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docs(docs): asdded and cleaned up docs
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<title>GridFire: src/include/gridfire/engine/views/engine_defined.h Source File</title>
docs(docs): rebuilt
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<a href="engine__defined_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="preprocessor">#pragma once</span></div>
<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span> </div>
<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="preprocessor">#include &quot;<a class="code" href="engine__view__abstract_8h.html">gridfire/engine/views/engine_view_abstract.h</a>&quot;</span></div>
<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span><span class="preprocessor">#include &quot;<a class="code" href="engine__abstract_8h.html">gridfire/engine/engine_abstract.h</a>&quot;</span></div>
<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span><span class="preprocessor">#include &quot;<a class="code" href="network__file_8h.html">gridfire/io/network_file.h</a>&quot;</span></div>
<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="preprocessor">#include &quot;<a class="code" href="network_8h.html">gridfire/network.h</a>&quot;</span></div>
<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span> </div>
<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span><span class="preprocessor">#include &quot;fourdst/config/config.h&quot;</span></div>
<div class="line"><a id="l00009" name="l00009"></a><span class="lineno"> 9</span><span class="preprocessor">#include &quot;fourdst/logging/logging.h&quot;</span></div>
<div class="line"><a id="l00010" name="l00010"></a><span class="lineno"> 10</span> </div>
<div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span><span class="preprocessor">#include &quot;quill/Logger.h&quot;</span></div>
<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span> </div>
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#include &lt;string&gt;</span></div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> </div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacegridfire.html">gridfire</a>{</div>
docs(docs): asdded and cleaned up docs
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<div class="foldopen" id="foldopen00016" data-start="{" data-end="};">
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"><a class="line" href="classgridfire_1_1_defined_engine_view.html"> 16</a></span> <span class="keyword">class </span><a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a9b319b4a1bd5a08381ebb183daf72c92">DefinedEngineView</a> : <span class="keyword">public</span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>, <span class="keyword">public</span> <a class="code hl_class" href="classgridfire_1_1_engine_view.html">EngineView</a>&lt;DynamicEngine&gt; {</div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> <span class="keyword">public</span>:</div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a9b319b4a1bd5a08381ebb183daf72c92">DefinedEngineView</a>(<span class="keyword">const</span> std::vector&lt;std::string&gt;&amp; peNames, <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>&amp; baseEngine);</div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>&amp; <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a69b9a5812ad8bda13f956acd0da24484">getBaseEngine</a>() <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> </div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// --- Engine Interface ---</span></div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> <span class="keyword">const</span> std::vector&lt;fourdst::atomic::Species&gt;&amp; <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a1a55f9748c45af6f13e16a6b6ceaa211">getNetworkSpecies</a>() <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> </div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// --- DynamicEngine Interface ---</span></div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> std::expected&lt;StepDerivatives&lt;double&gt;, <a class="code hl_struct" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a>&gt; <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d">calculateRHSAndEnergy</a>(</div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> <span class="keyword">const</span> std::vector&lt;double&gt;&amp; Y_defined,</div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> ) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#ad25c722eaee1f28f8ed7b4d33a1f69ae">generateJacobianMatrix</a>(</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> <span class="keyword">const</span> std::vector&lt;double&gt;&amp; Y_dynamic,</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> ) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a273b175049f5ce7b9208e931ad139e1b">getJacobianMatrixEntry</a>(</div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> <span class="keyword">const</span> <span class="keywordtype">int</span> i_defined,</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> <span class="keyword">const</span> <span class="keywordtype">int</span> j_defined</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> ) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#ad07221be49ae1b5133c5b987dafac3b6">generateStoichiometryMatrix</a>() <span class="keyword">override</span>;</div>
<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> <span class="keywordtype">int</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#afa2820971397114d788730cc33feefe2">getStoichiometryMatrixEntry</a>(</div>
