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< a href = "engine__graph_8cpp.html" > Go to the documentation of this file.< / a > < div class = "fragment" > < div class = "line" > < a id = "l00001" name = "l00001" > < / a > < span class = "lineno" > 1< / span > < span class = "preprocessor" > #include " < a class = "code" href = "engine__graph_8h.html" > gridfire/engine/engine_graph.h< / a > " < / span > < / div >
< div class = "line" > < a id = "l00002" name = "l00002" > < / a > < span class = "lineno" > 2< / span > < span class = "preprocessor" > #include " < a class = "code" href = "reaction_8h.html" > gridfire/reaction/reaction.h< / a > " < / span > < / div >
< div class = "line" > < a id = "l00003" name = "l00003" > < / a > < span class = "lineno" > 3< / span > < span class = "preprocessor" > #include " < a class = "code" href = "network_8h.html" > gridfire/network.h< / a > " < / span > < / div >
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< div class = "line" > < a id = "l00004" name = "l00004" > < / a > < span class = "lineno" > 4< / span > < span class = "preprocessor" > #include " < a class = "code" href = "screening__types_8h.html" > gridfire/screening/screening_types.h< / a > " < / span > < / div >
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< div class = "line" > < a id = "l00005" name = "l00005" > < / a > < span class = "lineno" > 5< / span > < span class = "preprocessor" > #include " < a class = "code" href = "priming_8h.html" > gridfire/engine/procedures/priming.h< / a > " < / span > < / div >
< div class = "line" > < a id = "l00006" name = "l00006" > < / a > < span class = "lineno" > 6< / span > < span class = "preprocessor" > #include " < a class = "code" href = "partition__ground_8h.html" > gridfire/partition/partition_ground.h< / a > " < / span > < / div >
< div class = "line" > < a id = "l00007" name = "l00007" > < / a > < span class = "lineno" > 7< / span > < span class = "preprocessor" > #include " < a class = "code" href = "construction_8h.html" > gridfire/engine/procedures/construction.h< / a > " < / span > < / div >
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< div class = "line" > < a id = "l00009" name = "l00009" > < / a > < span class = "lineno" > 9< / span > < span class = "preprocessor" > #include " fourdst/composition/species.h" < / span > < / div >
< div class = "line" > < a id = "l00010" name = "l00010" > < / a > < span class = "lineno" > 10< / span > < span class = "preprocessor" > #include " fourdst/composition/atomicSpecies.h" < / span > < / div >
< div class = "line" > < a id = "l00011" name = "l00011" > < / a > < span class = "lineno" > 11< / span > < / div >
< div class = "line" > < a id = "l00012" name = "l00012" > < / a > < span class = "lineno" > 12< / span > < span class = "preprocessor" > #include " quill/LogMacros.h" < / span > < / div >
< div class = "line" > < a id = "l00013" name = "l00013" > < / a > < span class = "lineno" > 13< / span > < / div >
< div class = "line" > < a id = "l00014" name = "l00014" > < / a > < span class = "lineno" > 14< / span > < span class = "preprocessor" > #include < cstdint> < / span > < / div >
< div class = "line" > < a id = "l00015" name = "l00015" > < / a > < span class = "lineno" > 15< / span > < span class = "preprocessor" > #include < iostream> < / span > < / div >
< div class = "line" > < a id = "l00016" name = "l00016" > < / a > < span class = "lineno" > 16< / span > < span class = "preprocessor" > #include < set> < / span > < / div >
< div class = "line" > < a id = "l00017" name = "l00017" > < / a > < span class = "lineno" > 17< / span > < span class = "preprocessor" > #include < stdexcept> < / span > < / div >
< div class = "line" > < a id = "l00018" name = "l00018" > < / a > < span class = "lineno" > 18< / span > < span class = "preprocessor" > #include < string> < / span > < / div >
< div class = "line" > < a id = "l00019" name = "l00019" > < / a > < span class = "lineno" > 19< / span > < span class = "preprocessor" > #include < string_view> < / span > < / div >
< div class = "line" > < a id = "l00020" name = "l00020" > < / a > < span class = "lineno" > 20< / span > < span class = "preprocessor" > #include < unordered_map> < / span > < / div >
< div class = "line" > < a id = "l00021" name = "l00021" > < / a > < span class = "lineno" > 21< / span > < span class = "preprocessor" > #include < utility> < / span > < / div >
< div class = "line" > < a id = "l00022" name = "l00022" > < / a > < span class = "lineno" > 22< / span > < span class = "preprocessor" > #include < vector> < / span > < / div >
< div class = "line" > < a id = "l00023" name = "l00023" > < / a > < span class = "lineno" > 23< / span > < span class = "preprocessor" > #include < fstream> < / span > < / div >
< div class = "line" > < a id = "l00024" name = "l00024" > < / a > < span class = "lineno" > 24< / span > < span class = "preprocessor" > #include < ranges> < / span > < / div >
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< div class = "line" > < a id = "l00026" name = "l00026" > < / a > < span class = "lineno" > 26< / span > < span class = "preprocessor" > #include < boost/numeric/odeint.hpp> < / span > < / div >
< div class = "line" > < a id = "l00027" name = "l00027" > < / a > < span class = "lineno" > 27< / span > < / div >
< div class = "line" > < a id = "l00028" name = "l00028" > < / a > < span class = "lineno" > 28< / span > < span class = "preprocessor" > #include " cppad/cppad.hpp" < / span > < / div >
< div class = "line" > < a id = "l00029" name = "l00029" > < / a > < span class = "lineno" > 29< / span > < span class = "preprocessor" > #include " cppad/utility/sparse_rc.hpp" < / span > < / div >
< div class = "line" > < a id = "l00030" name = "l00030" > < / a > < span class = "lineno" > 30< / span > < span class = "preprocessor" > #include " cppad/utility/sparse_rcv.hpp" < / span > < / div >
< div class = "line" > < a id = "l00031" name = "l00031" > < / a > < span class = "lineno" > 31< / span > < / div >
< div class = "line" > < a id = "l00032" name = "l00032" > < / a > < span class = "lineno" > 32< / span > < / div >
< div class = "line" > < a id = "l00033" name = "l00033" > < / a > < span class = "lineno" > 33< / span > < span class = "keyword" > namespace < / span > < a class = "code hl_namespace" href = "namespacegridfire.html" > gridfire< / a > {< / div >
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< div class = "foldopen" id = "foldopen00034" data-start = "{" data-end = "}" >
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< div class = "line" > < a id = "l00034" name = "l00034" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5" > 34< / a > < / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5" > GraphEngine::GraphEngine< / a > (< / div >
< div class = "line" > < a id = "l00035" name = "l00035" > < / a > < span class = "lineno" > 35< / span > < span class = "keyword" > const< / span > fourdst::composition::Composition & composition,< / div >
< div class = "line" > < a id = "l00036" name = "l00036" > < / a > < span class = "lineno" > 36< / span > < span class = "keyword" > const< / span > < a class = "code hl_typedef" href = "namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6" > BuildDepthType< / a > buildDepth< / div >
< div class = "line" > < a id = "l00037" name = "l00037" > < / a > < span class = "lineno" > 37< / span > ): < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5" > GraphEngine< / a > (composition, < a class = "code hl_namespace" href = "namespacegridfire_1_1partition.html" > partition< / a > ::GroundStatePartitionFunction(), buildDepth) {}< / div >
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< / div >
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< div class = "line" > < a id = "l00038" name = "l00038" > < / a > < span class = "lineno" > 38< / span > < / div >
< div class = "foldopen" id = "foldopen00039" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00039" name = "l00039" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a39d9838ed40bea71ee6c552bb5969026" > 39< / a > < / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5" > GraphEngine::GraphEngine< / a > (< / div >
< div class = "line" > < a id = "l00040" name = "l00040" > < / a > < span class = "lineno" > 40< / span > < span class = "keyword" > const< / span > fourdst::composition::Composition & composition,< / div >
< div class = "line" > < a id = "l00041" name = "l00041" > < / a > < span class = "lineno" > 41< / span > < span class = "keyword" > const< / span > < a class = "code hl_class" href = "classgridfire_1_1partition_1_1_partition_function.html" > partition::PartitionFunction< / a > & partitionFunction,< / div >
< div class = "line" > < a id = "l00042" name = "l00042" > < / a > < span class = "lineno" > 42< / span > < span class = "keyword" > const< / span > < a class = "code hl_typedef" href = "namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6" > BuildDepthType< / a > buildDepth) :< / div >
< div class = "line" > < a id = "l00043" name = "l00043" > < / a > < span class = "lineno" > 43< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > (< a class = "code hl_function" href = "namespacegridfire.html#aedddb89e400a6111f69bfe0c3fd4214e" > build_reaclib_nuclear_network< / a > (composition, buildDepth, false)),< / div >
< div class = "line" > < a id = "l00044" name = "l00044" > < / a > < span class = "lineno" > 44< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01" > m_depth< / a > (buildDepth),< / div >
< div class = "line" > < a id = "l00045" name = "l00045" > < / a > < span class = "lineno" > 45< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e" > m_partitionFunction< / a > (partitionFunction.clone())< / div >
< div class = "line" > < a id = "l00046" name = "l00046" > < / a > < span class = "lineno" > 46< / span > {< / div >
< div class = "line" > < a id = "l00047" name = "l00047" > < / a > < span class = "lineno" > 47< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f" > syncInternalMaps< / a > ();< / div >
< div class = "line" > < a id = "l00048" name = "l00048" > < / a > < span class = "lineno" > 48< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00049" name = "l00049" > < / a > < span class = "lineno" > 49< / span > < / div >
< div class = "foldopen" id = "foldopen00050" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00050" name = "l00050" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a1e7e851dfa21d41c2dc533ba56fc4c7b" > 50< / a > < / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5" > GraphEngine::GraphEngine< / a > (< / div >
< div class = "line" > < a id = "l00051" name = "l00051" > < / a > < span class = "lineno" > 51< / span > < span class = "keyword" > const< / span > < a class = "code hl_typedef" href = "namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" > reaction::LogicalReactionSet< / a > & reactions< / div >
< div class = "line" > < a id = "l00052" name = "l00052" > < / a > < span class = "lineno" > 52< / span > ) :< / div >
< div class = "line" > < a id = "l00053" name = "l00053" > < / a > < span class = "lineno" > 53< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > (reactions) {< / div >
< div class = "line" > < a id = "l00054" name = "l00054" > < / a > < span class = "lineno" > 54< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f" > syncInternalMaps< / a > ();< / div >
< div class = "line" > < a id = "l00055" name = "l00055" > < / a > < span class = "lineno" > 55< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00056" name = "l00056" > < / a > < span class = "lineno" > 56< / span > < / div >
< div class = "foldopen" id = "foldopen00057" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00057" name = "l00057" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#aaed3743a52246b0f7bf03995e1c12081" > 57< / a > < / span > std::expected< StepDerivatives< double> , < a class = "code hl_struct" href = "structgridfire_1_1expectations_1_1_stale_engine_error.html" > expectations::StaleEngineError< / a > > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#aaed3743a52246b0f7bf03995e1c12081" > GraphEngine::calculateRHSAndEnergy< / a > (< / div >
< div class = "line" > < a id = "l00058" name = "l00058" > < / a > < span class = "lineno" > 58< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l00059" name = "l00059" > < / a > < span class = "lineno" > 59< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00060" name = "l00060" > < / a > < span class = "lineno" > 60< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00061" name = "l00061" > < / a > < span class = "lineno" > 61< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00062" name = "l00062" > < / a > < span class = "lineno" > 62< / span > < span class = "keywordflow" > if< / span > (< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de" > m_usePrecomputation< / a > ) {< / div >
< div class = "line" > < a id = "l00063" name = "l00063" > < / a > < span class = "lineno" > 63< / span > std::vector< double> bare_rates;< / div >
< div class = "line" > < a id = "l00064" name = "l00064" > < / a > < span class = "lineno" > 64< / span > std::vector< double> bare_reverse_rates;< / div >
< div class = "line" > < a id = "l00065" name = "l00065" > < / a > < span class = "lineno" > 65< / span > bare_rates.reserve(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > .size());< / div >
< div class = "line" > < a id = "l00066" name = "l00066" > < / a > < span class = "lineno" > 66< / span > bare_reverse_rates.reserve(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > .size());< / div >
< div class = "line" > < a id = "l00067" name = "l00067" > < / a > < span class = "lineno" > 67< / span > < / div >
< div class = "line" > < a id = "l00068" name = "l00068" > < / a > < span class = "lineno" > 68< / span > < span class = "comment" > // TODO: Add cache to this< / span > < / div >
< div class = "line" > < a id = "l00069" name = "l00069" > < / a > < span class = "lineno" > 69< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > ) {< / div >
< div class = "line" > < a id = "l00070" name = "l00070" > < / a > < span class = "lineno" > 70< / span > bare_rates.push_back(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .calculate_rate(T9));< / div >
< div class = "line" > < a id = "l00071" name = "l00071" > < / a > < span class = "lineno" > 71< / span > bare_reverse_rates.push_back(< a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28" > calculateReverseRate< / a > (< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > , T9));< / div >
< div class = "line" > < a id = "l00072" name = "l00072" > < / a > < span class = "lineno" > 72< / span > }< / div >
< div class = "line" > < a id = "l00073" name = "l00073" > < / a > < span class = "lineno" > 73< / span > < / div >
< div class = "line" > < a id = "l00074" name = "l00074" > < / a > < span class = "lineno" > 74< / span > < span class = "comment" > // --- The public facing interface can always use the precomputed version since taping is done internally ---< / span > < / div >
< div class = "line" > < a id = "l00075" name = "l00075" > < / a > < span class = "lineno" > 75< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a97f98706b51fbe0d167ed81ffe58c438" > calculateAllDerivativesUsingPrecomputation< / a > (Y, bare_rates, bare_reverse_rates, T9, rho);< / div >
< div class = "line" > < a id = "l00076" name = "l00076" > < / a > < span class = "lineno" > 76< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00077" name = "l00077" > < / a > < span class = "lineno" > 77< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9" > calculateAllDerivatives< double> < / a > (Y, T9, rho);< / div >
< div class = "line" > < a id = "l00078" name = "l00078" > < / a > < span class = "lineno" > 78< / span > }< / div >
< div class = "line" > < a id = "l00079" name = "l00079" > < / a > < span class = "lineno" > 79< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00080" name = "l00080" > < / a > < span class = "lineno" > 80< / span > < / div >
< div class = "foldopen" id = "foldopen00081" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00081" name = "l00081" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f" > 81< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f" > GraphEngine::syncInternalMaps< / a > () {< / div >
< div class = "line" > < a id = "l00082" name = "l00082" > < / a > < span class = "lineno" > 82< / span > LOG_INFO(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Synchronizing internal maps for REACLIB graph network (serif::network::GraphNetwork)..." < / span > );< / div >
< div class = "line" > < a id = "l00083" name = "l00083" > < / a > < span class = "lineno" > 83< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa" > collectNetworkSpecies< / a > ();< / div >
< div class = "line" > < a id = "l00084" name = "l00084" > < / a > < span class = "lineno" > 84< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567" > populateReactionIDMap< / a > ();< / div >
< div class = "line" > < a id = "l00085" name = "l00085" > < / a > < span class = "lineno" > 85< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391" > populateSpeciesToIndexMap< / a > ();< / div >
< div class = "line" > < a id = "l00086" name = "l00086" > < / a > < span class = "lineno" > 86< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a29b338630c959449c15881935ac30746" > collectAtomicReverseRateAtomicBases< / a > ();< / div >
< div class = "line" > < a id = "l00087" name = "l00087" > < / a > < span class = "lineno" > 87< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38" > generateStoichiometryMatrix< / a > ();< / div >
< div class = "line" > < a id = "l00088" name = "l00088" > < / a > < span class = "lineno" > 88< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a8d0c0bd54a2908cff62dae7af0c149b5" > reserveJacobianMatrix< / a > ();< / div >
< div class = "line" > < a id = "l00089" name = "l00089" > < / a > < span class = "lineno" > 89< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889" > recordADTape< / a > ();< / div >
< div class = "line" > < a id = "l00090" name = "l00090" > < / a > < span class = "lineno" > 90< / span > < / div >
< div class = "line" > < a id = "l00091" name = "l00091" > < / a > < span class = "lineno" > 91< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > n = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876" > m_rhsADFun< / a > .Domain();< / div >
< div class = "line" > < a id = "l00092" name = "l00092" > < / a > < span class = "lineno" > 92< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > m = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876" > m_rhsADFun< / a > .Range();< / div >
< div class = "line" > < a id = "l00093" name = "l00093" > < / a > < span class = "lineno" > 93< / span > < / div >
< div class = "line" > < a id = "l00094" name = "l00094" > < / a > < span class = "lineno" > 94< / span > < span class = "keyword" > const< / span > std::vector< bool> select_domain(n, < span class = "keyword" > true< / span > );< / div >
< div class = "line" > < a id = "l00095" name = "l00095" > < / a > < span class = "lineno" > 95< / span > < span class = "keyword" > const< / span > std::vector< bool> select_range(m, < span class = "keyword" > true< / span > );< / div >
< div class = "line" > < a id = "l00096" name = "l00096" > < / a > < span class = "lineno" > 96< / span > < / div >
< div class = "line" > < a id = "l00097" name = "l00097" > < / a > < span class = "lineno" > 97< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876" > m_rhsADFun< / a > .subgraph_sparsity(select_domain, select_range, < span class = "keyword" > false< / span > , < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a19b2eea0e8d05ac90f9fd7120bdc6e06" > m_full_jacobian_sparsity_pattern< / a > );< / div >
< div class = "line" > < a id = "l00098" name = "l00098" > < / a > < span class = "lineno" > 98< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a250cc6350dc052fbdfdf9a02066e7891" > m_jac_work< / a > .clear();< / div >
< div class = "line" > < a id = "l00099" name = "l00099" > < / a > < span class = "lineno" > 99< / span > < / div >
< div class = "line" > < a id = "l00100" name = "l00100" > < / a > < span class = "lineno" > 100< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd" > precomputeNetwork< / a > ();< / div >
< div class = "line" > < a id = "l00101" name = "l00101" > < / a > < span class = "lineno" > 101< / span > LOG_INFO(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Internal maps synchronized. Network contains {} species and {} reactions." < / span > ,< / div >
< div class = "line" > < a id = "l00102" name = "l00102" > < / a > < span class = "lineno" > 102< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size(), < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > .size());< / div >
< div class = "line" > < a id = "l00103" name = "l00103" > < / a > < span class = "lineno" > 103< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00104" name = "l00104" > < / a > < span class = "lineno" > 104< / span > < / div >
