deploy: a1d4988

Custom_Group.html

@@ -92,12 +92,6 @@ <h1>Custom Symmetry Group Example<a class="headerlink" href="#custom-symmetry-gr
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/opt/hostedtoolcache/Python/3.8.14/x64/lib/python3.8/site-packages/symd/groups.py:442: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify &#39;dtype=object&#39; when creating the ndarray.
-  &quot;Trigonal&quot;: np.array(  # cubic, plus use b_y as shear
-</pre></div>
-</div>
-</div>
 </div>
 <section id="make-custom-group">
 <h2>Make custom group<a class="headerlink" href="#make-custom-group" title="Permalink to this headline"></a></h2>
@@ -200,7 +194,7 @@ <h2>Run<a class="headerlink" href="#run" title="Permalink to this headline"><
 </pre></div>
 </div>
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&quot;steps&quot;: 1000000, &quot;n_particles&quot;: 256, &quot;time_step&quot;: 0.005, &quot;seed&quot;: 435423, &quot;anderson_nu&quot;: 100, &quot;langevin_gamma&quot;: 0.5, &quot;bussi_taut&quot;: 0.5, &quot;thermostat_seed&quot;: 54344, &quot;rcut&quot;: 10, &quot;skin&quot;: 0.6000000000000001, &quot;temperature&quot;: 0.1, &quot;pressure&quot;: 0.25, &quot;box_update_period&quot;: 10, &quot;start_temperature&quot;: 0.1, &quot;thermostat&quot;: &quot;baoab&quot;, &quot;force_type&quot;: &quot;lj&quot;, &quot;final_positions&quot;: &quot;quasi/final_positions.dat&quot;, &quot;cell_log_file&quot;: &quot;quasi/cell_log_file.dat&quot;, &quot;print_period&quot;: 10000.0, &quot;cell&quot;: [38.0257, 0.0, 0.0, 37.0197], &quot;lj_epsilon&quot;: 1, &quot;lj_sigma&quot;: 1, &quot;images&quot;: [0, 0], &quot;wyckoffs&quot;: [{&quot;group&quot;: &quot;quasi/group-custom-00.json&quot;, &quot;n_particles&quot;: 1}], &quot;start_positions&quot;: &quot;quasi/final_positions.dat&quot;, &quot;group&quot;: &quot;quasi/group-custom.json&quot;, &quot;position_log_period&quot;: 1000, &quot;positions_log_file&quot;: &quot;quasi/positions.xyz&quot;}
-Info: You are running version fd57 of symd
+Info: You are running version a1d4 of symd
 Assuming you&#39;ll pass parameters via stdin. Waiting...
 Warning: assuming default value for velocity_log_period = 0
 Warning: assuming default value for force_log_period = 0
@@ -256,7 +250,7 @@ <h2>Run<a class="headerlink" href="#run" title="Permalink to this headline"><
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-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;matplotlib.lines.Line2D at 0x7fa8d4a02370&gt;]
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;matplotlib.lines.Line2D at 0x7f21bdfc92b0&gt;]
 </pre></div>
 </div>
 <img alt="_images/Custom_Group_7_1.png" src="_images/Custom_Group_7_1.png" />

Tutorial.html

@@ -102,12 +102,6 @@ <h1>Python Tutorial<a class="headerlink" href="#python-tutorial" title="Permalin
 </pre></div>
 </div>
 </div>
-<div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/opt/hostedtoolcache/Python/3.8.14/x64/lib/python3.8/site-packages/symd/groups.py:442: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify &#39;dtype=object&#39; when creating the ndarray.
-  &quot;Trigonal&quot;: np.array(  # cubic, plus use b_y as shear
-</pre></div>
-</div>
-</div>
 </div>
 <section id="a-group">
 <h2>A group<a class="headerlink" href="#a-group" title="Permalink to this headline"></a></h2>
@@ -328,8 +322,8 @@ <h2>Bravais Lattice<a class="headerlink" href="#bravais-lattice" title="Permalin
 </div>
 <div class="cell_output docutils container">
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>This lattice is Square
-[[2.13484562 0.        ]
- [0.         2.13484562]]
+[[2.11479269 0.        ]
+ [0.         2.11479269]]
 </pre></div>
 </div>
 </div>
@@ -351,11 +345,9 @@ <h2>Bravais Lattice<a class="headerlink" href="#bravais-lattice" title="Permalin
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>The volume of my cell is 4.5575658136274395
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>The volume of my cell is 4.472348120781142
 If I have 8 particles in asymmetric unit, there will be 64 in the unit cell
-</pre></div>
-</div>
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>If I want to have a number density of 0.6 with 8 particles,
+If I want to have a number density of 0.6 with 8 particles,
 my cell should be [5.163977476386405, 0.0, 0.0, 5.163977476386405]
 </pre></div>
 </div>

api.html

@@ -229,7 +229,7 @@
 <dd><p>Compute volume of given unit cell in arbitrary dimension</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>b</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.23)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a>) – lattice vectors as columns</p>
+<dd class="field-odd"><p><strong>b</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a>) – lattice vectors as columns</p>
 </dd>
 <dt class="field-even">Return type</dt>
 <dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></p>
@@ -321,12 +321,12 @@
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>cell</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.23)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a>) – unit cell as columns</p></li>
-<li><p><strong>projector</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>, <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.23)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a>]) – projector tensor or str of Bravais lattice</p></li>
+<li><p><strong>cell</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a>) – unit cell as columns</p></li>
+<li><p><strong>projector</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>, <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a>]) – projector tensor or str of Bravais lattice</p></li>
 </ul>
 </dd>
 <dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.23)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -341,7 +341,7 @@
 <dd class="field-odd"><p><strong>s</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>) – string in xyz notation</p>
 </dd>
 <dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.23)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a></p>
 </dd>
 <dt class="field-odd">Returns</dt>
 <dd class="field-odd"><p>np.ndarray: matrix</p>