<ahref="engine__adaptive_8cpp.html">Go to the documentation of this file.</a><divclass="fragment"><divclass="line"><aid="l00001"name="l00001"></a><spanclass="lineno"> 1</span><spanclass="preprocessor">#include "<aclass="code"href="engine__adaptive_8h.html">../../../include/gridfire/engine/views/engine_adaptive.h</a>"</span></div>
<divclass="line"><aid="l00025"name="l00025"></a><spanclass="lineno"> 25</span> LOG_TRACE_L1(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"Constructing species index map for adaptive engine view..."</span>);</div>
<divclass="line"><aid="l00039"name="l00039"></a><spanclass="lineno"> 39</span><spanclass="keyword">auto</span> it = fullSpeciesReverseMap.find(active_species);</div>
<divclass="line"><aid="l00043"name="l00043"></a><spanclass="lineno"> 43</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"Species '{}' not found in full species map."</span>, active_species.name());</div>
<divclass="line"><aid="l00045"name="l00045"></a><spanclass="lineno"> 45</span><spanclass="keywordflow">throw</span> std::runtime_error(<spanclass="stringliteral">"Species not found in full species map: "</span> + std::string(active_species.name()));</div>
<divclass="line"><aid="l00056"name="l00056"></a><spanclass="lineno"> 56</span><spanclass="comment">// --- Step 1: Create a reverse map using the reaction's unique ID as the key. ---</span></div>
<divclass="line"><aid="l00065"name="l00065"></a><spanclass="lineno"> 65</span><spanclass="comment">// --- Step 2: Build the final index map using the active reaction set. ---</span></div>
<divclass="line"><aid="l00070"name="l00070"></a><spanclass="lineno"> 70</span><spanclass="keyword">auto</span> it = fullReactionReverseMap.find(active_reaction_ptr.id());</div>
<divclass="line"><aid="l00075"name="l00075"></a><spanclass="lineno"> 75</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"Active reaction '{}' not found in base engine during reaction index map construction."</span>, active_reaction_ptr.id());</div>
<divclass="line"><aid="l00077"name="l00077"></a><spanclass="lineno"> 77</span><spanclass="keywordflow">throw</span> std::runtime_error(<spanclass="stringliteral">"Mismatch between active reactions and base engine."</span>);</div>
<divclass="line"><aid="l00086"name="l00086"></a><spanclass="lineno"> 86</span> LOG_TRACE_L1(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"Updating AdaptiveEngineView with new network input..."</span>);</div>
<divclass="line"><aid="l00113"name="l00113"></a><spanclass="lineno"> 113</span> LOG_INFO(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"AdaptiveEngineView updated successfully with {} active species and {} active reactions."</span>, <aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#af4bc9fc6e4afcd6a53c49ca6e2a95940">m_activeSpecies</a>.size(), <aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#a19fc7e02e216b797aa643fa35e429800">m_activeReactions</a>.size());</div>
<divclass="line"><aid="l00183"name="l00183"></a><spanclass="lineno"> 183</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"Reaction '{}' is not part of the active reactions in the adaptive engine view."</span>, <aclass="code hl_namespace"href="namespacegridfire_1_1reaction.html">reaction</a>.id());</div>
<divclass="line"><aid="l00185"name="l00185"></a><spanclass="lineno"> 185</span><spanclass="keywordflow">throw</span> std::runtime_error(<spanclass="stringliteral">"Reaction not found in active reactions: "</span> + std::string(<aclass="code hl_namespace"href="namespacegridfire_1_1reaction.html">reaction</a>.id()));</div>
<divclass="line"><aid="l00244"name="l00244"></a><spanclass="lineno"> 244</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"Culled index {} is out of bounds for species index map of size {}."</span>, culledSpeciesIndex, <aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#a5f66204a0ff5b27eed243afddecb0093">m_speciesIndexMap</a>.size());</div>