< div class = "line" > < a id = "l00105" name = "l00105" > < / a > < span class = "lineno" > 105< / span > < span class = "comment" > // --- Network Graph Construction Methods ---< / span > < / div >
< div class = "foldopen" id = "foldopen00106" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00106" name = "l00106" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa" > 106< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa" > GraphEngine::collectNetworkSpecies< / a > () {< / div >
< div class = "line" > < a id = "l00107" name = "l00107" > < / a > < span class = "lineno" > 107< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .clear();< / div >
< div class = "line" > < a id = "l00108" name = "l00108" > < / a > < span class = "lineno" > 108< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827" > m_networkSpeciesMap< / a > .clear();< / div >
2025-07-01 15:06:22 -04:00
< div class = "line" > < a id = "l00109" name = "l00109" > < / a > < span class = "lineno" > 109< / span > < / div >
2025-07-24 11:10:45 -04:00
< div class = "line" > < a id = "l00110" name = "l00110" > < / a > < span class = "lineno" > 110< / span > std::set< std::string_view> uniqueSpeciesNames;< / div >
< div class = "line" > < a id = "l00111" name = "l00111" > < / a > < span class = "lineno" > 111< / span > < / div >
< div class = "line" > < a id = "l00112" name = "l00112" > < / a > < span class = "lineno" > 112< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > ) {< / div >
< div class = "line" > < a id = "l00113" name = "l00113" > < / a > < span class = "lineno" > 113< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & reactant: < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants()) {< / div >
< div class = "line" > < a id = "l00114" name = "l00114" > < / a > < span class = "lineno" > 114< / span > uniqueSpeciesNames.insert(reactant.name());< / div >
< div class = "line" > < a id = "l00115" name = "l00115" > < / a > < span class = "lineno" > 115< / span > }< / div >
< div class = "line" > < a id = "l00116" name = "l00116" > < / a > < span class = "lineno" > 116< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & product: < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products()) {< / div >
< div class = "line" > < a id = "l00117" name = "l00117" > < / a > < span class = "lineno" > 117< / span > uniqueSpeciesNames.insert(product.name());< / div >
< div class = "line" > < a id = "l00118" name = "l00118" > < / a > < span class = "lineno" > 118< / span > }< / div >
< div class = "line" > < a id = "l00119" name = "l00119" > < / a > < span class = "lineno" > 119< / span > }< / div >
< div class = "line" > < a id = "l00120" name = "l00120" > < / a > < span class = "lineno" > 120< / span > < / div >
< div class = "line" > < a id = "l00121" name = "l00121" > < / a > < span class = "lineno" > 121< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & name: uniqueSpeciesNames) {< / div >
< div class = "line" > < a id = "l00122" name = "l00122" > < / a > < span class = "lineno" > 122< / span > < span class = "keyword" > auto< / span > it = fourdst::atomic::species.find(std::string(name));< / div >
< div class = "line" > < a id = "l00123" name = "l00123" > < / a > < span class = "lineno" > 123< / span > < span class = "keywordflow" > if< / span > (it != fourdst::atomic::species.end()) {< / div >
< div class = "line" > < a id = "l00124" name = "l00124" > < / a > < span class = "lineno" > 124< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .push_back(it-> second);< / div >
< div class = "line" > < a id = "l00125" name = "l00125" > < / a > < span class = "lineno" > 125< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827" > m_networkSpeciesMap< / a > .insert({name, it-> second});< / div >
< div class = "line" > < a id = "l00126" name = "l00126" > < / a > < span class = "lineno" > 126< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00127" name = "l00127" > < / a > < span class = "lineno" > 127< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Species ' {}' not found in global atomic species database." < / span > , name);< / div >
< div class = "line" > < a id = "l00128" name = "l00128" > < / a > < span class = "lineno" > 128< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00129" name = "l00129" > < / a > < span class = "lineno" > 129< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " Species not found in global atomic species database: " < / span > + std::string(name));< / div >
< div class = "line" > < a id = "l00130" name = "l00130" > < / a > < span class = "lineno" > 130< / span > }< / div >
< div class = "line" > < a id = "l00131" name = "l00131" > < / a > < span class = "lineno" > 131< / span > }< / div >
< div class = "line" > < a id = "l00132" name = "l00132" > < / a > < span class = "lineno" > 132< / span > < / div >
< div class = "line" > < a id = "l00133" name = "l00133" > < / a > < span class = "lineno" > 133< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00134" name = "l00134" > < / a > < span class = "lineno" > 134< / span > < / div >
< div class = "foldopen" id = "foldopen00135" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00135" name = "l00135" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567" > 135< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567" > GraphEngine::populateReactionIDMap< / a > () {< / div >
< div class = "line" > < a id = "l00136" name = "l00136" > < / a > < span class = "lineno" > 136< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Populating reaction ID map for REACLIB graph network (serif::network::GraphNetwork)..." < / span > );< / div >
< div class = "line" > < a id = "l00137" name = "l00137" > < / a > < span class = "lineno" > 137< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3" > m_reactionIDMap< / a > .clear();< / div >
< div class = "line" > < a id = "l00138" name = "l00138" > < / a > < span class = "lineno" > 138< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > auto< / span > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > ) {< / div >
< div class = "line" > < a id = "l00139" name = "l00139" > < / a > < span class = "lineno" > 139< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3" > m_reactionIDMap< / a > .emplace(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id(), & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > );< / div >
< div class = "line" > < a id = "l00140" name = "l00140" > < / a > < span class = "lineno" > 140< / span > }< / div >
< div class = "line" > < a id = "l00141" name = "l00141" > < / a > < span class = "lineno" > 141< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Populated {} reactions in the reaction ID map." < / span > , < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3" > m_reactionIDMap< / a > .size());< / div >
< div class = "line" > < a id = "l00142" name = "l00142" > < / a > < span class = "lineno" > 142< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00143" name = "l00143" > < / a > < span class = "lineno" > 143< / span > < / div >
< div class = "foldopen" id = "foldopen00144" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00144" name = "l00144" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391" > 144< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391" > GraphEngine::populateSpeciesToIndexMap< / a > () {< / div >
< div class = "line" > < a id = "l00145" name = "l00145" > < / a > < span class = "lineno" > 145< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7" > m_speciesToIndexMap< / a > .clear();< / div >
< div class = "line" > < a id = "l00146" name = "l00146" > < / a > < span class = "lineno" > 146< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size(); ++i) {< / div >
< div class = "line" > < a id = "l00147" name = "l00147" > < / a > < span class = "lineno" > 147< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7" > m_speciesToIndexMap< / a > .insert({< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > [i], i});< / div >
< div class = "line" > < a id = "l00148" name = "l00148" > < / a > < span class = "lineno" > 148< / span > }< / div >
< div class = "line" > < a id = "l00149" name = "l00149" > < / a > < span class = "lineno" > 149< / span > }< / div >
< / div >
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< div class = "line" > < a id = "l00150" name = "l00150" > < / a > < span class = "lineno" > 150< / span > < / div >
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< div class = "foldopen" id = "foldopen00151" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00151" name = "l00151" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a8d0c0bd54a2908cff62dae7af0c149b5" > 151< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a8d0c0bd54a2908cff62dae7af0c149b5" > GraphEngine::reserveJacobianMatrix< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00152" name = "l00152" > < / a > < span class = "lineno" > 152< / span > < span class = "comment" > // The implementation of this function (and others) constrains this nuclear network to a constant temperature and density during< / span > < / div >
< div class = "line" > < a id = "l00153" name = "l00153" > < / a > < span class = "lineno" > 153< / span > < span class = "comment" > // each evaluation.< / span > < / div >
< div class = "line" > < a id = "l00154" name = "l00154" > < / a > < span class = "lineno" > 154< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > numSpecies = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size();< / div >
< div class = "line" > < a id = "l00155" name = "l00155" > < / a > < span class = "lineno" > 155< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910" > m_jacobianMatrix< / a > .clear();< / div >
< div class = "line" > < a id = "l00156" name = "l00156" > < / a > < span class = "lineno" > 156< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910" > m_jacobianMatrix< / a > .resize(numSpecies, numSpecies, < span class = "keyword" > false< / span > ); < span class = "comment" > // Sparse matrix, no initial values< / span > < / div >
< div class = "line" > < a id = "l00157" name = "l00157" > < / a > < span class = "lineno" > 157< / span > LOG_TRACE_L2(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Jacobian matrix resized to {} rows and {} columns." < / span > ,< / div >
< div class = "line" > < a id = "l00158" name = "l00158" > < / a > < span class = "lineno" > 158< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910" > m_jacobianMatrix< / a > .size1(), < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910" > m_jacobianMatrix< / a > .size2());< / div >
< div class = "line" > < a id = "l00159" name = "l00159" > < / a > < span class = "lineno" > 159< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00160" name = "l00160" > < / a > < span class = "lineno" > 160< / span > < / div >
< div class = "line" > < a id = "l00161" name = "l00161" > < / a > < span class = "lineno" > 161< / span > < span class = "comment" > // --- Basic Accessors and Queries ---< / span > < / div >
< div class = "foldopen" id = "foldopen00162" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00162" name = "l00162" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767" > 162< / a > < / span > < span class = "keyword" > const< / span > std::vector< fourdst::atomic::Species> & < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767" > GraphEngine::getNetworkSpecies< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00163" name = "l00163" > < / a > < span class = "lineno" > 163< / span > < span class = "comment" > // Returns a constant reference to the vector of unique species in the network.< / span > < / div >
< div class = "line" > < a id = "l00164" name = "l00164" > < / a > < span class = "lineno" > 164< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Providing access to network species vector. Size: {}." < / span > , < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size());< / div >
< div class = "line" > < a id = "l00165" name = "l00165" > < / a > < span class = "lineno" > 165< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > ;< / div >
< div class = "line" > < a id = "l00166" name = "l00166" > < / a > < span class = "lineno" > 166< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00167" name = "l00167" > < / a > < span class = "lineno" > 167< / span > < / div >
< div class = "foldopen" id = "foldopen00168" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00168" name = "l00168" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da" > 168< / a > < / span > < span class = "keyword" > const< / span > < a class = "code hl_typedef" href = "namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" > reaction::LogicalReactionSet< / a > & < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da" > GraphEngine::getNetworkReactions< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00169" name = "l00169" > < / a > < span class = "lineno" > 169< / span > < span class = "comment" > // Returns a constant reference to the set of reactions in the network.< / span > < / div >
< div class = "line" > < a id = "l00170" name = "l00170" > < / a > < span class = "lineno" > 170< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Providing access to network reactions set. Size: {}." < / span > , < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > .size());< / div >
< div class = "line" > < a id = "l00171" name = "l00171" > < / a > < span class = "lineno" > 171< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > ;< / div >
< div class = "line" > < a id = "l00172" name = "l00172" > < / a > < span class = "lineno" > 172< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00173" name = "l00173" > < / a > < span class = "lineno" > 173< / span > < / div >
< div class = "foldopen" id = "foldopen00174" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00174" name = "l00174" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a371ba0881d6903ddb2d586faa61805d0" > 174< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a371ba0881d6903ddb2d586faa61805d0" > GraphEngine::setNetworkReactions< / a > (< span class = "keyword" > const< / span > < a class = "code hl_typedef" href = "namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" > reaction::LogicalReactionSet< / a > & reactions) {< / div >
< div class = "line" > < a id = "l00175" name = "l00175" > < / a > < span class = "lineno" > 175< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > = reactions;< / div >
< div class = "line" > < a id = "l00176" name = "l00176" > < / a > < span class = "lineno" > 176< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f" > syncInternalMaps< / a > ();< / div >
< div class = "line" > < a id = "l00177" name = "l00177" > < / a > < span class = "lineno" > 177< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00178" name = "l00178" > < / a > < span class = "lineno" > 178< / span > < / div >
< div class = "foldopen" id = "foldopen00179" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00179" name = "l00179" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b" > 179< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b" > GraphEngine::involvesSpecies< / a > (< span class = "keyword" > const< / span > fourdst::atomic::Species& species)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00180" name = "l00180" > < / a > < span class = "lineno" > 180< / span > < span class = "comment" > // Checks if a given species is present in the network' s species map for efficient lookup.< / span > < / div >
< div class = "line" > < a id = "l00181" name = "l00181" > < / a > < span class = "lineno" > 181< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > bool< / span > found = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827" > m_networkSpeciesMap< / a > .contains(species.name());< / div >
< div class = "line" > < a id = "l00182" name = "l00182" > < / a > < span class = "lineno" > 182< / span > LOG_DEBUG(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Checking if species ' {}' is involved in the network: {}." < / span > , species.name(), found ? < span class = "stringliteral" > " Yes" < / span > : < span class = "stringliteral" > " No" < / span > );< / div >
< div class = "line" > < a id = "l00183" name = "l00183" > < / a > < span class = "lineno" > 183< / span > < span class = "keywordflow" > return< / span > found;< / div >
< div class = "line" > < a id = "l00184" name = "l00184" > < / a > < span class = "lineno" > 184< / span > }< / div >
< / div >
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< div class = "line" > < a id = "l00185" name = "l00185" > < / a > < span class = "lineno" > 185< / span > < / div >
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< div class = "line" > < a id = "l00186" name = "l00186" > < / a > < span class = "lineno" > 186< / span > < span class = "comment" > // --- Validation Methods ---< / span > < / div >
< div class = "foldopen" id = "foldopen00187" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00187" name = "l00187" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be" > 187< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be" > GraphEngine::validateConservation< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00188" name = "l00188" > < / a > < span class = "lineno" > 188< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Validating mass (A) and charge (Z) conservation across all reactions in the network." < / span > );< / div >
< div class = "line" > < a id = "l00189" name = "l00189" > < / a > < span class = "lineno" > 189< / span > < / div >
< div class = "line" > < a id = "l00190" name = "l00190" > < / a > < span class = "lineno" > 190< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > ) {< / div >
< div class = "line" > < a id = "l00191" name = "l00191" > < / a > < span class = "lineno" > 191< / span > uint64_t totalReactantA = 0;< / div >
< div class = "line" > < a id = "l00192" name = "l00192" > < / a > < span class = "lineno" > 192< / span > uint64_t totalReactantZ = 0;< / div >
< div class = "line" > < a id = "l00193" name = "l00193" > < / a > < span class = "lineno" > 193< / span > uint64_t totalProductA = 0;< / div >
< div class = "line" > < a id = "l00194" name = "l00194" > < / a > < span class = "lineno" > 194< / span > uint64_t totalProductZ = 0;< / div >
< div class = "line" > < a id = "l00195" name = "l00195" > < / a > < span class = "lineno" > 195< / span > < / div >
< div class = "line" > < a id = "l00196" name = "l00196" > < / a > < span class = "lineno" > 196< / span > < span class = "comment" > // Calculate total A and Z for reactants< / span > < / div >
< div class = "line" > < a id = "l00197" name = "l00197" > < / a > < span class = "lineno" > 197< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & reactant : < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants()) {< / div >
< div class = "line" > < a id = "l00198" name = "l00198" > < / a > < span class = "lineno" > 198< / span > < span class = "keyword" > auto< / span > it = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827" > m_networkSpeciesMap< / a > .find(reactant.name());< / div >
< div class = "line" > < a id = "l00199" name = "l00199" > < / a > < span class = "lineno" > 199< / span > < span class = "keywordflow" > if< / span > (it != < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827" > m_networkSpeciesMap< / a > .end()) {< / div >
< div class = "line" > < a id = "l00200" name = "l00200" > < / a > < span class = "lineno" > 200< / span > totalReactantA += it-> second.a();< / div >
< div class = "line" > < a id = "l00201" name = "l00201" > < / a > < span class = "lineno" > 201< / span > totalReactantZ += it-> second.z();< / div >
< div class = "line" > < a id = "l00202" name = "l00202" > < / a > < span class = "lineno" > 202< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00203" name = "l00203" > < / a > < span class = "lineno" > 203< / span > < span class = "comment" > // This scenario indicates a severe data integrity issue:< / span > < / div >
< div class = "line" > < a id = "l00204" name = "l00204" > < / a > < span class = "lineno" > 204< / span > < span class = "comment" > // a reactant is part of a reaction but not in the network' s species map.< / span > < / div >
< div class = "line" > < a id = "l00205" name = "l00205" > < / a > < span class = "lineno" > 205< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " CRITICAL ERROR: Reactant species ' {}' in reaction ' {}' not found in network species map during conservation validation." < / span > ,< / div >
< div class = "line" > < a id = "l00206" name = "l00206" > < / a > < span class = "lineno" > 206< / span > reactant.name(), < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id());< / div >
< div class = "line" > < a id = "l00207" name = "l00207" > < / a > < span class = "lineno" > 207< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > false< / span > ;< / div >
< div class = "line" > < a id = "l00208" name = "l00208" > < / a > < span class = "lineno" > 208< / span > }< / div >
< div class = "line" > < a id = "l00209" name = "l00209" > < / a > < span class = "lineno" > 209< / span > }< / div >
