deploy: dfe93dd

_modules/arc/main.html

@@ -318,6 +318,8 @@ <h1>Source code for arc.main</h1><div class="highlight"><pre>
 <span class="sd">        trsh_ess_jobs (bool, optional): Whether to attempt troubleshooting failed ESS jobs. Default is ``True``.</span>
 <span class="sd">        output (dict, optional): Output dictionary with status and final QM file paths for all species.</span>
 <span class="sd">                                 Only used for restarting.</span>
+<span class="sd">        output_multi_spc (dict, optional): Output dictionary with status and final QM file paths for the multi species. </span>
+<span class="sd">                                           Only used for restarting.</span>
 <span class="sd">        running_jobs (dict, optional): A dictionary of jobs submitted in a precious ARC instance, used for restarting.</span>
 <span class="sd">        ts_adapters (list, optional): Entries represent different TS adapters.</span>
 <span class="sd">        report_e_elect (bool, optional): Whether to report electronic energy. Default is ``False``.</span>
@@ -344,6 +346,8 @@ <h1>Source code for arc.main</h1><div class="highlight"><pre>
 <span class="sd">            Job types not defined in adaptive levels will have non-adaptive (regular) levels.</span>
 <span class="sd">        output (dict): Output dictionary with status and final QM file paths for all species. Only used for restarting,</span>
 <span class="sd">                       the actual object used is in the Scheduler class.</span>
+<span class="sd">        output_multi_spc (dict): Output dictionary with status and final QM file paths for the multi species. </span>
+<span class="sd">                                 Only used for restarting, the actual object used is in the Scheduler class.</span>
 <span class="sd">        bac_type (str): The bond additivity correction type. &#39;p&#39; for Petersson- or &#39;m&#39; for Melius-type BAC.</span>
 <span class="sd">                        ``None`` to not use BAC.</span>
 <span class="sd">        arkane_level_of_theory (Level): The Arkane level of theory to use for AEC and BAC.</span>
@@ -422,6 +426,7 @@ <h1>Source code for arc.main</h1><div class="highlight"><pre>
                  <span class="n">opt_level</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">Level</span><span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
                  <span class="n">orbitals_level</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">Level</span><span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
                  <span class="n">output</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">dict</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+                 <span class="n">output_multi_spc</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">dict</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
                  <span class="n">project</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
                  <span class="n">project_directory</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
                  <span class="n">reactions</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">List</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="n">ARCReaction</span><span class="p">,</span> <span class="n">Reaction</span><span class="p">]]]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
@@ -455,6 +460,7 @@ <h1>Source code for arc.main</h1><div class="highlight"><pre>
         <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">project_directory</span><span class="p">):</span>
             <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">project_directory</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">=</span> <span class="n">output</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">output_multi_spc</span> <span class="o">=</span> <span class="n">output_multi_spc</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">standardize_output_paths</span><span class="p">()</span>  <span class="c1"># depends on self.project_directory</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">running_jobs</span> <span class="o">=</span> <span class="n">running_jobs</span> <span class="ow">or</span> <span class="nb">dict</span><span class="p">()</span>
         <span class="k">for</span> <span class="n">jobs</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">running_jobs</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
@@ -679,6 +685,7 @@ <h1>Source code for arc.main</h1><div class="highlight"><pre>
             <span class="n">restart_dict</span><span class="p">[</span><span class="s1">&#39;orbitals_level&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">orbitals_level</span><span class="o">.</span><span class="n">as_dict</span><span class="p">()</span> \
                 <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">orbitals_level</span><span class="p">,</span> <span class="p">(</span><span class="nb">dict</span><span class="p">,</span> <span class="nb">str</span><span class="p">))</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">orbitals_level</span>
         <span class="n">restart_dict</span><span class="p">[</span><span class="s1">&#39;output&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">output</span>
+        <span class="n">restart_dict</span><span class="p">[</span><span class="s1">&#39;output_multi_spc&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">output_multi_spc</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">output_multi_spc</span> <span class="k">else</span> <span class="nb">dict</span><span class="p">()</span>
         <span class="n">restart_dict</span><span class="p">[</span><span class="s1">&#39;project&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">project</span>
         <span class="n">restart_dict</span><span class="p">[</span><span class="s1">&#39;reactions&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">rxn</span><span class="o">.</span><span class="n">as_dict</span><span class="p">()</span> <span class="k">for</span> <span class="n">rxn</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">reactions</span><span class="p">]</span>
         <span class="n">restart_dict</span><span class="p">[</span><span class="s1">&#39;running_jobs&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">running_jobs</span>