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> <span class="keyword">const</span> <span class="keywordtype">int</span> speciesIndex_defined,</div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> <span class="keyword">const</span> <span class="keywordtype">int</span> reactionIndex_defined</div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> ) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032">calculateMolarReactionFlow</a>(</div>
<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a>&amp; <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>,</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> <span class="keyword">const</span> std::vector&lt;double&gt;&amp; Y_defined,</div>
<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
<div class="line"><a id="l00108" name="l00108"></a><span class="lineno"> 108</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
<div class="line"><a id="l00109" name="l00109"></a><span class="lineno"> 109</span> ) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a>&amp; <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#ae03b4f9afac03d4011a4d7cf0423535d">getNetworkReactions</a>() <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> </div>
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a9736edfb7c9148b60de30d50c0d3530d">setNetworkReactions</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a>&amp; reactions) <span class="keyword">override</span>;</div>
<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> [[nodiscard]] std::expected&lt;std::unordered_map&lt;fourdst::atomic::Species, double&gt;, <a class="code hl_struct" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a>&gt; <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#ac8daafabbc76f4b6811bede241a03d72">getSpeciesTimescales</a>(</div>
<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> <span class="keyword">const</span> std::vector&lt;double&gt;&amp; Y_defined,</div>
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> ) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> </div>
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span> [[nodiscard]] std::expected&lt;std::unordered_map&lt;fourdst::atomic::Species, double&gt;, <a class="code hl_struct" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a>&gt; <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a3d58e36ed8a6a0d82bb65e91090f7491">getSpeciesDestructionTimescales</a>(</div>
<div class="line"><a id="l00137" name="l00137"></a><span class="lineno"> 137</span> <span class="keyword">const</span> std::vector&lt;double&gt;&amp; Y_defined,</div>
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> ) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span></div>
<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</span> fourdst::composition::Composition <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#ae5762f395caea5381ec177507816b5ae">update</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) <span class="keyword">override</span>;</div>
<div class="line"><a id="l00154" name="l00154"></a><span class="lineno"> 154</span> </div>
<div class="line"><a id="l00155" name="l00155"></a><span class="lineno"> 155</span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a7d9e738dd28efb4d6127de7379169c87">isStale</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a>&amp; netIn) <span class="keyword">override</span>;</div>
<div class="line"><a id="l00156" name="l00156"></a><span class="lineno"> 156</span></div>
<div class="line"><a id="l00162" name="l00162"></a><span class="lineno"> 162</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#abf2da57c83c3c4c635cb301f53088258">setScreeningModel</a>(<a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> model) <span class="keyword">override</span>;</div>
<div class="line"><a id="l00163" name="l00163"></a><span class="lineno"> 163</span></div>
<div class="line"><a id="l00169" name="l00169"></a><span class="lineno"> 169</span> [[nodiscard]] <a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a3c657b82a0117118a4bb0ce7f624ae0c">getScreeningModel</a>() <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> </div>
<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</span> [[nodiscard]] <span class="keywordtype">int</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3">getSpeciesIndex</a>(<span class="keyword">const</span> fourdst::atomic::Species &amp;species) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> </div>
<div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span> [[nodiscard]] std::vector&lt;double&gt; <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a72789c1c3379594b65b560da50192de2">mapNetInToMolarAbundanceVector</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00174" name="l00174"></a><span class="lineno"> 174</span> </div>
<div class="line"><a id="l00175" name="l00175"></a><span class="lineno"> 175</span> [[nodiscard]] <a class="code hl_struct" href="structgridfire_1_1_priming_report.html">PrimingReport</a> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a13033abd3b44904f98b58c93e22da460">primeEngine</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) <span class="keyword">override</span>;</div>
<div class="line"><a id="l00176" name="l00176"></a><span class="lineno"> 176</span> <span class="keyword">protected</span>:</div>
<div class="line"><a id="l00177" name="l00177"></a><span class="lineno"><a class="line" href="classgridfire_1_1_defined_engine_view.html#a217d541f3fa777b1552f652fbb520382"> 177</a></span> <span class="keywordtype">bool</span> <a class="code hl_variable" href="classgridfire_1_1_defined_engine_view.html#a217d541f3fa777b1552f652fbb520382">m_isStale</a> = <span class="keyword">true</span>;</div>
