refactor(.gitignore): removed html/ from .gitignore
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@@ -105,99 +105,116 @@ $(function(){initNavTree('engine__abstract_8h_source.html',''); initResizable(tr
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<a href="engine__abstract_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="preprocessor">#pragma once</span></div>
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<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span> </div>
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<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="preprocessor">#include "<a class="code" href="reaction_8h.html">gridfire/reaction/reaction.h</a>"</span></div>
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<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span> </div>
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<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span><span class="preprocessor">#include <vector></span></div>
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<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="preprocessor">#include <unordered_map></span></div>
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<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span></div>
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<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> </div>
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<div class="foldopen" id="foldopen00021" data-start="{" data-end="}">
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<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"><a class="line" href="namespacegridfire.html"> 21</a></span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacegridfire.html">gridfire</a> {</div>
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<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span></div>
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<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> <span class="keyword">template</span><<span class="keyword">typename</span> T></div>
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<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"><a class="line" href="conceptgridfire_1_1_is_arithmetic_or_a_d.html"> 30</a></span> <span class="keyword">concept </span><a class="code hl_concept" href="conceptgridfire_1_1_is_arithmetic_or_a_d.html">IsArithmeticOrAD</a> = std::is_same_v<T, double> || std::is_same_v<T, CppAD::AD<double>>;</div>
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<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span></div>
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<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> <span class="keyword">template</span> <IsArithmeticOrAD T></div>
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<div class="foldopen" id="foldopen00050" data-start="{" data-end="};">
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<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"><a class="line" href="structgridfire_1_1_step_derivatives.html"> 50</a></span> <span class="keyword">struct </span><a class="code hl_struct" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a> {</div>
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<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"><a class="line" href="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d"> 51</a></span> std::vector<T> <a class="code hl_variable" href="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d">dydt</a>; </div>
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<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"><a class="line" href="structgridfire_1_1_step_derivatives.html#ab4aeb41be952c7b5844e1ee81fef9008"> 52</a></span> T <a class="code hl_variable" href="structgridfire_1_1_step_derivatives.html#ab4aeb41be952c7b5844e1ee81fef9008">nuclearEnergyGenerationRate</a> = T(0.0); </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="l00004" name="l00004"></a><span class="lineno"> 4</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="l00005" name="l00005"></a><span class="lineno"> 5</span><span class="preprocessor">#include "<a class="code" href="screening__abstract_8h.html">gridfire/screening/screening_abstract.h</a>"</span></div>
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<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="preprocessor">#include "<a class="code" href="screening__types_8h.html">gridfire/screening/screening_types.h</a>"</span></div>
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<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span> </div>
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<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span><span class="preprocessor">#include <vector></span></div>
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<div class="line"><a id="l00009" name="l00009"></a><span class="lineno"> 9</span><span class="preprocessor">#include <unordered_map></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="l00023" name="l00023"></a><span class="lineno"> 23</span> </div>
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<div class="foldopen" id="foldopen00024" data-start="{" data-end="}">
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<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"><a class="line" href="namespacegridfire.html"> 24</a></span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacegridfire.html">gridfire</a> {</div>
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<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span></div>
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<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> <span class="keyword">template</span><<span class="keyword">typename</span> T></div>
