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<div id="projectname">GridFire<span id="projectnumber"> 0.0.1a</span>
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<div id="projectbrief">General Purpose Nuclear Network</div>
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<a href="solver_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>
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<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span> </div>
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<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="preprocessor">#include "<a class="code" href="engine__graph_8h.html">gridfire/engine/engine_graph.h</a>"</span></div>
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<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span><span class="preprocessor">#include "<a class="code" href="engine__abstract_8h.html">gridfire/engine/engine_abstract.h</a>"</span></div>
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<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span><span class="preprocessor">#include "<a class="code" href="engine__adaptive_8h.html">gridfire/engine/engine_adaptive.h</a>"</span></div>
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<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="preprocessor">#include "<a class="code" href="network_8h.html">gridfire/network.h</a>"</span></div>
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<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span> </div>
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<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span><span class="preprocessor">#include "fourdst/logging/logging.h"</span></div>
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<div class="line"><a id="l00009" name="l00009"></a><span class="lineno"> 9</span><span class="preprocessor">#include "fourdst/config/config.h"</span></div>
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<div class="line"><a id="l00010" name="l00010"></a><span class="lineno"> 10</span> </div>
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<div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span><span class="preprocessor">#include "quill/Logger.h"</span></div>
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<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span> </div>
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<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#include "Eigen/Dense"</span></div>
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<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> </div>
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<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include <vector></span></div>
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<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> </div>
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<div class="foldopen" id="foldopen00017" data-start="{" data-end="}">
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<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"><a class="line" href="namespacegridfire_1_1solver.html"> 17</a></span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacegridfire_1_1solver.html">gridfire::solver</a> {</div>
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<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span></div>
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<div class="foldopen" id="foldopen00027" data-start="{" data-end="};">
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<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1dynamic_q_s_e_species_indices.html"> 27</a></span> <span class="keyword">struct </span><a class="code hl_struct" href="structgridfire_1_1solver_1_1dynamic_q_s_e_species_indices.html">dynamicQSESpeciesIndices</a> {</div>
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<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1dynamic_q_s_e_species_indices.html#ac6e0419abdd3c78b32e34c16c0543157"> 28</a></span> std::vector<size_t> <a class="code hl_variable" href="structgridfire_1_1solver_1_1dynamic_q_s_e_species_indices.html#ac6e0419abdd3c78b32e34c16c0543157">dynamicSpeciesIndices</a>; </div>
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<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1dynamic_q_s_e_species_indices.html#a7d4ba82d9e60a4914938ebebecaab4a2"> 29</a></span> std::vector<size_t> <a class="code hl_variable" href="structgridfire_1_1solver_1_1dynamic_q_s_e_species_indices.html#a7d4ba82d9e60a4914938ebebecaab4a2">QSESpeciesIndices</a>; </div>
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<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> };</div>
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</div>
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<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span></div>
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<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> <span class="keyword">template</span> <<span class="keyword">typename</span> EngineT></div>
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<div class="foldopen" id="foldopen00043" data-start="{" data-end="};">
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<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_network_solver_strategy.html"> 43</a></span> <span class="keyword">class </span><a class="code hl_function" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a01cbbec0eb5c3a60f50da38cdaf66505">NetworkSolverStrategy</a> {</div>
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<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> <span class="keyword">public</span>:</div>
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<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a01cbbec0eb5c3a60f50da38cdaf66505"> 49</a></span> <span class="keyword">explicit</span> <a class="code hl_function" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a01cbbec0eb5c3a60f50da38cdaf66505">NetworkSolverStrategy</a>(EngineT& engine) : <a class="code hl_variable" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a724924d94eaf82b67d9988a55c3261e8">m_engine</a>(engine) {};</div>
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<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span></div>
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<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a1693dc93f63599c89587d729aca8e318"> 54</a></span> <span class="keyword">virtual</span> <a class="code hl_function" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a1693dc93f63599c89587d729aca8e318">~NetworkSolverStrategy</a>() = <span class="keywordflow">default</span>;</div>
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<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span></div>
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<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#ace539b0482db171845ff1bd38d76b70f"> 61</a></span> <span class="keyword">virtual</span> <a class="code hl_struct" href="structgridfire_1_1_net_out.html">NetOut</a> <a class="code hl_function" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#ace539b0482db171845ff1bd38d76b70f">evaluate</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a>& netIn) = 0;</div>
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<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> <span class="keyword">protected</span>:</div>
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<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a724924d94eaf82b67d9988a55c3261e8"> 63</a></span> EngineT& <a class="code hl_variable" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a724924d94eaf82b67d9988a55c3261e8">m_engine</a>; </div>
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<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> };</div>
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</div>
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<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span></div>
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<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"><a class="line" href="namespacegridfire_1_1solver.html#a8118d08bc25e439754b43a3f5ecc1db3"> 69</a></span> <span class="keyword">using </span><a class="code hl_typedef" href="namespacegridfire_1_1solver.html#a8118d08bc25e439754b43a3f5ecc1db3">DynamicNetworkSolverStrategy</a> = <a class="code hl_class" href="classgridfire_1_1solver_1_1_network_solver_strategy.html">NetworkSolverStrategy<DynamicEngine></a>;</div>
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<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span></div>
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<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"><a class="line" href="namespacegridfire_1_1solver.html#af3b10822ab58b55365577755c1f4faf6"> 74</a></span> <span class="keyword">using </span><a class="code hl_typedef" href="namespacegridfire_1_1solver.html#af3b10822ab58b55365577755c1f4faf6">AdaptiveNetworkSolverStrategy</a> = <a class="code hl_class" href="classgridfire_1_1solver_1_1_network_solver_strategy.html">NetworkSolverStrategy<AdaptiveEngineView></a>;</div>
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<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span></div>
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<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"><a class="line" href="namespacegridfire_1_1solver.html#a5361d6cf364f0ba2f88285a60bb9cd92"> 79</a></span> <span class="keyword">using </span><a class="code hl_typedef" href="namespacegridfire_1_1solver.html#a5361d6cf364f0ba2f88285a60bb9cd92">StaticNetworkSolverStrategy</a> = <a class="code hl_class" href="classgridfire_1_1solver_1_1_network_solver_strategy.html">NetworkSolverStrategy<Engine></a>;</div>
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<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span></div>
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<div class="foldopen" id="foldopen00098" data-start="{" data-end="};">
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<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html"> 98</a></span> <span class="keyword">class </span><a class="code hl_class" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html">QSENetworkSolver</a> final : <span class="keyword">public</span> <a class="code hl_typedef" href="namespacegridfire_1_1solver.html#af3b10822ab58b55365577755c1f4faf6">AdaptiveNetworkSolverStrategy</a> {</div>
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<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> <span class="keyword">public</span>:</div>
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<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> <span class="keyword">using </span>AdaptiveNetworkSolverStrategy::AdaptiveNetworkSolverStrategy;</div>
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<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span></div>
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<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> <a class="code hl_struct" href="structgridfire_1_1_net_out.html">NetOut</a> <a class="code hl_function" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a53b5496db7fed6f345dca39656bf9c0e">evaluate</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a>& netIn) <span class="keyword">override</span>;</div>
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<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> <span class="keyword">private</span>: <span class="comment">// methods</span></div>
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<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> <a class="code hl_struct" href="structgridfire_1_1solver_1_1dynamic_q_s_e_species_indices.html">dynamicQSESpeciesIndices</a> <a class="code hl_function" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a5d81ee5bfcfd5e77fe52201ba9e63719">packSpeciesTypeIndexVectors</a>(</div>
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<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> <span class="keyword">const</span> std::vector<double>& Y,</div>
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<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span> ) <span class="keyword">const</span>;</div>
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<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"> 144</span></div>