<div class="line"><a id="l00178" name="l00178"></a><span class="lineno"><a class="line" href="classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195"> 178</a></span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>&amp; <a class="code hl_variable" href="classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195">m_baseEngine</a>;</div>
<div class="line"><a id="l00179" name="l00179"></a><span class="lineno"> 179</span> <span class="keyword">private</span>:</div>
<div class="line"><a id="l00180" name="l00180"></a><span class="lineno"><a class="line" href="classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3"> 180</a></span> quill::Logger* <a class="code hl_variable" href="classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3">m_logger</a> = fourdst::logging::LogManager::getInstance().getLogger(<span class="stringliteral">&quot;log&quot;</span>); </div>
<div class="line"><a id="l00182" name="l00182"></a><span class="lineno"><a class="line" href="classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae"> 182</a></span> std::vector&lt;fourdst::atomic::Species&gt; <a class="code hl_variable" href="classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae">m_activeSpecies</a>;</div>
<div class="line"><a id="l00184" name="l00184"></a><span class="lineno"><a class="line" href="classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965"> 184</a></span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> <a class="code hl_variable" href="classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965">m_activeReactions</a>;</div>
<div class="line"><a id="l00185" name="l00185"></a><span class="lineno"> 185</span></div>
<div class="line"><a id="l00187" name="l00187"></a><span class="lineno"><a class="line" href="classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e"> 187</a></span> std::vector&lt;size_t&gt; <a class="code hl_variable" href="classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e">m_speciesIndexMap</a>;</div>
<div class="line"><a id="l00189" name="l00189"></a><span class="lineno"><a class="line" href="classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd"> 189</a></span> std::vector&lt;size_t&gt; <a class="code hl_variable" href="classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd">m_reactionIndexMap</a>;</div>
<div class="line"><a id="l00190" name="l00190"></a><span class="lineno"> 190</span> <span class="keyword">private</span>:</div>
<div class="line"><a id="l00201" name="l00201"></a><span class="lineno"> 201</span> std::vector&lt;size_t&gt; <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a9ea4812bc697fe43f8aded14f8aa0985">constructSpeciesIndexMap</a>() <span class="keyword">const</span>;</div>
<div class="line"><a id="l00202" name="l00202"></a><span class="lineno"> 202</span></div>
<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</span> std::vector&lt;size_t&gt; <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#ab2514984afaaf8590c28ab71943fbe68">constructReactionIndexMap</a>() <span class="keyword">const</span>;</div>
<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span></div>
<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> std::vector&lt;double&gt; <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843">mapViewToFull</a>(<span class="keyword">const</span> std::vector&lt;double&gt;&amp; defined) <span class="keyword">const</span>;</div>
<div class="line"><a id="l00223" name="l00223"></a><span class="lineno"> 223</span></div>
<div class="line"><a id="l00231" name="l00231"></a><span class="lineno"> 231</span> std::vector&lt;double&gt; <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a2f59af6fb3516911de2a3e3ff0ed8873">mapFullToView</a>(<span class="keyword">const</span> std::vector&lt;double&gt;&amp; full) <span class="keyword">const</span>;</div>
<div class="line"><a id="l00232" name="l00232"></a><span class="lineno"> 232</span></div>
<div class="line"><a id="l00241" name="l00241"></a><span class="lineno"> 241</span> <span class="keywordtype">size_t</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#af6fb8c3c7894b505bd81d15f012f154a">mapViewToFullSpeciesIndex</a>(<span class="keywordtype">size_t</span> definedSpeciesIndex) <span class="keyword">const</span>;</div>
<div class="line"><a id="l00242" name="l00242"></a><span class="lineno"> 242</span></div>
<div class="line"><a id="l00251" name="l00251"></a><span class="lineno"> 251</span> <span class="keywordtype">size_t</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#aadf373d69a22fcd171a6c251466d53d1">mapViewToFullReactionIndex</a>(<span class="keywordtype">size_t</span> definedReactionIndex) <span class="keyword">const</span>;</div>
<div class="line"><a id="l00252" name="l00252"></a><span class="lineno"> 252</span> </div>
<div class="line"><a id="l00253" name="l00253"></a><span class="lineno"> 253</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0">validateNetworkState</a>() <span class="keyword">const</span>;</div>
<div class="line"><a id="l00254" name="l00254"></a><span class="lineno"> 254</span> </div>
<div class="line"><a id="l00255" name="l00255"></a><span class="lineno"> 255</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#adbc64284b5f5a3256867be46fa87c69e">collect</a>(<span class="keyword">const</span> std::vector&lt;std::string&gt;&amp; peNames);</div>
<div class="line"><a id="l00256" name="l00256"></a><span class="lineno"> 256</span> </div>
<div class="line"><a id="l00257" name="l00257"></a><span class="lineno"> 257</span> };</div>
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docs(docs): asdded and cleaned up docs