<divclass="line"><aid="l00246"name="l00246"></a><spanclass="lineno"> 246</span><spanclass="keywordflow">throw</span> std::out_of_range(<spanclass="stringliteral">"Culled index "</span> + std::to_string(culledSpeciesIndex) + <spanclass="stringliteral">" is out of bounds for species index map of size "</span> + std::to_string(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#a5f66204a0ff5b27eed243afddecb0093">m_speciesIndexMap</a>.size()) + <spanclass="stringliteral">"."</span>);</div>
<divclass="line"><aid="l00253"name="l00253"></a><spanclass="lineno"> 253</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"Culled index {} is out of bounds for reaction index map of size {}."</span>, culledReactionIndex, <aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#a21c6e33bbf8c18fd5b5eaabb469054de">m_reactionIndexMap</a>.size());</div>
<divclass="line"><aid="l00255"name="l00255"></a><spanclass="lineno"> 255</span><spanclass="keywordflow">throw</span> std::out_of_range(<spanclass="stringliteral">"Culled index "</span> + std::to_string(culledReactionIndex) + <spanclass="stringliteral">" is out of bounds for reaction index map of size "</span> + std::to_string(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#a21c6e33bbf8c18fd5b5eaabb469054de">m_reactionIndexMap</a>.size()) + <spanclass="stringliteral">"."</span>);</div>
<divclass="line"><aid="l00262"name="l00262"></a><spanclass="lineno"> 262</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"AdaptiveEngineView is stale. Please call update() before calculating RHS and energy."</span>);</div>
<divclass="line"><aid="l00264"name="l00264"></a><spanclass="lineno"> 264</span><spanclass="keywordflow">throw</span> std::runtime_error(<spanclass="stringliteral">"AdaptiveEngineView is stale. Please call update() before calculating RHS and energy."</span>);</div>
<divclass="line"><aid="l00280"name="l00280"></a><spanclass="lineno"> 280</span> LOG_TRACE_L2(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"Species '{}' not found in composition. Setting abundance to 0.0."</span>, species.name());</div>
<divclass="line"><aid="l00285"name="l00285"></a><spanclass="lineno"> 285</span><spanclass="keyword">const</span><spanclass="keywordtype">double</span> T9 = netIn.<aclass="code hl_variable"href="structgridfire_1_1_net_in.html#a5be0f5195a5cd1dd177b9fc5ab83a7be">temperature</a> / 1e9; <spanclass="comment">// Convert temperature from Kelvin to T9 (T9 = T / 1e9)</span></div>
<divclass="line"><aid="l00286"name="l00286"></a><spanclass="lineno"> 286</span><spanclass="keyword">const</span><spanclass="keywordtype">double</span> rho = netIn.<aclass="code hl_variable"href="structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577">density</a>; <spanclass="comment">// Density in g/cm^3</span></div>
<divclass="line"><aid="l00305"name="l00305"></a><spanclass="lineno"> 305</span><spanclass="keyword">constexpr</span><spanclass="keywordtype">double</span> ABUNDANCE_FLOOR = 1e-12; <spanclass="comment">// Abundance floor for a species to be considered part of the initial fuel</span></div>
<divclass="line"><aid="l00311"name="l00311"></a><spanclass="lineno"> 311</span> LOG_TRACE_L2(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"Network Connectivity Analysis: Species '{}' is part of the initial fuel."</span>, species.name());</div>
<divclass="line"><aid="l00348"name="l00348"></a><spanclass="lineno"> 348</span> LOG_TRACE_L1(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"Culling reactions based on flow rates..."</span>);</div>
<divclass="line"><aid="l00365"name="l00365"></a><spanclass="lineno"> 365</span> LOG_TRACE_L2(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"Maintaining reaction '{}' with zero flow due to reachable reactant '{}'."</span>, reactionPtr->id(), reactant.name());</div>
