Skip to content

Commit

Permalink
documentation added
Browse files Browse the repository at this point in the history
  • Loading branch information
akabiraka committed Aug 7, 2023
1 parent 46f919e commit 65709e9
Show file tree
Hide file tree
Showing 175 changed files with 18,289 additions and 0 deletions.
Binary file added docs/_images/88seqs_seqlen_vs_runtime.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_images/Bubbles.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_images/P5_flips.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_images/P5_qfactors.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_images/mcmc_algorithm.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_images/p5_wtmt_avg_coord.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_images/svr_rbf_perf_comparison_selex.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
320 changes: 320 additions & 0 deletions docs/_modules/index.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,320 @@


<!DOCTYPE html>


<html lang="en" >

<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &#8212; pyDNA-EPBD 1.0.0 documentation</title>



<script data-cfasync="false">
document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
document.documentElement.dataset.theme = localStorage.getItem("theme") || "light";
</script>

<!-- Loaded before other Sphinx assets -->
<link href="../_static/styles/theme.css?digest=e353d410970836974a52" rel="stylesheet" />
<link href="../_static/styles/bootstrap.css?digest=e353d410970836974a52" rel="stylesheet" />
<link href="../_static/styles/pydata-sphinx-theme.css?digest=e353d410970836974a52" rel="stylesheet" />


<link href="../_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=e353d410970836974a52" rel="stylesheet" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.1.2/webfonts/fa-solid-900.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2" />

<link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
<link rel="stylesheet" href="../_static/styles/sphinx-book-theme.css?digest=14f4ca6b54d191a8c7657f6c759bf11a5fb86285" type="text/css" />
<link rel="stylesheet" type="text/css" href="../_static/graphviz.css" />

<!-- Pre-loaded scripts that we'll load fully later -->
<link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=e353d410970836974a52" />
<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52" />

<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/doctools.js"></script>
<script src="../_static/sphinx_highlight.js"></script>
<script src="../_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
<script>DOCUMENTATION_OPTIONS.pagename = '_modules/index';</script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
</head>


<body data-bs-spy="scroll" data-bs-target=".bd-toc-nav" data-offset="180" data-bs-root-margin="0px 0px -60%" data-default-mode="">



<a class="skip-link" href="#main-content">Skip to main content</a>

<input type="checkbox"
class="sidebar-toggle"
name="__primary"
id="__primary"/>
<label class="overlay overlay-primary" for="__primary"></label>

<input type="checkbox"
class="sidebar-toggle"
name="__secondary"
id="__secondary"/>
<label class="overlay overlay-secondary" for="__secondary"></label>

<div class="search-button__wrapper">
<div class="search-button__overlay"></div>
<div class="search-button__search-container">
<form class="bd-search d-flex align-items-center"
action="../search.html"
method="get">
<i class="fa-solid fa-magnifying-glass"></i>
<input type="search"
class="form-control"
name="q"
id="search-input"
placeholder="Search..."
aria-label="Search..."
autocomplete="off"
autocorrect="off"
autocapitalize="off"
spellcheck="false"/>
<span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
</form></div>
</div>

<nav class="bd-header navbar navbar-expand-lg bd-navbar">
</nav>

<div class="bd-container">
<div class="bd-container__inner bd-page-width">

<div class="bd-sidebar-primary bd-sidebar">



<div class="sidebar-header-items sidebar-primary__section">




</div>

<div class="sidebar-primary-items__start sidebar-primary__section">
<div class="sidebar-primary-item">


<a class="navbar-brand logo" href="../index.html">





<p class="title logo__title">pyDNA-EPBD 1.0.0 documentation</p>

</a></div>
<div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
<div class="bd-toc-item navbar-nav active">
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="../modules/modules.html">pydna_epbd</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l2 has-children"><a class="reference internal" href="../modules/pydna_epbd.html">pydna_epbd package</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-2"><i class="fa-solid fa-chevron-down"></i></label><ul>
<li class="toctree-l3"><a class="reference internal" href="../modules/pydna_epbd.monitors.html">pydna_epbd.monitors package</a></li>
<li class="toctree-l3"><a class="reference internal" href="../modules/pydna_epbd.simulation.html">pydna_epbd.simulation package</a></li>
</ul>
</li>
</ul>
</li>
</ul>

</div>
</nav></div>
</div>


<div class="sidebar-primary-items__end sidebar-primary__section">
</div>

<div id="rtd-footer-container"></div>


</div>

<main id="main-content" class="bd-main">



<div class="sbt-scroll-pixel-helper"></div>

<div class="bd-content">
<div class="bd-article-container">

<div class="bd-header-article">
<div class="header-article-items header-article__inner">

<div class="header-article-items__start">

<div class="header-article-item"><label class="sidebar-toggle primary-toggle btn btn-sm" for="__primary" title="Toggle primary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
<span class="fa-solid fa-bars"></span>
</label></div>

