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< a href = "#pub-methods" > Public Member Functions< / a > |
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2025-07-31 10:54:31 -04:00
< p > < code > #include < engine_defined.h> < / code > < / p >
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Inheritance diagram for gridfire::DefinedEngineView:< / div >
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< img src = "classgridfire_1_1_defined_engine_view.png" usemap = "#gridfire::DefinedEngineView_map" alt = "" / >
< map id = "gridfire::DefinedEngineView_map" name = "gridfire::DefinedEngineView_map" >
< area href = "classgridfire_1_1_dynamic_engine.html" title = "Abstract class for engines supporting Jacobian and stoichiometry operations." alt = "gridfire::DynamicEngine" shape = "rect" coords = "0,56,238,80" / >
< area href = "classgridfire_1_1_engine_view.html" alt = "gridfire::EngineView< DynamicEngine >" shape = "rect" coords = "248,56,486,80" / >
< area href = "classgridfire_1_1_engine.html" title = "Abstract base class for a reaction network engine." alt = "gridfire::Engine" shape = "rect" coords = "0,0,238,24" / >
< area href = "classgridfire_1_1_file_defined_engine_view.html" alt = "gridfire::FileDefinedEngineView" shape = "rect" coords = "0,168,238,192" / >
< area href = "classgridfire_1_1_network_priming_engine_view.html" title = "Provides a view of a DynamicEngine filtered to reactions involving a specified priming species." alt = "gridfire::NetworkPrimingEngineView" shape = "rect" coords = "248,168,486,192" / >
< / map >
< / div > < / div >
< table class = "memberdecls" >
< tr class = "heading" > < td colspan = "2" > < h2 class = "groupheader" > < a id = "pub-methods" name = "pub-methods" > < / a >
Public Member Functions< / h2 > < / td > < / tr >
< tr class = "memitem:a9b319b4a1bd5a08381ebb183daf72c92" id = "r_a9b319b4a1bd5a08381ebb183daf72c92" > < td class = "memItemLeft" align = "right" valign = "top" >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a9b319b4a1bd5a08381ebb183daf72c92" > DefinedEngineView< / a > (const std::vector< std::string > & peNames, < a class = "el" href = "classgridfire_1_1_dynamic_engine.html" > DynamicEngine< / a > & baseEngine)< / td > < / tr >
< tr class = "separator:a9b319b4a1bd5a08381ebb183daf72c92" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a69b9a5812ad8bda13f956acd0da24484" id = "r_a69b9a5812ad8bda13f956acd0da24484" > < td class = "memItemLeft" align = "right" valign = "top" > const < a class = "el" href = "classgridfire_1_1_dynamic_engine.html" > DynamicEngine< / a > &   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a69b9a5812ad8bda13f956acd0da24484" > getBaseEngine< / a > () const override< / td > < / tr >
< tr class = "memdesc:a69b9a5812ad8bda13f956acd0da24484" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Access the underlying engine instance. < br / > < / td > < / tr >
< tr class = "separator:a69b9a5812ad8bda13f956acd0da24484" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a1a55f9748c45af6f13e16a6b6ceaa211" id = "r_a1a55f9748c45af6f13e16a6b6ceaa211" > < td class = "memItemLeft" align = "right" valign = "top" > const std::vector< fourdst::atomic::Species > &   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a1a55f9748c45af6f13e16a6b6ceaa211" > getNetworkSpecies< / a > () const override< / td > < / tr >
< tr class = "memdesc:a1a55f9748c45af6f13e16a6b6ceaa211" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Gets the list of active species in the network defined by the file. < br / > < / td > < / tr >
< tr class = "separator:a1a55f9748c45af6f13e16a6b6ceaa211" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a4b0d71367cb1d4c06bcd01251bbeb60d" id = "r_a4b0d71367cb1d4c06bcd01251bbeb60d" > < td class = "memItemLeft" align = "right" valign = "top" > std::expected< < a class = "el" href = "structgridfire_1_1_step_derivatives.html" > StepDerivatives< / a > < double > , < a class = "el" href = "structgridfire_1_1expectations_1_1_stale_engine_error.html" > expectations::StaleEngineError< / a > >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a4b0d71367cb1d4c06bcd01251bbeb60d" > calculateRHSAndEnergy< / a > (const std::vector< double > & Y_defined, const double T9, const double rho) const override< / td > < / tr >
< tr class = "memdesc:a4b0d71367cb1d4c06bcd01251bbeb60d" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Calculates the right-hand side (dY/dt) and energy generation for the active species. < br / > < / td > < / tr >
< tr class = "separator:a4b0d71367cb1d4c06bcd01251bbeb60d" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:ad25c722eaee1f28f8ed7b4d33a1f69ae" id = "r_ad25c722eaee1f28f8ed7b4d33a1f69ae" > < td class = "memItemLeft" align = "right" valign = "top" > void  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#ad25c722eaee1f28f8ed7b4d33a1f69ae" > generateJacobianMatrix< / a > (const std::vector< double > & Y_dynamic, const double T9, const double rho) const override< / td > < / tr >
< tr class = "memdesc:ad25c722eaee1f28f8ed7b4d33a1f69ae" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Generates the Jacobian matrix for the active species. < br / > < / td > < / tr >
< tr class = "separator:ad25c722eaee1f28f8ed7b4d33a1f69ae" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a273b175049f5ce7b9208e931ad139e1b" id = "r_a273b175049f5ce7b9208e931ad139e1b" > < td class = "memItemLeft" align = "right" valign = "top" > double  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a273b175049f5ce7b9208e931ad139e1b" > getJacobianMatrixEntry< / a > (const int i_defined, const int j_defined) const override< / td > < / tr >
< tr class = "memdesc:a273b175049f5ce7b9208e931ad139e1b" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Gets an entry from the Jacobian matrix for the active species. < br / > < / td > < / tr >
< tr class = "separator:a273b175049f5ce7b9208e931ad139e1b" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:ad07221be49ae1b5133c5b987dafac3b6" id = "r_ad07221be49ae1b5133c5b987dafac3b6" > < td class = "memItemLeft" align = "right" valign = "top" > void  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#ad07221be49ae1b5133c5b987dafac3b6" > generateStoichiometryMatrix< / a > () override< / td > < / tr >
< tr class = "memdesc:ad07221be49ae1b5133c5b987dafac3b6" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Generates the stoichiometry matrix for the active reactions and species. < br / > < / td > < / tr >
< tr class = "separator:ad07221be49ae1b5133c5b987dafac3b6" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:afa2820971397114d788730cc33feefe2" id = "r_afa2820971397114d788730cc33feefe2" > < td class = "memItemLeft" align = "right" valign = "top" > int  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#afa2820971397114d788730cc33feefe2" > getStoichiometryMatrixEntry< / a > (const int speciesIndex_defined, const int reactionIndex_defined) const override< / td > < / tr >
< tr class = "memdesc:afa2820971397114d788730cc33feefe2" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Gets an entry from the stoichiometry matrix for the active species and reactions. < br / > < / td > < / tr >
< tr class = "separator:afa2820971397114d788730cc33feefe2" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a142725470f96cba3edb48a29f1264032" id = "r_a142725470f96cba3edb48a29f1264032" > < td class = "memItemLeft" align = "right" valign = "top" > double  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a142725470f96cba3edb48a29f1264032" > calculateMolarReactionFlow< / a > (const < a class = "el" href = "classgridfire_1_1reaction_1_1_reaction.html" > reaction::Reaction< / a > & reaction, const std::vector< double > & Y_defined, const double T9, const double rho) const override< / td > < / tr >
< tr class = "memdesc:a142725470f96cba3edb48a29f1264032" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Calculates the molar reaction flow for a given reaction in the active network. < br / > < / td > < / tr >
< tr class = "separator:a142725470f96cba3edb48a29f1264032" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:ae03b4f9afac03d4011a4d7cf0423535d" id = "r_ae03b4f9afac03d4011a4d7cf0423535d" > < td class = "memItemLeft" align = "right" valign = "top" > const < a class = "el" href = "namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" > reaction::LogicalReactionSet< / a > &   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#ae03b4f9afac03d4011a4d7cf0423535d" > getNetworkReactions< / a > () const override< / td > < / tr >
< tr class = "memdesc:ae03b4f9afac03d4011a4d7cf0423535d" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Gets the set of active logical reactions in the network. < br / > < / td > < / tr >