<divclass="line"><aid="l00378"name="l00378"></a><spanclass="lineno"> 378</span> LOG_TRACE_L1(<aclass="code hl_variable"href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a>, <spanclass="stringliteral">"Culling reaction '{}' due to low flow rate or lack of connectivity."</span>, reactionPtr->id());</div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a048d4b1d41ecb4125a558d1b9ed7cb31"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a048d4b1d41ecb4125a558d1b9ed7cb31">gridfire::AdaptiveEngineView::calculateMolarReactionFlow</a></div><divclass="ttdeci">double calculateMolarReactionFlow(const reaction::Reaction &reaction, const std::vector< double >&Y_culled, double T9, double rho) const override</div><divclass="ttdoc">Calculates the molar reaction flow for a given reaction in the active network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00175">engine_adaptive.cpp:175</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a0ab1199f900a58f309c3c36532c9164f"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a0ab1199f900a58f309c3c36532c9164f">gridfire::AdaptiveEngineView::getScreeningModel</a></div><divclass="ttdeci">screening::ScreeningType getScreeningModel() const override</div><divclass="ttdoc">Gets the screening model from the base engine.</div><divclass="ttdef"><b>Definition</b><ahref="#l00220">engine_adaptive.cpp:220</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a0ed21f7e7c1034fc87b40d4116c4221b"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a0ed21f7e7c1034fc87b40d4116c4221b">gridfire::AdaptiveEngineView::findReachableSpecies</a></div><divclass="ttdeci">std::unordered_set< fourdst::atomic::Species > findReachableSpecies(const NetIn &netIn) const</div><divclass="ttdoc">Finds all species that are reachable from the initial fuel through the reaction network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00299">engine_adaptive.cpp:299</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a12cc2f352678fba9688363ba1876ab9c"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a12cc2f352678fba9688363ba1876ab9c">gridfire::AdaptiveEngineView::getNetworkReactions</a></div><divclass="ttdeci">const reaction::LogicalReactionSet & getNetworkReactions() const override</div><divclass="ttdoc">Gets the set of active logical reactions in the network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00192">engine_adaptive.cpp:192</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a14171a9ccc45a63996a967c72983de30"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a14171a9ccc45a63996a967c72983de30">gridfire::AdaptiveEngineView::m_config</a></div><divclass="ttdeci">Config & m_config</div><divclass="ttdoc">A reference to the singleton Config instance, used for retrieving configuration parameters.</div><divclass="ttdef"><b>Definition</b><ahref="engine__adaptive_8h_source.html#l00263">engine_adaptive.h:263</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a19fc7e02e216b797aa643fa35e429800"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a19fc7e02e216b797aa643fa35e429800">gridfire::AdaptiveEngineView::m_activeReactions</a></div><divclass="ttdeci">reaction::LogicalReactionSet m_activeReactions</div><divclass="ttdoc">The set of reactions that are currently active in the network.</div><divclass="ttdef"><b>Definition</b><ahref="engine__adaptive_8h_source.html#l00273">engine_adaptive.h:273</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a21c6e33bbf8c18fd5b5eaabb469054de"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a21c6e33bbf8c18fd5b5eaabb469054de">gridfire::AdaptiveEngineView::m_reactionIndexMap</a></div><divclass="ttdeci">std::vector< size_t > m_reactionIndexMap</div><divclass="ttdoc">A map from the indices of the active reactions to the indices of the corresponding reactions in the f...</div><divclass="ttdef"><b>Definition</b><ahref="engine__adaptive_8h_source.html#l00278">engine_adaptive.h:278</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a231193a61ba5a31e8eb92b0d4ce69111"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a231193a61ba5a31e8eb92b0d4ce69111">gridfire::AdaptiveEngineView::generateStoichiometryMatrix</a></div><divclass="ttdeci">void generateStoichiometryMatrix() override</div><divclass="ttdoc">Generates the stoichiometry matrix for the active reactions and species.