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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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<div class="headertitle"><div class="title">engine_graph.cpp</div></div>
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<a href="engine__graph_8cpp.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">#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="l00002" name="l00002"></a><span class="lineno"> 2</span><span class="preprocessor">#include "<a class="code" href="reaction_8h.html">gridfire/reaction/reaction.h</a>"</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="network_8h.html">gridfire/network.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="screening__types_8h.html">gridfire/screening/screening_types.h</a>"</span></div>
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<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span> </div>
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<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="preprocessor">#include "fourdst/composition/species.h"</span></div>
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<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span><span class="preprocessor">#include "fourdst/composition/atomicSpecies.h"</span></div>
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<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span> </div>
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<div class="line"><a id="l00009" name="l00009"></a><span class="lineno"> 9</span><span class="preprocessor">#include "quill/LogMacros.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 <cstdint></span></div>
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<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span><span class="preprocessor">#include <iostream></span></div>
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<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#include <set></span></div>
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<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="preprocessor">#include <stdexcept></span></div>
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<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include <string></span></div>
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<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="preprocessor">#include <string_view></span></div>
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<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="preprocessor">#include <unordered_map></span></div>
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<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#include <utility></span></div>
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<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span><span class="preprocessor">#include <vector></span></div>
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<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span><span class="preprocessor">#include <fstream></span></div>
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<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span> </div>
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<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span><span class="preprocessor">#include <boost/numeric/odeint.hpp></span></div>
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<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> </div>
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<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> </div>
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<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacegridfire.html">gridfire</a> {</div>
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<div class="foldopen" id="foldopen00026" data-start="{" data-end="}">
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<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a9f74786ff930ab72664b31f29d05a30c"> 26</a></span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a9f74786ff930ab72664b31f29d05a30c">GraphEngine::GraphEngine</a>(</div>
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<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> <span class="keyword">const</span> fourdst::composition::Composition &composition</div>
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<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span> ):</div>
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<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>(<a class="code hl_function" href="namespacegridfire.html#aa77f83539d9ae90e3bf541309bd9c83a">build_reaclib_nuclear_network</a>(composition, false)) {</div>
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<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">syncInternalMaps</a>();</div>
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<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd">precomputeNetwork</a>();</div>
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<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> }</div>
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</div>
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<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> </div>
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<div class="foldopen" id="foldopen00034" data-start="{" data-end="}">
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<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a1e7e851dfa21d41c2dc533ba56fc4c7b"> 34</a></span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a9f74786ff930ab72664b31f29d05a30c">GraphEngine::GraphEngine</a>(</div>
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<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &reactions</div>
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<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> ) :</div>
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<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>(reactions) {</div>
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<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">syncInternalMaps</a>();</div>
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<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd">precomputeNetwork</a>();</div>
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<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> }</div>
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</div>
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<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> </div>
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<div class="foldopen" id="foldopen00042" data-start="{" data-end="}">
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<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a8b3baf29829c7ae0a61430ea70632bbf"> 42</a></span> <a class="code hl_struct" href="structgridfire_1_1_step_derivatives.html">StepDerivatives<double></a> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a8b3baf29829c7ae0a61430ea70632bbf">GraphEngine::calculateRHSAndEnergy</a>(</div>
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<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">const</span> std::vector<double> &Y,</div>
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<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> )<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordflow">if</span> (<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de">m_usePrecomputation</a>) {</div>
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<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> std::vector<double> bare_rates;</div>
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<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> bare_rates.reserve(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size());</div>
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<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>: <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
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<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> bare_rates.push_back(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.calculate_rate(T9));</div>
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<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> }</div>
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<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> </div>
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<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> <span class="comment">// --- The public facing interface can always use the precomputed version since taping is done internally ---</span></div>
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<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> <span class="keywordflow">return</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a63639f4430d0889605c10839a6f32af9">calculateAllDerivativesUsingPrecomputation</a>(Y, bare_rates, T9, rho);</div>
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<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> } <span class="keywordflow">else</span> {</div>
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<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> <span class="keywordflow">return</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives<double></a>(Y, T9, rho);</div>
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<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> }</div>
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<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> }</div>
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</div>
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<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> </div>
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<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> </div>
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<div class="foldopen" id="foldopen00062" data-start="{" data-end="}">
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<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f"> 62</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">GraphEngine::syncInternalMaps</a>() {</div>
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<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa">collectNetworkSpecies</a>();</div>
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<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567">populateReactionIDMap</a>();</div>
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<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391">populateSpeciesToIndexMap</a>();</div>
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<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38">generateStoichiometryMatrix</a>();</div>
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<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a5a5458ed01923124f2d7e1f04f32f138">reserveJacobianMatrix</a>();</div>
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<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889">recordADTape</a>();</div>
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<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> }</div>
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</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="l00071" name="l00071"></a><span class="lineno"> 71</span> <span class="comment">// --- Network Graph Construction Methods ---</span></div>
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<div class="foldopen" id="foldopen00072" data-start="{" data-end="}">
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<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa"> 72</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa">GraphEngine::collectNetworkSpecies</a>() {</div>
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<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.clear();</div>
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<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.clear();</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="l00076" name="l00076"></a><span class="lineno"> 76</span> std::set<std::string_view> uniqueSpeciesNames;</div>
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<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> </div>
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<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>: <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
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<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& reactant: <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants()) {</div>
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<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> uniqueSpeciesNames.insert(reactant.name());</div>
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<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> }</div>
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<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& product: <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products()) {</div>
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<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> uniqueSpeciesNames.insert(product.name());</div>
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<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> }</div>
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<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> }</div>
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<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> </div>
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<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& name: uniqueSpeciesNames) {</div>
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<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span> <span class="keyword">auto</span> it = fourdst::atomic::species.find(std::string(name));</div>
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<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> <span class="keywordflow">if</span> (it != fourdst::atomic::species.end()) {</div>
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<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.push_back(it->second);</div>
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<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.insert({name, it->second});</div>
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<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> } <span class="keywordflow">else</span> {</div>
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<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Species '{}' not found in global atomic species database."</span>, name);</div>
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<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>->flush_log();</div>
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<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Species not found in global atomic species database: "</span> + std::string(name));</div>
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<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> }</div>
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<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> }</div>
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<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> </div>
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<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> }</div>
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</div>
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<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> </div>
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<div class="foldopen" id="foldopen00101" data-start="{" data-end="}">
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<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567"> 101</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567">GraphEngine::populateReactionIDMap</a>() {</div>
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<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Populating reaction ID map for REACLIB graph network (serif::network::GraphNetwork)..."</span>);</div>
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<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">m_reactionIDMap</a>.clear();</div>
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<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> <span class="keywordflow">for</span> (<span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>: <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
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<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">m_reactionIDMap</a>.emplace(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id(), &<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>);</div>
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<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> }</div>
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<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Populated {} reactions in the reaction ID map."</span>, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">m_reactionIDMap</a>.size());</div>
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<div class="line"><a id="l00108" name="l00108"></a><span class="lineno"> 108</span> }</div>
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</div>
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<div class="line"><a id="l00109" name="l00109"></a><span class="lineno"> 109</span> </div>
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<div class="foldopen" id="foldopen00110" data-start="{" data-end="}">
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<div class="line"><a id="l00110" name="l00110"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391"> 110</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391">GraphEngine::populateSpeciesToIndexMap</a>() {</div>
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<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a>.clear();</div>
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<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size(); ++i) {</div>
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<div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a>.insert({<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>[i], i});</div>
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<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span> }</div>
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<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> }</div>
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</div>
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<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> </div>
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<div class="foldopen" id="foldopen00117" data-start="{" data-end="}">
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<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a5a5458ed01923124f2d7e1f04f32f138"> 117</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a5a5458ed01923124f2d7e1f04f32f138">GraphEngine::reserveJacobianMatrix</a>() {</div>
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<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> <span class="comment">// The implementation of this function (and others) constrains this nuclear network to a constant temperature and density during</span></div>
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<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> <span class="comment">// each evaluation.</span></div>