< tr class = "separator:ae03b4f9afac03d4011a4d7cf0423535d" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a9736edfb7c9148b60de30d50c0d3530d" id = "r_a9736edfb7c9148b60de30d50c0d3530d" > < td class = "memItemLeft" align = "right" valign = "top" > void  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a9736edfb7c9148b60de30d50c0d3530d" > setNetworkReactions< / a > (const < a class = "el" href = "namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" > reaction::LogicalReactionSet< / a > & reactions) override< / td > < / tr >
< tr class = "separator:a9736edfb7c9148b60de30d50c0d3530d" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:ac8daafabbc76f4b6811bede241a03d72" id = "r_ac8daafabbc76f4b6811bede241a03d72" > < td class = "memItemLeft" align = "right" valign = "top" > std::expected< std::unordered_map< fourdst::atomic::Species, double > , < a class = "el" href = "structgridfire_1_1expectations_1_1_stale_engine_error.html" > expectations::StaleEngineError< / a > >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#ac8daafabbc76f4b6811bede241a03d72" > getSpeciesTimescales< / a > (const std::vector< double > & Y_defined, const double T9, const double rho) const override< / td > < / tr >
< tr class = "memdesc:ac8daafabbc76f4b6811bede241a03d72" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Computes timescales for all active species in the network. < br / > < / td > < / tr >
< tr class = "separator:ac8daafabbc76f4b6811bede241a03d72" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a3d58e36ed8a6a0d82bb65e91090f7491" id = "r_a3d58e36ed8a6a0d82bb65e91090f7491" > < td class = "memItemLeft" align = "right" valign = "top" > std::expected< std::unordered_map< fourdst::atomic::Species, double > , < a class = "el" href = "structgridfire_1_1expectations_1_1_stale_engine_error.html" > expectations::StaleEngineError< / a > >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a3d58e36ed8a6a0d82bb65e91090f7491" > getSpeciesDestructionTimescales< / a > (const std::vector< double > & Y_defined, const double T9, const double rho) const override< / td > < / tr >
< tr class = "separator:a3d58e36ed8a6a0d82bb65e91090f7491" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:ae5762f395caea5381ec177507816b5ae" id = "r_ae5762f395caea5381ec177507816b5ae" > < td class = "memItemLeft" align = "right" valign = "top" > fourdst::composition::Composition  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#ae5762f395caea5381ec177507816b5ae" > update< / a > (const < a class = "el" href = "structgridfire_1_1_net_in.html" > NetIn< / a > & netIn) override< / td > < / tr >
< tr class = "memdesc:ae5762f395caea5381ec177507816b5ae" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Updates the engine view if it is marked as stale. < br / > < / td > < / tr >
< tr class = "separator:ae5762f395caea5381ec177507816b5ae" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a7d9e738dd28efb4d6127de7379169c87" id = "r_a7d9e738dd28efb4d6127de7379169c87" > < td class = "memItemLeft" align = "right" valign = "top" > bool  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a7d9e738dd28efb4d6127de7379169c87" > isStale< / a > (const < a class = "el" href = "structgridfire_1_1_net_in.html" > NetIn< / a > & netIn) override< / td > < / tr >
< tr class = "separator:a7d9e738dd28efb4d6127de7379169c87" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:abf2da57c83c3c4c635cb301f53088258" id = "r_abf2da57c83c3c4c635cb301f53088258" > < td class = "memItemLeft" align = "right" valign = "top" > void  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#abf2da57c83c3c4c635cb301f53088258" > setScreeningModel< / a > (< a class = "el" href = "namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25" > screening::ScreeningType< / a > model) override< / td > < / tr >
< tr class = "memdesc:abf2da57c83c3c4c635cb301f53088258" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Sets the screening model for the base engine. < br / > < / td > < / tr >
< tr class = "separator:abf2da57c83c3c4c635cb301f53088258" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a3c657b82a0117118a4bb0ce7f624ae0c" id = "r_a3c657b82a0117118a4bb0ce7f624ae0c" > < td class = "memItemLeft" align = "right" valign = "top" > < a class = "el" href = "namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25" > screening::ScreeningType< / a >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a3c657b82a0117118a4bb0ce7f624ae0c" > getScreeningModel< / a > () const override< / td > < / tr >
< tr class = "memdesc:a3c657b82a0117118a4bb0ce7f624ae0c" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Gets the screening model from the base engine. < br / > < / td > < / tr >
< tr class = "separator:a3c657b82a0117118a4bb0ce7f624ae0c" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:abfee22688617ffe91c69be93049c89b3" id = "r_abfee22688617ffe91c69be93049c89b3" > < td class = "memItemLeft" align = "right" valign = "top" > int  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#abfee22688617ffe91c69be93049c89b3" > getSpeciesIndex< / a > (const fourdst::atomic::Species & species) const override< / td > < / tr >
< tr class = "separator:abfee22688617ffe91c69be93049c89b3" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a72789c1c3379594b65b560da50192de2" id = "r_a72789c1c3379594b65b560da50192de2" > < td class = "memItemLeft" align = "right" valign = "top" > std::vector< double >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a72789c1c3379594b65b560da50192de2" > mapNetInToMolarAbundanceVector< / a > (const < a class = "el" href = "structgridfire_1_1_net_in.html" > NetIn< / a > & netIn) const override< / td > < / tr >
< tr class = "separator:a72789c1c3379594b65b560da50192de2" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a13033abd3b44904f98b58c93e22da460" id = "r_a13033abd3b44904f98b58c93e22da460" > < td class = "memItemLeft" align = "right" valign = "top" > < a class = "el" href = "structgridfire_1_1_priming_report.html" > PrimingReport< / a >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a13033abd3b44904f98b58c93e22da460" > primeEngine< / a > (const < a class = "el" href = "structgridfire_1_1_net_in.html" > NetIn< / a > & netIn) override< / td > < / tr >
< tr class = "separator:a13033abd3b44904f98b58c93e22da460" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "inherit_header pub_methods_classgridfire_1_1_dynamic_engine" > < td colspan = "2" onclick = "javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_dynamic_engine')" > < img src = "closed.png" alt = "-" / >   Public Member Functions inherited from < a class = "el" href = "classgridfire_1_1_dynamic_engine.html" > gridfire::DynamicEngine< / a > < / td > < / tr >
< tr class = "memitem:a818d942efa843959393e4eed3263b7e7 inherit pub_methods_classgridfire_1_1_dynamic_engine" id = "r_a818d942efa843959393e4eed3263b7e7" > < td class = "memItemLeft" align = "right" valign = "top" > virtual void  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7" > generateJacobianMatrix< / a > (const std::vector< double > & Y_dynamic, double T9, double rho, const < a class = "el" href = "namespacegridfire.html#a898dfe22579e649935645cbd6f073178" > SparsityPattern< / a > & sparsityPattern) const< / td > < / tr >
< tr class = "separator:a818d942efa843959393e4eed3263b7e7 inherit pub_methods_classgridfire_1_1_dynamic_engine" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a04317b66ef14d519264bc30ee69f5bf9 inherit pub_methods_classgridfire_1_1_dynamic_engine" id = "r_a04317b66ef14d519264bc30ee69f5bf9" > < td class = "memItemLeft" align = "right" valign = "top" > virtual < a class = "el" href = "namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6" > BuildDepthType< / a >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9" > getDepth< / a > () const< / td > < / tr >
< tr class = "separator:a04317b66ef14d519264bc30ee69f5bf9 inherit pub_methods_classgridfire_1_1_dynamic_engine" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a4e2c8b896661b7a89beffe0066cb21cf inherit pub_methods_classgridfire_1_1_dynamic_engine" id = "r_a4e2c8b896661b7a89beffe0066cb21cf" > < td class = "memItemLeft" align = "right" valign = "top" > virtual void  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf" > rebuild< / a > (const fourdst::composition::Composition & comp, < a class = "el" href = "namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6" > BuildDepthType< / a > depth)< / td > < / tr >
< tr class = "separator:a4e2c8b896661b7a89beffe0066cb21cf inherit pub_methods_classgridfire_1_1_dynamic_engine" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "inherit_header pub_methods_classgridfire_1_1_engine" > < td colspan = "2" onclick = "javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine')" > < img src = "closed.png" alt = "-" / >   Public Member Functions inherited from < a class = "el" href = "classgridfire_1_1_engine.html" > gridfire::Engine< / a > < / td > < / tr >
< tr class = "memitem:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine" id = "r_a2e7970bed2100699f226f4141d5db037" > < td class = "memItemLeft" align = "right" valign = "top" > virtual  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037" > ~Engine< / a > ()=default< / td > < / tr >