</div><divclass="ttdef"><b>Definition</b><ahref="#l00160">engine_adaptive.cpp:160</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a256d14a333f9401039b826cc889761a8"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a256d14a333f9401039b826cc889761a8">gridfire::AdaptiveEngineView::mapCulledToFullSpeciesIndex</a></div><divclass="ttdeci">size_t mapCulledToFullSpeciesIndex(size_t culledSpeciesIndex) const</div><divclass="ttdoc">Maps a culled species index to a full species index.</div><divclass="ttdef"><b>Definition</b><ahref="#l00242">engine_adaptive.cpp:242</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a3d9d8e862d1c2f0a8ba460c57f6a7f44"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a3d9d8e862d1c2f0a8ba460c57f6a7f44">gridfire::AdaptiveEngineView::mapFullToCulled</a></div><divclass="ttdeci">std::vector< double > mapFullToCulled(const std::vector< double >&full) const</div><divclass="ttdoc">Maps a vector of full abundances to a vector of culled abundances.</div><divclass="ttdef"><b>Definition</b><ahref="#l00233">engine_adaptive.cpp:233</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a4710d218c8a0fd161e994ecd60b48e58"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a4710d218c8a0fd161e994ecd60b48e58">gridfire::AdaptiveEngineView::getJacobianMatrixEntry</a></div><divclass="ttdeci">double getJacobianMatrixEntry(const int i_culled, const int j_culled) const override</div><divclass="ttdoc">Gets an entry from the Jacobian matrix for the active species.</div><divclass="ttdef"><b>Definition</b><ahref="#l00149">engine_adaptive.cpp:149</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a4d38b46be9f25c7afe7ddd2b284253f8"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a4d38b46be9f25c7afe7ddd2b284253f8">gridfire::AdaptiveEngineView::m_baseEngine</a></div><divclass="ttdeci">DynamicEngine & m_baseEngine</div><divclass="ttdoc">The underlying engine to which this view delegates calculations.</div><divclass="ttdef"><b>Definition</b><ahref="engine__adaptive_8h_source.html#l00268">engine_adaptive.h:268</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a5f66204a0ff5b27eed243afddecb0093"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a5f66204a0ff5b27eed243afddecb0093">gridfire::AdaptiveEngineView::m_speciesIndexMap</a></div><divclass="ttdeci">std::vector< size_t > m_speciesIndexMap</div><divclass="ttdoc">A map from the indices of the active species to the indices of the corresponding species in the full ...</div><divclass="ttdef"><b>Definition</b><ahref="engine__adaptive_8h_source.html#l00276">engine_adaptive.h:276</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a63580db57e0f48f508906a11ccfd465e"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a63580db57e0f48f508906a11ccfd465e">gridfire::AdaptiveEngineView::m_isStale</a></div><divclass="ttdeci">bool m_isStale</div><divclass="ttdoc">A flag indicating whether the view is stale and needs to be updated.</div><divclass="ttdef"><b>Definition</b><ahref="engine__adaptive_8h_source.html#l00281">engine_adaptive.h:281</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a67b4ea8cad115394bb4a42cc39d696f9"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a67b4ea8cad115394bb4a42cc39d696f9">gridfire::AdaptiveEngineView::getStoichiometryMatrixEntry</a></div><divclass="ttdeci">int getStoichiometryMatrixEntry(const int speciesIndex_culled, const int reactionIndex_culled) const override</div><divclass="ttdoc">Gets an entry from the stoichiometry matrix for the active species and reactions.</div><divclass="ttdef"><b>Definition</b><ahref="#l00165">engine_adaptive.cpp:165</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a68695f056b660e91285b7e5a931612e1"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a68695f056b660e91285b7e5a931612e1">gridfire::AdaptiveEngineView::mapCulledToFull</a></div><divclass="ttdeci">std::vector< double > mapCulledToFull(const std::vector< double >&culled) const</div><divclass="ttdoc">Maps a vector of culled abundances to a vector of full abundances.