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docs(docs): asdded and cleaned up docs

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Emily Boudreaux
2025-07-24 11:10:45 -04:00
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@@ -116,18 +116,24 @@ Inheritance diagram for gridfire::DynamicEngine:</div>
<div class="center">
<img src="classgridfire_1_1_dynamic_engine.png" usemap="#gridfire::DynamicEngine_map" alt=""/>
<map id="gridfire::DynamicEngine_map" name="gridfire::DynamicEngine_map">
<area href="classgridfire_1_1_engine.html" title="Abstract base class for a reaction network engine." alt="gridfire::Engine" shape="rect" coords="201,0,392,24"/>
<area href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions." alt="gridfire::AdaptiveEngineView" shape="rect" coords="0,112,191,136"/>
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</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a0a2fb3435ee3271ab9c806f225c61a7f" id="r_a0a2fb3435ee3271ab9c806f225c61a7f"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0a2fb3435ee3271ab9c806f225c61a7f">generateJacobianMatrix</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho)=0</td></tr>
<tr class="memdesc:a0a2fb3435ee3271ab9c806f225c61a7f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate the Jacobian matrix for the current state. <br /></td></tr>
<tr class="separator:a0a2fb3435ee3271ab9c806f225c61a7f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a29bdd4231c29c3a4e524ad6ca66a127d" id="r_a29bdd4231c29c3a4e524ad6ca66a127d"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a29bdd4231c29c3a4e524ad6ca66a127d">generateJacobianMatrix</a> (const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho) const =0</td></tr>
<tr class="memdesc:a29bdd4231c29c3a4e524ad6ca66a127d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate the Jacobian matrix for the current state. <br /></td></tr>
<tr class="separator:a29bdd4231c29c3a4e524ad6ca66a127d"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a818d942efa843959393e4eed3263b7e7" id="r_a818d942efa843959393e4eed3263b7e7"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a818d942efa843959393e4eed3263b7e7">generateJacobianMatrix</a> (const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho, const <a class="el" href="namespacegridfire.html#a898dfe22579e649935645cbd6f073178">SparsityPattern</a> &amp;sparsityPattern) const</td></tr>
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<tr class="memdesc:a05d15ff35a6bc06a2fa7eda19838bd07"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get an entry from the previously generated Jacobian matrix. <br /></td></tr>
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@@ -143,18 +149,34 @@ Public Member Functions</h2></td></tr>
<tr class="memitem:ad2a82099edbb374bbb2c9509ccdb1037" id="r_ad2a82099edbb374bbb2c9509ccdb1037"><td class="memItemLeft" align="right" valign="top">virtual const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad2a82099edbb374bbb2c9509ccdb1037">getNetworkReactions</a> () const =0</td></tr>
<tr class="memdesc:ad2a82099edbb374bbb2c9509ccdb1037"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the set of logical reactions in the network. <br /></td></tr>
<tr class="separator:ad2a82099edbb374bbb2c9509ccdb1037"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5d8ba98b230d2849035ee2507728fa15" id="r_a5d8ba98b230d2849035ee2507728fa15"><td class="memItemLeft" align="right" valign="top">virtual std::unordered_map&lt; fourdst::atomic::Species, double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a5d8ba98b230d2849035ee2507728fa15">getSpeciesTimescales</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td></tr>
<tr class="memdesc:a5d8ba98b230d2849035ee2507728fa15"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute timescales for all species in the network. <br /></td></tr>
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<tr class="memitem:acd500e1cd788df1dc105d28a20dc5f4f" id="r_acd500e1cd788df1dc105d28a20dc5f4f"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#acd500e1cd788df1dc105d28a20dc5f4f">update</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn)=0</td></tr>
<tr class="memdesc:acd500e1cd788df1dc105d28a20dc5f4f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Update the internal state of the engine. <br /></td></tr>
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<tr class="memitem:a6772ac384b4c3d3e91712041e4aaa813" id="r_a6772ac384b4c3d3e91712041e4aaa813"><td class="memItemLeft" align="right" valign="top">virtual std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a6772ac384b4c3d3e91712041e4aaa813">getSpeciesTimescales</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td></tr>
<tr class="memdesc:a6772ac384b4c3d3e91712041e4aaa813"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute timescales for all species in the network. <br /></td></tr>
<tr class="separator:a6772ac384b4c3d3e91712041e4aaa813"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a6ca0f315f75252ca505507a61556dda6" id="r_a6ca0f315f75252ca505507a61556dda6"><td class="memItemLeft" align="right" valign="top">virtual std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a6ca0f315f75252ca505507a61556dda6">getSpeciesDestructionTimescales</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td></tr>
<tr class="separator:a6ca0f315f75252ca505507a61556dda6"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa799ff785e7e79bf35b11efd55f6282a" id="r_aa799ff785e7e79bf35b11efd55f6282a"><td class="memItemLeft" align="right" valign="top">virtual fourdst::composition::Composition&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aa799ff785e7e79bf35b11efd55f6282a">update</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn)=0</td></tr>