< tr class = "memdesc:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Virtual destructor. < br / > < / td > < / tr >
< tr class = "separator:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "inherit_header pub_methods_classgridfire_1_1_engine_view" > < td colspan = "2" onclick = "javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine_view')" > < img src = "closed.png" alt = "-" / >   Public Member Functions inherited from < a class = "el" href = "classgridfire_1_1_engine_view.html" > gridfire::EngineView< DynamicEngine > < / a > < / td > < / tr >
< tr class = "memitem:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view" id = "r_a994660f2d553f3a123512dc5eb421e74" > < td class = "memItemLeft" align = "right" valign = "top" > virtual  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74" > ~EngineView< / a > ()=default< / td > < / tr >
< tr class = "memdesc:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Virtual destructor. < br / > < / td > < / tr >
< tr class = "separator:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< / table > < table class = "memberdecls" >
< tr class = "heading" > < td colspan = "2" > < h2 class = "groupheader" > < a id = "pro-attribs" name = "pro-attribs" > < / a >
Protected Attributes< / h2 > < / td > < / tr >
< tr class = "memitem:a217d541f3fa777b1552f652fbb520382" id = "r_a217d541f3fa777b1552f652fbb520382" > < td class = "memItemLeft" align = "right" valign = "top" > bool  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a217d541f3fa777b1552f652fbb520382" > m_isStale< / a > = true< / td > < / tr >
< tr class = "separator:a217d541f3fa777b1552f652fbb520382" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a6e3243a8a8bcdce3282a8f82c5f98195" id = "r_a6e3243a8a8bcdce3282a8f82c5f98195" > < td class = "memItemLeft" align = "right" valign = "top" > < a class = "el" href = "classgridfire_1_1_dynamic_engine.html" > DynamicEngine< / a > &   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > < / td > < / tr >
< tr class = "separator:a6e3243a8a8bcdce3282a8f82c5f98195" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< / table > < table class = "memberdecls" >
< tr class = "heading" > < td colspan = "2" > < h2 class = "groupheader" > < a id = "pri-methods" name = "pri-methods" > < / a >
Private Member Functions< / h2 > < / td > < / tr >
< tr class = "memitem:a9ea4812bc697fe43f8aded14f8aa0985" id = "r_a9ea4812bc697fe43f8aded14f8aa0985" > < td class = "memItemLeft" align = "right" valign = "top" > std::vector< size_t >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a9ea4812bc697fe43f8aded14f8aa0985" > constructSpeciesIndexMap< / a > () const< / td > < / tr >
< tr class = "memdesc:a9ea4812bc697fe43f8aded14f8aa0985" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Constructs the species index map. < br / > < / td > < / tr >
< tr class = "separator:a9ea4812bc697fe43f8aded14f8aa0985" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:ab2514984afaaf8590c28ab71943fbe68" id = "r_ab2514984afaaf8590c28ab71943fbe68" > < td class = "memItemLeft" align = "right" valign = "top" > std::vector< size_t >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#ab2514984afaaf8590c28ab71943fbe68" > constructReactionIndexMap< / a > () const< / td > < / tr >
< tr class = "memdesc:ab2514984afaaf8590c28ab71943fbe68" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Constructs the reaction index map. < br / > < / td > < / tr >
< tr class = "separator:ab2514984afaaf8590c28ab71943fbe68" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a626ab005bfa08b201518c13627e1f843" id = "r_a626ab005bfa08b201518c13627e1f843" > < td class = "memItemLeft" align = "right" valign = "top" > std::vector< double >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a626ab005bfa08b201518c13627e1f843" > mapViewToFull< / a > (const std::vector< double > & defined) const< / td > < / tr >
< tr class = "memdesc:a626ab005bfa08b201518c13627e1f843" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Maps a vector of culled abundances to a vector of full abundances. < br / > < / td > < / tr >
< tr class = "separator:a626ab005bfa08b201518c13627e1f843" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a2f59af6fb3516911de2a3e3ff0ed8873" id = "r_a2f59af6fb3516911de2a3e3ff0ed8873" > < td class = "memItemLeft" align = "right" valign = "top" > std::vector< double >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a2f59af6fb3516911de2a3e3ff0ed8873" > mapFullToView< / a > (const std::vector< double > & full) const< / td > < / tr >
< tr class = "memdesc:a2f59af6fb3516911de2a3e3ff0ed8873" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Maps a vector of full abundances to a vector of culled abundances. < br / > < / td > < / tr >
< tr class = "separator:a2f59af6fb3516911de2a3e3ff0ed8873" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:af6fb8c3c7894b505bd81d15f012f154a" id = "r_af6fb8c3c7894b505bd81d15f012f154a" > < td class = "memItemLeft" align = "right" valign = "top" > size_t  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#af6fb8c3c7894b505bd81d15f012f154a" > mapViewToFullSpeciesIndex< / a > (size_t definedSpeciesIndex) const< / td > < / tr >
< tr class = "memdesc:af6fb8c3c7894b505bd81d15f012f154a" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Maps a culled species index to a full species index. < br / > < / td > < / tr >
< tr class = "separator:af6fb8c3c7894b505bd81d15f012f154a" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:aadf373d69a22fcd171a6c251466d53d1" id = "r_aadf373d69a22fcd171a6c251466d53d1" > < td class = "memItemLeft" align = "right" valign = "top" > size_t  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#aadf373d69a22fcd171a6c251466d53d1" > mapViewToFullReactionIndex< / a > (size_t definedReactionIndex) const< / td > < / tr >
< tr class = "memdesc:aadf373d69a22fcd171a6c251466d53d1" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Maps a culled reaction index to a full reaction index. < br / > < / td > < / tr >
< tr class = "separator:aadf373d69a22fcd171a6c251466d53d1" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a56bd041c2fc7fe4f1371c38c8c0443e0" id = "r_a56bd041c2fc7fe4f1371c38c8c0443e0" > < td class = "memItemLeft" align = "right" valign = "top" > void  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a56bd041c2fc7fe4f1371c38c8c0443e0" > validateNetworkState< / a > () const< / td > < / tr >
< tr class = "separator:a56bd041c2fc7fe4f1371c38c8c0443e0" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:adbc64284b5f5a3256867be46fa87c69e" id = "r_adbc64284b5f5a3256867be46fa87c69e" > < td class = "memItemLeft" align = "right" valign = "top" > void  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#adbc64284b5f5a3256867be46fa87c69e" > collect< / a > (const std::vector< std::string > & peNames)< / td > < / tr >
< tr class = "separator:adbc64284b5f5a3256867be46fa87c69e" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< / table > < table class = "memberdecls" >
< tr class = "heading" > < td colspan = "2" > < h2 class = "groupheader" > < a id = "pri-attribs" name = "pri-attribs" > < / a >
Private Attributes< / h2 > < / td > < / tr >
< tr class = "memitem:a4f4aa847ee80ad430de9b1cfdda6b4e3" id = "r_a4f4aa847ee80ad430de9b1cfdda6b4e3" > < td class = "memItemLeft" align = "right" valign = "top" > quill::Logger *  < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > = fourdst::logging::LogManager::getInstance().getLogger(" log" )< / td > < / tr >
< tr class = "memdesc:a4f4aa847ee80ad430de9b1cfdda6b4e3" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Active species in the defined engine. < br / > < / td > < / tr >
< tr class = "separator:a4f4aa847ee80ad430de9b1cfdda6b4e3" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a64e9c79a36d529e1b296fe5786e57aae" id = "r_a64e9c79a36d529e1b296fe5786e57aae" > < td class = "memItemLeft" align = "right" valign = "top" > std::vector< fourdst::atomic::Species >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > < / td > < / tr >
< tr class = "memdesc:a64e9c79a36d529e1b296fe5786e57aae" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Active reactions in the defined engine. < br / > < / td > < / tr >
< tr class = "separator:a64e9c79a36d529e1b296fe5786e57aae" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:a373d4a83f30527a1bfaf1d74ad14c965" id = "r_a373d4a83f30527a1bfaf1d74ad14c965" > < td class = "memItemLeft" align = "right" valign = "top" > < a class = "el" href = "namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" > reaction::LogicalReactionSet< / a >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#a373d4a83f30527a1bfaf1d74ad14c965" > m_activeReactions< / a > < / td > < / tr >