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<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"> 158</span> Eigen::VectorXd <a class="code hl_function" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a00d112f6087f6e3a93f4d40a519308d2">calculateSteadyStateAbundances</a>(</div>
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<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span> <span class="keyword">const</span> std::vector<double>& Y,</div>
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<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho,</div>
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<div class="line"><a id="l00162" name="l00162"></a><span class="lineno"> 162</span> <span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1solver_1_1dynamic_q_s_e_species_indices.html">dynamicQSESpeciesIndices</a>& indices</div>
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<div class="line"><a id="l00163" name="l00163"></a><span class="lineno"> 163</span> ) <span class="keyword">const</span>;</div>
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<div class="line"><a id="l00164" name="l00164"></a><span class="lineno"> 164</span></div>
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<div class="line"><a id="l00176" name="l00176"></a><span class="lineno"> 176</span> <a class="code hl_struct" href="structgridfire_1_1_net_out.html">NetOut</a> <a class="code hl_function" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#abaa567001df0007b714f474febae408b">initializeNetworkWithShortIgnition</a>(</div>
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<div class="line"><a id="l00177" name="l00177"></a><span class="lineno"> 177</span> <span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a>& netIn</div>
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<div class="line"><a id="l00178" name="l00178"></a><span class="lineno"> 178</span> ) <span class="keyword">const</span>;</div>
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<div class="line"><a id="l00179" name="l00179"></a><span class="lineno"> 179</span></div>
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<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a35f1f6ede393f15c8bb8862f3f1c3b07">shouldUpdateView</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a>& conditions) <span class="keyword">const</span>;</div>
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<div class="line"><a id="l00192" name="l00192"></a><span class="lineno"> 192</span> <span class="keyword">private</span>: <span class="comment">// Nested functors for ODE integration</span></div>
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<div class="foldopen" id="foldopen00201" data-start="{" data-end="};">
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<div class="line"><a id="l00201" name="l00201"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html"> 201</a></span> <span class="keyword">struct </span><a class="code hl_function" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a5353d8e6f27b6c435084a167bc009e46">RHSFunctor</a> {</div>
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<div class="line"><a id="l00202" name="l00202"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a0d8d28a6559cfed5e7cd683523d49b2c"> 202</a></span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a0d8d28a6559cfed5e7cd683523d49b2c">m_engine</a>; </div>
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<div class="line"><a id="l00203" name="l00203"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a3ac1ef529627d21f7d1ad718dc87f7f9"> 203</a></span> <span class="keyword">const</span> std::vector<size_t>& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a3ac1ef529627d21f7d1ad718dc87f7f9">m_dynamicSpeciesIndices</a>; </div>
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<div class="line"><a id="l00204" name="l00204"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a6be7259897a47ce480b289144b06e269"> 204</a></span> <span class="keyword">const</span> std::vector<size_t>& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a6be7259897a47ce480b289144b06e269">m_QSESpeciesIndices</a>; </div>
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<div class="line"><a id="l00205" name="l00205"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a02c23ef20d616bf5a591a274b66cd75a"> 205</a></span> <span class="keyword">const</span> Eigen::VectorXd& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a02c23ef20d616bf5a591a274b66cd75a">m_Y_QSE</a>; </div>
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<div class="line"><a id="l00206" name="l00206"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a35026100163c7cc6fdb4c2e4d988b8cb"> 206</a></span> <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a35026100163c7cc6fdb4c2e4d988b8cb">m_T9</a>; </div>
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<div class="line"><a id="l00207" name="l00207"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#adc0f8e655af42f414dcb220a7224f261"> 207</a></span> <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#adc0f8e655af42f414dcb220a7224f261">m_rho</a>; </div>
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<div class="line"><a id="l00208" name="l00208"></a><span class="lineno"> 208</span> </div>
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<div class="line"><a id="l00209" name="l00209"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a81f964b87457847d7de13fed18499283"> 209</a></span> <span class="keywordtype">bool</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a81f964b87457847d7de13fed18499283">m_isViewInitialized</a> = <span class="keyword">false</span>;</div>
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<div class="line"><a id="l00210" name="l00210"></a><span class="lineno"> 210</span></div>
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<div class="foldopen" id="foldopen00220" data-start="{" data-end="}">
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<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a5353d8e6f27b6c435084a167bc009e46"> 220</a></span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a5353d8e6f27b6c435084a167bc009e46">RHSFunctor</a>(</div>
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<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"> 221</span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>& engine,</div>
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<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> <span class="keyword">const</span> std::vector<size_t>& dynamicSpeciesIndices,</div>
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<div class="line"><a id="l00223" name="l00223"></a><span class="lineno"> 223</span> <span class="keyword">const</span> std::vector<size_t>& QSESpeciesIndices,</div>
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<div class="line"><a id="l00224" name="l00224"></a><span class="lineno"> 224</span> <span class="keyword">const</span> Eigen::VectorXd& Y_QSE,</div>
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<div class="line"><a id="l00225" name="l00225"></a><span class="lineno"> 225</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00226" name="l00226"></a><span class="lineno"> 226</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00227" name="l00227"></a><span class="lineno"> 227</span> ) :</div>
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<div class="line"><a id="l00228" name="l00228"></a><span class="lineno"> 228</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a0d8d28a6559cfed5e7cd683523d49b2c">m_engine</a>(engine),</div>
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<div class="line"><a id="l00229" name="l00229"></a><span class="lineno"> 229</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a3ac1ef529627d21f7d1ad718dc87f7f9">m_dynamicSpeciesIndices</a>(dynamicSpeciesIndices),</div>
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<div class="line"><a id="l00230" name="l00230"></a><span class="lineno"> 230</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a6be7259897a47ce480b289144b06e269">m_QSESpeciesIndices</a>(QSESpeciesIndices),</div>
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<div class="line"><a id="l00231" name="l00231"></a><span class="lineno"> 231</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a02c23ef20d616bf5a591a274b66cd75a">m_Y_QSE</a>(Y_QSE),</div>
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<div class="line"><a id="l00232" name="l00232"></a><span class="lineno"> 232</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a35026100163c7cc6fdb4c2e4d988b8cb">m_T9</a>(T9),</div>
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<div class="line"><a id="l00233" name="l00233"></a><span class="lineno"> 233</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#adc0f8e655af42f414dcb220a7224f261">m_rho</a>(rho) {}</div>
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</div>
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<div class="line"><a id="l00234" name="l00234"></a><span class="lineno"> 234</span></div>
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<div class="line"><a id="l00241" name="l00241"></a><span class="lineno"> 241</span> <span class="keywordtype">void</span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#ae0b6362d9c0a14e69c7a47233db6a86a">operator()</a>(</div>
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<div class="line"><a id="l00242" name="l00242"></a><span class="lineno"> 242</span> <span class="keyword">const</span> boost::numeric::ublas::vector<double>& YDynamic,</div>
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<div class="line"><a id="l00243" name="l00243"></a><span class="lineno"> 243</span> boost::numeric::ublas::vector<double>& dYdtDynamic,</div>
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<div class="line"><a id="l00244" name="l00244"></a><span class="lineno"> 244</span> <span class="keywordtype">double</span> t</div>
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<div class="line"><a id="l00245" name="l00245"></a><span class="lineno"> 245</span> ) <span class="keyword">const</span>;</div>
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<div class="line"><a id="l00246" name="l00246"></a><span class="lineno"> 246</span> </div>
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<div class="line"><a id="l00247" name="l00247"></a><span class="lineno"> 247</span> };</div>
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</div>
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<div class="line"><a id="l00248" name="l00248"></a><span class="lineno"> 248</span></div>
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<div class="foldopen" id="foldopen00259" data-start="{" data-end="};">
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<div class="line"><a id="l00259" name="l00259"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html"> 259</a></span> <span class="keyword">struct </span><a class="code hl_function" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#ab8222646cd32670a046b6c74909bd83a">JacobianFunctor</a> {</div>
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<div class="line"><a id="l00260" name="l00260"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#aaaa82eff96e6127a6de05444f730e43a"> 260</a></span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#aaaa82eff96e6127a6de05444f730e43a">m_engine</a>; </div>
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<div class="line"><a id="l00261" name="l00261"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a2071ce797f94ae1a3ea6d934748672ce"> 261</a></span> <span class="keyword">const</span> std::vector<size_t>& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a2071ce797f94ae1a3ea6d934748672ce">m_dynamicSpeciesIndices</a>; </div>
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<div class="line"><a id="l00262" name="l00262"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a1b92391170eb46771bd499aa8d115334"> 262</a></span> <span class="keyword">const</span> std::vector<size_t>& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a1b92391170eb46771bd499aa8d115334">m_QSESpeciesIndices</a>; </div>
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<div class="line"><a id="l00263" name="l00263"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a85f88639447a9a706008efece82ff289"> 263</a></span> <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a85f88639447a9a706008efece82ff289">m_T9</a>; </div>
