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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Documentation | Open TOPAS</title>
<link rel="stylesheet" href="assets/styles.css" />
</head>
<body>
<header>
<div class="navbar">
<h1>
<a class="logo-mark" href="index.html" aria-label="Open TOPAS home">
<img src="assets/img/Logo.png" alt="" />
</a>
</h1>
<button class="menu-toggle" type="button" aria-label="Toggle navigation" aria-expanded="false">
<span></span>
<span></span>
<span></span>
</button>
<nav id="primary-nav" class="nav-links" aria-label="Main navigation">
<a href="about.html">About</a>
<a href="download.html">Download</a>
<a href="documentation.html" aria-current="page">Documentation</a>
<a href="https://github.com/OpenTOPAS/OpenTOPAS/discussions" target="_blank" rel="noopener">
User Forum <span class="external-icon" aria-hidden="true">↗</span>
</a>
<a href="publications.html">Publications</a>
<a href="contact.html">Contact</a>
</nav>
</div>
</header>
<main>
<section class="section-inner" style="padding:4rem 1.5rem 3rem;">
<h2>Documentation Hub</h2>
<p>
Everything you need to install, operate, and contribute to OpenTOPAS—straight from the official manuals.
</p>
<div class="doc-grid">
<article class="card span-2 link-card" data-href="https://opentopas.readthedocs.io/en/latest/" tabindex="0">
<h4>Official Manual</h4>
<p>
The canonical reference for physics models, geometry components, scoring functions, graphics and release notes lives on Read the Docs.
</p>
<p><a href="https://opentopas.readthedocs.io/en/latest/" target="_blank" rel="noopener">OpenTOPAS on ReadTheDocs →</a></p>
<h4>Code Wiki (automatically generated by Gemini)</h4>
<p>
A description of the base code highlighting features can be found in this link.
</p>
<p><a href="https://codewiki.google/github.com/opentopas/opentopas" target="_blank" rel="noopener">OpenTOPAS on Code Wiki →</a></p>
</article>
<div class="install-row">
<article class="card link-card" data-href="https://github.com/OpenTOPAS/OpenTOPAS/blob/master/OpenTOPAS_quickStart_MacOS.md" tabindex="0">
<h4>Install · macOS</h4>
<p>
Follow the quickstart for Apple Silicon and Intel Macs, including dependency setup and
validation runs.
</p>
<p><a href="https://github.com/OpenTOPAS/OpenTOPAS/blob/master/OpenTOPAS_quickStart_MacOS.md" target="_blank" rel="noopener">macOS quickstart guide →</a></p>
</article>
<article class="card link-card" data-href="https://github.com/OpenTOPAS/OpenTOPAS/blob/master/OpenTOPAS_quickStart_Debian.md" tabindex="0">
<h4>Install · Debian / Ubuntu</h4>
<p>
Step-by-step instructions for Debian-based systems, covering apt packages, Geant4 data sets, and sanity
tests.
</p>
<p><a href="https://github.com/OpenTOPAS/OpenTOPAS/blob/master/OpenTOPAS_quickStart_Debian.md" target="_blank" rel="noopener">Debian quickstart guide →</a></p>
</article>
<article class="card link-card" data-href="https://github.com/OpenTOPAS/OpenTOPAS/blob/master/OpenTOPAS_quickStart_WSL.md" tabindex="0">
<h4>Install · Windows WSL</h4>
<p>
Use Windows Subsystem for Linux to run OpenTOPAS on Windows with near-native performance.
</p>
<p><a href="https://github.com/OpenTOPAS/OpenTOPAS/blob/master/OpenTOPAS_quickStart_WSL.md" target="_blank" rel="noopener">WSL quickstart guide →</a></p>
</article>
</div>
<article class="card span-2" tabindex="0">
<h4>Contribute via Fork</h4>
<p>
Keep contributions aligned with the `develop` branch and validate them through our qi-opentopas workflow.
</p>
<ol class="doc-steps">
<li>Fork <code>OpenTOPAS/OpenTOPAS</code>, create a feature branch off <code>develop</code>, and sync often.</li>
<li>Clone your fork <br /><code>git clone https://github.com/OpenTOPAS/qi-opentopas.git</code> for QA automation.</li>
<li>Run qi-opentopas checks locally (build, regression, formatting) before opening a Pull Request (PR).</li>
<li>Open the PR against <code>develop</code>, link related issues, and describe datasets/settings used.</li>
</ol>
<p><a href="https://github.com/OpenTOPAS/qi-opentopas" target="_blank" rel="noopener">qi-opentopas repository →</a></p>
</article>
<article class="card span-2" tabindex="0">
<h4>License & Usage</h4>
<p>
OpenTOPAS is distributed under the MIT License. Review the terms to understand how you can reuse and
redistribute the software.
</p>
<p><a href="download.html">Read the MIT License →</a></p>
</article>
<article class="card span-2" tabindex="0">
<h4>How to Cite?</h4>
<p>
Acknowledge the TOPAS collaboration by including these references in your publications:
</p>
<ol class="cite-list">
<li>
B. Faddegon, J. Ramos-Méndez, J. Schümann, A. McNamara, J. Shin, J. Perl, H. Paganetti. “The TOPAS Tool
for Particle Simulation, a Monte Carlo Simulation Tool for Physics, Biology and Clinical Research.”
<em>Phys Med.</em> 2020;72:114-121. PMID: 32247964. PMCID: PMC7192305.
</li>
<li>
J. Perl, J. Shin, J. Schümann, B. Faddegon, H. Paganetti. “TOPAS: an innovative proton Monte Carlo
platform for research and clinical applications.” <em>Med Phys.</em> 2012;39(11):6818-37.
</li>
</ol>
</article>
</div>
</section>
</main>
<footer>
<small>© <span id="year"></span> The TOPAS Collaboration</small>
</footer>
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</body>
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