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docs(docs): added doxygen html directory
2025-07-01 07:24:18 -04:00
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<div id="projectbrief">General Purpose Nuclear Network</div>
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<a href="#pub-methods">Public Member Functions</a> &#124;
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<div class="headertitle"><div class="title">gridfire::DynamicEngine Class Reference<span class="mlabels"><span class="mlabel abstract">abstract</span></span></div></div>
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<p>Abstract class for engines supporting Jacobian and stoichiometry operations.
<a href="#details">More...</a></p>
<p><code>#include &lt;<a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>&gt;</code></p>
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Inheritance diagram for gridfire::DynamicEngine:</div>
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docs(docs): asdded and cleaned up docs
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docs(docs): added doxygen html directory
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</map>
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<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>
docs(docs): asdded and cleaned up docs
2025-07-24 11:10:45 -04:00
<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>
<tr class="separator:a818d942efa843959393e4eed3263b7e7"><td class="memSeparator" colspan="2">&#160;</td></tr>
docs(docs): added doxygen html directory
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<tr class="memitem:a05d15ff35a6bc06a2fa7eda19838bd07" id="r_a05d15ff35a6bc06a2fa7eda19838bd07"><td class="memItemLeft" align="right" valign="top">virtual double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a05d15ff35a6bc06a2fa7eda19838bd07">getJacobianMatrixEntry</a> (int i, int j) const =0</td></tr>
<tr class="memdesc:a05d15ff35a6bc06a2fa7eda19838bd07"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get an entry from the previously generated Jacobian matrix. <br /></td></tr>
<tr class="separator:a05d15ff35a6bc06a2fa7eda19838bd07"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aeae6d84ef74d88fd2cdf07b82e98a16f" id="r_aeae6d84ef74d88fd2cdf07b82e98a16f"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aeae6d84ef74d88fd2cdf07b82e98a16f">generateStoichiometryMatrix</a> ()=0</td></tr>
<tr class="memdesc:aeae6d84ef74d88fd2cdf07b82e98a16f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate the stoichiometry matrix for the network. <br /></td></tr>
<tr class="separator:aeae6d84ef74d88fd2cdf07b82e98a16f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:afa108dd5227dbb1045e90d7b3bd8b84f" id="r_afa108dd5227dbb1045e90d7b3bd8b84f"><td class="memItemLeft" align="right" valign="top">virtual int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#afa108dd5227dbb1045e90d7b3bd8b84f">getStoichiometryMatrixEntry</a> (int speciesIndex, int reactionIndex) const =0</td></tr>
<tr class="memdesc:afa108dd5227dbb1045e90d7b3bd8b84f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get an entry from the stoichiometry matrix. <br /></td></tr>
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<tr class="memdesc:a6633b1757c41dd9e1c397333f4f9e785"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the molar reaction flow for a given reaction. <br /></td></tr>
<tr class="separator:a6633b1757c41dd9e1c397333f4f9e785"><td class="memSeparator" colspan="2">&#160;</td></tr>
refactor(.gitignore): removed html/ from .gitignore
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<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>
docs(docs): added doxygen html directory
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<tr class="memdesc:ad2a82099edbb374bbb2c9509ccdb1037"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the set of logical reactions in the network. <br /></td></tr>
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docs(docs): asdded and cleaned up docs
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<tr class="memitem:afb2ec904d88fc8aab516db4059d0e00f" id="r_afb2ec904d88fc8aab516db4059d0e00f"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#afb2ec904d88fc8aab516db4059d0e00f">setNetworkReactions</a> (const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;reactions)=0</td></tr>
<tr class="separator:afb2ec904d88fc8aab516db4059d0e00f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<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>
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<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>
refactor(.gitignore): removed html/ from .gitignore
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<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>
docs(docs): added extensive docs
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<tr class="memdesc:a3fb44b6f55563a2f590f31916528f2bd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Set the electron screening model. <br /></td></tr>
refactor(.gitignore): removed html/ from .gitignore
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<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>
docs(docs): added extensive docs
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<tr class="memdesc:a7a203f8e0f3a6744ddc912dfbcfdbcc0"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the current electron screening model. <br /></td></tr>
refactor(.gitignore): removed html/ from .gitignore
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docs(docs): asdded and cleaned up docs
2025-07-24 11:10:45 -04:00
<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>
docs(docs): added doxygen html directory
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<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>
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<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>
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<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>
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<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>
<p>Extends <a class="el" href="classgridfire_1_1_engine.html" title="Abstract base class for a reaction network engine.">Engine</a> with additional methods for:</p><ul>
<li>Generating and accessing the Jacobian matrix (for implicit solvers).</li>
<li>Generating and accessing the stoichiometry matrix.</li>
<li>Calculating molar reaction flows for individual reactions.</li>
<li>Accessing the set of logical reactions in the network.</li>
<li>Computing timescales for each species.</li>
</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>
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<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>
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</div><h2 class="groupheader">Member Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a6633b1757c41dd9e1c397333f4f9e785">&#9670;&#160;</a></span>calculateMolarReactionFlow()</h2>
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<td class="memname">virtual double gridfire::DynamicEngine::calculateMolarReactionFlow </td>
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<p>Calculate the molar reaction flow for a given reaction. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">reaction</td><td>The reaction for which to calculate the flow. </td></tr>
<tr><td class="paramname">Y</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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<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>
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<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="#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>
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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>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>
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<tr><td class="paramname">Y_dynamic</td><td>Vector of current abundances. </td></tr>
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<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </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>
