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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="scatter-gather-operations">
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<h1><span class="section-number">2.3.9. </span>Scatter/gather operations<a class="headerlink" href="#scatter-gather-operations" title="Link to this heading"></a></h1>
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<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">data</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">gather_atoms</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">)</span> <span class="c1"># return per-atom property of all atoms gathered into data, ordered by atom ID</span>
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<span class="c1"># name = "x", "charge", "type", etc</span>
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<span class="n">data</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">gather_atoms_concat</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">)</span> <span class="c1"># ditto, but concatenated atom values from each proc (unordered)</span>
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<span class="n">data</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">gather_atoms_subset</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">,</span><span class="n">ndata</span><span class="p">,</span><span class="n">ids</span><span class="p">)</span> <span class="c1"># ditto, but for subset of Ndata atoms with IDs</span>
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<span class="n">lmp</span><span class="o">.</span><span class="n">scatter_atoms</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> <span class="c1"># scatter per-atom property to all atoms from data, ordered by atom ID</span>
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<span class="c1"># name = "x", "charge", "type", etc</span>
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<span class="c1"># count = # of per-atom values, 1 or 3, etc</span>
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<span class="n">lmp</span><span class="o">.</span><span class="n">scatter_atoms_subset</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">,</span><span class="n">ndata</span><span class="p">,</span><span class="n">ids</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> <span class="c1"># ditto, but for subset of Ndata atoms with IDs</span>
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</pre></div>
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</div>
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<p>The gather methods collect peratom info of the requested type (atom
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coords, atom types, forces, etc) from all processors, and returns the
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same vector of values to each calling processor. The scatter
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functions do the inverse. They distribute a vector of peratom values,
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passed by all calling processors, to individual atoms, which may be
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owned by different processors.</p>
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<p>Note that the data returned by the gather methods,
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e.g. <code class="xref py py-meth docutils literal notranslate"><span class="pre">gather_atoms("x")</span></code>, is
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different from the data structure returned by
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<a class="reference internal" href="Python_module.html#lammps.lammps.extract_atom" title="lammps.lammps.extract_atom"><code class="xref py py-meth docutils literal notranslate"><span class="pre">extract_atom("x")</span></code></a> in four ways.
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(1) <code class="code docutils literal notranslate"><span class="pre">gather_atoms()</span></code> returns a vector which you index as x[i];
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<code class="code docutils literal notranslate"><span class="pre">extract_atom()</span></code> returns an array which you index as x[i][j].
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(2) <code class="code docutils literal notranslate"><span class="pre">gather_atoms()</span></code> orders the atoms by atom ID while
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<code class="code docutils literal notranslate"><span class="pre">extract_atom()</span></code> does not. (3) <code class="code docutils literal notranslate"><span class="pre">gather_atoms()</span></code> returns
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a list of all atoms in the simulation; <code class="code docutils literal notranslate"><span class="pre">extract_atoms()</span></code> returns just
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the atoms local to each processor. (4) Finally, the <code class="code docutils literal notranslate"><span class="pre">gather_atoms()</span></code>
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data structure is a copy of the atom coords stored internally in
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LAMMPS, whereas <code class="code docutils literal notranslate"><span class="pre">extract_atom()</span></code> returns an array that effectively
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points directly to the internal data. This means you can change
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values inside LAMMPS from Python by assigning a new values to the
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<code class="code docutils literal notranslate"><span class="pre">extract_atom()</span></code> array. To do this with the <code class="code docutils literal notranslate"><span class="pre">gather_atoms()</span></code> vector, you
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need to change values in the vector, then invoke the
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<code class="xref py py-meth docutils literal notranslate"><span class="pre">scatter_atoms("x")</span></code> method.</p>
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<p>For the scatter methods, the array of coordinates passed to must be a
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ctypes vector of ints or doubles, allocated and initialized something
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like this:</p>
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<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span><span class="w"> </span><span class="nn">ctypes</span><span class="w"> </span><span class="kn">import</span> <span class="n">c_double</span>
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<span class="n">natoms</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_natoms</span><span class="p">()</span>
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<span class="n">n3</span> <span class="o">=</span> <span class="mi">3</span><span class="o">*</span><span class="n">natoms</span>
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<span class="n">x</span> <span class="o">=</span> <span class="p">(</span><span class="n">n3</span><span class="o">*</span><span class="n">c_double</span><span class="p">)()</span>
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<span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span>
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<span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">y</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span>
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<span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span>
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<span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">2</span>
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<span class="o">...</span>
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<span class="n">x</span><span class="p">[</span><span class="n">n3</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="n">natoms</span>
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<span class="n">lmp</span><span class="o">.</span><span class="n">scatter_atoms</span><span class="p">(</span><span class="s2">"x"</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span>
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</pre></div>
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</div>
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<p>The coordinates can also be provided as arguments to the initializer of x:</p>
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<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span><span class="w"> </span><span class="nn">ctypes</span><span class="w"> </span><span class="kn">import</span> <span class="n">c_double</span>
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<span class="n">natoms</span> <span class="o">=</span> <span class="mi">2</span>
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<span class="n">n3</span> <span class="o">=</span> <span class="mi">3</span><span class="o">*</span><span class="n">natoms</span>
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<span class="c1"># init in constructor</span>
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<span class="n">x</span> <span class="o">=</span> <span class="p">(</span><span class="n">n3</span><span class="o">*</span><span class="n">c_double</span><span class="p">)(</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">)</span>
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<span class="n">lmp</span><span class="o">.</span><span class="n">scatter_atoms</span><span class="p">(</span><span class="s2">"x"</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span>
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<span class="c1"># or using a list</span>
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<span class="n">coords</span> <span class="o">=</span> <span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">2.0</span><span class="p">,</span> <span class="mf">3.0</span><span class="p">,</span> <span class="o">-</span><span class="mf">3.0</span><span class="p">,</span> <span class="o">-</span><span class="mf">2.0</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.0</span><span class="p">]</span>
|
|
<span class="n">x</span> <span class="o">=</span> <span class="p">(</span><span class="n">c_double</span><span class="o">*</span><span class="nb">len</span><span class="p">(</span><span class="n">coords</span><span class="p">))(</span><span class="o">*</span><span class="n">coords</span><span class="p">)</span>
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</pre></div>
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</div>
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<p>Alternatively, you can just change values in the vector returned by
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the gather methods, since they are also ctypes vectors.</p>
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