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<div class="line"><a id="l00264" name="l00264"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a0907f7b6c1a87baf5e39fbc17a30df82"> 264</a></span> <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a0907f7b6c1a87baf5e39fbc17a30df82">m_rho</a>; </div>
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<div class="line"><a id="l00265" name="l00265"></a><span class="lineno"> 265</span></div>
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<div class="foldopen" id="foldopen00274" data-start="{" data-end="}">
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<div class="line"><a id="l00274" name="l00274"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#ab8222646cd32670a046b6c74909bd83a"> 274</a></span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#ab8222646cd32670a046b6c74909bd83a">JacobianFunctor</a>(</div>
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<div class="line"><a id="l00275" name="l00275"></a><span class="lineno"> 275</span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>& engine,</div>
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<div class="line"><a id="l00276" name="l00276"></a><span class="lineno"> 276</span> <span class="keyword">const</span> std::vector<size_t>& dynamicSpeciesIndices,</div>
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<div class="line"><a id="l00277" name="l00277"></a><span class="lineno"> 277</span> <span class="keyword">const</span> std::vector<size_t>& QSESpeciesIndices,</div>
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<div class="line"><a id="l00278" name="l00278"></a><span class="lineno"> 278</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00279" name="l00279"></a><span class="lineno"> 279</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00280" name="l00280"></a><span class="lineno"> 280</span> ) :</div>
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<div class="line"><a id="l00281" name="l00281"></a><span class="lineno"> 281</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#aaaa82eff96e6127a6de05444f730e43a">m_engine</a>(engine),</div>
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<div class="line"><a id="l00282" name="l00282"></a><span class="lineno"> 282</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a2071ce797f94ae1a3ea6d934748672ce">m_dynamicSpeciesIndices</a>(dynamicSpeciesIndices),</div>
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<div class="line"><a id="l00283" name="l00283"></a><span class="lineno"> 283</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a1b92391170eb46771bd499aa8d115334">m_QSESpeciesIndices</a>(QSESpeciesIndices),</div>
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<div class="line"><a id="l00284" name="l00284"></a><span class="lineno"> 284</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a85f88639447a9a706008efece82ff289">m_T9</a>(T9),</div>
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<div class="line"><a id="l00285" name="l00285"></a><span class="lineno"> 285</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a0907f7b6c1a87baf5e39fbc17a30df82">m_rho</a>(rho) {}</div>
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</div>
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<div class="line"><a id="l00286" name="l00286"></a><span class="lineno"> 286</span></div>
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<div class="line"><a id="l00294" name="l00294"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a3668fae1e0f8e69ff3fd87275bf4a79d"> 294</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a3668fae1e0f8e69ff3fd87275bf4a79d">operator()</a>(</div>
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<div class="line"><a id="l00295" name="l00295"></a><span class="lineno"> 295</span> <span class="keyword">const</span> boost::numeric::ublas::vector<double>& YDynamic,</div>
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<div class="line"><a id="l00296" name="l00296"></a><span class="lineno"> 296</span> boost::numeric::ublas::matrix<double>& JDynamic,</div>
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<div class="line"><a id="l00297" name="l00297"></a><span class="lineno"> 297</span> <span class="keywordtype">double</span> t,</div>
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<div class="line"><a id="l00298" name="l00298"></a><span class="lineno"> 298</span> boost::numeric::ublas::vector<double>& dfdt</div>
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<div class="line"><a id="l00299" name="l00299"></a><span class="lineno"> 299</span> ) <span class="keyword">const</span>;</div>
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<div class="line"><a id="l00300" name="l00300"></a><span class="lineno"> 300</span> };</div>
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</div>
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<div class="line"><a id="l00301" name="l00301"></a><span class="lineno"> 301</span></div>
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<div class="line"><a id="l00308" name="l00308"></a><span class="lineno"> 308</span> <span class="keyword">template</span><<span class="keyword">typename</span> T></div>
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<div class="foldopen" id="foldopen00309" data-start="{" data-end="};">
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<div class="line"><a id="l00309" name="l00309"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html"> 309</a></span> <span class="keyword">struct </span><a class="code hl_function" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#af8650f704c2ca512c9c5b4562b3b0958">EigenFunctor</a> {</div>
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<div class="line"><a id="l00310" name="l00310"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ac4ec3c180a9778acdd604a9b80d25399"> 310</a></span> <span class="keyword">using </span><a class="code hl_typedef" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ac4ec3c180a9778acdd604a9b80d25399">InputType</a> = Eigen::Matrix<T, Eigen::Dynamic, 1>;</div>
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<div class="line"><a id="l00311" name="l00311"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abc86b32db81acf1b24feb3763dc4ddb0"> 311</a></span> <span class="keyword">using </span><a class="code hl_typedef" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abc86b32db81acf1b24feb3763dc4ddb0">OutputType</a> = Eigen::Matrix<T, Eigen::Dynamic, 1>;</div>
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<div class="line"><a id="l00312" name="l00312"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ad42fdb6d5ae06eaa6ddccf03eba0a50c"> 312</a></span> <span class="keyword">using </span><a class="code hl_typedef" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ad42fdb6d5ae06eaa6ddccf03eba0a50c">JacobianType</a> = Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic>;</div>
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<div class="line"><a id="l00313" name="l00313"></a><span class="lineno"> 313</span> </div>
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<div class="line"><a id="l00314" name="l00314"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a93b46ca95ddf9e4d21d02700621e6285"> 314</a></span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a93b46ca95ddf9e4d21d02700621e6285">m_engine</a>; </div>
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<div class="line"><a id="l00315" name="l00315"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#af4f10300bde1e8e07b896bfca6335401"> 315</a></span> <span class="keyword">const</span> std::vector<double>& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#af4f10300bde1e8e07b896bfca6335401">m_YDynamic</a>; </div>
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<div class="line"><a id="l00316" name="l00316"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a08ce53701b152f3ce108c1c18ce64de2"> 316</a></span> <span class="keyword">const</span> std::vector<size_t>& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a08ce53701b152f3ce108c1c18ce64de2">m_dynamicSpeciesIndices</a>; </div>
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<div class="line"><a id="l00317" name="l00317"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d"> 317</a></span> <span class="keyword">const</span> std::vector<size_t>& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>; </div>
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<div class="line"><a id="l00318" name="l00318"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a6771ae56ddd9058954b42ee92a378309"> 318</a></span> <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a6771ae56ddd9058954b42ee92a378309">m_T9</a>; </div>
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<div class="line"><a id="l00319" name="l00319"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ab0a0d4c166e97b971543cbbf2b0a1a2e"> 319</a></span> <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ab0a0d4c166e97b971543cbbf2b0a1a2e">m_rho</a>; </div>
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<div class="line"><a id="l00320" name="l00320"></a><span class="lineno"> 320</span></div>
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<div class="foldopen" id="foldopen00330" data-start="{" data-end="}">
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<div class="line"><a id="l00330" name="l00330"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#af8650f704c2ca512c9c5b4562b3b0958"> 330</a></span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#af8650f704c2ca512c9c5b4562b3b0958">EigenFunctor</a>(</div>
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<div class="line"><a id="l00331" name="l00331"></a><span class="lineno"> 331</span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>& engine,</div>
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<div class="line"><a id="l00332" name="l00332"></a><span class="lineno"> 332</span> <span class="keyword">const</span> std::vector<double>& YDynamic,</div>
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<div class="line"><a id="l00333" name="l00333"></a><span class="lineno"> 333</span> <span class="keyword">const</span> std::vector<size_t>& dynamicSpeciesIndices,</div>
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<div class="line"><a id="l00334" name="l00334"></a><span class="lineno"> 334</span> <span class="keyword">const</span> std::vector<size_t>& QSESpeciesIndices,</div>
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<div class="line"><a id="l00335" name="l00335"></a><span class="lineno"> 335</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00336" name="l00336"></a><span class="lineno"> 336</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00337" name="l00337"></a><span class="lineno"> 337</span> ) :</div>
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<div class="line"><a id="l00338" name="l00338"></a><span class="lineno"> 338</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a93b46ca95ddf9e4d21d02700621e6285">m_engine</a>(engine),</div>
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<div class="line"><a id="l00339" name="l00339"></a><span class="lineno"> 339</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#af4f10300bde1e8e07b896bfca6335401">m_YDynamic</a>(YDynamic),</div>
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<div class="line"><a id="l00340" name="l00340"></a><span class="lineno"> 340</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a08ce53701b152f3ce108c1c18ce64de2">m_dynamicSpeciesIndices</a>(dynamicSpeciesIndices),</div>
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<div class="line"><a id="l00341" name="l00341"></a><span class="lineno"> 341</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>(QSESpeciesIndices),</div>
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<div class="line"><a id="l00342" name="l00342"></a><span class="lineno"> 342</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a6771ae56ddd9058954b42ee92a378309">m_T9</a>(T9),</div>
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<div class="line"><a id="l00343" name="l00343"></a><span class="lineno"> 343</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ab0a0d4c166e97b971543cbbf2b0a1a2e">m_rho</a>(rho) {}</div>
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</div>
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<div class="line"><a id="l00344" name="l00344"></a><span class="lineno"> 344</span></div>