_modules/arc/scheduler.html

@@ -1347,18 +1347,22 @@ <h1>Source code for arc.scheduler</h1><div class="highlight"><pre>
                                                <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">species_dict</span><span class="p">[</span><span class="n">label</span><span class="p">]</span><span class="o">.</span><span class="n">get_xyz</span><span class="p">(</span><span class="n">generate</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">species_dict</span><span class="p">[</span><span class="n">label</span><span class="p">]</span><span class="o">.</span><span class="n">initial_xyz</span> <span class="ow">is</span> <span class="kc">None</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;Cannot execute opt job for </span><span class="si">{</span><span class="n">label</span><span class="si">}</span><span class="s1"> without xyz (got None for Species.initial_xyz)&#39;</span><span class="p">)</span>
+        <span class="n">label_single_spc</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="n">key</span> <span class="o">=</span> <span class="kc">None</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">species_dict</span><span class="p">[</span><span class="n">label</span><span class="p">]</span><span class="o">.</span><span class="n">multi_species</span><span class="p">:</span>
             <span class="n">key</span> <span class="o">=</span> <span class="s1">&#39;fine&#39;</span> <span class="k">if</span> <span class="n">fine</span> <span class="k">else</span> <span class="s1">&#39;opt&#39;</span>
             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">output_multi_spc</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">species_dict</span><span class="p">[</span><span class="n">label</span><span class="p">]</span><span class="o">.</span><span class="n">multi_species</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="kc">False</span><span class="p">):</span>
                 <span class="k">return</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">output_multi_spc</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">species_dict</span><span class="p">[</span><span class="n">label</span><span class="p">]</span><span class="o">.</span><span class="n">multi_species</span><span class="p">][</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
+            <span class="n">label_single_spc</span> <span class="o">=</span> <span class="n">label</span>
             <span class="n">label</span> <span class="o">=</span> <span class="p">[</span><span class="n">species</span><span class="o">.</span><span class="n">label</span> <span class="k">for</span> <span class="n">species</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">species_list</span>
                      <span class="k">if</span> <span class="n">species</span><span class="o">.</span><span class="n">multi_species</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">species_dict</span><span class="p">[</span><span class="n">label</span><span class="p">]</span><span class="o">.</span><span class="n">multi_species</span><span class="p">]</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">run_job</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="n">label</span><span class="p">,</span> 
                      <span class="n">xyz</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">species_dict</span><span class="p">[</span><span class="n">label</span><span class="p">]</span><span class="o">.</span><span class="n">initial_xyz</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">label</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
                      <span class="n">level_of_theory</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">opt_level</span><span class="p">,</span>
                      <span class="n">job_type</span><span class="o">=</span><span class="s1">&#39;opt&#39;</span><span class="p">,</span> 
-                     <span class="n">fine</span><span class="o">=</span><span class="n">fine</span><span class="p">)</span></div>
+                     <span class="n">fine</span><span class="o">=</span><span class="n">fine</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">label_single_spc</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">key</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">output_multi_spc</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">species_dict</span><span class="p">[</span><span class="n">label_single_spc</span><span class="p">]</span><span class="o">.</span><span class="n">multi_species</span><span class="p">][</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span></div>
 
 <div class="viewcode-block" id="Scheduler.run_composite_job"><a class="viewcode-back" href="../../api/scheduler.html#arc.scheduler.Scheduler.run_composite_job">[docs]</a>    <span class="k">def</span> <span class="nf">run_composite_job</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>

genindex.html

@@ -1429,8 +1429,12 @@ <h2 id="O">O</h2>
         <li><a href="api/scheduler.html#arc.scheduler.Scheduler.output">(arc.scheduler.Scheduler attribute)</a>
 </li>
       </ul></li>
-      <li><a href="api/scheduler.html#arc.scheduler.Scheduler.output_multi_spc">output_multi_spc (arc.scheduler.Scheduler attribute)</a>
+      <li><a href="api/main.html#arc.main.ARC.output_multi_spc">output_multi_spc (arc.main.ARC attribute)</a>
+
+      <ul>
+        <li><a href="api/scheduler.html#arc.scheduler.Scheduler.output_multi_spc">(arc.scheduler.Scheduler attribute)</a>
 </li>
+      </ul></li>
   </ul></td>
 </tr></table>