< div class = "line" > < a id = "l00210" name = "l00210" > < / a > < span class = "lineno" > 210< / span > < / div >
< div class = "line" > < a id = "l00211" name = "l00211" > < / a > < span class = "lineno" > 211< / span > < span class = "comment" > // Calculate total A and Z for products< / span > < / div >
< div class = "line" > < a id = "l00212" name = "l00212" > < / a > < span class = "lineno" > 212< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & product : < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products()) {< / div >
< div class = "line" > < a id = "l00213" name = "l00213" > < / a > < span class = "lineno" > 213< / span > < span class = "keyword" > auto< / span > it = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827" > m_networkSpeciesMap< / a > .find(product.name());< / div >
< div class = "line" > < a id = "l00214" name = "l00214" > < / a > < span class = "lineno" > 214< / span > < span class = "keywordflow" > if< / span > (it != < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827" > m_networkSpeciesMap< / a > .end()) {< / div >
< div class = "line" > < a id = "l00215" name = "l00215" > < / a > < span class = "lineno" > 215< / span > totalProductA += it-> second.a();< / div >
< div class = "line" > < a id = "l00216" name = "l00216" > < / a > < span class = "lineno" > 216< / span > totalProductZ += it-> second.z();< / div >
< div class = "line" > < a id = "l00217" name = "l00217" > < / a > < span class = "lineno" > 217< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00218" name = "l00218" > < / a > < span class = "lineno" > 218< / span > < span class = "comment" > // Similar critical error for product species< / span > < / div >
< div class = "line" > < a id = "l00219" name = "l00219" > < / a > < span class = "lineno" > 219< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " CRITICAL ERROR: Product species ' {}' in reaction ' {}' not found in network species map during conservation validation." < / span > ,< / div >
< div class = "line" > < a id = "l00220" name = "l00220" > < / a > < span class = "lineno" > 220< / span > product.name(), < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id());< / div >
< div class = "line" > < a id = "l00221" name = "l00221" > < / a > < span class = "lineno" > 221< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > false< / span > ;< / div >
< div class = "line" > < a id = "l00222" name = "l00222" > < / a > < span class = "lineno" > 222< / span > }< / div >
< div class = "line" > < a id = "l00223" name = "l00223" > < / a > < span class = "lineno" > 223< / span > }< / div >
< div class = "line" > < a id = "l00224" name = "l00224" > < / a > < span class = "lineno" > 224< / span > < / div >
< div class = "line" > < a id = "l00225" name = "l00225" > < / a > < span class = "lineno" > 225< / span > < span class = "comment" > // Compare totals for conservation< / span > < / div >
< div class = "line" > < a id = "l00226" name = "l00226" > < / a > < span class = "lineno" > 226< / span > < span class = "keywordflow" > if< / span > (totalReactantA != totalProductA) {< / div >
< div class = "line" > < a id = "l00227" name = "l00227" > < / a > < span class = "lineno" > 227< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Mass number (A) not conserved for reaction ' {}' : Reactants A={} vs Products A={}." < / span > ,< / div >
< div class = "line" > < a id = "l00228" name = "l00228" > < / a > < span class = "lineno" > 228< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id(), totalReactantA, totalProductA);< / div >
< div class = "line" > < a id = "l00229" name = "l00229" > < / a > < span class = "lineno" > 229< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > false< / span > ;< / div >
< div class = "line" > < a id = "l00230" name = "l00230" > < / a > < span class = "lineno" > 230< / span > }< / div >
< div class = "line" > < a id = "l00231" name = "l00231" > < / a > < span class = "lineno" > 231< / span > < span class = "keywordflow" > if< / span > (totalReactantZ != totalProductZ) {< / div >
< div class = "line" > < a id = "l00232" name = "l00232" > < / a > < span class = "lineno" > 232< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Atomic number (Z) not conserved for reaction ' {}' : Reactants Z={} vs Products Z={}." < / span > ,< / div >
< div class = "line" > < a id = "l00233" name = "l00233" > < / a > < span class = "lineno" > 233< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id(), totalReactantZ, totalProductZ);< / div >
< div class = "line" > < a id = "l00234" name = "l00234" > < / a > < span class = "lineno" > 234< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > false< / span > ;< / div >
< div class = "line" > < a id = "l00235" name = "l00235" > < / a > < span class = "lineno" > 235< / span > }< / div >
< div class = "line" > < a id = "l00236" name = "l00236" > < / a > < span class = "lineno" > 236< / span > }< / div >
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< div class = "line" > < a id = "l00237" name = "l00237" > < / a > < span class = "lineno" > 237< / span > < / div >
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< div class = "line" > < a id = "l00238" name = "l00238" > < / a > < span class = "lineno" > 238< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Mass (A) and charge (Z) conservation validated successfully for all reactions." < / span > );< / div >
< div class = "line" > < a id = "l00239" name = "l00239" > < / a > < span class = "lineno" > 239< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > true< / span > ; < span class = "comment" > // All reactions passed the conservation check< / span > < / div >
< div class = "line" > < a id = "l00240" name = "l00240" > < / a > < span class = "lineno" > 240< / span > }< / div >
< / div >
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< div class = "line" > < a id = "l00241" name = "l00241" > < / a > < span class = "lineno" > 241< / span > < / div >
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< div class = "foldopen" id = "foldopen00242" data-start = "{" data-end = "}" >
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< div class = "line" > < a id = "l00242" name = "l00242" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28" > 242< / a > < / span > < span class = "keywordtype" > double< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28" > GraphEngine::calculateReverseRate< / a > (< / div >
< div class = "line" > < a id = "l00243" name = "l00243" > < / a > < span class = "lineno" > 243< / span > < span class = "keyword" > const< / span > < a class = "code hl_class" href = "classgridfire_1_1reaction_1_1_reaction.html" > reaction::Reaction< / a > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > ,< / div >
< div class = "line" > < a id = "l00244" name = "l00244" > < / a > < span class = "lineno" > 244< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9< / div >
< div class = "line" > < a id = "l00245" name = "l00245" > < / a > < span class = "lineno" > 245< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00246" name = "l00246" > < / a > < span class = "lineno" > 246< / span > < span class = "keywordflow" > if< / span > (!< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc" > m_useReverseReactions< / a > ) {< / div >
< div class = "line" > < a id = "l00247" name = "l00247" > < / a > < span class = "lineno" > 247< / span > LOG_TRACE_L3_LIMIT_EVERY_N(std::numeric_limits< int> ::max(), < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Reverse reactions are disabled. Returning 0.0 for reverse rate of reaction ' {}' ." < / span > , < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id());< / div >
< div class = "line" > < a id = "l00248" name = "l00248" > < / a > < span class = "lineno" > 248< / span > < span class = "keywordflow" > return< / span > 0.0; < span class = "comment" > // If reverse reactions are not used, return 0.0< / span > < / div >
< div class = "line" > < a id = "l00249" name = "l00249" > < / a > < span class = "lineno" > 249< / span > }< / div >
< div class = "line" > < a id = "l00250" name = "l00250" > < / a > < span class = "lineno" > 250< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > temp = T9 * 1e9; < span class = "comment" > // Convert T9 to Kelvin< / span > < / div >
< div class = "line" > < a id = "l00251" name = "l00251" > < / a > < span class = "lineno" > 251< / span > < / div >
< div class = "line" > < a id = "l00252" name = "l00252" > < / a > < span class = "lineno" > 252< / span > < span class = "comment" > // In debug builds we check the units on kB to ensure it is in erg/K. This is removed in release builds to avoid overhead. (Note assert is a no-op in release builds)< / span > < / div >
< div class = "line" > < a id = "l00253" name = "l00253" > < / a > < span class = "lineno" > 253< / span > assert(Constants::getInstance().get(< span class = "stringliteral" > " kB" < / span > ).unit == < span class = "stringliteral" > " erg / K" < / span > );< / div >
< div class = "line" > < a id = "l00254" name = "l00254" > < / a > < span class = "lineno" > 254< / span > < / div >
< div class = "line" > < a id = "l00255" name = "l00255" > < / a > < span class = "lineno" > 255< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > kBMeV = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e" > m_constants< / a > .kB * 624151; < span class = "comment" > // Convert kB to MeV/K NOTE: This relies on the fact that m_constants.kB is in erg/K!< / span > < / div >
< div class = "line" > < a id = "l00256" name = "l00256" > < / a > < span class = "lineno" > 256< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > expFactor = std::exp(-< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .qValue() / (kBMeV * temp));< / div >
< div class = "line" > < a id = "l00257" name = "l00257" > < / a > < span class = "lineno" > 257< / span > < span class = "keywordtype" > double< / span > reverseRate = 0.0;< / div >
< div class = "line" > < a id = "l00258" name = "l00258" > < / a > < span class = "lineno" > 258< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > forwardRate = < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .calculate_rate(T9);< / div >
< div class = "line" > < a id = "l00259" name = "l00259" > < / a > < span class = "lineno" > 259< / span > < / div >
< div class = "line" > < a id = "l00260" name = "l00260" > < / a > < span class = "lineno" > 260< / span > < span class = "keywordflow" > if< / span > (< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants().size() == 2 & & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products().size() == 2) {< / div >
< div class = "line" > < a id = "l00261" name = "l00261" > < / a > < span class = "lineno" > 261< / span > reverseRate = < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755" > calculateReverseRateTwoBody< / a > (< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > , T9, forwardRate, expFactor);< / div >
< div class = "line" > < a id = "l00262" name = "l00262" > < / a > < span class = "lineno" > 262< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00263" name = "l00263" > < / a > < span class = "lineno" > 263< / span > LOG_WARNING_LIMIT_EVERY_N(1000000, < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Reverse rate calculation for reactions with more than two reactants or products is not implemented (reaction id {})." < / span > , < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .peName());< / div >
< div class = "line" > < a id = "l00264" name = "l00264" > < / a > < span class = "lineno" > 264< / span > }< / div >
< div class = "line" > < a id = "l00265" name = "l00265" > < / a > < span class = "lineno" > 265< / span > LOG_TRACE_L2_LIMIT_EVERY_N(1000, < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Calculated reverse rate for reaction ' {}' : {:.3E} at T9={:.3E}." < / span > , < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id(), reverseRate, T9);< / div >
< div class = "line" > < a id = "l00266" name = "l00266" > < / a > < span class = "lineno" > 266< / span > < span class = "keywordflow" > return< / span > reverseRate;< / div >
< div class = "line" > < a id = "l00267" name = "l00267" > < / a > < span class = "lineno" > 267< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00268" name = "l00268" > < / a > < span class = "lineno" > 268< / span > < / div >
< div class = "foldopen" id = "foldopen00269" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00269" name = "l00269" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755" > 269< / a > < / span > < span class = "keywordtype" > double< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755" > GraphEngine::calculateReverseRateTwoBody< / a > (< / div >
< div class = "line" > < a id = "l00270" name = "l00270" > < / a > < span class = "lineno" > 270< / span > < span class = "keyword" > const< / span > < a class = "code hl_class" href = "classgridfire_1_1reaction_1_1_reaction.html" > reaction::Reaction< / a > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > ,< / div >
< div class = "line" > < a id = "l00271" name = "l00271" > < / a > < span class = "lineno" > 271< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00272" name = "l00272" > < / a > < span class = "lineno" > 272< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > forwardRate,< / div >
< div class = "line" > < a id = "l00273" name = "l00273" > < / a > < span class = "lineno" > 273< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > expFactor< / div >
< div class = "line" > < a id = "l00274" name = "l00274" > < / a > < span class = "lineno" > 274< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00275" name = "l00275" > < / a > < span class = "lineno" > 275< / span > std::vector< double> reactantPartitionFunctions;< / div >
< div class = "line" > < a id = "l00276" name = "l00276" > < / a > < span class = "lineno" > 276< / span > std::vector< double> productPartitionFunctions;< / div >
< div class = "line" > < a id = "l00277" name = "l00277" > < / a > < span class = "lineno" > 277< / span > < / div >
< div class = "line" > < a id = "l00278" name = "l00278" > < / a > < span class = "lineno" > 278< / span > reactantPartitionFunctions.reserve(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants().size());< / div >
< div class = "line" > < a id = "l00279" name = "l00279" > < / a > < span class = "lineno" > 279< / span > productPartitionFunctions.reserve(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products().size());< / div >
< div class = "line" > < a id = "l00280" name = "l00280" > < / a > < span class = "lineno" > 280< / span > < / div >
< div class = "line" > < a id = "l00281" name = "l00281" > < / a > < span class = "lineno" > 281< / span > std::unordered_map< fourdst::atomic::Species, int> reactantMultiplicity;< / div >
< div class = "line" > < a id = "l00282" name = "l00282" > < / a > < span class = "lineno" > 282< / span > std::unordered_map< fourdst::atomic::Species, int> productMultiplicity;< / div >
< div class = "line" > < a id = "l00283" name = "l00283" > < / a > < span class = "lineno" > 283< / span > < / div >
< div class = "line" > < a id = "l00284" name = "l00284" > < / a > < span class = "lineno" > 284< / span > reactantMultiplicity.reserve(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants().size());< / div >
< div class = "line" > < a id = "l00285" name = "l00285" > < / a > < span class = "lineno" > 285< / span > productMultiplicity.reserve(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products().size());< / div >
< div class = "line" > < a id = "l00286" name = "l00286" > < / a > < span class = "lineno" > 286< / span > < / div >
< div class = "line" > < a id = "l00287" name = "l00287" > < / a > < span class = "lineno" > 287< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & reactant : < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants()) {< / div >
< div class = "line" > < a id = "l00288" name = "l00288" > < / a > < span class = "lineno" > 288< / span > reactantMultiplicity[reactant] += 1;< / div >
< div class = "line" > < a id = "l00289" name = "l00289" > < / a > < span class = "lineno" > 289< / span > }< / div >
< div class = "line" > < a id = "l00290" name = "l00290" > < / a > < span class = "lineno" > 290< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & product : < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products()) {< / div >
< div class = "line" > < a id = "l00291" name = "l00291" > < / a > < span class = "lineno" > 291< / span > productMultiplicity[product] += 1;< / div >
< div class = "line" > < a id = "l00292" name = "l00292" > < / a > < span class = "lineno" > 292< / span > }< / div >
< div class = "line" > < a id = "l00293" name = "l00293" > < / a > < span class = "lineno" > 293< / span > < span class = "keywordtype" > double< / span > reactantSymmetryFactor = 1.0;< / div >
< div class = "line" > < a id = "l00294" name = "l00294" > < / a > < span class = "lineno" > 294< / span > < span class = "keywordtype" > double< / span > productSymmetryFactor = 1.0;< / div >
< div class = "line" > < a id = "l00295" name = "l00295" > < / a > < span class = "lineno" > 295< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & count : reactantMultiplicity | std::views::values) {< / div >
< div class = "line" > < a id = "l00296" name = "l00296" > < / a > < span class = "lineno" > 296< / span > reactantSymmetryFactor *= std::tgamma(count + 1);< / div >
< div class = "line" > < a id = "l00297" name = "l00297" > < / a > < span class = "lineno" > 297< / span > }< / div >
< div class = "line" > < a id = "l00298" name = "l00298" > < / a > < span class = "lineno" > 298< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & count : productMultiplicity | std::views::values) {< / div >
< div class = "line" > < a id = "l00299" name = "l00299" > < / a > < span class = "lineno" > 299< / span > productSymmetryFactor *= std::tgamma(count + 1);< / div >
< div class = "line" > < a id = "l00300" name = "l00300" > < / a > < span class = "lineno" > 300< / span > }< / div >
< div class = "line" > < a id = "l00301" name = "l00301" > < / a > < span class = "lineno" > 301< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > symmetryFactor = reactantSymmetryFactor / productSymmetryFactor;< / div >
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< div class = "line" > < a id = "l00302" name = "l00302" > < / a > < span class = "lineno" > 302< / span > < / div >
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< div class = "line" > < a id = "l00303" name = "l00303" > < / a > < span class = "lineno" > 303< / span > < span class = "comment" > // Accumulate mass terms< / span > < / div >
< div class = "line" > < a id = "l00304" name = "l00304" > < / a > < span class = "lineno" > 304< / span > < span class = "keyword" > auto< / span > mass_op = [](< span class = "keywordtype" > double< / span > acc, < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species) { < span class = "keywordflow" > return< / span > acc * species.a(); };< / div >
< div class = "line" > < a id = "l00305" name = "l00305" > < / a > < span class = "lineno" > 305< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > massNumerator = std::accumulate(< / div >
< div class = "line" > < a id = "l00306" name = "l00306" > < / a > < span class = "lineno" > 306< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants().begin(),< / div >
< div class = "line" > < a id = "l00307" name = "l00307" > < / a > < span class = "lineno" > 307< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants().end(),< / div >
< div class = "line" > < a id = "l00308" name = "l00308" > < / a > < span class = "lineno" > 308< / span > 1.0,< / div >
< div class = "line" > < a id = "l00309" name = "l00309" > < / a > < span class = "lineno" > 309< / span > mass_op< / div >
< div class = "line" > < a id = "l00310" name = "l00310" > < / a > < span class = "lineno" > 310< / span > );< / div >
< div class = "line" > < a id = "l00311" name = "l00311" > < / a > < span class = "lineno" > 311< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > massDenominator = std::accumulate(< / div >
< div class = "line" > < a id = "l00312" name = "l00312" > < / a > < span class = "lineno" > 312< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products().begin(),< / div >
< div class = "line" > < a id = "l00313" name = "l00313" > < / a > < span class = "lineno" > 313< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products().end(),< / div >
< div class = "line" > < a id = "l00314" name = "l00314" > < / a > < span class = "lineno" > 314< / span > 1.0,< / div >
< div class = "line" > < a id = "l00315" name = "l00315" > < / a > < span class = "lineno" > 315< / span > mass_op< / div >
< div class = "line" > < a id = "l00316" name = "l00316" > < / a > < span class = "lineno" > 316< / span > );< / div >
< div class = "line" > < a id = "l00317" name = "l00317" > < / a > < span class = "lineno" > 317< / span > < / div >
< div class = "line" > < a id = "l00318" name = "l00318" > < / a > < span class = "lineno" > 318< / span > < span class = "comment" > // Accumulate partition functions< / span > < / div >