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<div class="line"><a id="l00351" name="l00351"></a><span class="lineno"> 351</span> <span class="keywordtype">int</span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a91c9c7c40c061dcfb6e57524e696676e">operator()</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ac4ec3c180a9778acdd604a9b80d25399">InputType</a>& v_QSE, <a class="code hl_typedef" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abc86b32db81acf1b24feb3763dc4ddb0">OutputType</a>& f_QSE) <span class="keyword">const</span>;</div>
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<div class="line"><a id="l00352" name="l00352"></a><span class="lineno"> 352</span></div>
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<div class="line"><a id="l00359" name="l00359"></a><span class="lineno"> 359</span> <span class="keywordtype">int</span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ac46bd712296b03f31af1573f6a0f5644">df</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ac4ec3c180a9778acdd604a9b80d25399">InputType</a>& v_QSE, <a class="code hl_typedef" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ad42fdb6d5ae06eaa6ddccf03eba0a50c">JacobianType</a>& J_QSE) <span class="keyword">const</span>;</div>
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<div class="line"><a id="l00360" name="l00360"></a><span class="lineno"> 360</span> };</div>
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</div>
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<div class="line"><a id="l00361" name="l00361"></a><span class="lineno"> 361</span> <span class="keyword">private</span>:</div>
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<div class="line"><a id="l00362" name="l00362"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a428b49fa7878559665363de06f1a44a7"> 362</a></span> quill::Logger* <a class="code hl_variable" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a428b49fa7878559665363de06f1a44a7">m_logger</a> = fourdst::logging::LogManager::getInstance().getLogger(<span class="stringliteral">"log"</span>); </div>
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<div class="line"><a id="l00363" name="l00363"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a7d19b6e50db34d38c81afec76bbedee1"> 363</a></span> fourdst::config::Config& <a class="code hl_variable" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a7d19b6e50db34d38c81afec76bbedee1">m_config</a> = fourdst::config::Config::getInstance(); </div>
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<div class="line"><a id="l00364" name="l00364"></a><span class="lineno"> 364</span> </div>
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<div class="line"><a id="l00365" name="l00365"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#ab07e68fd418ab058f890502d191b3f18"> 365</a></span> <span class="keywordtype">bool</span> <a class="code hl_variable" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#ab07e68fd418ab058f890502d191b3f18">m_isViewInitialized</a> = <span class="keyword">false</span>; </div>
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<div class="line"><a id="l00366" name="l00366"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a3c9d46c8f5c519854cd65309a588772f"> 366</a></span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a> <a class="code hl_variable" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a3c9d46c8f5c519854cd65309a588772f">m_lastSeenConditions</a>; </div>
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<div class="line"><a id="l00367" name="l00367"></a><span class="lineno"> 367</span> };</div>
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</div>
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<div class="line"><a id="l00368" name="l00368"></a><span class="lineno"> 368</span></div>
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<div class="foldopen" id="foldopen00379" data-start="{" data-end="};">
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<div class="line"><a id="l00379" name="l00379"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_direct_network_solver.html"> 379</a></span> <span class="keyword">class </span><a class="code hl_class" href="classgridfire_1_1solver_1_1_direct_network_solver.html">DirectNetworkSolver</a> final : <span class="keyword">public</span> <a class="code hl_typedef" href="namespacegridfire_1_1solver.html#a8118d08bc25e439754b43a3f5ecc1db3">DynamicNetworkSolverStrategy</a> {</div>
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<div class="line"><a id="l00380" name="l00380"></a><span class="lineno"> 380</span> <span class="keyword">public</span>:</div>
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<div class="line"><a id="l00385" name="l00385"></a><span class="lineno"> 385</span> <span class="keyword">using </span>DynamicNetworkSolverStrategy::DynamicNetworkSolverStrategy;</div>
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<div class="line"><a id="l00386" name="l00386"></a><span class="lineno"> 386</span></div>
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<div class="line"><a id="l00392" name="l00392"></a><span class="lineno"> 392</span> <a class="code hl_struct" href="structgridfire_1_1_net_out.html">NetOut</a> <a class="code hl_function" href="classgridfire_1_1solver_1_1_direct_network_solver.html#a0e8a4b8ef656e0b084d11bea982e412a">evaluate</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a>& netIn) <span class="keyword">override</span>;</div>
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<div class="line"><a id="l00393" name="l00393"></a><span class="lineno"> 393</span> <span class="keyword">private</span>:</div>
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<div class="foldopen" id="foldopen00402" data-start="{" data-end="};">
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<div class="line"><a id="l00402" name="l00402"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html"> 402</a></span> <span class="keyword">struct </span><a class="code hl_function" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#aed201b52ea757069c17a49e9638b3d3c">RHSFunctor</a> {</div>
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<div class="line"><a id="l00403" name="l00403"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a04f8c84e46e6fbd0977e50fda4829d1a"> 403</a></span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a04f8c84e46e6fbd0977e50fda4829d1a">m_engine</a>; </div>
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<div class="line"><a id="l00404" name="l00404"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a082844f1eae0609e66620575210e8823"> 404</a></span> <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a082844f1eae0609e66620575210e8823">m_T9</a>; </div>
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<div class="line"><a id="l00405" name="l00405"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a7d4f7f04c4ee6f0b519194f87aa265e7"> 405</a></span> <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a7d4f7f04c4ee6f0b519194f87aa265e7">m_rho</a>; </div>
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<div class="line"><a id="l00406" name="l00406"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#ac4a1af03d2a4fbc5cc2407b8a6833147"> 406</a></span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#ac4a1af03d2a4fbc5cc2407b8a6833147">m_numSpecies</a>; </div>
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<div class="line"><a id="l00407" name="l00407"></a><span class="lineno"> 407</span></div>
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<div class="foldopen" id="foldopen00414" data-start="{" data-end="}">
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<div class="line"><a id="l00414" name="l00414"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#aed201b52ea757069c17a49e9638b3d3c"> 414</a></span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#aed201b52ea757069c17a49e9638b3d3c">RHSFunctor</a>(</div>
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<div class="line"><a id="l00415" name="l00415"></a><span class="lineno"> 415</span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>& engine,</div>
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<div class="line"><a id="l00416" name="l00416"></a><span class="lineno"> 416</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00417" name="l00417"></a><span class="lineno"> 417</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00418" name="l00418"></a><span class="lineno"> 418</span> ) :</div>
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<div class="line"><a id="l00419" name="l00419"></a><span class="lineno"> 419</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a04f8c84e46e6fbd0977e50fda4829d1a">m_engine</a>(engine),</div>
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<div class="line"><a id="l00420" name="l00420"></a><span class="lineno"> 420</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a082844f1eae0609e66620575210e8823">m_T9</a>(T9),</div>
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<div class="line"><a id="l00421" name="l00421"></a><span class="lineno"> 421</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a7d4f7f04c4ee6f0b519194f87aa265e7">m_rho</a>(rho),</div>
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<div class="line"><a id="l00422" name="l00422"></a><span class="lineno"> 422</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#ac4a1af03d2a4fbc5cc2407b8a6833147">m_numSpecies</a>(engine.getNetworkSpecies().size()) {}</div>
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</div>
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<div class="line"><a id="l00423" name="l00423"></a><span class="lineno"> 423</span></div>
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<div class="line"><a id="l00430" name="l00430"></a><span class="lineno"> 430</span> <span class="keywordtype">void</span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a3a7542b6c6b4c86b6fe53f54d7232919">operator()</a>(</div>
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<div class="line"><a id="l00431" name="l00431"></a><span class="lineno"> 431</span> <span class="keyword">const</span> boost::numeric::ublas::vector<double>& Y,</div>
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<div class="line"><a id="l00432" name="l00432"></a><span class="lineno"> 432</span> boost::numeric::ublas::vector<double>& dYdt,</div>
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<div class="line"><a id="l00433" name="l00433"></a><span class="lineno"> 433</span> <span class="keywordtype">double</span> t</div>
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<div class="line"><a id="l00434" name="l00434"></a><span class="lineno"> 434</span> ) <span class="keyword">const</span>;</div>
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<div class="line"><a id="l00435" name="l00435"></a><span class="lineno"> 435</span> };</div>
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</div>
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<div class="line"><a id="l00436" name="l00436"></a><span class="lineno"> 436</span></div>
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<div class="foldopen" id="foldopen00444" data-start="{" data-end="};">
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<div class="line"><a id="l00444" name="l00444"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html"> 444</a></span> <span class="keyword">struct </span><a class="code hl_function" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#afd2a548ffb907b0fb1fa28993ea99f25">JacobianFunctor</a> {</div>
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<div class="line"><a id="l00445" name="l00445"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a56f8b2b222fb2a7dac190ead0babfdd0"> 445</a></span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>& <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a56f8b2b222fb2a7dac190ead0babfdd0">m_engine</a>; </div>
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<div class="line"><a id="l00446" name="l00446"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a88f5fc48a555b369f1e2688d6bb67b83"> 446</a></span> <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a88f5fc48a555b369f1e2688d6bb67b83">m_T9</a>; </div>
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<div class="line"><a id="l00447" name="l00447"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a932c41aa9f1aa38e56a03b27cd2ccda4"> 447</a></span> <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a932c41aa9f1aa38e56a03b27cd2ccda4">m_rho</a>; </div>
