https://readdy.github.io/validation.html">Validation</a>
<a class="side-nav-item" href="https://readdy.github.io/benchmark.html">Benchmark</a>
<div class="nav-supergroup-delimiter">
<b>Advanced topics</b>
</div>
<a class="side-nav-item active" href="https://readdy.github.io/cookbook.html">Cookbook</a>
<a class="side-nav-item" href="https://readdy.github.io/development.html">Development</a>
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<b>Legal notices</b>
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</nav>
<div class="github-wrapper">
<a href="https://github.com/readdy/readdy" style="width: 16rem; height:100%; position:absolute; top:0; left:0;">
<div class="github-text">ReaDDy on GitHub</div>
<div class="side-logo logo-github"></div>
</a>
</div>
<div class="side-logo logo-cmb"><a href="https://www.mi.fu-berlin.de/en/math/groups/comp-mol-bio/"></a></div>
</div>
</div>
<div class="main-container" id="unique-main-container">
<div class="main notebook">
<article>
<div class="docpage-heading"><h1>Cookbook</h1></div>
<p>Useful code snippets and hints</p>
<h3 id="continue-simulation-while-overwriting-old-checkpoints-and-output">Continue simulation while overwriting old checkpoints and output</h3>
<noscript><pre>400: Invalid request</pre></noscript>
<script src="https://gist.github.com/f5e7e395071929f2c2c321794d2dfb59.js"> </script>
<h3 id="record-and-read-out-trajectory-with-c-interface">Record and read out trajectory with C++ interface</h3>
<noscript><pre>400: Invalid request</pre></noscript>
<script src="https://gist.github.com/0a2e87192a0d0976e484d4a23cf78a01.js"> </script>
<h3 id="low-level-simulation-using-the-kernel-directly">Low level simulation using the kernel directly</h3>
<p>Full example on <a href="https://github.com/chrisfroe/readdy-sim-lowlevel">this repository</a></p>
<noscript><pre>400: Invalid request</pre></noscript>
<script src="https://gist.github.com/4694d2709a2d33659c989b1a33ca20bc.js"> </script>
</article>
<div class="foot">
© Copyright 2020 <a href="https://www.mi.fu-berlin.de/en/math/groups/comp-mol-bio/">AI4Science (former CMB) Group</a>
</div>
</div>
</div>
<script src="https://readdy.github.io/libraries/perfect-scrollbar/js/perfect-scrollbar.min.js"></script>
<script src="https://readdy.github.io/assets/js/scrollbar.js"></script>
</body>
</html>