docs(docs): added extensive docs
This commit is contained in:
@@ -144,7 +144,7 @@ $(function(){initNavTree('engine__defined_8cpp_source.html',''); initResizable(t
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<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> )<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ae3f99002ab2c56a5bcdec00839f8628f">validateNetworkState</a>();</div>
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<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> </div>
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<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> <span class="keyword">const</span> <span class="keyword">auto</span> Y_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ac231044e37e0962f664f8465e1ccb022">mapViewToFull</a>(Y_defined);</div>
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<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> <span class="keyword">const</span> <span class="keyword">auto</span> Y_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#adba3c11b11a04b2907c1635210d73dee">mapViewToFull</a>(Y_defined);</div>
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<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> <span class="keyword">const</span> <span class="keyword">auto</span> [dydt, nuclearEnergyGenerationRate] = <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81">m_baseEngine</a>.calculateRHSAndEnergy(Y_full, T9, rho);</div>
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<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> </div>
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<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> <a class="code hl_struct" href="structgridfire_1_1_step_derivatives.html">StepDerivatives<double></a> definedResults;</div>
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@@ -162,7 +162,7 @@ $(function(){initNavTree('engine__defined_8cpp_source.html',''); initResizable(t
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<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> ) {</div>
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<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ae3f99002ab2c56a5bcdec00839f8628f">validateNetworkState</a>();</div>
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<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> </div>
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<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> <span class="keyword">const</span> <span class="keyword">auto</span> Y_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ac231044e37e0962f664f8465e1ccb022">mapViewToFull</a>(Y_defined);</div>
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<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> <span class="keyword">const</span> <span class="keyword">auto</span> Y_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#adba3c11b11a04b2907c1635210d73dee">mapViewToFull</a>(Y_defined);</div>
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<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81">m_baseEngine</a>.generateJacobianMatrix(Y_full, T9, rho);</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>
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@@ -174,8 +174,8 @@ $(function(){initNavTree('engine__defined_8cpp_source.html',''); initResizable(t
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<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> )<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ae3f99002ab2c56a5bcdec00839f8628f">validateNetworkState</a>();</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="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> i_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf">mapViewToFullSpeciesIndex</a>(i_defined);</div>
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<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> j_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf">mapViewToFullSpeciesIndex</a>(j_defined);</div>
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<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> i_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#aa2373955ef5b0eabf7a57c7208e38bb1">mapViewToFullSpeciesIndex</a>(i_defined);</div>
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<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> j_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#aa2373955ef5b0eabf7a57c7208e38bb1">mapViewToFullSpeciesIndex</a>(j_defined);</div>
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<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> </div>
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<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81">m_baseEngine</a>.getJacobianMatrixEntry(i_full, j_full);</div>
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<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> }</div>
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@@ -196,8 +196,8 @@ $(function(){initNavTree('engine__defined_8cpp_source.html',''); initResizable(t
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<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> )<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ae3f99002ab2c56a5bcdec00839f8628f">validateNetworkState</a>();</div>
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<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> </div>
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<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> i_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf">mapViewToFullSpeciesIndex</a>(speciesIndex_defined);</div>
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<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> j_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ae7d6f0ff9076d59d1245c047bbd1bdb9">mapViewToFullReactionIndex</a>(reactionIndex_defined);</div>
