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docs(docs): added extensive docs

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Emily Boudreaux
2025-07-01 15:06:22 -04:00
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@@ -176,24 +176,24 @@ $(function(){initNavTree('engine__abstract_8h_source.html',''); initResizable(tr
<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</span> <span class="keywordtype">double</span> T9,</div>
<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span> <span class="keywordtype">double</span> rho</div>
<div class="line"><a id="l00215" name="l00215"></a><span class="lineno"> 215</span> ) <span class="keyword">const</span> = 0;</div>
<div class="line"><a id="l00216" name="l00216"></a><span class="lineno"> 216</span> </div>
<div class="line"><a id="l00217" name="l00217"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f"> 217</a></span> <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f">update</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a>&amp; netIn) = 0;</div>
<div class="line"><a id="l00218" name="l00218"></a><span class="lineno"> 218</span> </div>
<div class="line"><a id="l00219" name="l00219"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd"> 219</a></span> <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">setScreeningModel</a>(<a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> model) = 0;</div>
<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span> </div>
<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0"> 221</a></span> [[nodiscard]] <span class="keyword">virtual</span> <a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">getScreeningModel</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> };</div>
<div class="line"><a id="l00216" name="l00216"></a><span class="lineno"> 216</span></div>
<div class="line"><a id="l00237" name="l00237"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f"> 237</a></span> <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f">update</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a>&amp; netIn) = 0;</div>
<div class="line"><a id="l00238" name="l00238"></a><span class="lineno"> 238</span></div>
<div class="line"><a id="l00255" name="l00255"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd"> 255</a></span> <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">setScreeningModel</a>(<a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> model) = 0;</div>
<div class="line"><a id="l00256" name="l00256"></a><span class="lineno"> 256</span></div>
<div class="line"><a id="l00267" name="l00267"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0"> 267</a></span> [[nodiscard]] <span class="keyword">virtual</span> <a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">getScreeningModel</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a id="l00268" name="l00268"></a><span class="lineno"> 268</span> };</div>
</div>
<div class="line"><a id="l00223" name="l00223"></a><span class="lineno"> 223</span>}</div>
<div class="line"><a id="l00269" name="l00269"></a><span class="lineno"> 269</span>}</div>
</div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><div class="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><div class="ttdef"><b>Definition</b> <a href="#l00121">engine_abstract.h:121</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a05d15ff35a6bc06a2fa7eda19838bd07"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">gridfire::DynamicEngine::getJacobianMatrixEntry</a></div><div class="ttdeci">virtual double getJacobianMatrixEntry(int i, int j) const =0</div><div class="ttdoc">Get an entry from the previously generated Jacobian matrix.</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a0a2fb3435ee3271ab9c806f225c61a7f"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f">gridfire::DynamicEngine::generateJacobianMatrix</a></div><div class="ttdeci">virtual void generateJacobianMatrix(const std::vector&lt; double &gt; &amp;Y, double T9, double rho)=0</div><div class="ttdoc">Generate the Jacobian matrix for the current state.</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a3fb44b6f55563a2f590f31916528f2bd"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">gridfire::DynamicEngine::setScreeningModel</a></div><div class="ttdeci">virtual void setScreeningModel(screening::ScreeningType model)=0</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a3fb44b6f55563a2f590f31916528f2bd"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">gridfire::DynamicEngine::setScreeningModel</a></div><div class="ttdeci">virtual void setScreeningModel(screening::ScreeningType model)=0</div><div class="ttdoc">Set the electron screening model.