Automated documentation rebuild

Author: github-actions

_sources/users/rmg/input.rst.txt

@@ -965,6 +965,7 @@ Miscellaneous options::
         units='si',
         generateOutputHTML=True,
         generatePlots=False,
+		generatePESDiagrams=False,
         saveSimulationProfiles=True,
         verboseComments=False,
         saveEdgeSpecies=True,
@@ -986,6 +987,8 @@ HTML file for your model containing all the species and reactions.  Turning this
 
 Setting ``generatePlots`` to ``True`` will generate a number of plots describing the statistics of the RMG job, including the reaction model core and edge size and memory use versus  execution time. These will be placed in the output directory in the plot/ folder.
 
+Setting ``generatePESDiagrams`` to ``True`` will generate potential energy surface diagrams for each pressure dependent network in the model.  These diagrams will be saved in the ``pdep/`` folder in the output directory. Only applicable if pressure dependence is enabled.
+
 Setting ``saveSimulationProfiles`` to ``True`` will make RMG save csv files of the simulation in .csv files in the ``solver/`` folder.  The filename will be ``simulation_1_26.csv`` where the first number corresponds to the reaciton system, and the second number corresponds to the total number of species at the point of the simulation.  Therefore, the highest second number will indicate the latest simulation that RMG has complete while enlarging the core model.  The information inside the csv file will provide the time, reactor volume in m^3, as well as mole fractions of the individual species.
 
 Setting ``verboseComments`` to ``True`` will make RMG generate chemkin files with complete verbose commentary for the kinetic and thermo parameters.  This will be helpful in debugging what values are being averaged for the kinetics.  Note that this may produce very large files.

reference/arkane/pdep.html

@@ -192,12 +192,15 @@ <h1>arkane.PressureDependenceJob<a class="headerlink" href="#arkane-pressuredepe
 
 <dl class="py method">
 <dt class="sig sig-object py" id="arkane.PressureDependenceJob.draw">
-<span class="sig-name descname"><span class="pre">draw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_directory</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pdf'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#arkane.PressureDependenceJob.draw" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">draw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_directory</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pdf'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename_stem</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'network'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#arkane.PressureDependenceJob.draw" title="Permalink to this definition">¶</a></dt>
 <dd><p>Generate a PDF drawing of the pressure-dependent reaction network.
 This requires that Cairo and its Python wrapper be available; if not,
 the drawing is not generated.</p>
 <p>You may also generate different formats of drawings, by changing format to
 one of the following: <cite>pdf</cite>, <cite>svg</cite>, <cite>png</cite>.</p>
+<p>The default filename stem is ‘network’, which will result in a file
+named ‘network.pdf’ in the specified output directory. You can change
+this by passing a different <cite>filename_stem</cite> argument.</p>
 </dd></dl>
 