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<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> i_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#aa2373955ef5b0eabf7a57c7208e38bb1">mapViewToFullSpeciesIndex</a>(speciesIndex_defined);</div>
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<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> j_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#a74217a1f8fd8e6daff969cb17885315c">mapViewToFullReactionIndex</a>(reactionIndex_defined);</div>
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<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81">m_baseEngine</a>.getStoichiometryMatrixEntry(i_full, j_full);</div>
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<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> }</div>
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</div>
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@@ -216,7 +216,7 @@ $(function(){initNavTree('engine__defined_8cpp_source.html',''); initResizable(t
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<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432">m_logger</a> -> flush_log();</div>
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<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Reaction not found in active reactions: "</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="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> <span class="keyword">const</span> <span class="keyword">auto</span> Y_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ac231044e37e0962f664f8465e1ccb022">mapViewToFull</a>(Y_defined);</div>
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<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> <span class="keyword">const</span> <span class="keyword">auto</span> Y_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#adba3c11b11a04b2907c1635210d73dee">mapViewToFull</a>(Y_defined);</div>
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<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81">m_baseEngine</a>.calculateMolarReactionFlow(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>, Y_full, T9, rho);</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>
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@@ -237,7 +237,7 @@ $(function(){initNavTree('engine__defined_8cpp_source.html',''); initResizable(t
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<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span> )<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span> <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ae3f99002ab2c56a5bcdec00839f8628f">validateNetworkState</a>();</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> <span class="keyword">const</span> <span class="keyword">auto</span> Y_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ac231044e37e0962f664f8465e1ccb022">mapViewToFull</a>(Y_defined);</div>
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<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> <span class="keyword">const</span> <span class="keyword">auto</span> Y_full = <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#adba3c11b11a04b2907c1635210d73dee">mapViewToFull</a>(Y_defined);</div>
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<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> <span class="keyword">const</span> <span class="keyword">auto</span> fullTimescales = <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81">m_baseEngine</a>.getSpeciesTimescales(Y_full, T9, rho);</div>
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<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> </div>
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<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> std::unordered_map<Species, double> definedTimescales;</div>
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@@ -405,7 +405,7 @@ $(function(){initNavTree('engine__defined_8cpp_source.html',''); initResizable(t
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</div>
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<div class="line"><a id="l00266" name="l00266"></a><span class="lineno"> 266</span> </div>
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<div class="foldopen" id="foldopen00267" data-start="{" data-end="}">
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<div class="line"><a id="l00267" name="l00267"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#ac231044e37e0962f664f8465e1ccb022"> 267</a></span> std::vector<double> <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ac231044e37e0962f664f8465e1ccb022">FileDefinedEngineView::mapViewToFull</a>(<span class="keyword">const</span> std::vector<double>& culled)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00267" name="l00267"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#adba3c11b11a04b2907c1635210d73dee"> 267</a></span> std::vector<double> <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#adba3c11b11a04b2907c1635210d73dee">FileDefinedEngineView::mapViewToFull</a>(<span class="keyword">const</span> std::vector<double>& culled)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00268" name="l00268"></a><span class="lineno"> 268</span> std::vector<double> full(<a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81">m_baseEngine</a>.getNetworkSpecies().size(), 0.0);</div>
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<div class="line"><a id="l00269" name="l00269"></a><span class="lineno"> 269</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i_culled = 0; i_culled < culled.size(); ++i_culled) {</div>
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<div class="line"><a id="l00270" name="l00270"></a><span class="lineno"> 270</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> i_full = <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#aebd4a1a584f2784f1df3d503645be03b">m_speciesIndexMap</a>[i_culled];</div>