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<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"><a class="line" href="conceptgridfire_1_1_is_arithmetic_or_a_d.html"> 33</a></span> <span class="keyword">concept </span><a class="code hl_concept" href="conceptgridfire_1_1_is_arithmetic_or_a_d.html">IsArithmeticOrAD</a> = std::is_same_v<T, double> || std::is_same_v<T, CppAD::AD<double>>;</div>
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<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span></div>
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<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> <span class="keyword">template</span> <IsArithmeticOrAD T></div>
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<div class="foldopen" id="foldopen00053" data-start="{" data-end="};">
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<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"><a class="line" href="structgridfire_1_1_step_derivatives.html"> 53</a></span> <span class="keyword">struct </span><a class="code hl_struct" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a> {</div>
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<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"><a class="line" href="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d"> 54</a></span> std::vector<T> <a class="code hl_variable" href="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d">dydt</a>; </div>
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<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"><a class="line" href="structgridfire_1_1_step_derivatives.html#ab4aeb41be952c7b5844e1ee81fef9008"> 55</a></span> T <a class="code hl_variable" href="structgridfire_1_1_step_derivatives.html#ab4aeb41be952c7b5844e1ee81fef9008">nuclearEnergyGenerationRate</a> = T(0.0); </div>
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<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> };</div>
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</div>
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<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</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_engine.html"> 72</a></span> <span class="keyword">class </span><a class="code hl_class" href="classgridfire_1_1_engine.html">Engine</a> {</div>
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<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> <span class="keyword">public</span>:</div>
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<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"><a class="line" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037"> 77</a></span> <span class="keyword">virtual</span> <a class="code hl_function" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>() = <span class="keywordflow">default</span>;</div>
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<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span></div>
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<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"><a class="line" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3"> 83</a></span> <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector<fourdst::atomic::Species>& <a class="code hl_function" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">getNetworkSpecies</a>() <span class="keyword">const</span> = 0;</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="l00097" name="l00097"></a><span class="lineno"><a class="line" href="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2"> 97</a></span> <span class="keyword">virtual</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_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">calculateRHSAndEnergy</a>(</div>
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<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> <span class="keyword">const</span> std::vector<double>& Y,</div>
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<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> ) <span class="keyword">const</span> = 0;</div>
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<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> };</div>
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<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span></div>
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<div class="foldopen" id="foldopen00075" data-start="{" data-end="};">
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<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"><a class="line" href="classgridfire_1_1_engine.html"> 75</a></span> <span class="keyword">class </span><a class="code hl_class" href="classgridfire_1_1_engine.html">Engine</a> {</div>
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<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> <span class="keyword">public</span>:</div>
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<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"><a class="line" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037"> 80</a></span> <span class="keyword">virtual</span> <a class="code hl_function" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>() = <span class="keywordflow">default</span>;</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="l00086" name="l00086"></a><span class="lineno"><a class="line" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3"> 86</a></span> [[nodiscard]] <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector<fourdst::atomic::Species>& <a class="code hl_function" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">getNetworkSpecies</a>() <span class="keyword">const</span> = 0;</div>
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<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span></div>
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<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"><a class="line" href="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2"> 100</a></span> [[nodiscard]] <span class="keyword">virtual</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_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">calculateRHSAndEnergy</a>(</div>