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<div class="line"><a id="l00448" name="l00448"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a3f624142212b5e6ff65f5706953fe353"> 448</a></span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a3f624142212b5e6ff65f5706953fe353">m_numSpecies</a>; </div>
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<div class="line"><a id="l00449" name="l00449"></a><span class="lineno"> 449</span></div>
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<div class="foldopen" id="foldopen00456" data-start="{" data-end="}">
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<div class="line"><a id="l00456" name="l00456"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#afd2a548ffb907b0fb1fa28993ea99f25"> 456</a></span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#afd2a548ffb907b0fb1fa28993ea99f25">JacobianFunctor</a>(</div>
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<div class="line"><a id="l00457" name="l00457"></a><span class="lineno"> 457</span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>& engine,</div>
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<div class="line"><a id="l00458" name="l00458"></a><span class="lineno"> 458</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00459" name="l00459"></a><span class="lineno"> 459</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00460" name="l00460"></a><span class="lineno"> 460</span> ) :</div>
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<div class="line"><a id="l00461" name="l00461"></a><span class="lineno"> 461</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a56f8b2b222fb2a7dac190ead0babfdd0">m_engine</a>(engine),</div>
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<div class="line"><a id="l00462" name="l00462"></a><span class="lineno"> 462</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a88f5fc48a555b369f1e2688d6bb67b83">m_T9</a>(T9),</div>
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<div class="line"><a id="l00463" name="l00463"></a><span class="lineno"> 463</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a932c41aa9f1aa38e56a03b27cd2ccda4">m_rho</a>(rho),</div>
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<div class="line"><a id="l00464" name="l00464"></a><span class="lineno"> 464</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a3f624142212b5e6ff65f5706953fe353">m_numSpecies</a>(engine.getNetworkSpecies().size()) {}</div>
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</div>
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<div class="line"><a id="l00465" name="l00465"></a><span class="lineno"> 465</span></div>
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<div class="line"><a id="l00473" name="l00473"></a><span class="lineno"> 473</span> <span class="keywordtype">void</span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#ad4fc0b406218aa2f567f5c61a4eda3c9">operator()</a>(</div>
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<div class="line"><a id="l00474" name="l00474"></a><span class="lineno"> 474</span> <span class="keyword">const</span> boost::numeric::ublas::vector<double>& Y,</div>
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<div class="line"><a id="l00475" name="l00475"></a><span class="lineno"> 475</span> boost::numeric::ublas::matrix<double>& J,</div>
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<div class="line"><a id="l00476" name="l00476"></a><span class="lineno"> 476</span> <span class="keywordtype">double</span> t,</div>
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<div class="line"><a id="l00477" name="l00477"></a><span class="lineno"> 477</span> boost::numeric::ublas::vector<double>& dfdt</div>
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<div class="line"><a id="l00478" name="l00478"></a><span class="lineno"> 478</span> ) <span class="keyword">const</span>;</div>
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<div class="line"><a id="l00479" name="l00479"></a><span class="lineno"> 479</span> </div>
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<div class="line"><a id="l00480" name="l00480"></a><span class="lineno"> 480</span> };</div>
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</div>
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<div class="line"><a id="l00481" name="l00481"></a><span class="lineno"> 481</span> </div>
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<div class="line"><a id="l00482" name="l00482"></a><span class="lineno"> 482</span> <span class="keyword">private</span>:</div>
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<div class="line"><a id="l00483" name="l00483"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_direct_network_solver.html#a093aa89fd23c2fe03266e286871c7079"> 483</a></span> quill::Logger* <a class="code hl_variable" href="classgridfire_1_1solver_1_1_direct_network_solver.html#a093aa89fd23c2fe03266e286871c7079">m_logger</a> = fourdst::logging::LogManager::getInstance().getLogger(<span class="stringliteral">"log"</span>); </div>
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<div class="line"><a id="l00484" name="l00484"></a><span class="lineno"><a class="line" href="classgridfire_1_1solver_1_1_direct_network_solver.html#a0d1b52d06b0521e7c556d75cd8d2ffe6"> 484</a></span> fourdst::config::Config& <a class="code hl_variable" href="classgridfire_1_1solver_1_1_direct_network_solver.html#a0d1b52d06b0521e7c556d75cd8d2ffe6">m_config</a> = fourdst::config::Config::getInstance(); </div>
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<div class="line"><a id="l00485" name="l00485"></a><span class="lineno"> 485</span> };</div>
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</div>
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<div class="line"><a id="l00486" name="l00486"></a><span class="lineno"> 486</span> </div>
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<div class="line"><a id="l00487" name="l00487"></a><span class="lineno"> 487</span> <span class="keyword">template</span><<span class="keyword">typename</span> T></div>
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<div class="foldopen" id="foldopen00488" data-start="{" data-end="}">
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<div class="line"><a id="l00488" name="l00488"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a91c9c7c40c061dcfb6e57524e696676e"> 488</a></span> <span class="keywordtype">int</span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a91c9c7c40c061dcfb6e57524e696676e">QSENetworkSolver::EigenFunctor<T>::operator()</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ac4ec3c180a9778acdd604a9b80d25399">InputType</a> &v_QSE, <a class="code hl_typedef" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abc86b32db81acf1b24feb3763dc4ddb0">OutputType</a> &f_QSE)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00489" name="l00489"></a><span class="lineno"> 489</span> std::vector<double> YFull(<a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a93b46ca95ddf9e4d21d02700621e6285">m_engine</a>.getNetworkSpecies().size(), 0.0);</div>
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<div class="line"><a id="l00490" name="l00490"></a><span class="lineno"> 490</span> Eigen::VectorXd Y_QSE(v_QSE.array().exp());</div>
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<div class="line"><a id="l00491" name="l00491"></a><span class="lineno"> 491</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a08ce53701b152f3ce108c1c18ce64de2">m_dynamicSpeciesIndices</a>.size(); ++i) {</div>
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<div class="line"><a id="l00492" name="l00492"></a><span class="lineno"> 492</span> YFull[<a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a08ce53701b152f3ce108c1c18ce64de2">m_dynamicSpeciesIndices</a>[i]] = <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#af4f10300bde1e8e07b896bfca6335401">m_YDynamic</a>[i];</div>
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<div class="line"><a id="l00493" name="l00493"></a><span class="lineno"> 493</span> }</div>
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<div class="line"><a id="l00494" name="l00494"></a><span class="lineno"> 494</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>.size(); ++i) {</div>
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<div class="line"><a id="l00495" name="l00495"></a><span class="lineno"> 495</span> YFull[<a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>[i]] = Y_QSE(i);</div>
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<div class="line"><a id="l00496" name="l00496"></a><span class="lineno"> 496</span> }</div>
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<div class="line"><a id="l00497" name="l00497"></a><span class="lineno"> 497</span> <span class="keyword">const</span> <span class="keyword">auto</span> [full_dYdt, specificEnergyGenerationRate] = <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a93b46ca95ddf9e4d21d02700621e6285">m_engine</a>.calculateRHSAndEnergy(YFull, <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a6771ae56ddd9058954b42ee92a378309">m_T9</a>, <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ab0a0d4c166e97b971543cbbf2b0a1a2e">m_rho</a>);</div>
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<div class="line"><a id="l00498" name="l00498"></a><span class="lineno"> 498</span> f_QSE.resize(<a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>.size());</div>
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<div class="line"><a id="l00499" name="l00499"></a><span class="lineno"> 499</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>.size(); ++i) {</div>
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<div class="line"><a id="l00500" name="l00500"></a><span class="lineno"> 500</span> f_QSE(i) = full_dYdt[<a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>[i]];</div>
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<div class="line"><a id="l00501" name="l00501"></a><span class="lineno"> 501</span> }</div>
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<div class="line"><a id="l00502" name="l00502"></a><span class="lineno"> 502</span> </div>
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<div class="line"><a id="l00503" name="l00503"></a><span class="lineno"> 503</span> <span class="keywordflow">return</span> 0; <span class="comment">// Success</span></div>
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<div class="line"><a id="l00504" name="l00504"></a><span class="lineno"> 504</span> }</div>
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</div>
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<div class="line"><a id="l00505" name="l00505"></a><span class="lineno"> 505</span> </div>
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<div class="line"><a id="l00506" name="l00506"></a><span class="lineno"> 506</span> <span class="keyword">template</span> <<span class="keyword">typename</span> T></div>
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<div class="foldopen" id="foldopen00507" data-start="{" data-end="}">
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<div class="line"><a id="l00507" name="l00507"></a><span class="lineno"><a class="line" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ac46bd712296b03f31af1573f6a0f5644"> 507</a></span> <span class="keywordtype">int</span> <a class="code hl_function" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ac46bd712296b03f31af1573f6a0f5644">QSENetworkSolver::EigenFunctor<T>::df</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ac4ec3c180a9778acdd604a9b80d25399">InputType</a>& v_QSE, <a class="code hl_typedef" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ad42fdb6d5ae06eaa6ddccf03eba0a50c">JacobianType</a>& J_QSE)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00508" name="l00508"></a><span class="lineno"> 508</span> std::vector<double> YFull(<a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a93b46ca95ddf9e4d21d02700621e6285">m_engine</a>.getNetworkSpecies().size(), 0.0);</div>
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<div class="line"><a id="l00509" name="l00509"></a><span class="lineno"> 509</span> Eigen::VectorXd Y_QSE(v_QSE.array().exp());</div>
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<div class="line"><a id="l00510" name="l00510"></a><span class="lineno"> 510</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a08ce53701b152f3ce108c1c18ce64de2">m_dynamicSpeciesIndices</a>.size(); ++i) {</div>