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<div class="line"><a id="l00258" name="l00258"></a><span class="lineno"> 258</span> </div>
<div class="foldopen" id="foldopen00259" data-start="{" data-end="};">
<div class="line"><a id="l00259" name="l00259"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html"> 259</a></span> <span class="keyword">class </span><a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#a8f2f64bab0f516ed2a6fd529912e0acd">FileDefinedEngineView</a> final: <span class="keyword">public</span> <a class="code hl_function" href="classgridfire_1_1_defined_engine_view.html#a9b319b4a1bd5a08381ebb183daf72c92">DefinedEngineView</a> {</div>
<div class="line"><a id="l00260" name="l00260"></a><span class="lineno"> 260</span> <span class="keyword">public</span>:</div>
<div class="line"><a id="l00261" name="l00261"></a><span class="lineno"> 261</span> <span class="keyword">explicit</span> <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#a8f2f64bab0f516ed2a6fd529912e0acd">FileDefinedEngineView</a>(</div>
<div class="line"><a id="l00262" name="l00262"></a><span class="lineno"> 262</span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>&amp; baseEngine,</div>
<div class="line"><a id="l00263" name="l00263"></a><span class="lineno"> 263</span> <span class="keyword">const</span> std::string&amp; fileName,</div>
<div class="line"><a id="l00264" name="l00264"></a><span class="lineno"> 264</span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a>&amp; parser</div>
<div class="line"><a id="l00265" name="l00265"></a><span class="lineno"> 265</span> );</div>
<div class="line"><a id="l00266" name="l00266"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#ae0c35d8963b6ed05aeb88089ce301718"> 266</a></span> std::string <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ae0c35d8963b6ed05aeb88089ce301718">getNetworkFile</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#a1b343998b93955025a589b2b4541e33b">m_fileName</a>; }</div>
<div class="line"><a id="l00267" name="l00267"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#aea834dc382ff1d663040db4532ea928f"> 267</a></span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a>&amp; <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#aea834dc382ff1d663040db4532ea928f">getParser</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500">m_parser</a>; }</div>
<div class="line"><a id="l00268" name="l00268"></a><span class="lineno"> 268</span> <span class="keyword">private</span>:</div>
<div class="line"><a id="l00269" name="l00269"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#a63f8f85e75ecaab6fa39d48d7a846187"> 269</a></span> <span class="keyword">using </span><a class="code hl_typedef" href="classgridfire_1_1_file_defined_engine_view.html#a63f8f85e75ecaab6fa39d48d7a846187">Config</a> = fourdst::config::Config;</div>
<div class="line"><a id="l00270" name="l00270"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#acbb1a9bcb775e6d50de512a333afed08"> 270</a></span> <span class="keyword">using </span><a class="code hl_typedef" href="classgridfire_1_1_file_defined_engine_view.html#acbb1a9bcb775e6d50de512a333afed08">LogManager</a> = fourdst::logging::LogManager;</div>
<div class="line"><a id="l00271" name="l00271"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#a7a80966c023ae722239491af58609362"> 271</a></span> <a class="code hl_typedef" href="classgridfire_1_1_file_defined_engine_view.html#a63f8f85e75ecaab6fa39d48d7a846187">Config</a>&amp; <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#a7a80966c023ae722239491af58609362">m_config</a> = Config::getInstance();</div>
<div class="line"><a id="l00272" name="l00272"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432"> 272</a></span> quill::Logger* <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432">m_logger</a> = LogManager::getInstance().getLogger(<span class="stringliteral">&quot;log&quot;</span>);</div>
<div class="line"><a id="l00273" name="l00273"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#a1b343998b93955025a589b2b4541e33b"> 273</a></span> std::string <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#a1b343998b93955025a589b2b4541e33b">m_fileName</a>;</div>
<div class="line"><a id="l00275" name="l00275"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500"> 275</a></span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a>&amp; <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500">m_parser</a>;</div>
<div class="line"><a id="l00276" name="l00276"></a><span class="lineno"> 276</span> };</div>
</div>
<div class="line"><a id="l00277" name="l00277"></a><span class="lineno"> 277</span>}</div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a13033abd3b44904f98b58c93e22da460"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a13033abd3b44904f98b58c93e22da460">gridfire::DefinedEngineView::primeEngine</a></div><div class="ttdeci">PrimingReport primeEngine(const NetIn &amp;netIn) override</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00212">engine_defined.cpp:212</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a142725470f96cba3edb48a29f1264032"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032">gridfire::DefinedEngineView::calculateMolarReactionFlow</a></div><div class="ttdeci">double calculateMolarReactionFlow(const reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</div><div class="ttdoc">Calculates the molar reaction flow for a given reaction in the active network.