<tr class="memdesc:aa799ff785e7e79bf35b11efd55f6282a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Update the internal state of the engine. <br /></td></tr>
<tr class="separator:aa799ff785e7e79bf35b11efd55f6282a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a942e65ced17ca602482cc42e469d6398" id="r_a942e65ced17ca602482cc42e469d6398"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a942e65ced17ca602482cc42e469d6398">isStale</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn)=0</td></tr>
<tr class="separator:a942e65ced17ca602482cc42e469d6398"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a3fb44b6f55563a2f590f31916528f2bd" id="r_a3fb44b6f55563a2f590f31916528f2bd"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a3fb44b6f55563a2f590f31916528f2bd">setScreeningModel</a> (<a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> model)=0</td></tr>
<tr class="memdesc:a3fb44b6f55563a2f590f31916528f2bd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Set the electron screening model. <br /></td></tr>
<tr class="separator:a3fb44b6f55563a2f590f31916528f2bd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7a203f8e0f3a6744ddc912dfbcfdbcc0" id="r_a7a203f8e0f3a6744ddc912dfbcfdbcc0"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a7a203f8e0f3a6744ddc912dfbcfdbcc0">getScreeningModel</a> () const =0</td></tr>
<tr class="memdesc:a7a203f8e0f3a6744ddc912dfbcfdbcc0"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the current electron screening model. <br /></td></tr>
<tr class="separator:a7a203f8e0f3a6744ddc912dfbcfdbcc0"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad3d56a8b9161b9cc7f4da51f6bf7e8c9" id="r_ad3d56a8b9161b9cc7f4da51f6bf7e8c9"><td class="memItemLeft" align="right" valign="top">virtual int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad3d56a8b9161b9cc7f4da51f6bf7e8c9">getSpeciesIndex</a> (const fourdst::atomic::Species &amp;species) const =0</td></tr>
<tr class="separator:ad3d56a8b9161b9cc7f4da51f6bf7e8c9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a55f1b7e5ebe2840e1d7c54665ca5411a" id="r_a55f1b7e5ebe2840e1d7c54665ca5411a"><td class="memItemLeft" align="right" valign="top">virtual std::vector&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a55f1b7e5ebe2840e1d7c54665ca5411a">mapNetInToMolarAbundanceVector</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) const =0</td></tr>
<tr class="separator:a55f1b7e5ebe2840e1d7c54665ca5411a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a21c34f59c080a853fafa38a25175124e" id="r_a21c34f59c080a853fafa38a25175124e"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="structgridfire_1_1_priming_report.html">PrimingReport</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a21c34f59c080a853fafa38a25175124e">primeEngine</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn)=0</td></tr>
<tr class="separator:a21c34f59c080a853fafa38a25175124e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a04317b66ef14d519264bc30ee69f5bf9" id="r_a04317b66ef14d519264bc30ee69f5bf9"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a> () const</td></tr>
<tr class="separator:a04317b66ef14d519264bc30ee69f5bf9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a4e2c8b896661b7a89beffe0066cb21cf" id="r_a4e2c8b896661b7a89beffe0066cb21cf"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a4e2c8b896661b7a89beffe0066cb21cf">rebuild</a> (const fourdst::composition::Composition &amp;comp, <a class="el" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a> depth)</td></tr>
<tr class="separator:a4e2c8b896661b7a89beffe0066cb21cf"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pub_methods_classgridfire_1_1_engine"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td></tr>
<tr class="memitem:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine" id="r_a2e7970bed2100699f226f4141d5db037"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a> ()=default</td></tr>
<tr class="memdesc:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor. <br /></td></tr>
@@ -162,9 +184,9 @@ Public Member Functions</h2></td></tr>
<tr class="memitem:a020e1b493d6964cafdad08fde697ceb3 inherit pub_methods_classgridfire_1_1_engine" id="r_a020e1b493d6964cafdad08fde697ceb3"><td class="memItemLeft" align="right" valign="top">virtual const std::vector&lt; fourdst::atomic::Species &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">getNetworkSpecies</a> () const =0</td></tr>
<tr class="memdesc:a020e1b493d6964cafdad08fde697ceb3 inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the list of species in the network. <br /></td></tr>
<tr class="separator:a020e1b493d6964cafdad08fde697ceb3 inherit pub_methods_classgridfire_1_1_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac8b56124b6b49cd1802addb74a9a47c2 inherit pub_methods_classgridfire_1_1_engine" id="r_ac8b56124b6b49cd1802addb74a9a47c2"><td class="memItemLeft" align="right" valign="top">virtual <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="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td></tr>
<tr class="memdesc:ac8b56124b6b49cd1802addb74a9a47c2 inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the right-hand side (dY/dt) and energy generation. <br /></td></tr>
<tr class="separator:ac8b56124b6b49cd1802addb74a9a47c2 inherit pub_methods_classgridfire_1_1_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a89f714d19b84a93a004a7afbb487a6cb inherit pub_methods_classgridfire_1_1_engine" id="r_a89f714d19b84a93a004a7afbb487a6cb"><td class="memItemLeft" align="right" valign="top">virtual std::expected&lt; <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td></tr>