< tr class = "memdesc:a373d4a83f30527a1bfaf1d74ad14c965" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Maps indices of active species to indices in the full network. < br / > < / td > < / tr >
< tr class = "separator:a373d4a83f30527a1bfaf1d74ad14c965" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:acc4976262e208d1dd2185ebccbdd275e" id = "r_acc4976262e208d1dd2185ebccbdd275e" > < td class = "memItemLeft" align = "right" valign = "top" > std::vector< size_t >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#acc4976262e208d1dd2185ebccbdd275e" > m_speciesIndexMap< / a > < / td > < / tr >
< tr class = "memdesc:acc4976262e208d1dd2185ebccbdd275e" > < td class = "mdescLeft" >   < / td > < td class = "mdescRight" > Maps indices of active reactions to indices in the full network. < br / > < / td > < / tr >
< tr class = "separator:acc4976262e208d1dd2185ebccbdd275e" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< tr class = "memitem:affda6d60651c53ee02532806104671bd" id = "r_affda6d60651c53ee02532806104671bd" > < td class = "memItemLeft" align = "right" valign = "top" > std::vector< size_t >   < / td > < td class = "memItemRight" valign = "bottom" > < a class = "el" href = "#affda6d60651c53ee02532806104671bd" > m_reactionIndexMap< / a > < / td > < / tr >
< tr class = "separator:affda6d60651c53ee02532806104671bd" > < td class = "memSeparator" colspan = "2" >   < / td > < / tr >
< / table >
2025-07-31 10:54:31 -04:00
< h2 class = "groupheader" > Constructor & Destructor Documentation< / h2 >
2025-07-24 11:10:45 -04:00
< a id = "a9b319b4a1bd5a08381ebb183daf72c92" name = "a9b319b4a1bd5a08381ebb183daf72c92" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a9b319b4a1bd5a08381ebb183daf72c92" > ◆   < / a > < / span > DefinedEngineView()< / h2 >
< div class = "memitem" >
< div class = "memproto" >
< table class = "memname" >
< tr >
< td class = "memname" > gridfire::DefinedEngineView::DefinedEngineView < / td >
< td > (< / td >
< td class = "paramtype" > const std::vector< std::string > & < / td > < td class = "paramname" > < span class = "paramname" > < em > peNames< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > < a class = "el" href = "classgridfire_1_1_dynamic_engine.html" > DynamicEngine< / a > & < / td > < td class = "paramname" > < span class = "paramname" > < em > baseEngine< / em > < / span >   )< / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< / div >
< / div >
< h2 class = "groupheader" > Member Function Documentation< / h2 >
< a id = "a142725470f96cba3edb48a29f1264032" name = "a142725470f96cba3edb48a29f1264032" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a142725470f96cba3edb48a29f1264032" > ◆   < / a > < / span > calculateMolarReactionFlow()< / h2 >
< div class = "memitem" >
< div class = "memproto" >
< table class = "mlabels" >
< tr >
< td class = "mlabels-left" >
< table class = "memname" >
< tr >
< td class = "memname" > double gridfire::DefinedEngineView::calculateMolarReactionFlow < / td >
< td > (< / td >
< td class = "paramtype" > const < a class = "el" href = "classgridfire_1_1reaction_1_1_reaction.html" > reaction::Reaction< / a > & < / td > < td class = "paramname" > < span class = "paramname" > < em > reaction< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const std::vector< double > & < / td > < td class = "paramname" > < span class = "paramname" > < em > Y_defined< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const double< / td > < td class = "paramname" > < span class = "paramname" > < em > T9< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const double< / td > < td class = "paramname" > < span class = "paramname" > < em > rho< / em > < / span >   ) const< / td >
< / tr >
< / table >
< / td >
< td class = "mlabels-right" >
< span class = "mlabels" > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Calculates the molar reaction flow for a given reaction in the active network. < / p >
< dl class = "params" > < dt > Parameters< / dt > < dd >
< table class = "params" >
< tr > < td class = "paramname" > reaction< / td > < td > The reaction for which to calculate the flow. < / td > < / tr >
< tr > < td class = "paramname" > Y_defined< / td > < td > Vector of current abundances for the active species. < / td > < / tr >
< tr > < td class = "paramname" > T9< / td > < td > Temperature in units of 10^9 K. < / td > < / tr >
< tr > < td class = "paramname" > rho< / td > < td > Density in g/cm^3. < / td > < / tr >
< / table >
< / dd >
< / dl >
< dl class = "section return" > < dt > Returns< / dt > < dd > Molar flow rate for the reaction (e.g., mol/g/s).< / dd > < / dl >
< dl class = "exception" > < dt > Exceptions< / dt > < dd >
< table class = "exception" >
< tr > < td class = "paramname" > std::runtime_error< / td > < td > If the view is stale or if the reaction is not in the active set. < / td > < / tr >
< / table >
< / dd >
< / dl >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785" > gridfire::DynamicEngine< / a > .< / p >
< / div >
< / div >
< a id = "a4b0d71367cb1d4c06bcd01251bbeb60d" name = "a4b0d71367cb1d4c06bcd01251bbeb60d" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a4b0d71367cb1d4c06bcd01251bbeb60d" > ◆   < / a > < / span > calculateRHSAndEnergy()< / h2 >
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< td class = "memname" > std::expected< < a class = "el" href = "structgridfire_1_1_step_derivatives.html" > StepDerivatives< / a > < double > , < a class = "el" href = "structgridfire_1_1expectations_1_1_stale_engine_error.html" > expectations::StaleEngineError< / a > > gridfire::DefinedEngineView::calculateRHSAndEnergy < / td >
< td > (< / td >
< td class = "paramtype" > const std::vector< double > & < / td > < td class = "paramname" > < span class = "paramname" > < em > Y_defined< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const double< / td > < td class = "paramname" > < span class = "paramname" > < em > T9< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const double< / td > < td class = "paramname" > < span class = "paramname" > < em > rho< / em > < / span >   ) const< / td >
< / tr >
< / table >
< / td >
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< span class = "mlabels" > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
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< / table >
< / div > < div class = "memdoc" >
< p > Calculates the right-hand side (dY/dt) and energy generation for the active species. < / p >
< dl class = "params" > < dt > Parameters< / dt > < dd >
< table class = "params" >
< tr > < td class = "paramname" > Y_defined< / td > < td > A vector of abundances for the active species. < / td > < / tr >
< tr > < td class = "paramname" > T9< / td > < td > The temperature in units of 10^9 K. < / td > < / tr >
< tr > < td class = "paramname" > rho< / td > < td > The density in g/cm^3. < / td > < / tr >
< / table >
< / dd >
< / dl >
< dl class = "section return" > < dt > Returns< / dt > < dd > A < a class = "el" href = "structgridfire_1_1_step_derivatives.html" title = "Structure holding derivatives and energy generation for a network step." > StepDerivatives< / a > struct containing the derivatives of the active species and the nuclear energy generation rate.< / dd > < / dl >
< dl class = "exception" > < dt > Exceptions< / dt > < dd >
< table class = "exception" >
< tr > < td class = "paramname" > std::runtime_error< / td > < td > If the view is stale (i.e., < code > < a class = "el" href = "#ae5762f395caea5381ec177507816b5ae" title = "Updates the engine view if it is marked as stale." > update()< / a > < / code > has not been called after < code > setNetworkFile()< / code > ). < / td > < / tr >
< / table >
< / dd >
< / dl >
< p > Implements < a class = "el" href = "classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb" > gridfire::Engine< / a > .< / p >
< / div >
< / div >
< a id = "adbc64284b5f5a3256867be46fa87c69e" name = "adbc64284b5f5a3256867be46fa87c69e" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#adbc64284b5f5a3256867be46fa87c69e" > ◆   < / a > < / span > collect()< / h2 >
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< td class = "memname" > void gridfire::DefinedEngineView::collect < / td >
< td > (< / td >
< td class = "paramtype" > const std::vector< std::string > & < / td > < td class = "paramname" > < span class = "paramname" > < em > peNames< / em > < / span > < / td > < td > )< / td >
< td > < / td >
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< / td >
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< span class = "mlabels" > < span class = "mlabel private" > private< / span > < / span > < / td >
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< / div > < div class = "memdoc" >
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< a id = "ab2514984afaaf8590c28ab71943fbe68" name = "ab2514984afaaf8590c28ab71943fbe68" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#ab2514984afaaf8590c28ab71943fbe68" > ◆   < / a > < / span > constructReactionIndexMap()< / h2 >