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@@ -427,7 +427,7 @@ $(function(){initNavTree('engine__defined_8cpp_source.html',''); initResizable(t
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</div>
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<div class="line"><a id="l00284" name="l00284"></a><span class="lineno"> 284</span> </div>
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<div class="foldopen" id="foldopen00285" data-start="{" data-end="}">
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<div class="line"><a id="l00285" name="l00285"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf"> 285</a></span> <span class="keywordtype">size_t</span> <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf">FileDefinedEngineView::mapViewToFullSpeciesIndex</a>(<span class="keywordtype">size_t</span> culledSpeciesIndex)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00285" name="l00285"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#aa2373955ef5b0eabf7a57c7208e38bb1"> 285</a></span> <span class="keywordtype">size_t</span> <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#aa2373955ef5b0eabf7a57c7208e38bb1">FileDefinedEngineView::mapViewToFullSpeciesIndex</a>(<span class="keywordtype">size_t</span> culledSpeciesIndex)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00286" name="l00286"></a><span class="lineno"> 286</span> <span class="keywordflow">if</span> (culledSpeciesIndex < 0 || culledSpeciesIndex >= <span class="keyword">static_cast<</span><span class="keywordtype">int</span><span class="keyword">></span>(<a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#aebd4a1a584f2784f1df3d503645be03b">m_speciesIndexMap</a>.size())) {</div>
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<div class="line"><a id="l00287" name="l00287"></a><span class="lineno"> 287</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432">m_logger</a>, <span class="stringliteral">"Defined index {} is out of bounds for species index map of size {}."</span>, culledSpeciesIndex, <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#aebd4a1a584f2784f1df3d503645be03b">m_speciesIndexMap</a>.size());</div>
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<div class="line"><a id="l00288" name="l00288"></a><span class="lineno"> 288</span> <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432">m_logger</a>->flush_log();</div>
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@@ -438,7 +438,7 @@ $(function(){initNavTree('engine__defined_8cpp_source.html',''); initResizable(t
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</div>
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<div class="line"><a id="l00293" name="l00293"></a><span class="lineno"> 293</span> </div>
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<div class="foldopen" id="foldopen00294" data-start="{" data-end="}">
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<div class="line"><a id="l00294" name="l00294"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#ae7d6f0ff9076d59d1245c047bbd1bdb9"> 294</a></span> <span class="keywordtype">size_t</span> <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#ae7d6f0ff9076d59d1245c047bbd1bdb9">FileDefinedEngineView::mapViewToFullReactionIndex</a>(<span class="keywordtype">size_t</span> culledReactionIndex)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00294" name="l00294"></a><span class="lineno"><a class="line" href="classgridfire_1_1_file_defined_engine_view.html#a74217a1f8fd8e6daff969cb17885315c"> 294</a></span> <span class="keywordtype">size_t</span> <a class="code hl_function" href="classgridfire_1_1_file_defined_engine_view.html#a74217a1f8fd8e6daff969cb17885315c">FileDefinedEngineView::mapViewToFullReactionIndex</a>(<span class="keywordtype">size_t</span> culledReactionIndex)<span class="keyword"> const </span>{</div>
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<div class="line"><a id="l00295" name="l00295"></a><span class="lineno"> 295</span> <span class="keywordflow">if</span> (culledReactionIndex < 0 || culledReactionIndex >= <span class="keyword">static_cast<</span><span class="keywordtype">int</span><span class="keyword">></span>(<a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#af0a77a4749a15aae87bdecfccbd1736e">m_reactionIndexMap</a>.size())) {</div>
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<div class="line"><a id="l00296" name="l00296"></a><span class="lineno"> 296</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432">m_logger</a>, <span class="stringliteral">"Defined index {} is out of bounds for reaction index map of size {}."</span>, culledReactionIndex, <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#af0a77a4749a15aae87bdecfccbd1736e">m_reactionIndexMap</a>.size());</div>
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<div class="line"><a id="l00297" name="l00297"></a><span class="lineno"> 297</span> <a class="code hl_variable" href="classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432">m_logger</a>->flush_log();</div>
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@@ -459,44 +459,44 @@ $(function(){initNavTree('engine__defined_8cpp_source.html',''); initResizable(t