<tr class="memdesc:a89f714d19b84a93a004a7afbb487a6cb inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the right-hand side (dY/dt) and energy generation. <br /></td></tr>
<tr class="separator:a89f714d19b84a93a004a7afbb487a6cb inherit pub_methods_classgridfire_1_1_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Abstract class for engines supporting Jacobian and stoichiometry operations. </p>
@@ -177,7 +199,7 @@ Public Member Functions</h2></td></tr>
</ul>
<p>Intended usage: Derive from this class to implement engines that support advanced solver features such as implicit integration, sensitivity analysis, QSE (Quasi-Steady-State Equilibrium) handling, and more. </p>
<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00121">121</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00130">130</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
</div><h2 class="groupheader">Member Function Documentation</h2>
<a id="a6633b1757c41dd9e1c397333f4f9e785" name="a6633b1757c41dd9e1c397333f4f9e785"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a6633b1757c41dd9e1c397333f4f9e785">&#9670;&#160;</a></span>calculateMolarReactionFlow()</h2>
@@ -229,12 +251,12 @@ Public Member Functions</h2></td></tr>
<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>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a048d4b1d41ecb4125a558d1b9ed7cb31">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ac371fb66fd0a76a04df204c9dd9a05ef">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">gridfire::GraphEngine</a>.</p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a048d4b1d41ecb4125a558d1b9ed7cb31">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a79eb9c108d694a27ec913ed0143aa044">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a6224f546ba66b1257506b1fc9f47195a">PyDynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a0a2fb3435ee3271ab9c806f225c61a7f">&#9670;&#160;</a></span>generateJacobianMatrix()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a29bdd4231c29c3a4e524ad6ca66a127d">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[1/2]</span></h2>
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<td class="memname">virtual void gridfire::DynamicEngine::generateJacobianMatrix </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_dynamic</em></span>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;)</td>
<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
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<p>Generate the Jacobian matrix for the current state. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">Y</td><td>Vector of current abundances. </td></tr>
<tr><td class="paramname">Y_dynamic</td><td>Vector of current abundances. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3.</td></tr>
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@@ -276,7 +298,50 @@ Public Member Functions</h2></td></tr>
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<p>This method must compute and store the Jacobian matrix (∂(dY/dt)_i/∂Y_j) for the current state. The matrix can then be accessed via <a class="el" href="#a05d15ff35a6bc06a2fa7eda19838bd07" title="Get an entry from the previously generated Jacobian matrix.">getJacobianMatrixEntry()</a>. </p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac9aab6f60e80a9228b2b19b1b10449ef">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a48b2451f96b8f5511ffc4071519c0810">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#ae347ff0316e532e0298ec8c913908105">gridfire::GraphEngine</a>.</p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a03fc187d3d306b9058103b9522cbbaeb">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#ad25c722eaee1f28f8ed7b4d33a1f69ae">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#acdf5ad8765290ea2b78170235aea391d">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a5bd40c752db1badcd600797c9113121d">PyDynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a818d942efa843959393e4eed3263b7e7">&#9670;&#160;</a></span>generateJacobianMatrix() <span class="overload">[2/2]</span></h2>
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<td class="memname">virtual void gridfire::DynamicEngine::generateJacobianMatrix </td>
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<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_dynamic</em></span>, </td>
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<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
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<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>, </td>
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<td class="paramtype">const <a class="el" href="namespacegridfire.html#a898dfe22579e649935645cbd6f073178">SparsityPattern</a> &amp;</td> <td class="paramname"><span class="paramname"><em>sparsityPattern</em></span>&#160;) const</td>
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<p>Reimplemented in <a class="el" href="classgridfire_1_1_graph_engine.html#a9687eef88c97eeb7f8680acb230f8ac1">gridfire::GraphEngine</a>, and <a class="el" href="class_py_dynamic_engine.html#aa0f1fd3f0c0185395193d1b6897d64c5">PyDynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00148">148</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
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<p>Generate the stoichiometry matrix for the network. </p>