< div class = "line" > < a id = "l00319" name = "l00319" > < / a > < span class = "lineno" > 319< / span > < span class = "keyword" > auto< / span > pf_op = [& ](< span class = "keywordtype" > double< / span > acc, < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species) {< / div >
< div class = "line" > < a id = "l00320" name = "l00320" > < / a > < span class = "lineno" > 320< / span > < span class = "keywordflow" > return< / span > acc * < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e" > m_partitionFunction< / a > -> evaluate(species.z(), species.a(), T9);< / div >
< div class = "line" > < a id = "l00321" name = "l00321" > < / a > < span class = "lineno" > 321< / span > };< / div >
< div class = "line" > < a id = "l00322" name = "l00322" > < / a > < span class = "lineno" > 322< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > partitionFunctionNumerator = std::accumulate(< / div >
< div class = "line" > < a id = "l00323" name = "l00323" > < / a > < span class = "lineno" > 323< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants().begin(),< / div >
< div class = "line" > < a id = "l00324" name = "l00324" > < / a > < span class = "lineno" > 324< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants().end(),< / div >
< div class = "line" > < a id = "l00325" name = "l00325" > < / a > < span class = "lineno" > 325< / span > 1.0,< / div >
< div class = "line" > < a id = "l00326" name = "l00326" > < / a > < span class = "lineno" > 326< / span > pf_op< / div >
< div class = "line" > < a id = "l00327" name = "l00327" > < / a > < span class = "lineno" > 327< / span > );< / div >
< div class = "line" > < a id = "l00328" name = "l00328" > < / a > < span class = "lineno" > 328< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > partitionFunctionDenominator = std::accumulate(< / div >
< div class = "line" > < a id = "l00329" name = "l00329" > < / a > < span class = "lineno" > 329< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products().begin(),< / div >
< div class = "line" > < a id = "l00330" name = "l00330" > < / a > < span class = "lineno" > 330< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products().end(),< / div >
< div class = "line" > < a id = "l00331" name = "l00331" > < / a > < span class = "lineno" > 331< / span > 1.0,< / div >
< div class = "line" > < a id = "l00332" name = "l00332" > < / a > < span class = "lineno" > 332< / span > pf_op< / div >
< div class = "line" > < a id = "l00333" name = "l00333" > < / a > < span class = "lineno" > 333< / span > );< / div >
< div class = "line" > < a id = "l00334" name = "l00334" > < / a > < span class = "lineno" > 334< / span > < / div >
< div class = "line" > < a id = "l00335" name = "l00335" > < / a > < span class = "lineno" > 335< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > CT = std::pow(massNumerator/massDenominator, 1.5) *< / div >
< div class = "line" > < a id = "l00336" name = "l00336" > < / a > < span class = "lineno" > 336< / span > (partitionFunctionNumerator/partitionFunctionDenominator);< / div >
< div class = "line" > < a id = "l00337" name = "l00337" > < / a > < span class = "lineno" > 337< / span > < / div >
< div class = "line" > < a id = "l00338" name = "l00338" > < / a > < span class = "lineno" > 338< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > reverseRate = forwardRate * symmetryFactor * CT * expFactor;< / div >
< div class = "line" > < a id = "l00339" name = "l00339" > < / a > < span class = "lineno" > 339< / span > < span class = "keywordflow" > if< / span > (!std::isfinite(reverseRate)) {< / div >
< div class = "line" > < a id = "l00340" name = "l00340" > < / a > < span class = "lineno" > 340< / span > < span class = "keywordflow" > return< / span > 0.0; < span class = "comment" > // If the reverse rate is not finite, return 0.0< / span > < / div >
< div class = "line" > < a id = "l00341" name = "l00341" > < / a > < span class = "lineno" > 341< / span > }< / div >
< div class = "line" > < a id = "l00342" name = "l00342" > < / a > < span class = "lineno" > 342< / span > < span class = "keywordflow" > return< / span > reverseRate; < span class = "comment" > // Return the calculated reverse rate< / span > < / div >
< div class = "line" > < a id = "l00343" name = "l00343" > < / a > < span class = "lineno" > 343< / span > < / div >
< div class = "line" > < a id = "l00344" name = "l00344" > < / a > < span class = "lineno" > 344< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00345" name = "l00345" > < / a > < span class = "lineno" > 345< / span > < / div >
< div class = "foldopen" id = "foldopen00346" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00346" name = "l00346" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#af28950c5af3a92eb03a1a64ed0f913e7" > 346< / a > < / span > < span class = "keywordtype" > double< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#af28950c5af3a92eb03a1a64ed0f913e7" > GraphEngine::calculateReverseRateTwoBodyDerivative< / a > (< / div >
< div class = "line" > < a id = "l00347" name = "l00347" > < / a > < span class = "lineno" > 347< / span > < span class = "keyword" > const< / span > < a class = "code hl_class" href = "classgridfire_1_1reaction_1_1_reaction.html" > reaction::Reaction< / a > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > ,< / div >
< div class = "line" > < a id = "l00348" name = "l00348" > < / a > < span class = "lineno" > 348< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00349" name = "l00349" > < / a > < span class = "lineno" > 349< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > reverseRate< / div >
< div class = "line" > < a id = "l00350" name = "l00350" > < / a > < span class = "lineno" > 350< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00351" name = "l00351" > < / a > < span class = "lineno" > 351< / span > < span class = "keywordflow" > if< / span > (!< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc" > m_useReverseReactions< / a > ) {< / div >
< div class = "line" > < a id = "l00352" name = "l00352" > < / a > < span class = "lineno" > 352< / span > LOG_TRACE_L3_LIMIT_EVERY_N(std::numeric_limits< int> ::max(), < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Reverse reactions are disabled. Returning 0.0 for reverse rate of reaction ' {}' ." < / span > , < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id());< / div >
< div class = "line" > < a id = "l00353" name = "l00353" > < / a > < span class = "lineno" > 353< / span > < span class = "keywordflow" > return< / span > 0.0; < span class = "comment" > // If reverse reactions are not used, return 0.0< / span > < / div >
< div class = "line" > < a id = "l00354" name = "l00354" > < / a > < span class = "lineno" > 354< / span > }< / div >
< div class = "line" > < a id = "l00355" name = "l00355" > < / a > < span class = "lineno" > 355< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > d_log_kFwd = < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .calculate_forward_rate_log_derivative(T9);< / div >
< div class = "line" > < a id = "l00356" name = "l00356" > < / a > < span class = "lineno" > 356< / span > < / div >
< div class = "line" > < a id = "l00357" name = "l00357" > < / a > < span class = "lineno" > 357< / span > < span class = "keyword" > auto< / span > log_deriv_pf_op = [& ](< span class = "keywordtype" > double< / span > acc, < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species) {< / div >
< div class = "line" > < a id = "l00358" name = "l00358" > < / a > < span class = "lineno" > 358< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > g = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e" > m_partitionFunction< / a > -> evaluate(species.z(), species.a(), T9);< / div >
< div class = "line" > < a id = "l00359" name = "l00359" > < / a > < span class = "lineno" > 359< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > dg_dT = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e" > m_partitionFunction< / a > -> evaluateDerivative(species.z(), species.a(), T9);< / div >
< div class = "line" > < a id = "l00360" name = "l00360" > < / a > < span class = "lineno" > 360< / span > < span class = "keywordflow" > return< / span > (g == 0.0) ? acc : acc + (dg_dT / g);< / div >
< div class = "line" > < a id = "l00361" name = "l00361" > < / a > < span class = "lineno" > 361< / span > };< / div >
< div class = "line" > < a id = "l00362" name = "l00362" > < / a > < span class = "lineno" > 362< / span > < / div >
< div class = "line" > < a id = "l00363" name = "l00363" > < / a > < span class = "lineno" > 363< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > reactant_log_derivative_sum = std::accumulate(< / div >
< div class = "line" > < a id = "l00364" name = "l00364" > < / a > < span class = "lineno" > 364< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants().begin(),< / div >
< div class = "line" > < a id = "l00365" name = "l00365" > < / a > < span class = "lineno" > 365< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants().end(),< / div >
< div class = "line" > < a id = "l00366" name = "l00366" > < / a > < span class = "lineno" > 366< / span > 0.0,< / div >
< div class = "line" > < a id = "l00367" name = "l00367" > < / a > < span class = "lineno" > 367< / span > log_deriv_pf_op< / div >
< div class = "line" > < a id = "l00368" name = "l00368" > < / a > < span class = "lineno" > 368< / span > );< / div >
< div class = "line" > < a id = "l00369" name = "l00369" > < / a > < span class = "lineno" > 369< / span > < / div >
< div class = "line" > < a id = "l00370" name = "l00370" > < / a > < span class = "lineno" > 370< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > product_log_derivative_sum = std::accumulate(< / div >
< div class = "line" > < a id = "l00371" name = "l00371" > < / a > < span class = "lineno" > 371< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products().begin(),< / div >
< div class = "line" > < a id = "l00372" name = "l00372" > < / a > < span class = "lineno" > 372< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products().end(),< / div >
< div class = "line" > < a id = "l00373" name = "l00373" > < / a > < span class = "lineno" > 373< / span > 0.0,< / div >
< div class = "line" > < a id = "l00374" name = "l00374" > < / a > < span class = "lineno" > 374< / span > log_deriv_pf_op< / div >
< div class = "line" > < a id = "l00375" name = "l00375" > < / a > < span class = "lineno" > 375< / span > );< / div >
< div class = "line" > < a id = "l00376" name = "l00376" > < / a > < span class = "lineno" > 376< / span > < / div >
< div class = "line" > < a id = "l00377" name = "l00377" > < / a > < span class = "lineno" > 377< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > d_log_C = reactant_log_derivative_sum - product_log_derivative_sum;< / div >
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< div class = "line" > < a id = "l00378" name = "l00378" > < / a > < span class = "lineno" > 378< / span > < / div >
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< div class = "line" > < a id = "l00379" name = "l00379" > < / a > < span class = "lineno" > 379< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > d_log_exp = < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .qValue() / (< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e" > m_constants< / a > .kB * T9 * T9);< / div >
< div class = "line" > < a id = "l00380" name = "l00380" > < / a > < span class = "lineno" > 380< / span > < / div >
< div class = "line" > < a id = "l00381" name = "l00381" > < / a > < span class = "lineno" > 381< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > log_total_derivative = d_log_kFwd + d_log_C + d_log_exp;< / div >
< div class = "line" > < a id = "l00382" name = "l00382" > < / a > < span class = "lineno" > 382< / span > < / div >
< div class = "line" > < a id = "l00383" name = "l00383" > < / a > < span class = "lineno" > 383< / span > < span class = "keywordflow" > return< / span > reverseRate * log_total_derivative; < span class = "comment" > // Return the derivative of the reverse rate with respect to T9< / span > < / div >
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< div class = "line" > < a id = "l00384" name = "l00384" > < / a > < span class = "lineno" > 384< / span > < / div >
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< div class = "line" > < a id = "l00385" name = "l00385" > < / a > < span class = "lineno" > 385< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00386" name = "l00386" > < / a > < span class = "lineno" > 386< / span > < / div >
< div class = "foldopen" id = "foldopen00387" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00387" name = "l00387" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#ae7a210d9ab13ad5fb0c612f027acabd0" > 387< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#ae7a210d9ab13ad5fb0c612f027acabd0" > GraphEngine::isUsingReverseReactions< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00388" name = "l00388" > < / a > < span class = "lineno" > 388< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc" > m_useReverseReactions< / a > ;< / div >
< div class = "line" > < a id = "l00389" name = "l00389" > < / a > < span class = "lineno" > 389< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00390" name = "l00390" > < / a > < span class = "lineno" > 390< / span > < / div >
< div class = "foldopen" id = "foldopen00391" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00391" name = "l00391" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197" > 391< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197" > GraphEngine::setUseReverseReactions< / a > (< span class = "keyword" > const< / span > < span class = "keywordtype" > bool< / span > useReverse) {< / div >
< div class = "line" > < a id = "l00392" name = "l00392" > < / a > < span class = "lineno" > 392< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc" > m_useReverseReactions< / a > = useReverse;< / div >
< div class = "line" > < a id = "l00393" name = "l00393" > < / a > < span class = "lineno" > 393< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00394" name = "l00394" > < / a > < span class = "lineno" > 394< / span > < / div >
< div class = "foldopen" id = "foldopen00395" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00395" name = "l00395" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda" > 395< / a > < / span > < span class = "keywordtype" > int< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda" > GraphEngine::getSpeciesIndex< / a > (< span class = "keyword" > const< / span > fourdst::atomic::Species & species)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00396" name = "l00396" > < / a > < span class = "lineno" > 396< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7" > m_speciesToIndexMap< / a > .at(species); < span class = "comment" > // Returns the index of the species in the stoichiometry matrix< / span > < / div >
< div class = "line" > < a id = "l00397" name = "l00397" > < / a > < span class = "lineno" > 397< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00398" name = "l00398" > < / a > < span class = "lineno" > 398< / span > < / div >
< div class = "foldopen" id = "foldopen00399" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00399" name = "l00399" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a27f3a928e1f6bbe7e847cffed6db729f" > 399< / a > < / span > std::vector< double> < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a27f3a928e1f6bbe7e847cffed6db729f" > GraphEngine::mapNetInToMolarAbundanceVector< / a > (< span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_net_in.html" > NetIn< / a > & netIn)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00400" name = "l00400" > < / a > < span class = "lineno" > 400< / span > std::vector< double> Y(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size(), 0.0); < span class = "comment" > // Initialize with zeros< / span > < / div >
< div class = "line" > < a id = "l00401" name = "l00401" > < / a > < span class = "lineno" > 401< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & [symbol, entry] : netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1" > composition< / a > ) {< / div >
< div class = "line" > < a id = "l00402" name = "l00402" > < / a > < span class = "lineno" > 402< / span > Y[< a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda" > getSpeciesIndex< / a > (entry.isotope())] = netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1" > composition< / a > .getMolarAbundance(symbol); < span class = "comment" > // Map species to their molar abundance< / span > < / div >
< div class = "line" > < a id = "l00403" name = "l00403" > < / a > < span class = "lineno" > 403< / span > }< / div >
< div class = "line" > < a id = "l00404" name = "l00404" > < / a > < span class = "lineno" > 404< / span > < span class = "keywordflow" > return< / span > Y; < span class = "comment" > // Return the vector of molar abundances< / span > < / div >
< div class = "line" > < a id = "l00405" name = "l00405" > < / a > < span class = "lineno" > 405< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00406" name = "l00406" > < / a > < span class = "lineno" > 406< / span > < / div >
< div class = "foldopen" id = "foldopen00407" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00407" name = "l00407" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#ae7a371be61ab09b3fa4a93f05bd44e5e" > 407< / a > < / span > < a class = "code hl_struct" href = "structgridfire_1_1_priming_report.html" > PrimingReport< / a > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#ae7a371be61ab09b3fa4a93f05bd44e5e" > GraphEngine::primeEngine< / a > (< span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_net_in.html" > NetIn< / a > & netIn) {< / div >
< div class = "line" > < a id = "l00408" name = "l00408" > < / a > < span class = "lineno" > 408< / span > < a class = "code hl_struct" href = "structgridfire_1_1_net_in.html" > NetIn< / a > fullNetIn;< / div >
< div class = "line" > < a id = "l00409" name = "l00409" > < / a > < span class = "lineno" > 409< / span > fourdst::composition::Composition composition;< / div >
< div class = "line" > < a id = "l00410" name = "l00410" > < / a > < span class = "lineno" > 410< / span > < / div >
< div class = "line" > < a id = "l00411" name = "l00411" > < / a > < span class = "lineno" > 411< / span > std::vector< std::string> symbols;< / div >
< div class = "line" > < a id = "l00412" name = "l00412" > < / a > < span class = "lineno" > 412< / span > symbols.reserve(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size());< / div >
< div class = "line" > < a id = "l00413" name = "l00413" > < / a > < span class = "lineno" > 413< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & symbol: < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > ) {< / div >
< div class = "line" > < a id = "l00414" name = "l00414" > < / a > < span class = "lineno" > 414< / span > symbols.emplace_back(symbol.name());< / div >
< div class = "line" > < a id = "l00415" name = "l00415" > < / a > < span class = "lineno" > 415< / span > }< / div >
< div class = "line" > < a id = "l00416" name = "l00416" > < / a > < span class = "lineno" > 416< / span > composition.registerSymbol(symbols);< / div >
< div class = "line" > < a id = "l00417" name = "l00417" > < / a > < span class = "lineno" > 417< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & [symbol, entry] : netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1" > composition< / a > ) {< / div >
< div class = "line" > < a id = "l00418" name = "l00418" > < / a > < span class = "lineno" > 418< / span > < span class = "keywordflow" > if< / span > (< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827" > m_networkSpeciesMap< / a > .contains(symbol)) {< / div >
< div class = "line" > < a id = "l00419" name = "l00419" > < / a > < span class = "lineno" > 419< / span > composition.setMassFraction(symbol, entry.mass_fraction());< / div >
< div class = "line" > < a id = "l00420" name = "l00420" > < / a > < span class = "lineno" > 420< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00421" name = "l00421" > < / a > < span class = "lineno" > 421< / span > composition.setMassFraction(symbol, 0.0);< / div >
< div class = "line" > < a id = "l00422" name = "l00422" > < / a > < span class = "lineno" > 422< / span > }< / div >
< div class = "line" > < a id = "l00423" name = "l00423" > < / a > < span class = "lineno" > 423< / span > }< / div >
< div class = "line" > < a id = "l00424" name = "l00424" > < / a > < span class = "lineno" > 424< / span > composition.finalize(< span class = "keyword" > true< / span > );< / div >
< div class = "line" > < a id = "l00425" name = "l00425" > < / a > < span class = "lineno" > 425< / span > fullNetIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1" > composition< / a > = composition;< / div >