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</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="ttc" id="aclassgridfire_1_1_dynamic_engine_html"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><div class="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00121">engine_abstract.h:121</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a0a9b07176cb93b54c677b6ce71fda500"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500">gridfire::FileDefinedEngineView::m_parser</a></div><div class="ttdeci">const io::NetworkFileParser & m_parser</div><div class="ttdoc">Parser for the network file.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00078">engine_defined.h:78</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a0ef8804780d13bbfce0856237bb00470"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a0ef8804780d13bbfce0856237bb00470">gridfire::FileDefinedEngineView::getJacobianMatrixEntry</a></div><div class="ttdeci">double getJacobianMatrixEntry(const int i_defined, const int j_defined) const override</div><div class="ttdoc">Get an entry from the previously generated Jacobian matrix.</div><div class="ttdef"><b>Definition</b> <a href="#l00056">engine_defined.cpp:56</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a1b343998b93955025a589b2b4541e33b"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a1b343998b93955025a589b2b4541e33b">gridfire::FileDefinedEngineView::m_fileName</a></div><div class="ttdeci">std::string m_fileName</div><div class="ttdoc">Name of the file defining the reaction set considered by the engine view.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00077">engine_defined.h:77</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a27a5163157cc15c4cb3b99a5d3564dbd"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a27a5163157cc15c4cb3b99a5d3564dbd">gridfire::FileDefinedEngineView::generateStoichiometryMatrix</a></div><div class="ttdeci">void generateStoichiometryMatrix() override</div><div class="ttdoc">Generate the stoichiometry matrix for the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00068">engine_defined.cpp:68</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a299a0c61aa4f26029c770013c9feff5e"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a299a0c61aa4f26029c770013c9feff5e">gridfire::FileDefinedEngineView::m_activeSpecies</a></div><div class="ttdeci">std::vector< fourdst::atomic::Species > m_activeSpecies</div><div class="ttdoc">Active species in the defined engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00080">engine_defined.h:80</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a2c1d88b06568f9ea4c65e794d012ebfb"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a2c1d88b06568f9ea4c65e794d012ebfb">gridfire::FileDefinedEngineView::calculateRHSAndEnergy</a></div><div class="ttdeci">StepDerivatives< double > calculateRHSAndEnergy(const std::vector< double > &Y_defined, const double T9, const double rho) const override</div><div class="ttdoc">Calculate the right-hand side (dY/dt) and energy generation.</div><div class="ttdef"><b>Definition</b> <a href="#l00029">engine_defined.cpp:29</a></div></div>
|
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a3b5162b7be35405285ef9f825ec2663b"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a3b5162b7be35405285ef9f825ec2663b">gridfire::FileDefinedEngineView::buildFromFile</a></div><div class="ttdeci">void buildFromFile(const std::string &fileName)</div><div class="ttdef"><b>Definition</b> <a href="#l00208">engine_defined.cpp:208</a></div></div>
|
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a48b2451f96b8f5511ffc4071519c0810"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a48b2451f96b8f5511ffc4071519c0810">gridfire::FileDefinedEngineView::generateJacobianMatrix</a></div><div class="ttdeci">void generateJacobianMatrix(const std::vector< double > &Y_defined, const double T9, const double rho) override</div><div class="ttdoc">Generate the Jacobian matrix for the current state.</div><div class="ttdef"><b>Definition</b> <a href="#l00045">engine_defined.cpp:45</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a4c8b273c5cb3d470567c5691b68493a3"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a4c8b273c5cb3d470567c5691b68493a3">gridfire::FileDefinedEngineView::getBaseEngine</a></div><div class="ttdeci">const DynamicEngine & getBaseEngine() const override</div><div class="ttdoc">Access the underlying engine instance.</div><div class="ttdef"><b>Definition</b> <a href="#l00021">engine_defined.cpp:21</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a0a9b07176cb93b54c677b6ce71fda500"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500">gridfire::FileDefinedEngineView::m_parser</a></div><div class="ttdeci">const io::NetworkFileParser & m_parser</div><div class="ttdoc">Active species in the defined engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00235">engine_defined.h:235</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a0ef8804780d13bbfce0856237bb00470"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a0ef8804780d13bbfce0856237bb00470">gridfire::FileDefinedEngineView::getJacobianMatrixEntry</a></div><div class="ttdeci">double getJacobianMatrixEntry(const int i_defined, const int j_defined) const override</div><div class="ttdoc">Gets an entry from the Jacobian matrix for the active species.</div><div class="ttdef"><b>Definition</b> <a href="#l00056">engine_defined.cpp:56</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a1b343998b93955025a589b2b4541e33b"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a1b343998b93955025a589b2b4541e33b">gridfire::FileDefinedEngineView::m_fileName</a></div><div class="ttdeci">std::string m_fileName</div><div class="ttdoc">Parser for the network file.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00233">engine_defined.h:233</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a27a5163157cc15c4cb3b99a5d3564dbd"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a27a5163157cc15c4cb3b99a5d3564dbd">gridfire::FileDefinedEngineView::generateStoichiometryMatrix</a></div><div class="ttdeci">void generateStoichiometryMatrix() override</div><div class="ttdoc">Generates the stoichiometry matrix for the active reactions and species.</div><div class="ttdef"><b>Definition</b> <a href="#l00068">engine_defined.cpp:68</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a299a0c61aa4f26029c770013c9feff5e"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a299a0c61aa4f26029c770013c9feff5e">gridfire::FileDefinedEngineView::m_activeSpecies</a></div><div class="ttdeci">std::vector< fourdst::atomic::Species > m_activeSpecies</div><div class="ttdoc">Active reactions in the defined engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00238">engine_defined.h:238</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a2c1d88b06568f9ea4c65e794d012ebfb"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a2c1d88b06568f9ea4c65e794d012ebfb">gridfire::FileDefinedEngineView::calculateRHSAndEnergy</a></div><div class="ttdeci">StepDerivatives< double > calculateRHSAndEnergy(const std::vector< double > &Y_defined, const double T9, const double rho) const override</div><div class="ttdoc">Calculates the right-hand side (dY/dt) and energy generation for the active species.