<p>This method must compute and store the stoichiometry matrix, which encodes the net change of each species in each reaction. </p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a231193a61ba5a31e8eb92b0d4ce69111">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a27a5163157cc15c4cb3b99a5d3564dbd">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38">gridfire::GraphEngine</a>.</p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a231193a61ba5a31e8eb92b0d4ce69111">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#ad07221be49ae1b5133c5b987dafac3b6">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#abe76a46784b1ebc8ad67a9eec40d369a">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a2066649ca11a869c054079ea12d8d0e9">PyDynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a04317b66ef14d519264bc30ee69f5bf9">&#9670;&#160;</a></span>getDepth()</h2>
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<td class="memname">virtual <a class="el" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a> gridfire::DynamicEngine::getDepth </td>
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<p>Reimplemented in <a class="el" href="classgridfire_1_1_graph_engine.html#a166a5f4349580f9aa0b930afec73fcc4">gridfire::GraphEngine</a>, and <a class="el" href="class_py_dynamic_engine.html#adba68716d832b6100e08d32fbc36f13c">PyDynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00305">305</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
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</dd>
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<dl class="section return"><dt>Returns</dt><dd>Value of the Jacobian matrix at (i, j).</dd></dl>
<p>The Jacobian must have been generated by <a class="el" href="#a0a2fb3435ee3271ab9c806f225c61a7f" title="Generate the Jacobian matrix for the current state.">generateJacobianMatrix()</a> before calling this. </p>
<p>The Jacobian must have been generated by <a class="el" href="#a29bdd4231c29c3a4e524ad6ca66a127d" title="Generate the Jacobian matrix for the current state.">generateJacobianMatrix()</a> before calling this. </p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4710d218c8a0fd161e994ecd60b48e58">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a0ef8804780d13bbfce0856237bb00470">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c">gridfire::GraphEngine</a>.</p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4710d218c8a0fd161e994ecd60b48e58">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a273b175049f5ce7b9208e931ad139e1b">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ac961484383e86d9712a424728e068633">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a1c888bbc0618f1ae02d9a53e45f3c159">PyDynamicEngine</a>.</p>
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<p>Get the set of logical reactions in the network. </p>
<dl class="section return"><dt>Returns</dt><dd>Reference to the LogicalReactionSet containing all reactions. </dd></dl>
<dl class="section return"><dt>Returns</dt><dd>Reference to the <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" title="A set of logical reactions.">LogicalReactionSet</a> containing all reactions. </dd></dl>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a12cc2f352678fba9688363ba1876ab9c">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a5bbea17b69cc8f81bc251a04f4435a0c">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da">gridfire::GraphEngine</a>.</p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a12cc2f352678fba9688363ba1876ab9c">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#ae03b4f9afac03d4011a4d7cf0423535d">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ad751f2c1306895ee74a61f2071ca96eb">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a5988cfba247631ba6c00795cafda9a38">PyDynamicEngine</a>.</p>
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@@ -411,12 +505,12 @@ Public Member Functions</h2></td></tr>
<div class="ttc" id="anamespacegridfire_1_1screening_html_aa82aafbc4f8c28d0a75b60798e3a7d25"><div class="ttname"><a href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">gridfire::screening::ScreeningType</a></div><div class="ttdeci">ScreeningType</div><div class="ttdoc">Enumerates the available plasma screening models.</div><div class="ttdef"><b>Definition</b> <a href="screening__types_8h_source.html#l00015">screening_types.h:15</a></div></div>
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<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a0ab1199f900a58f309c3c36532c9164f">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#adbc50f397445f92b810d80cf329b8626">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a">gridfire::GraphEngine</a>.</p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a0ab1199f900a58f309c3c36532c9164f">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a3c657b82a0117118a4bb0ce7f624ae0c">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a7bfb4e6fec2f337a1dea69e3d4f1fc82">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#ab4cfdca5e15957c5cef75ffa6dedeee5">PyDynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a5d8ba98b230d2849035ee2507728fa15">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a6ca0f315f75252ca505507a61556dda6">&#9670;&#160;</a></span>getSpeciesDestructionTimescales()</h2>
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<td class="memname">virtual std::unordered_map&lt; fourdst::atomic::Species, double &gt; gridfire::DynamicEngine::getSpeciesTimescales </td>
<td class="memname">virtual std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::DynamicEngine::getSpeciesDestructionTimescales </td>