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00091">engine_defined.cpp:91</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a1a55f9748c45af6f13e16a6b6ceaa211"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a1a55f9748c45af6f13e16a6b6ceaa211">gridfire::DefinedEngineView::getNetworkSpecies</a></div><div class="ttdeci">const std::vector&lt; fourdst::atomic::Species &gt; &amp; getNetworkSpecies() const override</div><div class="ttdoc">Gets the list of active species in the network defined by the file.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00026">engine_defined.cpp:26</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a217d541f3fa777b1552f652fbb520382"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a217d541f3fa777b1552f652fbb520382">gridfire::DefinedEngineView::m_isStale</a></div><div class="ttdeci">bool m_isStale</div><div class="ttdef"><b>Definition</b> <a href="#l00177">engine_defined.h:177</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a273b175049f5ce7b9208e931ad139e1b"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a273b175049f5ce7b9208e931ad139e1b">gridfire::DefinedEngineView::getJacobianMatrixEntry</a></div><div class="ttdeci">double getJacobianMatrixEntry(const int i_defined, const int j_defined) const override</div><div class="ttdoc">Gets an entry from the Jacobian matrix for the active species.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00062">engine_defined.cpp:62</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a2f59af6fb3516911de2a3e3ff0ed8873"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a2f59af6fb3516911de2a3e3ff0ed8873">gridfire::DefinedEngineView::mapFullToView</a></div><div class="ttdeci">std::vector&lt; double &gt; mapFullToView(const std::vector&lt; double &gt; &amp;full) const</div><div class="ttdoc">Maps a vector of full abundances to a vector of culled abundances.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00286">engine_defined.cpp:286</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a373d4a83f30527a1bfaf1d74ad14c965"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965">gridfire::DefinedEngineView::m_activeReactions</a></div><div class="ttdeci">reaction::LogicalReactionSet m_activeReactions</div><div class="ttdoc">Maps indices of active species to indices in the full network.</div><div class="ttdef"><b>Definition</b> <a href="#l00184">engine_defined.h:184</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a3c657b82a0117118a4bb0ce7f624ae0c"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a3c657b82a0117118a4bb0ce7f624ae0c">gridfire::DefinedEngineView::getScreeningModel</a></div><div class="ttdeci">screening::ScreeningType getScreeningModel() const override</div><div class="ttdoc">Gets the screening model from the base engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00184">engine_defined.cpp:184</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a3d58e36ed8a6a0d82bb65e91090f7491"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a3d58e36ed8a6a0d82bb65e91090f7491">gridfire::DefinedEngineView::getSpeciesDestructionTimescales</a></div><div class="ttdeci">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, expectations::StaleEngineError &gt; getSpeciesDestructionTimescales(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00146">engine_defined.cpp:146</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a4b0d71367cb1d4c06bcd01251bbeb60d"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d">gridfire::DefinedEngineView::calculateRHSAndEnergy</a></div><div class="ttdeci">std::expected&lt; StepDerivatives&lt; double &gt;, expectations::StaleEngineError &gt; calculateRHSAndEnergy(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</div><div class="ttdoc">Calculates the right-hand side (dY/dt) and energy generation for the active species.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00030">engine_defined.cpp:30</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a4f4aa847ee80ad430de9b1cfdda6b4e3"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3">gridfire::DefinedEngineView::m_logger</a></div><div class="ttdeci">quill::Logger * m_logger</div><div class="ttdoc">Active species in the defined engine.</div><div class="ttdef"><b>Definition</b> <a href="#l00180">engine_defined.h:180</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a56bd041c2fc7fe4f1371c38c8c0443e0"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0">gridfire::DefinedEngineView::validateNetworkState</a></div><div class="ttdeci">void validateNetworkState() const</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00313">engine_defined.cpp:313</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a626ab005bfa08b201518c13627e1f843"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843">gridfire::DefinedEngineView::mapViewToFull</a></div><div class="ttdeci">std::vector&lt; double &gt; mapViewToFull(const std::vector&lt; double &gt; &amp;defined) const</div><div class="ttdoc">Maps a vector of culled abundances to a vector of full abundances.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00277">engine_defined.cpp:277</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a64e9c79a36d529e1b296fe5786e57aae"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae">gridfire::DefinedEngineView::m_activeSpecies</a></div><div class="ttdeci">std::vector&lt; fourdst::atomic::Species &gt; m_activeSpecies</div><div class="ttdoc">Active reactions in the defined engine.</div><div class="ttdef"><b>Definition</b> <a href="#l00182">engine_defined.h:182</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a69b9a5812ad8bda13f956acd0da24484"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a69b9a5812ad8bda13f956acd0da24484">gridfire::DefinedEngineView::getBaseEngine</a></div><div class="ttdeci">const DynamicEngine &amp; getBaseEngine() const override</div><div class="ttdoc">Access the underlying engine instance.