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docs(docs): rebuild with more usage examples

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Emily Boudreaux
2025-07-30 15:12:46 -04:00
parent 24870ffcbc
commit cd60ae5c1e
79 changed files with 5050 additions and 4496 deletions
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docs/html/classgridfire_1_1_graph_engine.html
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@@ -261,9 +261,6 @@ Private Member Functions</h2></td></tr>
<tr class="memitem:acf4cfccea20f5cb31c9886bf233a28be" id="r_acf4cfccea20f5cb31c9886bf233a28be"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#acf4cfccea20f5cb31c9886bf233a28be">validateConservation</a> () const</td></tr>
<tr class="memdesc:acf4cfccea20f5cb31c9886bf233a28be"><td class="mdescLeft">&#160;</td><td class="mdescRight">Validates mass and charge conservation across all reactions. <br /></td></tr>
<tr class="separator:acf4cfccea20f5cb31c9886bf233a28be"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aeeafeab40a5f4dbfae78bdc87e25e93f" id="r_aeeafeab40a5f4dbfae78bdc87e25e93f"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aeeafeab40a5f4dbfae78bdc87e25e93f">validateComposition</a> (const fourdst::composition::Composition &amp;composition, double culling, double T9)</td></tr>
<tr class="memdesc:aeeafeab40a5f4dbfae78bdc87e25e93f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Validates the composition against the current reaction set. <br /></td></tr>
<tr class="separator:aeeafeab40a5f4dbfae78bdc87e25e93f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a97f98706b51fbe0d167ed81ffe58c438" id="r_a97f98706b51fbe0d167ed81ffe58c438"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a97f98706b51fbe0d167ed81ffe58c438">calculateAllDerivativesUsingPrecomputation</a> (const std::vector&lt; double &gt; &amp;Y_in, const std::vector&lt; double &gt; &amp;bare_rates, const std::vector&lt; double &gt; &amp;bare_reverse_rates, double T9, double rho) const</td></tr>
<tr class="separator:a97f98706b51fbe0d167ed81ffe58c438"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5e96b5a0b34c8932f0e14eabda57f1a4" id="r_a5e96b5a0b34c8932f0e14eabda57f1a4"><td class="memTemplParams" colspan="2">template&lt;IsArithmeticOrAD T&gt; </td></tr>
@@ -358,7 +355,7 @@ Private Attributes</h2></td></tr>
</ul>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="engine__abstract_8h.html" title="Abstract interfaces for reaction network engines in GridFire.">engine_abstract.h</a> </dd></dl>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00101">101</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00100">100</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
<a id="afad967546b611d9c005268760feb75d5" name="afad967546b611d9c005268760feb75d5"></a>
<h2 class="memtitle"><span class="permalink"><a href="#afad967546b611d9c005268760feb75d5">&#9670;&#160;</a></span>GraphEngine() <span class="overload">[1/3]</span></h2>
@@ -518,7 +515,7 @@ Private Attributes</h2></td></tr>
<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives&lt;ADDouble&gt;</a> containing dY/dt and energy generation rate.</dd></dl>
<p>This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state using automatic differentiation. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00616">616</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00594">594</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -566,7 +563,7 @@ Private Attributes</h2></td></tr>
<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives&lt;double&gt;</a> containing dY/dt and energy generation rate.</dd></dl>
<p>This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state using double precision arithmetic. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00608">608</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00586">586</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -622,7 +619,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives&lt;T&gt;</a> containing dY/dt and energy generation rate.</dd></dl>
<p>This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00745">745</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00715">715</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00470">470</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00448">448</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -724,7 +721,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00645">645</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00623">623</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -786,7 +783,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<dl class="section return"><dt>Returns</dt><dd>Molar flow rate for the reaction (e.g., mol/g/s).</dd></dl>
<p>This method computes the net rate at which the given reaction proceeds under the current state. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00826">826</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00796">796</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00667">667</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00648">648</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00262">262</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00242">242</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00291">291</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00269">269</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00368">368</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00346">346</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00969">969</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00947">947</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1090,7 +1087,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
</dl>
<p>Example usage: </p><div class="fragment"><div class="line">engine.exportToCSV(<span class="stringliteral">&quot;network.csv&quot;</span>);</div>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00810">810</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00788">788</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1125,7 +1122,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
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<p>Example usage: </p><div class="fragment"><div class="line">engine.exportToDot(<span class="stringliteral">&quot;network.dot&quot;</span>);</div>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00762">762</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00740">740</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1175,7 +1172,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a29bdd4231c29c3a4e524ad6ca66a127d">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00654">654</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00632">632</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1218,7 +1215,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Reimplemented from <a class="el" href="classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00687">687</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00665">665</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1250,7 +1247,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00567">567</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00545">545</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Reimplemented from <a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00456">456</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00434">434</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1324,7 +1321,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00744">744</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00722">722</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1360,7 +1357,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