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<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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<td class="memname">virtual void gridfire::DynamicEngine::generateJacobianMatrix </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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<h2 class="memtitle"><span class="permalink"><a href="#aeae6d84ef74d88fd2cdf07b82e98a16f">&#9670;&#160;</a></span>generateStoichiometryMatrix()</h2>
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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>
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<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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<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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<p>Get an entry from the previously generated Jacobian matrix. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">i</td><td>Row index (species index). </td></tr>
<tr><td class="paramname">j</td><td>Column index (species index). </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>Value of the Jacobian matrix at (i, j).</dd></dl>
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<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>
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<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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<td class="memname">virtual const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp; gridfire::DynamicEngine::getNetworkReactions </td>
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<p>Get the set of logical reactions in the network. </p>
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<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>
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<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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<td class="memname">virtual <a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> gridfire::DynamicEngine::getScreeningModel </td>
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<p>Get the current electron screening model. </p>
<dl class="section return"><dt>Returns</dt><dd>The currently active screening model type.</dd></dl>
<dl class="section user"><dt>Usage Example:</dt><dd><div class="fragment"><div class="line"><a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> currentModel = myEngine.getScreeningModel();</div>
<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_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="#a6ca0f315f75252ca505507a61556dda6">&#9670;&#160;</a></span>getSpeciesDestructionTimescales()</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::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>
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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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<p>Compute timescales for all species in the network. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">Y</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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<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>
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<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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<h2 class="memtitle"><span class="permalink"><a href="#afa108dd5227dbb1045e90d7b3bd8b84f">&#9670;&#160;</a></span>getStoichiometryMatrixEntry()</h2>
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<td class="memname">virtual int gridfire::DynamicEngine::getStoichiometryMatrixEntry </td>
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<p>Get an entry from the stoichiometry matrix. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">speciesIndex</td><td>Index of the species. </td></tr>
<tr><td class="paramname">reactionIndex</td><td>Index of the reaction. </td></tr>
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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>
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<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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<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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<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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<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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<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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<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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<h2 class="memtitle"><span class="permalink"><a href="#a3fb44b6f55563a2f590f31916528f2bd">&#9670;&#160;</a></span>setScreeningModel()</h2>
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<td class="memname">virtual void gridfire::DynamicEngine::setScreeningModel </td>
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<td class="paramtype"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a></td> <td class="paramname"><span class="paramname"><em>model</em></span></td><td>)</td>
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<p>Set the electron screening model. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">model</td><td>The type of screening model to use for reaction rate calculations.</td></tr>
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<p>This method allows changing the screening model at runtime. Screening corrections account for the electrostatic shielding of nuclei by electrons, which affects reaction rates in dense stellar plasmas.</p>
<dl class="section user"><dt>Usage Example:</dt><dd><div class="fragment"><div class="line">myEngine.setScreeningModel(<a class="code hl_enumvalue" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25a32c7d8943bec86a6d7d5e03598670ca8">screening::ScreeningType::WEAK</a>);</div>
<div class="ttc" id="anamespacegridfire_1_1screening_html_aa82aafbc4f8c28d0a75b60798e3a7d25a32c7d8943bec86a6d7d5e03598670ca8"><div class="ttname"><a href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25a32c7d8943bec86a6d7d5e03598670ca8">gridfire::screening::ScreeningType::WEAK</a></div><div class="ttdeci">@ WEAK</div><div class="ttdoc">Weak screening model (Salpeter, 1954).</div><div class="ttdef"><b>Definition</b> <a href="screening__types_8h_source.html#l00035">screening_types.h:35</a></div></div>
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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>
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<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="#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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<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>Update the internal state of the engine. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">netIn</td><td>A struct containing the current network input, such as temperature, density, and composition.</td></tr>
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<p>This method is intended to be implemented by derived classes to update their internal state based on the provided network conditions. For example, an adaptive engine might use this to re-evaluate which reactions and species are active. For other engines that do not support manually updating, this method might do nothing.</p>
<dl class="section user"><dt>Usage Example:</dt><dd><div class="fragment"><div class="line"><a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a> input = { ... };</div>
<div class="line">myEngine.update(input);</div>
<div class="ttc" id="astructgridfire_1_1_net_in_html"><div class="ttname"><a href="structgridfire_1_1_net_in.html">gridfire::NetIn</a></div><div class="ttdef"><b>Definition</b> <a href="network_8h_source.html#l00053">network.h:53</a></div></div>
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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>
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<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>
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<li>src/include/gridfire/engine/<a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a></li>
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