< div class = "line" > < a id = "l00426" name = "l00426" > < / a > < span class = "lineno" > 426< / span > fullNetIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a5be0f5195a5cd1dd177b9fc5ab83a7be" > temperature< / a > = netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a5be0f5195a5cd1dd177b9fc5ab83a7be" > temperature< / a > ;< / div >
< div class = "line" > < a id = "l00427" name = "l00427" > < / a > < span class = "lineno" > 427< / span > fullNetIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577" > density< / a > = netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577" > density< / a > ;< / div >
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< div class = "line" > < a id = "l00428" name = "l00428" > < / a > < span class = "lineno" > 428< / span > < / div >
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< div class = "line" > < a id = "l00429" name = "l00429" > < / a > < span class = "lineno" > 429< / span > < span class = "keyword" > auto< / span > primingReport = < a class = "code hl_function" href = "namespacegridfire.html#acd0bfdfbce4e84af102d62ff8a797c9f" > primeNetwork< / a > (fullNetIn, *< span class = "keyword" > this< / span > );< / div >
< div class = "line" > < a id = "l00430" name = "l00430" > < / a > < span class = "lineno" > 430< / span > < / div >
< div class = "line" > < a id = "l00431" name = "l00431" > < / a > < span class = "lineno" > 431< / span > < span class = "keywordflow" > return< / span > primingReport;< / div >
< div class = "line" > < a id = "l00432" name = "l00432" > < / a > < span class = "lineno" > 432< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00433" name = "l00433" > < / a > < span class = "lineno" > 433< / span > < / div >
< div class = "foldopen" id = "foldopen00434" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00434" name = "l00434" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a166a5f4349580f9aa0b930afec73fcc4" > 434< / a > < / span > < a class = "code hl_typedef" href = "namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6" > BuildDepthType< / a > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a166a5f4349580f9aa0b930afec73fcc4" > GraphEngine::getDepth< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00435" name = "l00435" > < / a > < span class = "lineno" > 435< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01" > m_depth< / a > ;< / div >
< div class = "line" > < a id = "l00436" name = "l00436" > < / a > < span class = "lineno" > 436< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00437" name = "l00437" > < / a > < span class = "lineno" > 437< / span > < / div >
< div class = "foldopen" id = "foldopen00438" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00438" name = "l00438" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#ad9d6c70ace5cbbf7f3aa7b31fce39490" > 438< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#ad9d6c70ace5cbbf7f3aa7b31fce39490" > GraphEngine::rebuild< / a > (< span class = "keyword" > const< / span > fourdst::composition::Composition& comp, < span class = "keyword" > const< / span > < a class = "code hl_typedef" href = "namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6" > BuildDepthType< / a > depth) {< / div >
< div class = "line" > < a id = "l00439" name = "l00439" > < / a > < span class = "lineno" > 439< / span > < span class = "keywordflow" > if< / span > (depth != < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01" > m_depth< / a > ) {< / div >
< div class = "line" > < a id = "l00440" name = "l00440" > < / a > < span class = "lineno" > 440< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01" > m_depth< / a > = depth;< / div >
< div class = "line" > < a id = "l00441" name = "l00441" > < / a > < span class = "lineno" > 441< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > = < a class = "code hl_function" href = "namespacegridfire.html#aedddb89e400a6111f69bfe0c3fd4214e" > build_reaclib_nuclear_network< / a > (comp, < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01" > m_depth< / a > , < span class = "keyword" > false< / span > );< / div >
< div class = "line" > < a id = "l00442" name = "l00442" > < / a > < span class = "lineno" > 442< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f" > syncInternalMaps< / a > (); < span class = "comment" > // Resync internal maps after changing the depth< / span > < / div >
< div class = "line" > < a id = "l00443" name = "l00443" > < / a > < span class = "lineno" > 443< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00444" name = "l00444" > < / a > < span class = "lineno" > 444< / span > LOG_DEBUG(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Rebuild requested with the same depth. No changes made to the network." < / span > );< / div >
< div class = "line" > < a id = "l00445" name = "l00445" > < / a > < span class = "lineno" > 445< / span > }< / div >
< div class = "line" > < a id = "l00446" name = "l00446" > < / a > < span class = "lineno" > 446< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00447" name = "l00447" > < / a > < span class = "lineno" > 447< / span > < / div >
< div class = "foldopen" id = "foldopen00448" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00448" name = "l00448" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a97f98706b51fbe0d167ed81ffe58c438" > 448< / a > < / span > < a class = "code hl_struct" href = "structgridfire_1_1_step_derivatives.html" > StepDerivatives< double> < / a > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a97f98706b51fbe0d167ed81ffe58c438" > GraphEngine::calculateAllDerivativesUsingPrecomputation< / a > (< / div >
< div class = "line" > < a id = "l00449" name = "l00449" > < / a > < span class = "lineno" > 449< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_in,< / div >
< div class = "line" > < a id = "l00450" name = "l00450" > < / a > < span class = "lineno" > 450< / span > < span class = "keyword" > const< / span > std::vector< double> & bare_rates,< / div >
< div class = "line" > < a id = "l00451" name = "l00451" > < / a > < span class = "lineno" > 451< / span > < span class = "keyword" > const< / span > std::vector< double> & bare_reverse_rates,< / div >
< div class = "line" > < a id = "l00452" name = "l00452" > < / a > < span class = "lineno" > 452< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00453" name = "l00453" > < / a > < span class = "lineno" > 453< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00454" name = "l00454" > < / a > < span class = "lineno" > 454< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00455" name = "l00455" > < / a > < span class = "lineno" > 455< / span > < span class = "comment" > // --- Calculate screening factors ---< / span > < / div >
< div class = "line" > < a id = "l00456" name = "l00456" > < / a > < span class = "lineno" > 456< / span > < span class = "keyword" > const< / span > std::vector< double> screeningFactors = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#af17cf3762abac3efcab9a8e87c961210" > m_screeningModel< / a > -> calculateScreeningFactors(< / div >
< div class = "line" > < a id = "l00457" name = "l00457" > < / a > < span class = "lineno" > 457< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > ,< / div >
< div class = "line" > < a id = "l00458" name = "l00458" > < / a > < span class = "lineno" > 458< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > ,< / div >
< div class = "line" > < a id = "l00459" name = "l00459" > < / a > < span class = "lineno" > 459< / span > Y_in,< / div >
< div class = "line" > < a id = "l00460" name = "l00460" > < / a > < span class = "lineno" > 460< / span > T9,< / div >
< div class = "line" > < a id = "l00461" name = "l00461" > < / a > < span class = "lineno" > 461< / span > rho< / div >
< div class = "line" > < a id = "l00462" name = "l00462" > < / a > < span class = "lineno" > 462< / span > );< / div >
< div class = "line" > < a id = "l00463" name = "l00463" > < / a > < span class = "lineno" > 463< / span > < / div >
< div class = "line" > < a id = "l00464" name = "l00464" > < / a > < span class = "lineno" > 464< / span > < span class = "comment" > // --- Optimized loop ---< / span > < / div >
< div class = "line" > < a id = "l00465" name = "l00465" > < / a > < span class = "lineno" > 465< / span > std::vector< double> molarReactionFlows;< / div >
< div class = "line" > < a id = "l00466" name = "l00466" > < / a > < span class = "lineno" > 466< / span > molarReactionFlows.reserve(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3" > m_precomputedReactions< / a > .size());< / div >
< div class = "line" > < a id = "l00467" name = "l00467" > < / a > < span class = "lineno" > 467< / span > < / div >
< div class = "line" > < a id = "l00468" name = "l00468" > < / a > < span class = "lineno" > 468< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & precomp : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3" > m_precomputedReactions< / a > ) {< / div >
< div class = "line" > < a id = "l00469" name = "l00469" > < / a > < span class = "lineno" > 469< / span > < span class = "keywordtype" > double< / span > forwardAbundanceProduct = 1.0;< / div >
< div class = "line" > < a id = "l00470" name = "l00470" > < / a > < span class = "lineno" > 470< / span > < span class = "comment" > // bool below_threshold = false;< / span > < / div >
< div class = "line" > < a id = "l00471" name = "l00471" > < / a > < span class = "lineno" > 471< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < precomp.unique_reactant_indices.size(); ++i) {< / div >
< div class = "line" > < a id = "l00472" name = "l00472" > < / a > < span class = "lineno" > 472< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > reactantIndex = precomp.unique_reactant_indices[i];< / div >
< div class = "line" > < a id = "l00473" name = "l00473" > < / a > < span class = "lineno" > 473< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > power = precomp.reactant_powers[i];< / div >
< div class = "line" > < a id = "l00474" name = "l00474" > < / a > < span class = "lineno" > 474< / span > < span class = "comment" > // const double abundance = Y_in[reactantIndex];< / span > < / div >
< div class = "line" > < a id = "l00475" name = "l00475" > < / a > < span class = "lineno" > 475< / span > < span class = "comment" > // if (abundance < MIN_ABUNDANCE_THRESHOLD) {< / span > < / div >
< div class = "line" > < a id = "l00476" name = "l00476" > < / a > < span class = "lineno" > 476< / span > < span class = "comment" > // below_threshold = true;< / span > < / div >
< div class = "line" > < a id = "l00477" name = "l00477" > < / a > < span class = "lineno" > 477< / span > < span class = "comment" > // break;< / span > < / div >
< div class = "line" > < a id = "l00478" name = "l00478" > < / a > < span class = "lineno" > 478< / span > < span class = "comment" > // }< / span > < / div >
< div class = "line" > < a id = "l00479" name = "l00479" > < / a > < span class = "lineno" > 479< / span > < / div >
< div class = "line" > < a id = "l00480" name = "l00480" > < / a > < span class = "lineno" > 480< / span > forwardAbundanceProduct *= std::pow(Y_in[reactantIndex], power);< / div >
< div class = "line" > < a id = "l00481" name = "l00481" > < / a > < span class = "lineno" > 481< / span > }< / div >
< div class = "line" > < a id = "l00482" name = "l00482" > < / a > < span class = "lineno" > 482< / span > < span class = "comment" > // if (below_threshold) {< / span > < / div >
< div class = "line" > < a id = "l00483" name = "l00483" > < / a > < span class = "lineno" > 483< / span > < span class = "comment" > // molarReactionFlows.push_back(0.0);< / span > < / div >
< div class = "line" > < a id = "l00484" name = "l00484" > < / a > < span class = "lineno" > 484< / span > < span class = "comment" > // continue; // Skip this reaction if any reactant is below the abundance threshold< / span > < / div >
< div class = "line" > < a id = "l00485" name = "l00485" > < / a > < span class = "lineno" > 485< / span > < span class = "comment" > // }< / span > < / div >
< div class = "line" > < a id = "l00486" name = "l00486" > < / a > < span class = "lineno" > 486< / span > < / div >
< div class = "line" > < a id = "l00487" name = "l00487" > < / a > < span class = "lineno" > 487< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > bare_rate = bare_rates[precomp.reaction_index];< / div >
< div class = "line" > < a id = "l00488" name = "l00488" > < / a > < span class = "lineno" > 488< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > screeningFactor = screeningFactors[precomp.reaction_index];< / div >
< div class = "line" > < a id = "l00489" name = "l00489" > < / a > < span class = "lineno" > 489< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > numReactants = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > [precomp.reaction_index].reactants().size();< / div >
< div class = "line" > < a id = "l00490" name = "l00490" > < / a > < span class = "lineno" > 490< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > numProducts = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > [precomp.reaction_index].products().size();< / div >
< div class = "line" > < a id = "l00491" name = "l00491" > < / a > < span class = "lineno" > 491< / span > < / div >
< div class = "line" > < a id = "l00492" name = "l00492" > < / a > < span class = "lineno" > 492< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > forwardMolarReactionFlow =< / div >
< div class = "line" > < a id = "l00493" name = "l00493" > < / a > < span class = "lineno" > 493< / span > screeningFactor *< / div >
< div class = "line" > < a id = "l00494" name = "l00494" > < / a > < span class = "lineno" > 494< / span > bare_rate *< / div >
< div class = "line" > < a id = "l00495" name = "l00495" > < / a > < span class = "lineno" > 495< / span > precomp.symmetry_factor *< / div >
< div class = "line" > < a id = "l00496" name = "l00496" > < / a > < span class = "lineno" > 496< / span > forwardAbundanceProduct *< / div >
< div class = "line" > < a id = "l00497" name = "l00497" > < / a > < span class = "lineno" > 497< / span > std::pow(rho, numReactants > 1 ? numReactants - 1 : 0.0);< / div >
< div class = "line" > < a id = "l00498" name = "l00498" > < / a > < span class = "lineno" > 498< / span > < / div >
< div class = "line" > < a id = "l00499" name = "l00499" > < / a > < span class = "lineno" > 499< / span > < span class = "keywordtype" > double< / span > reverseMolarReactionFlow = 0.0;< / div >
< div class = "line" > < a id = "l00500" name = "l00500" > < / a > < span class = "lineno" > 500< / span > < span class = "keywordflow" > if< / span > (precomp.reverse_symmetry_factor != 0.0 and < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc" > m_useReverseReactions< / a > ) {< / div >
< div class = "line" > < a id = "l00501" name = "l00501" > < / a > < span class = "lineno" > 501< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > bare_reverse_rate = bare_reverse_rates[precomp.reaction_index];< / div >
< div class = "line" > < a id = "l00502" name = "l00502" > < / a > < span class = "lineno" > 502< / span > < span class = "keywordtype" > double< / span > reverseAbundanceProduct = 1.0;< / div >
< div class = "line" > < a id = "l00503" name = "l00503" > < / a > < span class = "lineno" > 503< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < precomp.unique_product_indices.size(); ++i) {< / div >
< div class = "line" > < a id = "l00504" name = "l00504" > < / a > < span class = "lineno" > 504< / span > reverseAbundanceProduct *= std::pow(Y_in[precomp.unique_product_indices[i]], precomp.product_powers[i]);< / div >
< div class = "line" > < a id = "l00505" name = "l00505" > < / a > < span class = "lineno" > 505< / span > }< / div >
< div class = "line" > < a id = "l00506" name = "l00506" > < / a > < span class = "lineno" > 506< / span > reverseMolarReactionFlow = screeningFactor *< / div >
< div class = "line" > < a id = "l00507" name = "l00507" > < / a > < span class = "lineno" > 507< / span > bare_reverse_rate *< / div >
< div class = "line" > < a id = "l00508" name = "l00508" > < / a > < span class = "lineno" > 508< / span > precomp.reverse_symmetry_factor *< / div >
< div class = "line" > < a id = "l00509" name = "l00509" > < / a > < span class = "lineno" > 509< / span > reverseAbundanceProduct *< / div >
< div class = "line" > < a id = "l00510" name = "l00510" > < / a > < span class = "lineno" > 510< / span > std::pow(rho, numProducts > 1 ? numProducts - 1 : 0.0);< / div >
< div class = "line" > < a id = "l00511" name = "l00511" > < / a > < span class = "lineno" > 511< / span > }< / div >
< div class = "line" > < a id = "l00512" name = "l00512" > < / a > < span class = "lineno" > 512< / span > < / div >
< div class = "line" > < a id = "l00513" name = "l00513" > < / a > < span class = "lineno" > 513< / span > molarReactionFlows.push_back(forwardMolarReactionFlow - reverseMolarReactionFlow);< / div >
< div class = "line" > < a id = "l00514" name = "l00514" > < / a > < span class = "lineno" > 514< / span > < / div >
< div class = "line" > < a id = "l00515" name = "l00515" > < / a > < span class = "lineno" > 515< / span > }< / div >
< div class = "line" > < a id = "l00516" name = "l00516" > < / a > < span class = "lineno" > 516< / span > < / div >
< div class = "line" > < a id = "l00517" name = "l00517" > < / a > < span class = "lineno" > 517< / span > < span class = "comment" > // --- Assemble molar abundance derivatives ---< / span > < / div >
< div class = "line" > < a id = "l00518" name = "l00518" > < / a > < span class = "lineno" > 518< / span > < a class = "code hl_struct" href = "structgridfire_1_1_step_derivatives.html" > StepDerivatives< double> < / a > result;< / div >
< div class = "line" > < a id = "l00519" name = "l00519" > < / a > < span class = "lineno" > 519< / span > result.< a class = "code hl_variable" href = "structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d" > dydt< / a > .assign(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size(), 0.0); < span class = "comment" > // Initialize derivatives to zero< / span > < / div >
< div class = "line" > < a id = "l00520" name = "l00520" > < / a > < span class = "lineno" > 520< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > j = 0; j < < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3" > m_precomputedReactions< / a > .size(); ++j) {< / div >
< div class = "line" > < a id = "l00521" name = "l00521" > < / a > < span class = "lineno" > 521< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & precomp = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3" > m_precomputedReactions< / a > [j];< / div >
< div class = "line" > < a id = "l00522" name = "l00522" > < / a > < span class = "lineno" > 522< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > R_j = molarReactionFlows[j];< / div >
< div class = "line" > < a id = "l00523" name = "l00523" > < / a > < span class = "lineno" > 523< / span > < / div >
< div class = "line" > < a id = "l00524" name = "l00524" > < / a > < span class = "lineno" > 524< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < precomp.affected_species_indices.size(); ++i) {< / div >
< div class = "line" > < a id = "l00525" name = "l00525" > < / a > < span class = "lineno" > 525< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > speciesIndex = precomp.affected_species_indices[i];< / div >
< div class = "line" > < a id = "l00526" name = "l00526" > < / a > < span class = "lineno" > 526< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > stoichiometricCoefficient = precomp.stoichiometric_coefficients[i];< / div >
< div class = "line" > < a id = "l00527" name = "l00527" > < / a > < span class = "lineno" > 527< / span > < / div >
< div class = "line" > < a id = "l00528" name = "l00528" > < / a > < span class = "lineno" > 528< / span > < span class = "comment" > // Update the derivative for this species< / span > < / div >
< div class = "line" > < a id = "l00529" name = "l00529" > < / a > < span class = "lineno" > 529< / span > result.< a class = "code hl_variable" href = "structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d" > dydt< / a > [speciesIndex] += < span class = "keyword" > static_cast< < / span > < span class = "keywordtype" > double< / span > < span class = "keyword" > > < / span > (stoichiometricCoefficient) * R_j;< / div >
< div class = "line" > < a id = "l00530" name = "l00530" > < / a > < span class = "lineno" > 530< / span > }< / div >
< div class = "line" > < a id = "l00531" name = "l00531" > < / a > < span class = "lineno" > 531< / span > }< / div >
< div class = "line" > < a id = "l00532" name = "l00532" > < / a > < span class = "lineno" > 532< / span > < / div >
< div class = "line" > < a id = "l00533" name = "l00533" > < / a > < span class = "lineno" > 533< / span > < span class = "comment" > // --- Calculate the nuclear energy generation rate ---< / span > < / div >
< div class = "line" > < a id = "l00534" name = "l00534" > < / a > < span class = "lineno" > 534< / span > < span class = "keywordtype" > double< / span > massProductionRate = 0.0; < span class = "comment" > // [mol][s^-1]< / span > < / div >
< div class = "line" > < a id = "l00535" name = "l00535" > < / a > < span class = "lineno" > 535< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size(); ++i) {< / div >