</div><div class="ttdef"><b>Definition</b> <a href="#l00029">engine_defined.cpp:29</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a3b5162b7be35405285ef9f825ec2663b"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a3b5162b7be35405285ef9f825ec2663b">gridfire::FileDefinedEngineView::buildFromFile</a></div><div class="ttdeci">void buildFromFile(const std::string &fileName)</div><div class="ttdoc">Builds the active species and reaction sets from a file.</div><div class="ttdef"><b>Definition</b> <a href="#l00208">engine_defined.cpp:208</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a48b2451f96b8f5511ffc4071519c0810"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a48b2451f96b8f5511ffc4071519c0810">gridfire::FileDefinedEngineView::generateJacobianMatrix</a></div><div class="ttdeci">void generateJacobianMatrix(const std::vector< double > &Y_defined, const double T9, const double rho) override</div><div class="ttdoc">Generates the Jacobian matrix for the active species.</div><div class="ttdef"><b>Definition</b> <a href="#l00045">engine_defined.cpp:45</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a4c8b273c5cb3d470567c5691b68493a3"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a4c8b273c5cb3d470567c5691b68493a3">gridfire::FileDefinedEngineView::getBaseEngine</a></div><div class="ttdeci">const DynamicEngine & getBaseEngine() const override</div><div class="ttdoc">Gets the base engine.</div><div class="ttdef"><b>Definition</b> <a href="#l00021">engine_defined.cpp:21</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a51ba09ff01fdcac1125d42f276c9a0a7"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a51ba09ff01fdcac1125d42f276c9a0a7">gridfire::FileDefinedEngineView::constructSpeciesIndexMap</a></div><div class="ttdeci">std::vector< size_t > constructSpeciesIndexMap() const</div><div class="ttdoc">Constructs the species index map.</div><div class="ttdef"><b>Definition</b> <a href="#l00147">engine_defined.cpp:147</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a5bbea17b69cc8f81bc251a04f4435a0c"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a5bbea17b69cc8f81bc251a04f4435a0c">gridfire::FileDefinedEngineView::getNetworkReactions</a></div><div class="ttdeci">const reaction::LogicalReactionSet & getNetworkReactions() const override</div><div class="ttdoc">Get the set of logical reactions in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00102">engine_defined.cpp:102</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a6e421bc748933be31bed9ff53f12b595"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a6e421bc748933be31bed9ff53f12b595">gridfire::FileDefinedEngineView::m_isStale</a></div><div class="ttdeci">bool m_isStale</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00086">engine_defined.h:86</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a8bb583e039b49608272997ed2d3387fa"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a8bb583e039b49608272997ed2d3387fa">gridfire::FileDefinedEngineView::getNetworkSpecies</a></div><div class="ttdeci">const std::vector< fourdst::atomic::Species > & getNetworkSpecies() const override</div><div class="ttdoc">Get the list of species in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00025">engine_defined.cpp:25</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf">gridfire::FileDefinedEngineView::mapViewToFullSpeciesIndex</a></div><div class="ttdeci">size_t mapViewToFullSpeciesIndex(size_t culledSpeciesIndex) const</div><div class="ttdoc">Maps a culled species index to a full species index.</div><div class="ttdef"><b>Definition</b> <a href="#l00285">engine_defined.cpp:285</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a8f2f64bab0f516ed2a6fd529912e0acd"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a8f2f64bab0f516ed2a6fd529912e0acd">gridfire::FileDefinedEngineView::FileDefinedEngineView</a></div><div class="ttdeci">FileDefinedEngineView(DynamicEngine &baseEngine, const std::string &fileName, const io::NetworkFileParser &parser)</div><div class="ttdef"><b>Definition</b> <a href="#l00008">engine_defined.cpp:8</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a92f14da849e99d07c1ff1347addb9263"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a92f14da849e99d07c1ff1347addb9263">gridfire::FileDefinedEngineView::setNetworkFile</a></div><div class="ttdeci">void setNetworkFile(const std::string &fileName)</div><div class="ttdef"><b>Definition</b> <a href="#l00133">engine_defined.cpp:133</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a5bbea17b69cc8f81bc251a04f4435a0c"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a5bbea17b69cc8f81bc251a04f4435a0c">gridfire::FileDefinedEngineView::getNetworkReactions</a></div><div class="ttdeci">const reaction::LogicalReactionSet & getNetworkReactions() const override</div><div class="ttdoc">Gets the set of active logical reactions in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00102">engine_defined.cpp:102</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a6e421bc748933be31bed9ff53f12b595"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a6e421bc748933be31bed9ff53f12b595">gridfire::FileDefinedEngineView::m_isStale</a></div><div class="ttdeci">bool m_isStale</div><div class="ttdoc">A flag indicating whether the view is stale and needs to be updated.