</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a5d8ba98b230d2849035ee2507728fa15"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15">gridfire::DynamicEngine::getSpeciesTimescales</a></div><div class="ttdeci">virtual std::unordered_map&lt; fourdst::atomic::Species, double &gt; getSpeciesTimescales(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</div><div class="ttdoc">Compute timescales for all species in the network.</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a6633b1757c41dd9e1c397333f4f9e785"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine::calculateMolarReactionFlow</a></div><div class="ttdeci">virtual double calculateMolarReactionFlow(const reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</div><div class="ttdoc">Calculate the molar reaction flow for a given reaction.</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a7a203f8e0f3a6744ddc912dfbcfdbcc0"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">gridfire::DynamicEngine::getScreeningModel</a></div><div class="ttdeci">virtual screening::ScreeningType getScreeningModel() const =0</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_acd500e1cd788df1dc105d28a20dc5f4f"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f">gridfire::DynamicEngine::update</a></div><div class="ttdeci">virtual void update(const NetIn &amp;netIn)=0</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a7a203f8e0f3a6744ddc912dfbcfdbcc0"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">gridfire::DynamicEngine::getScreeningModel</a></div><div class="ttdeci">virtual screening::ScreeningType getScreeningModel() const =0</div><div class="ttdoc">Get the current electron screening model.</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_acd500e1cd788df1dc105d28a20dc5f4f"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f">gridfire::DynamicEngine::update</a></div><div class="ttdeci">virtual void update(const NetIn &amp;netIn)=0</div><div class="ttdoc">Update the internal state of the engine.</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_ad2a82099edbb374bbb2c9509ccdb1037"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">gridfire::DynamicEngine::getNetworkReactions</a></div><div class="ttdeci">virtual const reaction::LogicalReactionSet &amp; getNetworkReactions() const =0</div><div class="ttdoc">Get the set of logical reactions in the network.</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_aeae6d84ef74d88fd2cdf07b82e98a16f"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">gridfire::DynamicEngine::generateStoichiometryMatrix</a></div><div class="ttdeci">virtual void generateStoichiometryMatrix()=0</div><div class="ttdoc">Generate the stoichiometry matrix for the network.</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_afa108dd5227dbb1045e90d7b3bd8b84f"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">gridfire::DynamicEngine::getStoichiometryMatrixEntry</a></div><div class="ttdeci">virtual int getStoichiometryMatrixEntry(int speciesIndex, int reactionIndex) const =0</div><div class="ttdoc">Get an entry from the stoichiometry matrix.</div></div>
@@ -205,7 +205,7 @@ $(function(){initNavTree('engine__abstract_8h_source.html',''); initResizable(tr
<div class="ttc" id="aconceptgridfire_1_1_is_arithmetic_or_a_d_html"><div class="ttname"><a href="conceptgridfire_1_1_is_arithmetic_or_a_d.html">gridfire::IsArithmeticOrAD</a></div><div class="ttdoc">Concept for types allowed in engine calculations.</div><div class="ttdef"><b>Definition</b> <a href="#l00033">engine_abstract.h:33</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1reaction_html"><div class="ttname"><a href="namespacegridfire_1_1reaction.html">gridfire::reaction</a></div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00025">reaction.h:25</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1reaction_html_aa86f08712565f278adacc7cd2361eb31"><div class="ttname"><a href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a></div><div class="ttdeci">TemplatedReactionSet&lt; LogicalReaction &gt; LogicalReactionSet</div><div class="ttdoc">A set of logical reactions.</div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00557">reaction.h:557</a></div></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="ttdef"><b>Definition</b> <a href="screening__types_8h_source.html#l00008">screening_types.h:8</a></div></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>
<div class="ttc" id="anamespacegridfire_html"><div class="ttname"><a href="namespacegridfire.html">gridfire</a></div><div class="ttdef"><b>Definition</b> <a href="#l00024">engine_abstract.h:24</a></div></div>
<div class="ttc" id="anetwork_8h_html"><div class="ttname"><a href="network_8h.html">network.h</a></div></div>
<div class="ttc" id="areaction_8h_html"><div class="ttname"><a href="reaction_8h.html">reaction.h</a></div><div class="ttdoc">Defines classes for representing and managing nuclear reactions.</div></div>