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<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span> <span class="keywordtype">size_t</span> numSpecies = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size();</div>
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<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.clear();</div>
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<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.resize(numSpecies, numSpecies, <span class="keyword">false</span>); <span class="comment">// Sparse matrix, no initial values</span></div>
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<div class="line"><a id="l00123" name="l00123"></a><span class="lineno"> 123</span> LOG_TRACE_L2(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Jacobian matrix resized to {} rows and {} columns."</span>,</div>
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<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.size1(), <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.size2());</div>
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<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> }</div>
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</div>
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<div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</span> </div>
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<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span> <span class="comment">// --- Basic Accessors and Queries ---</span></div>
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<div class="foldopen" id="foldopen00128" data-start="{" data-end="}">
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<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767"> 128</a></span> <span class="keyword">const</span> std::vector<fourdst::atomic::Species>& <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767">GraphEngine::getNetworkSpecies</a>()<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> <span class="comment">// Returns a constant reference to the vector of unique species in the network.</span></div>
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<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> LOG_TRACE_L3(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Providing access to network species vector. Size: {}."</span>, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size());</div>
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<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>;</div>
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<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> }</div>
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</div>
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<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span> </div>
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<div class="foldopen" id="foldopen00134" data-start="{" data-end="}">
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<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da"> 134</a></span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a>& <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da">GraphEngine::getNetworkReactions</a>()<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> <span class="comment">// Returns a constant reference to the set of reactions in the network.</span></div>
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<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span> LOG_TRACE_L3(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Providing access to network reactions set. Size: {}."</span>, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size());</div>
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<div class="line"><a id="l00137" name="l00137"></a><span class="lineno"> 137</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>;</div>
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<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> }</div>
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</div>
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<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> </div>
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<div class="foldopen" id="foldopen00140" data-start="{" data-end="}">
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<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b"> 140</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b">GraphEngine::involvesSpecies</a>(<span class="keyword">const</span> fourdst::atomic::Species& species)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span> <span class="comment">// Checks if a given species is present in the network's species map for efficient lookup.</span></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">bool</span> found = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.contains(species.name());</div>
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<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span> LOG_DEBUG(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Checking if species '{}' is involved in the network: {}."</span>, species.name(), found ? <span class="stringliteral">"Yes"</span> : <span class="stringliteral">"No"</span>);</div>
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<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"> 144</span> <span class="keywordflow">return</span> found;</div>
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<div class="line"><a id="l00145" name="l00145"></a><span class="lineno"> 145</span> }</div>
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</div>
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<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"> 146</span> </div>
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<div class="line"><a id="l00147" name="l00147"></a><span class="lineno"> 147</span> <span class="comment">// --- Validation Methods ---</span></div>
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<div class="foldopen" id="foldopen00148" data-start="{" data-end="}">
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<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be"> 148</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be">GraphEngine::validateConservation</a>()<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00149" name="l00149"></a><span class="lineno"> 149</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Validating mass (A) and charge (Z) conservation across all reactions in the network."</span>);</div>
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<div class="line"><a id="l00150" name="l00150"></a><span class="lineno"> 150</span> </div>
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<div class="line"><a id="l00151" name="l00151"></a><span class="lineno"> 151</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a> : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
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<div class="line"><a id="l00152" name="l00152"></a><span class="lineno"> 152</span> uint64_t totalReactantA = 0;</div>
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<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</span> uint64_t totalReactantZ = 0;</div>
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<div class="line"><a id="l00154" name="l00154"></a><span class="lineno"> 154</span> uint64_t totalProductA = 0;</div>
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<div class="line"><a id="l00155" name="l00155"></a><span class="lineno"> 155</span> uint64_t totalProductZ = 0;</div>
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<div class="line"><a id="l00156" name="l00156"></a><span class="lineno"> 156</span> </div>
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<div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</span> <span class="comment">// Calculate total A and Z for reactants</span></div>
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<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"> 158</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& reactant : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants()) {</div>
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<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span> <span class="keyword">auto</span> it = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.find(reactant.name());</div>
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<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> <span class="keywordflow">if</span> (it != <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.end()) {</div>
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<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span> totalReactantA += it->second.a();</div>
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<div class="line"><a id="l00162" name="l00162"></a><span class="lineno"> 162</span> totalReactantZ += it->second.z();</div>
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<div class="line"><a id="l00163" name="l00163"></a><span class="lineno"> 163</span> } <span class="keywordflow">else</span> {</div>
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<div class="line"><a id="l00164" name="l00164"></a><span class="lineno"> 164</span> <span class="comment">// This scenario indicates a severe data integrity issue:</span></div>
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<div class="line"><a id="l00165" name="l00165"></a><span class="lineno"> 165</span> <span class="comment">// a reactant is part of a reaction but not in the network's species map.</span></div>
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<div class="line"><a id="l00166" name="l00166"></a><span class="lineno"> 166</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"CRITICAL ERROR: Reactant species '{}' in reaction '{}' not found in network species map during conservation validation."</span>,</div>
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<div class="line"><a id="l00167" name="l00167"></a><span class="lineno"> 167</span> reactant.name(), <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id());</div>
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<div class="line"><a id="l00168" name="l00168"></a><span class="lineno"> 168</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
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<div class="line"><a id="l00169" name="l00169"></a><span class="lineno"> 169</span> }</div>
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<div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> }</div>
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<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</span> </div>
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<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> <span class="comment">// Calculate total A and Z for products</span></div>
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<div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& product : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products()) {</div>
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<div class="line"><a id="l00174" name="l00174"></a><span class="lineno"> 174</span> <span class="keyword">auto</span> it = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.find(product.name());</div>
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<div class="line"><a id="l00175" name="l00175"></a><span class="lineno"> 175</span> <span class="keywordflow">if</span> (it != <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.end()) {</div>
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<div class="line"><a id="l00176" name="l00176"></a><span class="lineno"> 176</span> totalProductA += it->second.a();</div>
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<div class="line"><a id="l00177" name="l00177"></a><span class="lineno"> 177</span> totalProductZ += it->second.z();</div>
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<div class="line"><a id="l00178" name="l00178"></a><span class="lineno"> 178</span> } <span class="keywordflow">else</span> {</div>
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<div class="line"><a id="l00179" name="l00179"></a><span class="lineno"> 179</span> <span class="comment">// Similar critical error for product species</span></div>
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<div class="line"><a id="l00180" name="l00180"></a><span class="lineno"> 180</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"CRITICAL ERROR: Product species '{}' in reaction '{}' not found in network species map during conservation validation."</span>,</div>
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<div class="line"><a id="l00181" name="l00181"></a><span class="lineno"> 181</span> product.name(), <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id());</div>
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<div class="line"><a id="l00182" name="l00182"></a><span class="lineno"> 182</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
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<div class="line"><a id="l00183" name="l00183"></a><span class="lineno"> 183</span> }</div>
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<div class="line"><a id="l00184" name="l00184"></a><span class="lineno"> 184</span> }</div>
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<div class="line"><a id="l00185" name="l00185"></a><span class="lineno"> 185</span> </div>
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<div class="line"><a id="l00186" name="l00186"></a><span class="lineno"> 186</span> <span class="comment">// Compare totals for conservation</span></div>
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<div class="line"><a id="l00187" name="l00187"></a><span class="lineno"> 187</span> <span class="keywordflow">if</span> (totalReactantA != totalProductA) {</div>
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<div class="line"><a id="l00188" name="l00188"></a><span class="lineno"> 188</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Mass number (A) not conserved for reaction '{}': Reactants A={} vs Products A={}."</span>,</div>
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<div class="line"><a id="l00189" name="l00189"></a><span class="lineno"> 189</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id(), totalReactantA, totalProductA);</div>
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<div class="line"><a id="l00190" name="l00190"></a><span class="lineno"> 190</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
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<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span> }</div>
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<div class="line"><a id="l00192" name="l00192"></a><span class="lineno"> 192</span> <span class="keywordflow">if</span> (totalReactantZ != totalProductZ) {</div>
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<div class="line"><a id="l00193" name="l00193"></a><span class="lineno"> 193</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Atomic number (Z) not conserved for reaction '{}': Reactants Z={} vs Products Z={}."</span>,</div>
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<div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id(), totalReactantZ, totalProductZ);</div>
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<div class="line"><a id="l00195" name="l00195"></a><span class="lineno"> 195</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
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<div class="line"><a id="l00196" name="l00196"></a><span class="lineno"> 196</span> }</div>
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<div class="line"><a id="l00197" name="l00197"></a><span class="lineno"> 197</span> }</div>
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<div class="line"><a id="l00198" name="l00198"></a><span class="lineno"> 198</span> </div>
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<div class="line"><a id="l00199" name="l00199"></a><span class="lineno"> 199</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Mass (A) and charge (Z) conservation validated successfully for all reactions."</span>);</div>
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<div class="line"><a id="l00200" name="l00200"></a><span class="lineno"> 200</span> <span class="keywordflow">return</span> <span class="keyword">true</span>; <span class="comment">// All reactions passed the conservation check</span></div>
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<div class="line"><a id="l00201" name="l00201"></a><span class="lineno"> 201</span> }</div>
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</div>
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<div class="line"><a id="l00202" name="l00202"></a><span class="lineno"> 202</span> </div>
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<div class="foldopen" id="foldopen00203" data-start="{" data-end="}">
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<div class="line"><a id="l00203" name="l00203"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#aeeafeab40a5f4dbfae78bdc87e25e93f"> 203</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aeeafeab40a5f4dbfae78bdc87e25e93f">GraphEngine::validateComposition</a>(<span class="keyword">const</span> fourdst::composition::Composition &composition, <span class="keywordtype">double</span> culling, <span class="keywordtype">double</span> T9) {</div>
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<div class="line"><a id="l00204" name="l00204"></a><span class="lineno"> 204</span> <span class="comment">// Check if the requested network has already been cached.</span></div>
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<div class="line"><a id="l00205" name="l00205"></a><span class="lineno"> 205</span> <span class="comment">// PERF: Rebuilding this should be pretty fast but it may be a good point of optimization in the future.</span></div>
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<div class="line"><a id="l00206" name="l00206"></a><span class="lineno"> 206</span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> validationReactionSet = <a class="code hl_function" href="namespacegridfire.html#aa77f83539d9ae90e3bf541309bd9c83a">build_reaclib_nuclear_network</a>(composition, <span class="keyword">false</span>);</div>
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<div class="line"><a id="l00207" name="l00207"></a><span class="lineno"> 207</span> <span class="comment">// TODO: need some more robust method here to</span></div>
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<div class="line"><a id="l00208" name="l00208"></a><span class="lineno"> 208</span> <span class="comment">// A. Build the basic network from the composition's species with non zero mass fractions.</span></div>
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<div class="line"><a id="l00209" name="l00209"></a><span class="lineno"> 209</span> <span class="comment">// B. rebuild a new composition from the reaction set's reactants + products (with the mass fractions from the things that are only products set to 0)</span></div>
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<div class="line"><a id="l00210" name="l00210"></a><span class="lineno"> 210</span> <span class="comment">// C. Rebuild the reaction set from the new composition</span></div>
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<div class="line"><a id="l00211" name="l00211"></a><span class="lineno"> 211</span> <span class="comment">// D. Cull reactions where all reactants have mass fractions below the culling threshold.</span></div>
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<div class="line"><a id="l00212" name="l00212"></a><span class="lineno"> 212</span> <span class="comment">// E. Be careful about maintaining caching through all of this</span></div>