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00022">engine_defined.cpp:22</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a6e3243a8a8bcdce3282a8f82c5f98195"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195">gridfire::DefinedEngineView::m_baseEngine</a></div><div class="ttdeci">DynamicEngine &amp; m_baseEngine</div><div class="ttdef"><b>Definition</b> <a href="#l00178">engine_defined.h:178</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a72789c1c3379594b65b560da50192de2"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a72789c1c3379594b65b560da50192de2">gridfire::DefinedEngineView::mapNetInToMolarAbundanceVector</a></div><div class="ttdeci">std::vector&lt; double &gt; mapNetInToMolarAbundanceVector(const NetIn &amp;netIn) const override</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00201">engine_defined.cpp:201</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a7d9e738dd28efb4d6127de7379169c87"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a7d9e738dd28efb4d6127de7379169c87">gridfire::DefinedEngineView::isStale</a></div><div class="ttdeci">bool isStale(const NetIn &amp;netIn) override</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00175">engine_defined.cpp:175</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a9736edfb7c9148b60de30d50c0d3530d"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a9736edfb7c9148b60de30d50c0d3530d">gridfire::DefinedEngineView::setNetworkReactions</a></div><div class="ttdeci">void setNetworkReactions(const reaction::LogicalReactionSet &amp;reactions) override</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00114">engine_defined.cpp:114</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a9b319b4a1bd5a08381ebb183daf72c92"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a9b319b4a1bd5a08381ebb183daf72c92">gridfire::DefinedEngineView::DefinedEngineView</a></div><div class="ttdeci">DefinedEngineView(const std::vector&lt; std::string &gt; &amp;peNames, DynamicEngine &amp;baseEngine)</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00017">engine_defined.cpp:17</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_a9ea4812bc697fe43f8aded14f8aa0985"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#a9ea4812bc697fe43f8aded14f8aa0985">gridfire::DefinedEngineView::constructSpeciesIndexMap</a></div><div class="ttdeci">std::vector&lt; size_t &gt; constructSpeciesIndexMap() const</div><div class="ttdoc">Constructs the species index map.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00216">engine_defined.cpp:216</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_aadf373d69a22fcd171a6c251466d53d1"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#aadf373d69a22fcd171a6c251466d53d1">gridfire::DefinedEngineView::mapViewToFullReactionIndex</a></div><div class="ttdeci">size_t mapViewToFullReactionIndex(size_t definedReactionIndex) const</div><div class="ttdoc">Maps a culled reaction index to a full reaction index.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00304">engine_defined.cpp:304</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_ab2514984afaaf8590c28ab71943fbe68"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#ab2514984afaaf8590c28ab71943fbe68">gridfire::DefinedEngineView::constructReactionIndexMap</a></div><div class="ttdeci">std::vector&lt; size_t &gt; constructReactionIndexMap() const</div><div class="ttdoc">Constructs the reaction index map.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00245">engine_defined.cpp:245</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_abf2da57c83c3c4c635cb301f53088258"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#abf2da57c83c3c4c635cb301f53088258">gridfire::DefinedEngineView::setScreeningModel</a></div><div class="ttdeci">void setScreeningModel(screening::ScreeningType model) override</div><div class="ttdoc">Sets the screening model for the base engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00180">engine_defined.cpp:180</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_abfee22688617ffe91c69be93049c89b3"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3">gridfire::DefinedEngineView::getSpeciesIndex</a></div><div class="ttdeci">int getSpeciesIndex(const fourdst::atomic::Species &amp;species) const override</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00188">engine_defined.cpp:188</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_ac8daafabbc76f4b6811bede241a03d72"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#ac8daafabbc76f4b6811bede241a03d72">gridfire::DefinedEngineView::getSpeciesTimescales</a></div><div class="ttdeci">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, expectations::StaleEngineError &gt; getSpeciesTimescales(const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</div><div class="ttdoc">Computes timescales for all active species in the network.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00122">engine_defined.cpp:122</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_acc4976262e208d1dd2185ebccbdd275e"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e">gridfire::DefinedEngineView::m_speciesIndexMap</a></div><div class="ttdeci">std::vector&lt; size_t &gt; m_speciesIndexMap</div><div class="ttdoc">Maps indices of active reactions to indices in the full network.