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< td class = "memname" > std::vector< size_t > gridfire::DefinedEngineView::constructReactionIndexMap < / td >
< td > (< / td >
< td class = "paramname" > < span class = "paramname" > < em > < / em > < / span > < / td > < td > )< / td >
< td > const< / td >
< / tr >
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< span class = "mlabels" > < span class = "mlabel private" > private< / span > < / span > < / td >
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< p > Constructs the reaction index map. < / p >
< dl class = "section return" > < dt > Returns< / dt > < dd > A vector mapping defined reaction indices to full reaction indices.< / dd > < / dl >
< p > This method creates a map from the indices of the active reactions to the indices of the corresponding reactions in the full network.< / p >
< dl class = "exception" > < dt > Exceptions< / dt > < dd >
< table class = "exception" >
< tr > < td class = "paramname" > std::runtime_error< / td > < td > If an active reaction is not found in the base engine's reaction list. < / td > < / tr >
< / table >
< / dd >
< / dl >
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< a id = "a9ea4812bc697fe43f8aded14f8aa0985" name = "a9ea4812bc697fe43f8aded14f8aa0985" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a9ea4812bc697fe43f8aded14f8aa0985" > ◆   < / a > < / span > constructSpeciesIndexMap()< / h2 >
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< td class = "memname" > std::vector< size_t > gridfire::DefinedEngineView::constructSpeciesIndexMap < / td >
< td > (< / td >
< td class = "paramname" > < span class = "paramname" > < em > < / em > < / span > < / td > < td > )< / td >
< td > const< / td >
< / tr >
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< span class = "mlabels" > < span class = "mlabel private" > private< / span > < / span > < / td >
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< p > Constructs the species index map. < / p >
< dl class = "section return" > < dt > Returns< / dt > < dd > A vector mapping defined species indices to full species indices.< / dd > < / dl >
< p > This method creates a map from the indices of the active species to the indices of the corresponding species in the full network.< / p >
< dl class = "exception" > < dt > Exceptions< / dt > < dd >
< table class = "exception" >
< tr > < td class = "paramname" > std::runtime_error< / td > < td > If an active species is not found in the base engine's species list. < / td > < / tr >
< / table >
< / dd >
< / dl >
< / div >
< / div >
< a id = "ad25c722eaee1f28f8ed7b4d33a1f69ae" name = "ad25c722eaee1f28f8ed7b4d33a1f69ae" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#ad25c722eaee1f28f8ed7b4d33a1f69ae" > ◆   < / a > < / span > generateJacobianMatrix()< / h2 >
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< td class = "memname" > void gridfire::DefinedEngineView::generateJacobianMatrix < / td >
< td > (< / td >
< td class = "paramtype" > const std::vector< double > & < / td > < td class = "paramname" > < span class = "paramname" > < em > Y_dynamic< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const double< / td > < td class = "paramname" > < span class = "paramname" > < em > T9< / em > < / span > , < / td >
< / tr >
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< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const double< / td > < td class = "paramname" > < span class = "paramname" > < em > rho< / em > < / span >   ) const< / td >
< / tr >
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< / td >
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< span class = "mlabels" > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
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< / table >
< / div > < div class = "memdoc" >
< p > Generates the Jacobian matrix for the active species. < / p >
< dl class = "params" > < dt > Parameters< / dt > < dd >
< table class = "params" >
< tr > < td class = "paramname" > Y_dynamic< / td > < td > A vector of abundances for the active species. < / td > < / tr >
< tr > < td class = "paramname" > T9< / td > < td > The temperature in units of 10^9 K. < / td > < / tr >
< tr > < td class = "paramname" > rho< / td > < td > The density in g/cm^3.< / td > < / tr >
< / table >
< / dd >
< / dl >
< dl class = "exception" > < dt > Exceptions< / dt > < dd >
< table class = "exception" >
< tr > < td class = "paramname" > std::runtime_error< / td > < td > If the view is stale. < / td > < / tr >
< / table >
< / dd >
< / dl >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a29bdd4231c29c3a4e524ad6ca66a127d" > gridfire::DynamicEngine< / a > .< / p >
< / div >
< / div >
< a id = "ad07221be49ae1b5133c5b987dafac3b6" name = "ad07221be49ae1b5133c5b987dafac3b6" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#ad07221be49ae1b5133c5b987dafac3b6" > ◆   < / a > < / span > generateStoichiometryMatrix()< / h2 >
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< td class = "memname" > void gridfire::DefinedEngineView::generateStoichiometryMatrix < / td >
< td > (< / td >
< td class = "paramname" > < span class = "paramname" > < em > < / em > < / span > < / td > < td > )< / td >
< td > < / td >
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< / td >
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< span class = "mlabels" > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
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< p > Generates the stoichiometry matrix for the active reactions and species. < / p >
< dl class = "exception" > < dt > Exceptions< / dt > < dd >
< table class = "exception" >
< tr > < td class = "paramname" > std::runtime_error< / td > < td > If the view is stale. < / td > < / tr >
< / table >
< / dd >
< / dl >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f" > gridfire::DynamicEngine< / a > .< / p >
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< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a69b9a5812ad8bda13f956acd0da24484" > ◆   < / a > < / span > getBaseEngine()< / h2 >
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< td class = "memname" > const < a class = "el" href = "classgridfire_1_1_dynamic_engine.html" > DynamicEngine< / a > & gridfire::DefinedEngineView::getBaseEngine < / td >
< td > (< / td >
< td class = "paramname" > < span class = "paramname" > < em > < / em > < / span > < / td > < td > )< / td >
< td > const< / td >
< / tr >
< / table >
< / td >
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< span class = "mlabels" > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
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< p > Access the underlying engine instance. < / p >
< dl class = "section return" > < dt > Returns< / dt > < dd > Const reference to the underlying engine.< / dd > < / dl >
< p > This method must be implemented by derived classes to provide access to the base engine. The returned reference should remain valid for the lifetime of the < a class = "el" href = "classgridfire_1_1_engine_view.html" title = "Abstract base class for a "view" of a reaction network engine." > EngineView< / a > .< / p >
< p > Example: < / p > < div class = "fragment" > < div class = "line" > < span class = "keyword" > const< / span > < a class = "code hl_class" href = "classgridfire_1_1_dynamic_engine.html" > DynamicEngine< / a > & engine = myView.getBaseEngine();< / div >
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< div class = "ttc" id = "aclassgridfire_1_1_dynamic_engine_html" > < div class = "ttname" > < a href = "classgridfire_1_1_dynamic_engine.html" > gridfire::DynamicEngine< / a > < / div > < div class = "ttdoc" > Abstract class for engines supporting Jacobian and stoichiometry operations.< / div > < div class = "ttdef" > < b > Definition< / b > engine_abstract.h:130< / div > < / div >
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< / div > <!-- fragment -->
< p > Implements < a class = "el" href = "classgridfire_1_1_engine_view.html#ad294227f8b5cf6d970c349eabf5447a6" > gridfire::EngineView< DynamicEngine > < / a > .< / p >
< / div >
< / div >
< a id = "a273b175049f5ce7b9208e931ad139e1b" name = "a273b175049f5ce7b9208e931ad139e1b" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a273b175049f5ce7b9208e931ad139e1b" > ◆   < / a > < / span > getJacobianMatrixEntry()< / h2 >
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< td class = "memname" > double gridfire::DefinedEngineView::getJacobianMatrixEntry < / td >
< td > (< / td >
< td class = "paramtype" > const int< / td > < td class = "paramname" > < span class = "paramname" > < em > i_defined< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const int< / td > < td class = "paramname" > < span class = "paramname" > < em > j_defined< / em > < / span >   ) const< / td >
