docs(docs): rebuilt docs with loads more detail for triggers and weak reactions
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@@ -105,58 +105,57 @@ $(function(){initNavTree('classgridfire_1_1_multiscale_partitioning_engine_view.
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<p>This is the complete list of members for <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#af13e764c118a6cc51847384e9c70e05b">analyzeTimescalePoolConnectivity</a>(const std::vector< std::vector< size_t > > &timescale_pools, const std::vector< double > &Y, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#aae0865e361dfeb23984d70409fdd9f39">buildConnectivityGraph</a>(const std::unordered_set< size_t > &fast_reaction_indices) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#ae3875c61dc916c0982ed122c2e272d94">buildConnectivityGraph</a>(const std::vector< size_t > &species_pool) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a79eb9c108d694a27ec913ed0143aa044">calculateMolarReactionFlow</a>(const reaction::Reaction &reaction, const std::vector< double > &Y_full, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a716d7357e944e8394d8b8e0b5e7625eb">calculateRHSAndEnergy</a>(const std::vector< double > &Y_full, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#ac206840057bac65b7f7738e6dfd1047a">constructCandidateGroups</a>(const std::vector< std::vector< size_t > > &candidate_pools, const std::vector< double > &Y, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a4bc879246c6fbd8633b05052858df51d">equilibrateNetwork</a>(const std::vector< double > &Y, double T9, double rho)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a05e45017bbb772c586f483bd527004ee">analyzeTimescalePoolConnectivity</a>(const std::vector< std::vector< fourdst::atomic::Species > > &timescale_pools, const fourdst::composition::Composition &comp, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a5d1c11f3c0883385833462dd088f6f89">buildConnectivityGraph</a>(const std::vector< fourdst::atomic::Species > &species_pool) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a99f9116d5a18afcbf0e808ef111d1be8">calculateEpsDerivatives</a>(const fourdst::composition::Composition &comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a87687a960f263a4e1bc035e4d0a345db">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_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a5c1ab19bc3394a5d29241ef02073c4cb">calculateRHSAndEnergy</a>(const fourdst::composition::Composition &comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#aaabaae8e33ca8a05a2aa1f374e792795">constructCandidateGroups</a>(const std::vector< std::vector< fourdst::atomic::Species > > &candidate_pools, const fourdst::composition::Composition &comp, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a2f0c45d4e2b2f9de5d961088f3ab0a9a">equilibrateNetwork</a>(const fourdst::composition::Composition &comp, double T9, double rho)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b17f94386882ea1524147782b7a1ddc">equilibrateNetwork</a>(const NetIn &netIn)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#acff59a15abac30eee16e9fa7b355fb18">exportToDot</a>(const std::string &filename, const std::vector< double > &Y, const double T9, const double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#acdf5ad8765290ea2b78170235aea391d">generateJacobianMatrix</a>(const std::vector< double > &Y_full, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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#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_multiscale_partitioning_engine_view.html#adfa1e133c49c0ef78b374d37e90a3372">exportToDot</a>(const std::string &filename, const fourdst::composition::Composition &Y, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ab9f71bc9a1c0f98ec9cc1c7da00fd975">generateJacobianMatrix</a>(const fourdst::composition::Composition &comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#abe76a46784b1ebc8ad67a9eec40d369a">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a22bd1f0e821ed415611d75bac67063d1">getBaseEngine</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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#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_multiscale_partitioning_engine_view.html#a1e04e8cb8c84b1bd033ac599accf0888">getDynamicSpecies</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c82e4e082d1c82b1b090ac9847c7c5e">getFastSpecies</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ac961484383e86d9712a424728e068633">getJacobianMatrixEntry</a>(int i_full, int j_full) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#ad751f2c1306895ee74a61f2071ca96eb">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a586da5402750151fee5db2666785b6e4">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_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a253e51d6dc7226a863a123683049af61">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a696f74f5135bbd62169b6577f92fee80">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a7bfb4e6fec2f337a1dea69e3d4f1fc82">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#aa38c367ef3c74d012ccd10521cd5a727">getSpeciesDestructionTimescales</a>(const std::vector< double > &Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a91d32b7197fcb27ee697d5bfde960f3f">getSpeciesIndex</a>(const fourdst::atomic::Species &species) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a560612347bbd5b7b380e990624d01105">getSpeciesTimescales</a>(const std::vector< double > &Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a510b920dea726aef859ac1f6d051807e">getStoichiometryMatrixEntry</a>(int speciesIndex, int reactionIndex) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a54ca8004fbd8d6d3ea6f67efeb5dbc8d">identifyMeanSlowestPool</a>(const std::vector< std::vector< size_t > > &pools, const std::vector< double > &Y, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a1a14b0c7ec882b2ad2370f7aa729b9f9">getSpeciesDestructionTimescales</a>(const fourdst::composition::Composition &comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a8db21995e6878f4043f3a5a45bf36d5e">getSpeciesIndex</a>(const fourdst::atomic::Species &species) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#aea2c3d2ae6ddf77bd4a9b07b86f3306b">getSpeciesTimescales</a>(const fourdst::composition::Composition &comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a7140384baaaa0bd05ca448a0d8fec471">getStoichiometryMatrixEntry</a>(const