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Deployed d848e9e to 0.4 with MkDocs 1.6.1 and mike 2.1.3
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github-actions committed Nov 23, 2024
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351 changes: 308 additions & 43 deletions 0.4/api/atomcell/index.html
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179 changes: 162 additions & 17 deletions 0.4/api/atoms/index.html
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12 changes: 11 additions & 1 deletion 0.4/api/bbox/index.html
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Expand Up @@ -1468,6 +1468,11 @@ <h1 id="atomlibbbox"><code>atomlib.bbox</code></h1>








<div class="doc doc-children">


Expand All @@ -1493,6 +1498,11 @@ <h2 id="atomlib.bbox.BBox3D" class="doc doc-heading">

<p>3D axis-aligned bounding box, with corners <code>min</code> and <code>max</code>.</p>






<details class="quote">
<summary>Source code in <code>atomlib/bbox.py</code></summary>
<div class="language-python highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"><a href="#__codelineno-0-18"> 18</a></span>
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</span>

</h3>
<div class="language-python doc-signature highlight"><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="n">inner</span><span class="p">:</span> <span class="n"><a class="autorefs autorefs-external" title="numpy.ndarray" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray">ndarray</a></span> <span class="o">=</span> <span class="n"><a class="autorefs autorefs-external" title="numpy.stack" href="https://numpy.org/doc/stable/reference/generated/numpy.stack.html#numpy.stack">stack</a></span><span class="p">((</span><span class="n"><a class="autorefs autorefs-internal" title="atomlib.bbox.BBox3D.min" href="#atomlib.bbox.BBox3D.min">min</a></span><span class="p">,</span> <span class="n"><a class="autorefs autorefs-internal" title="atomlib.bbox.BBox3D.max" href="#atomlib.bbox.BBox3D.max">max</a></span><span class="p">),</span> <span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
<div class="language-python doc-signature highlight"><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="n">inner</span><span class="p">:</span> <span class="n"><a class="autorefs autorefs-external" title="numpy.ndarray" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray">ndarray</a></span> <span class="o">=</span> <span class="n"><a class="autorefs autorefs-external" title="numpy.stack" href="https://numpy.org/doc/stable/reference/generated/numpy.stack.html#numpy.stack">stack</a></span><span class="p">((</span><span class="n"><a class="autorefs autorefs-internal" title="atomlib.bbox.BBox3D.min" href="#atomlib.bbox.BBox3D.min">min</a></span><span class="p">,</span> <span class="n"><a class="autorefs autorefs-internal" title="atomlib.bbox.BBox3D.max" href="#atomlib.bbox.BBox3D.max">max</a></span><span class="p">),</span> <span class="n"><span title="numpy.stack(axis)">axis</span></span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
</span></code></pre></div>

<div class="doc doc-contents ">
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65 changes: 52 additions & 13 deletions 0.4/api/cell/index.html
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125 changes: 95 additions & 30 deletions 0.4/api/defect/index.html
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Expand Up @@ -1330,6 +1330,11 @@ <h1 id="atomlibdefect"><code>atomlib.defect</code></h1>