 <dl class="py method">

reference/rmg/main.html

@@ -172,43 +172,46 @@ <h1>rmgpy.rmg.main.RMG<a class="headerlink" href="#rmgpy-rmg-main-rmg" title="Pe
 <tr class="row-even"><td><p><cite>generate_plots</cite></p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">True</span></code> to generate plots of the job execution statistics after each iteration, <code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise</p></td>
 </tr>
-<tr class="row-odd"><td><p><cite>verbose_comments</cite></p></td>
+<tr class="row-odd"><td><p><cite>generate_PES_diagrams</cite></p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">True</span></code> to generate potential energy surface diagrams for pressure dependent networks in the model, <code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise</p></td>
+</tr>
+<tr class="row-even"><td><p><cite>verbose_comments</cite></p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">True</span></code> to keep the verbose comments for database estimates, <code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise</p></td>
 </tr>
-<tr class="row-even"><td><p><cite>save_edge_species</cite></p></td>
+<tr class="row-odd"><td><p><cite>save_edge_species</cite></p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">True</span></code> to save chemkin and HTML files of the edge species, <code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise</p></td>
 </tr>
-<tr class="row-odd"><td><p><cite>keep_irreversible</cite></p></td>
+<tr class="row-even"><td><p><cite>keep_irreversible</cite></p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">True</span></code> to keep ireversibility of library reactions as is (‘&lt;=&gt;’ or ‘=&gt;’). <code class="docutils literal notranslate"><span class="pre">False</span></code> (default) to force all library reactions to be reversible (‘&lt;=&gt;’)</p></td>
 </tr>
-<tr class="row-even"><td><p><cite>trimolecular_product_reversible</cite></p></td>
+<tr class="row-odd"><td><p><cite>trimolecular_product_reversible</cite></p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">True</span></code> (default) to allow families with trimolecular products to react in the reverse direction, <code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise</p></td>
 </tr>
-<tr class="row-odd"><td><p><cite>pressure_dependence</cite></p></td>
+<tr class="row-even"><td><p><cite>pressure_dependence</cite></p></td>
 <td><p>Whether to process unimolecular (pressure-dependent) reaction networks</p></td>
 </tr>
-<tr class="row-even"><td><p><cite>quantum_mechanics</cite></p></td>
+<tr class="row-odd"><td><p><cite>quantum_mechanics</cite></p></td>
 <td><p>Whether to apply quantum mechanical calculations instead of group additivity to certain molecular types.</p></td>
 </tr>
-<tr class="row-odd"><td><p><cite>ml_estimator</cite></p></td>
+<tr class="row-even"><td><p><cite>ml_estimator</cite></p></td>
 <td><p>To use thermo estimation with machine learning</p></td>
 </tr>
-<tr class="row-even"><td><p><cite>ml_settings</cite></p></td>
+<tr class="row-odd"><td><p><cite>ml_settings</cite></p></td>
 <td><p>Settings for ML estimation</p></td>
 </tr>
-<tr class="row-odd"><td><p><cite>walltime</cite></p></td>
+<tr class="row-even"><td><p><cite>walltime</cite></p></td>
 <td><p>The maximum amount of CPU time in the form DD:HH:MM:SS to expend on this job; used to stop gracefully so we can still get profiling information</p></td>
 </tr>
-<tr class="row-even"><td><p><cite>max_iterations</cite></p></td>
+<tr class="row-odd"><td><p><cite>max_iterations</cite></p></td>
 <td><p>The maximum number of RMG iterations allowed, after which the job will terminate</p></td>
 </tr>
-<tr class="row-odd"><td><p><cite>kinetics_datastore</cite></p></td>
+<tr class="row-even"><td><p><cite>kinetics_datastore</cite></p></td>
 <td><p><code class="docutils literal notranslate"><span class="pre">True</span></code> if storing details of each kinetic database entry in text file, <code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise</p></td>
 </tr>
-<tr class="row-even"><td><p><cite>initialization_time</cite></p></td>
+<tr class="row-odd"><td><p><cite>initialization_time</cite></p></td>
 <td><p>The time at which the job was initiated, in seconds since the epoch (i.e. from time.time())</p></td>
 </tr>
-<tr class="row-odd"><td><p><cite>done</cite></p></td>
+<tr class="row-even"><td><p><cite>done</cite></p></td>
 <td><p>Whether the job has completed (there is nothing new to add)</p></td>
 </tr>
 </tbody>

searchindex.js

@@ -215,6 +215,7 @@ <h2><span class="section-number">5.2. </span>1,3-hexadiene pyrolysis<a class="he
     <span class="n">units</span><span class="o">=</span><span class="s1">&#39;si&#39;</span><span class="p">,</span>
     <span class="n">generateOutputHTML</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
     <span class="n">generatePlots</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+    <span class="n">generatePESDiagrams</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
 <span class="p">)</span>
 </pre></div>
 </div>
@@ -442,6 +443,8 @@ <h2><span class="section-number">5.3. </span>Commented input file<a class="heade
     <span class="n">generateOutputHTML</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
     <span class="c1"># generates plots of the RMG&#39;s performance statistics. Not helpful if you just want a model.</span>
     <span class="n">generatePlots</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+    <span class="c1"># generates potential energy surface diagrams for pressure dependent networks in the model.</span>
+    <span class="n">generatePESDiagrams</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
     <span class="c1"># saves mole fraction of species in &#39;solver/&#39; to help you create plots</span>
     <span class="n">saveSimulationProfiles</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
     <span class="c1"># gets RMG to output comments on where kinetics were obtained in the chemkin file.</span>