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<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> <span class="keyword">const</span> std::vector<double>& Y,</div>
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<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> ) <span class="keyword">const</span> = 0;</div>
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<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> };</div>
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</div>
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<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span></div>
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<div class="foldopen" id="foldopen00118" data-start="{" data-end="};">
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<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html"> 118</a></span> <span class="keyword">class </span><a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> : <span class="keyword">public</span> <a class="code hl_class" href="classgridfire_1_1_engine.html">Engine</a> {</div>
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<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> <span class="keyword">public</span>:</div>
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<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f"> 130</a></span> <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f">generateJacobianMatrix</a>(</div>
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<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> <span class="keyword">const</span> std::vector<double>& Y,</div>
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<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> <span class="keywordtype">double</span> T9, <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span> ) = 0;</div>
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<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span></div>
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<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07"> 144</a></span> <span class="keyword">virtual</span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">getJacobianMatrixEntry</a>(</div>
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<div class="line"><a id="l00145" name="l00145"></a><span class="lineno"> 145</span> <span class="keywordtype">int</span> i,</div>
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<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"> 146</span> <span class="keywordtype">int</span> j</div>
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<div class="line"><a id="l00147" name="l00147"></a><span class="lineno"> 147</span> ) <span class="keyword">const</span> = 0;</div>
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<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"> 148</span></div>
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<div class="line"><a id="l00155" name="l00155"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f"> 155</a></span> <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">generateStoichiometryMatrix</a>() = 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="l00166" name="l00166"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f"> 166</a></span> <span class="keyword">virtual</span> <span class="keywordtype">int</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">getStoichiometryMatrixEntry</a>(</div>
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<div class="line"><a id="l00167" name="l00167"></a><span class="lineno"> 167</span> <span class="keywordtype">int</span> speciesIndex,</div>
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<div class="line"><a id="l00168" name="l00168"></a><span class="lineno"> 168</span> <span class="keywordtype">int</span> reactionIndex</div>
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<div class="line"><a id="l00169" name="l00169"></a><span class="lineno"> 169</span> ) <span class="keyword">const</span> = 0;</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="l00183" name="l00183"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785"> 183</a></span> <span class="keyword">virtual</span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">calculateMolarReactionFlow</a>(</div>
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<div class="line"><a id="l00184" name="l00184"></a><span class="lineno"> 184</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="l00185" name="l00185"></a><span class="lineno"> 185</span> <span class="keyword">const</span> std::vector<double>& Y,</div>
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<div class="line"><a id="l00186" name="l00186"></a><span class="lineno"> 186</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00187" name="l00187"></a><span class="lineno"> 187</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00188" name="l00188"></a><span class="lineno"> 188</span> ) <span class="keyword">const</span> = 0;</div>
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<div class="line"><a id="l00189" name="l00189"></a><span class="lineno"> 189</span></div>
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<div class="line"><a id="l00195" name="l00195"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037"> 195</a></span> <span class="keyword">virtual</span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">reaction::LogicalReactionSet</a>& <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">getNetworkReactions</a>() <span class="keyword">const</span> = 0;</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="l00208" name="l00208"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15"> 208</a></span> <span class="keyword">virtual</span> std::unordered_map<fourdst::atomic::Species, double> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15">getSpeciesTimescales</a>(</div>