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Expand Down Expand Up @@ -1457,7 +1462,9 @@ <h2 id="atomlib.defect.stacking_fault" class="doc doc-heading">
</thead>
<tbody>
<tr class="doc-section-item">
<td><code>atoms</code></td>
<td>
<code>atoms</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Structure to add fault to</p>
Expand All @@ -1471,7 +1478,9 @@ <h2 id="atomlib.defect.stacking_fault" class="doc doc-heading">
</td>
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<td><code>pos</code></td>
<td>
<code>pos</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Position on fault plane</p>
Expand All @@ -1485,7 +1494,9 @@ <h2 id="atomlib.defect.stacking_fault" class="doc doc-heading">
</td>
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<td><code>shift</code></td>
<td>
<code>shift</code>
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<div class="doc-md-description">
<p>Vector to shift by</p>
Expand All @@ -1499,7 +1510,9 @@ <h2 id="atomlib.defect.stacking_fault" class="doc doc-heading">
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<td><code>plane</code></td>
<td>
<code>plane</code>
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<div class="doc-md-description">
<p>Normal to fault plane</p>
Expand Down Expand Up @@ -1709,7 +1722,9 @@ <h2 id="atomlib.defect.disloc_edge" class="doc doc-heading">
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<td><code>atoms</code></td>
<td>
<code>atoms</code>
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<p>Structure to add edge dislocation to</p>
Expand All @@ -1723,7 +1738,9 @@ <h2 id="atomlib.defect.disloc_edge" class="doc doc-heading">
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<td><code>center</code></td>
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<code>center</code>
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<p>Position on dislocation line</p>
Expand All @@ -1737,7 +1754,9 @@ <h2 id="atomlib.defect.disloc_edge" class="doc doc-heading">
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<td><code>b</code></td>
<td>
<code>b</code>
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<div class="doc-md-description">
<p>Burgers vector of dislocation (FS/RH convention)</p>
Expand All @@ -1751,7 +1770,9 @@ <h2 id="atomlib.defect.disloc_edge" class="doc doc-heading">
</td>
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<td><code>t</code></td>
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<code>t</code>
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<div class="doc-md-description">
<p>Tangent vector of dislocation</p>
Expand All @@ -1765,7 +1786,9 @@ <h2 id="atomlib.defect.disloc_edge" class="doc doc-heading">
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<td><code>cut</code></td>
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<code>cut</code>
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<div class="doc-md-description">
<p>Cut plane to create dislocation on</p>
Expand All @@ -1783,7 +1806,9 @@ <h2 id="atomlib.defect.disloc_edge" class="doc doc-heading">
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<td><code>poisson</code></td>
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<code>poisson</code>
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<div class="doc-md-description">
<p>Poisson ratio of material</p>
Expand Down Expand Up @@ -2123,7 +2148,9 @@ <h2 id="atomlib.defect.disloc_screw" class="doc doc-heading">
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<td><code>atoms</code></td>
<td>
<code>atoms</code>
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<div class="doc-md-description">
<p>Structure to add screw dislocation to</p>
Expand All @@ -2137,7 +2164,9 @@ <h2 id="atomlib.defect.disloc_screw" class="doc doc-heading">
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<td><code>center</code></td>
<td>
<code>center</code>
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<div class="doc-md-description">
<p>Position on dislocation line</p>
Expand All @@ -2151,7 +2180,9 @@ <h2 id="atomlib.defect.disloc_screw" class="doc doc-heading">
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<td><code>b</code></td>
<td>
<code>b</code>
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<div class="doc-md-description">
<p>Burgers vector of dislocation (FS/RH convention)</p>
Expand All @@ -2165,7 +2196,9 @@ <h2 id="atomlib.defect.disloc_screw" class="doc doc-heading">
</td>
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<td><code>cut</code></td>
<td>
<code>cut</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Cut plane to create dislocation on</p>
Expand All @@ -2183,7 +2216,9 @@ <h2 id="atomlib.defect.disloc_screw" class="doc doc-heading">
</td>
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<td><code>sign</code></td>
<td>
<code>sign</code>
</td>