</div><divclass="ttdef"><b>Definition</b><ahref="#l00224">engine_adaptive.cpp:224</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a7b276b7210be588263395bdb0497fc6d"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a7b276b7210be588263395bdb0497fc6d">gridfire::AdaptiveEngineView::calculateRHSAndEnergy</a></div><divclass="ttdeci">StepDerivatives< double > calculateRHSAndEnergy(const std::vector< double >&Y_culled, const double T9, const double rho) const override</div><divclass="ttdoc">Calculates the right-hand side (dY/dt) and energy generation for the active species.</div><divclass="ttdef"><b>Definition</b><ahref="#l00120">engine_adaptive.cpp:120</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a7d61e73f5158f1574cda3edc90c51f7e"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a7d61e73f5158f1574cda3edc90c51f7e">gridfire::AdaptiveEngineView::update</a></div><divclass="ttdeci">void update(const NetIn &netIn) override</div><divclass="ttdoc">Updates the active species and reactions based on the current conditions.</div><divclass="ttdef"><b>Definition</b><ahref="#l00085">engine_adaptive.cpp:85</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a89614f4a48f60c4170a0197f45303e7c"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a89614f4a48f60c4170a0197f45303e7c">gridfire::AdaptiveEngineView::constructReactionIndexMap</a></div><divclass="ttdeci">std::vector< size_t > constructReactionIndexMap() const</div><divclass="ttdoc">Constructs the reaction index map.</div><divclass="ttdef"><b>Definition</b><ahref="#l00053">engine_adaptive.cpp:53</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a896d29325b4233e83d9298850b617a2d"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a896d29325b4233e83d9298850b617a2d">gridfire::AdaptiveEngineView::constructSpeciesIndexMap</a></div><divclass="ttdeci">std::vector< size_t > constructSpeciesIndexMap() const</div><divclass="ttdoc">Constructs the species index map.</div><divclass="ttdef"><b>Definition</b><ahref="#l00024">engine_adaptive.cpp:24</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a91e742642d8a8d9ec0620779927e5101"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a91e742642d8a8d9ec0620779927e5101">gridfire::AdaptiveEngineView::mapCulledToFullReactionIndex</a></div><divclass="ttdeci">size_t mapCulledToFullReactionIndex(size_t culledReactionIndex) const</div><divclass="ttdoc">Maps a culled reaction index to a full reaction index.</div><divclass="ttdef"><b>Definition</b><ahref="#l00251">engine_adaptive.cpp:251</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_a93b38d0fdc4647f6f7340172dae17872"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#a93b38d0fdc4647f6f7340172dae17872">gridfire::AdaptiveEngineView::getSpeciesTimescales</a></div><divclass="ttdeci">std::unordered_map< fourdst::atomic::Species, double > getSpeciesTimescales(const std::vector< double >&Y_culled, double T9, double rho) const override</div><divclass="ttdoc">Computes timescales for all active species in the network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00196">engine_adaptive.cpp:196</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_aa79fb382c98461b02a2c30668491e6c5"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#aa79fb382c98461b02a2c30668491e6c5">gridfire::AdaptiveEngineView::finalizeActiveSet</a></div><divclass="ttdeci">void finalizeActiveSet(const std::vector< const reaction::LogicalReaction * >&finalReactions)</div><divclass="ttdoc">Finalizes the set of active species and reactions.</div><divclass="ttdef"><b>Definition</b><ahref="#l00385">engine_adaptive.cpp:385</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_aae4ddbef1c4e2202fd236221a4bf376b"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#aae4ddbef1c4e2202fd236221a4bf376b">gridfire::AdaptiveEngineView::setScreeningModel</a></div><divclass="ttdeci">void setScreeningModel(screening::ScreeningType model) override</div><divclass="ttdoc">Sets the screening model for the base engine.