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<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</span> </div>
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<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span> </div>
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<div class="line"><a id="l00215" name="l00215"></a><span class="lineno"> 215</span> <span class="comment">// This allows for dynamic network modification while retaining caching for networks which are very similar.</span></div>
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<div class="line"><a id="l00216" name="l00216"></a><span class="lineno"> 216</span> <span class="keywordflow">if</span> (validationReactionSet != <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
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<div class="line"><a id="l00217" name="l00217"></a><span class="lineno"> 217</span> LOG_DEBUG(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Reaction set not cached. Rebuilding the reaction set for T9={} and culling={}."</span>, T9, culling);</div>
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<div class="line"><a id="l00218" name="l00218"></a><span class="lineno"> 218</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a> = validationReactionSet;</div>
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<div class="line"><a id="l00219" name="l00219"></a><span class="lineno"> 219</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">syncInternalMaps</a>(); <span class="comment">// Re-sync internal maps after updating reactions. Note this will also retrace the AD tape.</span></div>
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<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span> }</div>
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<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"> 221</span> }</div>
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</div>
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<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> </div>
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<div class="foldopen" id="foldopen00223" data-start="{" data-end="}">
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<div class="line"><a id="l00223" name="l00223"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a63639f4430d0889605c10839a6f32af9"> 223</a></span> <a class="code hl_struct" href="structgridfire_1_1_step_derivatives.html">StepDerivatives<double></a> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a63639f4430d0889605c10839a6f32af9">GraphEngine::calculateAllDerivativesUsingPrecomputation</a>(</div>
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<div class="line"><a id="l00224" name="l00224"></a><span class="lineno"> 224</span> <span class="keyword">const</span> std::vector<double> &Y_in,</div>
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<div class="line"><a id="l00225" name="l00225"></a><span class="lineno"> 225</span> <span class="keyword">const</span> std::vector<double> &bare_rates,</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> T9,</div>
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<div class="line"><a id="l00227" name="l00227"></a><span class="lineno"> 227</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00228" name="l00228"></a><span class="lineno"> 228</span> )<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00229" name="l00229"></a><span class="lineno"> 229</span> <span class="comment">// --- Calculate screening factors ---</span></div>
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<div class="line"><a id="l00230" name="l00230"></a><span class="lineno"> 230</span> <span class="keyword">const</span> std::vector<double> screeningFactors = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#af17cf3762abac3efcab9a8e87c961210">m_screeningModel</a>->calculateScreeningFactors(</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="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>,</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="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>,</div>
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<div class="line"><a id="l00233" name="l00233"></a><span class="lineno"> 233</span> Y_in,</div>
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<div class="line"><a id="l00234" name="l00234"></a><span class="lineno"> 234</span> T9,</div>
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<div class="line"><a id="l00235" name="l00235"></a><span class="lineno"> 235</span> rho</div>
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<div class="line"><a id="l00236" name="l00236"></a><span class="lineno"> 236</span> );</div>
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<div class="line"><a id="l00237" name="l00237"></a><span class="lineno"> 237</span> </div>
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<div class="line"><a id="l00238" name="l00238"></a><span class="lineno"> 238</span> <span class="comment">// --- Optimized loop ---</span></div>
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<div class="line"><a id="l00239" name="l00239"></a><span class="lineno"> 239</span> std::vector<double> molarReactionFlows;</div>
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<div class="line"><a id="l00240" name="l00240"></a><span class="lineno"> 240</span> molarReactionFlows.reserve(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>.size());</div>
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<div class="line"><a id="l00241" name="l00241"></a><span class="lineno"> 241</span> </div>
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<div class="line"><a id="l00242" name="l00242"></a><span class="lineno"> 242</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& precomp : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>) {</div>
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<div class="line"><a id="l00243" name="l00243"></a><span class="lineno"> 243</span> <span class="keywordtype">double</span> abundanceProduct = 1.0;</div>
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<div class="line"><a id="l00244" name="l00244"></a><span class="lineno"> 244</span> <span class="keywordtype">bool</span> below_threshold = <span class="keyword">false</span>;</div>
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<div class="line"><a id="l00245" name="l00245"></a><span class="lineno"> 245</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < precomp.unique_reactant_indices.size(); ++i) {</div>
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<div class="line"><a id="l00246" name="l00246"></a><span class="lineno"> 246</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> reactantIndex = precomp.unique_reactant_indices[i];</div>
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<div class="line"><a id="l00247" name="l00247"></a><span class="lineno"> 247</span> <span class="keyword">const</span> <span class="keywordtype">int</span> power = precomp.reactant_powers[i];</div>
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<div class="line"><a id="l00248" name="l00248"></a><span class="lineno"> 248</span> <span class="keyword">const</span> <span class="keywordtype">double</span> abundance = Y_in[reactantIndex];</div>
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<div class="line"><a id="l00249" name="l00249"></a><span class="lineno"> 249</span> <span class="keywordflow">if</span> (abundance < <a class="code hl_variable" href="namespacegridfire.html#a96c062f94713921e5d7568ecedcdcb06">MIN_ABUNDANCE_THRESHOLD</a>) {</div>
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<div class="line"><a id="l00250" name="l00250"></a><span class="lineno"> 250</span> below_threshold = <span class="keyword">true</span>;</div>
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<div class="line"><a id="l00251" name="l00251"></a><span class="lineno"> 251</span> <span class="keywordflow">break</span>;</div>
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<div class="line"><a id="l00252" name="l00252"></a><span class="lineno"> 252</span> }</div>
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<div class="line"><a id="l00253" name="l00253"></a><span class="lineno"> 253</span> </div>
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<div class="line"><a id="l00254" name="l00254"></a><span class="lineno"> 254</span> abundanceProduct *= std::pow(Y_in[reactantIndex], power);</div>
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<div class="line"><a id="l00255" name="l00255"></a><span class="lineno"> 255</span> }</div>
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<div class="line"><a id="l00256" name="l00256"></a><span class="lineno"> 256</span> <span class="keywordflow">if</span> (below_threshold) {</div>
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<div class="line"><a id="l00257" name="l00257"></a><span class="lineno"> 257</span> molarReactionFlows.push_back(0.0);</div>
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<div class="line"><a id="l00258" name="l00258"></a><span class="lineno"> 258</span> <span class="keywordflow">continue</span>; <span class="comment">// Skip this reaction if any reactant is below the abundance threshold</span></div>
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<div class="line"><a id="l00259" name="l00259"></a><span class="lineno"> 259</span> }</div>
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<div class="line"><a id="l00260" name="l00260"></a><span class="lineno"> 260</span> </div>
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<div class="line"><a id="l00261" name="l00261"></a><span class="lineno"> 261</span> <span class="keyword">const</span> <span class="keywordtype">double</span> bare_rate = bare_rates[precomp.reaction_index];</div>
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<div class="line"><a id="l00262" name="l00262"></a><span class="lineno"> 262</span> <span class="keyword">const</span> <span class="keywordtype">double</span> screeningFactor = screeningFactors[precomp.reaction_index];</div>
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<div class="line"><a id="l00263" name="l00263"></a><span class="lineno"> 263</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> numReactants = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>[precomp.reaction_index].reactants().size();</div>
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<div class="line"><a id="l00264" name="l00264"></a><span class="lineno"> 264</span> </div>
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<div class="line"><a id="l00265" name="l00265"></a><span class="lineno"> 265</span> <span class="keyword">const</span> <span class="keywordtype">double</span> molarReactionFlow =</div>
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<div class="line"><a id="l00266" name="l00266"></a><span class="lineno"> 266</span> screeningFactor *</div>
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<div class="line"><a id="l00267" name="l00267"></a><span class="lineno"> 267</span> bare_rate *</div>
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<div class="line"><a id="l00268" name="l00268"></a><span class="lineno"> 268</span> precomp.symmetry_factor *</div>
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<div class="line"><a id="l00269" name="l00269"></a><span class="lineno"> 269</span> abundanceProduct *</div>
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<div class="line"><a id="l00270" name="l00270"></a><span class="lineno"> 270</span> std::pow(rho, numReactants);</div>
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<div class="line"><a id="l00271" name="l00271"></a><span class="lineno"> 271</span> </div>
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<div class="line"><a id="l00272" name="l00272"></a><span class="lineno"> 272</span> molarReactionFlows.push_back(molarReactionFlow);</div>
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<div class="line"><a id="l00273" name="l00273"></a><span class="lineno"> 273</span> }</div>
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<div class="line"><a id="l00274" name="l00274"></a><span class="lineno"> 274</span> </div>
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<div class="line"><a id="l00275" name="l00275"></a><span class="lineno"> 275</span> <span class="comment">// --- Assemble molar abundance derivatives ---</span></div>
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<div class="line"><a id="l00276" name="l00276"></a><span class="lineno"> 276</span> <a class="code hl_struct" href="structgridfire_1_1_step_derivatives.html">StepDerivatives<double></a> result;</div>
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<div class="line"><a id="l00277" name="l00277"></a><span class="lineno"> 277</span> result.<a class="code hl_variable" href="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d">dydt</a>.assign(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size(), 0.0); <span class="comment">// Initialize derivatives to zero</span></div>
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<div class="line"><a id="l00278" name="l00278"></a><span class="lineno"> 278</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j < <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>.size(); ++j) {</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="keyword">auto</span>& precomp = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>[j];</div>
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<div class="line"><a id="l00280" name="l00280"></a><span class="lineno"> 280</span> <span class="keyword">const</span> <span class="keywordtype">double</span> R_j = molarReactionFlows[j];</div>
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<div class="line"><a id="l00281" name="l00281"></a><span class="lineno"> 281</span> </div>
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<div class="line"><a id="l00282" name="l00282"></a><span class="lineno"> 282</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < precomp.affected_species_indices.size(); ++i) {</div>
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<div class="line"><a id="l00283" name="l00283"></a><span class="lineno"> 283</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> speciesIndex = precomp.affected_species_indices[i];</div>
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<div class="line"><a id="l00284" name="l00284"></a><span class="lineno"> 284</span> <span class="keyword">const</span> <span class="keywordtype">int</span> stoichiometricCoefficient = precomp.stoichiometric_coefficients[i];</div>
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<div class="line"><a id="l00285" name="l00285"></a><span class="lineno"> 285</span> </div>
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<div class="line"><a id="l00286" name="l00286"></a><span class="lineno"> 286</span> <span class="comment">// Update the derivative for this species</span></div>
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<div class="line"><a id="l00287" name="l00287"></a><span class="lineno"> 287</span> result.<a class="code hl_variable" href="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d">dydt</a>[speciesIndex] += <span class="keyword">static_cast<</span><span class="keywordtype">double</span><span class="keyword">></span>(stoichiometricCoefficient) * R_j / rho;</div>
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<div class="line"><a id="l00288" name="l00288"></a><span class="lineno"> 288</span> }</div>
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<div class="line"><a id="l00289" name="l00289"></a><span class="lineno"> 289</span> }</div>
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<div class="line"><a id="l00290" name="l00290"></a><span class="lineno"> 290</span> </div>
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<div class="line"><a id="l00291" name="l00291"></a><span class="lineno"> 291</span> <span class="comment">// --- Calculate the nuclear energy generation rate ---</span></div>
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<div class="line"><a id="l00292" name="l00292"></a><span class="lineno"> 292</span> <span class="keywordtype">double</span> massProductionRate = 0.0; <span class="comment">// [mol][s^-1]</span></div>
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<div class="line"><a id="l00293" name="l00293"></a><span class="lineno"> 293</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size(); ++i) {</div>
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<div class="line"><a id="l00294" name="l00294"></a><span class="lineno"> 294</span> <span class="keyword">const</span> <span class="keyword">auto</span>& species = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>[i];</div>
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<div class="line"><a id="l00295" name="l00295"></a><span class="lineno"> 295</span> massProductionRate += result.<a class="code hl_variable" href="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d">dydt</a>[i] * species.mass() * <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">m_constants</a>.u;</div>
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<div class="line"><a id="l00296" name="l00296"></a><span class="lineno"> 296</span> }</div>
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<div class="line"><a id="l00297" name="l00297"></a><span class="lineno"> 297</span> result.<a class="code hl_variable" href="structgridfire_1_1_step_derivatives.html#ab4aeb41be952c7b5844e1ee81fef9008">nuclearEnergyGenerationRate</a> = -massProductionRate * <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">m_constants</a>.Na * <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">m_constants</a>.c * <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">m_constants</a>.c; <span class="comment">// [erg][s^-1][g^-1]</span></div>
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<div class="line"><a id="l00298" name="l00298"></a><span class="lineno"> 298</span> <span class="keywordflow">return</span> result;</div>
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<div class="line"><a id="l00299" name="l00299"></a><span class="lineno"> 299</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="l00302" name="l00302"></a><span class="lineno"> 302</span> <span class="comment">// --- Generate Stoichiometry Matrix ---</span></div>
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<div class="foldopen" id="foldopen00303" data-start="{" data-end="}">
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<div class="line"><a id="l00303" name="l00303"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38"> 303</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38">GraphEngine::generateStoichiometryMatrix</a>() {</div>
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<div class="line"><a id="l00304" name="l00304"></a><span class="lineno"> 304</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Generating stoichiometry matrix..."</span>);</div>
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<div class="line"><a id="l00305" name="l00305"></a><span class="lineno"> 305</span> </div>
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<div class="line"><a id="l00306" name="l00306"></a><span class="lineno"> 306</span> <span class="comment">// Task 1: Set dimensions and initialize the matrix</span></div>
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<div class="line"><a id="l00307" name="l00307"></a><span class="lineno"> 307</span> <span class="keywordtype">size_t</span> numSpecies = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size();</div>
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<div class="line"><a id="l00308" name="l00308"></a><span class="lineno"> 308</span> <span class="keywordtype">size_t</span> numReactions = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size();</div>