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<div class="line"><a id="l00511" name="l00511"></a><span class="lineno"> 511</span> YFull[<a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a08ce53701b152f3ce108c1c18ce64de2">m_dynamicSpeciesIndices</a>[i]] = <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#af4f10300bde1e8e07b896bfca6335401">m_YDynamic</a>[i];</div>
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<div class="line"><a id="l00512" name="l00512"></a><span class="lineno"> 512</span> }</div>
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<div class="line"><a id="l00513" name="l00513"></a><span class="lineno"> 513</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>.size(); ++i) {</div>
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<div class="line"><a id="l00514" name="l00514"></a><span class="lineno"> 514</span> YFull[<a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>[i]] = Y_QSE(i);</div>
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<div class="line"><a id="l00515" name="l00515"></a><span class="lineno"> 515</span> }</div>
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<div class="line"><a id="l00516" name="l00516"></a><span class="lineno"> 516</span> </div>
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<div class="line"><a id="l00517" name="l00517"></a><span class="lineno"> 517</span> <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a93b46ca95ddf9e4d21d02700621e6285">m_engine</a>.generateJacobianMatrix(YFull, <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a6771ae56ddd9058954b42ee92a378309">m_T9</a>, <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ab0a0d4c166e97b971543cbbf2b0a1a2e">m_rho</a>);</div>
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<div class="line"><a id="l00518" name="l00518"></a><span class="lineno"> 518</span> </div>
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<div class="line"><a id="l00519" name="l00519"></a><span class="lineno"> 519</span> Eigen::MatrixXd J_orig(<a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>.size(), <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>.size());</div>
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<div class="line"><a id="l00520" name="l00520"></a><span class="lineno"> 520</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>.size(); ++i) {</div>
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<div class="line"><a id="l00521" name="l00521"></a><span class="lineno"> 521</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j < <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>.size(); ++j) {</div>
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<div class="line"><a id="l00522" name="l00522"></a><span class="lineno"> 522</span> J_orig(i, j) = <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a93b46ca95ddf9e4d21d02700621e6285">m_engine</a>.getJacobianMatrixEntry(<a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>[i], <a class="code hl_variable" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">m_QSESpeciesIndices</a>[j]);</div>
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<div class="line"><a id="l00523" name="l00523"></a><span class="lineno"> 523</span> }</div>
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<div class="line"><a id="l00524" name="l00524"></a><span class="lineno"> 524</span> }</div>
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<div class="line"><a id="l00525" name="l00525"></a><span class="lineno"> 525</span> </div>
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<div class="line"><a id="l00526" name="l00526"></a><span class="lineno"> 526</span> J_QSE = J_orig;</div>
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<div class="line"><a id="l00527" name="l00527"></a><span class="lineno"> 527</span> <span class="keywordflow">for</span> (<span class="keywordtype">long</span> j = 0; j < J_QSE.cols(); ++j) {</div>
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<div class="line"><a id="l00528" name="l00528"></a><span class="lineno"> 528</span> J_QSE.col(j) *= Y_QSE(j); <span class="comment">// Chain rule for log space</span></div>
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<div class="line"><a id="l00529" name="l00529"></a><span class="lineno"> 529</span> }</div>
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<div class="line"><a id="l00530" name="l00530"></a><span class="lineno"> 530</span> <span class="keywordflow">return</span> 0; <span class="comment">// Success</span></div>
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<div class="line"><a id="l00531" name="l00531"></a><span class="lineno"> 531</span> }</div>
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</div>
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<div class="line"><a id="l00532" name="l00532"></a><span class="lineno"> 532</span> </div>
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<div class="line"><a id="l00533" name="l00533"></a><span class="lineno"> 533</span> </div>
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<div class="line"><a id="l00534" name="l00534"></a><span class="lineno"> 534</span>}</div>
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</div>
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<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#l00118">engine_abstract.h:118</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_direct_network_solver_html"><div class="ttname"><a href="classgridfire_1_1solver_1_1_direct_network_solver.html">gridfire::solver::DirectNetworkSolver</a></div><div class="ttdoc">A network solver that directly integrates the reaction network ODEs.</div><div class="ttdef"><b>Definition</b> <a href="#l00379">solver.h:379</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_direct_network_solver_html_a093aa89fd23c2fe03266e286871c7079"><div class="ttname"><a href="classgridfire_1_1solver_1_1_direct_network_solver.html#a093aa89fd23c2fe03266e286871c7079">gridfire::solver::DirectNetworkSolver::m_logger</a></div><div class="ttdeci">quill::Logger * m_logger</div><div class="ttdoc">Logger instance.</div><div class="ttdef"><b>Definition</b> <a href="#l00483">solver.h:483</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_direct_network_solver_html_a0d1b52d06b0521e7c556d75cd8d2ffe6"><div class="ttname"><a href="classgridfire_1_1solver_1_1_direct_network_solver.html#a0d1b52d06b0521e7c556d75cd8d2ffe6">gridfire::solver::DirectNetworkSolver::m_config</a></div><div class="ttdeci">fourdst::config::Config & m_config</div><div class="ttdoc">Configuration instance.</div><div class="ttdef"><b>Definition</b> <a href="#l00484">solver.h:484</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_direct_network_solver_html_a0e8a4b8ef656e0b084d11bea982e412a"><div class="ttname"><a href="classgridfire_1_1solver_1_1_direct_network_solver.html#a0e8a4b8ef656e0b084d11bea982e412a">gridfire::solver::DirectNetworkSolver::evaluate</a></div><div class="ttdeci">NetOut evaluate(const NetIn &netIn) override</div><div class="ttdoc">Evaluates the network for a given timestep using direct integration.</div><div class="ttdef"><b>Definition</b> <a href="solver_8cpp_source.html#l00308">solver.cpp:308</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_network_solver_strategy_html"><div class="ttname"><a href="classgridfire_1_1solver_1_1_network_solver_strategy.html">gridfire::solver::NetworkSolverStrategy</a></div><div class="ttdoc">Abstract base class for network solver strategies.</div><div class="ttdef"><b>Definition</b> <a href="#l00043">solver.h:43</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_network_solver_strategy_html_a01cbbec0eb5c3a60f50da38cdaf66505"><div class="ttname"><a href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a01cbbec0eb5c3a60f50da38cdaf66505">gridfire::solver::NetworkSolverStrategy::NetworkSolverStrategy</a></div><div class="ttdeci">NetworkSolverStrategy(EngineT &engine)</div><div class="ttdoc">Constructor for the NetworkSolverStrategy.</div><div class="ttdef"><b>Definition</b> <a href="#l00049">solver.h:49</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_network_solver_strategy_html_a1693dc93f63599c89587d729aca8e318"><div class="ttname"><a href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a1693dc93f63599c89587d729aca8e318">gridfire::solver::NetworkSolverStrategy::~NetworkSolverStrategy</a></div><div class="ttdeci">virtual ~NetworkSolverStrategy()=default</div><div class="ttdoc">Virtual destructor.</div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_network_solver_strategy_html_a724924d94eaf82b67d9988a55c3261e8"><div class="ttname"><a href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a724924d94eaf82b67d9988a55c3261e8">gridfire::solver::NetworkSolverStrategy< DynamicEngine >::m_engine</a></div><div class="ttdeci">DynamicEngine & m_engine</div><div class="ttdef"><b>Definition</b> <a href="#l00063">solver.h:63</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_network_solver_strategy_html_ace539b0482db171845ff1bd38d76b70f"><div class="ttname"><a href="classgridfire_1_1solver_1_1_network_solver_strategy.html#ace539b0482db171845ff1bd38d76b70f">gridfire::solver::NetworkSolverStrategy::evaluate</a></div><div class="ttdeci">virtual NetOut evaluate(const NetIn &netIn)=0</div><div class="ttdoc">Evaluates the network for a given timestep.</div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_q_s_e_network_solver_html"><div class="ttname"><a href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html">gridfire::solver::QSENetworkSolver</a></div><div class="ttdoc">A network solver that uses a Quasi-Steady-State Equilibrium (QSE) approach.</div><div class="ttdef"><b>Definition</b> <a href="#l00098">solver.h:98</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_q_s_e_network_solver_html_a00d112f6087f6e3a93f4d40a519308d2"><div class="ttname"><a href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a00d112f6087f6e3a93f4d40a519308d2">gridfire::solver::QSENetworkSolver::calculateSteadyStateAbundances</a></div><div class="ttdeci">Eigen::VectorXd calculateSteadyStateAbundances(const std::vector< double > &Y, const double T9, const double rho, const dynamicQSESpeciesIndices &indices) const</div><div class="ttdoc">Calculates the steady-state abundances of the QSE species.</div><div class="ttdef"><b>Definition</b> <a href="solver_8cpp_source.html#l00187">solver.cpp:187</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_q_s_e_network_solver_html_a35f1f6ede393f15c8bb8862f3f1c3b07"><div class="ttname"><a href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a35f1f6ede393f15c8bb8862f3f1c3b07">gridfire::solver::QSENetworkSolver::shouldUpdateView</a></div><div class="ttdeci">bool shouldUpdateView(const NetIn &conditions) const</div><div class="ttdoc">Determines whether the adaptive engine view should be updated.</div><div class="ttdef"><b>Definition</b> <a href="solver_8cpp_source.html#l00241">solver.cpp:241</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_q_s_e_network_solver_html_a3c9d46c8f5c519854cd65309a588772f"><div class="ttname"><a href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a3c9d46c8f5c519854cd65309a588772f">gridfire::solver::QSENetworkSolver::m_lastSeenConditions</a></div><div class="ttdeci">NetIn m_lastSeenConditions</div><div class="ttdoc">The last seen input conditions.</div><div class="ttdef"><b>Definition</b> <a href="#l00366">solver.h:366</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_q_s_e_network_solver_html_a428b49fa7878559665363de06f1a44a7"><div class="ttname"><a href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a428b49fa7878559665363de06f1a44a7">gridfire::solver::QSENetworkSolver::m_logger</a></div><div class="ttdeci">quill::Logger * m_logger</div><div class="ttdoc">Logger instance.</div><div class="ttdef"><b>Definition</b> <a href="#l00362">solver.h:362</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_q_s_e_network_solver_html_a53b5496db7fed6f345dca39656bf9c0e"><div class="ttname"><a href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a53b5496db7fed6f345dca39656bf9c0e">gridfire::solver::QSENetworkSolver::evaluate</a></div><div class="ttdeci">NetOut evaluate(const NetIn &netIn) override</div><div class="ttdoc">Evaluates the network for a given timestep using the QSE approach.