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00248">engine_defined.h:248</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a74217a1f8fd8e6daff969cb17885315c"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a74217a1f8fd8e6daff969cb17885315c">gridfire::FileDefinedEngineView::mapViewToFullReactionIndex</a></div><div class="ttdeci">size_t mapViewToFullReactionIndex(size_t definedReactionIndex) const</div><div class="ttdoc">Maps a culled reaction index to a full reaction index.</div><div class="ttdef"><b>Definition</b> <a href="#l00294">engine_defined.cpp:294</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a8bb583e039b49608272997ed2d3387fa"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a8bb583e039b49608272997ed2d3387fa">gridfire::FileDefinedEngineView::getNetworkSpecies</a></div><div class="ttdeci">const std::vector< fourdst::atomic::Species > & getNetworkSpecies() const override</div><div class="ttdoc">Gets the list of active species in the network defined by the file.</div><div class="ttdef"><b>Definition</b> <a href="#l00025">engine_defined.cpp:25</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a8f2f64bab0f516ed2a6fd529912e0acd"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a8f2f64bab0f516ed2a6fd529912e0acd">gridfire::FileDefinedEngineView::FileDefinedEngineView</a></div><div class="ttdeci">FileDefinedEngineView(DynamicEngine &baseEngine, const std::string &fileName, const io::NetworkFileParser &parser)</div><div class="ttdoc">Constructs a FileDefinedEngineView.</div><div class="ttdef"><b>Definition</b> <a href="#l00008">engine_defined.cpp:8</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a92f14da849e99d07c1ff1347addb9263"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a92f14da849e99d07c1ff1347addb9263">gridfire::FileDefinedEngineView::setNetworkFile</a></div><div class="ttdeci">void setNetworkFile(const std::string &fileName)</div><div class="ttdoc">Sets a new network file to define the active reactions.</div><div class="ttdef"><b>Definition</b> <a href="#l00133">engine_defined.cpp:133</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a97e5ee4651dbe6754678fe96e4702fee"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a97e5ee4651dbe6754678fe96e4702fee">gridfire::FileDefinedEngineView::mapFullToView</a></div><div class="ttdeci">std::vector< double > mapFullToView(const std::vector< double > &full) const</div><div class="ttdoc">Maps a vector of full abundances to a vector of culled abundances.</div><div class="ttdef"><b>Definition</b> <a href="#l00276">engine_defined.cpp:276</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a9d93633ed4ab68de94b7274f879a0432"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432">gridfire::FileDefinedEngineView::m_logger</a></div><div class="ttdeci">quill::Logger * m_logger</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00074">engine_defined.h:74</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a9da9224f5c99a5068f3d8cbf066e4693"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a9da9224f5c99a5068f3d8cbf066e4693">gridfire::FileDefinedEngineView::getStoichiometryMatrixEntry</a></div><div class="ttdeci">int getStoichiometryMatrixEntry(const int speciesIndex_defined, const int reactionIndex_defined) const override</div><div class="ttdoc">Get an entry from the stoichiometry matrix.</div><div class="ttdef"><b>Definition</b> <a href="#l00074">engine_defined.cpp:74</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ac231044e37e0962f664f8465e1ccb022"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ac231044e37e0962f664f8465e1ccb022">gridfire::FileDefinedEngineView::mapViewToFull</a></div><div class="ttdeci">std::vector< double > mapViewToFull(const std::vector< double > &culled) const</div><div class="ttdoc">Maps a vector of culled abundances to a vector of full abundances.</div><div class="ttdef"><b>Definition</b> <a href="#l00267">engine_defined.cpp:267</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ac371fb66fd0a76a04df204c9dd9a05ef"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ac371fb66fd0a76a04df204c9dd9a05ef">gridfire::FileDefinedEngineView::calculateMolarReactionFlow</a></div><div class="ttdeci">double calculateMolarReactionFlow(const reaction::Reaction &reaction, const std::vector< double > &Y_defined, const double T9, const double rho) const override</div><div class="ttdoc">Calculate the molar reaction flow for a given reaction.</div><div class="ttdef"><b>Definition</b> <a href="#l00085">engine_defined.cpp:85</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ace3568eadaba69e7357b4386c5ca3eb0"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ace3568eadaba69e7357b4386c5ca3eb0">gridfire::FileDefinedEngineView::update</a></div><div class="ttdeci">void update(const NetIn &netIn) override</div><div class="ttdef"><b>Definition</b> <a href="#l00127">engine_defined.cpp:127</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ace3c6ea4841318c08695973ab3dcddc6"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ace3c6ea4841318c08695973ab3dcddc6">gridfire::FileDefinedEngineView::getSpeciesTimescales</a></div><div class="ttdeci">std::unordered_map< fourdst::atomic::Species, double > getSpeciesTimescales(const std::vector< double > &Y_defined, const double T9, const double rho) const override</div><div class="ttdoc">Compute timescales for all species in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00108">engine_defined.cpp:108</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ad8454c98fa9a4bb45dc81059bc51fc81"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81">gridfire::FileDefinedEngineView::m_baseEngine</a></div><div class="ttdeci">DynamicEngine & m_baseEngine</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00076">engine_defined.h:76</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ad96bbee6d3d37b50d9236a975ef704c0"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ad96bbee6d3d37b50d9236a975ef704c0">gridfire::FileDefinedEngineView::setScreeningModel</a></div><div class="ttdeci">void setScreeningModel(screening::ScreeningType