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< span class = "mlabels" > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
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< p > Gets an entry from the Jacobian matrix for the active species. < / p >
< dl class = "params" > < dt > Parameters< / dt > < dd >
< table class = "params" >
< tr > < td class = "paramname" > i_defined< / td > < td > The row index (species index) in the defined matrix. < / td > < / tr >
< tr > < td class = "paramname" > j_defined< / td > < td > The column index (species index) in the defined matrix. < / td > < / tr >
< / table >
< / dd >
< / dl >
< dl class = "section return" > < dt > Returns< / dt > < dd > The value of the Jacobian matrix at (i_defined, j_defined).< / dd > < / dl >
< dl class = "exception" > < dt > Exceptions< / dt > < dd >
< table class = "exception" >
< tr > < td class = "paramname" > std::runtime_error< / td > < td > If the view is stale. < / td > < / tr >
< tr > < td class = "paramname" > std::out_of_range< / td > < td > If an index is out of bounds. < / td > < / tr >
< / table >
< / dd >
< / dl >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07" > gridfire::DynamicEngine< / a > .< / p >
< / div >
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< a id = "ae03b4f9afac03d4011a4d7cf0423535d" name = "ae03b4f9afac03d4011a4d7cf0423535d" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#ae03b4f9afac03d4011a4d7cf0423535d" > ◆   < / a > < / span > getNetworkReactions()< / h2 >
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< td class = "memname" > const < a class = "el" href = "namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" > reaction::LogicalReactionSet< / a > & gridfire::DefinedEngineView::getNetworkReactions < / td >
< td > (< / td >
< td class = "paramname" > < span class = "paramname" > < em > < / em > < / span > < / td > < td > )< / td >
< td > const< / td >
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< p > Gets the set of active logical reactions in the network. < / p >
< dl class = "section return" > < dt > Returns< / dt > < dd > Reference to the < a class = "el" href = "namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" title = "A set of logical reactions." > LogicalReactionSet< / a > containing all active reactions.< / dd > < / dl >
< dl class = "exception" > < dt > Exceptions< / dt > < dd >
< table class = "exception" >
< tr > < td class = "paramname" > std::runtime_error< / td > < td > If the view is stale. < / td > < / tr >
< / table >
< / dd >
< / dl >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037" > gridfire::DynamicEngine< / a > .< / p >
< / div >
< / div >
< a id = "a1a55f9748c45af6f13e16a6b6ceaa211" name = "a1a55f9748c45af6f13e16a6b6ceaa211" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a1a55f9748c45af6f13e16a6b6ceaa211" > ◆   < / a > < / span > getNetworkSpecies()< / h2 >
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< td class = "memname" > const std::vector< Species > & gridfire::DefinedEngineView::getNetworkSpecies < / td >
< td > (< / td >
< td class = "paramname" > < span class = "paramname" > < em > < / em > < / span > < / td > < td > )< / td >
< td > const< / td >
< / tr >
< / table >
< / td >
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< span class = "mlabels" > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
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< p > Gets the list of active species in the network defined by the file. < / p >
< dl class = "section return" > < dt > Returns< / dt > < dd > A const reference to the vector of active species. < / dd > < / dl >
< p > Implements < a class = "el" href = "classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3" > gridfire::Engine< / a > .< / p >
< / div >
< / div >
< a id = "a3c657b82a0117118a4bb0ce7f624ae0c" name = "a3c657b82a0117118a4bb0ce7f624ae0c" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a3c657b82a0117118a4bb0ce7f624ae0c" > ◆   < / a > < / span > getScreeningModel()< / h2 >
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< td class = "memname" > < a class = "el" href = "namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25" > screening::ScreeningType< / a > gridfire::DefinedEngineView::getScreeningModel < / td >
< td > (< / td >
< td class = "paramname" > < span class = "paramname" > < em > < / em > < / span > < / td > < td > )< / td >
< td > const< / td >
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< / td >
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< span class = "mlabels" > < span class = "mlabel nodiscard" > nodiscard< / span > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Gets the screening model from the base engine. < / p >
< dl class = "section return" > < dt > Returns< / dt > < dd > The current screening model type. < / dd > < / dl >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0" > gridfire::DynamicEngine< / a > .< / p >
< / div >
< / div >
< a id = "a3d58e36ed8a6a0d82bb65e91090f7491" name = "a3d58e36ed8a6a0d82bb65e91090f7491" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a3d58e36ed8a6a0d82bb65e91090f7491" > ◆   < / a > < / span > getSpeciesDestructionTimescales()< / h2 >
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< td class = "memname" > std::expected< std::unordered_map< fourdst::atomic::Species, double > , < a class = "el" href = "structgridfire_1_1expectations_1_1_stale_engine_error.html" > expectations::StaleEngineError< / a > > gridfire::DefinedEngineView::getSpeciesDestructionTimescales < / td >
< td > (< / td >
< td class = "paramtype" > const std::vector< double > & < / td > < td class = "paramname" > < span class = "paramname" > < em > Y_defined< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const double< / td > < td class = "paramname" > < span class = "paramname" > < em > T9< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const double< / td > < td class = "paramname" > < span class = "paramname" > < em > rho< / em > < / span >   ) const< / td >
< / tr >
< / table >
< / td >
< td class = "mlabels-right" >
< span class = "mlabels" > < span class = "mlabel nodiscard" > nodiscard< / span > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a6ca0f315f75252ca505507a61556dda6" > gridfire::DynamicEngine< / a > .< / p >
< / div >
< / div >
< a id = "abfee22688617ffe91c69be93049c89b3" name = "abfee22688617ffe91c69be93049c89b3" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#abfee22688617ffe91c69be93049c89b3" > ◆   < / a > < / span > getSpeciesIndex()< / h2 >
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< td class = "memname" > int gridfire::DefinedEngineView::getSpeciesIndex < / td >
< td > (< / td >
< td class = "paramtype" > const fourdst::atomic::Species & < / td > < td class = "paramname" > < span class = "paramname" > < em > species< / em > < / span > < / td > < td > )< / td >
< td > const< / td >
< / tr >
< / table >
< / td >
< td class = "mlabels-right" >
< span class = "mlabels" > < span class = "mlabel nodiscard" > nodiscard< / span > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#ad3d56a8b9161b9cc7f4da51f6bf7e8c9" > gridfire::DynamicEngine< / a > .< / p >
< / div >
< / div >
< a id = "ac8daafabbc76f4b6811bede241a03d72" name = "ac8daafabbc76f4b6811bede241a03d72" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#ac8daafabbc76f4b6811bede241a03d72" > ◆   < / a > < / span > getSpeciesTimescales()< / h2 >
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< td class = "memname" > std::expected< std::unordered_map< Species, double > , < a class = "el" href = "structgridfire_1_1expectations_1_1_stale_engine_error.html" > expectations::StaleEngineError< / a > > gridfire::DefinedEngineView::getSpeciesTimescales < / td >
< td > (< / td >
< td class = "paramtype" > const std::vector< double > & < / td > < td class = "paramname" > < span class = "paramname" > < em > Y_defined< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const double< / td > < td class = "paramname" > < span class = "paramname" > < em > T9< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const double< / td > < td class = "paramname" > < span class = "paramname" > < em > rho< / em > < / span >   ) const< / td >
< / tr >
< / table >
< / td >
< td class = "mlabels-right" >
< span class = "mlabels" > < span class = "mlabel nodiscard" > nodiscard< / span > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Computes timescales for all active species in the network. < / p >
< dl class = "params" > < dt > Parameters< / dt > < dd >
< table class = "params" >
< tr > < td class = "paramname" > Y_defined< / td > < td > Vector of current abundances for the active species. < / td > < / tr >
< tr > < td class = "paramname" > T9< / td > < td > Temperature in units of 10^9 K. < / td > < / tr >
< tr > < td class = "paramname" > rho< / td > < td > Density in g/cm^3. < / td > < / tr >