</div><div class="ttdef"><b>Definition</b> <a href="solver_8cpp_source.html#l00023">solver.cpp:23</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_q_s_e_network_solver_html_a5d81ee5bfcfd5e77fe52201ba9e63719"><div class="ttname"><a href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a5d81ee5bfcfd5e77fe52201ba9e63719">gridfire::solver::QSENetworkSolver::packSpeciesTypeIndexVectors</a></div><div class="ttdeci">dynamicQSESpeciesIndices packSpeciesTypeIndexVectors(const std::vector< double > &Y, const double T9, const double rho) const</div><div class="ttdoc">Packs the species indices into vectors based on their type (dynamic or QSE).</div><div class="ttdef"><b>Definition</b> <a href="solver_8cpp_source.html#l00119">solver.cpp:119</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_q_s_e_network_solver_html_a7d19b6e50db34d38c81afec76bbedee1"><div class="ttname"><a href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a7d19b6e50db34d38c81afec76bbedee1">gridfire::solver::QSENetworkSolver::m_config</a></div><div class="ttdeci">fourdst::config::Config & m_config</div><div class="ttdoc">Configuration instance.</div><div class="ttdef"><b>Definition</b> <a href="#l00363">solver.h:363</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_q_s_e_network_solver_html_ab07e68fd418ab058f890502d191b3f18"><div class="ttname"><a href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#ab07e68fd418ab058f890502d191b3f18">gridfire::solver::QSENetworkSolver::m_isViewInitialized</a></div><div class="ttdeci">bool m_isViewInitialized</div><div class="ttdoc">Flag indicating whether the adaptive engine view has been initialized.</div><div class="ttdef"><b>Definition</b> <a href="#l00365">solver.h:365</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1solver_1_1_q_s_e_network_solver_html_abaa567001df0007b714f474febae408b"><div class="ttname"><a href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#abaa567001df0007b714f474febae408b">gridfire::solver::QSENetworkSolver::initializeNetworkWithShortIgnition</a></div><div class="ttdeci">NetOut initializeNetworkWithShortIgnition(const NetIn &netIn) const</div><div class="ttdoc">Initializes the network with a short ignition phase.</div><div class="ttdef"><b>Definition</b> <a href="solver_8cpp_source.html#l00202">solver.cpp:202</a></div></div>
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<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>
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<div class="ttc" id="aengine__adaptive_8h_html"><div class="ttname"><a href="engine__adaptive_8h.html">engine_adaptive.h</a></div></div>
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<div class="ttc" id="aengine__graph_8h_html"><div class="ttname"><a href="engine__graph_8h.html">engine_graph.h</a></div></div>
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<div class="ttc" id="anamespacegridfire_1_1solver_html"><div class="ttname"><a href="namespacegridfire_1_1solver.html">gridfire::solver</a></div><div class="ttdef"><b>Definition</b> <a href="#l00017">solver.h:17</a></div></div>
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<div class="ttc" id="anamespacegridfire_1_1solver_html_a5361d6cf364f0ba2f88285a60bb9cd92"><div class="ttname"><a href="namespacegridfire_1_1solver.html#a5361d6cf364f0ba2f88285a60bb9cd92">gridfire::solver::StaticNetworkSolverStrategy</a></div><div class="ttdeci">NetworkSolverStrategy< Engine > StaticNetworkSolverStrategy</div><div class="ttdoc">Type alias for a network solver strategy that uses a static Engine.</div><div class="ttdef"><b>Definition</b> <a href="#l00079">solver.h:79</a></div></div>
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<div class="ttc" id="anamespacegridfire_1_1solver_html_a8118d08bc25e439754b43a3f5ecc1db3"><div class="ttname"><a href="namespacegridfire_1_1solver.html#a8118d08bc25e439754b43a3f5ecc1db3">gridfire::solver::DynamicNetworkSolverStrategy</a></div><div class="ttdeci">NetworkSolverStrategy< DynamicEngine > DynamicNetworkSolverStrategy</div><div class="ttdoc">Type alias for a network solver strategy that uses a DynamicEngine.</div><div class="ttdef"><b>Definition</b> <a href="#l00069">solver.h:69</a></div></div>
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<div class="ttc" id="anamespacegridfire_1_1solver_html_af3b10822ab58b55365577755c1f4faf6"><div class="ttname"><a href="namespacegridfire_1_1solver.html#af3b10822ab58b55365577755c1f4faf6">gridfire::solver::AdaptiveNetworkSolverStrategy</a></div><div class="ttdeci">NetworkSolverStrategy< AdaptiveEngineView > AdaptiveNetworkSolverStrategy</div><div class="ttdoc">Type alias for a network solver strategy that uses an AdaptiveEngineView.</div><div class="ttdef"><b>Definition</b> <a href="#l00074">solver.h:74</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>
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<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_net_out_html"><div class="ttname"><a href="structgridfire_1_1_net_out.html">gridfire::NetOut</a></div><div class="ttdef"><b>Definition</b> <a href="network_8h_source.html#l00065">network.h:65</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor_html_a3f624142212b5e6ff65f5706953fe353"><div class="ttname"><a href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a3f624142212b5e6ff65f5706953fe353">gridfire::solver::DirectNetworkSolver::JacobianFunctor::m_numSpecies</a></div><div class="ttdeci">const size_t m_numSpecies</div><div class="ttdoc">The number of species in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00448">solver.h:448</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor_html_a56f8b2b222fb2a7dac190ead0babfdd0"><div class="ttname"><a href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a56f8b2b222fb2a7dac190ead0babfdd0">gridfire::solver::DirectNetworkSolver::JacobianFunctor::m_engine</a></div><div class="ttdeci">DynamicEngine & m_engine</div><div class="ttdoc">The engine used to evaluate the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00445">solver.h:445</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor_html_a88f5fc48a555b369f1e2688d6bb67b83"><div class="ttname"><a href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a88f5fc48a555b369f1e2688d6bb67b83">gridfire::solver::DirectNetworkSolver::JacobianFunctor::m_T9</a></div><div class="ttdeci">const double m_T9</div><div class="ttdoc">Temperature in units of 10^9 K.</div><div class="ttdef"><b>Definition</b> <a href="#l00446">solver.h:446</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor_html_a932c41aa9f1aa38e56a03b27cd2ccda4"><div class="ttname"><a href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a932c41aa9f1aa38e56a03b27cd2ccda4">gridfire::solver::DirectNetworkSolver::JacobianFunctor::m_rho</a></div><div class="ttdeci">const double m_rho</div><div class="ttdoc">Density in g/cm^3.</div><div class="ttdef"><b>Definition</b> <a href="#l00447">solver.h:447</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor_html_ad4fc0b406218aa2f567f5c61a4eda3c9"><div class="ttname"><a href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#ad4fc0b406218aa2f567f5c61a4eda3c9">gridfire::solver::DirectNetworkSolver::JacobianFunctor::operator()</a></div><div class="ttdeci">void operator()(const boost::numeric::ublas::vector< double > &Y, boost::numeric::ublas::matrix< double > &J, double t, boost::numeric::ublas::vector< double > &dfdt) const</div><div class="ttdoc">Calculates the Jacobian matrix.</div><div class="ttdef"><b>Definition</b> <a href="solver_8cpp_source.html#l00386">solver.cpp:386</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor_html_afd2a548ffb907b0fb1fa28993ea99f25"><div class="ttname"><a href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#afd2a548ffb907b0fb1fa28993ea99f25">gridfire::solver::DirectNetworkSolver::JacobianFunctor::JacobianFunctor</a></div><div class="ttdeci">JacobianFunctor(DynamicEngine &engine, const double T9, const double rho)</div><div class="ttdoc">Constructor for the JacobianFunctor.</div><div class="ttdef"><b>Definition</b> <a href="#l00456">solver.h:456</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor_html_a04f8c84e46e6fbd0977e50fda4829d1a"><div class="ttname"><a href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a04f8c84e46e6fbd0977e50fda4829d1a">gridfire::solver::DirectNetworkSolver::RHSFunctor::m_engine</a></div><div class="ttdeci">DynamicEngine & m_engine</div><div class="ttdoc">The engine used to evaluate the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00403">solver.h:403</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor_html_a082844f1eae0609e66620575210e8823"><div class="ttname"><a href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a082844f1eae0609e66620575210e8823">gridfire::solver::DirectNetworkSolver::RHSFunctor::m_T9</a></div><div class="ttdeci">const double m_T9</div><div class="ttdoc">Temperature in units of 10^9 K.</div><div class="ttdef"><b>Definition</b> <a href="#l00404">solver.h:404</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor_html_a3a7542b6c6b4c86b6fe53f54d7232919"><div class="ttname"><a href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a3a7542b6c6b4c86b6fe53f54d7232919">gridfire::solver::DirectNetworkSolver::RHSFunctor::operator()</a></div><div class="ttdeci">void operator()(const boost::numeric::ublas::vector< double > &Y, boost::numeric::ublas::vector< double > &dYdt, double t) const</div><div class="ttdoc">Calculates the time derivatives of the species abundances.</div><div class="ttdef"><b>Definition</b> <a href="solver_8cpp_source.html#l00374">solver.cpp:374</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor_html_a7d4f7f04c4ee6f0b519194f87aa265e7"><div class="ttname"><a href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a7d4f7f04c4ee6f0b519194f87aa265e7">gridfire::solver::DirectNetworkSolver::RHSFunctor::m_rho</a></div><div class="ttdeci">const double m_rho</div><div class="ttdoc">Density in g/cm^3.</div><div class="ttdef"><b>Definition</b> <a href="#l00405">solver.h:405</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor_html_ac4a1af03d2a4fbc5cc2407b8a6833147"><div class="ttname"><a href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#ac4a1af03d2a4fbc5cc2407b8a6833147">gridfire::solver::DirectNetworkSolver::RHSFunctor::m_numSpecies</a></div><div class="ttdeci">const size_t m_numSpecies</div><div class="ttdoc">The number of species in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00406">solver.h:406</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor_html_aed201b52ea757069c17a49e9638b3d3c"><div class="ttname"><a href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#aed201b52ea757069c17a49e9638b3d3c">gridfire::solver::DirectNetworkSolver::RHSFunctor::RHSFunctor</a></div><div class="ttdeci">RHSFunctor(DynamicEngine &engine, const double T9, const double rho)</div><div class="ttdoc">Constructor for the RHSFunctor.</div><div class="ttdef"><b>Definition</b> <a href="#l00414">solver.h:414</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor_html_a08ce53701b152f3ce108c1c18ce64de2"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a08ce53701b152f3ce108c1c18ce64de2">gridfire::solver::QSENetworkSolver::EigenFunctor::m_dynamicSpeciesIndices</a></div><div class="ttdeci">const std::vector< size_t > & m_dynamicSpeciesIndices</div><div class="ttdoc">Indices of the dynamic species.</div><div class="ttdef"><b>Definition</b> <a href="#l00316">solver.h:316</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor_html_a6771ae56ddd9058954b42ee92a378309"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a6771ae56ddd9058954b42ee92a378309">gridfire::solver::QSENetworkSolver::EigenFunctor::m_T9</a></div><div class="ttdeci">const double m_T9</div><div class="ttdoc">Temperature in units of 10^9 K.</div><div class="ttdef"><b>Definition</b> <a href="#l00318">solver.h:318</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor_html_a91c9c7c40c061dcfb6e57524e696676e"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a91c9c7c40c061dcfb6e57524e696676e">gridfire::solver::QSENetworkSolver::EigenFunctor::operator()</a></div><div class="ttdeci">int operator()(const InputType &v_QSE, OutputType &f_QSE) const</div><div class="ttdoc">Calculates the residual vector for the QSE species.</div><div class="ttdef"><b>Definition</b> <a href="#l00488">solver.h:488</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor_html_a93b46ca95ddf9e4d21d02700621e6285"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a93b46ca95ddf9e4d21d02700621e6285">gridfire::solver::QSENetworkSolver::EigenFunctor::m_engine</a></div><div class="ttdeci">DynamicEngine & m_engine</div><div class="ttdoc">The engine used to evaluate the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00314">solver.h:314</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor_html_ab0a0d4c166e97b971543cbbf2b0a1a2e"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ab0a0d4c166e97b971543cbbf2b0a1a2e">gridfire::solver::QSENetworkSolver::EigenFunctor::m_rho</a></div><div class="ttdeci">const double m_rho</div><div class="ttdoc">Density in g/cm^3.