model) override</div><div class="ttdef"><b>Definition</b> <a href="#l00139">engine_defined.cpp:139</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_adbc50f397445f92b810d80cf329b8626"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#adbc50f397445f92b810d80cf329b8626">gridfire::FileDefinedEngineView::getScreeningModel</a></div><div class="ttdeci">screening::ScreeningType getScreeningModel() const override</div><div class="ttdef"><b>Definition</b> <a href="#l00143">engine_defined.cpp:143</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ae012da2b1f6169cb13e6075a73353ab2"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ae012da2b1f6169cb13e6075a73353ab2">gridfire::FileDefinedEngineView::m_activeReactions</a></div><div class="ttdeci">reaction::LogicalReactionSet m_activeReactions</div><div class="ttdoc">Active reactions in the defined engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00081">engine_defined.h:81</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ae3f99002ab2c56a5bcdec00839f8628f"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ae3f99002ab2c56a5bcdec00839f8628f">gridfire::FileDefinedEngineView::validateNetworkState</a></div><div class="ttdeci">void validateNetworkState() const</div><div class="ttdef"><b>Definition</b> <a href="#l00303">engine_defined.cpp:303</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ae7d6f0ff9076d59d1245c047bbd1bdb9"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ae7d6f0ff9076d59d1245c047bbd1bdb9">gridfire::FileDefinedEngineView::mapViewToFullReactionIndex</a></div><div class="ttdeci">size_t mapViewToFullReactionIndex(size_t culledReactionIndex) const</div><div class="ttdoc">Maps a culled reaction index to a full reaction index.</div><div class="ttdef"><b>Definition</b> <a href="#l00294">engine_defined.cpp:294</a></div></div>
|
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a9d93633ed4ab68de94b7274f879a0432"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432">gridfire::FileDefinedEngineView::m_logger</a></div><div class="ttdeci">quill::Logger * m_logger</div><div class="ttdoc">A pointer to the logger instance.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00228">engine_defined.h:228</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a9da9224f5c99a5068f3d8cbf066e4693"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#a9da9224f5c99a5068f3d8cbf066e4693">gridfire::FileDefinedEngineView::getStoichiometryMatrixEntry</a></div><div class="ttdeci">int getStoichiometryMatrixEntry(const int speciesIndex_defined, const int reactionIndex_defined) const override</div><div class="ttdoc">Gets an entry from the stoichiometry matrix for the active species and reactions.</div><div class="ttdef"><b>Definition</b> <a href="#l00074">engine_defined.cpp:74</a></div></div>
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||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_aa2373955ef5b0eabf7a57c7208e38bb1"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#aa2373955ef5b0eabf7a57c7208e38bb1">gridfire::FileDefinedEngineView::mapViewToFullSpeciesIndex</a></div><div class="ttdeci">size_t mapViewToFullSpeciesIndex(size_t definedSpeciesIndex) const</div><div class="ttdoc">Maps a culled species index to a full species index.</div><div class="ttdef"><b>Definition</b> <a href="#l00285">engine_defined.cpp:285</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ac371fb66fd0a76a04df204c9dd9a05ef"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ac371fb66fd0a76a04df204c9dd9a05ef">gridfire::FileDefinedEngineView::calculateMolarReactionFlow</a></div><div class="ttdeci">double calculateMolarReactionFlow(const reaction::Reaction &reaction, const std::vector< double > &Y_defined, const double T9, const double rho) const override</div><div class="ttdoc">Calculates the molar reaction flow for a given reaction in the active network.</div><div class="ttdef"><b>Definition</b> <a href="#l00085">engine_defined.cpp:85</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ace3568eadaba69e7357b4386c5ca3eb0"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ace3568eadaba69e7357b4386c5ca3eb0">gridfire::FileDefinedEngineView::update</a></div><div class="ttdeci">void update(const NetIn &netIn) override</div><div class="ttdoc">Updates the engine view if it is marked as stale.</div><div class="ttdef"><b>Definition</b> <a href="#l00127">engine_defined.cpp:127</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ace3c6ea4841318c08695973ab3dcddc6"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ace3c6ea4841318c08695973ab3dcddc6">gridfire::FileDefinedEngineView::getSpeciesTimescales</a></div><div class="ttdeci">std::unordered_map< fourdst::atomic::Species, double > getSpeciesTimescales(const std::vector< double > &Y_defined, const double T9, const double rho) const override</div><div class="ttdoc">Computes timescales for all active species in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00108">engine_defined.cpp:108</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ad8454c98fa9a4bb45dc81059bc51fc81"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81">gridfire::FileDefinedEngineView::m_baseEngine</a></div><div class="ttdeci">DynamicEngine & m_baseEngine</div><div class="ttdoc">The underlying engine to which this view delegates calculations.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00231">engine_defined.h:231</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ad96bbee6d3d37b50d9236a975ef704c0"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ad96bbee6d3d37b50d9236a975ef704c0">gridfire::FileDefinedEngineView::setScreeningModel</a></div><div class="ttdeci">void setScreeningModel(screening::ScreeningType model) override</div><div class="ttdoc">Sets the screening model for the base engine.