< / table >
< / dd >
< / dl >
< dl class = "section return" > < dt > Returns< / dt > < dd > Map from Species to their characteristic timescales (s).< / dd > < / dl >
< dl class = "exception" > < dt > Exceptions< / dt > < dd >
< table class = "exception" >
< tr > < td class = "paramname" > std::runtime_error< / td > < td > If the view is stale. < / td > < / tr >
< / table >
< / dd >
< / dl >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a6772ac384b4c3d3e91712041e4aaa813" > gridfire::DynamicEngine< / a > .< / p >
< / div >
< / div >
< a id = "afa2820971397114d788730cc33feefe2" name = "afa2820971397114d788730cc33feefe2" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#afa2820971397114d788730cc33feefe2" > ◆   < / a > < / span > getStoichiometryMatrixEntry()< / h2 >
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< td class = "memname" > int gridfire::DefinedEngineView::getStoichiometryMatrixEntry < / td >
< td > (< / td >
< td class = "paramtype" > const int< / td > < td class = "paramname" > < span class = "paramname" > < em > speciesIndex_defined< / em > < / span > , < / td >
< / tr >
< tr >
< td class = "paramkey" > < / td >
< td > < / td >
< td class = "paramtype" > const int< / td > < td class = "paramname" > < span class = "paramname" > < em > reactionIndex_defined< / em > < / span >   ) const< / td >
< / tr >
< / table >
< / td >
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< span class = "mlabels" > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Gets an entry from the stoichiometry matrix for the active species and reactions. < / p >
< dl class = "params" > < dt > Parameters< / dt > < dd >
< table class = "params" >
< tr > < td class = "paramname" > speciesIndex_defined< / td > < td > The index of the species in the defined species list. < / td > < / tr >
< tr > < td class = "paramname" > reactionIndex_defined< / td > < td > The index of the reaction in the defined reaction list. < / td > < / tr >
< / table >
< / dd >
< / dl >
< dl class = "section return" > < dt > Returns< / dt > < dd > The stoichiometric coefficient for the given species and reaction.< / dd > < / dl >
< dl class = "exception" > < dt > Exceptions< / dt > < dd >
< table class = "exception" >
< tr > < td class = "paramname" > std::runtime_error< / td > < td > If the view is stale. < / td > < / tr >
< tr > < td class = "paramname" > std::out_of_range< / td > < td > If an index is out of bounds. < / td > < / tr >
< / table >
< / dd >
< / dl >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f" > gridfire::DynamicEngine< / a > .< / p >
< / div >
< / div >
< a id = "a7d9e738dd28efb4d6127de7379169c87" name = "a7d9e738dd28efb4d6127de7379169c87" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a7d9e738dd28efb4d6127de7379169c87" > ◆   < / a > < / span > isStale()< / h2 >
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< td class = "memname" > bool gridfire::DefinedEngineView::isStale < / td >
< td > (< / td >
< td class = "paramtype" > const < a class = "el" href = "structgridfire_1_1_net_in.html" > NetIn< / a > & < / td > < td class = "paramname" > < span class = "paramname" > < em > netIn< / em > < / span > < / td > < td > )< / td >
< td > < / td >
< / tr >
< / table >
< / td >
< td class = "mlabels-right" >
< span class = "mlabels" > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a942e65ced17ca602482cc42e469d6398" > gridfire::DynamicEngine< / a > .< / p >
< / div >
< / div >
< a id = "a2f59af6fb3516911de2a3e3ff0ed8873" name = "a2f59af6fb3516911de2a3e3ff0ed8873" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a2f59af6fb3516911de2a3e3ff0ed8873" > ◆   < / a > < / span > mapFullToView()< / h2 >
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< td class = "memname" > std::vector< double > gridfire::DefinedEngineView::mapFullToView < / td >
< td > (< / td >
< td class = "paramtype" > const std::vector< double > & < / td > < td class = "paramname" > < span class = "paramname" > < em > full< / em > < / span > < / td > < td > )< / td >
< td > const< / td >
< / tr >
< / table >
< / td >
< td class = "mlabels-right" >
< span class = "mlabels" > < span class = "mlabel private" > private< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Maps a vector of full abundances to a vector of culled abundances. < / p >
< dl class = "params" > < dt > Parameters< / dt > < dd >
< table class = "params" >
< tr > < td class = "paramname" > full< / td > < td > A vector of abundances for the full network. < / td > < / tr >
< / table >
< / dd >
< / dl >
< dl class = "section return" > < dt > Returns< / dt > < dd > A vector of abundances for the active species, with the abundances of the active species copied from the full vector. < / dd > < / dl >
< / div >
< / div >
< a id = "a72789c1c3379594b65b560da50192de2" name = "a72789c1c3379594b65b560da50192de2" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a72789c1c3379594b65b560da50192de2" > ◆   < / a > < / span > mapNetInToMolarAbundanceVector()< / h2 >
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< td class = "memname" > std::vector< double > gridfire::DefinedEngineView::mapNetInToMolarAbundanceVector < / td >
< td > (< / td >
< td class = "paramtype" > const < a class = "el" href = "structgridfire_1_1_net_in.html" > NetIn< / a > & < / td > < td class = "paramname" > < span class = "paramname" > < em > netIn< / em > < / span > < / td > < td > )< / td >
< td > const< / td >
< / tr >
< / table >
< / td >
< td class = "mlabels-right" >
< span class = "mlabels" > < span class = "mlabel nodiscard" > nodiscard< / span > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a55f1b7e5ebe2840e1d7c54665ca5411a" > gridfire::DynamicEngine< / a > .< / p >
< / div >
< / div >
< a id = "a626ab005bfa08b201518c13627e1f843" name = "a626ab005bfa08b201518c13627e1f843" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a626ab005bfa08b201518c13627e1f843" > ◆   < / a > < / span > mapViewToFull()< / h2 >
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< td class = "memname" > std::vector< double > gridfire::DefinedEngineView::mapViewToFull < / td >
< td > (< / td >
< td class = "paramtype" > const std::vector< double > & < / td > < td class = "paramname" > < span class = "paramname" > < em > defined< / em > < / span > < / td > < td > )< / td >
< td > const< / td >
< / tr >
< / table >
< / td >
< td class = "mlabels-right" >
< span class = "mlabels" > < span class = "mlabel private" > private< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Maps a vector of culled abundances to a vector of full abundances. < / p >
< dl class = "params" > < dt > Parameters< / dt > < dd >
< table class = "params" >
< tr > < td class = "paramname" > defined< / td > < td > A vector of abundances for the active species. < / td > < / tr >
< / table >
< / dd >
< / dl >
< dl class = "section return" > < dt > Returns< / dt > < dd > A vector of abundances for the full network, with the abundances of the active species copied from the defined vector. < / dd > < / dl >
< / div >
< / div >
< a id = "aadf373d69a22fcd171a6c251466d53d1" name = "aadf373d69a22fcd171a6c251466d53d1" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#aadf373d69a22fcd171a6c251466d53d1" > ◆   < / a > < / span > mapViewToFullReactionIndex()< / h2 >
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< td class = "memname" > size_t gridfire::DefinedEngineView::mapViewToFullReactionIndex < / td >
< td > (< / td >
< td class = "paramtype" > size_t< / td > < td class = "paramname" > < span class = "paramname" > < em > definedReactionIndex< / em > < / span > < / td > < td > )< / td >
< td > const< / td >
< / tr >
< / table >
< / td >
< td class = "mlabels-right" >
< span class = "mlabels" > < span class = "mlabel private" > private< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Maps a culled reaction index to a full reaction index. < / p >
< dl class = "params" > < dt > Parameters< / dt > < dd >
< table class = "params" >
< tr > < td class = "paramname" > definedReactionIndex< / td > < td > The index of the reaction in the defined reaction list. < / td > < / tr >
< / table >
< / dd >
< / dl >
< dl class = "section return" > < dt > Returns< / dt > < dd > The index of the corresponding reaction in the full network.< / dd > < / dl >
< dl class = "exception" > < dt > Exceptions< / dt > < dd >
< table class = "exception" >
< tr > < td class = "paramname" > std::out_of_range< / td > < td > If the defined index is out of bounds for the reaction index map. < / td > < / tr >
< / table >
< / dd >
< / dl >
< / div >
< / div >
< a id = "af6fb8c3c7894b505bd81d15f012f154a" name = "af6fb8c3c7894b505bd81d15f012f154a" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#af6fb8c3c7894b505bd81d15f012f154a" > ◆   < / a > < / span > mapViewToFullSpeciesIndex()< / h2 >
< div class = "memitem" >
< div class = "memproto" >
< table class = "mlabels" >
