<ahref="engine__graph_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__graph_8h.html">gridfire/engine/engine_graph.h</a>"</span></div>
<divclass="line"><aid="l00054"name="l00054"></a><spanclass="lineno"> 54</span><spanclass="comment">// --- The public facing interface can always use the precomputed version since taping is done internally ---</span></div>
<divclass="line"><aid="l00088"name="l00088"></a><spanclass="lineno"> 88</span><spanclass="keyword">auto</span> it = fourdst::atomic::species.find(std::string(name));</div>
<divclass="line"><aid="l00093"name="l00093"></a><spanclass="lineno"> 93</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Species '{}' not found in global atomic species database."</span>, name);</div>
<divclass="line"><aid="l00095"name="l00095"></a><spanclass="lineno"> 95</span><spanclass="keywordflow">throw</span> std::runtime_error(<spanclass="stringliteral">"Species not found in global atomic species database: "</span> + std::string(name));</div>
<divclass="line"><aid="l00107"name="l00107"></a><spanclass="lineno"> 107</span> LOG_TRACE_L1(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Populated {} reactions in the reaction ID map."</span>, <aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">m_reactionIDMap</a>.size());</div>
<divclass="line"><aid="l00118"name="l00118"></a><spanclass="lineno"> 118</span><spanclass="comment">// The implementation of this function (and others) constrains this nuclear network to a constant temperature and density during</span></div>
<divclass="line"><aid="l00119"name="l00119"></a><spanclass="lineno"> 119</span><spanclass="comment">// each evaluation.</span></div>
<divclass="line"><aid="l00129"name="l00129"></a><spanclass="lineno"> 129</span><spanclass="comment">// Returns a constant reference to the vector of unique species in the network.</span></div>
<divclass="line"><aid="l00130"name="l00130"></a><spanclass="lineno"> 130</span> LOG_TRACE_L3(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Providing access to network species vector. Size: {}."</span>, <aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size());</div>
<divclass="line"><aid="l00135"name="l00135"></a><spanclass="lineno"> 135</span><spanclass="comment">// Returns a constant reference to the set of reactions in the network.</span></div>
<divclass="line"><aid="l00141"name="l00141"></a><spanclass="lineno"> 141</span><spanclass="comment">// Checks if a given species is present in the network's species map for efficient lookup.</span></div>
<divclass="line"><aid="l00142"name="l00142"></a><spanclass="lineno"> 142</span><spanclass="keyword">const</span><spanclass="keywordtype">bool</span> found = <aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.contains(species.name());</div>
<divclass="line"><aid="l00143"name="l00143"></a><spanclass="lineno"> 143</span> LOG_DEBUG(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Checking if species '{}' is involved in the network: {}."</span>, species.name(), found ? <spanclass="stringliteral">"Yes"</span> : <spanclass="stringliteral">"No"</span>);</div>
<divclass="line"><aid="l00149"name="l00149"></a><spanclass="lineno"> 149</span> LOG_TRACE_L1(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Validating mass (A) and charge (Z) conservation across all reactions in the network."</span>);</div>
<divclass="line"><aid="l00157"name="l00157"></a><spanclass="lineno"> 157</span><spanclass="comment">// Calculate total A and Z for reactants</span></div>
<divclass="line"><aid="l00164"name="l00164"></a><spanclass="lineno"> 164</span><spanclass="comment">// This scenario indicates a severe data integrity issue:</span></div>
<divclass="line"><aid="l00165"name="l00165"></a><spanclass="lineno"> 165</span><spanclass="comment">// a reactant is part of a reaction but not in the network's species map.</span></div>
<divclass="line"><aid="l00166"name="l00166"></a><spanclass="lineno"> 166</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"CRITICAL ERROR: Reactant species '{}' in reaction '{}' not found in network species map during conservation validation."</span>,</div>
<divclass="line"><aid="l00172"name="l00172"></a><spanclass="lineno"> 172</span><spanclass="comment">// Calculate total A and Z for products</span></div>
<divclass="line"><aid="l00179"name="l00179"></a><spanclass="lineno"> 179</span><spanclass="comment">// Similar critical error for product species</span></div>
<divclass="line"><aid="l00180"name="l00180"></a><spanclass="lineno"> 180</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"CRITICAL ERROR: Product species '{}' in reaction '{}' not found in network species map during conservation validation."</span>,</div>