</div><divclass="ttdef"><b>Definition</b><ahref="#l00216">engine_adaptive.cpp:216</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_abdbaf4b87629efe43ac1255dad424c0c"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#abdbaf4b87629efe43ac1255dad424c0c">gridfire::AdaptiveEngineView::calculateAllReactionFlows</a></div><divclass="ttdeci">std::vector< ReactionFlow > calculateAllReactionFlows(const NetIn &netIn, std::vector< double >&out_Y_Full) const</div><divclass="ttdoc">Calculates the molar reaction flow rate for all reactions in the full network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00268">engine_adaptive.cpp:268</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_ac5bdbe46f87d38d9f23ece5743dcd193"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">gridfire::AdaptiveEngineView::m_logger</a></div><divclass="ttdeci">quill::Logger * m_logger</div><divclass="ttdoc">A pointer to the logger instance, used for logging messages.</div><divclass="ttdef"><b>Definition</b><ahref="engine__adaptive_8h_source.html#l00265">engine_adaptive.h:265</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_ac83a8efe25c0e5b9bf7756ac3a500bb1"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#ac83a8efe25c0e5b9bf7756ac3a500bb1">gridfire::AdaptiveEngineView::getNetworkSpecies</a></div><divclass="ttdeci">const std::vector< fourdst::atomic::Species >& getNetworkSpecies() const override</div><divclass="ttdoc">Gets the list of active species in the network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00116">engine_adaptive.cpp:116</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_ac9aab6f60e80a9228b2b19b1b10449ef"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#ac9aab6f60e80a9228b2b19b1b10449ef">gridfire::AdaptiveEngineView::generateJacobianMatrix</a></div><divclass="ttdeci">void generateJacobianMatrix(const std::vector< double >&Y_culled, const double T9, const double rho) override</div><divclass="ttdoc">Generates the Jacobian matrix for the active species.</div><divclass="ttdef"><b>Definition</b><ahref="#l00138">engine_adaptive.cpp:138</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_ad599363cdd457e72e2e2937b0222c455"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#ad599363cdd457e72e2e2937b0222c455">gridfire::AdaptiveEngineView::AdaptiveEngineView</a></div><divclass="ttdeci">AdaptiveEngineView(DynamicEngine &baseEngine)</div><divclass="ttdoc">Constructs an AdaptiveEngineView.</div><divclass="ttdef"><b>Definition</b><ahref="#l00013">engine_adaptive.cpp:13</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_aedc0dedb51c81e03f253cc409a5d5c40"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#aedc0dedb51c81e03f253cc409a5d5c40">gridfire::AdaptiveEngineView::validateState</a></div><divclass="ttdeci">void validateState() const</div><divclass="ttdoc">Validates that the AdaptiveEngineView is not stale.</div><divclass="ttdef"><b>Definition</b><ahref="#l00260">engine_adaptive.cpp:260</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_af4bc9fc6e4afcd6a53c49ca6e2a95940"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#af4bc9fc6e4afcd6a53c49ca6e2a95940">gridfire::AdaptiveEngineView::m_activeSpecies</a></div><divclass="ttdeci">std::vector< fourdst::atomic::Species > m_activeSpecies</div><divclass="ttdoc">The set of species that are currently active in the network.</div><divclass="ttdef"><b>Definition</b><ahref="engine__adaptive_8h_source.html#l00271">engine_adaptive.h:271</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_dynamic_engine_html"><divclass="ttname"><ahref="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><divclass="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><divclass="ttdef"><b>Definition</b><ahref="engine__abstract_8h_source.html#l00121">engine_abstract.h:121</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1reaction_1_1_reaction_html"><divclass="ttname"><ahref="classgridfire_1_1reaction_1_1_reaction.html">gridfire::reaction::Reaction</a></div><divclass="ttdoc">Represents a single nuclear reaction from a specific data source.</div><divclass="ttdef"><b>Definition</b><ahref="reaction_8h_source.html#l00072">reaction.h:72</a></div></div>