fourdst::atomic::Species &species, const reaction::Reaction &reaction) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a70f4a0c4123b7f78305f64eb11beeeeb">identifyMeanSlowestPool</a>(const std::vector< std::vector< fourdst::atomic::Species > > &pools, const fourdst::composition::Composition &comp, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#ae7847959fc5af2b83f5446dd73567b46">isStale</a>(const NetIn &netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a445d7447f2cf18f755fc8b8b288e68cb">m_activeReactionIndices</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a57d97b11e80fa78ab5f509fce1f156b8">m_activeSpeciesIndices</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a4656c05b8235dbf4ec698b03a716a8c8">m_algebraic_species</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a53862719dd73f98bc69eecde090cf655">m_algebraic_species_indices</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a3af2b37ce21829d9554d702cad074470">m_algebraic_abundances</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a4656c05b8235dbf4ec698b03a716a8c8">m_algebraic_species</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93">m_baseEngine</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a">m_cacheStats</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#aec6126b5c4a397d090790d7b75f9f70f">m_dynamic_species</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a38b4f0373c3bd81503889650c0bb69bb">m_dynamic_species_indices</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e">m_qse_abundance_cache</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
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||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b4aa04a1e641204e4fd82361b0e39c6">m_qse_groups</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#aada497e8df74a295fdf5df7d7cdf64e0">mapNetInToMolarAbundanceVector</a>(const NetIn &netIn) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a0df457c0f0f6f403a295335c84fd828f">MultiscalePartitioningEngineView</a>(GraphEngine &baseEngine)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ad4d29ee55f89384807616d1068797067">partitionByTimescale</a>(const std::vector< double > &Y_full, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a7d26945df5395b9317552a3989c42d1c">partitionNetwork</a>(const std::vector< double > &Y, double T9, double rho)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a98b11ffe498846f5a3a72f08504346b7">partitionNetwork</a>(const NetIn &netIn)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a05730ced13ac5331060ca011f0da6235">primeEngine</a>(const NetIn &netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a34b5fdb2078e748edfbe6846ecadd681">QSEPartition</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_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_multiscale_partitioning_engine_view.html#acb5fa7f03cd89b8c1b6b9ffdf3abb12e">setNetworkReactions</a>(const reaction::LogicalReactionSet &reactions) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a1a0c0a0ade632eb10f0eecab828a059f">setScreeningModel</a>(screening::ScreeningType model) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a3c5fcb8e3396d74359fd601554c9ffa9">solveQSEAbundances</a>(const std::vector< double > &Y_full, double T9, double rho)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a6bee75b5a6e508e6eebf83f0d48c50b8">update</a>(const NetIn &netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#aa55ed182301d216264daae3e6dfd8917">validateGroupsWithFluxAnalysis</a>(const std::vector< QSEGroup > &candidate_groups, const std::vector< double > &Y, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_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="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>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e">m_qse_abundance_cache</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b4aa04a1e641204e4fd82361b0e39c6">m_qse_groups</a></td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#aada497e8df74a295fdf5df7d7cdf64e0">mapNetInToMolarAbundanceVector</a>(const NetIn &netIn) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a0df457c0f0f6f403a295335c84fd828f">MultiscalePartitioningEngineView</a>(GraphEngine &baseEngine)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a7aa4eb7a0d6e6d04b3e1aa1b1fb7f3f6">partitionByTimescale</a>(const fourdst::composition::Composition &comp, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a3c327a40d7c667043826002975baa2b4">partitionNetwork</a>(const fourdst::composition::Composition &comp, double T9, double rho)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
|
||||
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a98b11ffe498846f5a3a72f08504346b7">partitionNetwork</a>(const NetIn &netIn)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></td><td class="entry"></td></tr>
|
||||
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a05730ced13ac5331060ca011f0da6235">primeEngine</a>(const NetIn &netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a34b5fdb2078e748edfbe6846ecadd681">QSEPartition</a> typedef</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_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="even"><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#af99f5e4871808188d00379c1c35868fe">setNetworkReactions</a>(const reaction::ReactionSet &reactions) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a1a0c0a0ade632eb10f0eecab828a059f">setScreeningModel</a>(screening::ScreeningType model) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a40ce2c18063cd56cffd58419b9ae96bf">solveQSEAbundances</a>(const fourdst::composition::Composition &comp, double T9, double rho)</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#a6bee75b5a6e508e6eebf83f0d48c50b8">update</a>(const NetIn &netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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_multiscale_partitioning_engine_view.html#ad94c6fa2281d9104471631c6b90f411e">validateGroupsWithFluxAnalysis</a>(const std::vector< QSEGroup > &candidate_groups, const fourdst::composition::Composition &comp, double T9, double rho) const</td><td class="entry"><a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</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>
|
||||
</table></div><!-- contents -->
|
||||
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Reference in New Issue
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