<divclass="line"><aid="l00188"name="l00188"></a><spanclass="lineno"> 188</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Mass number (A) not conserved for reaction '{}': Reactants A={} vs Products A={}."</span>,</div>
<divclass="line"><aid="l00193"name="l00193"></a><spanclass="lineno"> 193</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Atomic number (Z) not conserved for reaction '{}': Reactants Z={} vs Products Z={}."</span>,</div>
<divclass="line"><aid="l00199"name="l00199"></a><spanclass="lineno"> 199</span> LOG_TRACE_L1(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Mass (A) and charge (Z) conservation validated successfully for all reactions."</span>);</div>
<divclass="line"><aid="l00200"name="l00200"></a><spanclass="lineno"> 200</span><spanclass="keywordflow">return</span><spanclass="keyword">true</span>; <spanclass="comment">// All reactions passed the conservation check</span></div>
<divclass="line"><aid="l00204"name="l00204"></a><spanclass="lineno"> 204</span><spanclass="comment">// Check if the requested network has already been cached.</span></div>
<divclass="line"><aid="l00205"name="l00205"></a><spanclass="lineno"> 205</span><spanclass="comment">// PERF: Rebuilding this should be pretty fast but it may be a good point of optimization in the future.</span></div>
<divclass="line"><aid="l00207"name="l00207"></a><spanclass="lineno"> 207</span><spanclass="comment">// TODO: need some more robust method here to</span></div>
<divclass="line"><aid="l00208"name="l00208"></a><spanclass="lineno"> 208</span><spanclass="comment">// A. Build the basic network from the composition's species with non zero mass fractions.</span></div>
<divclass="line"><aid="l00209"name="l00209"></a><spanclass="lineno"> 209</span><spanclass="comment">// B. rebuild a new composition from the reaction set's reactants + products (with the mass fractions from the things that are only products set to 0)</span></div>
<divclass="line"><aid="l00210"name="l00210"></a><spanclass="lineno"> 210</span><spanclass="comment">// C. Rebuild the reaction set from the new composition</span></div>
<divclass="line"><aid="l00211"name="l00211"></a><spanclass="lineno"> 211</span><spanclass="comment">// D. Cull reactions where all reactants have mass fractions below the culling threshold.</span></div>
<divclass="line"><aid="l00212"name="l00212"></a><spanclass="lineno"> 212</span><spanclass="comment">// E. Be careful about maintaining caching through all of this</span></div>
<divclass="line"><aid="l00215"name="l00215"></a><spanclass="lineno"> 215</span><spanclass="comment">// This allows for dynamic network modification while retaining caching for networks which are very similar.</span></div>
<divclass="line"><aid="l00217"name="l00217"></a><spanclass="lineno"> 217</span> LOG_DEBUG(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Reaction set not cached. Rebuilding the reaction set for T9={} and culling={}."</span>, T9, culling);</div>
<divclass="line"><aid="l00219"name="l00219"></a><spanclass="lineno"> 219</span><aclass="code hl_function"href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">syncInternalMaps</a>(); <spanclass="comment">// Re-sync internal maps after updating reactions. Note this will also retrace the AD tape.</span></div>
<divclass="line"><aid="l00247"name="l00247"></a><spanclass="lineno"> 247</span><spanclass="keyword">const</span><spanclass="keywordtype">int</span> power = precomp.reactant_powers[i];</div>
<divclass="line"><aid="l00258"name="l00258"></a><spanclass="lineno"> 258</span><spanclass="keywordflow">continue</span>; <spanclass="comment">// Skip this reaction if any reactant is below the abundance threshold</span></div>
<divclass="line"><aid="l00286"name="l00286"></a><spanclass="lineno"> 286</span><spanclass="comment">// Update the derivative for this species</span></div>
<divclass="line"><aid="l00291"name="l00291"></a><spanclass="lineno"> 291</span><spanclass="comment">// --- Calculate the nuclear energy generation rate ---</span></div>
<divclass="line"><aid="l00306"name="l00306"></a><spanclass="lineno"> 306</span><spanclass="comment">// Task 1: Set dimensions and initialize the matrix</span></div>
<divclass="line"><aid="l00314"name="l00314"></a><spanclass="lineno"> 314</span><spanclass="comment">// Task 2: Populate the stoichiometry matrix</span></div>
<divclass="line"><aid="l00315"name="l00315"></a><spanclass="lineno"> 315</span><spanclass="comment">// Iterate through all reactions, assign them a column index, and fill in their stoichiometric coefficients.</span></div>
