<ahref="engine__adaptive_8h.html">Go to the documentation of this file.</a><divclass="fragment"><divclass="line"><aid="l00001"name="l00001"></a><spanclass="lineno"> 1</span><spanclass="preprocessor">#pragma once</span></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="engine__adaptive_8cpp_source.html#l00175">engine_adaptive.cpp:175</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="engine__adaptive_8cpp_source.html#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="ttdef"><b>Definition</b><ahref="#l00234">engine_adaptive.h:234</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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#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="ttdef"><b>Definition</b><ahref="#l00237">engine_adaptive.h:237</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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#l00196">engine_adaptive.cpp:196</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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#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="engine__adaptive_8cpp_source.html#l00260">engine_adaptive.cpp:260</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_adaptive_engine_view_html_aee095b30a9dce5fcb5ae2fa1d2aa192c"><divclass="ttname"><ahref="classgridfire_1_1_adaptive_engine_view.html#aee095b30a9dce5fcb5ae2fa1d2aa192c">gridfire::AdaptiveEngineView::getBaseEngine</a></div><divclass="ttdeci">const DynamicEngine & getBaseEngine() const override</div><divclass="ttdoc">Gets the base engine.</div><divclass="ttdef"><b>Definition</b><ahref="#l00226">engine_adaptive.h:226</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_1_engine_view_html"><divclass="ttname"><ahref="classgridfire_1_1_engine_view.html">gridfire::EngineView</a></div><divclass="ttdoc">Abstract base class for a "view" of a reaction network engine.</div><divclass="ttdef"><b>Definition</b><ahref="engine__view__abstract_8h_source.html#l00074">engine_view_abstract.h:74</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1reaction_1_1_logical_reaction_html"><divclass="ttname"><ahref="classgridfire_1_1reaction_1_1_logical_reaction.html">gridfire::reaction::LogicalReaction</a></div><divclass="ttdoc">Represents a "logical" reaction that aggregates rates from multiple sources.</div><divclass="ttdef"><b>Definition</b><ahref="reaction_8h_source.html#l00308">reaction.h:308</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="aengine__abstract_8h_html"><divclass="ttname"><ahref="engine__abstract_8h.html">engine_abstract.h</a></div><divclass="ttdoc">Abstract interfaces for reaction network engines in GridFire.</div></div>
<divclass="ttc"id="aengine__view__abstract_8h_html"><divclass="ttname"><ahref="engine__view__abstract_8h.html">engine_view_abstract.h</a></div><divclass="ttdoc">Abstract interfaces for engine "views" in GridFire.</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="astructgridfire_1_1_adaptive_engine_view_1_1_reaction_flow_html"><divclass="ttname"><ahref="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html">gridfire::AdaptiveEngineView::ReactionFlow</a></div><divclass="ttdoc">A struct to hold a reaction and its flow rate.</div><divclass="ttdef"><b>Definition</b><ahref="#l00251">engine_adaptive.h:251</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>
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