lass="p">(</span><span class="bp">self</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;A matrix where the entry A[i, j, :] is the vector</span>
<span class="sd">        self.cartesian_pos[j] - self.cartesian_pos[i].</span>

<span class="sd">        For periodic systems the distance of an atom from itself is the</span>
<span class="sd">        smallest displacement of an atom from one of it&#39;s periodic copies, and</span>
<span class="sd">        the distance of two different ato