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<div class="line"><a id="l00209" name="l00209"></a><span class="lineno"> 209</span> <span class="keyword">const</span> std::vector<double>& Y,</div>
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<div class="line"><a id="l00210" name="l00210"></a><span class="lineno"> 210</span> <span class="keywordtype">double</span> T9,</div>
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<div class="line"><a id="l00211" name="l00211"></a><span class="lineno"> 211</span> <span class="keywordtype">double</span> rho</div>
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<div class="line"><a id="l00212" name="l00212"></a><span class="lineno"> 212</span> ) <span class="keyword">const</span> = 0;</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="l00106" name="l00106"></a><span class="lineno"> 106</span></div>
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<div class="foldopen" id="foldopen00121" data-start="{" data-end="};">
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<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html"> 121</a></span> <span class="keyword">class </span><a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> : <span class="keyword">public</span> <a class="code hl_class" href="classgridfire_1_1_engine.html">Engine</a> {</div>
|
||||
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> <span class="keyword">public</span>:</div>
|
||||
<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f"> 133</a></span> <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f">generateJacobianMatrix</a>(</div>
|
||||
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> <span class="keyword">const</span> std::vector<double>& Y,</div>
|
||||
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> <span class="keywordtype">double</span> T9, <span class="keywordtype">double</span> rho</div>
|
||||
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span> ) = 0;</div>
|
||||
<div class="line"><a id="l00137" name="l00137"></a><span class="lineno"> 137</span></div>
|
||||
<div class="line"><a id="l00147" name="l00147"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07"> 147</a></span> [[nodiscard]] <span class="keyword">virtual</span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">getJacobianMatrixEntry</a>(</div>
|
||||
<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"> 148</span> <span class="keywordtype">int</span> i,</div>
|
||||
<div class="line"><a id="l00149" name="l00149"></a><span class="lineno"> 149</span> <span class="keywordtype">int</span> j</div>
|
||||
<div class="line"><a id="l00150" name="l00150"></a><span class="lineno"> 150</span> ) <span class="keyword">const</span> = 0;</div>
|
||||
<div class="line"><a id="l00151" name="l00151"></a><span class="lineno"> 151</span></div>
|
||||
<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f"> 158</a></span> <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">generateStoichiometryMatrix</a>() = 0;</div>
|
||||
<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span></div>
|
||||
<div class="line"><a id="l00169" name="l00169"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f"> 169</a></span> [[nodiscard]] <span class="keyword">virtual</span> <span class="keywordtype">int</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">getStoichiometryMatrixEntry</a>(</div>
|
||||
<div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> <span class="keywordtype">int</span> speciesIndex,</div>
|
||||
<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</span> <span class="keywordtype">int</span> reactionIndex</div>
|
||||
<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> ) <span class="keyword">const</span> = 0;</div>
|
||||
<div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span></div>
|
||||
<div class="line"><a id="l00186" name="l00186"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785"> 186</a></span> [[nodiscard]] <span class="keyword">virtual</span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">calculateMolarReactionFlow</a>(</div>
|
||||
<div class="line"><a id="l00187" name="l00187"></a><span class="lineno"> 187</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>
|
||||
<div class="line"><a id="l00188" name="l00188"></a><span class="lineno"> 188</span> <span class="keyword">const</span> std::vector<double>& Y,</div>
|
||||
<div class="line"><a id="l00189" name="l00189"></a><span class="lineno"> 189</span> <span class="keywordtype">double</span> T9,</div>
|
||||
<div class="line"><a id="l00190" name="l00190"></a><span class="lineno"> 190</span> <span class="keywordtype">double</span> rho</div>
|
||||
<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span> ) <span class="keyword">const</span> = 0;</div>
|
||||
<div class="line"><a id="l00192" name="l00192"></a><span class="lineno"> 192</span></div>
|
||||
<div class="line"><a id="l00198" name="l00198"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037"> 198</a></span> [[nodiscard]] <span class="keyword">virtual</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_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">getNetworkReactions</a>() <span class="keyword">const</span> = 0;</div>
|
||||
<div class="line"><a id="l00199" name="l00199"></a><span class="lineno"> 199</span></div>
|
||||
<div class="line"><a id="l00211" name="l00211"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15"> 211</a></span> [[nodiscard]] <span class="keyword">virtual</span> std::unordered_map<fourdst::atomic::Species, double> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15">getSpeciesTimescales</a>(</div>
|
||||
<div class="line"><a id="l00212" name="l00212"></a><span class="lineno"> 212</span> <span class="keyword">const</span> std::vector<double>& Y,</div>
