Update documentation

_sources/observables.md.txt

@@ -171,6 +171,13 @@ Print the energy associated to all (or a subset of) the external forces acting o
 * `type = force_energy`: the observable type.
 * `[print_group = <string>]`: limit the energy computation to the forces belonging to a specific group of forces. This can be set by adding a `group_name` option to the [desired external forces](forces.md#common-options). If not set, all external forces will be considered.
 
+## External force acting on particle(s)
+
+Print the force vector acting on all (or a subset of all) particles due to external forces. This observable supports the `update_every` option.
+
+* `type = external_force`: the observable type.
+* `particles`: list of comma-separated particle indexes whose force vectors should be printed.
+
 ## Configuration
 
 Print an [oxDNA configuration](configurations.md#configuration-file).

index.html

@@ -185,6 +185,7 @@ <h1>oxDNA<a class="headerlink" href="#oxdna" title="Permalink to this heading">
 <li class="toctree-l2"><a class="reference internal" href="observables.html#interaction-energy-between-pairs-of-particles">Interaction energy between pairs of particles</a></li>
 <li class="toctree-l2"><a class="reference internal" href="observables.html#stretched-bonds">Stretched bonds</a></li>
 <li class="toctree-l2"><a class="reference internal" href="observables.html#energy-associated-to-the-external-forces">Energy associated to the external forces</a></li>
+<li class="toctree-l2"><a class="reference internal" href="observables.html#external-force-acting-on-particle-s">External force acting on particle(s)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="observables.html#configuration">Configuration</a></li>
 <li class="toctree-l2"><a class="reference internal" href="observables.html#pressure">Pressure</a></li>
 <li class="toctree-l2"><a class="reference internal" href="observables.html#stress-autocorrelation">Stress autocorrelation</a></li>

oat/cli.html

@@ -460,9 +460,10 @@ <h3>Named Arguments<a class="headerlink" href="#Named Arguments" title="Permalin
 <h2>Distance<a class="headerlink" href="#distance" title="Permalink to this heading"></a></h2>
 <p><p>Finds the ensemble of distances between any two particles in the system</p>
 </p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">oat</span> <span class="n">distance</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">i</span> <span class="nb">input</span> <span class="p">[</span><span class="nb">input</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">-</span><span class="n">o</span> <span class="n">output_file</span><span class="p">]</span>
- <span class="p">[</span><span class="o">-</span><span class="n">f</span> <span class="o">&lt;</span><span class="n">histogram</span><span class="o">/</span><span class="n">trajectory</span><span class="o">/</span><span class="n">both</span><span class="o">&gt;</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">d</span> <span class="n">data_file</span><span class="p">]</span>
- <span class="p">[</span><span class="o">-</span><span class="n">n</span> <span class="n">names</span> <span class="p">[</span><span class="n">names</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">-</span><span class="n">p</span> <span class="n">num_cpus</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">c</span><span class="p">]</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">oat</span> <span class="n">distance</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span>
+ <span class="p">[</span><span class="o">-</span><span class="n">i</span> <span class="nb">input</span> <span class="n">p1</span> <span class="n">p2</span> <span class="n">p1</span> <span class="n">p2</span><span class="o">...</span><span class="p">)</span> <span class="p">[</span><span class="nb">input</span> <span class="n">p1</span> <span class="n">p2</span> <span class="p">(</span><span class="n">p1</span> <span class="n">p2</span><span class="o">...</span> <span class="o">...</span><span class="p">]]</span>
+ <span class="p">[</span><span class="o">-</span><span class="n">o</span> <span class="n">output_file</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">f</span> <span class="o">&lt;</span><span class="n">histogram</span><span class="o">/</span><span class="n">trajectory</span><span class="o">/</span><span class="n">both</span><span class="o">&gt;</span><span class="p">]</span>
+ <span class="p">[</span><span class="o">-</span><span class="n">d</span> <span class="n">data_file</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">n</span> <span class="n">names</span> <span class="p">[</span><span class="n">names</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">-</span><span class="n">p</span> <span class="n">num_cpus</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">c</span><span class="p">]</span>
 </pre></div>
 </div>
 <section id="Named Arguments">
@@ -973,7 +974,7 @@ <h3>Named Arguments<a class="headerlink" href="#Named Arguments" title="Permalin
 <h2>Subset trajectory<a class="headerlink" href="#subset-trajectory" title="Permalink to this heading"></a></h2>
 <p><p>Extracts parts of a structure into separate trajectories</p>
 </p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">oat</span> <span class="n">subset_trajectory</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">i</span> <span class="n">index</span> <span class="n">index</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">p</span> <span class="n">num_cpus</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">f</span><span class="p">]</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">oat</span> <span class="n">subset_trajectory</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">i</span> <span class="n">index</span> <span class="n">outfile</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">p</span> <span class="n">num_cpus</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">f</span><span class="p">]</span>
  <span class="n">trajectory</span> <span class="n">topology</span>
 </pre></div>
 </div>
@@ -1008,7 +1009,9 @@ <h3>Named Arguments<a class="headerlink" href="#Named Arguments" title="Permalin
 <h2>Superimpose<a class="headerlink" href="#superimpose" title="Permalink to this heading"></a></h2>
 <p><p>superimposes one or more structures sharing a topology to a reference structure</p>
 </p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">oat</span> <span class="n">superimpose</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">i</span> <span class="n">index_file</span><span class="p">]</span> <span class="n">reference</span> <span class="n">victims</span> <span class="p">[</span><span class="n">victims</span> <span class="o">...</span><span class="p">]</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">oat</span> <span class="n">superimpose</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">i</span> <span class="n">index_file</span><span class="p">]</span>
+ <span class="p">[</span><span class="o">-</span><span class="n">o</span> <span class="n">output_names</span> <span class="p">[</span><span class="n">output_names</span> <span class="o">...</span><span class="p">]]</span>
+ <span class="n">reference</span> <span class="n">victims</span> <span class="p">[</span><span class="n">victims</span> <span class="o">...</span><span class="p">]</span>
 </pre></div>
 </div>
 <section id="Positional Arguments">
@@ -1028,6 +1031,9 @@ <h3>Named Arguments<a class="headerlink" href="#Named Arguments" title="Permalin
 <dt><kbd>-i</kbd></dt>
 <dd><p>Align to only a subset of particles from a space-separated list in the provided file</p>
 </dd>
+<dt><kbd>-o</kbd></dt>
+<dd><p>The names of the output files (defaults to inputname_a.dat)</p>
+</dd>
 </dl>
 </section>
 </section>