<divclass="line"><aid="l00318"name="l00318"></a><spanclass="lineno"> 318</span><spanclass="comment">// Get the net stoichiometry for the current reaction</span></div>
<divclass="line"><aid="l00321"name="l00321"></a><spanclass="lineno"> 321</span><spanclass="comment">// Iterate through the species and their coefficients in the stoichiometry map</span></div>
<divclass="line"><aid="l00323"name="l00323"></a><spanclass="lineno"> 323</span><spanclass="comment">// Find the row index for this species</span></div>
<divclass="line"><aid="l00324"name="l00324"></a><spanclass="lineno"> 324</span><spanclass="keyword">auto</span> it = <aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a>.find(species);</div>
<divclass="line"><aid="l00327"name="l00327"></a><spanclass="lineno"> 327</span><spanclass="comment">// Set the matrix element. Boost.uBLAS handles sparse insertion.</span></div>
<divclass="line"><aid="l00330"name="l00330"></a><spanclass="lineno"> 330</span><spanclass="comment">// This scenario should ideally not happen if m_networkSpeciesMap and m_speciesToIndexMap are correctly synced</span></div>
<divclass="line"><aid="l00331"name="l00331"></a><spanclass="lineno"> 331</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"CRITICAL ERROR: Species '{}' from reaction '{}' stoichiometry not found in species to index map."</span>,</div>
<divclass="line"><aid="l00334"name="l00334"></a><spanclass="lineno"> 334</span><spanclass="keywordflow">throw</span> std::runtime_error(<spanclass="stringliteral">"Species not found in species to index map: "</span> + std::string(species.name()));</div>
<divclass="line"><aid="l00337"name="l00337"></a><spanclass="lineno"> 337</span> reactionColumnIndex++; <spanclass="comment">// Move to the next column for the next reaction</span></div>
<divclass="line"><aid="l00340"name="l00340"></a><spanclass="lineno"> 340</span> LOG_TRACE_L1(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Stoichiometry matrix population complete. Number of non-zero elements: {}."</span>,</div>
<divclass="line"><aid="l00341"name="l00341"></a><spanclass="lineno"> 341</span><aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a>.nnz()); <spanclass="comment">// Assuming nnz() exists for compressed_matrix</span></div>
<divclass="line"><aid="l00395"name="l00395"></a><spanclass="lineno"> 395</span><spanclass="comment">// 1. Pack the input variables into a vector for CppAD</span></div>
<divclass="line"><aid="l00396"name="l00396"></a><spanclass="lineno"> 396</span> std::vector<double> adInput(numSpecies + 2, 0.0); <spanclass="comment">// +2 for T9 and rho</span></div>
<divclass="line"><aid="l00397"name="l00397"></a><spanclass="lineno"> 397</span><spanclass="keywordflow">for</span> (<spanclass="keywordtype">size_t</span> i = 0; i < numSpecies; ++i) {</div>
<divclass="line"><aid="l00441"name="l00441"></a><spanclass="lineno"> 441</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Failed to open file for writing: {}"</span>, filename);</div>
<divclass="line"><aid="l00443"name="l00443"></a><spanclass="lineno"> 443</span><spanclass="keywordflow">throw</span> std::runtime_error(<spanclass="stringliteral">"Failed to open file for writing: "</span> + filename);</div>
<divclass="line"><aid="l00458"name="l00458"></a><spanclass="lineno"> 458</span><spanclass="comment">// 2. Define all reactions as intermediate nodes and connect them</span></div>
<divclass="line"><aid="l00461"name="l00461"></a><spanclass="lineno"> 461</span><spanclass="comment">// Create a unique ID for the reaction node</span></div>
<divclass="line"><aid="l00464"name="l00464"></a><spanclass="lineno"> 464</span><spanclass="comment">// Define the reaction node (small, black dot)</span></div>
<divclass="line"><aid="l00467"name="l00467"></a><spanclass="lineno"> 467</span><spanclass="comment">// Draw edges from reactants to the reaction node</span></div>
<divclass="line"><aid="l00472"name="l00472"></a><spanclass="lineno"> 472</span><spanclass="comment">// Draw edges from the reaction node to products</span></div>
<divclass="line"><aid="l00489"name="l00489"></a><spanclass="lineno"> 489</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Failed to open file for writing: {}"</span>, filename);</div>
<divclass="line"><aid="l00491"name="l00491"></a><spanclass="lineno"> 491</span><spanclass="keywordflow">throw</span> std::runtime_error(<spanclass="stringliteral">"Failed to open file for writing: "</span> + filename);</div>
<divclass="line"><aid="l00495"name="l00495"></a><spanclass="lineno"> 495</span><spanclass="comment">// Dynamic cast to REACLIBReaction to access specific properties</span></div>