|
||||
<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</span> <span class="keywordtype">double</span> T9,</div>
|
||||
<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span> <span class="keywordtype">double</span> rho</div>
|
||||
<div class="line"><a id="l00215" name="l00215"></a><span class="lineno"> 215</span> ) <span class="keyword">const</span> = 0;</div>
|
||||
<div class="line"><a id="l00216" name="l00216"></a><span class="lineno"> 216</span> </div>
|
||||
<div class="line"><a id="l00217" name="l00217"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f"> 217</a></span> <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f">update</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a>& netIn) = 0;</div>
|
||||
<div class="line"><a id="l00218" name="l00218"></a><span class="lineno"> 218</span> </div>
|
||||
<div class="line"><a id="l00219" name="l00219"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd"> 219</a></span> <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">setScreeningModel</a>(<a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> model) = 0;</div>
|
||||
<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span> </div>
|
||||
<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"><a class="line" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0"> 221</a></span> [[nodiscard]] <span class="keyword">virtual</span> <a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> <a class="code hl_function" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">getScreeningModel</a>() <span class="keyword">const</span> = 0;</div>
|
||||
<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> };</div>
|
||||
</div>
|
||||
<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span>}</div>
|
||||
<div class="line"><a id="l00223" name="l00223"></a><span class="lineno"> 223</span>}</div>
|
||||
</div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><div class="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><div class="ttdef"><b>Definition</b> <a href="#l00118">engine_abstract.h:118</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><div class="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><div class="ttdef"><b>Definition</b> <a href="#l00121">engine_abstract.h:121</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a05d15ff35a6bc06a2fa7eda19838bd07"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">gridfire::DynamicEngine::getJacobianMatrixEntry</a></div><div class="ttdeci">virtual double getJacobianMatrixEntry(int i, int j) const =0</div><div class="ttdoc">Get an entry from the previously generated Jacobian matrix.</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a0a2fb3435ee3271ab9c806f225c61a7f"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f">gridfire::DynamicEngine::generateJacobianMatrix</a></div><div class="ttdeci">virtual void generateJacobianMatrix(const std::vector< double > &Y, double T9, double rho)=0</div><div class="ttdoc">Generate the Jacobian matrix for the current state.</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a3fb44b6f55563a2f590f31916528f2bd"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">gridfire::DynamicEngine::setScreeningModel</a></div><div class="ttdeci">virtual void setScreeningModel(screening::ScreeningType model)=0</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a5d8ba98b230d2849035ee2507728fa15"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15">gridfire::DynamicEngine::getSpeciesTimescales</a></div><div class="ttdeci">virtual std::unordered_map< fourdst::atomic::Species, double > getSpeciesTimescales(const std::vector< double > &Y, double T9, double rho) const =0</div><div class="ttdoc">Compute timescales for all species in the network.</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a6633b1757c41dd9e1c397333f4f9e785"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine::calculateMolarReactionFlow</a></div><div class="ttdeci">virtual double calculateMolarReactionFlow(const reaction::Reaction &reaction, const std::vector< double > &Y, double T9, double rho) const =0</div><div class="ttdoc">Calculate the molar reaction flow for a given reaction.</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_a7a203f8e0f3a6744ddc912dfbcfdbcc0"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">gridfire::DynamicEngine::getScreeningModel</a></div><div class="ttdeci">virtual screening::ScreeningType getScreeningModel() const =0</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_acd500e1cd788df1dc105d28a20dc5f4f"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f">gridfire::DynamicEngine::update</a></div><div class="ttdeci">virtual void update(const NetIn &netIn)=0</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_ad2a82099edbb374bbb2c9509ccdb1037"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">gridfire::DynamicEngine::getNetworkReactions</a></div><div class="ttdeci">virtual const reaction::LogicalReactionSet & getNetworkReactions() const =0</div><div class="ttdoc">Get the set of logical reactions in the network.</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_aeae6d84ef74d88fd2cdf07b82e98a16f"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">gridfire::DynamicEngine::generateStoichiometryMatrix</a></div><div class="ttdeci">virtual void generateStoichiometryMatrix()=0</div><div class="ttdoc">Generate the stoichiometry matrix for the network.</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html_afa108dd5227dbb1045e90d7b3bd8b84f"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">gridfire::DynamicEngine::getStoichiometryMatrixEntry</a></div><div class="ttdeci">virtual int getStoichiometryMatrixEntry(int speciesIndex, int reactionIndex) const =0</div><div class="ttdoc">Get an entry from the stoichiometry matrix.</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_engine_html"><div class="ttname"><a href="classgridfire_1_1_engine.html">gridfire::Engine</a></div><div class="ttdoc">Abstract base class for a reaction network engine.