</div><div class="ttdef"><b>Definition</b> <a href="#l00319">solver.h:319</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor_html_abaf28fdd93e881ef56c24f541be7492d"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">gridfire::solver::QSENetworkSolver::EigenFunctor::m_QSESpeciesIndices</a></div><div class="ttdeci">const std::vector< size_t > & m_QSESpeciesIndices</div><div class="ttdoc">Indices of the QSE species.</div><div class="ttdef"><b>Definition</b> <a href="#l00317">solver.h:317</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor_html_abc86b32db81acf1b24feb3763dc4ddb0"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abc86b32db81acf1b24feb3763dc4ddb0">gridfire::solver::QSENetworkSolver::EigenFunctor::OutputType</a></div><div class="ttdeci">Eigen::Matrix< T, Eigen::Dynamic, 1 > OutputType</div><div class="ttdef"><b>Definition</b> <a href="#l00311">solver.h:311</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor_html_ac46bd712296b03f31af1573f6a0f5644"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ac46bd712296b03f31af1573f6a0f5644">gridfire::solver::QSENetworkSolver::EigenFunctor::df</a></div><div class="ttdeci">int df(const InputType &v_QSE, JacobianType &J_QSE) const</div><div class="ttdoc">Calculates the Jacobian matrix for the QSE species.</div><div class="ttdef"><b>Definition</b> <a href="#l00507">solver.h:507</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor_html_ac4ec3c180a9778acdd604a9b80d25399"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ac4ec3c180a9778acdd604a9b80d25399">gridfire::solver::QSENetworkSolver::EigenFunctor::InputType</a></div><div class="ttdeci">Eigen::Matrix< T, Eigen::Dynamic, 1 > InputType</div><div class="ttdef"><b>Definition</b> <a href="#l00310">solver.h:310</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor_html_ad42fdb6d5ae06eaa6ddccf03eba0a50c"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#ad42fdb6d5ae06eaa6ddccf03eba0a50c">gridfire::solver::QSENetworkSolver::EigenFunctor::JacobianType</a></div><div class="ttdeci">Eigen::Matrix< T, Eigen::Dynamic, Eigen::Dynamic > JacobianType</div><div class="ttdef"><b>Definition</b> <a href="#l00312">solver.h:312</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor_html_af4f10300bde1e8e07b896bfca6335401"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#af4f10300bde1e8e07b896bfca6335401">gridfire::solver::QSENetworkSolver::EigenFunctor::m_YDynamic</a></div><div class="ttdeci">const std::vector< double > & m_YDynamic</div><div class="ttdoc">Abundances of the dynamic species.</div><div class="ttdef"><b>Definition</b> <a href="#l00315">solver.h:315</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor_html_af8650f704c2ca512c9c5b4562b3b0958"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#af8650f704c2ca512c9c5b4562b3b0958">gridfire::solver::QSENetworkSolver::EigenFunctor::EigenFunctor</a></div><div class="ttdeci">EigenFunctor(DynamicEngine &engine, const std::vector< double > &YDynamic, const std::vector< size_t > &dynamicSpeciesIndices, const std::vector< size_t > &QSESpeciesIndices, const double T9, const double rho)</div><div class="ttdoc">Constructor for the EigenFunctor.</div><div class="ttdef"><b>Definition</b> <a href="#l00330">solver.h:330</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor_html_a0907f7b6c1a87baf5e39fbc17a30df82"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a0907f7b6c1a87baf5e39fbc17a30df82">gridfire::solver::QSENetworkSolver::JacobianFunctor::m_rho</a></div><div class="ttdeci">const double m_rho</div><div class="ttdoc">Density in g/cm^3.</div><div class="ttdef"><b>Definition</b> <a href="#l00264">solver.h:264</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor_html_a1b92391170eb46771bd499aa8d115334"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a1b92391170eb46771bd499aa8d115334">gridfire::solver::QSENetworkSolver::JacobianFunctor::m_QSESpeciesIndices</a></div><div class="ttdeci">const std::vector< size_t > & m_QSESpeciesIndices</div><div class="ttdoc">Indices of the QSE species.</div><div class="ttdef"><b>Definition</b> <a href="#l00262">solver.h:262</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor_html_a2071ce797f94ae1a3ea6d934748672ce"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a2071ce797f94ae1a3ea6d934748672ce">gridfire::solver::QSENetworkSolver::JacobianFunctor::m_dynamicSpeciesIndices</a></div><div class="ttdeci">const std::vector< size_t > & m_dynamicSpeciesIndices</div><div class="ttdoc">Indices of the dynamic species.</div><div class="ttdef"><b>Definition</b> <a href="#l00261">solver.h:261</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor_html_a3668fae1e0f8e69ff3fd87275bf4a79d"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a3668fae1e0f8e69ff3fd87275bf4a79d">gridfire::solver::QSENetworkSolver::JacobianFunctor::operator()</a></div><div class="ttdeci">void operator()(const boost::numeric::ublas::vector< double > &YDynamic, boost::numeric::ublas::matrix< double > &JDynamic, double t, boost::numeric::ublas::vector< double > &dfdt) const</div><div class="ttdoc">Calculates the Jacobian matrix of the ODEs for the dynamic species.</div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor_html_a85f88639447a9a706008efece82ff289"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a85f88639447a9a706008efece82ff289">gridfire::solver::QSENetworkSolver::JacobianFunctor::m_T9</a></div><div class="ttdeci">const double m_T9</div><div class="ttdoc">Temperature in units of 10^9 K.</div><div class="ttdef"><b>Definition</b> <a href="#l00263">solver.h:263</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor_html_aaaa82eff96e6127a6de05444f730e43a"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#aaaa82eff96e6127a6de05444f730e43a">gridfire::solver::QSENetworkSolver::JacobianFunctor::m_engine</a></div><div class="ttdeci">DynamicEngine & m_engine</div><div class="ttdoc">The engine used to evaluate the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00260">solver.h:260</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor_html_ab8222646cd32670a046b6c74909bd83a"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#ab8222646cd32670a046b6c74909bd83a">gridfire::solver::QSENetworkSolver::JacobianFunctor::JacobianFunctor</a></div><div class="ttdeci">JacobianFunctor(DynamicEngine &engine, const std::vector< size_t > &dynamicSpeciesIndices, const std::vector< size_t > &QSESpeciesIndices, const double T9, const double rho)</div><div class="ttdoc">Constructor for the JacobianFunctor.</div><div class="ttdef"><b>Definition</b> <a href="#l00274">solver.h:274</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor_html_a02c23ef20d616bf5a591a274b66cd75a"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a02c23ef20d616bf5a591a274b66cd75a">gridfire::solver::QSENetworkSolver::RHSFunctor::m_Y_QSE</a></div><div class="ttdeci">const Eigen::VectorXd & m_Y_QSE</div><div class="ttdoc">Steady-state abundances of the QSE species.</div><div class="ttdef"><b>Definition</b> <a href="#l00205">solver.h:205</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor_html_a0d8d28a6559cfed5e7cd683523d49b2c"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a0d8d28a6559cfed5e7cd683523d49b2c">gridfire::solver::QSENetworkSolver::RHSFunctor::m_engine</a></div><div class="ttdeci">DynamicEngine & m_engine</div><div class="ttdoc">The engine used to evaluate the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00202">solver.h:202</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor_html_a35026100163c7cc6fdb4c2e4d988b8cb"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a35026100163c7cc6fdb4c2e4d988b8cb">gridfire::solver::QSENetworkSolver::RHSFunctor::m_T9</a></div><div class="ttdeci">const double m_T9</div><div class="ttdoc">Temperature in units of 10^9 K.</div><div class="ttdef"><b>Definition</b> <a href="#l00206">solver.h:206</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor_html_a3ac1ef529627d21f7d1ad718dc87f7f9"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a3ac1ef529627d21f7d1ad718dc87f7f9">gridfire::solver::QSENetworkSolver::RHSFunctor::m_dynamicSpeciesIndices</a></div><div class="ttdeci">const std::vector< size_t > & m_dynamicSpeciesIndices</div><div class="ttdoc">Indices of the dynamic species.</div><div class="ttdef"><b>Definition</b> <a href="#l00203">solver.h:203</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor_html_a5353d8e6f27b6c435084a167bc009e46"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a5353d8e6f27b6c435084a167bc009e46">gridfire::solver::QSENetworkSolver::RHSFunctor::RHSFunctor</a></div><div class="ttdeci">RHSFunctor(DynamicEngine &engine, const std::vector< size_t > &dynamicSpeciesIndices, const std::vector< size_t > &QSESpeciesIndices, const Eigen::VectorXd &Y_QSE, const double T9, const double rho)</div><div class="ttdoc">Constructor for the RHSFunctor.</div><div class="ttdef"><b>Definition</b> <a href="#l00220">solver.h:220</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor_html_a6be7259897a47ce480b289144b06e269"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a6be7259897a47ce480b289144b06e269">gridfire::solver::QSENetworkSolver::RHSFunctor::m_QSESpeciesIndices</a></div><div class="ttdeci">const std::vector< size_t > & m_QSESpeciesIndices</div><div class="ttdoc">Indices of the QSE species.</div><div class="ttdef"><b>Definition</b> <a href="#l00204">solver.h:204</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor_html_a81f964b87457847d7de13fed18499283"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a81f964b87457847d7de13fed18499283">gridfire::solver::QSENetworkSolver::RHSFunctor::m_isViewInitialized</a></div><div class="ttdeci">bool m_isViewInitialized</div><div class="ttdef"><b>Definition</b> <a href="#l00209">solver.h:209</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor_html_adc0f8e655af42f414dcb220a7224f261"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#adc0f8e655af42f414dcb220a7224f261">gridfire::solver::QSENetworkSolver::RHSFunctor::m_rho</a></div><div class="ttdeci">const double m_rho</div><div class="ttdoc">Density in g/cm^3.</div><div class="ttdef"><b>Definition</b> <a href="#l00207">solver.h:207</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor_html_ae0b6362d9c0a14e69c7a47233db6a86a"><div class="ttname"><a href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#ae0b6362d9c0a14e69c7a47233db6a86a">gridfire::solver::QSENetworkSolver::RHSFunctor::operator()</a></div><div class="ttdeci">void operator()(const boost::numeric::ublas::vector< double > &YDynamic, boost::numeric::ublas::vector< double > &dYdtDynamic, double t) const</div><div class="ttdoc">Calculates the time derivatives of the dynamic species.</div><div class="ttdef"><b>Definition</b> <a href="solver_8cpp_source.html#l00283">solver.cpp:283</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1dynamic_q_s_e_species_indices_html"><div class="ttname"><a href="structgridfire_1_1solver_1_1dynamic_q_s_e_species_indices.html">gridfire::solver::dynamicQSESpeciesIndices</a></div><div class="ttdoc">Structure to hold indices of dynamic and QSE species.</div><div class="ttdef"><b>Definition</b> <a href="#l00027">solver.h:27</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1dynamic_q_s_e_species_indices_html_a7d4ba82d9e60a4914938ebebecaab4a2"><div class="ttname"><a href="structgridfire_1_1solver_1_1dynamic_q_s_e_species_indices.html#a7d4ba82d9e60a4914938ebebecaab4a2">gridfire::solver::dynamicQSESpeciesIndices::QSESpeciesIndices</a></div><div class="ttdeci">std::vector< size_t > QSESpeciesIndices</div><div class="ttdoc">Indices of fast species that are in QSE.</div><div class="ttdef"><b>Definition</b> <a href="#l00029">solver.h:29</a></div></div>
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<div class="ttc" id="astructgridfire_1_1solver_1_1dynamic_q_s_e_species_indices_html_ac6e0419abdd3c78b32e34c16c0543157"><div class="ttname"><a href="structgridfire_1_1solver_1_1dynamic_q_s_e_species_indices.html#ac6e0419abdd3c78b32e34c16c0543157">gridfire::solver::dynamicQSESpeciesIndices::dynamicSpeciesIndices</a></div><div class="ttdeci">std::vector< size_t > dynamicSpeciesIndices</div><div class="ttdoc">Indices of slow species that are not in QSE.</div><div class="ttdef"><b>Definition</b> <a href="#l00028">solver.h:28</a></div></div>
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