users/rmg/examples.html

@@ -933,6 +933,7 @@ <h3><span class="section-number">4.10.5. </span>Maximum size of adduct for which
     <span class="n">units</span><span class="o">=</span><span class="s1">&#39;si&#39;</span><span class="p">,</span>
     <span class="n">generateOutputHTML</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
     <span class="n">generatePlots</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+            <span class="n">generatePESDiagrams</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
     <span class="n">saveSimulationProfiles</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
     <span class="n">verboseComments</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
     <span class="n">saveEdgeSpecies</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
@@ -949,6 +950,7 @@ <h3><span class="section-number">4.10.5. </span>Maximum size of adduct for which
 <p>Setting <code class="docutils literal notranslate"><span class="pre">generateOutputHTML</span></code> to <code class="docutils literal notranslate"><span class="pre">True</span></code> will let RMG know that you want to save 2-D images (png files in the local <code class="docutils literal notranslate"><span class="pre">species</span></code> folder) of all species in the generated core model.  It will save a visualized
 HTML file for your model containing all the species and reactions.  Turning this feature off by setting it to <code class="docutils literal notranslate"><span class="pre">False</span></code> may save memory if running large jobs.</p>
 <p>Setting <code class="docutils literal notranslate"><span class="pre">generatePlots</span></code> to <code class="docutils literal notranslate"><span class="pre">True</span></code> will generate a number of plots describing the statistics of the RMG job, including the reaction model core and edge size and memory use versus  execution time. These will be placed in the output directory in the plot/ folder.</p>
+<p>Setting <code class="docutils literal notranslate"><span class="pre">generatePESDiagrams</span></code> to <code class="docutils literal notranslate"><span class="pre">True</span></code> will generate potential energy surface diagrams for each pressure dependent network in the model.  These diagrams will be saved in the <code class="docutils literal notranslate"><span class="pre">pdep/</span></code> folder in the output directory. Only applicable if pressure dependence is enabled.</p>
 <p>Setting <code class="docutils literal notranslate"><span class="pre">saveSimulationProfiles</span></code> to <code class="docutils literal notranslate"><span class="pre">True</span></code> will make RMG save csv files of the simulation in .csv files in the <code class="docutils literal notranslate"><span class="pre">solver/</span></code> folder.  The filename will be <code class="docutils literal notranslate"><span class="pre">simulation_1_26.csv</span></code> where the first number corresponds to the reaciton system, and the second number corresponds to the total number of species at the point of the simulation.  Therefore, the highest second number will indicate the latest simulation that RMG has complete while enlarging the core model.  The information inside the csv file will provide the time, reactor volume in m^3, as well as mole fractions of the individual species.</p>
 <p>Setting <code class="docutils literal notranslate"><span class="pre">verboseComments</span></code> to <code class="docutils literal notranslate"><span class="pre">True</span></code> will make RMG generate chemkin files with complete verbose commentary for the kinetic and thermo parameters.  This will be helpful in debugging what values are being averaged for the kinetics.  Note that this may produce very large files.</p>
 <p>Setting <code class="docutils literal notranslate"><span class="pre">saveEdgeSpecies</span></code> to <code class="docutils literal notranslate"><span class="pre">True</span></code> will make RMG generate chemkin files of the edge reactions in addition to the core model in files such as <code class="docutils literal notranslate"><span class="pre">chem_edge.inp</span></code> and <code class="docutils literal notranslate"><span class="pre">chem_edge_annotated.inp</span></code> files located inside the <code class="docutils literal notranslate"><span class="pre">chemkin</span></code> folder.  These files will be helpful in viewing RMG’s estimate for edge reactions and seeing if certain reactions one expects are actually in the edge or not.</p>