</div><div class="ttdef"><b>Definition</b> <a href="#l00072">engine_abstract.h:72</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_engine_html"><div class="ttname"><a href="classgridfire_1_1_engine.html">gridfire::Engine</a></div><div class="ttdoc">Abstract base class for a reaction network engine.</div><div class="ttdef"><b>Definition</b> <a href="#l00075">engine_abstract.h:75</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_engine_html_a020e1b493d6964cafdad08fde697ceb3"><div class="ttname"><a href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">gridfire::Engine::getNetworkSpecies</a></div><div class="ttdeci">virtual const std::vector< fourdst::atomic::Species > & getNetworkSpecies() const =0</div><div class="ttdoc">Get the list of species in the network.</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_engine_html_a2e7970bed2100699f226f4141d5db037"><div class="ttname"><a href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">gridfire::Engine::~Engine</a></div><div class="ttdeci">virtual ~Engine()=default</div><div class="ttdoc">Virtual destructor.</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_engine_html_ac8b56124b6b49cd1802addb74a9a47c2"><div class="ttname"><a href="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">gridfire::Engine::calculateRHSAndEnergy</a></div><div class="ttdeci">virtual StepDerivatives< double > calculateRHSAndEnergy(const std::vector< double > &Y, double T9, double rho) const =0</div><div class="ttdoc">Calculate the right-hand side (dY/dt) and energy generation.</div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1reaction_1_1_logical_reaction_set_html"><div class="ttname"><a href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">gridfire::reaction::LogicalReactionSet</a></div><div class="ttdoc">A collection of LogicalReaction objects.</div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00554">reaction.h:554</a></div></div>
|
||||
<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#l00071">reaction.h:71</a></div></div>
|
||||
<div class="ttc" id="aconceptgridfire_1_1_is_arithmetic_or_a_d_html"><div class="ttname"><a href="conceptgridfire_1_1_is_arithmetic_or_a_d.html">gridfire::IsArithmeticOrAD</a></div><div class="ttdoc">Concept for types allowed in engine calculations.</div><div class="ttdef"><b>Definition</b> <a href="#l00030">engine_abstract.h:30</a></div></div>
|
||||
<div class="ttc" id="anamespacegridfire_1_1reaction_html"><div class="ttname"><a href="namespacegridfire_1_1reaction.html">gridfire::reaction</a></div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00024">reaction.h:24</a></div></div>
|
||||
<div class="ttc" id="anamespacegridfire_html"><div class="ttname"><a href="namespacegridfire.html">gridfire</a></div><div class="ttdef"><b>Definition</b> <a href="#l00021">engine_abstract.h:21</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1reaction_1_1_reaction_html"><div class="ttname"><a href="classgridfire_1_1reaction_1_1_reaction.html">gridfire::reaction::Reaction</a></div><div class="ttdoc">Represents a single nuclear reaction from a specific data source.</div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00072">reaction.h:72</a></div></div>
|
||||
<div class="ttc" id="aconceptgridfire_1_1_is_arithmetic_or_a_d_html"><div class="ttname"><a href="conceptgridfire_1_1_is_arithmetic_or_a_d.html">gridfire::IsArithmeticOrAD</a></div><div class="ttdoc">Concept for types allowed in engine calculations.</div><div class="ttdef"><b>Definition</b> <a href="#l00033">engine_abstract.h:33</a></div></div>
|
||||
<div class="ttc" id="anamespacegridfire_1_1reaction_html"><div class="ttname"><a href="namespacegridfire_1_1reaction.html">gridfire::reaction</a></div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00025">reaction.h:25</a></div></div>
|
||||
<div class="ttc" id="anamespacegridfire_1_1reaction_html_aa86f08712565f278adacc7cd2361eb31"><div class="ttname"><a href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a></div><div class="ttdeci">TemplatedReactionSet< 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>
|
||||
<div class="ttc" id="anamespacegridfire_1_1screening_html_aa82aafbc4f8c28d0a75b60798e3a7d25"><div class="ttname"><a href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">gridfire::screening::ScreeningType</a></div><div class="ttdeci">ScreeningType</div><div class="ttdef"><b>Definition</b> <a href="screening__types_8h_source.html#l00008">screening_types.h:8</a></div></div>
|
||||
<div class="ttc" id="anamespacegridfire_html"><div class="ttname"><a href="namespacegridfire.html">gridfire</a></div><div class="ttdef"><b>Definition</b> <a href="#l00024">engine_abstract.h:24</a></div></div>
|
||||
<div class="ttc" id="anetwork_8h_html"><div class="ttname"><a href="network_8h.html">network.h</a></div></div>
|
||||
<div class="ttc" id="areaction_8h_html"><div class="ttname"><a href="reaction_8h.html">reaction.h</a></div><div class="ttdoc">Defines classes for representing and managing nuclear reactions.</div></div>
|
||||
<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="#l00050">engine_abstract.h:50</a></div></div>
|
||||
<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="#l00052">engine_abstract.h:52</a></div></div>
|
||||
<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="#l00051">engine_abstract.h:51</a></div></div>
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<div class="ttc" id="ascreening__abstract_8h_html"><div class="ttname"><a href="screening__abstract_8h.html">screening_abstract.h</a></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_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="#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="#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="#l00054">engine_abstract.h:54</a></div></div>
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