deploy: 6fda63e

_modules/arc/species/converter.html

@@ -1544,12 +1544,14 @@ <h1>Source code for arc.species.converter</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span>
     <span class="n">xyz</span> <span class="o">=</span> <span class="n">check_xyz_dict</span><span class="p">(</span><span class="n">xyz</span><span class="p">)</span>
 
-    <span class="k">if</span> <span class="n">xyz</span><span class="p">[</span><span class="s1">&#39;symbols&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="p">(</span><span class="s1">&#39;O&#39;</span><span class="p">,</span> <span class="s1">&#39;O&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="n">multiplicity</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
-        <span class="n">coords</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">xyz</span><span class="p">[</span><span class="s1">&#39;coords&#39;</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
-        <span class="n">vector</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="n">coords</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-        <span class="k">if</span> <span class="nb">float</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">vector</span><span class="p">,</span> <span class="n">vector</span><span class="p">)</span> <span class="o">**</span> <span class="mf">0.5</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mf">1.4</span><span class="p">:</span>
-            <span class="c1"># Special case for O2 triplet</span>
-            <span class="k">return</span> <span class="n">Molecule</span><span class="p">(</span><span class="n">smiles</span><span class="o">=</span><span class="s1">&#39;[O][O]&#39;</span><span class="p">),</span> <span class="n">Molecule</span><span class="p">(</span><span class="n">smiles</span><span class="o">=</span><span class="s1">&#39;[O][O]&#39;</span><span class="p">)</span>
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">xyz</span><span class="p">[</span><span class="s1">&#39;symbols&#39;</span><span class="p">])</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
+        <span class="k">for</span> <span class="n">element</span><span class="p">,</span> <span class="n">bond_length</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">([</span><span class="s1">&#39;O&#39;</span><span class="p">,</span> <span class="s1">&#39;S&#39;</span><span class="p">],</span> <span class="p">[</span><span class="mf">1.4</span><span class="p">,</span> <span class="mf">2.1</span><span class="p">]):</span>
+            <span class="k">if</span> <span class="n">xyz</span><span class="p">[</span><span class="s1">&#39;symbols&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="p">(</span><span class="n">element</span><span class="p">,</span> <span class="n">element</span><span class="p">)</span> <span class="ow">and</span> <span class="n">multiplicity</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
+                <span class="n">coords</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">xyz</span><span class="p">[</span><span class="s1">&#39;coords&#39;</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
+                <span class="n">vector</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="n">coords</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="k">if</span> <span class="nb">float</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">vector</span><span class="p">,</span> <span class="n">vector</span><span class="p">)</span> <span class="o">**</span> <span class="mf">0.5</span><span class="p">)</span> <span class="o">&lt;</span> <span class="n">bond_length</span><span class="p">:</span>
+                    <span class="c1"># Special case for O2 and S2 triplet</span>
+                    <span class="k">return</span> <span class="n">Molecule</span><span class="p">(</span><span class="n">smiles</span><span class="o">=</span><span class="sa">f</span><span class="s1">&#39;[</span><span class="si">{</span><span class="n">element</span><span class="si">}</span><span class="s1">][</span><span class="si">{</span><span class="n">element</span><span class="si">}</span><span class="s1">]&#39;</span><span class="p">),</span> <span class="n">Molecule</span><span class="p">(</span><span class="n">smiles</span><span class="o">=</span><span class="sa">f</span><span class="s1">&#39;[</span><span class="si">{</span><span class="n">element</span><span class="si">}</span><span class="s1">][</span><span class="si">{</span><span class="n">element</span><span class="si">}</span><span class="s1">]&#39;</span><span class="p">)</span>
 
     <span class="c1"># 1. Generate a molecule with no bond order information with atoms ordered as in xyz.</span>
     <span class="n">mol_graph</span> <span class="o">=</span> <span class="n">MolGraph</span><span class="p">(</span><span class="n">symbols</span><span class="o">=</span><span class="n">xyz</span><span class="p">[</span><span class="s1">&#39;symbols&#39;</span><span class="p">],</span> <span class="n">coords</span><span class="o">=</span><span class="n">xyz</span><span class="p">[</span><span class="s1">&#39;coords&#39;</span><span class="p">])</span>

_modules/arc/species/species.html

@@ -1747,11 +1747,6 @@ <h1>Source code for arc.species.species</h1><div class="highlight"><pre>
         <span class="k">if</span> <span class="n">xyz</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">return</span> <span class="kc">None</span>
 
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">xyz</span><span class="p">[</span><span class="s1">&#39;symbols&#39;</span><span class="p">])</span> <span class="o">==</span> <span class="mi">2</span> <span class="ow">and</span> <span class="n">xyz</span><span class="p">[</span><span class="s1">&#39;symbols&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="n">xyz</span><span class="p">[</span><span class="s1">&#39;symbols&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> \
-                <span class="ow">and</span> <span class="n">xyz</span><span class="p">[</span><span class="s1">&#39;symbols&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;O&#39;</span><span class="p">,</span> <span class="s1">&#39;S&#39;</span><span class="p">]</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">multiplicity</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
-            <span class="c1"># Hard-coded for triplet O2 and S2: Don&#39;t perceive mol.</span>
-            <span class="k">return</span> <span class="kc">None</span>
-
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">mol</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mol</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">xyz</span><span class="p">[</span><span class="s1">&#39;symbols&#39;</span><span class="p">]):</span>
                 <span class="k">raise</span> <span class="n">SpeciesError</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;The number of atoms in the molecule and in the coordinates of </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">label</span><span class="si">}</span><span class="s1"> is different.&#39;</span>