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lorenzo-rovigatti · Jun 26, 2024 · 55ab634 · 55ab634
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diff --git a/_sources/oxpy/index.md.txt b/_sources/oxpy/index.md.txt
@@ -33,7 +33,20 @@ with oxpy.Context():
 	# and the interaction energy between the first two particles
 	print("Interaction energy between particle 0 and particle 1:", manager.config_info().interaction.pair_interaction(particles[0], particles[1]))
 ```
-
+
+:::{warning}
+There is a known issue that makes the code segfault whenever multiple `with oxpy.Context()` are used in a single script. In these cases a simple workaround is to add a `del manager` instruction at the end of the `with` code block, like this:
+
+```python
+for _ in range(N_sims):
+   with oxpy.Context():
+      manager = oxpy.OxpyManager("input")
+      manager.run(N_steps)
+      del manager # <-- if you comment this line the script will segfault
+```
+
+:::
+
 If you want, you can initialise the input file yourself and change some of the options before initialising the manager:
 
 ```python
@@ -67,7 +80,7 @@ conf_file = init_conf.dat
 trajectory_file = trajectory.dat
 energy_file = energy.dat
 ```
-	
+
 ## An example of a simple analysis
 
 Here we loop over all the configurations stored in an oxDNA trajectory file, printing the position of the first particle. 

diff --git a/oat/api.html b/oat/api.html
diff --git a/oat/utils.html b/oat/utils.html
diff --git a/oxpy/index.html b/oxpy/index.html
@@ -139,6 +139,17 @@ <h2>An example of a simple simulation<a class="headerlink" href="#an-example-of-
 	<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Interaction energy between particle 0 and particle 1:&quot;</span><span class="p">,</span> <span class="n">manager</span><span class="o">.</span><span class="n">config_info</span><span class="p">()</span><span class="o">.</span><span class="n">interaction</span><span class="o">.</span><span class="n">pair_interaction</span><span class="p">(</span><span class="n">particles</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">particles</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
 </pre></div>
 </div>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>There is a known issue that makes the code segfault whenever multiple <code class="docutils literal notranslate"><span class="pre">with</span> <span class="pre">oxpy.Context()</span></code> are used in a single script. In these cases a simple workaround is to add a <code class="docutils literal notranslate"><span class="pre">del</span> <span class="pre">manager</span></code> instruction at the end of the <code class="docutils literal notranslate"><span class="pre">with</span></code> code block, like this:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">N_sims</span><span class="p">):</span>
+   <span class="k">with</span> <span class="n">oxpy</span><span class="o">.</span><span class="n">Context</span><span class="p">():</span>
+      <span class="n">manager</span> <span class="o">=</span> <span class="n">oxpy</span><span class="o">.</span><span class="n">OxpyManager</span><span class="p">(</span><span class="s2">&quot;input&quot;</span><span class="p">)</span>
+      <span class="n">manager</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">N_steps</span><span class="p">)</span>
+      <span class="k">del</span> <span class="n">manager</span> <span class="c1"># &lt;-- if you comment this line the script will segfault</span>
+</pre></div>
+</div>
+</div>
 <p>If you want, you can initialise the input file yourself and change some of the options before initialising the manager:</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">my_input</span> <span class="o">=</span> <span class="n">oxpy</span><span class="o">.</span><span class="n">InputFile</span><span class="p">()</span>
 <span class="n">my_input</span><span class="o">.</span><span class="n">init_from_filename</span><span class="p">(</span><span class="s2">&quot;input&quot;</span><span class="p">)</span>

diff --git a/oxpy/modules/core/core.html b/oxpy/modules/core/core.html
@@ -506,7 +506,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd class="field-odd"><p>The position of the site.</p>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></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 v1.26)">numpy.ndarray</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)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -520,7 +520,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd class="field-odd"><p>The position of the site.</p>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></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 v1.26)">numpy.ndarray</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)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -534,7 +534,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd class="field-odd"><p>The position of the site.</p>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></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 v1.26)">numpy.ndarray</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)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -556,7 +556,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd class="field-odd"><p>The position of the site.</p>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></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 v1.26)">numpy.ndarray</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)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -570,7 +570,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd class="field-odd"><p>The position of the site.</p>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></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 v1.26)">numpy.ndarray</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)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -584,7 +584,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd class="field-odd"><p>The position of the site.</p>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></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 v1.26)">numpy.ndarray</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)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -598,7 +598,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd class="field-odd"><p>The position of the site.</p>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></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 v1.26)">numpy.ndarray</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)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -612,7 +612,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd class="field-odd"><p>The position of the site.</p>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></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 v1.26)">numpy.ndarray</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)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -626,7 +626,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd class="field-odd"><p>The position of the site.</p>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></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 v1.26)">numpy.ndarray</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)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -640,7 +640,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd class="field-odd"><p>The position of the site.</p>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></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 v1.26)">numpy.ndarray</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)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -763,7 +763,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd><p>Set the distance vector used by the <cite>pair_interaction_*</cite> methods when they are called with <cite>compute_r = False</cite> (see <a class="reference internal" href="#oxpy.core.BaseInteraction.pair_interaction" title="oxpy.core.BaseInteraction.pair_interaction"><code class="xref py py-meth docutils literal notranslate"><span class="pre">pair_interaction()</span></code></a> for additional details).</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>r</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.26)"><em>numpy.ndarray</em></a>) – The distance vector to be stored.</p>
+<dd class="field-odd"><p><strong>r</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.0)"><em>numpy.ndarray</em></a>) – The distance vector to be stored.</p>
 </dd>
 </dl>
 </dd></dl>
@@ -1005,7 +1005,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd class="field-even"><p>The absolute (unwrapped) position of the given particle.</p>
 </dd>
 <dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.26)">numpy.ndarray</a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.0)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -1042,7 +1042,7 @@ <h1>The core module<a class="headerlink" href="#the-core-module" title="Permalin
 <dd class="field-even"><p>The distance vector connecting <cite>p</cite> to <cite>q</cite>.</p>
 </dd>
 <dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.26)">numpy.ndarray</a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.0)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>

diff --git a/oxpy/modules/core/forces.html b/oxpy/modules/core/forces.html
@@ -203,7 +203,7 @@ <h1>The core.forces module<a class="headerlink" href="#the-core-forces-module" t
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>step</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – The current time step.</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.26)"><em>numpy.ndarray</em></a>) – The position where the force should be computed.</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.0)"><em>numpy.ndarray</em></a>) – The position where the force should be computed.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
@@ -241,14 +241,14 @@ <h1>The core.forces module<a class="headerlink" href="#the-core-forces-module" t
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>step</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – The current time step.</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.26)"><em>numpy.ndarray</em></a>) – The position where the force should be computed.</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.0)"><em>numpy.ndarray</em></a>) – The position where the force should be computed.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
 <dd class="field-even"><p>The computed force vector.</p>
 </dd>
 <dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.26)">numpy.ndarray</a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.0)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>

diff --git a/searchindex.js b/searchindex.js