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 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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+config: 24beb70a714f877bcc3d224ae7d685fd
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Tutorials/CCP5-June-2021.html

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   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Motivation &mdash; quippy 694dc9c documentation</title>
+  <title>Motivation &mdash; quippy 8e99b0a documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
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 <div role="search">
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@@ -133,13 +133,13 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <center><p><img alt="41da55aa12594826ae724cfb415aeaa2" src="../_images/warwick-logo.png" /></p>
+  <center><p><img alt="8a8b156d67834d99895cdd5aa38576b4" src="../_images/warwick-logo.png" /></p>
 <h1><p>Quantum Mechanics and Interatomic Potentials – the QUIP code</p>
 </h1><h3><p>James Kermode</p>
 </h3><p>Warwick Centre for Predictive Modelling / School of Engineering University of Warwick</p>
 <h4><p>CCP5++ Software Seminar - 17th June 2021</p>
-</h4><table bgcolor="#ffffff"><tr><td><p><img alt="187278d5f5234ffc885605838b15a4fd" class="no-scaled-link" src="../_images/WCPM_logo_text.png" style="width: 100%;" /></p>
-</td><td><p><img alt="2822f5f1c34c4ccbbf05b6c098ff4b95" class="no-scaled-link" src="../_images/hybrid.png" style="width: 100%;" /></p>
+</h4><table bgcolor="#ffffff"><tr><td><p><img alt="2d791609e8f4496e8f86ea424de27464" class="no-scaled-link" src="../_images/WCPM_logo_text.png" style="width: 100%;" /></p>
+</td><td><p><img alt="12e00b341fbf475ab45bcf135719a582" class="no-scaled-link" src="../_images/hybrid.png" style="width: 100%;" /></p>
 </td></tr></table></center><p><em>These slides will subsequently be made available at https://libatoms.github.io/QUIP/Tutorials</em></p>
 <div class="nbinput nblast docutils container">
 <div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
@@ -190,7 +190,7 @@ <h1>Motivation<a class="headerlink" href="#Motivation" title="Permalink to this
 </ul>
 </li>
 </ul>
-<center><p><img alt="fd7740e6ec4548928844188e5f964614" class="no-scaled-link" src="../_images/multiscale.png" style="width: 80%;" /></p>
+<center><p><img alt="ea5a0887b0ac4011bc061cb01e0ffa02" class="no-scaled-link" src="../_images/multiscale.png" style="width: 80%;" /></p>
 </center><p><em>Image credit: Gábor Csányi</em></p>
 </section>
 <section id="The-QUIP-code">
@@ -408,7 +408,7 @@ <h1>Using QUIP with Python and the Atomic Simulation Environment<a class="header
 <li><p><a class="reference external" href="https://jupyter.org/">jupyter</a>/IPython notebooks encourage reproducible research</p></li>
 <li><p><a class="reference external" href="https://jupyter.org/">anaconda</a> distribution and package management system</p></li>
 </ul>
-<center><p><img alt="9b4f8da879654c2f9b091472b6b05bc5" class="no-scaled-link" src="../_images/scipy-stack.png" style="width: 70%;" /></p>
+<center><p><img alt="a78e4d5a4b4845c6a2b5e2bd5a6bfee9" class="no-scaled-link" src="../_images/scipy-stack.png" style="width: 70%;" /></p>
 </center><p><a class="reference external" href="http://www.scipy.org">http://www.scipy.org</a></p>
 </section>
 <section id="Atomic-Simulation-Environment-(ASE)">
@@ -418,7 +418,7 @@ <h1>Atomic Simulation Environment (ASE)<a class="headerlink" href="#Atomic-Simul
 <li><p>Wide range of calculators, very similar data model for Atoms objects to QUIP</p></li>
 <li><p>Can use many codes as drop-in replacements:</p></li>
 </ul>
-<center><p><img alt="35f28b17c46c4467bff9503708eadf35" class="no-scaled-link" src="../_images/ase-calculators.png" style="width: 60%;" /></p>
+<center><p><img alt="65e32547de39460ea19599e61e2ada9a" class="no-scaled-link" src="../_images/ase-calculators.png" style="width: 60%;" /></p>
 </center><p><a class="reference external" href="https://wiki.fysik.dtu.dk/ase/">https://wiki.fysik.dtu.dk/ase/</a></p>
 </section>
 <section id="quippy-demo:-analysing-GAP-models-with-predictive-variance">