<divclass="ttc"id="anamespacegridfire_1_1reaction_html_aa86f08712565f278adacc7cd2361eb31"><divclass="ttname"><ahref="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a></div><divclass="ttdeci">TemplatedReactionSet< LogicalReaction > LogicalReactionSet</div><divclass="ttdoc">A set of logical reactions.</div><divclass="ttdef"><b>Definition</b><ahref="reaction_8h_source.html#l00557">reaction.h:557</a></div></div>
<divclass="ttc"id="anamespacegridfire_1_1screening_html_aa82aafbc4f8c28d0a75b60798e3a7d25"><divclass="ttname"><ahref="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">gridfire::screening::ScreeningType</a></div><divclass="ttdeci">ScreeningType</div><divclass="ttdoc">Enumerates the available plasma screening models.</div><divclass="ttdef"><b>Definition</b><ahref="screening__types_8h_source.html#l00015">screening_types.h:15</a></div></div>
<divclass="ttc"id="astructgridfire_1_1_net_in_html_a06f0dff9f8927b7cf2da3004c8fa1577"><divclass="ttname"><ahref="structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577">gridfire::NetIn::density</a></div><divclass="ttdeci">double density</div><divclass="ttdoc">Density in g/cm^3.</div><divclass="ttdef"><b>Definition</b><ahref="network_8h_source.html#l00058">network.h:58</a></div></div>
<divclass="ttc"id="astructgridfire_1_1_net_in_html_a13058f4929e72c1187abbebcddb8aed1"><divclass="ttname"><ahref="structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1">gridfire::NetIn::composition</a></div><divclass="ttdeci">fourdst::composition::Composition composition</div><divclass="ttdoc">Composition of the network.</div><divclass="ttdef"><b>Definition</b><ahref="network_8h_source.html#l00054">network.h:54</a></div></div>
<divclass="ttc"id="astructgridfire_1_1_net_in_html_a5be0f5195a5cd1dd177b9fc5ab83a7be"><divclass="ttname"><ahref="structgridfire_1_1_net_in.html#a5be0f5195a5cd1dd177b9fc5ab83a7be">gridfire::NetIn::temperature</a></div><divclass="ttdeci">double temperature</div><divclass="ttdoc">Temperature in Kelvin.</div><divclass="ttdef"><b>Definition</b><ahref="network_8h_source.html#l00057">network.h:57</a></div></div>
<divclass="ttc"id="astructgridfire_1_1_step_derivatives_html"><divclass="ttname"><ahref="structgridfire_1_1_step_derivatives.html">gridfire::StepDerivatives</a></div><divclass="ttdoc">Structure holding derivatives and energy generation for a network step.</div><divclass="ttdef"><b>Definition</b><ahref="engine__abstract_8h_source.html#l00053">engine_abstract.h:53</a></div></div>
<divclass="ttc"id="astructgridfire_1_1_step_derivatives_html_ab4aeb41be952c7b5844e1ee81fef9008"><divclass="ttname"><ahref="structgridfire_1_1_step_derivatives.html#ab4aeb41be952c7b5844e1ee81fef9008">gridfire::StepDerivatives::nuclearEnergyGenerationRate</a></div><divclass="ttdeci">T nuclearEnergyGenerationRate</div><divclass="ttdoc">Specific energy generation rate (e.g., erg/g/s).</div><divclass="ttdef"><b>Definition</b><ahref="engine__abstract_8h_source.html#l00055">engine_abstract.h:55</a></div></div>
<divclass="ttc"id="astructgridfire_1_1_step_derivatives_html_ae0de268b86c2404379409c4feae0b34d"><divclass="ttname"><ahref="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d">gridfire::StepDerivatives::dydt</a></div><divclass="ttdeci">std::vector< T > dydt</div><divclass="ttdoc">Derivatives of abundances (dY/dt for each species).</div><divclass="ttdef"><b>Definition</b><ahref="engine__abstract_8h_source.html#l00054">engine_abstract.h:54</a></div></div>
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