Automated documentation rebuild

Author: github-actions

_sources/users/rmg/input.rst.txt

@@ -879,6 +879,39 @@ to turn off pressure dependence for all molecules larger than the given number
 of atoms (16 in the above example).
 
 
+Completed Pressure-Dependent Networks
+--------------------------------------
+
+Sometimes you have a pressure-dependent network that has been studied in great 
+detail and included in a seed mechanism or reaction library (such as CH2O2), 
+and you don't want RMG to add additional reactions to that network. Adding 
+RMG's estimates to a thoroughly studied network will likely make your model 
+worse, as the original authors would have included any important reactions.
+
+You can specify that certain networks should not be expanded further using the
+``completedNetworks`` parameter within the ``pressureDependence()`` block. This 
+parameter takes a list of chemical formulas identifying the networks that should 
+be considered complete. For example::
+
+    pressureDependence(
+        method='modified strong collision',
+        maximumGrainSize=(0.5,'kcal/mol'),
+        minimumNumberOfGrains=250,
+        temperatures=(300,2000,'K',8),
+        pressures=(0.01,100,'bar',5),
+        interpolation=('Chebyshev', 6, 4),
+        maximumAtoms=16,
+        completedNetworks=['CH2O2'],
+    )
+
+Multiple networks can be specified in the list::
+
+    completedNetworks=['CH2O2', 'C2H6'],
+
+When a network is marked as completed, RMG will not add any new reactions to it,
+though reactions already present in seed mechanisms will still be used.
+
+
 .. _uncertaintyanalysis:
 
 Uncertainty Analysis

genindex.html

@@ -116,6 +116,8 @@ <h2 id="A">A</h2>
         <li><a href="reference/molecule/molecule.html#rmgpy.molecule.Molecule.add_bond">(rmgpy.molecule.Molecule method)</a>
 </li>
       </ul></li>
+      <li><a href="reference/rmg/coreedgereactionmodel.html#rmgpy.rmg.model.CoreEdgeReactionModel.add_completed_pdep_network">add_completed_pdep_network() (rmgpy.rmg.model.CoreEdgeReactionModel method)</a>
+</li>
       <li><a href="reference/molecule/graph.html#rmgpy.molecule.graph.Graph.add_edge">add_edge() (rmgpy.molecule.graph.Graph method)</a>
 
       <ul>
@@ -245,11 +247,11 @@ <h2 id="A">A</h2>
 </li>
       </ul></li>
       <li><a href="reference/data/reactionrecipe.html#rmgpy.data.kinetics.ReactionRecipe.apply_forward">apply_forward() (rmgpy.data.kinetics.ReactionRecipe method)</a>
-</li>
-      <li><a href="reference/pdep/reaction.html#rmgpy.pdep.reaction.apply_inverse_laplace_transform_method">apply_inverse_laplace_transform_method() (in module rmgpy.pdep.reaction)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="reference/pdep/reaction.html#rmgpy.pdep.reaction.apply_inverse_laplace_transform_method">apply_inverse_laplace_transform_method() (in module rmgpy.pdep.reaction)</a>
+</li>
       <li><a href="reference/rmg/coreedgereactionmodel.html#rmgpy.rmg.model.CoreEdgeReactionModel.apply_kinetics_to_reaction">apply_kinetics_to_reaction() (rmgpy.rmg.model.CoreEdgeReactionModel method)</a>
 </li>
       <li><a href="reference/pdep/methods.html#rmgpy.pdep.msc.apply_modified_strong_collision_method">apply_modified_strong_collision_method() (in module rmgpy.pdep.msc)</a>

objects.inv

@@ -102,6 +102,12 @@ <h1>rmgpy.rmg.model.CoreEdgeReactionModel<a class="headerlink" href="#rmgpy-rmg-
 </tr>
 </tbody>
 </table>
+<dl class="py method">
+<dt class="sig sig-object py" id="rmgpy.rmg.model.CoreEdgeReactionModel.add_completed_pdep_network">
+<span class="sig-name descname"><span class="pre">add_completed_pdep_network</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">formula</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#rmgpy.rmg.model.CoreEdgeReactionModel.add_completed_pdep_network" title="Permalink to this definition">¶</a></dt>
+<dd><p>Add a completed pressure-dependent network formula to the set.</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="rmgpy.rmg.model.CoreEdgeReactionModel.add_new_surface_objects">
 <span class="sig-name descname"><span class="pre">add_new_surface_objects</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">obj</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_surface_species</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_surface_reactions</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reaction_system</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#rmgpy.rmg.model.CoreEdgeReactionModel.add_new_surface_objects" title="Permalink to this definition">¶</a></dt>
@@ -516,6 +522,7 @@ <h3><a href="../../contents.html">Table of Contents</a></h3>
     <ul>
 <li><a class="reference internal" href="#">rmgpy.rmg.model.CoreEdgeReactionModel</a><ul>
 <li><a class="reference internal" href="#rmgpy.rmg.model.CoreEdgeReactionModel"><code class="docutils literal notranslate"><span class="pre">CoreEdgeReactionModel</span></code></a><ul>
+<li><a class="reference internal" href="#rmgpy.rmg.model.CoreEdgeReactionModel.add_completed_pdep_network"><code class="docutils literal notranslate"><span class="pre">CoreEdgeReactionModel.add_completed_pdep_network()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.rmg.model.CoreEdgeReactionModel.add_new_surface_objects"><code class="docutils literal notranslate"><span class="pre">CoreEdgeReactionModel.add_new_surface_objects()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.rmg.model.CoreEdgeReactionModel.add_reaction_library_to_edge"><code class="docutils literal notranslate"><span class="pre">CoreEdgeReactionModel.add_reaction_library_to_edge()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.rmg.model.CoreEdgeReactionModel.add_reaction_library_to_output"><code class="docutils literal notranslate"><span class="pre">CoreEdgeReactionModel.add_reaction_library_to_output()</span></code></a></li>