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<dl class="section return"><dt>Returns</dt><dd>Map of species to their stoichiometric coefficients. </dd></dl>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00749">749</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00727">727</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00641">641</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00619">619</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1486,7 +1483,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00629">629</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00607">607</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6ca0f315f75252ca505507a61556dda6">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00883">883</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00861">861</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1553,7 +1550,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad3d56a8b9161b9cc7f4da51f6bf7e8c9">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00417">417</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00395">395</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6772ac384b4c3d3e91712041e4aaa813">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00864">864</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00842">842</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00755">755</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00733">733</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00637">637</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00615">615</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a942e65ced17ca602482cc42e469d6398">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00920">920</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00898">898</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00409">409</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00387">387</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a55f1b7e5ebe2840e1d7c54665ca5411a">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00421">421</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00399">399</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00982">982</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00960">960</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a21c34f59c080a853fafa38a25175124e">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00429">429</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00407">407</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Reimplemented from <a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00460">460</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00438">438</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00924">924</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00902">902</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00633">633</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00611">611</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00624">624</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00602">602</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00413">413</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00391">391</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -2193,54 +2190,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aa799ff785e7e79bf35b11efd55f6282a">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00908">908</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aeeafeab40a5f4dbfae78bdc87e25e93f">&#9670;&#160;</a></span>validateComposition()</h2>
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<td class="memname">void gridfire::GraphEngine::validateComposition </td>
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<td class="paramtype">const fourdst::composition::Composition &amp;</td> <td class="paramname"><span class="paramname"><em>composition</em></span>, </td>
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<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>culling</em></span>, </td>
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<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>&#160;)</td>
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<p>Validates the composition against the current reaction set. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">composition</td><td>The composition to validate. </td></tr>
<tr><td class="paramname">culling</td><td>The culling threshold to use. </td></tr>
<tr><td class="paramname">T9</td><td>The temperature to use.</td></tr>
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<p>This method validates the composition against the current reaction set. If the composition is not compatible with the reaction set, the reaction set is rebuilt from the composition. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00242">242</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00886">886</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00467">467</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00466">466</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00448">448</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00447">447</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00451">451</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00450">450</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00476">476</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00475">475</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2394,7 +2344,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Full sparsity pattern for the Jacobian matrix. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00465">465</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00464">464</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2420,7 +2370,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Work object for sparse Jacobian calculations. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00464">464</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00463">463</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2446,7 +2396,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Jacobian matrix (species x species). </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00462">462</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00461">461</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2470,7 +2420,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00449">449</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00448">448</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2496,7 +2446,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Vector of unique species in the network. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00456">456</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00455">455</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2522,7 +2472,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Map from species name to Species object. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00457">457</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00456">456</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2548,7 +2498,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Partition function for the network. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00479">479</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00478">478</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>Precomputed reactions for efficiency. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00478">478</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00477">477</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2600,7 +2550,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a performance bottleneck. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00454">454</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00453">453</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>Set of REACLIB reactions in the network. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00453">453</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00452">452</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>CppAD function for the right-hand side of the ODE. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00463">463</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00462">462</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00470">470</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00469">469</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>Screening type for the reaction network. Default to no screening. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00469">469</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00468">468</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>Map from species to their index in the stoichiometry matrix. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00458">458</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00457">457</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>Stoichiometry matrix (species x reactions). </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00460">460</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00459">459</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>Flag to enable or disable using precomputed reactions for efficiency. Mathematically, this should not change the results. Generally end users should not need to change this. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00472">472</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00471">471</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>Flag to enable or disable reverse reactions. If false, only forward reactions are considered. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00474">474</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00473">473</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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