Tutorials/adaptive-qmmm-references.html

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-  <title>References &mdash; quippy 694dc9c documentation</title>
+  <title>References &mdash; quippy 8e99b0a documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
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Tutorials/adaptive-qmmm-solutions.html

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   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Solutions &mdash; quippy 694dc9c documentation</title>
+  <title>Solutions &mdash; quippy 8e99b0a documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css" />
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Tutorials/adaptive-qmmm-step0.html

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   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Introduction &mdash; quippy 694dc9c documentation</title>
+  <title>Introduction &mdash; quippy 8e99b0a documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
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Tutorials/adaptive-qmmm-step1.html

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Step 1: Setup of the Silicon model system &mdash; quippy 694dc9c documentation</title>
+  <title>Step 1: Setup of the Silicon model system &mdash; quippy 8e99b0a documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css" />
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@@ -243,7 +243,7 @@ <h3>Import the relevant modules and functions<a class="headerlink" href="#import
 <cite>AtomEye</cite> see its <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">web page</a> or the documentation
 for the <code class="xref py py-mod docutils literal notranslate"><span class="pre">qlab</span></code> and <code class="xref py py-mod docutils literal notranslate"><span class="pre">atomeye</span></code> modules.</p>
 <p>Now, we initialise the Stillinger-Weber (SW) classical interatomic
-potential using quippy’s <a class="reference internal" href="../potential.html#quippy.potential.Potential" title="quippy.potential.Potential"><code class="xref py py-class docutils literal notranslate"><span class="pre">Potential</span></code></a> class</p>
+potential using quippy’s <code class="xref py py-class docutils literal notranslate"><span class="pre">Potential</span></code> class</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mm_pot</span> <span class="o">=</span> <span class="n">Potential</span><span class="p">(</span><span class="s1">&#39;IP SW&#39;</span><span class="p">,</span> <span class="n">param_filename</span><span class="o">=</span><span class="s1">&#39;params.xml&#39;</span><span class="p">)</span>
 </pre></div>
 </div>