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<div class="line"><a id="l00309" name="l00309"></a><span class="lineno"> 309</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a>.resize(numSpecies, numReactions, <span class="keyword">false</span>);</div>
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<div class="line"><a id="l00310" name="l00310"></a><span class="lineno"> 310</span> </div>
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<div class="line"><a id="l00311" name="l00311"></a><span class="lineno"> 311</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Stoichiometry matrix initialized with dimensions: {} rows (species) x {} columns (reactions)."</span>,</div>
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<div class="line"><a id="l00312" name="l00312"></a><span class="lineno"> 312</span> numSpecies, numReactions);</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"> 314</span> <span class="comment">// Task 2: Populate the stoichiometry matrix</span></div>
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<div class="line"><a id="l00315" name="l00315"></a><span class="lineno"> 315</span> <span class="comment">// Iterate through all reactions, assign them a column index, and fill in their stoichiometric coefficients.</span></div>
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<div class="line"><a id="l00316" name="l00316"></a><span class="lineno"> 316</span> <span class="keywordtype">size_t</span> reactionColumnIndex = 0;</div>
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<div class="line"><a id="l00317" name="l00317"></a><span class="lineno"> 317</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a> : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
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<div class="line"><a id="l00318" name="l00318"></a><span class="lineno"> 318</span> <span class="comment">// Get the net stoichiometry for the current reaction</span></div>
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<div class="line"><a id="l00319" name="l00319"></a><span class="lineno"> 319</span> std::unordered_map<fourdst::atomic::Species, int> netStoichiometry = <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.stoichiometry();</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="line"><a id="l00321" name="l00321"></a><span class="lineno"> 321</span> <span class="comment">// Iterate through the species and their coefficients in the stoichiometry map</span></div>
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<div class="line"><a id="l00322" name="l00322"></a><span class="lineno"> 322</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& [species, coefficient] : netStoichiometry) {</div>
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<div class="line"><a id="l00323" name="l00323"></a><span class="lineno"> 323</span> <span class="comment">// Find the row index for this species</span></div>
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<div class="line"><a id="l00324" name="l00324"></a><span class="lineno"> 324</span> <span class="keyword">auto</span> it = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a>.find(species);</div>
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<div class="line"><a id="l00325" name="l00325"></a><span class="lineno"> 325</span> <span class="keywordflow">if</span> (it != <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a>.end()) {</div>
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<div class="line"><a id="l00326" name="l00326"></a><span class="lineno"> 326</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> speciesRowIndex = it->second;</div>
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<div class="line"><a id="l00327" name="l00327"></a><span class="lineno"> 327</span> <span class="comment">// Set the matrix element. Boost.uBLAS handles sparse insertion.</span></div>
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<div class="line"><a id="l00328" name="l00328"></a><span class="lineno"> 328</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a>(speciesRowIndex, reactionColumnIndex) = coefficient;</div>
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<div class="line"><a id="l00329" name="l00329"></a><span class="lineno"> 329</span> } <span class="keywordflow">else</span> {</div>
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<div class="line"><a id="l00330" name="l00330"></a><span class="lineno"> 330</span> <span class="comment">// This scenario should ideally not happen if m_networkSpeciesMap and m_speciesToIndexMap are correctly synced</span></div>
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<div class="line"><a id="l00331" name="l00331"></a><span class="lineno"> 331</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"CRITICAL ERROR: Species '{}' from reaction '{}' stoichiometry not found in species to index map."</span>,</div>
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<div class="line"><a id="l00332" name="l00332"></a><span class="lineno"> 332</span> species.name(), <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id());</div>
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<div class="line"><a id="l00333" name="l00333"></a><span class="lineno"> 333</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a> -> flush_log();</div>
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<div class="line"><a id="l00334" name="l00334"></a><span class="lineno"> 334</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Species not found in species to index map: "</span> + std::string(species.name()));</div>
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<div class="line"><a id="l00335" name="l00335"></a><span class="lineno"> 335</span> }</div>
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<div class="line"><a id="l00336" name="l00336"></a><span class="lineno"> 336</span> }</div>
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<div class="line"><a id="l00337" name="l00337"></a><span class="lineno"> 337</span> reactionColumnIndex++; <span class="comment">// Move to the next column for the next reaction</span></div>
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<div class="line"><a id="l00338" name="l00338"></a><span class="lineno"> 338</span> }</div>
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<div class="line"><a id="l00339" name="l00339"></a><span class="lineno"> 339</span> </div>
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<div class="line"><a id="l00340" name="l00340"></a><span class="lineno"> 340</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Stoichiometry matrix population complete. Number of non-zero elements: {}."</span>,</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="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a>.nnz()); <span class="comment">// Assuming nnz() exists for compressed_matrix</span></div>
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<div class="line"><a id="l00342" name="l00342"></a><span class="lineno"> 342</span> }</div>
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</div>
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<div class="line"><a id="l00343" name="l00343"></a><span class="lineno"> 343</span> </div>
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<div class="foldopen" id="foldopen00344" data-start="{" data-end="}">
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<div class="line"><a id="l00344" name="l00344"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#aaf4d54e4b774ab8ec8eabec006579d31"> 344</a></span> <a class="code hl_struct" href="structgridfire_1_1_step_derivatives.html">StepDerivatives<double></a> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">GraphEngine::calculateAllDerivatives</a>(</div>
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<div class="line"><a id="l00345" name="l00345"></a><span class="lineno"> 345</span> <span class="keyword">const</span> std::vector<double> &Y_in,</div>
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<div class="line"><a id="l00346" name="l00346"></a><span class="lineno"> 346</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00347" name="l00347"></a><span class="lineno"> 347</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00348" name="l00348"></a><span class="lineno"> 348</span> )<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00349" name="l00349"></a><span class="lineno"> 349</span> <span class="keywordflow">return</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives<double></a>(Y_in, T9, rho);</div>
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<div class="line"><a id="l00350" name="l00350"></a><span class="lineno"> 350</span> }</div>
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</div>
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<div class="line"><a id="l00351" name="l00351"></a><span class="lineno"> 351</span> </div>
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<div class="foldopen" id="foldopen00352" data-start="{" data-end="}">
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<div class="line"><a id="l00352" name="l00352"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a71a3d1181b90c3becdc5d9a3da05b9c9"> 352</a></span> <a class="code hl_struct" href="structgridfire_1_1_step_derivatives.html">StepDerivatives<ADDouble></a> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">GraphEngine::calculateAllDerivatives</a>(</div>
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<div class="line"><a id="l00353" name="l00353"></a><span class="lineno"> 353</span> <span class="keyword">const</span> std::vector<ADDouble> &Y_in,</div>
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<div class="line"><a id="l00354" name="l00354"></a><span class="lineno"> 354</span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc">ADDouble</a> &T9,</div>
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<div class="line"><a id="l00355" name="l00355"></a><span class="lineno"> 355</span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc">ADDouble</a> &rho</div>
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<div class="line"><a id="l00356" name="l00356"></a><span class="lineno"> 356</span> )<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00357" name="l00357"></a><span class="lineno"> 357</span> <span class="keywordflow">return</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives<ADDouble></a>(Y_in, T9, rho);</div>
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<div class="line"><a id="l00358" name="l00358"></a><span class="lineno"> 358</span> }</div>
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</div>
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<div class="line"><a id="l00359" name="l00359"></a><span class="lineno"> 359</span> </div>
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<div class="foldopen" id="foldopen00360" data-start="{" data-end="}">
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<div class="line"><a id="l00360" name="l00360"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f"> 360</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f">GraphEngine::setScreeningModel</a>(<span class="keyword">const</span> <a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> model) {</div>
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<div class="line"><a id="l00361" name="l00361"></a><span class="lineno"> 361</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#af17cf3762abac3efcab9a8e87c961210">m_screeningModel</a> = <a class="code hl_function" href="namespacegridfire_1_1screening.html#a6ca8556d27ac373e176f5b23437c416e">screening::selectScreeningModel</a>(model);</div>
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<div class="line"><a id="l00362" name="l00362"></a><span class="lineno"> 362</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a52edc3e88f1e8fc497e1e63972d63c80">m_screeningType</a> = model;</div>
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<div class="line"><a id="l00363" name="l00363"></a><span class="lineno"> 363</span> }</div>
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</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="foldopen" id="foldopen00365" data-start="{" data-end="}">
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<div class="line"><a id="l00365" name="l00365"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a"> 365</a></span> <a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a">GraphEngine::getScreeningModel</a>()<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00366" name="l00366"></a><span class="lineno"> 366</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a52edc3e88f1e8fc497e1e63972d63c80">m_screeningType</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="foldopen00369" data-start="{" data-end="}">
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<div class="line"><a id="l00369" name="l00369"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1"> 369</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1">GraphEngine::setPrecomputation</a>(<span class="keyword">const</span> <span class="keywordtype">bool</span> precompute) {</div>
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<div class="line"><a id="l00370" name="l00370"></a><span class="lineno"> 370</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de">m_usePrecomputation</a> = precompute;</div>
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<div class="line"><a id="l00371" name="l00371"></a><span class="lineno"> 371</span> }</div>
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</div>
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<div class="line"><a id="l00372" name="l00372"></a><span class="lineno"> 372</span> </div>
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<div class="foldopen" id="foldopen00373" data-start="{" data-end="}">
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<div class="line"><a id="l00373" name="l00373"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f"> 373</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f">GraphEngine::isPrecomputationEnabled</a>()<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00374" name="l00374"></a><span class="lineno"> 374</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de">m_usePrecomputation</a>;</div>
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<div class="line"><a id="l00375" name="l00375"></a><span class="lineno"> 375</span> }</div>
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</div>
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<div class="line"><a id="l00376" name="l00376"></a><span class="lineno"> 376</span> </div>
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<div class="foldopen" id="foldopen00377" data-start="{" data-end="}">
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<div class="line"><a id="l00377" name="l00377"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f"> 377</a></span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">GraphEngine::calculateMolarReactionFlow</a>(</div>
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<div class="line"><a id="l00378" name="l00378"></a><span class="lineno"> 378</span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>,</div>
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<div class="line"><a id="l00379" name="l00379"></a><span class="lineno"> 379</span> <span class="keyword">const</span> std::vector<double> &Y,</div>
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<div class="line"><a id="l00380" name="l00380"></a><span class="lineno"> 380</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00381" name="l00381"></a><span class="lineno"> 381</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00382" name="l00382"></a><span class="lineno"> 382</span> )<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00383" name="l00383"></a><span class="lineno"> 383</span> <span class="keywordflow">return</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">calculateMolarReactionFlow<double></a>(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>, Y, T9, rho);</div>
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<div class="line"><a id="l00384" name="l00384"></a><span class="lineno"> 384</span> }</div>
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</div>
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<div class="line"><a id="l00385" name="l00385"></a><span class="lineno"> 385</span> </div>
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<div class="foldopen" id="foldopen00386" data-start="{" data-end="}">
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<div class="line"><a id="l00386" name="l00386"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#ae347ff0316e532e0298ec8c913908105"> 386</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#ae347ff0316e532e0298ec8c913908105">GraphEngine::generateJacobianMatrix</a>(</div>
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<div class="line"><a id="l00387" name="l00387"></a><span class="lineno"> 387</span> <span class="keyword">const</span> std::vector<double> &Y,</div>
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<div class="line"><a id="l00388" name="l00388"></a><span class="lineno"> 388</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00389" name="l00389"></a><span class="lineno"> 389</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00390" name="l00390"></a><span class="lineno"> 390</span> ) {</div>
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<div class="line"><a id="l00391" name="l00391"></a><span class="lineno"> 391</span> </div>
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<div class="line"><a id="l00392" name="l00392"></a><span class="lineno"> 392</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Generating jacobian matrix for T9={}, rho={}.."</span>, T9, rho);</div>
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<div class="line"><a id="l00393" name="l00393"></a><span class="lineno"> 393</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> numSpecies = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size();</div>
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<div class="line"><a id="l00394" name="l00394"></a><span class="lineno"> 394</span> </div>
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<div class="line"><a id="l00395" name="l00395"></a><span class="lineno"> 395</span> <span class="comment">// 1. Pack the input variables into a vector for CppAD</span></div>
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<div class="line"><a id="l00396" name="l00396"></a><span class="lineno"> 396</span> std::vector<double> adInput(numSpecies + 2, 0.0); <span class="comment">// +2 for T9 and rho</span></div>
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<div class="line"><a id="l00397" name="l00397"></a><span class="lineno"> 397</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < numSpecies; ++i) {</div>
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<div class="line"><a id="l00398" name="l00398"></a><span class="lineno"> 398</span> adInput[i] = Y[i];</div>
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<div class="line"><a id="l00399" name="l00399"></a><span class="lineno"> 399</span> }</div>
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<div class="line"><a id="l00400" name="l00400"></a><span class="lineno"> 400</span> adInput[numSpecies] = T9; <span class="comment">// T9</span></div>
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<div class="line"><a id="l00401" name="l00401"></a><span class="lineno"> 401</span> adInput[numSpecies + 1] = rho; <span class="comment">// rho</span></div>
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<div class="line"><a id="l00402" name="l00402"></a><span class="lineno"> 402</span> </div>