</div>


<div class="header-article-items__end">

<div class="header-article-item">

<div class="article-header-buttons">



<button onclick="toggleFullScreen()"
class="btn btn-sm btn-fullscreen-button"
title="Fullscreen mode"
data-bs-placement="bottom" data-bs-toggle="tooltip"
>


<span class="btn__icon-container">
<i class="fas fa-expand"></i>
</span>

</button>


<script>
document.write(`
<button class="theme-switch-button btn btn-sm btn-outline-primary navbar-btn rounded-circle" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
<span class="theme-switch" data-mode="light"><i class="fa-solid fa-sun"></i></span>
<span class="theme-switch" data-mode="dark"><i class="fa-solid fa-moon"></i></span>
<span class="theme-switch" data-mode="auto"><i class="fa-solid fa-circle-half-stroke"></i></span>
</button>
`);
</script>

<script>
document.write(`
<button class="btn btn-sm navbar-btn search-button search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
<i class="fa-solid fa-magnifying-glass"></i>
</button>
`);
</script>

</div></div>

</div>

</div>
</div>



<div id="jb-print-docs-body" class="onlyprint">
<h1></h1>
<!-- Table of contents -->
<div id="print-main-content">
<div id="jb-print-toc">

</div>
</div>
</div>



<div id="searchbox"></div>
<article class="bd-article" role="main">

<h1>All modules for which code is available</h1>
<ul><li><a href="pydna_epbd/configs.html">pydna_epbd.configs</a></li>
<li><a href="pydna_epbd/input_reader.html">pydna_epbd.input_reader</a></li>
<li><a href="pydna_epbd/monitors/all_monitors.html">pydna_epbd.monitors.all_monitors</a></li>
<li><a href="pydna_epbd/monitors/bubble_monitor.html">pydna_epbd.monitors.bubble_monitor</a></li>
<li><a href="pydna_epbd/monitors/coord_monitor.html">pydna_epbd.monitors.coord_monitor</a></li>
<li><a href="pydna_epbd/monitors/energy_monitor.html">pydna_epbd.monitors.energy_monitor</a></li>
<li><a href="pydna_epbd/monitors/flipping_monitor.html">pydna_epbd.monitors.flipping_monitor</a></li>
<li><a href="pydna_epbd/monitors/flipping_monitor_verbose.html">pydna_epbd.monitors.flipping_monitor_verbose</a></li>
<li><a href="pydna_epbd/monitors/melting_and_fraction_many_monitor.html">pydna_epbd.monitors.melting_and_fraction_many_monitor</a></li>
<li><a href="pydna_epbd/monitors/melting_and_fraction_monitor.html">pydna_epbd.monitors.melting_and_fraction_monitor</a></li>
<li><a href="pydna_epbd/monitors/monitor.html">pydna_epbd.monitors.monitor</a></li>
<li><a href="pydna_epbd/pickle_utils.html">pydna_epbd.pickle_utils</a></li>
<li><a href="pydna_epbd/run.html">pydna_epbd.run</a></li>
<li><a href="pydna_epbd/simulation/aggregate_outputs_and_write.html">pydna_epbd.simulation.aggregate_outputs_and_write</a></li>
<li><a href="pydna_epbd/simulation/dna.html">pydna_epbd.simulation.dna</a></li>
<li><a href="pydna_epbd/simulation/mc_simulation.html">pydna_epbd.simulation.mc_simulation</a></li>
<li><a href="pydna_epbd/simulation/simulation_steps.html">pydna_epbd.simulation.simulation_steps</a></li>
</ul>

</article>




<footer class="bd-footer-article">

<div class="footer-article-items footer-article__inner">

<div class="footer-article-item"><!-- Previous / next buttons -->
<div class="prev-next-area">
</div></div>

</div>

</footer>

</div>




</div>
<footer class="bd-footer-content">

<div class="bd-footer-content__inner container">

<div class="footer-item">

<p class="component-author">
By Anowarul Kabir, Manish Bhattarai, Kim Rasmussen, Amarda Shehu, Anny Usheva, Alan Bishop and Boian Alexandrov
</p>

</div>

<div class="footer-item">

<p class="copyright">

© Copyright 2023, LANL.
<br/>

</p>

</div>

<div class="footer-item">

</div>

<div class="footer-item">

</div>

</div>
</footer>


</main>
</div>
</div>

<!-- Scripts loaded after <body> so the DOM is not blocked -->
<script src="../_static/scripts/bootstrap.js?digest=e353d410970836974a52"></script>
<script src="../_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52"></script>

<footer class="bd-footer">
</footer>
</body>
</html>
Loading

0 comments on commit 65709e9

Please sign in to comment.