docs(docs): rebuilt docs with loads more detail for triggers and weak reactions
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@@ -106,53 +106,54 @@ $(function(){initNavTree('classgridfire_1_1_adaptive_engine_view.html',''); init
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<p>This is the complete list of members for <a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a>, including all inherited members.</p>
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<table class="directory">
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ad599363cdd457e72e2e2937b0222c455">AdaptiveEngineView</a>(DynamicEngine &baseEngine)</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#abdbaf4b87629efe43ac1255dad424c0c">calculateAllReactionFlows</a>(const NetIn &netIn, std::vector< double > &out_Y_Full) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a048d4b1d41ecb4125a558d1b9ed7cb31">calculateMolarReactionFlow</a>(const reaction::Reaction &reaction, const std::vector< double > &Y_culled, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#af703ad17ea65ffff4b75bf8ccc00e5d5">calculateRHSAndEnergy</a>(const std::vector< double > &Y_culled, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#afec39b2faa34ea65c5488dd8e11ba3c3">Config</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a89614f4a48f60c4170a0197f45303e7c">constructReactionIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a896d29325b4233e83d9298850b617a2d">constructSpeciesIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a42417e96fe9fd623458af109401daf08">cullReactionsByFlow</a>(const std::vector< ReactionFlow > &allFlows, const std::unordered_set< fourdst::atomic::Species > &reachableSpecies, const std::vector< double > &Y_full, double maxFlow) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aa79fb382c98461b02a2c30668491e6c5">finalizeActiveSet</a>(const std::vector< const reaction::LogicalReaction * > &finalReactions)</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a0ed21f7e7c1034fc87b40d4116c4221b">findReachableSpecies</a>(const NetIn &netIn) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a03fc187d3d306b9058103b9522cbbaeb">generateJacobianMatrix</a>(const std::vector< double > &Y_dynamic, const double T9, const double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7">gridfire::DynamicEngine::generateJacobianMatrix</a>(const std::vector< double > &Y_dynamic, double T9, double rho, const SparsityPattern &sparsityPattern) const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a231193a61ba5a31e8eb92b0d4ce69111">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aee095b30a9dce5fcb5ae2fa1d2aa192c">getBaseEngine</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4710d218c8a0fd161e994ecd60b48e58">getJacobianMatrixEntry</a>(const int i_culled, const int j_culled) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a12cc2f352678fba9688363ba1876ab9c">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac83a8efe25c0e5b9bf7756ac3a500bb1">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a0ab1199f900a58f309c3c36532c9164f">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a522e78bce9ff062939572248d57f8cea">getSpeciesDestructionTimescales</a>(const std::vector< double > &Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a9055feb245524a5a9549ace935f059ff">getSpeciesIndex</a>(const fourdst::atomic::Species &species) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4e856d6d4d2fc220952bbb7e6b2f85d9">getSpeciesTimescales</a>(const std::vector< double > &Y_culled, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a67b4ea8cad115394bb4a42cc39d696f9">getStoichiometryMatrixEntry</a>(const int speciesIndex_culled, const int reactionIndex_culled) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ad268c9942655e5c9605148fe07718e88">isStale</a>(const NetIn &netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a5eaf7c3a4e28cd3a4f34979b88a80103">LogManager</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a19fc7e02e216b797aa643fa35e429800">m_activeReactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#af4bc9fc6e4afcd6a53c49ca6e2a95940">m_activeSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4d38b46be9f25c7afe7ddd2b284253f8">m_baseEngine</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a14171a9ccc45a63996a967c72983de30">m_config</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a63580db57e0f48f508906a11ccfd465e">m_isStale</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a21c6e33bbf8c18fd5b5eaabb469054de">m_reactionIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a5f66204a0ff5b27eed243afddecb0093">m_speciesIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a68695f056b660e91285b7e5a931612e1">mapCulledToFull</a>(const std::vector< double > &culled) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a91e742642d8a8d9ec0620779927e5101">mapCulledToFullReactionIndex</a>(size_t culledReactionIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a256d14a333f9401039b826cc889761a8">mapCulledToFullSpeciesIndex</a>(size_t culledSpeciesIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a3d9d8e862d1c2f0a8ba460c57f6a7f44">mapFullToCulled</a>(const std::vector< double > &full) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7d0237956bf3ec7230bc51d88e7f8019">mapNetInToMolarAbundanceVector</a>(const NetIn &netIn) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a70005361262bc180d4417b608661e3c3">primeEngine</a>(const NetIn &netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">rebuild</a>(const fourdst::composition::Composition &comp, BuildDepthType depth)</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a823c665ba89452aa2b3d5422fa5d313f">rescueEdgeSpeciesDestructionChannel</a>(const std::vector< double > &Y_full, const double T9, const double rho, const std::vector< fourdst::atomic::Species > &activeSpecies, const reaction::LogicalReactionSet &activeReactions) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4ff60b5214ec0bdaf683feb6615573a5">RescueSet</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7b3a6b3ab0a52f0f84d2b142e74ea672">setNetworkReactions</a>(const reaction::LogicalReactionSet &reactions) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aae4ddbef1c4e2202fd236221a4bf376b">setScreeningModel</a>(screening::ScreeningType model) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a2a7ecf985a326b4bea43e00cf9ee43dd">update</a>(const NetIn &netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aedc0dedb51c81e03f253cc409a5d5c40">validateState</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView< DynamicEngine ></a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ab5397d217039f096acededd4d2779780">calculateAllReactionFlows</a>(const NetIn &netIn) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a5d1b50afd2fba6af75e976a4f9c9dcbc">calculateEpsDerivatives</a>(const fourdst::composition::Composition &comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a3c1e27b45051c4ba481a2b87513982ed">calculateMolarReactionFlow</a>(const reaction::Reaction &reaction, const fourdst::composition::Composition &comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac5545d546166de94514871d7ad7b8669">calculateRHSAndEnergy</a>(const fourdst::composition::Composition &comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#afec39b2faa34ea65c5488dd8e11ba3c3">Config</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a89614f4a48f60c4170a0197f45303e7c">constructReactionIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a896d29325b4233e83d9298850b617a2d">constructSpeciesIndexMap</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a95fbfb7f2bdbf80195f1ea0aff8d62fb">cullReactionsByFlow</a>(const std::vector< ReactionFlow > &allFlows, const std::unordered_set< fourdst::atomic::Species > &reachableSpecies, const fourdst::composition::Composition &comp, double maxFlow) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7b8b3a786b973e4383e721358e61b7ed">finalizeActiveSet</a>(const std::vector< const reaction::Reaction * > &finalReactions)</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a0ed21f7e7c1034fc87b40d4116c4221b">findReachableSpecies</a>(const NetIn &netIn) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a8da7664cf483cba7f979f855a74c3559">generateJacobianMatrix</a>(const fourdst::composition::Composition &comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a11d602a708af4629f51873b17f7b8dbd">gridfire::DynamicEngine::generateJacobianMatrix</a>(const fourdst::composition::Composition &comp, double T9, double rho, const SparsityPattern &sparsityPattern) const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a231193a61ba5a31e8eb92b0d4ce69111">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aee095b30a9dce5fcb5ae2fa1d2aa192c">getBaseEngine</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#adf3b8a5734983509ca02b7a1a480119f">getJacobianMatrixEntry</a>(const fourdst::atomic::Species &rowSpecies, const fourdst::atomic::Species &colSpecies) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a3247c1e6a76de5622223ee7b5ca3452a">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac83a8efe25c0e5b9bf7756ac3a500bb1">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a0ab1199f900a58f309c3c36532c9164f">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aa861db5f6fc4e85fb51f524e4e1367c6">getSpeciesDestructionTimescales</a>(const fourdst::composition::Composition &comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#abb811382522c31f6456787edd4f59ace">getSpeciesIndex</a>(const fourdst::atomic::Species &species) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a57a218c5a145f589531777c8615b7408">getSpeciesTimescales</a>(const fourdst::composition::Composition &comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#abe2ca6426e10cc6a10090eecf7098dbe">getStoichiometryMatrixEntry</a>(const fourdst::atomic::Species &species, const reaction::Reaction &reaction) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ad268c9942655e5c9605148fe07718e88">isStale</a>(const NetIn &netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a5eaf7c3a4e28cd3a4f34979b88a80103">LogManager</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ab5ab06941bf6d97007d0a76658bf2aa6">m_activeReactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#af4bc9fc6e4afcd6a53c49ca6e2a95940">m_activeSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4d38b46be9f25c7afe7ddd2b284253f8">m_baseEngine</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a14171a9ccc45a63996a967c72983de30">m_config</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a63580db57e0f48f508906a11ccfd465e">m_isStale</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac5bdbe46f87d38d9f23ece5743dcd193">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a21c6e33bbf8c18fd5b5eaabb469054de">m_reactionIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a5f66204a0ff5b27eed243afddecb0093">m_speciesIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a68695f056b660e91285b7e5a931612e1">mapCulledToFull</a>(const std::vector< double > &culled) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a91e742642d8a8d9ec0620779927e5101">mapCulledToFullReactionIndex</a>(size_t culledReactionIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a256d14a333f9401039b826cc889761a8">mapCulledToFullSpeciesIndex</a>(size_t culledSpeciesIndex) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a3d9d8e862d1c2f0a8ba460c57f6a7f44">mapFullToCulled</a>(const std::vector< double > &full) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7d0237956bf3ec7230bc51d88e7f8019">mapNetInToMolarAbundanceVector</a>(const NetIn &netIn) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a70005361262bc180d4417b608661e3c3">primeEngine</a>(const NetIn &netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">rebuild</a>(const fourdst::composition::Composition &comp, BuildDepthType depth)</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a0439f464865b4c01bad0f6be6055c3fc">rescueEdgeSpeciesDestructionChannel</a>(const fourdst::composition::Composition &comp, double T9, double rho, const std::vector< fourdst::atomic::Species > &activeSpecies, const reaction::ReactionSet &activeReactions) const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac674338ddcbae4c33dd84b0441631806">RescueSet</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#adedc8547568d643473bdfcc86040b488">setNetworkReactions</a>(const reaction::ReactionSet &reactions) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aae4ddbef1c4e2202fd236221a4bf376b">setScreeningModel</a>(screening::ScreeningType model) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a2a7ecf985a326b4bea43e00cf9ee43dd">update</a>(const NetIn &netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aedc0dedb51c81e03f253cc409a5d5c40">validateState</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView< DynamicEngine ></a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
|
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Reference in New Issue
Block a user