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<div class="line"><a id="l00403" name="l00403"></a><span class="lineno"> 403</span> <span class="comment">// 2. Calculate the full jacobian</span></div>
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<div class="line"><a id="l00404" name="l00404"></a><span class="lineno"> 404</span> <span class="keyword">const</span> std::vector<double> dotY = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a>.Jacobian(adInput);</div>
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<div class="line"><a id="l00405" name="l00405"></a><span class="lineno"> 405</span> </div>
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<div class="line"><a id="l00406" name="l00406"></a><span class="lineno"> 406</span> <span class="comment">// 3. Pack jacobian vector into sparse matrix</span></div>
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<div class="line"><a id="l00407" name="l00407"></a><span class="lineno"> 407</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.clear();</div>
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<div class="line"><a id="l00408" name="l00408"></a><span class="lineno"> 408</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < numSpecies; ++i) {</div>
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<div class="line"><a id="l00409" name="l00409"></a><span class="lineno"> 409</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j < numSpecies; ++j) {</div>
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<div class="line"><a id="l00410" name="l00410"></a><span class="lineno"> 410</span> <span class="keyword">const</span> <span class="keywordtype">double</span> value = dotY[i * (numSpecies + 2) + j];</div>
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<div class="line"><a id="l00411" name="l00411"></a><span class="lineno"> 411</span> <span class="keywordflow">if</span> (std::abs(value) > <a class="code hl_variable" href="namespacegridfire.html#ae01b1738df1921db565bcbd68dd6cf64">MIN_JACOBIAN_THRESHOLD</a>) {</div>
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<div class="line"><a id="l00412" name="l00412"></a><span class="lineno"> 412</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>(i, j) = value;</div>
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<div class="line"><a id="l00413" name="l00413"></a><span class="lineno"> 413</span> }</div>
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<div class="line"><a id="l00414" name="l00414"></a><span class="lineno"> 414</span> }</div>
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<div class="line"><a id="l00415" name="l00415"></a><span class="lineno"> 415</span> }</div>
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<div class="line"><a id="l00416" name="l00416"></a><span class="lineno"> 416</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Jacobian matrix generated with dimensions: {} rows x {} columns."</span>, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.size1(), <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.size2());</div>
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<div class="line"><a id="l00417" name="l00417"></a><span class="lineno"> 417</span> }</div>
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</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="foldopen" id="foldopen00419" data-start="{" data-end="}">
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<div class="line"><a id="l00419" name="l00419"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c"> 419</a></span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c">GraphEngine::getJacobianMatrixEntry</a>(<span class="keyword">const</span> <span class="keywordtype">int</span> i, <span class="keyword">const</span> <span class="keywordtype">int</span> j)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00420" name="l00420"></a><span class="lineno"> 420</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>(i, j);</div>
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<div class="line"><a id="l00421" name="l00421"></a><span class="lineno"> 421</span> }</div>
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</div>
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<div class="line"><a id="l00422" name="l00422"></a><span class="lineno"> 422</span> </div>
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<div class="foldopen" id="foldopen00423" data-start="{" data-end="}">
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<div class="line"><a id="l00423" name="l00423"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9"> 423</a></span> std::unordered_map<fourdst::atomic::Species, int> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9">GraphEngine::getNetReactionStoichiometry</a>(</div>
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<div class="line"><a id="l00424" name="l00424"></a><span class="lineno"> 424</span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a></div>
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<div class="line"><a id="l00425" name="l00425"></a><span class="lineno"> 425</span> ) {</div>
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<div class="line"><a id="l00426" name="l00426"></a><span class="lineno"> 426</span> <span class="keywordflow">return</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.stoichiometry();</div>
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<div class="line"><a id="l00427" name="l00427"></a><span class="lineno"> 427</span> }</div>
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</div>
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<div class="line"><a id="l00428" name="l00428"></a><span class="lineno"> 428</span> </div>
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<div class="foldopen" id="foldopen00429" data-start="{" data-end="}">
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<div class="line"><a id="l00429" name="l00429"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152"> 429</a></span> <span class="keywordtype">int</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152">GraphEngine::getStoichiometryMatrixEntry</a>(</div>
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<div class="line"><a id="l00430" name="l00430"></a><span class="lineno"> 430</span> <span class="keyword">const</span> <span class="keywordtype">int</span> speciesIndex,</div>
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<div class="line"><a id="l00431" name="l00431"></a><span class="lineno"> 431</span> <span class="keyword">const</span> <span class="keywordtype">int</span> reactionIndex</div>
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<div class="line"><a id="l00432" name="l00432"></a><span class="lineno"> 432</span> )<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00433" name="l00433"></a><span class="lineno"> 433</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a>(speciesIndex, reactionIndex);</div>
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<div class="line"><a id="l00434" name="l00434"></a><span class="lineno"> 434</span> }</div>
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</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 class="foldopen" id="foldopen00436" data-start="{" data-end="}">
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<div class="line"><a id="l00436" name="l00436"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929"> 436</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929">GraphEngine::exportToDot</a>(<span class="keyword">const</span> std::string &filename)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00437" name="l00437"></a><span class="lineno"> 437</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Exporting network graph to DOT file: {}"</span>, filename);</div>
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<div class="line"><a id="l00438" name="l00438"></a><span class="lineno"> 438</span> </div>
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<div class="line"><a id="l00439" name="l00439"></a><span class="lineno"> 439</span> std::ofstream dotFile(filename);</div>
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<div class="line"><a id="l00440" name="l00440"></a><span class="lineno"> 440</span> <span class="keywordflow">if</span> (!dotFile.is_open()) {</div>
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<div class="line"><a id="l00441" name="l00441"></a><span class="lineno"> 441</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Failed to open file for writing: {}"</span>, filename);</div>
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<div class="line"><a id="l00442" name="l00442"></a><span class="lineno"> 442</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>->flush_log();</div>
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<div class="line"><a id="l00443" name="l00443"></a><span class="lineno"> 443</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Failed to open file for writing: "</span> + filename);</div>
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<div class="line"><a id="l00444" name="l00444"></a><span class="lineno"> 444</span> }</div>
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<div class="line"><a id="l00445" name="l00445"></a><span class="lineno"> 445</span> </div>
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<div class="line"><a id="l00446" name="l00446"></a><span class="lineno"> 446</span> dotFile << <span class="stringliteral">"digraph NuclearReactionNetwork {\n"</span>;</div>
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<div class="line"><a id="l00447" name="l00447"></a><span class="lineno"> 447</span> dotFile << <span class="stringliteral">" graph [rankdir=LR, splines=true, overlap=false, bgcolor=\"#f0f0f0\"];\n"</span>;</div>
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<div class="line"><a id="l00448" name="l00448"></a><span class="lineno"> 448</span> dotFile << <span class="stringliteral">" node [shape=circle, style=filled, fillcolor=\"#a7c7e7\", fontname=\"Helvetica\"];\n"</span>;</div>
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<div class="line"><a id="l00449" name="l00449"></a><span class="lineno"> 449</span> dotFile << <span class="stringliteral">" edge [fontname=\"Helvetica\", fontsize=10];\n\n"</span>;</div>
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<div class="line"><a id="l00450" name="l00450"></a><span class="lineno"> 450</span> </div>
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<div class="line"><a id="l00451" name="l00451"></a><span class="lineno"> 451</span> <span class="comment">// 1. Define all species as nodes</span></div>
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<div class="line"><a id="l00452" name="l00452"></a><span class="lineno"> 452</span> dotFile << <span class="stringliteral">" // --- Species Nodes ---\n"</span>;</div>
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<div class="line"><a id="l00453" name="l00453"></a><span class="lineno"> 453</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& species : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>) {</div>
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<div class="line"><a id="l00454" name="l00454"></a><span class="lineno"> 454</span> dotFile << <span class="stringliteral">" \""</span> << species.name() << <span class="stringliteral">"\" [label=\""</span> << species.name() << <span class="stringliteral">"\"];\n"</span>;</div>
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<div class="line"><a id="l00455" name="l00455"></a><span class="lineno"> 455</span> }</div>
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<div class="line"><a id="l00456" name="l00456"></a><span class="lineno"> 456</span> dotFile << <span class="stringliteral">"\n"</span>;</div>
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<div class="line"><a id="l00457" name="l00457"></a><span class="lineno"> 457</span> </div>
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<div class="line"><a id="l00458" name="l00458"></a><span class="lineno"> 458</span> <span class="comment">// 2. Define all reactions as intermediate nodes and connect them</span></div>
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<div class="line"><a id="l00459" name="l00459"></a><span class="lineno"> 459</span> dotFile << <span class="stringliteral">" // --- Reaction Edges ---\n"</span>;</div>
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<div class="line"><a id="l00460" name="l00460"></a><span class="lineno"> 460</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a> : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
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<div class="line"><a id="l00461" name="l00461"></a><span class="lineno"> 461</span> <span class="comment">// Create a unique ID for the reaction node</span></div>
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<div class="line"><a id="l00462" name="l00462"></a><span class="lineno"> 462</span> std::string reactionNodeId = <span class="stringliteral">"reaction_"</span> + std::string(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id());</div>
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<div class="line"><a id="l00463" name="l00463"></a><span class="lineno"> 463</span> </div>
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<div class="line"><a id="l00464" name="l00464"></a><span class="lineno"> 464</span> <span class="comment">// Define the reaction node (small, black dot)</span></div>
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<div class="line"><a id="l00465" name="l00465"></a><span class="lineno"> 465</span> dotFile << <span class="stringliteral">" \""</span> << reactionNodeId << <span class="stringliteral">"\" [shape=point, fillcolor=black, width=0.1, height=0.1, label=\"\"];\n"</span>;</div>
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<div class="line"><a id="l00466" name="l00466"></a><span class="lineno"> 466</span> </div>
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<div class="line"><a id="l00467" name="l00467"></a><span class="lineno"> 467</span> <span class="comment">// Draw edges from reactants to the reaction node</span></div>
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<div class="line"><a id="l00468" name="l00468"></a><span class="lineno"> 468</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& reactant : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants()) {</div>
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<div class="line"><a id="l00469" name="l00469"></a><span class="lineno"> 469</span> dotFile << <span class="stringliteral">" \""</span> << reactant.name() << <span class="stringliteral">"\" -> \""</span> << reactionNodeId << <span class="stringliteral">"\";\n"</span>;</div>
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<div class="line"><a id="l00470" name="l00470"></a><span class="lineno"> 470</span> }</div>
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<div class="line"><a id="l00471" name="l00471"></a><span class="lineno"> 471</span> </div>
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<div class="line"><a id="l00472" name="l00472"></a><span class="lineno"> 472</span> <span class="comment">// Draw edges from the reaction node to products</span></div>
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<div class="line"><a id="l00473" name="l00473"></a><span class="lineno"> 473</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& product : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products()) {</div>
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<div class="line"><a id="l00474" name="l00474"></a><span class="lineno"> 474</span> dotFile << <span class="stringliteral">" \""</span> << reactionNodeId << <span class="stringliteral">"\" -> \""</span> << product.name() << <span class="stringliteral">"\" [label=\""</span> << <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.qValue() << <span class="stringliteral">" MeV\"];\n"</span>;</div>
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<div class="line"><a id="l00475" name="l00475"></a><span class="lineno"> 475</span> }</div>
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<div class="line"><a id="l00476" name="l00476"></a><span class="lineno"> 476</span> dotFile << <span class="stringliteral">"\n"</span>;</div>
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<div class="line"><a id="l00477" name="l00477"></a><span class="lineno"> 477</span> }</div>
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<div class="line"><a id="l00478" name="l00478"></a><span class="lineno"> 478</span> </div>
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<div class="line"><a id="l00479" name="l00479"></a><span class="lineno"> 479</span> dotFile << <span class="stringliteral">"}\n"</span>;</div>
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<div class="line"><a id="l00480" name="l00480"></a><span class="lineno"> 480</span> dotFile.close();</div>
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<div class="line"><a id="l00481" name="l00481"></a><span class="lineno"> 481</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Successfully exported network to {}"</span>, filename);</div>
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<div class="line"><a id="l00482" name="l00482"></a><span class="lineno"> 482</span> }</div>
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</div>
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<div class="line"><a id="l00483" name="l00483"></a><span class="lineno"> 483</span> </div>
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<div class="foldopen" id="foldopen00484" data-start="{" data-end="}">
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<div class="line"><a id="l00484" name="l00484"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95"> 484</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95">GraphEngine::exportToCSV</a>(<span class="keyword">const</span> std::string &filename)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00485" name="l00485"></a><span class="lineno"> 485</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Exporting network graph to CSV file: {}"</span>, filename);</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> std::ofstream csvFile(filename, std::ios::out | std::ios::trunc);</div>
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<div class="line"><a id="l00488" name="l00488"></a><span class="lineno"> 488</span> <span class="keywordflow">if</span> (!csvFile.is_open()) {</div>
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<div class="line"><a id="l00489" name="l00489"></a><span class="lineno"> 489</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Failed to open file for writing: {}"</span>, filename);</div>
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<div class="line"><a id="l00490" name="l00490"></a><span class="lineno"> 490</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>->flush_log();</div>
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<div class="line"><a id="l00491" name="l00491"></a><span class="lineno"> 491</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Failed to open file for writing: "</span> + filename);</div>
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<div class="line"><a id="l00492" name="l00492"></a><span class="lineno"> 492</span> }</div>
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<div class="line"><a id="l00493" name="l00493"></a><span class="lineno"> 493</span> csvFile << <span class="stringliteral">"Reaction;Reactants;Products;Q-value;sources;rates\n"</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="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a> : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
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<div class="line"><a id="l00495" name="l00495"></a><span class="lineno"> 495</span> <span class="comment">// Dynamic cast to REACLIBReaction to access specific properties</span></div>