<divclass="line"><aid="l00555"name="l00555"></a><spanclass="lineno"> 555</span><spanclass="comment">// No-op for GraphEngine, as it does not support manually triggering updates.</span></div>
<divclass="line"><aid="l00559"name="l00559"></a><spanclass="lineno"> 559</span> LOG_TRACE_L1(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Recording AD tape for the RHS calculation..."</span>);</div>
<divclass="line"><aid="l00561"name="l00561"></a><spanclass="lineno"> 561</span><spanclass="comment">// Task 1: Set dimensions and initialize the matrix</span></div>
<divclass="line"><aid="l00564"name="l00564"></a><spanclass="lineno"> 564</span> LOG_ERROR(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"Cannot record AD tape: No species in the network."</span>);</div>
<divclass="line"><aid="l00566"name="l00566"></a><spanclass="lineno"> 566</span><spanclass="keywordflow">throw</span> std::runtime_error(<spanclass="stringliteral">"Cannot record AD tape: No species in the network."</span>);</div>
<divclass="line"><aid="l00568"name="l00568"></a><spanclass="lineno"> 568</span><spanclass="keyword">const</span><spanclass="keywordtype">size_t</span> numADInputs = numSpecies + 2; <spanclass="comment">// Note here that by not letting T9 and rho be independent variables, we are constraining the network to a constant temperature and density during each evaluation.</span></div>
<divclass="line"><aid="l00572"name="l00572"></a><spanclass="lineno"> 572</span><spanclass="comment">// We also initialize the dummy variable for tape recording (these tell CppAD what the derivative chain looks like).</span></div>
<divclass="line"><aid="l00573"name="l00573"></a><spanclass="lineno"> 573</span><spanclass="comment">// Their numeric values are irrelevant except for in so far as they avoid numerical instabilities.</span></div>
<divclass="line"><aid="l00575"name="l00575"></a><spanclass="lineno"> 575</span><spanclass="comment">// Distribute total mass fraction uniformly between species in the dummy variable space</span></div>
<divclass="line"><aid="l00582"name="l00582"></a><spanclass="lineno"> 582</span><spanclass="comment">// This also beings the tape recording process.</span></div>
<divclass="line"><aid="l00586"name="l00586"></a><spanclass="lineno"> 586</span><spanclass="keywordflow">for</span>(<spanclass="keywordtype">size_t</span> i = 0; i < numSpecies; ++i) {</div>
<divclass="line"><aid="l00593"name="l00593"></a><spanclass="lineno"> 593</span><spanclass="comment">// 5. Call the actual templated function</span></div>
<divclass="line"><aid="l00594"name="l00594"></a><spanclass="lineno"> 594</span><spanclass="comment">// We let T9 and rho be constant, so we pass them as fixed values.</span></div>
<divclass="line"><aid="l00599"name="l00599"></a><spanclass="lineno"> 599</span> LOG_TRACE_L1(<aclass="code hl_variable"href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <spanclass="stringliteral">"AD tape recorded successfully for the RHS calculation. Number of independent variables: {}."</span>,</div>
<divclass="line"><aid="l00606"name="l00606"></a><spanclass="lineno"> 606</span><spanclass="comment">// --- Reverse map for fast species lookups ---</span></div>
<divclass="line"><aid="l00620"name="l00620"></a><spanclass="lineno"> 620</span><spanclass="comment">// --- Precompute reactant information ---</span></div>
<divclass="line"><aid="l00621"name="l00621"></a><spanclass="lineno"> 621</span><spanclass="comment">// Count occurrences for each reactant to determine powers and symmetry</span></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a0ed390f3e598ebba4e245ac90bb78767"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767">gridfire::GraphEngine::getNetworkSpecies</a></div><divclass="ttdeci">const std::vector< fourdst::atomic::Species >& getNetworkSpecies() const override</div><divclass="ttdoc">Gets the list of species in the network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00128">engine_graph.cpp:128</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a191cff35402d3c97c82c5c966a39d0de"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de">gridfire::GraphEngine::m_usePrecomputation</a></div><divclass="ttdeci">bool m_usePrecomputation</div><divclass="ttdoc">Flag to enable or disable using precomputed reactions for efficiency. Mathematically,...