Tutorials/adaptive-qmmm-step2.html

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Step 2: Classical MD simulation of fracture in Si &mdash; quippy 694dc9c documentation</title>
+  <title>Step 2: Classical MD simulation of fracture in Si &mdash; quippy 8e99b0a documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css" />
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           </a>
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@@ -240,7 +240,7 @@ <h3>Setup of the constraints<a class="headerlink" href="#setup-of-the-constraint
 <h3>Setup of the potential<a class="headerlink" href="#setup-of-the-potential" title="Permalink to this heading"></a></h3>
 <p>Before starting the MD simulation, the SW classical potential must be
 initialised and attached to the <cite>atoms</cite> object.  As in <cite>Step 1</cite>, we
-use quippy’s <a class="reference internal" href="../potential.html#quippy.potential.Potential" title="quippy.potential.Potential"><code class="xref py py-class docutils literal notranslate"><span class="pre">Potential</span></code></a> class, but now we
+use quippy’s <code class="xref py py-class docutils literal notranslate"><span class="pre">Potential</span></code> class, but now we
 need to pass the <cite>cutoff_skin</cite> parameter, which is used to decide when
 the neighbour list needs to be updated (see the attribute
 <code class="xref py py-attr docutils literal notranslate"><span class="pre">cutoff_skin</span></code>). Moreover, we request
@@ -496,7 +496,7 @@ <h3>Milestone 2.2<a class="headerlink" href="#milestone-2-2" title="Permalink to
 near zero temperature, and it is common to use the second term to
 define a per-atom stress tensor.</p>
 <p>Note, however, that this requires a definition of the atomic volume. By default
-the <a class="reference internal" href="../potential.html#quippy.potential.Potential.get_stresses" title="quippy.potential.Potential.get_stresses"><code class="xref py py-meth docutils literal notranslate"><span class="pre">get_stresses()</span></code></a> function simply divides the
+the <code class="xref py py-meth docutils literal notranslate"><span class="pre">get_stresses()</span></code> function simply divides the
 total cell volume by the number of atoms to get the volume per atom. This is
 not a very good approximation for our cell, which contains a lot of empty
 vacuum, so the volume per atom comes out much too large, and the stress
@@ -521,7 +521,7 @@ <h3>Milestone 2.2<a class="headerlink" href="#milestone-2-2" title="Permalink to
 obeys the expected <span class="math notranslate nohighlight">\(1/\sqrt{r}\)</span> divergence near the crack tip, and tends
 to a constant value ahead of the crack, due to the thin strip loading. <em>Hint:</em>
 use a mask to select the relevant atoms, as we did when fixing the edge atoms
-above. You can use the matplotlib <a class="reference external" href="https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.plot.html#matplotlib.pyplot.plot" title="(in Matplotlib v3.8.4)"><code class="xref py py-func docutils literal notranslate"><span class="pre">plot()</span></code></a> function to
+above. You can use the matplotlib <a class="reference external" href="https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.plot.html#matplotlib.pyplot.plot" title="(in Matplotlib v3.9.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">plot()</span></code></a> function to
 produce a plot.</p>
 </section>
 <section id="time-averaged-stress-field">
@@ -647,7 +647,7 @@ <h3>Milestone 2.2<a class="headerlink" href="#milestone-2-2" title="Permalink to
 <p>The following plot shows the evolution of <cite>G</cite> (blue) and of the
 position of the crack (red; stored as <cite>crack_pos_x</cite>). Note that a
 second vertical axis can be produced with the
-<a class="reference external" href="https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.twinx.html#matplotlib.pyplot.twinx" title="(in Matplotlib v3.8.4)"><code class="xref py py-func docutils literal notranslate"><span class="pre">twinx()</span></code></a> function.</p>
+<a class="reference external" href="https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.twinx.html#matplotlib.pyplot.twinx" title="(in Matplotlib v3.9.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">twinx()</span></code></a> function.</p>
 <a class="reference internal image-reference" href="../_images/energy-release-rate-crack-position.png"><img alt="../_images/energy-release-rate-crack-position.png" class="align-center" src="../_images/energy-release-rate-crack-position.png" style="width: 600px;" /></a>
 <p>In this case the crack actually arrests for a while at around <span class="math notranslate nohighlight">\(t
 = 6\)</span> ps. This is another characteristic feature of non-brittle

Tutorials/adaptive-qmmm-step3.html

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   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Step 3: LOTF hybrid MD simulation of fracture in Si &mdash; quippy 694dc9c documentation</title>
+  <title>Step 3: LOTF hybrid MD simulation of fracture in Si &mdash; quippy 8e99b0a documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
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               <img src="../_static/hybrid.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                694dc9c
+                8e99b0a
               </div>
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@@ -160,7 +160,7 @@ <h4>Setup of the QM and QM/MM potentials<a class="headerlink" href="#setup-of-th
 and MM forces.</p>
 <p>Leave the initialisiton of the SW classical potential as it is. After this, we
 want to add some lines of code to setup the QM potential. Using the same
-<a class="reference internal" href="../potential.html#quippy.potential.Potential" title="quippy.potential.Potential"><code class="xref py py-class docutils literal notranslate"><span class="pre">Potential</span></code></a> class, we initialise now the Density
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Potential</span></code> class, we initialise now the Density
 functional tight binding (DFTB) potential. This is done by passing the new QM
 <cite>qm_init_args</cite> as the <cite>init_args</cite> parameter and the same XML file as before for
 the <cite>param_filename</cite> to the Potential constructor (note that the single file

Tutorials/adaptive-qmmm-theory.html

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   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
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-  <title>Theoretical background &mdash; quippy 694dc9c documentation</title>
+  <title>Theoretical background &mdash; quippy 8e99b0a documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css" />
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           </a>
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Tutorials/adaptive-qmmm.html

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-  <title>Adaptive QM/MM MD of Fracture in Silicon &mdash; quippy 694dc9c documentation</title>
+  <title>Adaptive QM/MM MD of Fracture in Silicon &mdash; quippy 8e99b0a documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
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           </a>
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+                8e99b0a
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