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<div class="line"><a id="l00496" name="l00496"></a><span class="lineno"> 496</span> csvFile << <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id() << <span class="stringliteral">";"</span>;</div>
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<div class="line"><a id="l00497" name="l00497"></a><span class="lineno"> 497</span> <span class="comment">// Reactants</span></div>
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<div class="line"><a id="l00498" name="l00498"></a><span class="lineno"> 498</span> <span class="keywordtype">int</span> count = 0;</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="keyword">const</span> <span class="keyword">auto</span>& reactant : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants()) {</div>
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<div class="line"><a id="l00500" name="l00500"></a><span class="lineno"> 500</span> csvFile << reactant.name();</div>
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<div class="line"><a id="l00501" name="l00501"></a><span class="lineno"> 501</span> <span class="keywordflow">if</span> (++count < <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants().size()) {</div>
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<div class="line"><a id="l00502" name="l00502"></a><span class="lineno"> 502</span> csvFile << <span class="stringliteral">","</span>;</div>
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<div class="line"><a id="l00503" name="l00503"></a><span class="lineno"> 503</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 class="line"><a id="l00505" name="l00505"></a><span class="lineno"> 505</span> csvFile << <span class="stringliteral">";"</span>;</div>
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<div class="line"><a id="l00506" name="l00506"></a><span class="lineno"> 506</span> count = 0;</div>
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<div class="line"><a id="l00507" name="l00507"></a><span class="lineno"> 507</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& product : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products()) {</div>
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<div class="line"><a id="l00508" name="l00508"></a><span class="lineno"> 508</span> csvFile << product.name();</div>
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<div class="line"><a id="l00509" name="l00509"></a><span class="lineno"> 509</span> <span class="keywordflow">if</span> (++count < <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products().size()) {</div>
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<div class="line"><a id="l00510" name="l00510"></a><span class="lineno"> 510</span> csvFile << <span class="stringliteral">","</span>;</div>
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<div class="line"><a id="l00511" name="l00511"></a><span class="lineno"> 511</span> }</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> csvFile << <span class="stringliteral">";"</span> << <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.qValue() << <span class="stringliteral">";"</span>;</div>
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<div class="line"><a id="l00514" name="l00514"></a><span class="lineno"> 514</span> <span class="comment">// Reaction coefficients</span></div>
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<div class="line"><a id="l00515" name="l00515"></a><span class="lineno"> 515</span> <span class="keyword">auto</span> sources = <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.sources();</div>
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<div class="line"><a id="l00516" name="l00516"></a><span class="lineno"> 516</span> count = 0;</div>
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<div class="line"><a id="l00517" name="l00517"></a><span class="lineno"> 517</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& source : sources) {</div>
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<div class="line"><a id="l00518" name="l00518"></a><span class="lineno"> 518</span> csvFile << source;</div>
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<div class="line"><a id="l00519" name="l00519"></a><span class="lineno"> 519</span> <span class="keywordflow">if</span> (++count < sources.size()) {</div>
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<div class="line"><a id="l00520" name="l00520"></a><span class="lineno"> 520</span> csvFile << <span class="stringliteral">","</span>;</div>
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<div class="line"><a id="l00521" name="l00521"></a><span class="lineno"> 521</span> }</div>
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<div class="line"><a id="l00522" name="l00522"></a><span class="lineno"> 522</span> }</div>
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<div class="line"><a id="l00523" name="l00523"></a><span class="lineno"> 523</span> csvFile << <span class="stringliteral">";"</span>;</div>
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<div class="line"><a id="l00524" name="l00524"></a><span class="lineno"> 524</span> <span class="comment">// Reaction coefficients</span></div>
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<div class="line"><a id="l00525" name="l00525"></a><span class="lineno"> 525</span> count = 0;</div>
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<div class="line"><a id="l00526" name="l00526"></a><span class="lineno"> 526</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& rates : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>) {</div>
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<div class="line"><a id="l00527" name="l00527"></a><span class="lineno"> 527</span> csvFile << rates;</div>
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<div class="line"><a id="l00528" name="l00528"></a><span class="lineno"> 528</span> <span class="keywordflow">if</span> (++count < <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.size()) {</div>
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<div class="line"><a id="l00529" name="l00529"></a><span class="lineno"> 529</span> csvFile << <span class="stringliteral">","</span>;</div>
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<div class="line"><a id="l00530" name="l00530"></a><span class="lineno"> 530</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 class="line"><a id="l00532" name="l00532"></a><span class="lineno"> 532</span> csvFile << <span class="stringliteral">"\n"</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> csvFile.close();</div>
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<div class="line"><a id="l00535" name="l00535"></a><span class="lineno"> 535</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Successfully exported network graph to {}"</span>, filename);</div>
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<div class="line"><a id="l00536" name="l00536"></a><span class="lineno"> 536</span> }</div>
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</div>
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<div class="line"><a id="l00537" name="l00537"></a><span class="lineno"> 537</span> </div>
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<div class="foldopen" id="foldopen00538" data-start="{" data-end="}">
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<div class="line"><a id="l00538" name="l00538"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a26215593544c3a52597194602e4e25dd"> 538</a></span> std::unordered_map<fourdst::atomic::Species, double> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a26215593544c3a52597194602e4e25dd">GraphEngine::getSpeciesTimescales</a>(<span class="keyword">const</span> std::vector<double> &Y, <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00539" name="l00539"></a><span class="lineno"> 539</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00540" name="l00540"></a><span class="lineno"> 540</span> <span class="keyword">auto</span> [dydt, _] = <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives<double></a>(Y, T9, rho);</div>
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<div class="line"><a id="l00541" name="l00541"></a><span class="lineno"> 541</span> std::unordered_map<fourdst::atomic::Species, double> speciesTimescales;</div>
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<div class="line"><a id="l00542" name="l00542"></a><span class="lineno"> 542</span> speciesTimescales.reserve(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size());</div>
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<div class="line"><a id="l00543" name="l00543"></a><span class="lineno"> 543</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size(); ++i) {</div>
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<div class="line"><a id="l00544" name="l00544"></a><span class="lineno"> 544</span> <span class="keywordtype">double</span> timescale = std::numeric_limits<double>::infinity();</div>
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<div class="line"><a id="l00545" name="l00545"></a><span class="lineno"> 545</span> <span class="keyword">const</span> <span class="keyword">auto</span> species = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>[i];</div>
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<div class="line"><a id="l00546" name="l00546"></a><span class="lineno"> 546</span> <span class="keywordflow">if</span> (std::abs(dydt[i]) > 0.0) {</div>
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<div class="line"><a id="l00547" name="l00547"></a><span class="lineno"> 547</span> timescale = std::abs(Y[i] / dydt[i]);</div>
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<div class="line"><a id="l00548" name="l00548"></a><span class="lineno"> 548</span> }</div>
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<div class="line"><a id="l00549" name="l00549"></a><span class="lineno"> 549</span> speciesTimescales.emplace(species, timescale);</div>
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<div class="line"><a id="l00550" name="l00550"></a><span class="lineno"> 550</span> }</div>
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<div class="line"><a id="l00551" name="l00551"></a><span class="lineno"> 551</span> <span class="keywordflow">return</span> speciesTimescales;</div>
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<div class="line"><a id="l00552" name="l00552"></a><span class="lineno"> 552</span> }</div>
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</div>
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<div class="line"><a id="l00553" name="l00553"></a><span class="lineno"> 553</span> </div>
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<div class="foldopen" id="foldopen00554" data-start="{" data-end="}">
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<div class="line"><a id="l00554" name="l00554"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a51b4cedf9b00de79fb6eef243631b04d"> 554</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a51b4cedf9b00de79fb6eef243631b04d">GraphEngine::update</a>(<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="l00555" name="l00555"></a><span class="lineno"> 555</span> <span class="comment">// No-op for GraphEngine, as it does not support manually triggering updates.</span></div>
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<div class="line"><a id="l00556" name="l00556"></a><span class="lineno"> 556</span> }</div>
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</div>
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<div class="line"><a id="l00557" name="l00557"></a><span class="lineno"> 557</span> </div>
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<div class="foldopen" id="foldopen00558" data-start="{" data-end="}">
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<div class="line"><a id="l00558" name="l00558"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889"> 558</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889">GraphEngine::recordADTape</a>() {</div>
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<div class="line"><a id="l00559" name="l00559"></a><span class="lineno"> 559</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Recording AD tape for the RHS calculation..."</span>);</div>
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<div class="line"><a id="l00560" name="l00560"></a><span class="lineno"> 560</span> </div>
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<div class="line"><a id="l00561" name="l00561"></a><span class="lineno"> 561</span> <span class="comment">// Task 1: Set dimensions and initialize the matrix</span></div>
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<div class="line"><a id="l00562" name="l00562"></a><span class="lineno"> 562</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> numSpecies = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size();</div>
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<div class="line"><a id="l00563" name="l00563"></a><span class="lineno"> 563</span> <span class="keywordflow">if</span> (numSpecies == 0) {</div>
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<div class="line"><a id="l00564" name="l00564"></a><span class="lineno"> 564</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Cannot record AD tape: No species in the network."</span>);</div>
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<div class="line"><a id="l00565" name="l00565"></a><span class="lineno"> 565</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>->flush_log();</div>
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<div class="line"><a id="l00566" name="l00566"></a><span class="lineno"> 566</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Cannot record AD tape: No species in the network."</span>);</div>
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<div class="line"><a id="l00567" name="l00567"></a><span class="lineno"> 567</span> }</div>
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<div class="line"><a id="l00568" name="l00568"></a><span class="lineno"> 568</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> numADInputs = numSpecies + 2; <span class="comment">// Note here that by not letting T9 and rho be independent variables, we are constraining the network to a constant temperature and density during each evaluation.</span></div>
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<div class="line"><a id="l00569" name="l00569"></a><span class="lineno"> 569</span> </div>
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<div class="line"><a id="l00570" name="l00570"></a><span class="lineno"> 570</span> <span class="comment">// --- CppAD Tape Recording ---</span></div>
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<div class="line"><a id="l00571" name="l00571"></a><span class="lineno"> 571</span> <span class="comment">// 1. Declare independent variable (adY)</span></div>
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<div class="line"><a id="l00572" name="l00572"></a><span class="lineno"> 572</span> <span class="comment">// We also initialize the dummy variable for tape recording (these tell CppAD what the derivative chain looks like).</span></div>
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<div class="line"><a id="l00573" name="l00573"></a><span class="lineno"> 573</span> <span class="comment">// Their numeric values are irrelevant except for in so far as they avoid numerical instabilities.</span></div>
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<div class="line"><a id="l00574" name="l00574"></a><span class="lineno"> 574</span> </div>
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<div class="line"><a id="l00575" name="l00575"></a><span class="lineno"> 575</span> <span class="comment">// Distribute total mass fraction uniformly between species in the dummy variable space</span></div>
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<div class="line"><a id="l00576" name="l00576"></a><span class="lineno"> 576</span> <span class="keyword">const</span> <span class="keyword">auto</span> uniformMassFraction = <span class="keyword">static_cast<</span>CppAD::AD<double><span class="keyword">></span>(1.0 / <span class="keyword">static_cast<</span><span class="keywordtype">double</span><span class="keyword">></span>(numSpecies));</div>
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<div class="line"><a id="l00577" name="l00577"></a><span class="lineno"> 577</span> std::vector<CppAD::AD<double>> adInput(numADInputs, uniformMassFraction);</div>
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<div class="line"><a id="l00578" name="l00578"></a><span class="lineno"> 578</span> adInput[numSpecies] = 1.0; <span class="comment">// Dummy T9</span></div>
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<div class="line"><a id="l00579" name="l00579"></a><span class="lineno"> 579</span> adInput[numSpecies + 1] = 1.0; <span class="comment">// Dummy rho</span></div>
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<div class="line"><a id="l00580" name="l00580"></a><span class="lineno"> 580</span> </div>
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<div class="line"><a id="l00581" name="l00581"></a><span class="lineno"> 581</span> <span class="comment">// 3. Declare independent variables (what CppAD will differentiate wrt.)</span></div>
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<div class="line"><a id="l00582" name="l00582"></a><span class="lineno"> 582</span> <span class="comment">// This also beings the tape recording process.</span></div>
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<div class="line"><a id="l00583" name="l00583"></a><span class="lineno"> 583</span> CppAD::Independent(adInput);</div>
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<div class="line"><a id="l00584" name="l00584"></a><span class="lineno"> 584</span> </div>
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<div class="line"><a id="l00585" name="l00585"></a><span class="lineno"> 585</span> std::vector<CppAD::AD<double>> adY(numSpecies);</div>
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<div class="line"><a id="l00586" name="l00586"></a><span class="lineno"> 586</span> <span class="keywordflow">for</span>(<span class="keywordtype">size_t</span> i = 0; i < numSpecies; ++i) {</div>
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<div class="line"><a id="l00587" name="l00587"></a><span class="lineno"> 587</span> adY[i] = adInput[i];</div>
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<div class="line"><a id="l00588" name="l00588"></a><span class="lineno"> 588</span> }</div>
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<div class="line"><a id="l00589" name="l00589"></a><span class="lineno"> 589</span> <span class="keyword">const</span> CppAD::AD<double> adT9 = adInput[numSpecies];</div>
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<div class="line"><a id="l00590" name="l00590"></a><span class="lineno"> 590</span> <span class="keyword">const</span> CppAD::AD<double> adRho = adInput[numSpecies + 1];</div>
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<div class="line"><a id="l00591" name="l00591"></a><span class="lineno"> 591</span> </div>
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<div class="line"><a id="l00592" name="l00592"></a><span class="lineno"> 592</span> </div>
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<div class="line"><a id="l00593" name="l00593"></a><span class="lineno"> 593</span> <span class="comment">// 5. Call the actual templated function</span></div>
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<div class="line"><a id="l00594" name="l00594"></a><span class="lineno"> 594</span> <span class="comment">// We let T9 and rho be constant, so we pass them as fixed values.</span></div>