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<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
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<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a522e78bce9ff062939572248d57f8cea">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a3d58e36ed8a6a0d82bb65e91090f7491">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#aef8f6bde24d27345067b71084330c7da">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#aa38c367ef3c74d012ccd10521cd5a727">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a020044829e0146427ed4830e5b02c4f3">PyDynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ad3d56a8b9161b9cc7f4da51f6bf7e8c9">&#9670;&#160;</a></span>getSpeciesIndex()</h2>
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<td class="memname">virtual int gridfire::DynamicEngine::getSpeciesIndex </td>
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<td class="paramtype">const fourdst::atomic::Species &amp;</td> <td class="paramname"><span class="paramname"><em>species</em></span></td><td>)</td>
<td> const</td>
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<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a9055feb245524a5a9549ace935f059ff">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a91d32b7197fcb27ee697d5bfde960f3f">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a2ee1d745c1c21b9fcb652c96c42f1091">PyDynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a6772ac384b4c3d3e91712041e4aaa813">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
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<td class="memname">virtual std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::DynamicEngine::getSpeciesTimescales </td>
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<dl class="section return"><dt>Returns</dt><dd>Map from Species to their characteristic timescales (s).</dd></dl>
<p>This method estimates the timescale for abundance change of each species, which can be used for timestep control, diagnostics, and reaction network culling. </p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a93b38d0fdc4647f6f7340172dae17872">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ace3c6ea4841318c08695973ab3dcddc6">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a26215593544c3a52597194602e4e25dd">gridfire::GraphEngine</a>.</p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4e856d6d4d2fc220952bbb7e6b2f85d9">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#ac8daafabbc76f4b6811bede241a03d72">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a65f9f33cddb0bbd1da7c9d0cff23d581">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a560612347bbd5b7b380e990624d01105">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a02a4c86c9637a3c9c9ca8ddd82ecff22">PyDynamicEngine</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>Stoichiometric coefficient for the species in the reaction.</dd></dl>
<p>The stoichiometry matrix must have been generated by <a class="el" href="#aeae6d84ef74d88fd2cdf07b82e98a16f" title="Generate the stoichiometry matrix for the network.">generateStoichiometryMatrix()</a>. </p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a67b4ea8cad115394bb4a42cc39d696f9">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a9da9224f5c99a5068f3d8cbf066e4693">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152">gridfire::GraphEngine</a>.</p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a67b4ea8cad115394bb4a42cc39d696f9">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#afa2820971397114d788730cc33feefe2">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a510b920dea726aef859ac1f6d051807e">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#ab48ef6db18da20024aa563a91fa16f83">PyDynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a942e65ced17ca602482cc42e469d6398">&#9670;&#160;</a></span>isStale()</h2>
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<td class="memname">virtual bool gridfire::DynamicEngine::isStale </td>
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<td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td> <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
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<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ad268c9942655e5c9605148fe07718e88">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a7d9e738dd28efb4d6127de7379169c87">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#af04a9f8a629d6f6c58c477af0f1ab9e5">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ae7847959fc5af2b83f5446dd73567b46">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a55bf19ed7534a312a36faf74753f7b14">PyDynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a55f1b7e5ebe2840e1d7c54665ca5411a">&#9670;&#160;</a></span>mapNetInToMolarAbundanceVector()</h2>
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<td class="memname">virtual std::vector&lt; double &gt; gridfire::DynamicEngine::mapNetInToMolarAbundanceVector </td>
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<td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td> <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
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<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7d0237956bf3ec7230bc51d88e7f8019">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a72789c1c3379594b65b560da50192de2">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a27f3a928e1f6bbe7e847cffed6db729f">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#aada497e8df74a295fdf5df7d7cdf64e0">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#a61bb4b430fe740cfb2c24e5cc673e4ac">PyDynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a21c34f59c080a853fafa38a25175124e">&#9670;&#160;</a></span>primeEngine()</h2>