oat/utils.html

@@ -778,7 +778,7 @@ <h2>Rye reader<a class="headerlink" href="#rye-reader" title="Permalink to this
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>traj_info</strong> (<a class="reference internal" href="#oxDNA_analysis_tools.UTILS.data_structures.TrajInfo" title="oxDNA_analysis_tools.UTILS.data_structures.TrajInfo"><em>TrajInfo</em></a>) – The trajectory info</p></li>
 <li><p><strong>top_info</strong> (<a class="reference internal" href="#oxDNA_analysis_tools.UTILS.data_structures.TopInfo" title="oxDNA_analysis_tools.UTILS.data_structures.TopInfo"><em>TopInfo</em></a>) – The topology info</p></li>
-<li><p><strong>ntopart</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 number of confs to read at a time</p></li>
+<li><p><strong>chunk_size</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 number of confs to read at a time. Defaults to config.get_chunk_size()</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>

observables.html

@@ -70,6 +70,7 @@
 <li class="toctree-l2"><a class="reference internal" href="#interaction-energy-between-pairs-of-particles">Interaction energy between pairs of particles</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#stretched-bonds">Stretched bonds</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#energy-associated-to-the-external-forces">Energy associated to the external forces</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#external-force-acting-on-particle-s">External force acting on particle(s)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#configuration">Configuration</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#pressure">Pressure</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#stress-autocorrelation">Stress autocorrelation</a></li>
@@ -296,6 +297,14 @@ <h2>Energy associated to the external forces<a class="headerlink" href="#energy-
 <li><p><code class="docutils literal notranslate"><span class="pre">[print_group</span> <span class="pre">=</span> <span class="pre">&lt;string&gt;]</span></code>: limit the energy computation to the forces belonging to a specific group of forces. This can be set by adding a <code class="docutils literal notranslate"><span class="pre">group_name</span></code> option to the <a class="reference internal" href="forces.html#common-options"><span class="std std-ref">desired external forces</span></a>. If not set, all external forces will be considered.</p></li>
 </ul>
 </section>
+<section id="external-force-acting-on-particle-s">
+<h2>External force acting on particle(s)<a class="headerlink" href="#external-force-acting-on-particle-s" title="Permalink to this heading"></a></h2>
+<p>Print the force vector acting on all (or a subset of all) particles due to external forces. This observable supports the <code class="docutils literal notranslate"><span class="pre">update_every</span></code> option.</p>
+<ul class="simple">
+<li><p><code class="docutils literal notranslate"><span class="pre">type</span> <span class="pre">=</span> <span class="pre">external_force</span></code>: the observable type.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">particles</span></code>: list of comma-separated particle indexes whose force vectors should be printed.</p></li>
+</ul>
+</section>
 <section id="configuration">
 <h2>Configuration<a class="headerlink" href="#configuration" title="Permalink to this heading"></a></h2>
 <p>Print an <a class="reference internal" href="configurations.html#configuration-file"><span class="std std-ref">oxDNA configuration</span></a>.</p>