< div class = "line" > < a id = "l00536" name = "l00536" > < / a > < span class = "lineno" > 536< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > [i];< / div >
< div class = "line" > < a id = "l00537" name = "l00537" > < / a > < span class = "lineno" > 537< / span > massProductionRate += result.< a class = "code hl_variable" href = "structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d" > dydt< / a > [i] * species.mass() * < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e" > m_constants< / a > .u;< / div >
< div class = "line" > < a id = "l00538" name = "l00538" > < / a > < span class = "lineno" > 538< / span > }< / div >
< div class = "line" > < a id = "l00539" name = "l00539" > < / a > < span class = "lineno" > 539< / span > result.< a class = "code hl_variable" href = "structgridfire_1_1_step_derivatives.html#ab4aeb41be952c7b5844e1ee81fef9008" > nuclearEnergyGenerationRate< / a > = -massProductionRate * < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e" > m_constants< / a > .Na * < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e" > m_constants< / a > .c * < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e" > m_constants< / a > .c; < span class = "comment" > // [erg][s^-1][g^-1]< / span > < / div >
< div class = "line" > < a id = "l00540" name = "l00540" > < / a > < span class = "lineno" > 540< / span > < span class = "keywordflow" > return< / span > result;< / div >
< div class = "line" > < a id = "l00541" name = "l00541" > < / a > < span class = "lineno" > 541< / span > < / div >
< div class = "line" > < a id = "l00542" name = "l00542" > < / a > < span class = "lineno" > 542< / span > }< / div >
2025-07-24 11:10:45 -04:00
< / div >
2025-07-30 15:12:46 -04:00
< div class = "line" > < a id = "l00543" name = "l00543" > < / a > < span class = "lineno" > 543< / span > < / div >
< div class = "line" > < a id = "l00544" name = "l00544" > < / a > < span class = "lineno" > 544< / span > < span class = "comment" > // --- Generate Stoichiometry Matrix ---< / span > < / div >
< div class = "foldopen" id = "foldopen00545" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00545" name = "l00545" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38" > 545< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38" > GraphEngine::generateStoichiometryMatrix< / a > () {< / div >
< div class = "line" > < a id = "l00546" name = "l00546" > < / a > < span class = "lineno" > 546< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Generating stoichiometry matrix..." < / span > );< / div >
< div class = "line" > < a id = "l00547" name = "l00547" > < / a > < span class = "lineno" > 547< / span > < / div >
< div class = "line" > < a id = "l00548" name = "l00548" > < / a > < span class = "lineno" > 548< / span > < span class = "comment" > // Task 1: Set dimensions and initialize the matrix< / span > < / div >
< div class = "line" > < a id = "l00549" name = "l00549" > < / a > < span class = "lineno" > 549< / span > < span class = "keywordtype" > size_t< / span > numSpecies = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size();< / div >
< div class = "line" > < a id = "l00550" name = "l00550" > < / a > < span class = "lineno" > 550< / span > < span class = "keywordtype" > size_t< / span > numReactions = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > .size();< / div >
< div class = "line" > < a id = "l00551" name = "l00551" > < / a > < span class = "lineno" > 551< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24" > m_stoichiometryMatrix< / a > .resize(numSpecies, numReactions, < span class = "keyword" > false< / span > );< / div >
< div class = "line" > < a id = "l00552" name = "l00552" > < / a > < span class = "lineno" > 552< / span > < / div >
< div class = "line" > < a id = "l00553" name = "l00553" > < / a > < span class = "lineno" > 553< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Stoichiometry matrix initialized with dimensions: {} rows (species) x {} columns (reactions)." < / span > ,< / div >
< div class = "line" > < a id = "l00554" name = "l00554" > < / a > < span class = "lineno" > 554< / span > numSpecies, numReactions);< / div >
< div class = "line" > < a id = "l00555" name = "l00555" > < / a > < span class = "lineno" > 555< / span > < / div >
< div class = "line" > < a id = "l00556" name = "l00556" > < / a > < span class = "lineno" > 556< / span > < span class = "comment" > // Task 2: Populate the stoichiometry matrix< / span > < / div >
< div class = "line" > < a id = "l00557" name = "l00557" > < / a > < span class = "lineno" > 557< / span > < span class = "comment" > // Iterate through all reactions, assign them a column index, and fill in their stoichiometric coefficients.< / span > < / div >
< div class = "line" > < a id = "l00558" name = "l00558" > < / a > < span class = "lineno" > 558< / span > < span class = "keywordtype" > size_t< / span > reactionColumnIndex = 0;< / div >
< div class = "line" > < a id = "l00559" name = "l00559" > < / a > < span class = "lineno" > 559< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > ) {< / div >
< div class = "line" > < a id = "l00560" name = "l00560" > < / a > < span class = "lineno" > 560< / span > < span class = "comment" > // Get the net stoichiometry for the current reaction< / span > < / div >
< div class = "line" > < a id = "l00561" name = "l00561" > < / a > < span class = "lineno" > 561< / span > std::unordered_map< fourdst::atomic::Species, int> netStoichiometry = < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .stoichiometry();< / div >
< div class = "line" > < a id = "l00562" name = "l00562" > < / a > < span class = "lineno" > 562< / span > < / div >
< div class = "line" > < a id = "l00563" name = "l00563" > < / a > < span class = "lineno" > 563< / span > < span class = "comment" > // Iterate through the species and their coefficients in the stoichiometry map< / span > < / div >
< div class = "line" > < a id = "l00564" name = "l00564" > < / a > < span class = "lineno" > 564< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & [species, coefficient] : netStoichiometry) {< / div >
< div class = "line" > < a id = "l00565" name = "l00565" > < / a > < span class = "lineno" > 565< / span > < span class = "comment" > // Find the row index for this species< / span > < / div >
< div class = "line" > < a id = "l00566" name = "l00566" > < / a > < span class = "lineno" > 566< / span > < span class = "keyword" > auto< / span > it = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7" > m_speciesToIndexMap< / a > .find(species);< / div >
< div class = "line" > < a id = "l00567" name = "l00567" > < / a > < span class = "lineno" > 567< / span > < span class = "keywordflow" > if< / span > (it != < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7" > m_speciesToIndexMap< / a > .end()) {< / div >
< div class = "line" > < a id = "l00568" name = "l00568" > < / a > < span class = "lineno" > 568< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > speciesRowIndex = it-> second;< / div >
< div class = "line" > < a id = "l00569" name = "l00569" > < / a > < span class = "lineno" > 569< / span > < span class = "comment" > // Set the matrix element. Boost.uBLAS handles sparse insertion.< / span > < / div >
< div class = "line" > < a id = "l00570" name = "l00570" > < / a > < span class = "lineno" > 570< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24" > m_stoichiometryMatrix< / a > (speciesRowIndex, reactionColumnIndex) = coefficient;< / div >
< div class = "line" > < a id = "l00571" name = "l00571" > < / a > < span class = "lineno" > 571< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00572" name = "l00572" > < / a > < span class = "lineno" > 572< / span > < span class = "comment" > // This scenario should ideally not happen if m_networkSpeciesMap and m_speciesToIndexMap are correctly synced< / span > < / div >
< div class = "line" > < a id = "l00573" name = "l00573" > < / a > < span class = "lineno" > 573< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " CRITICAL ERROR: Species ' {}' from reaction ' {}' stoichiometry not found in species to index map." < / span > ,< / div >
< div class = "line" > < a id = "l00574" name = "l00574" > < / a > < span class = "lineno" > 574< / span > species.name(), < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id());< / div >
< div class = "line" > < a id = "l00575" name = "l00575" > < / a > < span class = "lineno" > 575< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00576" name = "l00576" > < / a > < span class = "lineno" > 576< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " Species not found in species to index map: " < / span > + std::string(species.name()));< / div >
< div class = "line" > < a id = "l00577" name = "l00577" > < / a > < span class = "lineno" > 577< / span > }< / div >
< div class = "line" > < a id = "l00578" name = "l00578" > < / a > < span class = "lineno" > 578< / span > }< / div >
< div class = "line" > < a id = "l00579" name = "l00579" > < / a > < span class = "lineno" > 579< / span > reactionColumnIndex++; < span class = "comment" > // Move to the next column for the next reaction< / span > < / div >
< div class = "line" > < a id = "l00580" name = "l00580" > < / a > < span class = "lineno" > 580< / span > }< / div >
< div class = "line" > < a id = "l00581" name = "l00581" > < / a > < span class = "lineno" > 581< / span > < / div >
< div class = "line" > < a id = "l00582" name = "l00582" > < / a > < span class = "lineno" > 582< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Stoichiometry matrix population complete. Number of non-zero elements: {}." < / span > ,< / div >
< div class = "line" > < a id = "l00583" name = "l00583" > < / a > < span class = "lineno" > 583< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24" > m_stoichiometryMatrix< / a > .nnz()); < span class = "comment" > // Assuming nnz() exists for compressed_matrix< / span > < / div >
< div class = "line" > < a id = "l00584" name = "l00584" > < / a > < span class = "lineno" > 584< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00585" name = "l00585" > < / a > < span class = "lineno" > 585< / span > < / div >
< div class = "foldopen" id = "foldopen00586" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00586" name = "l00586" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#aaf4d54e4b774ab8ec8eabec006579d31" > 586< / a > < / span > < a class = "code hl_struct" href = "structgridfire_1_1_step_derivatives.html" > StepDerivatives< double> < / a > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9" > GraphEngine::calculateAllDerivatives< / a > (< / div >
< div class = "line" > < a id = "l00587" name = "l00587" > < / a > < span class = "lineno" > 587< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_in,< / div >
< div class = "line" > < a id = "l00588" name = "l00588" > < / a > < span class = "lineno" > 588< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00589" name = "l00589" > < / a > < span class = "lineno" > 589< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00590" name = "l00590" > < / a > < span class = "lineno" > 590< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00591" name = "l00591" > < / a > < span class = "lineno" > 591< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9" > calculateAllDerivatives< double> < / a > (Y_in, T9, rho);< / div >
< div class = "line" > < a id = "l00592" name = "l00592" > < / a > < span class = "lineno" > 592< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00593" name = "l00593" > < / a > < span class = "lineno" > 593< / span > < / div >
< div class = "foldopen" id = "foldopen00594" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00594" name = "l00594" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a71a3d1181b90c3becdc5d9a3da05b9c9" > 594< / a > < / span > < a class = "code hl_struct" href = "structgridfire_1_1_step_derivatives.html" > StepDerivatives< ADDouble> < / a > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9" > GraphEngine::calculateAllDerivatives< / a > (< / div >
< div class = "line" > < a id = "l00595" name = "l00595" > < / a > < span class = "lineno" > 595< / span > < span class = "keyword" > const< / span > std::vector< ADDouble> & Y_in,< / div >
< div class = "line" > < a id = "l00596" name = "l00596" > < / a > < span class = "lineno" > 596< / span > < span class = "keyword" > const< / span > < a class = "code hl_typedef" href = "namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc" > ADDouble< / a > & T9,< / div >
< div class = "line" > < a id = "l00597" name = "l00597" > < / a > < span class = "lineno" > 597< / span > < span class = "keyword" > const< / span > < a class = "code hl_typedef" href = "namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc" > ADDouble< / a > & rho< / div >
< div class = "line" > < a id = "l00598" name = "l00598" > < / a > < span class = "lineno" > 598< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00599" name = "l00599" > < / a > < span class = "lineno" > 599< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9" > calculateAllDerivatives< ADDouble> < / a > (Y_in, T9, rho);< / div >
< div class = "line" > < a id = "l00600" name = "l00600" > < / a > < span class = "lineno" > 600< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00601" name = "l00601" > < / a > < span class = "lineno" > 601< / span > < / div >
< div class = "foldopen" id = "foldopen00602" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00602" name = "l00602" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f" > 602< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f" > GraphEngine::setScreeningModel< / a > (< span class = "keyword" > const< / span > < a class = "code hl_enumeration" href = "namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25" > screening::ScreeningType< / a > model) {< / div >
< div class = "line" > < a id = "l00603" name = "l00603" > < / a > < span class = "lineno" > 603< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#af17cf3762abac3efcab9a8e87c961210" > m_screeningModel< / a > = < a class = "code hl_function" href = "namespacegridfire_1_1screening.html#a6ca8556d27ac373e176f5b23437c416e" > screening::selectScreeningModel< / a > (model);< / div >
< div class = "line" > < a id = "l00604" name = "l00604" > < / a > < span class = "lineno" > 604< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a52edc3e88f1e8fc497e1e63972d63c80" > m_screeningType< / a > = model;< / div >
< div class = "line" > < a id = "l00605" name = "l00605" > < / a > < span class = "lineno" > 605< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00606" name = "l00606" > < / a > < span class = "lineno" > 606< / span > < / div >
< div class = "foldopen" id = "foldopen00607" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00607" name = "l00607" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a" > 607< / a > < / span > < a class = "code hl_enumeration" href = "namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25" > screening::ScreeningType< / a > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a" > GraphEngine::getScreeningModel< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00608" name = "l00608" > < / a > < span class = "lineno" > 608< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a52edc3e88f1e8fc497e1e63972d63c80" > m_screeningType< / a > ;< / div >
< div class = "line" > < a id = "l00609" name = "l00609" > < / a > < span class = "lineno" > 609< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00610" name = "l00610" > < / a > < span class = "lineno" > 610< / span > < / div >
< div class = "foldopen" id = "foldopen00611" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00611" name = "l00611" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1" > 611< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1" > GraphEngine::setPrecomputation< / a > (< span class = "keyword" > const< / span > < span class = "keywordtype" > bool< / span > precompute) {< / div >
< div class = "line" > < a id = "l00612" name = "l00612" > < / a > < span class = "lineno" > 612< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de" > m_usePrecomputation< / a > = precompute;< / div >
< div class = "line" > < a id = "l00613" name = "l00613" > < / a > < span class = "lineno" > 613< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00614" name = "l00614" > < / a > < span class = "lineno" > 614< / span > < / div >
< div class = "foldopen" id = "foldopen00615" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00615" name = "l00615" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f" > 615< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f" > GraphEngine::isPrecomputationEnabled< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00616" name = "l00616" > < / a > < span class = "lineno" > 616< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de" > m_usePrecomputation< / a > ;< / div >
< div class = "line" > < a id = "l00617" name = "l00617" > < / a > < span class = "lineno" > 617< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00618" name = "l00618" > < / a > < span class = "lineno" > 618< / span > < / div >
< div class = "foldopen" id = "foldopen00619" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00619" name = "l00619" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#add98ece49ec5c538bddf3cc77004fe44" > 619< / a > < / span > < span class = "keyword" > const< / span > < a class = "code hl_class" href = "classgridfire_1_1partition_1_1_partition_function.html" > partition::PartitionFunction< / a > & < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#add98ece49ec5c538bddf3cc77004fe44" > GraphEngine::getPartitionFunction< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00620" name = "l00620" > < / a > < span class = "lineno" > 620< / span > < span class = "keywordflow" > return< / span > *< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e" > m_partitionFunction< / a > ;< / div >
< div class = "line" > < a id = "l00621" name = "l00621" > < / a > < span class = "lineno" > 621< / span > }< / div >
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< / div >
2025-07-30 15:12:46 -04:00
< div class = "line" > < a id = "l00622" name = "l00622" > < / a > < span class = "lineno" > 622< / span > < / div >
< div class = "foldopen" id = "foldopen00623" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00623" name = "l00623" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f" > 623< / a > < / span > < span class = "keywordtype" > double< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f" > GraphEngine::calculateMolarReactionFlow< / a > (< / div >
< div class = "line" > < a id = "l00624" name = "l00624" > < / a > < span class = "lineno" > 624< / span > < span class = "keyword" > const< / span > < a class = "code hl_class" href = "classgridfire_1_1reaction_1_1_reaction.html" > reaction::Reaction< / a > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > ,< / div >
< div class = "line" > < a id = "l00625" name = "l00625" > < / a > < span class = "lineno" > 625< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l00626" name = "l00626" > < / a > < span class = "lineno" > 626< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00627" name = "l00627" > < / a > < span class = "lineno" > 627< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00628" name = "l00628" > < / a > < span class = "lineno" > 628< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00629" name = "l00629" > < / a > < span class = "lineno" > 629< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f" > calculateMolarReactionFlow< double> < / a > (< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > , Y, T9, rho);< / div >
< div class = "line" > < a id = "l00630" name = "l00630" > < / a > < span class = "lineno" > 630< / span > }< / div >
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< / div >
2025-07-30 15:12:46 -04:00
< div class = "line" > < a id = "l00631" name = "l00631" > < / a > < span class = "lineno" > 631< / span > < / div >
< div class = "foldopen" id = "foldopen00632" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00632" name = "l00632" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119" > 632< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119" > GraphEngine::generateJacobianMatrix< / a > (< / div >
< div class = "line" > < a id = "l00633" name = "l00633" > < / a > < span class = "lineno" > 633< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_dynamic,< / div >
< div class = "line" > < a id = "l00634" name = "l00634" > < / a > < span class = "lineno" > 634< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00635" name = "l00635" > < / a > < span class = "lineno" > 635< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00636" name = "l00636" > < / a > < span class = "lineno" > 636< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00637" name = "l00637" > < / a > < span class = "lineno" > 637< / span > < / div >