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<td class="memname">virtual <a class="el" href="structgridfire_1_1_priming_report.html">PrimingReport</a> gridfire::DynamicEngine::primeEngine </td>
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<td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td> <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
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<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a70005361262bc180d4417b608661e3c3">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a13033abd3b44904f98b58c93e22da460">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#ae7a371be61ab09b3fa4a93f05bd44e5e">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a05730ced13ac5331060ca011f0da6235">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#ac22a10412be6649bf379e6d61113c878">PyDynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a4e2c8b896661b7a89beffe0066cb21cf">&#9670;&#160;</a></span>rebuild()</h2>
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<td class="memname">virtual void gridfire::DynamicEngine::rebuild </td>
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<td class="paramtype">const fourdst::composition::Composition &amp;</td> <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
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<td class="paramtype"><a class="el" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a></td> <td class="paramname"><span class="paramname"><em>depth</em></span>&#160;)</td>
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<p>Reimplemented in <a class="el" href="classgridfire_1_1_graph_engine.html#ad9d6c70ace5cbbf7f3aa7b31fce39490">gridfire::GraphEngine</a>, and <a class="el" href="class_py_dynamic_engine.html#a3d30a9116825ab2c5c209bc2712126bc">PyDynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00309">309</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#afb2ec904d88fc8aab516db4059d0e00f">&#9670;&#160;</a></span>setNetworkReactions()</h2>
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<td class="paramtype">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;</td> <td class="paramname"><span class="paramname"><em>reactions</em></span></td><td>)</td>
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<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7b3a6b3ab0a52f0f84d2b142e74ea672">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a9736edfb7c9148b60de30d50c0d3530d">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a371ba0881d6903ddb2d586faa61805d0">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#acb5fa7f03cd89b8c1b6b9ffdf3abb12e">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#afd818c408c64d207e71b1a90426328d6">PyDynamicEngine</a>.</p>
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<dl class="section post"><dt>Postcondition</dt><dd>The engine will use the specified screening model for subsequent rate calculations. </dd></dl>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aae4ddbef1c4e2202fd236221a4bf376b">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ad96bbee6d3d37b50d9236a975ef704c0">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f">gridfire::GraphEngine</a>.</p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aae4ddbef1c4e2202fd236221a4bf376b">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#abf2da57c83c3c4c635cb301f53088258">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a1a0c0a0ade632eb10f0eecab828a059f">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#afa3abfd612033336a656f092721c14ac">PyDynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#acd500e1cd788df1dc105d28a20dc5f4f">&#9670;&#160;</a></span>update()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#aa799ff785e7e79bf35b11efd55f6282a">&#9670;&#160;</a></span>update()</h2>
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<td class="memname">virtual fourdst::composition::Composition gridfire::DynamicEngine::update </td>
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<dl class="section post"><dt>Postcondition</dt><dd>The internal state of the engine is updated to reflect the new conditions. </dd></dl>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7d61e73f5158f1574cda3edc90c51f7e">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ace3568eadaba69e7357b4386c5ca3eb0">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a51b4cedf9b00de79fb6eef243631b04d">gridfire::GraphEngine</a>.</p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a2a7ecf985a326b4bea43e00cf9ee43dd">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#ae5762f395caea5381ec177507816b5ae">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a5ac7cff23e70bd07ba7e510b753e2ab6">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a6bee75b5a6e508e6eebf83f0d48c50b8">gridfire::MultiscalePartitioningEngineView</a>, and <a class="el" href="class_py_dynamic_engine.html#af8e6a8cd44f278535d7bcc9a896d6da8">PyDynamicEngine</a>.</p>
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<hr/>The documentation for this class was generated from the following file:<ul>
<li>src/network/include/gridfire/engine/<a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a></li>
<li>src/include/gridfire/engine/<a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a></li>
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