</div><div class="ttdef"><b>Definition</b> <a href="#l00139">engine_defined.cpp:139</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_adba3c11b11a04b2907c1635210d73dee"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#adba3c11b11a04b2907c1635210d73dee">gridfire::FileDefinedEngineView::mapViewToFull</a></div><div class="ttdeci">std::vector< double > mapViewToFull(const std::vector< double > &defined) const</div><div class="ttdoc">Maps a vector of culled abundances to a vector of full abundances.</div><div class="ttdef"><b>Definition</b> <a href="#l00267">engine_defined.cpp:267</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_adbc50f397445f92b810d80cf329b8626"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#adbc50f397445f92b810d80cf329b8626">gridfire::FileDefinedEngineView::getScreeningModel</a></div><div class="ttdeci">screening::ScreeningType getScreeningModel() const override</div><div class="ttdoc">Gets the screening model from the base engine.</div><div class="ttdef"><b>Definition</b> <a href="#l00143">engine_defined.cpp:143</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ae012da2b1f6169cb13e6075a73353ab2"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ae012da2b1f6169cb13e6075a73353ab2">gridfire::FileDefinedEngineView::m_activeReactions</a></div><div class="ttdeci">reaction::LogicalReactionSet m_activeReactions</div><div class="ttdoc">Maps indices of active species to indices in the full network.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00240">engine_defined.h:240</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ae3f99002ab2c56a5bcdec00839f8628f"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ae3f99002ab2c56a5bcdec00839f8628f">gridfire::FileDefinedEngineView::validateNetworkState</a></div><div class="ttdeci">void validateNetworkState() const</div><div class="ttdoc">Validates that the FileDefinedEngineView is not stale.</div><div class="ttdef"><b>Definition</b> <a href="#l00303">engine_defined.cpp:303</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_aebb3f3548f8781506f31580706810a4e"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#aebb3f3548f8781506f31580706810a4e">gridfire::FileDefinedEngineView::constructReactionIndexMap</a></div><div class="ttdeci">std::vector< size_t > constructReactionIndexMap() const</div><div class="ttdoc">Constructs the reaction index map.</div><div class="ttdef"><b>Definition</b> <a href="#l00176">engine_defined.cpp:176</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_aebd4a1a584f2784f1df3d503645be03b"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#aebd4a1a584f2784f1df3d503645be03b">gridfire::FileDefinedEngineView::m_speciesIndexMap</a></div><div class="ttdeci">std::vector< size_t > m_speciesIndexMap</div><div class="ttdoc">Maps indices of active species to indices in the full network.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00083">engine_defined.h:83</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_af0a77a4749a15aae87bdecfccbd1736e"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#af0a77a4749a15aae87bdecfccbd1736e">gridfire::FileDefinedEngineView::m_reactionIndexMap</a></div><div class="ttdeci">std::vector< size_t > m_reactionIndexMap</div><div class="ttdoc">Maps indices of active reactions to indices in the full network.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00084">engine_defined.h:84</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1io_1_1_network_file_parser_html"><div class="ttname"><a href="classgridfire_1_1io_1_1_network_file_parser.html">gridfire::io::NetworkFileParser</a></div><div class="ttdef"><b>Definition</b> <a href="network__file_8h_source.html#l00017">network_file.h:17</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_aebd4a1a584f2784f1df3d503645be03b"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#aebd4a1a584f2784f1df3d503645be03b">gridfire::FileDefinedEngineView::m_speciesIndexMap</a></div><div class="ttdeci">std::vector< size_t > m_speciesIndexMap</div><div class="ttdoc">Maps indices of active reactions to indices in the full network.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00243">engine_defined.h:243</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_af0a77a4749a15aae87bdecfccbd1736e"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#af0a77a4749a15aae87bdecfccbd1736e">gridfire::FileDefinedEngineView::m_reactionIndexMap</a></div><div class="ttdeci">std::vector< size_t > m_reactionIndexMap</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00245">engine_defined.h:245</a></div></div>
|
||||
<div class="ttc" id="aclassgridfire_1_1io_1_1_network_file_parser_html"><div class="ttname"><a href="classgridfire_1_1io_1_1_network_file_parser.html">gridfire::io::NetworkFileParser</a></div><div class="ttdoc">An abstract base class for network file parsers.</div><div class="ttdef"><b>Definition</b> <a href="network__file_8h_source.html#l00038">network_file.h:38</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="aengine__defined_8h_html"><div class="ttname"><a href="engine__defined_8h.html">engine_defined.h</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_1_1screening_html_aa82aafbc4f8c28d0a75b60798e3a7d25"><div class="ttname"><a href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">gridfire::screening::ScreeningType</a></div><div class="ttdeci">ScreeningType</div><div class="ttdoc">Enumerates the available plasma screening models.</div><div class="ttdef"><b>Definition</b> <a href="screening__types_8h_source.html#l00015">screening_types.h:15</a></div></div>
|
||||
<div class="ttc" id="anamespacegridfire_html"><div class="ttname"><a href="namespacegridfire.html">gridfire</a></div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00024">engine_abstract.h:24</a></div></div>
|
||||
<div class="ttc" id="astructgridfire_1_1_net_in_html"><div class="ttname"><a href="structgridfire_1_1_net_in.html">gridfire::NetIn</a></div><div class="ttdef"><b>Definition</b> <a href="network_8h_source.html#l00053">network.h:53</a></div></div>
|
||||
<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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