</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00347">engine_graph.h:347</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a26215593544c3a52597194602e4e25dd"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a26215593544c3a52597194602e4e25dd">gridfire::GraphEngine::getSpeciesTimescales</a></div><divclass="ttdeci">std::unordered_map< fourdst::atomic::Species, double > getSpeciesTimescales(const std::vector< double >&Y, double T9, double rho) const override</div><divclass="ttdoc">Computes timescales for all species in the network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00538">engine_graph.cpp:538</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a26602e1b3c610780a47b5a6511d6d567"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567">gridfire::GraphEngine::populateReactionIDMap</a></div><divclass="ttdeci">void populateReactionIDMap()</div><divclass="ttdoc">Populates the reaction ID map.</div><divclass="ttdef"><b>Definition</b><ahref="#l00101">engine_graph.cpp:101</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a2e22b111f6d00ecc9e3804a71f1ce876"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">gridfire::GraphEngine::m_rhsADFun</a></div><divclass="ttdeci">CppAD::ADFun< double > m_rhsADFun</div><divclass="ttdoc">CppAD function for the right-hand side of the ODE.</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00342">engine_graph.h:342</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a2f1718c89d4aaad028102724d18fa910"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">gridfire::GraphEngine::m_jacobianMatrix</a></div><divclass="ttdeci">boost::numeric::ublas::compressed_matrix< double > m_jacobianMatrix</div><divclass="ttdoc">Jacobian matrix (species x species).</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00340">engine_graph.h:340</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a303e6093591cde91430f866a04a8be7c"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c">gridfire::GraphEngine::getJacobianMatrixEntry</a></div><divclass="ttdeci">double getJacobianMatrixEntry(const int i, const int j) const override</div><divclass="ttdoc">Gets an entry from the previously generated Jacobian matrix.</div><divclass="ttdef"><b>Definition</b><ahref="#l00419">engine_graph.cpp:419</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a30e09ed0bce6aa5fc89beaa316a7b827"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">gridfire::GraphEngine::m_networkSpeciesMap</a></div><divclass="ttdeci">std::unordered_map< std::string_view, fourdst::atomic::Species > m_networkSpeciesMap</div><divclass="ttdoc">Map from species name to Species object.</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00336">engine_graph.h:336</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a47202c43342b96480070874bffce1391"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391">gridfire::GraphEngine::populateSpeciesToIndexMap</a></div><divclass="ttdeci">void populateSpeciesToIndexMap()</div><divclass="ttdoc">Populates the species-to-index map.</div><divclass="ttdef"><b>Definition</b><ahref="#l00110">engine_graph.cpp:110</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a51b4cedf9b00de79fb6eef243631b04d"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a51b4cedf9b00de79fb6eef243631b04d">gridfire::GraphEngine::update</a></div><divclass="ttdeci">void update(const NetIn &netIn) override</div><divclass="ttdoc">Update the internal state of the engine.</div><divclass="ttdef"><b>Definition</b><ahref="#l00554">engine_graph.cpp:554</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a52edc3e88f1e8fc497e1e63972d63c80"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a52edc3e88f1e8fc497e1e63972d63c80">gridfire::GraphEngine::m_screeningType</a></div><divclass="ttdeci">screening::ScreeningType m_screeningType</div><divclass="ttdoc">Screening type for the reaction network. Default to no screening.</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00344">engine_graph.h:344</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a5a5458ed01923124f2d7e1f04f32f138"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a5a5458ed01923124f2d7e1f04f32f138">gridfire::GraphEngine::reserveJacobianMatrix</a></div><divclass="ttdeci">void reserveJacobianMatrix()</div><divclass="ttdoc">Reserves space for the Jacobian matrix.</div><divclass="ttdef"><b>Definition</b><ahref="#l00117">engine_graph.cpp:117</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a5d431d5385b1219ba29689eb29601ea3"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">gridfire::GraphEngine::m_precomputedReactions</a></div><divclass="ttdeci">std::vector< PrecomputedReaction > m_precomputedReactions</div><divclass="ttdoc">Precomputed reactions for efficiency.