reference/rmg/coreedgereactionmodel.html

@@ -486,6 +486,11 @@ <h2><span class="section-number">5.3. </span>Commented input file<a class="heade
     <span class="c1"># turns off pressure dependence for molecules with number of atoms greater than the number specified below</span>
     <span class="c1"># this is due to faster internal rate of energy transfer for larger molecules</span>
     <span class="n">maximumAtoms</span><span class="o">=</span><span class="mi">15</span><span class="p">,</span>
+    <span class="c1"># (optional) list of networks that have been thoroughly studied and should not be expanded</span>
+    <span class="c1"># by RMG. This is useful when you have a detailed mechanism for a specific network (e.g., from</span>
+    <span class="c1"># a seed mechanism or reaction library) and don&#39;t want RMG to add its own estimates which may</span>
+    <span class="c1"># make the model worse. Specify networks by their chemical formula, e.g., [&#39;CH2O2&#39;, &#39;C2H6&#39;]</span>
+    <span class="c1"># completedNetworks=[&#39;CH2O2&#39;],</span>
 <span class="p">)</span>
 
 <span class="c1"># optional block adds constraints on what RMG can output.</span>

searchindex.js

@@ -846,6 +846,36 @@ <h3><span class="section-number">4.10.5. </span>Maximum size of adduct for which
 <p>to turn off pressure dependence for all molecules larger than the given number
 of atoms (16 in the above example).</p>
 </section>
+<section id="completed-pressure-dependent-networks">
+<h3><span class="section-number">4.10.6. </span>Completed Pressure-Dependent Networks<a class="headerlink" href="#completed-pressure-dependent-networks" title="Permalink to this heading">¶</a></h3>
+<p>Sometimes you have a pressure-dependent network that has been studied in great
+detail and included in a seed mechanism or reaction library (such as CH2O2),
+and you don’t want RMG to add additional reactions to that network. Adding
+RMG’s estimates to a thoroughly studied network will likely make your model
+worse, as the original authors would have included any important reactions.</p>
+<p>You can specify that certain networks should not be expanded further using the
+<code class="docutils literal notranslate"><span class="pre">completedNetworks</span></code> parameter within the <code class="docutils literal notranslate"><span class="pre">pressureDependence()</span></code> block. This
+parameter takes a list of chemical formulas identifying the networks that should
+be considered complete. For example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pressureDependence</span><span class="p">(</span>
+    <span class="n">method</span><span class="o">=</span><span class="s1">&#39;modified strong collision&#39;</span><span class="p">,</span>
+    <span class="n">maximumGrainSize</span><span class="o">=</span><span class="p">(</span><span class="mf">0.5</span><span class="p">,</span><span class="s1">&#39;kcal/mol&#39;</span><span class="p">),</span>
+    <span class="n">minimumNumberOfGrains</span><span class="o">=</span><span class="mi">250</span><span class="p">,</span>
+    <span class="n">temperatures</span><span class="o">=</span><span class="p">(</span><span class="mi">300</span><span class="p">,</span><span class="mi">2000</span><span class="p">,</span><span class="s1">&#39;K&#39;</span><span class="p">,</span><span class="mi">8</span><span class="p">),</span>
+    <span class="n">pressures</span><span class="o">=</span><span class="p">(</span><span class="mf">0.01</span><span class="p">,</span><span class="mi">100</span><span class="p">,</span><span class="s1">&#39;bar&#39;</span><span class="p">,</span><span class="mi">5</span><span class="p">),</span>
+    <span class="n">interpolation</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;Chebyshev&#39;</span><span class="p">,</span> <span class="mi">6</span><span class="p">,</span> <span class="mi">4</span><span class="p">),</span>
+    <span class="n">maximumAtoms</span><span class="o">=</span><span class="mi">16</span><span class="p">,</span>
+    <span class="n">completedNetworks</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;CH2O2&#39;</span><span class="p">],</span>
+<span class="p">)</span>
+</pre></div>
+</div>
+<p>Multiple networks can be specified in the list:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">completedNetworks</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;CH2O2&#39;</span><span class="p">,</span> <span class="s1">&#39;C2H6&#39;</span><span class="p">],</span>
+</pre></div>
+</div>
+<p>When a network is marked as completed, RMG will not add any new reactions to it,
+though reactions already present in seed mechanisms will still be used.</p>
+</section>
 </section>
 <section id="uncertainty-analysis">
 <span id="uncertaintyanalysis"></span><h2><span class="section-number">4.11. </span>Uncertainty Analysis<a class="headerlink" href="#uncertainty-analysis" title="Permalink to this heading">¶</a></h2>
@@ -1115,6 +1145,7 @@ <h3><a href="../../contents.html">Table of Contents</a></h3>
 <li><a class="reference internal" href="#temperature-and-pressure-for-the-interpolation-scheme">4.10.3. Temperature and pressure for the interpolation scheme</a></li>
 <li><a class="reference internal" href="#interpolation-scheme">4.10.4. Interpolation scheme</a></li>
 <li><a class="reference internal" href="#maximum-size-of-adduct-for-which-pressure-dependence-kinetics-be-generated">4.10.5. Maximum size of adduct for which pressure dependence kinetics be generated</a></li>
+<li><a class="reference internal" href="#completed-pressure-dependent-networks">4.10.6. Completed Pressure-Dependent Networks</a></li>
 </ul>
 </li>
 <li><a class="reference internal" href="#uncertainty-analysis">4.11. Uncertainty Analysis</a></li>