< div class = "line" > < a id = "l00638" name = "l00638" > < / a > < span class = "lineno" > 638< / span > LOG_TRACE_L1_LIMIT_EVERY_N(1000, < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Generating jacobian matrix for T9={}, rho={}.." < / span > , T9, rho);< / div >
< div class = "line" > < a id = "l00639" name = "l00639" > < / a > < span class = "lineno" > 639< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > numSpecies = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size();< / div >
< div class = "line" > < a id = "l00640" name = "l00640" > < / a > < span class = "lineno" > 640< / span > < / div >
< div class = "line" > < a id = "l00641" name = "l00641" > < / a > < span class = "lineno" > 641< / span > < span class = "comment" > // 1. Pack the input variables into a vector for CppAD< / span > < / div >
< div class = "line" > < a id = "l00642" name = "l00642" > < / a > < span class = "lineno" > 642< / span > std::vector< double> adInput(numSpecies + 2, 0.0); < span class = "comment" > // +2 for T9 and rho< / span > < / div >
< div class = "line" > < a id = "l00643" name = "l00643" > < / a > < span class = "lineno" > 643< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < numSpecies; ++i) {< / div >
< div class = "line" > < a id = "l00644" name = "l00644" > < / a > < span class = "lineno" > 644< / span > adInput[i] = std::max(Y_dynamic[i], 1e-99); < span class = "comment" > // regularize the jacobian...< / span > < / div >
< div class = "line" > < a id = "l00645" name = "l00645" > < / a > < span class = "lineno" > 645< / span > }< / div >
< div class = "line" > < a id = "l00646" name = "l00646" > < / a > < span class = "lineno" > 646< / span > adInput[numSpecies] = T9; < span class = "comment" > // T9< / span > < / div >
< div class = "line" > < a id = "l00647" name = "l00647" > < / a > < span class = "lineno" > 647< / span > adInput[numSpecies + 1] = rho; < span class = "comment" > // rho< / span > < / div >
< div class = "line" > < a id = "l00648" name = "l00648" > < / a > < span class = "lineno" > 648< / span > < / div >
< div class = "line" > < a id = "l00649" name = "l00649" > < / a > < span class = "lineno" > 649< / span > < span class = "comment" > // 2. Calculate the full jacobian< / span > < / div >
< div class = "line" > < a id = "l00650" name = "l00650" > < / a > < span class = "lineno" > 650< / span > < span class = "keyword" > const< / span > std::vector< double> dotY = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876" > m_rhsADFun< / a > .Jacobian(adInput);< / div >
< div class = "line" > < a id = "l00651" name = "l00651" > < / a > < span class = "lineno" > 651< / span > < / div >
< div class = "line" > < a id = "l00652" name = "l00652" > < / a > < span class = "lineno" > 652< / span > < span class = "comment" > // 3. Pack jacobian vector into sparse matrix< / span > < / div >
< div class = "line" > < a id = "l00653" name = "l00653" > < / a > < span class = "lineno" > 653< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910" > m_jacobianMatrix< / a > .clear();< / div >
< div class = "line" > < a id = "l00654" name = "l00654" > < / a > < span class = "lineno" > 654< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < numSpecies; ++i) {< / div >
< div class = "line" > < a id = "l00655" name = "l00655" > < / a > < span class = "lineno" > 655< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > j = 0; j < numSpecies; ++j) {< / div >
< div class = "line" > < a id = "l00656" name = "l00656" > < / a > < span class = "lineno" > 656< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > value = dotY[i * (numSpecies + 2) + j];< / div >
< div class = "line" > < a id = "l00657" name = "l00657" > < / a > < span class = "lineno" > 657< / span > < span class = "keywordflow" > if< / span > (std::abs(value) > < a class = "code hl_variable" href = "namespacegridfire.html#ae01b1738df1921db565bcbd68dd6cf64" > MIN_JACOBIAN_THRESHOLD< / a > || i == j) { < span class = "comment" > // Always keep diagonal elements to avoid pathological stiffness< / span > < / div >
< div class = "line" > < a id = "l00658" name = "l00658" > < / a > < span class = "lineno" > 658< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910" > m_jacobianMatrix< / a > (i, j) = value;< / div >
< div class = "line" > < a id = "l00659" name = "l00659" > < / a > < span class = "lineno" > 659< / span > }< / div >
< div class = "line" > < a id = "l00660" name = "l00660" > < / a > < span class = "lineno" > 660< / span > }< / div >
< div class = "line" > < a id = "l00661" name = "l00661" > < / a > < span class = "lineno" > 661< / span > }< / div >
< div class = "line" > < a id = "l00662" name = "l00662" > < / a > < span class = "lineno" > 662< / span > LOG_TRACE_L1_LIMIT_EVERY_N(1000, < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Jacobian matrix generated with dimensions: {} rows x {} columns." < / span > , < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910" > m_jacobianMatrix< / a > .size1(), < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910" > m_jacobianMatrix< / a > .size2());< / div >
< div class = "line" > < a id = "l00663" name = "l00663" > < / a > < span class = "lineno" > 663< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00664" name = "l00664" > < / a > < span class = "lineno" > 664< / span > < / div >
< div class = "foldopen" id = "foldopen00665" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00665" name = "l00665" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a9687eef88c97eeb7f8680acb230f8ac1" > 665< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119" > GraphEngine::generateJacobianMatrix< / a > (< / div >
< div class = "line" > < a id = "l00666" name = "l00666" > < / a > < span class = "lineno" > 666< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_dynamic,< / div >
< div class = "line" > < a id = "l00667" name = "l00667" > < / a > < span class = "lineno" > 667< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00668" name = "l00668" > < / a > < span class = "lineno" > 668< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho,< / div >
< div class = "line" > < a id = "l00669" name = "l00669" > < / a > < span class = "lineno" > 669< / span > < span class = "keyword" > const< / span > < a class = "code hl_typedef" href = "namespacegridfire.html#a898dfe22579e649935645cbd6f073178" > SparsityPattern< / a > & sparsityPattern< / div >
< div class = "line" > < a id = "l00670" name = "l00670" > < / a > < span class = "lineno" > 670< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00671" name = "l00671" > < / a > < span class = "lineno" > 671< / span > < span class = "comment" > // --- Pack the input variables into a vector for CppAD ---< / span > < / div >
< div class = "line" > < a id = "l00672" name = "l00672" > < / a > < span class = "lineno" > 672< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > numSpecies = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size();< / div >
< div class = "line" > < a id = "l00673" name = "l00673" > < / a > < span class = "lineno" > 673< / span > std::vector< double> x(numSpecies + 2, 0.0);< / div >
< div class = "line" > < a id = "l00674" name = "l00674" > < / a > < span class = "lineno" > 674< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < numSpecies; ++i) {< / div >
< div class = "line" > < a id = "l00675" name = "l00675" > < / a > < span class = "lineno" > 675< / span > x[i] = Y_dynamic[i];< / div >
< div class = "line" > < a id = "l00676" name = "l00676" > < / a > < span class = "lineno" > 676< / span > }< / div >
< div class = "line" > < a id = "l00677" name = "l00677" > < / a > < span class = "lineno" > 677< / span > x[numSpecies] = T9;< / div >
< div class = "line" > < a id = "l00678" name = "l00678" > < / a > < span class = "lineno" > 678< / span > x[numSpecies + 1] = rho;< / div >
< div class = "line" > < a id = "l00679" name = "l00679" > < / a > < span class = "lineno" > 679< / span > < / div >
< div class = "line" > < a id = "l00680" name = "l00680" > < / a > < span class = "lineno" > 680< / span > < span class = "comment" > // --- Convert into CppAD Sparsity pattern ---< / span > < / div >
< div class = "line" > < a id = "l00681" name = "l00681" > < / a > < span class = "lineno" > 681< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > nnz = sparsityPattern.size(); < span class = "comment" > // Number of non-zero entries in the sparsity pattern< / span > < / div >
< div class = "line" > < a id = "l00682" name = "l00682" > < / a > < span class = "lineno" > 682< / span > std::vector< size_t> row_indices(nnz);< / div >
< div class = "line" > < a id = "l00683" name = "l00683" > < / a > < span class = "lineno" > 683< / span > std::vector< size_t> col_indices(nnz);< / div >
< div class = "line" > < a id = "l00684" name = "l00684" > < / a > < span class = "lineno" > 684< / span > < / div >
< div class = "line" > < a id = "l00685" name = "l00685" > < / a > < span class = "lineno" > 685< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > k = 0; k < nnz; ++k) {< / div >
< div class = "line" > < a id = "l00686" name = "l00686" > < / a > < span class = "lineno" > 686< / span > row_indices[k] = sparsityPattern[k].first;< / div >
< div class = "line" > < a id = "l00687" name = "l00687" > < / a > < span class = "lineno" > 687< / span > col_indices[k] = sparsityPattern[k].second;< / div >
< div class = "line" > < a id = "l00688" name = "l00688" > < / a > < span class = "lineno" > 688< / span > }< / div >
< div class = "line" > < a id = "l00689" name = "l00689" > < / a > < span class = "lineno" > 689< / span > < / div >
< div class = "line" > < a id = "l00690" name = "l00690" > < / a > < span class = "lineno" > 690< / span > std::vector< double> values(nnz);< / div >
< div class = "line" > < a id = "l00691" name = "l00691" > < / a > < span class = "lineno" > 691< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > num_rows_jac = numSpecies;< / div >
< div class = "line" > < a id = "l00692" name = "l00692" > < / a > < span class = "lineno" > 692< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > num_cols_jac = numSpecies + 2; < span class = "comment" > // +2 for T9 and rho< / span > < / div >
< div class = "line" > < a id = "l00693" name = "l00693" > < / a > < span class = "lineno" > 693< / span > < / div >
< div class = "line" > < a id = "l00694" name = "l00694" > < / a > < span class = "lineno" > 694< / span > CppAD::sparse_rc< std::vector< size_t> > CppAD_sparsity_pattern(num_rows_jac, num_cols_jac, nnz);< / div >
< div class = "line" > < a id = "l00695" name = "l00695" > < / a > < span class = "lineno" > 695< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > k = 0; k < nnz; ++k) {< / div >
< div class = "line" > < a id = "l00696" name = "l00696" > < / a > < span class = "lineno" > 696< / span > CppAD_sparsity_pattern.set(k, sparsityPattern[k].first, sparsityPattern[k].second);< / div >
< div class = "line" > < a id = "l00697" name = "l00697" > < / a > < span class = "lineno" > 697< / span > }< / div >
< div class = "line" > < a id = "l00698" name = "l00698" > < / a > < span class = "lineno" > 698< / span > < / div >
< div class = "line" > < a id = "l00699" name = "l00699" > < / a > < span class = "lineno" > 699< / span > CppAD::sparse_rcv< std::vector< size_t> , std::vector< double> > jac_subset(CppAD_sparsity_pattern);< / div >
< div class = "line" > < a id = "l00700" name = "l00700" > < / a > < span class = "lineno" > 700< / span > < / div >
< div class = "line" > < a id = "l00701" name = "l00701" > < / a > < span class = "lineno" > 701< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876" > m_rhsADFun< / a > .sparse_jac_rev(< / div >
< div class = "line" > < a id = "l00702" name = "l00702" > < / a > < span class = "lineno" > 702< / span > x,< / div >
< div class = "line" > < a id = "l00703" name = "l00703" > < / a > < span class = "lineno" > 703< / span > jac_subset, < span class = "comment" > // Sparse Jacobian output< / span > < / div >
< div class = "line" > < a id = "l00704" name = "l00704" > < / a > < span class = "lineno" > 704< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a19b2eea0e8d05ac90f9fd7120bdc6e06" > m_full_jacobian_sparsity_pattern< / a > ,< / div >
< div class = "line" > < a id = "l00705" name = "l00705" > < / a > < span class = "lineno" > 705< / span > < span class = "stringliteral" > " cppad" < / span > ,< / div >
< div class = "line" > < a id = "l00706" name = "l00706" > < / a > < span class = "lineno" > 706< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a250cc6350dc052fbdfdf9a02066e7891" > m_jac_work< / a > < span class = "comment" > // Work vector for CppAD< / span > < / div >
< div class = "line" > < a id = "l00707" name = "l00707" > < / a > < span class = "lineno" > 707< / span > );< / div >
< div class = "line" > < a id = "l00708" name = "l00708" > < / a > < span class = "lineno" > 708< / span > < / div >
< div class = "line" > < a id = "l00709" name = "l00709" > < / a > < span class = "lineno" > 709< / span > < span class = "comment" > // --- Convert the sparse Jacobian back to the Boost uBLAS format ---< / span > < / div >
< div class = "line" > < a id = "l00710" name = "l00710" > < / a > < span class = "lineno" > 710< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910" > m_jacobianMatrix< / a > .clear();< / div >
< div class = "line" > < a id = "l00711" name = "l00711" > < / a > < span class = "lineno" > 711< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > k = 0; k < nnz; ++k) {< / div >
< div class = "line" > < a id = "l00712" name = "l00712" > < / a > < span class = "lineno" > 712< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > row = jac_subset.row()[k];< / div >
< div class = "line" > < a id = "l00713" name = "l00713" > < / a > < span class = "lineno" > 713< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > col = jac_subset.col()[k];< / div >
< div class = "line" > < a id = "l00714" name = "l00714" > < / a > < span class = "lineno" > 714< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > value = jac_subset.val()[k];< / div >
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< div class = "line" > < a id = "l00715" name = "l00715" > < / a > < span class = "lineno" > 715< / span > < / div >
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< div class = "line" > < a id = "l00716" name = "l00716" > < / a > < span class = "lineno" > 716< / span > < span class = "keywordflow" > if< / span > (std::abs(value) > < a class = "code hl_variable" href = "namespacegridfire.html#ae01b1738df1921db565bcbd68dd6cf64" > MIN_JACOBIAN_THRESHOLD< / a > ) {< / div >
< div class = "line" > < a id = "l00717" name = "l00717" > < / a > < span class = "lineno" > 717< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910" > m_jacobianMatrix< / a > (row, col) = value; < span class = "comment" > // Insert into the sparse matrix< / span > < / div >
< div class = "line" > < a id = "l00718" name = "l00718" > < / a > < span class = "lineno" > 718< / span > }< / div >
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< div class = "line" > < a id = "l00719" name = "l00719" > < / a > < span class = "lineno" > 719< / span > }< / div >
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< div class = "line" > < a id = "l00720" name = "l00720" > < / a > < span class = "lineno" > 720< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00721" name = "l00721" > < / a > < span class = "lineno" > 721< / span > < / div >
< div class = "foldopen" id = "foldopen00722" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00722" name = "l00722" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c" > 722< / a > < / span > < span class = "keywordtype" > double< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c" > GraphEngine::getJacobianMatrixEntry< / a > (< span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > i, < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > j)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00723" name = "l00723" > < / a > < span class = "lineno" > 723< / span > < span class = "comment" > // LOG_TRACE_L3(m_logger, " Getting jacobian matrix entry for {},{} = {}" , i, j, m_jacobianMatrix(i, j));< / span > < / div >
< div class = "line" > < a id = "l00724" name = "l00724" > < / a > < span class = "lineno" > 724< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910" > m_jacobianMatrix< / a > (i, j);< / div >
< div class = "line" > < a id = "l00725" name = "l00725" > < / a > < span class = "lineno" > 725< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00726" name = "l00726" > < / a > < span class = "lineno" > 726< / span > < / div >
< div class = "foldopen" id = "foldopen00727" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00727" name = "l00727" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9" > 727< / a > < / span > std::unordered_map< fourdst::atomic::Species, int> < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9" > GraphEngine::getNetReactionStoichiometry< / a > (< / div >
< div class = "line" > < a id = "l00728" name = "l00728" > < / a > < span class = "lineno" > 728< / span > < span class = "keyword" > const< / span > < a class = "code hl_class" href = "classgridfire_1_1reaction_1_1_reaction.html" > reaction::Reaction< / a > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > < / div >
< div class = "line" > < a id = "l00729" name = "l00729" > < / a > < span class = "lineno" > 729< / span > ) {< / div >
< div class = "line" > < a id = "l00730" name = "l00730" > < / a > < span class = "lineno" > 730< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .stoichiometry();< / div >
< div class = "line" > < a id = "l00731" name = "l00731" > < / a > < span class = "lineno" > 731< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00732" name = "l00732" > < / a > < span class = "lineno" > 732< / span > < / div >
< div class = "foldopen" id = "foldopen00733" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00733" name = "l00733" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152" > 733< / a > < / span > < span class = "keywordtype" > int< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152" > GraphEngine::getStoichiometryMatrixEntry< / a > (< / div >
< div class = "line" > < a id = "l00734" name = "l00734" > < / a > < span class = "lineno" > 734< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > speciesIndex,< / div >
< div class = "line" > < a id = "l00735" name = "l00735" > < / a > < span class = "lineno" > 735< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > reactionIndex< / div >
< div class = "line" > < a id = "l00736" name = "l00736" > < / a > < span class = "lineno" > 736< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00737" name = "l00737" > < / a > < span class = "lineno" > 737< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24" > m_stoichiometryMatrix< / a > (speciesIndex, reactionIndex);< / div >
< div class = "line" > < a id = "l00738" name = "l00738" > < / a > < span class = "lineno" > 738< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00739" name = "l00739" > < / a > < span class = "lineno" > 739< / span > < / div >
< div class = "foldopen" id = "foldopen00740" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00740" name = "l00740" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929" > 740< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929" > GraphEngine::exportToDot< / a > (< span class = "keyword" > const< / span > std::string & filename)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00741" name = "l00741" > < / a > < span class = "lineno" > 741< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Exporting network graph to DOT file: {}" < / span > , filename);< / div >
< div class = "line" > < a id = "l00742" name = "l00742" > < / a > < span class = "lineno" > 742< / span > < / div >
< div class = "line" > < a id = "l00743" name = "l00743" > < / a > < span class = "lineno" > 743< / span > std::ofstream dotFile(filename);< / div >
< div class = "line" > < a id = "l00744" name = "l00744" > < / a > < span class = "lineno" > 744< / span > < span class = "keywordflow" > if< / span > (!dotFile.is_open()) {< / div >
< div class = "line" > < a id = "l00745" name = "l00745" > < / a > < span class = "lineno" > 745< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Failed to open file for writing: {}" < / span > , filename);< / div >
< div class = "line" > < a id = "l00746" name = "l00746" > < / a > < span class = "lineno" > 746< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00747" name = "l00747" > < / a > < span class = "lineno" > 747< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " Failed to open file for writing: " < / span > + filename);< / div >
< div class = "line" > < a id = "l00748" name = "l00748" > < / a > < span class = "lineno" > 748< / span > }< / div >
< div class = "line" > < a id = "l00749" name = "l00749" > < / a > < span class = "lineno" > 749< / span > < / div >
< div class = "line" > < a id = "l00750" name = "l00750" > < / a > < span class = "lineno" > 750< / span > dotFile < < < span class = "stringliteral" > " digraph NuclearReactionNetwork {\n" < / span > ;< / div >