</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00349">engine_graph.h:349</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a5d6cc63b99b467c2a976d1fbaaa1dfa3"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">gridfire::GraphEngine::m_reactionIDMap</a></div><divclass="ttdeci">std::unordered_map< std::string_view, reaction::Reaction * > m_reactionIDMap</div><divclass="ttdoc">Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a ...</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00333">engine_graph.h:333</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a697f2004e0d02c59e83c7890742d7c9a"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a">gridfire::GraphEngine::getScreeningModel</a></div><divclass="ttdeci">screening::ScreeningType getScreeningModel() const override</div><divclass="ttdoc">Get the current electron screening model.</div><divclass="ttdef"><b>Definition</b><ahref="#l00365">engine_graph.cpp:365</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a6b5feaf788bade212b7c8df7ac8c8152"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152">gridfire::GraphEngine::getStoichiometryMatrixEntry</a></div><divclass="ttdeci">int getStoichiometryMatrixEntry(const int speciesIndex, const int reactionIndex) const override</div><divclass="ttdoc">Gets an entry from the stoichiometry matrix.</div><divclass="ttdef"><b>Definition</b><ahref="#l00429">engine_graph.cpp:429</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a8110e687844f921438bb517e1d8ce62f"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f">gridfire::GraphEngine::setScreeningModel</a></div><divclass="ttdeci">void setScreeningModel(screening::ScreeningType) override</div><divclass="ttdoc">Set the electron screening model.</div><divclass="ttdef"><b>Definition</b><ahref="#l00360">engine_graph.cpp:360</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a832e2fe066381811a3e0464806ff5e95"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95">gridfire::GraphEngine::exportToCSV</a></div><divclass="ttdeci">void exportToCSV(const std::string &filename) const</div><divclass="ttdoc">Exports the network to a CSV file for analysis.</div><divclass="ttdef"><b>Definition</b><ahref="#l00484">engine_graph.cpp:484</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a8b3baf29829c7ae0a61430ea70632bbf"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a8b3baf29829c7ae0a61430ea70632bbf">gridfire::GraphEngine::calculateRHSAndEnergy</a></div><divclass="ttdeci">StepDerivatives< double > calculateRHSAndEnergy(const std::vector< double >&Y, const double T9, const double rho) const override</div><divclass="ttdoc">Calculates the right-hand side (dY/dt) and energy generation rate.</div><divclass="ttdef"><b>Definition</b><ahref="#l00042">engine_graph.cpp:42</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a8c29d8bbde407e913be5eb77efb2c0c9"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9">gridfire::GraphEngine::getNetReactionStoichiometry</a></div><divclass="ttdeci">static std::unordered_map< fourdst::atomic::Species, int > getNetReactionStoichiometry(const reaction::Reaction &reaction)</div><divclass="ttdoc">Gets the net stoichiometry for a given reaction.</div><divclass="ttdef"><b>Definition</b><ahref="#l00423">engine_graph.cpp:423</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a9245642b741f215e52861d00e756fb3f"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">gridfire::GraphEngine::calculateMolarReactionFlow</a></div><divclass="ttdeci">double calculateMolarReactionFlow(const reaction::Reaction &reaction, const std::vector< double >&Y, const double T9, const double rho) const override</div><divclass="ttdoc">Calculates the molar reaction flow for a given reaction.</div><divclass="ttdef"><b>Definition</b><ahref="#l00377">engine_graph.cpp:377</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a92d26068ba139e47d335f5fe9e2814cc"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">gridfire::GraphEngine::m_networkSpecies</a></div><divclass="ttdeci">std::vector< fourdst::atomic::Species > m_networkSpecies</div><divclass="ttdoc">Vector of unique species in the network.</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00335">engine_graph.h:335</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a95563f6bc86007d9ee053a0f1e15b889"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889">gridfire::GraphEngine::recordADTape</a></div><divclass="ttdeci">void recordADTape()</div><divclass="ttdoc">Records the AD tape for the right-hand side of the ODE.