</div><div class="ttdef"><b>Definition</b> <a href="#l00187">engine_defined.h:187</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_ad07221be49ae1b5133c5b987dafac3b6"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#ad07221be49ae1b5133c5b987dafac3b6">gridfire::DefinedEngineView::generateStoichiometryMatrix</a></div><div class="ttdeci">void generateStoichiometryMatrix() override</div><div class="ttdoc">Generates the stoichiometry matrix for the active reactions and species.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00074">engine_defined.cpp:74</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_ad25c722eaee1f28f8ed7b4d33a1f69ae"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#ad25c722eaee1f28f8ed7b4d33a1f69ae">gridfire::DefinedEngineView::generateJacobianMatrix</a></div><div class="ttdeci">void generateJacobianMatrix(const std::vector&lt; double &gt; &amp;Y_dynamic, const double T9, const double rho) const override</div><div class="ttdoc">Generates the Jacobian matrix for the active species.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00051">engine_defined.cpp:51</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_adbc64284b5f5a3256867be46fa87c69e"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#adbc64284b5f5a3256867be46fa87c69e">gridfire::DefinedEngineView::collect</a></div><div class="ttdeci">void collect(const std::vector&lt; std::string &gt; &amp;peNames)</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00321">engine_defined.cpp:321</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_ae03b4f9afac03d4011a4d7cf0423535d"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#ae03b4f9afac03d4011a4d7cf0423535d">gridfire::DefinedEngineView::getNetworkReactions</a></div><div class="ttdeci">const reaction::LogicalReactionSet &amp; getNetworkReactions() const override</div><div class="ttdoc">Gets the set of active logical reactions in the network.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00108">engine_defined.cpp:108</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_ae5762f395caea5381ec177507816b5ae"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#ae5762f395caea5381ec177507816b5ae">gridfire::DefinedEngineView::update</a></div><div class="ttdeci">fourdst::composition::Composition update(const NetIn &amp;netIn) override</div><div class="ttdoc">Updates the engine view if it is marked as stale.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00171">engine_defined.cpp:171</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_af6fb8c3c7894b505bd81d15f012f154a"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#af6fb8c3c7894b505bd81d15f012f154a">gridfire::DefinedEngineView::mapViewToFullSpeciesIndex</a></div><div class="ttdeci">size_t mapViewToFullSpeciesIndex(size_t definedSpeciesIndex) const</div><div class="ttdoc">Maps a culled species index to a full species index.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00295">engine_defined.cpp:295</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_afa2820971397114d788730cc33feefe2"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#afa2820971397114d788730cc33feefe2">gridfire::DefinedEngineView::getStoichiometryMatrixEntry</a></div><div class="ttdeci">int getStoichiometryMatrixEntry(const int speciesIndex_defined, const int reactionIndex_defined) const override</div><div class="ttdoc">Gets an entry from the stoichiometry matrix for the active species and reactions.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00080">engine_defined.cpp:80</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html_affda6d60651c53ee02532806104671bd"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd">gridfire::DefinedEngineView::m_reactionIndexMap</a></div><div class="ttdeci">std::vector&lt; size_t &gt; m_reactionIndexMap</div><div class="ttdef"><b>Definition</b> <a href="#l00189">engine_defined.h:189</a></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="engine__abstract_8h_source.html#l00130">engine_abstract.h:130</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_engine_view_html"><div class="ttname"><a href="classgridfire_1_1_engine_view.html">gridfire::EngineView</a></div><div class="ttdoc">Abstract base class for a &quot;view&quot; of a reaction network engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__view__abstract_8h_source.html#l00074">engine_view_abstract.h:74</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a0a9b07176cb93b54c677b6ce71fda500"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500">gridfire::FileDefinedEngineView::m_parser</a></div><div class="ttdeci">const io::NetworkFileParser &amp; m_parser</div><div class="ttdef"><b>Definition</b> <a href="#l00275">engine_defined.h:275</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a1b343998b93955025a589b2b4541e33b"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a1b343998b93955025a589b2b4541e33b">gridfire::FileDefinedEngineView::m_fileName</a></div><div class="ttdeci">std::string m_fileName</div><div class="ttdoc">Parser for the network file.</div><div class="ttdef"><b>Definition</b> <a href="#l00273">engine_defined.h:273</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a63f8f85e75ecaab6fa39d48d7a846187"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a63f8f85e75ecaab6fa39d48d7a846187">gridfire::FileDefinedEngineView::Config</a></div><div class="ttdeci">fourdst::config::Config Config</div><div class="ttdef"><b>Definition</b> <a href="#l00269">engine_defined.h:269</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a7a80966c023ae722239491af58609362"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a7a80966c023ae722239491af58609362">gridfire::FileDefinedEngineView::m_config</a></div><div class="ttdeci">Config &amp; m_config</div><div class="ttdef"><b>Definition</b> <a href="#l00271">engine_defined.h:271</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a8f2f64bab0f516ed2a6fd529912e0acd"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a8f2f64bab0f516ed2a6fd529912e0acd">gridfire::FileDefinedEngineView::FileDefinedEngineView</a></div><div class="ttdeci">FileDefinedEngineView(DynamicEngine &amp;baseEngine, const std::string &amp;fileName, const io::NetworkFileParser &amp;parser)</div><div class="ttdoc">FileDefinedEngineView Implementation ///.