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<div class="line"><a id="l00595" name="l00595"></a><span class="lineno"> 595</span> <span class="keyword">auto</span> [dydt, nuclearEnergyGenerationRate] = <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives<CppAD::AD<double></a>>(adY, adT9, adRho);</div>
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<div class="line"><a id="l00596" name="l00596"></a><span class="lineno"> 596</span> </div>
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<div class="line"><a id="l00597" name="l00597"></a><span class="lineno"> 597</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a>.Dependent(adInput, dydt);</div>
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<div class="line"><a id="l00598" name="l00598"></a><span class="lineno"> 598</span> </div>
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<div class="line"><a id="l00599" name="l00599"></a><span class="lineno"> 599</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"AD tape recorded successfully for the RHS calculation. Number of independent variables: {}."</span>,</div>
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<div class="line"><a id="l00600" name="l00600"></a><span class="lineno"> 600</span> adInput.size());</div>
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<div class="line"><a id="l00601" name="l00601"></a><span class="lineno"> 601</span> }</div>
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</div>
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<div class="line"><a id="l00602" name="l00602"></a><span class="lineno"> 602</span> </div>
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<div class="foldopen" id="foldopen00603" data-start="{" data-end="}">
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<div class="line"><a id="l00603" name="l00603"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd"> 603</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd">GraphEngine::precomputeNetwork</a>() {</div>
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<div class="line"><a id="l00604" name="l00604"></a><span class="lineno"> 604</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Pre-computing constant components of GraphNetwork state..."</span>);</div>
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<div class="line"><a id="l00605" name="l00605"></a><span class="lineno"> 605</span> </div>
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<div class="line"><a id="l00606" name="l00606"></a><span class="lineno"> 606</span> <span class="comment">// --- Reverse map for fast species lookups ---</span></div>
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<div class="line"><a id="l00607" name="l00607"></a><span class="lineno"> 607</span> std::unordered_map<fourdst::atomic::Species, size_t> speciesIndexMap;</div>
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<div class="line"><a id="l00608" name="l00608"></a><span class="lineno"> 608</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size(); ++i) {</div>
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<div class="line"><a id="l00609" name="l00609"></a><span class="lineno"> 609</span> speciesIndexMap[<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>[i]] = i;</div>
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<div class="line"><a id="l00610" name="l00610"></a><span class="lineno"> 610</span> }</div>
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<div class="line"><a id="l00611" name="l00611"></a><span class="lineno"> 611</span> </div>
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<div class="line"><a id="l00612" name="l00612"></a><span class="lineno"> 612</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>.clear();</div>
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<div class="line"><a id="l00613" name="l00613"></a><span class="lineno"> 613</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>.reserve(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size());</div>
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<div class="line"><a id="l00614" name="l00614"></a><span class="lineno"> 614</span> </div>
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<div class="line"><a id="l00615" name="l00615"></a><span class="lineno"> 615</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size(); ++i) {</div>
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<div class="line"><a id="l00616" name="l00616"></a><span class="lineno"> 616</span> <span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a> = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>[i];</div>
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<div class="line"><a id="l00617" name="l00617"></a><span class="lineno"> 617</span> <a class="code hl_struct" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html">PrecomputedReaction</a> precomp;</div>
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<div class="line"><a id="l00618" name="l00618"></a><span class="lineno"> 618</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a93635f6940d3534e949f402503c3d497">reaction_index</a> = i;</div>
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<div class="line"><a id="l00619" name="l00619"></a><span class="lineno"> 619</span> </div>
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<div class="line"><a id="l00620" name="l00620"></a><span class="lineno"> 620</span> <span class="comment">// --- Precompute reactant information ---</span></div>
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<div class="line"><a id="l00621" name="l00621"></a><span class="lineno"> 621</span> <span class="comment">// Count occurrences for each reactant to determine powers and symmetry</span></div>
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<div class="line"><a id="l00622" name="l00622"></a><span class="lineno"> 622</span> std::unordered_map<size_t, int> reactantCounts;</div>
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<div class="line"><a id="l00623" name="l00623"></a><span class="lineno"> 623</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& reactant: <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants()) {</div>
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<div class="line"><a id="l00624" name="l00624"></a><span class="lineno"> 624</span> <span class="keywordtype">size_t</span> reactantIndex = speciesIndexMap.at(reactant);</div>
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<div class="line"><a id="l00625" name="l00625"></a><span class="lineno"> 625</span> reactantCounts[reactantIndex]++;</div>
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<div class="line"><a id="l00626" name="l00626"></a><span class="lineno"> 626</span> }</div>
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<div class="line"><a id="l00627" name="l00627"></a><span class="lineno"> 627</span> </div>
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<div class="line"><a id="l00628" name="l00628"></a><span class="lineno"> 628</span> <span class="keywordtype">double</span> symmetryDenominator = 1.0;</div>
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<div class="line"><a id="l00629" name="l00629"></a><span class="lineno"> 629</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& [index, count] : reactantCounts) {</div>
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<div class="line"><a id="l00630" name="l00630"></a><span class="lineno"> 630</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a510e380116e2e6d9158cf00fedac2666">unique_reactant_indices</a>.push_back(index);</div>
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<div class="line"><a id="l00631" name="l00631"></a><span class="lineno"> 631</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a03d596c88289e21e7bd18711e3a1f275">reactant_powers</a>.push_back(count);</div>
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<div class="line"><a id="l00632" name="l00632"></a><span class="lineno"> 632</span> </div>
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<div class="line"><a id="l00633" name="l00633"></a><span class="lineno"> 633</span> symmetryDenominator *= 1.0/std::tgamma(count + 1);</div>
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<div class="line"><a id="l00634" name="l00634"></a><span class="lineno"> 634</span> }</div>
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<div class="line"><a id="l00635" name="l00635"></a><span class="lineno"> 635</span> </div>
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<div class="line"><a id="l00636" name="l00636"></a><span class="lineno"> 636</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#ac42504e868c0b9fd9ac9a405ea739f0e">symmetry_factor</a> = symmetryDenominator;</div>
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<div class="line"><a id="l00637" name="l00637"></a><span class="lineno"> 637</span> </div>
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<div class="line"><a id="l00638" name="l00638"></a><span class="lineno"> 638</span> <span class="comment">// --- Precompute stoichiometry information ---</span></div>
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<div class="line"><a id="l00639" name="l00639"></a><span class="lineno"> 639</span> <span class="keyword">const</span> <span class="keyword">auto</span> stoichiometryMap = <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.stoichiometry();</div>
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<div class="line"><a id="l00640" name="l00640"></a><span class="lineno"> 640</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3e2e67e532970738d20491ea56b170f3">affected_species_indices</a>.reserve(stoichiometryMap.size());</div>
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<div class="line"><a id="l00641" name="l00641"></a><span class="lineno"> 641</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a7a7e9167b19e339e0d69544b9c00e79c">stoichiometric_coefficients</a>.reserve(stoichiometryMap.size());</div>
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<div class="line"><a id="l00642" name="l00642"></a><span class="lineno"> 642</span> </div>
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<div class="line"><a id="l00643" name="l00643"></a><span class="lineno"> 643</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& [species, coeff] : stoichiometryMap) {</div>
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<div class="line"><a id="l00644" name="l00644"></a><span class="lineno"> 644</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3e2e67e532970738d20491ea56b170f3">affected_species_indices</a>.push_back(speciesIndexMap.at(species));</div>
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<div class="line"><a id="l00645" name="l00645"></a><span class="lineno"> 645</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a7a7e9167b19e339e0d69544b9c00e79c">stoichiometric_coefficients</a>.push_back(coeff);</div>
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<div class="line"><a id="l00646" name="l00646"></a><span class="lineno"> 646</span> }</div>
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<div class="line"><a id="l00647" name="l00647"></a><span class="lineno"> 647</span> </div>
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<div class="line"><a id="l00648" name="l00648"></a><span class="lineno"> 648</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>.push_back(std::move(precomp));</div>
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<div class="line"><a id="l00649" name="l00649"></a><span class="lineno"> 649</span> }</div>
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<div class="line"><a id="l00650" name="l00650"></a><span class="lineno"> 650</span> }</div>
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</div>
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<div class="line"><a id="l00651" name="l00651"></a><span class="lineno"> 651</span>}</div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a015f8975701f028c29835d3a9794e00f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f">gridfire::GraphEngine::isPrecomputationEnabled</a></div><div class="ttdeci">bool isPrecomputationEnabled() const</div><div class="ttdef"><b>Definition</b> <a href="#l00373">engine_graph.cpp:373</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a0ed390f3e598ebba4e245ac90bb78767"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767">gridfire::GraphEngine::getNetworkSpecies</a></div><div class="ttdeci">const std::vector< fourdst::atomic::Species > & getNetworkSpecies() const override</div><div class="ttdoc">Gets the list of species in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00128">engine_graph.cpp:128</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a10c01bc20ae668c2857efb2a1783098e"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">gridfire::GraphEngine::m_constants</a></div><div class="ttdeci">constants m_constants</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00330">engine_graph.h:330</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a191cff35402d3c97c82c5c966a39d0de"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de">gridfire::GraphEngine::m_usePrecomputation</a></div><div class="ttdeci">bool m_usePrecomputation</div><div class="ttdoc">Flag to enable or disable using precomputed reactions for efficiency. Mathematically,...</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00347">engine_graph.h:347</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a26215593544c3a52597194602e4e25dd"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a26215593544c3a52597194602e4e25dd">gridfire::GraphEngine::getSpeciesTimescales</a></div><div class="ttdeci">std::unordered_map< fourdst::atomic::Species, double > getSpeciesTimescales(const std::vector< double > &Y, double T9, double rho) const override</div><div class="ttdoc">Computes timescales for all species in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00538">engine_graph.cpp:538</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a26602e1b3c610780a47b5a6511d6d567"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567">gridfire::GraphEngine::populateReactionIDMap</a></div><div class="ttdeci">void populateReactionIDMap()</div><div class="ttdoc">Populates the reaction ID map.</div><div class="ttdef"><b>Definition</b> <a href="#l00101">engine_graph.cpp:101</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a2e22b111f6d00ecc9e3804a71f1ce876"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">gridfire::GraphEngine::m_rhsADFun</a></div><div class="ttdeci">CppAD::ADFun< double > m_rhsADFun</div><div class="ttdoc">CppAD function for the right-hand side of the ODE.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00342">engine_graph.h:342</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a2f1718c89d4aaad028102724d18fa910"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">gridfire::GraphEngine::m_jacobianMatrix</a></div><div class="ttdeci">boost::numeric::ublas::compressed_matrix< double > m_jacobianMatrix</div><div class="ttdoc">Jacobian matrix (species x species).</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00340">engine_graph.h:340</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a303e6093591cde91430f866a04a8be7c"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c">gridfire::GraphEngine::getJacobianMatrixEntry</a></div><div class="ttdeci">double getJacobianMatrixEntry(const int i, const int j) const override</div><div class="ttdoc">Gets an entry from the previously generated Jacobian matrix.</div><div class="ttdef"><b>Definition</b> <a href="#l00419">engine_graph.cpp:419</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a30e09ed0bce6aa5fc89beaa316a7b827"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">gridfire::GraphEngine::m_networkSpeciesMap</a></div><div class="ttdeci">std::unordered_map< std::string_view, fourdst::atomic::Species > m_networkSpeciesMap</div><div class="ttdoc">Map from species name to Species object.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00336">engine_graph.h:336</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a47202c43342b96480070874bffce1391"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391">gridfire::GraphEngine::populateSpeciesToIndexMap</a></div><div class="ttdeci">void populateSpeciesToIndexMap()</div><div class="ttdoc">Populates the species-to-index map.</div><div class="ttdef"><b>Definition</b> <a href="#l00110">engine_graph.cpp:110</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a483979fc154adc88d029b3b672066d53"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">gridfire::GraphEngine::m_logger</a></div><div class="ttdeci">quill::Logger * m_logger</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00328">engine_graph.h:328</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a51b4cedf9b00de79fb6eef243631b04d"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a51b4cedf9b00de79fb6eef243631b04d">gridfire::GraphEngine::update</a></div><div class="ttdeci">void update(const NetIn &netIn) override</div><div class="ttdoc">Update the internal state of the engine.</div><div class="ttdef"><b>Definition</b> <a href="#l00554">engine_graph.cpp:554</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a52edc3e88f1e8fc497e1e63972d63c80"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a52edc3e88f1e8fc497e1e63972d63c80">gridfire::GraphEngine::m_screeningType</a></div><div class="ttdeci">screening::ScreeningType m_screeningType</div><div class="ttdoc">Screening type for the reaction network. Default to no screening.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00344">engine_graph.h:344</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a5a5458ed01923124f2d7e1f04f32f138"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a5a5458ed01923124f2d7e1f04f32f138">gridfire::GraphEngine::reserveJacobianMatrix</a></div><div class="ttdeci">void reserveJacobianMatrix()</div><div class="ttdoc">Reserves space for the Jacobian matrix.</div><div class="ttdef"><b>Definition</b> <a href="#l00117">engine_graph.cpp:117</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a5d431d5385b1219ba29689eb29601ea3"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">gridfire::GraphEngine::m_precomputedReactions</a></div><div class="ttdeci">std::vector< PrecomputedReaction > m_precomputedReactions</div><div class="ttdoc">Precomputed reactions for efficiency.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00349">engine_graph.h:349</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a5d6cc63b99b467c2a976d1fbaaa1dfa3"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">gridfire::GraphEngine::m_reactionIDMap</a></div><div class="ttdeci">std::unordered_map< std::string_view, reaction::Reaction * > m_reactionIDMap</div><div class="ttdoc">Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a ...</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00333">engine_graph.h:333</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a63639f4430d0889605c10839a6f32af9"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a63639f4430d0889605c10839a6f32af9">gridfire::GraphEngine::calculateAllDerivativesUsingPrecomputation</a></div><div class="ttdeci">StepDerivatives< double > calculateAllDerivativesUsingPrecomputation(const std::vector< double > &Y_in, const std::vector< double > &bare_rates, double T9, double rho) const</div><div class="ttdef"><b>Definition</b> <a href="#l00223">engine_graph.cpp:223</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a697f2004e0d02c59e83c7890742d7c9a"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a">gridfire::GraphEngine::getScreeningModel</a></div><div class="ttdeci">screening::ScreeningType getScreeningModel() const override</div><div class="ttdoc">Get the current electron screening model.</div><div class="ttdef"><b>Definition</b> <a href="#l00365">engine_graph.cpp:365</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a6b5feaf788bade212b7c8df7ac8c8152"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152">gridfire::GraphEngine::getStoichiometryMatrixEntry</a></div><div class="ttdeci">int getStoichiometryMatrixEntry(const int speciesIndex, const int reactionIndex) const override</div><div class="ttdoc">Gets an entry from the stoichiometry matrix.