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<div class="doc-md-description">
<p>Sign of screw dislocation (True means positive)</p>
Expand Down Expand Up @@ -2407,7 +2442,9 @@ <h2 id="atomlib.defect.disloc_loop_z" class="doc doc-heading">
</thead>
<tbody>
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<td><code>atoms</code></td>
<td>
<code>atoms</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Structure to add dislocation loop to</p>
Expand All @@ -2421,7 +2458,9 @@ <h2 id="atomlib.defect.disloc_loop_z" class="doc doc-heading">
</td>
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<td><code>center</code></td>
<td>
<code>center</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Center of dislocation loop</p>
Expand All @@ -2435,7 +2474,9 @@ <h2 id="atomlib.defect.disloc_loop_z" class="doc doc-heading">
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<td><code>b</code></td>
<td>
<code>b</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Burgers vector of dislocation (defined so travelling upwards leads to a plastic displacment of <code>b</code>).</p>
Expand All @@ -2449,7 +2490,9 @@ <h2 id="atomlib.defect.disloc_loop_z" class="doc doc-heading">
</td>
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<td><code>loop_r</code></td>
<td>
<code>loop_r</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Radius of dislocation loop</p>
Expand All @@ -2463,7 +2506,9 @@ <h2 id="atomlib.defect.disloc_loop_z" class="doc doc-heading">
</td>
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<td><code>poisson</code></td>
<td>
<code>poisson</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Poisson ratio of material</p>
Expand Down Expand Up @@ -2664,7 +2709,9 @@ <h2 id="atomlib.defect.disloc_square_z" class="doc doc-heading">
</thead>
<tbody>
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<td><code>atoms</code></td>
<td>
<code>atoms</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Structure to add dislocation loop to</p>
Expand All @@ -2678,7 +2725,9 @@ <h2 id="atomlib.defect.disloc_square_z" class="doc doc-heading">
</td>
</tr>
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<td><code>center</code></td>
<td>
<code>center</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Center of dislocation loop</p>
Expand All @@ -2692,7 +2741,9 @@ <h2 id="atomlib.defect.disloc_square_z" class="doc doc-heading">
</td>
</tr>
<tr class="doc-section-item">
<td><code>b</code></td>
<td>
<code>b</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Burgers vector of dislocation (defined so travelling upwards leads to a plastic displacment of <code>b</code>).</p>
Expand All @@ -2706,7 +2757,9 @@ <h2 id="atomlib.defect.disloc_square_z" class="doc doc-heading">
</td>
</tr>
<tr class="doc-section-item">
<td><code>loop_r</code></td>
<td>
<code>loop_r</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Radius (side length/2) of dislocation loop</p>
Expand All @@ -2720,7 +2773,9 @@ <h2 id="atomlib.defect.disloc_square_z" class="doc doc-heading">
</td>
</tr>
<tr class="doc-section-item">
<td><code>poisson</code></td>
<td>
<code>poisson</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Poisson ratio of material</p>
Expand Down Expand Up @@ -2856,7 +2911,9 @@ <h2 id="atomlib.defect.disloc_poly_z" class="doc doc-heading">
</thead>
<tbody>
<tr class="doc-section-item">
<td><code>atoms</code></td>
<td>
<code>atoms</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Structure to add dislocation loop to</p>
Expand All @@ -2870,7 +2927,9 @@ <h2 id="atomlib.defect.disloc_poly_z" class="doc doc-heading">
</td>
</tr>
<tr class="doc-section-item">
<td><code>b</code></td>
<td>
<code>b</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Burgers vector of dislocation (defined so travelling upwards leads to a plastic displacment of <code>b</code>).</p>
Expand All @@ -2884,7 +2943,9 @@ <h2 id="atomlib.defect.disloc_poly_z" class="doc doc-heading">
</td>
</tr>
<tr class="doc-section-item">
<td><code>poly</code></td>
<td>
<code>poly</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>2D polygon defining dislocation line. It is placed in the plane <code>z=center[2]</code>.</p>
Expand All @@ -2898,7 +2959,9 @@ <h2 id="atomlib.defect.disloc_poly_z" class="doc doc-heading">
</td>
</tr>
<tr class="doc-section-item">
<td><code>center</code></td>
<td>
<code>center</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Center of dislocation loop (defaults to zero, applying no displacement to the gven polygon).</p>
Expand All @@ -2916,7 +2979,9 @@ <h2 id="atomlib.defect.disloc_poly_z" class="doc doc-heading">
</td>
</tr>
<tr class="doc-section-item">
<td><code>poisson</code></td>
<td>
<code>poisson</code>
</td>
<td class="doc-param-details">
<div class="doc-md-description">
<p>Poisson ratio of material</p>
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