</div><divclass="ttdef"><b>Definition</b><ahref="#l00558">engine_graph.cpp:558</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_a9f74786ff930ab72664b31f29d05a30c"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#a9f74786ff930ab72664b31f29d05a30c">gridfire::GraphEngine::GraphEngine</a></div><divclass="ttdeci">GraphEngine(const fourdst::composition::Composition &composition)</div><divclass="ttdoc">Constructs a GraphEngine from a composition.</div><divclass="ttdef"><b>Definition</b><ahref="#l00026">engine_graph.cpp:26</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_aa6202cee0c3c481eda77cc9a91bc126b"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b">gridfire::GraphEngine::involvesSpecies</a></div><divclass="ttdeci">bool involvesSpecies(const fourdst::atomic::Species &species) const</div><divclass="ttdoc">Checks if a given species is involved in the network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00140">engine_graph.cpp:140</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_acb7c4f5108b0efeae48ad15598e808c3"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">gridfire::GraphEngine::m_reactions</a></div><divclass="ttdeci">reaction::LogicalReactionSet m_reactions</div><divclass="ttdoc">Set of REACLIB reactions in the network.</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00332">engine_graph.h:332</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_acdce8d87e23a2cd1504bc9472e538c0f"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">gridfire::GraphEngine::syncInternalMaps</a></div><divclass="ttdeci">void syncInternalMaps()</div><divclass="ttdoc">Synchronizes the internal maps.</div><divclass="ttdef"><b>Definition</b><ahref="#l00062">engine_graph.cpp:62</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_acf4cfccea20f5cb31c9886bf233a28be"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be">gridfire::GraphEngine::validateConservation</a></div><divclass="ttdeci">bool validateConservation() const</div><divclass="ttdoc">Validates mass and charge conservation across all reactions.</div><divclass="ttdef"><b>Definition</b><ahref="#l00148">engine_graph.cpp:148</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_ad1cb5fd32efc37668e2d9ecf0c72ad24"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">gridfire::GraphEngine::m_stoichiometryMatrix</a></div><divclass="ttdeci">boost::numeric::ublas::compressed_matrix< int > m_stoichiometryMatrix</div><divclass="ttdoc">Stoichiometry matrix (species x reactions).</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00339">engine_graph.h:339</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_ad45650d10fc5dff1673ae3f806d067da"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da">gridfire::GraphEngine::getNetworkReactions</a></div><divclass="ttdeci">const reaction::LogicalReactionSet & getNetworkReactions() const override</div><divclass="ttdoc">Gets the set of logical reactions in the network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00134">engine_graph.cpp:134</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_ad8237c252145a75092202d00f5e1ddf7"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">gridfire::GraphEngine::m_speciesToIndexMap</a></div><divclass="ttdeci">std::unordered_map< fourdst::atomic::Species, size_t > m_speciesToIndexMap</div><divclass="ttdoc">Map from species to their index in the stoichiometry matrix.</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00337">engine_graph.h:337</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_adac8c7d62bae76e17fc060e86dadd929"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929">gridfire::GraphEngine::exportToDot</a></div><divclass="ttdeci">void exportToDot(const std::string &filename) const</div><divclass="ttdoc">Exports the network to a DOT file for visualization.</div><divclass="ttdef"><b>Definition</b><ahref="#l00436">engine_graph.cpp:436</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_ae347ff0316e532e0298ec8c913908105"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#ae347ff0316e532e0298ec8c913908105">gridfire::GraphEngine::generateJacobianMatrix</a></div><divclass="ttdeci">void generateJacobianMatrix(const std::vector< double >&Y, const double T9, const double rho) override</div><divclass="ttdoc">Generates the Jacobian matrix for the current state.