</div><div class="ttdef"><b>Definition</b> <a href="#l00429">engine_graph.cpp:429</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a6c5410878496abc349ba30b691cdf0f1"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1">gridfire::GraphEngine::setPrecomputation</a></div><div class="ttdeci">void setPrecomputation(bool precompute)</div><div class="ttdef"><b>Definition</b> <a href="#l00369">engine_graph.cpp:369</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a8110e687844f921438bb517e1d8ce62f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f">gridfire::GraphEngine::setScreeningModel</a></div><div class="ttdeci">void setScreeningModel(screening::ScreeningType) override</div><div class="ttdoc">Set the electron screening model.</div><div class="ttdef"><b>Definition</b> <a href="#l00360">engine_graph.cpp:360</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a832e2fe066381811a3e0464806ff5e95"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95">gridfire::GraphEngine::exportToCSV</a></div><div class="ttdeci">void exportToCSV(const std::string &filename) const</div><div class="ttdoc">Exports the network to a CSV file for analysis.</div><div class="ttdef"><b>Definition</b> <a href="#l00484">engine_graph.cpp:484</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a8b3baf29829c7ae0a61430ea70632bbf"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a8b3baf29829c7ae0a61430ea70632bbf">gridfire::GraphEngine::calculateRHSAndEnergy</a></div><div class="ttdeci">StepDerivatives< double > calculateRHSAndEnergy(const std::vector< double > &Y, const double T9, const double rho) const override</div><div class="ttdoc">Calculates the right-hand side (dY/dt) and energy generation rate.</div><div class="ttdef"><b>Definition</b> <a href="#l00042">engine_graph.cpp:42</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a8c29d8bbde407e913be5eb77efb2c0c9"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9">gridfire::GraphEngine::getNetReactionStoichiometry</a></div><div class="ttdeci">static std::unordered_map< fourdst::atomic::Species, int > getNetReactionStoichiometry(const reaction::Reaction &reaction)</div><div class="ttdoc">Gets the net stoichiometry for a given reaction.</div><div class="ttdef"><b>Definition</b> <a href="#l00423">engine_graph.cpp:423</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a9245642b741f215e52861d00e756fb3f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">gridfire::GraphEngine::calculateMolarReactionFlow</a></div><div class="ttdeci">double calculateMolarReactionFlow(const reaction::Reaction &reaction, const std::vector< double > &Y, const double T9, const double rho) const override</div><div class="ttdoc">Calculates the molar reaction flow for a given reaction.</div><div class="ttdef"><b>Definition</b> <a href="#l00377">engine_graph.cpp:377</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a92644bc333bff69c5685be4552ca12fd"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd">gridfire::GraphEngine::precomputeNetwork</a></div><div class="ttdeci">void precomputeNetwork()</div><div class="ttdef"><b>Definition</b> <a href="#l00603">engine_graph.cpp:603</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a92d26068ba139e47d335f5fe9e2814cc"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">gridfire::GraphEngine::m_networkSpecies</a></div><div class="ttdeci">std::vector< fourdst::atomic::Species > m_networkSpecies</div><div class="ttdoc">Vector of unique species in the network.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00335">engine_graph.h:335</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a95563f6bc86007d9ee053a0f1e15b889"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889">gridfire::GraphEngine::recordADTape</a></div><div class="ttdeci">void recordADTape()</div><div class="ttdoc">Records the AD tape for the right-hand side of the ODE.</div><div class="ttdef"><b>Definition</b> <a href="#l00558">engine_graph.cpp:558</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a9f74786ff930ab72664b31f29d05a30c"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a9f74786ff930ab72664b31f29d05a30c">gridfire::GraphEngine::GraphEngine</a></div><div class="ttdeci">GraphEngine(const fourdst::composition::Composition &composition)</div><div class="ttdoc">Constructs a GraphEngine from a composition.</div><div class="ttdef"><b>Definition</b> <a href="#l00026">engine_graph.cpp:26</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_aa6202cee0c3c481eda77cc9a91bc126b"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b">gridfire::GraphEngine::involvesSpecies</a></div><div class="ttdeci">bool involvesSpecies(const fourdst::atomic::Species &species) const</div><div class="ttdoc">Checks if a given species is involved in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00140">engine_graph.cpp:140</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_acb7c4f5108b0efeae48ad15598e808c3"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">gridfire::GraphEngine::m_reactions</a></div><div class="ttdeci">reaction::LogicalReactionSet m_reactions</div><div class="ttdoc">Set of REACLIB reactions in the network.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00332">engine_graph.h:332</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_acdce8d87e23a2cd1504bc9472e538c0f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">gridfire::GraphEngine::syncInternalMaps</a></div><div class="ttdeci">void syncInternalMaps()</div><div class="ttdoc">Synchronizes the internal maps.</div><div class="ttdef"><b>Definition</b> <a href="#l00062">engine_graph.cpp:62</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_acf4cfccea20f5cb31c9886bf233a28be"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be">gridfire::GraphEngine::validateConservation</a></div><div class="ttdeci">bool validateConservation() const</div><div class="ttdoc">Validates mass and charge conservation across all reactions.</div><div class="ttdef"><b>Definition</b> <a href="#l00148">engine_graph.cpp:148</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ad1cb5fd32efc37668e2d9ecf0c72ad24"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">gridfire::GraphEngine::m_stoichiometryMatrix</a></div><div class="ttdeci">boost::numeric::ublas::compressed_matrix< int > m_stoichiometryMatrix</div><div class="ttdoc">Stoichiometry matrix (species x reactions).</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00339">engine_graph.h:339</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ad45650d10fc5dff1673ae3f806d067da"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da">gridfire::GraphEngine::getNetworkReactions</a></div><div class="ttdeci">const reaction::LogicalReactionSet & getNetworkReactions() const override</div><div class="ttdoc">Gets the set of logical reactions in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00134">engine_graph.cpp:134</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ad8237c252145a75092202d00f5e1ddf7"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">gridfire::GraphEngine::m_speciesToIndexMap</a></div><div class="ttdeci">std::unordered_map< fourdst::atomic::Species, size_t > m_speciesToIndexMap</div><div class="ttdoc">Map from species to their index in the stoichiometry matrix.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00337">engine_graph.h:337</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_adac8c7d62bae76e17fc060e86dadd929"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929">gridfire::GraphEngine::exportToDot</a></div><div class="ttdeci">void exportToDot(const std::string &filename) const</div><div class="ttdoc">Exports the network to a DOT file for visualization.</div><div class="ttdef"><b>Definition</b> <a href="#l00436">engine_graph.cpp:436</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ae347ff0316e532e0298ec8c913908105"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ae347ff0316e532e0298ec8c913908105">gridfire::GraphEngine::generateJacobianMatrix</a></div><div class="ttdeci">void generateJacobianMatrix(const std::vector< double > &Y, const double T9, const double rho) override</div><div class="ttdoc">Generates the Jacobian matrix for the current state.</div><div class="ttdef"><b>Definition</b> <a href="#l00386">engine_graph.cpp:386</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_aed726d36ee2b3796beff6067a1e4db38"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38">gridfire::GraphEngine::generateStoichiometryMatrix</a></div><div class="ttdeci">void generateStoichiometryMatrix() override</div><div class="ttdoc">Generates the stoichiometry matrix for the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00303">engine_graph.cpp:303</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_aedf42d83bfcc28313b6b6454034d2efa"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa">gridfire::GraphEngine::collectNetworkSpecies</a></div><div class="ttdeci">void collectNetworkSpecies()</div><div class="ttdoc">Collects the unique species in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00072">engine_graph.cpp:72</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_aeeafeab40a5f4dbfae78bdc87e25e93f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#aeeafeab40a5f4dbfae78bdc87e25e93f">gridfire::GraphEngine::validateComposition</a></div><div class="ttdeci">void validateComposition(const fourdst::composition::Composition &composition, double culling, double T9)</div><div class="ttdoc">Validates the composition against the current reaction set.</div><div class="ttdef"><b>Definition</b> <a href="#l00203">engine_graph.cpp:203</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_af17cf3762abac3efcab9a8e87c961210"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#af17cf3762abac3efcab9a8e87c961210">gridfire::GraphEngine::m_screeningModel</a></div><div class="ttdeci">std::unique_ptr< screening::ScreeningModel > m_screeningModel</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00345">engine_graph.h:345</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_af41df9ce979b6410e12642cb093916c9"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">gridfire::GraphEngine::calculateAllDerivatives</a></div><div class="ttdeci">StepDerivatives< T > calculateAllDerivatives(const std::vector< T > &Y_in, T T9, T rho) const</div><div class="ttdoc">Calculates all derivatives (dY/dt) and the energy generation rate.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00521">engine_graph.h:521</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1reaction_1_1_reaction_html"><div class="ttname"><a href="classgridfire_1_1reaction_1_1_reaction.html">gridfire::reaction::Reaction</a></div><div class="ttdoc">Represents a single nuclear reaction from a specific data source.</div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00072">reaction.h:72</a></div></div>
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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_1reaction_html"><div class="ttname"><a href="namespacegridfire_1_1reaction.html">gridfire::reaction</a></div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00025">reaction.h:25</a></div></div>
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<div class="ttc" id="anamespacegridfire_1_1reaction_html_aa86f08712565f278adacc7cd2361eb31"><div class="ttname"><a href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a></div><div class="ttdeci">TemplatedReactionSet< LogicalReaction > LogicalReactionSet</div><div class="ttdoc">A set of logical reactions.</div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00557">reaction.h:557</a></div></div>
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<div class="ttc" id="anamespacegridfire_1_1screening_html_a6ca8556d27ac373e176f5b23437c416e"><div class="ttname"><a href="namespacegridfire_1_1screening.html#a6ca8556d27ac373e176f5b23437c416e">gridfire::screening::selectScreeningModel</a></div><div class="ttdeci">std::unique_ptr< ScreeningModel > selectScreeningModel(ScreeningType type)</div><div class="ttdoc">A factory function to select and create a screening model.</div><div class="ttdef"><b>Definition</b> <a href="screening__types_8cpp_source.html#l00009">screening_types.cpp:9</a></div></div>
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<div class="ttc" id="anamespacegridfire_1_1screening_html_aa82aafbc4f8c28d0a75b60798e3a7d25"><div class="ttname"><a href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">gridfire::screening::ScreeningType</a></div><div class="ttdeci">ScreeningType</div><div class="ttdoc">Enumerates the available plasma screening models.</div><div class="ttdef"><b>Definition</b> <a href="screening__types_8h_source.html#l00015">screening_types.h:15</a></div></div>
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<div class="ttc" id="anamespacegridfire_html"><div class="ttname"><a href="namespacegridfire.html">gridfire</a></div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00024">engine_abstract.h:24</a></div></div>
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<div class="ttc" id="anamespacegridfire_html_a1121d0b2d005195333412559fa29d3cc"><div class="ttname"><a href="namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc">gridfire::ADDouble</a></div><div class="ttdeci">CppAD::AD< double > ADDouble</div><div class="ttdoc">Alias for CppAD AD type for double precision.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00034">engine_graph.h:34</a></div></div>
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<div class="ttc" id="anamespacegridfire_html_a96c062f94713921e5d7568ecedcdcb06"><div class="ttname"><a href="namespacegridfire.html#a96c062f94713921e5d7568ecedcdcb06">gridfire::MIN_ABUNDANCE_THRESHOLD</a></div><div class="ttdeci">static constexpr double MIN_ABUNDANCE_THRESHOLD</div><div class="ttdoc">Minimum abundance threshold below which species are ignored.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00056">engine_graph.h:56</a></div></div>
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<div class="ttc" id="anamespacegridfire_html_aa77f83539d9ae90e3bf541309bd9c83a"><div class="ttname"><a href="namespacegridfire.html#aa77f83539d9ae90e3bf541309bd9c83a">gridfire::build_reaclib_nuclear_network</a></div><div class="ttdeci">reaction::LogicalReactionSet build_reaclib_nuclear_network(const fourdst::composition::Composition &composition, bool reverse)</div><div class="ttdef"><b>Definition</b> <a href="network_8cpp_source.html#l00064">network.cpp:64</a></div></div>
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<div class="ttc" id="anamespacegridfire_html_ae01b1738df1921db565bcbd68dd6cf64"><div class="ttname"><a href="namespacegridfire.html#ae01b1738df1921db565bcbd68dd6cf64">gridfire::MIN_JACOBIAN_THRESHOLD</a></div><div class="ttdeci">static constexpr double MIN_JACOBIAN_THRESHOLD</div><div class="ttdoc">Minimum value for Jacobian matrix entries.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00064">engine_graph.h:64</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="areaction_8h_html"><div class="ttname"><a href="reaction_8h.html">reaction.h</a></div><div class="ttdoc">Defines classes for representing and managing nuclear reactions.</div></div>
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<div class="ttc" id="ascreening__types_8h_html"><div class="ttname"><a href="screening__types_8h.html">screening_types.h</a></div></div>
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<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html">gridfire::GraphEngine::PrecomputedReaction</a></div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00311">engine_graph.h:311</a></div></div>
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<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a03d596c88289e21e7bd18711e3a1f275"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a03d596c88289e21e7bd18711e3a1f275">gridfire::GraphEngine::PrecomputedReaction::reactant_powers</a></div><div class="ttdeci">std::vector< int > reactant_powers</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00314">engine_graph.h:314</a></div></div>
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<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a3e2e67e532970738d20491ea56b170f3"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3e2e67e532970738d20491ea56b170f3">gridfire::GraphEngine::PrecomputedReaction::affected_species_indices</a></div><div class="ttdeci">std::vector< size_t > affected_species_indices</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00316">engine_graph.h:316</a></div></div>
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<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a510e380116e2e6d9158cf00fedac2666"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a510e380116e2e6d9158cf00fedac2666">gridfire::GraphEngine::PrecomputedReaction::unique_reactant_indices</a></div><div class="ttdeci">std::vector< size_t > unique_reactant_indices</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00313">engine_graph.h:313</a></div></div>
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<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a7a7e9167b19e339e0d69544b9c00e79c"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a7a7e9167b19e339e0d69544b9c00e79c">gridfire::GraphEngine::PrecomputedReaction::stoichiometric_coefficients</a></div><div class="ttdeci">std::vector< int > stoichiometric_coefficients</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00317">engine_graph.h:317</a></div></div>
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<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a93635f6940d3534e949f402503c3d497"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a93635f6940d3534e949f402503c3d497">gridfire::GraphEngine::PrecomputedReaction::reaction_index</a></div><div class="ttdeci">size_t reaction_index</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00312">engine_graph.h:312</a></div></div>
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<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_ac42504e868c0b9fd9ac9a405ea739f0e"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#ac42504e868c0b9fd9ac9a405ea739f0e">gridfire::GraphEngine::PrecomputedReaction::symmetry_factor</a></div><div class="ttdeci">double symmetry_factor</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00315">engine_graph.h:315</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_step_derivatives_html"><div class="ttname"><a href="structgridfire_1_1_step_derivatives.html">gridfire::StepDerivatives</a></div><div class="ttdoc">Structure holding derivatives and energy generation for a network step.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00053">engine_abstract.h:53</a></div></div>
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<div class="ttc" id="astructgridfire_1_1_step_derivatives_html_ab4aeb41be952c7b5844e1ee81fef9008"><div class="ttname"><a href="structgridfire_1_1_step_derivatives.html#ab4aeb41be952c7b5844e1ee81fef9008">gridfire::StepDerivatives::nuclearEnergyGenerationRate</a></div><div class="ttdeci">T nuclearEnergyGenerationRate</div><div class="ttdoc">Specific energy generation rate (e.g., erg/g/s).</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00055">engine_abstract.h:55</a></div></div>
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<div class="ttc" id="astructgridfire_1_1_step_derivatives_html_ae0de268b86c2404379409c4feae0b34d"><div class="ttname"><a href="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d">gridfire::StepDerivatives::dydt</a></div><div class="ttdeci">std::vector< T > dydt</div><div class="ttdoc">Derivatives of abundances (dY/dt for each species).</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00054">engine_abstract.h:54</a></div></div>
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