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00379">engine_defined.cpp:379</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a9d93633ed4ab68de94b7274f879a0432"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432">gridfire::FileDefinedEngineView::m_logger</a></div><div class="ttdeci">quill::Logger * m_logger</div><div class="ttdef"><b>Definition</b> <a href="#l00272">engine_defined.h:272</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_acbb1a9bcb775e6d50de512a333afed08"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#acbb1a9bcb775e6d50de512a333afed08">gridfire::FileDefinedEngineView::LogManager</a></div><div class="ttdeci">fourdst::logging::LogManager LogManager</div><div class="ttdef"><b>Definition</b> <a href="#l00270">engine_defined.h:270</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ae0c35d8963b6ed05aeb88089ce301718"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ae0c35d8963b6ed05aeb88089ce301718">gridfire::FileDefinedEngineView::getNetworkFile</a></div><div class="ttdeci">std::string getNetworkFile() const</div><div class="ttdef"><b>Definition</b> <a href="#l00266">engine_defined.h:266</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_aea834dc382ff1d663040db4532ea928f"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#aea834dc382ff1d663040db4532ea928f">gridfire::FileDefinedEngineView::getParser</a></div><div class="ttdeci">const io::NetworkFileParser &amp; getParser() const</div><div class="ttdef"><b>Definition</b> <a href="#l00267">engine_defined.h:267</a></div></div>
<div class="ttc" id="aclassgridfire_1_1io_1_1_network_file_parser_html"><div class="ttname"><a href="classgridfire_1_1io_1_1_network_file_parser.html">gridfire::io::NetworkFileParser</a></div><div class="ttdoc">An abstract base class for network file parsers.</div><div class="ttdef"><b>Definition</b> <a href="network__file_8h_source.html#l00022">network_file.h:22</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1reaction_1_1_reaction_html"><div class="ttname"><a href="classgridfire_1_1reaction_1_1_reaction.html">gridfire::reaction::Reaction</a></div><div class="ttdoc">Represents a single nuclear reaction from a specific data source.</div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00072">reaction.h:72</a></div></div>
<div class="ttc" id="aengine__abstract_8h_html"><div class="ttname"><a href="engine__abstract_8h.html">engine_abstract.h</a></div><div class="ttdoc">Abstract interfaces for reaction network engines in GridFire.</div></div>
<div class="ttc" id="aengine__view__abstract_8h_html"><div class="ttname"><a href="engine__view__abstract_8h.html">engine_view_abstract.h</a></div><div class="ttdoc">Abstract interfaces for engine &quot;views&quot; in GridFire.</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>
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<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#l00563">reaction.h:563</a></div></div>
docs(docs): added extensive docs
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<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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<div class="ttc" id="anamespacegridfire_html"><div class="ttname"><a href="namespacegridfire.html">gridfire</a></div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00031">engine_abstract.h:31</a></div></div>
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<div class="ttc" id="anetwork_8h_html"><div class="ttname"><a href="network_8h.html">network.h</a></div></div>
<div class="ttc" id="anetwork__file_8h_html"><div class="ttname"><a href="network__file_8h.html">network_file.h</a></div></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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<div class="ttc" id="astructgridfire_1_1_priming_report_html"><div class="ttname"><a href="structgridfire_1_1_priming_report.html">gridfire::PrimingReport</a></div><div class="ttdoc">Captures the result of a network priming operation.</div><div class="ttdef"><b>Definition</b> <a href="reporting_8h_source.html#l00067">reporting.h:67</a></div></div>
<div class="ttc" id="astructgridfire_1_1expectations_1_1_stale_engine_error_html"><div class="ttname"><a href="structgridfire_1_1expectations_1_1_stale_engine_error.html">gridfire::expectations::StaleEngineError</a></div><div class="ttdef"><b>Definition</b> <a href="expected__engine_8h_source.html#l00044">expected_engine.h:44</a></div></div>
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docs(docs): asdded and cleaned up docs
2025-07-24 11:10:45 -04:00
<li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_b0856f6b0d80ccb263b2f415c91f9e17.html">include</a></li><li class="navelem"><a class="el" href="dir_3626e0c0e3c5d7812d6b277dfa4ec364.html">gridfire</a></li><li class="navelem"><a class="el" href="dir_aff155d61c3b73b9ab7dcdc908c4d49e.html">engine</a></li><li class="navelem"><a class="el" href="dir_d5492b42d970deba31f48df1b35a6c47.html">views</a></li><li class="navelem"><a class="el" href="engine__defined_8h.html">engine_defined.h</a></li>
docs(docs): rebuilt
2025-07-01 11:40:58 -04:00
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