</div><divclass="ttdef"><b>Definition</b><ahref="#l00386">engine_graph.cpp:386</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_aed726d36ee2b3796beff6067a1e4db38"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38">gridfire::GraphEngine::generateStoichiometryMatrix</a></div><divclass="ttdeci">void generateStoichiometryMatrix() override</div><divclass="ttdoc">Generates the stoichiometry matrix for the network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00303">engine_graph.cpp:303</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_aedf42d83bfcc28313b6b6454034d2efa"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa">gridfire::GraphEngine::collectNetworkSpecies</a></div><divclass="ttdeci">void collectNetworkSpecies()</div><divclass="ttdoc">Collects the unique species in the network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00072">engine_graph.cpp:72</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_aeeafeab40a5f4dbfae78bdc87e25e93f"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#aeeafeab40a5f4dbfae78bdc87e25e93f">gridfire::GraphEngine::validateComposition</a></div><divclass="ttdeci">void validateComposition(const fourdst::composition::Composition &composition, double culling, double T9)</div><divclass="ttdoc">Validates the composition against the current reaction set.</div><divclass="ttdef"><b>Definition</b><ahref="#l00203">engine_graph.cpp:203</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_graph_engine_html_af41df9ce979b6410e12642cb093916c9"><divclass="ttname"><ahref="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">gridfire::GraphEngine::calculateAllDerivatives</a></div><divclass="ttdeci">StepDerivatives< T > calculateAllDerivatives(const std::vector< T >&Y_in, T T9, T rho) const</div><divclass="ttdoc">Calculates all derivatives (dY/dt) and the energy generation rate.</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00521">engine_graph.h:521</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_a6ca8556d27ac373e176f5b23437c416e"><divclass="ttname"><ahref="namespacegridfire_1_1screening.html#a6ca8556d27ac373e176f5b23437c416e">gridfire::screening::selectScreeningModel</a></div><divclass="ttdeci">std::unique_ptr< ScreeningModel > selectScreeningModel(ScreeningType type)</div><divclass="ttdoc">A factory function to select and create a screening model.</div><divclass="ttdef"><b>Definition</b><ahref="screening__types_8cpp_source.html#l00009">screening_types.cpp:9</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="anamespacegridfire_html_a1121d0b2d005195333412559fa29d3cc"><divclass="ttname"><ahref="namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc">gridfire::ADDouble</a></div><divclass="ttdeci">CppAD::AD< double > ADDouble</div><divclass="ttdoc">Alias for CppAD AD type for double precision.</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00034">engine_graph.h:34</a></div></div>
<divclass="ttc"id="anamespacegridfire_html_a96c062f94713921e5d7568ecedcdcb06"><divclass="ttname"><ahref="namespacegridfire.html#a96c062f94713921e5d7568ecedcdcb06">gridfire::MIN_ABUNDANCE_THRESHOLD</a></div><divclass="ttdeci">static constexpr double MIN_ABUNDANCE_THRESHOLD</div><divclass="ttdoc">Minimum abundance threshold below which species are ignored.</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00056">engine_graph.h:56</a></div></div>
<divclass="ttc"id="anamespacegridfire_html_ae01b1738df1921db565bcbd68dd6cf64"><divclass="ttname"><ahref="namespacegridfire.html#ae01b1738df1921db565bcbd68dd6cf64">gridfire::MIN_JACOBIAN_THRESHOLD</a></div><divclass="ttdeci">static constexpr double MIN_JACOBIAN_THRESHOLD</div><divclass="ttdoc">Minimum value for Jacobian matrix entries.</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00064">engine_graph.h:64</a></div></div>
<divclass="ttc"id="areaction_8h_html"><divclass="ttname"><ahref="reaction_8h.html">reaction.h</a></div><divclass="ttdoc">Defines classes for representing and managing nuclear reactions.</div></div>
<divclass="ttc"id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a03d596c88289e21e7bd18711e3a1f275"><divclass="ttname"><ahref="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a03d596c88289e21e7bd18711e3a1f275">gridfire::GraphEngine::PrecomputedReaction::reactant_powers</a></div><divclass="ttdeci">std::vector< int > reactant_powers</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00314">engine_graph.h:314</a></div></div>
<divclass="ttc"id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a7a7e9167b19e339e0d69544b9c00e79c"><divclass="ttname"><ahref="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a7a7e9167b19e339e0d69544b9c00e79c">gridfire::GraphEngine::PrecomputedReaction::stoichiometric_coefficients</a></div><divclass="ttdeci">std::vector< int > stoichiometric_coefficients</div><divclass="ttdef"><b>Definition</b><ahref="engine__graph_8h_source.html#l00317">engine_graph.h:317</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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