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< td class = "mlabels-left" >
< table class = "memname" >
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< td class = "memname" > size_t gridfire::DefinedEngineView::mapViewToFullSpeciesIndex < / td >
< td > (< / td >
< td class = "paramtype" > size_t< / td > < td class = "paramname" > < span class = "paramname" > < em > definedSpeciesIndex< / em > < / span > < / td > < td > )< / td >
< td > const< / td >
< / tr >
< / table >
< / td >
< td class = "mlabels-right" >
< span class = "mlabels" > < span class = "mlabel private" > private< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Maps a culled species index to a full species index. < / p >
< dl class = "params" > < dt > Parameters< / dt > < dd >
< table class = "params" >
< tr > < td class = "paramname" > definedSpeciesIndex< / td > < td > The index of the species in the defined species list. < / td > < / tr >
< / table >
< / dd >
< / dl >
< dl class = "section return" > < dt > Returns< / dt > < dd > The index of the corresponding species in the full network.< / dd > < / dl >
< dl class = "exception" > < dt > Exceptions< / dt > < dd >
< table class = "exception" >
< tr > < td class = "paramname" > std::out_of_range< / td > < td > If the defined index is out of bounds for the species index map. < / td > < / tr >
< / table >
< / dd >
< / dl >
< / div >
< / div >
< a id = "a13033abd3b44904f98b58c93e22da460" name = "a13033abd3b44904f98b58c93e22da460" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a13033abd3b44904f98b58c93e22da460" > ◆   < / a > < / span > primeEngine()< / h2 >
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< td class = "memname" > < a class = "el" href = "structgridfire_1_1_priming_report.html" > PrimingReport< / a > gridfire::DefinedEngineView::primeEngine < / td >
< td > (< / td >
< td class = "paramtype" > const < a class = "el" href = "structgridfire_1_1_net_in.html" > NetIn< / a > & < / td > < td class = "paramname" > < span class = "paramname" > < em > netIn< / em > < / span > < / td > < td > )< / td >
< td > < / td >
< / tr >
< / table >
< / td >
< td class = "mlabels-right" >
< span class = "mlabels" > < span class = "mlabel nodiscard" > nodiscard< / span > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a21c34f59c080a853fafa38a25175124e" > gridfire::DynamicEngine< / a > .< / p >
< / div >
< / div >
< a id = "a9736edfb7c9148b60de30d50c0d3530d" name = "a9736edfb7c9148b60de30d50c0d3530d" > < / a >
< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a9736edfb7c9148b60de30d50c0d3530d" > ◆   < / a > < / span > setNetworkReactions()< / h2 >
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< td class = "memname" > void gridfire::DefinedEngineView::setNetworkReactions < / td >
< td > (< / td >
< td class = "paramtype" > const < a class = "el" href = "namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" > reaction::LogicalReactionSet< / a > & < / td > < td class = "paramname" > < span class = "paramname" > < em > reactions< / em > < / span > < / td > < td > )< / td >
< td > < / td >
< / tr >
< / table >
< / td >
< td class = "mlabels-right" >
< span class = "mlabels" > < span class = "mlabel override" > override< / span > < span class = "mlabel virtual" > virtual< / span > < / span > < / td >
< / tr >
< / table >
< / div > < div class = "memdoc" >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#afb2ec904d88fc8aab516db4059d0e00f" > gridfire::DynamicEngine< / a > .< / p >
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< td class = "memname" > void gridfire::DefinedEngineView::setScreeningModel < / td >
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< td class = "paramtype" > < a class = "el" href = "namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25" > screening::ScreeningType< / a > < / td > < td class = "paramname" > < span class = "paramname" > < em > model< / em > < / span > < / td > < td > )< / td >
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< p > Sets the screening model for the base engine. < / p >
< dl class = "params" > < dt > Parameters< / dt > < dd >
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< tr > < td class = "paramname" > model< / td > < td > The screening model to set. < / td > < / tr >
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< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd" > gridfire::DynamicEngine< / a > .< / p >
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< td class = "memname" > fourdst::composition::Composition gridfire::DefinedEngineView::update < / td >
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< td class = "paramtype" > const < a class = "el" href = "structgridfire_1_1_net_in.html" > NetIn< / a > & < / td > < td class = "paramname" > < span class = "paramname" > < em > netIn< / em > < / span > < / td > < td > )< / td >
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< p > Updates the engine view if it is marked as stale. < / p >
< p > This method checks if the view is stale (e.g., after < code > setNetworkFile< / code > was called). If it is, it rebuilds the active network from the currently set file. The < code > netIn< / code > parameter is not used by this implementation but is required by the interface.< / p >
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< tr > < td class = "paramname" > netIn< / td > < td > The current network input (unused).< / td > < / tr >
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< dl class = "section post" > < dt > Postcondition< / dt > < dd > If the view was stale, it is rebuilt and is no longer stale. < / dd > < / dl >
< p > Implements < a class = "el" href = "classgridfire_1_1_dynamic_engine.html#aa799ff785e7e79bf35b11efd55f6282a" > gridfire::DynamicEngine< / a > .< / p >
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< td class = "memname" > void gridfire::DefinedEngineView::validateNetworkState < / td >
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< h2 class = "groupheader" > Member Data Documentation< / h2 >
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< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a373d4a83f30527a1bfaf1d74ad14c965" > ◆   < / a > < / span > m_activeReactions< / h2 >
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< td class = "memname" > < a class = "el" href = "namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" > reaction::LogicalReactionSet< / a > gridfire::DefinedEngineView::m_activeReactions< / td >
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< p > Maps indices of active species to indices in the full network. < / p >
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< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a64e9c79a36d529e1b296fe5786e57aae" > ◆   < / a > < / span > m_activeSpecies< / h2 >
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< td class = "memname" > std::vector< fourdst::atomic::Species> gridfire::DefinedEngineView::m_activeSpecies< / td >
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< p > Active reactions in the defined engine. < / p >
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< h2 class = "memtitle" > < span class = "permalink" > < a href = "#a6e3243a8a8bcdce3282a8f82c5f98195" > ◆   < / a > < / span > m_baseEngine< / h2 >
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< td class = "memname" > < a class = "el" href = "classgridfire_1_1_dynamic_engine.html" > DynamicEngine< / a > & gridfire::DefinedEngineView::m_baseEngine< / td >
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< td class = "memname" > bool gridfire::DefinedEngineView::m_isStale = true< / td >
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< td class = "memname" > quill::Logger* gridfire::DefinedEngineView::m_logger = fourdst::logging::LogManager::getInstance().getLogger(" log" )< / td >
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< p > Active species in the defined engine. < / p >
< p > Logger instance for trace and debug information. < / p >
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< p > Maps indices of active reactions to indices in the full network. < / p >
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< hr / > The documentation for this class was generated from the following files:< ul >
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< li > src/include/gridfire/engine/views/< a class = "el" href = "engine__defined_8h.html" > engine_defined.h< / a > < / li >
< li > src/lib/engine/views/< a class = "el" href = "engine__defined_8cpp.html" > engine_defined.cpp< / a > < / li >
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< li class = "footer" > Generated by < a href = "https://www.doxygen.org/index.html" > < img class = "footer" src = "doxygen.svg" width = "104" height = "31" alt = "doxygen" / > < / a > 1.13.2 < / li >
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