< div class = "line" > < a id = "l00751" name = "l00751" > < / a > < span class = "lineno" > 751< / span > dotFile < < < span class = "stringliteral" > " graph [rankdir=LR, splines=true, overlap=false, bgcolor=\" #f0f0f0\" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00752" name = "l00752" > < / a > < span class = "lineno" > 752< / span > dotFile < < < span class = "stringliteral" > " node [shape=circle, style=filled, fillcolor=\" #a7c7e7\" , fontname=\" Helvetica\" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00753" name = "l00753" > < / a > < span class = "lineno" > 753< / span > dotFile < < < span class = "stringliteral" > " edge [fontname=\" Helvetica\" , fontsize=10];\n\n" < / span > ;< / div >
< div class = "line" > < a id = "l00754" name = "l00754" > < / a > < span class = "lineno" > 754< / span > < / div >
< div class = "line" > < a id = "l00755" name = "l00755" > < / a > < span class = "lineno" > 755< / span > < span class = "comment" > // 1. Define all species as nodes< / span > < / div >
< div class = "line" > < a id = "l00756" name = "l00756" > < / a > < span class = "lineno" > 756< / span > dotFile < < < span class = "stringliteral" > " // --- Species Nodes ---\n" < / span > ;< / div >
< div class = "line" > < a id = "l00757" name = "l00757" > < / a > < span class = "lineno" > 757< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > ) {< / div >
< div class = "line" > < a id = "l00758" name = "l00758" > < / a > < span class = "lineno" > 758< / span > dotFile < < < span class = "stringliteral" > " \" " < / span > < < species.name() < < < span class = "stringliteral" > " \" [label=\" " < / span > < < species.name() < < < span class = "stringliteral" > " \" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00759" name = "l00759" > < / a > < span class = "lineno" > 759< / span > }< / div >
< div class = "line" > < a id = "l00760" name = "l00760" > < / a > < span class = "lineno" > 760< / span > dotFile < < < span class = "stringliteral" > " \n" < / span > ;< / div >
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< div class = "line" > < a id = "l00761" name = "l00761" > < / a > < span class = "lineno" > 761< / span > < / div >
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< div class = "line" > < a id = "l00762" name = "l00762" > < / a > < span class = "lineno" > 762< / span > < span class = "comment" > // 2. Define all reactions as intermediate nodes and connect them< / span > < / div >
< div class = "line" > < a id = "l00763" name = "l00763" > < / a > < span class = "lineno" > 763< / span > dotFile < < < span class = "stringliteral" > " // --- Reaction Edges ---\n" < / span > ;< / div >
< div class = "line" > < a id = "l00764" name = "l00764" > < / a > < span class = "lineno" > 764< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > ) {< / div >
< div class = "line" > < a id = "l00765" name = "l00765" > < / a > < span class = "lineno" > 765< / span > < span class = "comment" > // Create a unique ID for the reaction node< / span > < / div >
< div class = "line" > < a id = "l00766" name = "l00766" > < / a > < span class = "lineno" > 766< / span > std::string reactionNodeId = < span class = "stringliteral" > " reaction_" < / span > + std::string(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id());< / div >
< div class = "line" > < a id = "l00767" name = "l00767" > < / a > < span class = "lineno" > 767< / span > < / div >
< div class = "line" > < a id = "l00768" name = "l00768" > < / a > < span class = "lineno" > 768< / span > < span class = "comment" > // Define the reaction node (small, black dot)< / span > < / div >
< div class = "line" > < a id = "l00769" name = "l00769" > < / a > < span class = "lineno" > 769< / span > dotFile < < < span class = "stringliteral" > " \" " < / span > < < reactionNodeId < < < span class = "stringliteral" > " \" [shape=point, fillcolor=black, width=0.1, height=0.1, label=\" \" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00770" name = "l00770" > < / a > < span class = "lineno" > 770< / span > < / div >
< div class = "line" > < a id = "l00771" name = "l00771" > < / a > < span class = "lineno" > 771< / span > < span class = "comment" > // Draw edges from reactants to the reaction node< / span > < / div >
< div class = "line" > < a id = "l00772" name = "l00772" > < / a > < span class = "lineno" > 772< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & reactant : < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants()) {< / div >
< div class = "line" > < a id = "l00773" name = "l00773" > < / a > < span class = "lineno" > 773< / span > dotFile < < < span class = "stringliteral" > " \" " < / span > < < reactant.name() < < < span class = "stringliteral" > " \" -> \" " < / span > < < reactionNodeId < < < span class = "stringliteral" > " \" ;\n" < / span > ;< / div >
< div class = "line" > < a id = "l00774" name = "l00774" > < / a > < span class = "lineno" > 774< / span > }< / div >
< div class = "line" > < a id = "l00775" name = "l00775" > < / a > < span class = "lineno" > 775< / span > < / div >
< div class = "line" > < a id = "l00776" name = "l00776" > < / a > < span class = "lineno" > 776< / span > < span class = "comment" > // Draw edges from the reaction node to products< / span > < / div >
< div class = "line" > < a id = "l00777" name = "l00777" > < / a > < span class = "lineno" > 777< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & product : < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products()) {< / div >
< div class = "line" > < a id = "l00778" name = "l00778" > < / a > < span class = "lineno" > 778< / span > dotFile < < < span class = "stringliteral" > " \" " < / span > < < reactionNodeId < < < span class = "stringliteral" > " \" -> \" " < / span > < < product.name() < < < span class = "stringliteral" > " \" [label=\" " < / span > < < < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .qValue() < < < span class = "stringliteral" > " MeV\" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00779" name = "l00779" > < / a > < span class = "lineno" > 779< / span > }< / div >
< div class = "line" > < a id = "l00780" name = "l00780" > < / a > < span class = "lineno" > 780< / span > dotFile < < < span class = "stringliteral" > " \n" < / span > ;< / div >
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< div class = "line" > < a id = "l00781" name = "l00781" > < / a > < span class = "lineno" > 781< / span > }< / div >
2025-07-30 15:12:46 -04:00
< div class = "line" > < a id = "l00782" name = "l00782" > < / a > < span class = "lineno" > 782< / span > < / div >
< div class = "line" > < a id = "l00783" name = "l00783" > < / a > < span class = "lineno" > 783< / span > dotFile < < < span class = "stringliteral" > " }\n" < / span > ;< / div >
< div class = "line" > < a id = "l00784" name = "l00784" > < / a > < span class = "lineno" > 784< / span > dotFile.close();< / div >
< div class = "line" > < a id = "l00785" name = "l00785" > < / a > < span class = "lineno" > 785< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Successfully exported network to {}" < / span > , filename);< / div >
< div class = "line" > < a id = "l00786" name = "l00786" > < / a > < span class = "lineno" > 786< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00787" name = "l00787" > < / a > < span class = "lineno" > 787< / span > < / div >
< div class = "foldopen" id = "foldopen00788" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00788" name = "l00788" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95" > 788< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95" > GraphEngine::exportToCSV< / a > (< span class = "keyword" > const< / span > std::string & filename)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00789" name = "l00789" > < / a > < span class = "lineno" > 789< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Exporting network graph to CSV file: {}" < / span > , filename);< / div >
< div class = "line" > < a id = "l00790" name = "l00790" > < / a > < span class = "lineno" > 790< / span > < / div >
< div class = "line" > < a id = "l00791" name = "l00791" > < / a > < span class = "lineno" > 791< / span > std::ofstream csvFile(filename, std::ios::out | std::ios::trunc);< / div >
< div class = "line" > < a id = "l00792" name = "l00792" > < / a > < span class = "lineno" > 792< / span > < span class = "keywordflow" > if< / span > (!csvFile.is_open()) {< / div >
< div class = "line" > < a id = "l00793" name = "l00793" > < / a > < span class = "lineno" > 793< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Failed to open file for writing: {}" < / span > , filename);< / div >
< div class = "line" > < a id = "l00794" name = "l00794" > < / a > < span class = "lineno" > 794< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00795" name = "l00795" > < / a > < span class = "lineno" > 795< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " Failed to open file for writing: " < / span > + filename);< / div >
< div class = "line" > < a id = "l00796" name = "l00796" > < / a > < span class = "lineno" > 796< / span > }< / div >
< div class = "line" > < a id = "l00797" name = "l00797" > < / a > < span class = "lineno" > 797< / span > csvFile < < < span class = "stringliteral" > " Reaction;Reactants;Products;Q-value;sources;rates\n" < / span > ;< / div >
< div class = "line" > < a id = "l00798" name = "l00798" > < / a > < span class = "lineno" > 798< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > ) {< / div >
< div class = "line" > < a id = "l00799" name = "l00799" > < / a > < span class = "lineno" > 799< / span > < span class = "comment" > // Dynamic cast to REACLIBReaction to access specific properties< / span > < / div >
< div class = "line" > < a id = "l00800" name = "l00800" > < / a > < span class = "lineno" > 800< / span > csvFile < < < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id() < < < span class = "stringliteral" > " ;" < / span > ;< / div >
< div class = "line" > < a id = "l00801" name = "l00801" > < / a > < span class = "lineno" > 801< / span > < span class = "comment" > // Reactants< / span > < / div >
< div class = "line" > < a id = "l00802" name = "l00802" > < / a > < span class = "lineno" > 802< / span > < span class = "keywordtype" > size_t< / span > count = 0;< / div >
< div class = "line" > < a id = "l00803" name = "l00803" > < / a > < span class = "lineno" > 803< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & reactant : < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants()) {< / div >
< div class = "line" > < a id = "l00804" name = "l00804" > < / a > < span class = "lineno" > 804< / span > csvFile < < reactant.name();< / div >
< div class = "line" > < a id = "l00805" name = "l00805" > < / a > < span class = "lineno" > 805< / span > < span class = "keywordflow" > if< / span > (++count < < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants().size()) {< / div >
< div class = "line" > < a id = "l00806" name = "l00806" > < / a > < span class = "lineno" > 806< / span > csvFile < < < span class = "stringliteral" > " ," < / span > ;< / div >
< div class = "line" > < a id = "l00807" name = "l00807" > < / a > < span class = "lineno" > 807< / span > }< / div >
< div class = "line" > < a id = "l00808" name = "l00808" > < / a > < span class = "lineno" > 808< / span > }< / div >
< div class = "line" > < a id = "l00809" name = "l00809" > < / a > < span class = "lineno" > 809< / span > csvFile < < < span class = "stringliteral" > " ;" < / span > ;< / div >
< div class = "line" > < a id = "l00810" name = "l00810" > < / a > < span class = "lineno" > 810< / span > count = 0;< / div >
< div class = "line" > < a id = "l00811" name = "l00811" > < / a > < span class = "lineno" > 811< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & product : < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products()) {< / div >
< div class = "line" > < a id = "l00812" name = "l00812" > < / a > < span class = "lineno" > 812< / span > csvFile < < product.name();< / div >
< div class = "line" > < a id = "l00813" name = "l00813" > < / a > < span class = "lineno" > 813< / span > < span class = "keywordflow" > if< / span > (++count < < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products().size()) {< / div >
< div class = "line" > < a id = "l00814" name = "l00814" > < / a > < span class = "lineno" > 814< / span > csvFile < < < span class = "stringliteral" > " ," < / span > ;< / div >
< div class = "line" > < a id = "l00815" name = "l00815" > < / a > < span class = "lineno" > 815< / span > }< / div >
< div class = "line" > < a id = "l00816" name = "l00816" > < / a > < span class = "lineno" > 816< / span > }< / div >
< div class = "line" > < a id = "l00817" name = "l00817" > < / a > < span class = "lineno" > 817< / span > csvFile < < < span class = "stringliteral" > " ;" < / span > < < < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .qValue() < < < span class = "stringliteral" > " ;" < / span > ;< / div >
< div class = "line" > < a id = "l00818" name = "l00818" > < / a > < span class = "lineno" > 818< / span > < span class = "comment" > // Reaction coefficients< / span > < / div >
< div class = "line" > < a id = "l00819" name = "l00819" > < / a > < span class = "lineno" > 819< / span > < span class = "keyword" > auto< / span > sources = < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .sources();< / div >
< div class = "line" > < a id = "l00820" name = "l00820" > < / a > < span class = "lineno" > 820< / span > count = 0;< / div >
< div class = "line" > < a id = "l00821" name = "l00821" > < / a > < span class = "lineno" > 821< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & source : sources) {< / div >
< div class = "line" > < a id = "l00822" name = "l00822" > < / a > < span class = "lineno" > 822< / span > csvFile < < source;< / div >
< div class = "line" > < a id = "l00823" name = "l00823" > < / a > < span class = "lineno" > 823< / span > < span class = "keywordflow" > if< / span > (++count < sources.size()) {< / div >
< div class = "line" > < a id = "l00824" name = "l00824" > < / a > < span class = "lineno" > 824< / span > csvFile < < < span class = "stringliteral" > " ," < / span > ;< / div >
< div class = "line" > < a id = "l00825" name = "l00825" > < / a > < span class = "lineno" > 825< / span > }< / div >
< div class = "line" > < a id = "l00826" name = "l00826" > < / a > < span class = "lineno" > 826< / span > }< / div >
< div class = "line" > < a id = "l00827" name = "l00827" > < / a > < span class = "lineno" > 827< / span > csvFile < < < span class = "stringliteral" > " ;" < / span > ;< / div >
< div class = "line" > < a id = "l00828" name = "l00828" > < / a > < span class = "lineno" > 828< / span > < span class = "comment" > // Reaction coefficients< / span > < / div >
< div class = "line" > < a id = "l00829" name = "l00829" > < / a > < span class = "lineno" > 829< / span > count = 0;< / div >
< div class = "line" > < a id = "l00830" name = "l00830" > < / a > < span class = "lineno" > 830< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & rates : < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > ) {< / div >
< div class = "line" > < a id = "l00831" name = "l00831" > < / a > < span class = "lineno" > 831< / span > csvFile < < rates;< / div >
< div class = "line" > < a id = "l00832" name = "l00832" > < / a > < span class = "lineno" > 832< / span > < span class = "keywordflow" > if< / span > (++count < < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .size()) {< / div >
< div class = "line" > < a id = "l00833" name = "l00833" > < / a > < span class = "lineno" > 833< / span > csvFile < < < span class = "stringliteral" > " ," < / span > ;< / div >
< div class = "line" > < a id = "l00834" name = "l00834" > < / a > < span class = "lineno" > 834< / span > }< / div >
< div class = "line" > < a id = "l00835" name = "l00835" > < / a > < span class = "lineno" > 835< / span > }< / div >
< div class = "line" > < a id = "l00836" name = "l00836" > < / a > < span class = "lineno" > 836< / span > csvFile < < < span class = "stringliteral" > " \n" < / span > ;< / div >
< div class = "line" > < a id = "l00837" name = "l00837" > < / a > < span class = "lineno" > 837< / span > }< / div >
< div class = "line" > < a id = "l00838" name = "l00838" > < / a > < span class = "lineno" > 838< / span > csvFile.close();< / div >
< div class = "line" > < a id = "l00839" name = "l00839" > < / a > < span class = "lineno" > 839< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Successfully exported network graph to {}" < / span > , filename);< / div >
< div class = "line" > < a id = "l00840" name = "l00840" > < / a > < span class = "lineno" > 840< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00841" name = "l00841" > < / a > < span class = "lineno" > 841< / span > < / div >
< div class = "foldopen" id = "foldopen00842" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00842" name = "l00842" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a65f9f33cddb0bbd1da7c9d0cff23d581" > 842< / a > < / span > std::expected< std::unordered_map< fourdst::atomic::Species, double> , < a class = "code hl_struct" href = "structgridfire_1_1expectations_1_1_stale_engine_error.html" > expectations::StaleEngineError< / a > > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a65f9f33cddb0bbd1da7c9d0cff23d581" > GraphEngine::getSpeciesTimescales< / a > (< / div >
< div class = "line" > < a id = "l00843" name = "l00843" > < / a > < span class = "lineno" > 843< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l00844" name = "l00844" > < / a > < span class = "lineno" > 844< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00845" name = "l00845" > < / a > < span class = "lineno" > 845< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00846" name = "l00846" > < / a > < span class = "lineno" > 846< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00847" name = "l00847" > < / a > < span class = "lineno" > 847< / span > < span class = "keyword" > auto< / span > [dydt, _] = < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9" > calculateAllDerivatives< double> < / a > (Y, T9, rho);< / div >
< div class = "line" > < a id = "l00848" name = "l00848" > < / a > < span class = "lineno" > 848< / span > std::unordered_map< fourdst::atomic::Species, double> speciesTimescales;< / div >
< div class = "line" > < a id = "l00849" name = "l00849" > < / a > < span class = "lineno" > 849< / span > speciesTimescales.reserve(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size());< / div >
< div class = "line" > < a id = "l00850" name = "l00850" > < / a > < span class = "lineno" > 850< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size(); ++i) {< / div >
< div class = "line" > < a id = "l00851" name = "l00851" > < / a > < span class = "lineno" > 851< / span > < span class = "keywordtype" > double< / span > timescale = std::numeric_limits< double> ::infinity();< / div >
< div class = "line" > < a id = "l00852" name = "l00852" > < / a > < span class = "lineno" > 852< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > species = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > [i];< / div >
< div class = "line" > < a id = "l00853" name = "l00853" > < / a > < span class = "lineno" > 853< / span > < span class = "keywordflow" > if< / span > (std::abs(dydt[i]) > 0.0) {< / div >
< div class = "line" > < a id = "l00854" name = "l00854" > < / a > < span class = "lineno" > 854< / span > timescale = std::abs(Y[i] / dydt[i]);< / div >
< div class = "line" > < a id = "l00855" name = "l00855" > < / a > < span class = "lineno" > 855< / span > }< / div >
< div class = "line" > < a id = "l00856" name = "l00856" > < / a > < span class = "lineno" > 856< / span > speciesTimescales.emplace(species, timescale);< / div >
< div class = "line" > < a id = "l00857" name = "l00857" > < / a > < span class = "lineno" > 857< / span > }< / div >
< div class = "line" > < a id = "l00858" name = "l00858" > < / a > < span class = "lineno" > 858< / span > < span class = "keywordflow" > return< / span > speciesTimescales;< / div >
< div class = "line" > < a id = "l00859" name = "l00859" > < / a > < span class = "lineno" > 859< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00860" name = "l00860" > < / a > < span class = "lineno" > 860< / span > < / div >
< div class = "foldopen" id = "foldopen00861" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00861" name = "l00861" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#aef8f6bde24d27345067b71084330c7da" > 861< / a > < / span > std::expected< std::unordered_map< fourdst::atomic::Species, double> , < a class = "code hl_struct" href = "structgridfire_1_1expectations_1_1_stale_engine_error.html" > expectations::StaleEngineError< / a > > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#aef8f6bde24d27345067b71084330c7da" > GraphEngine::getSpeciesDestructionTimescales< / a > (< / div >
< div class = "line" > < a id = "l00862" name = "l00862" > < / a > < span class = "lineno" > 862< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l00863" name = "l00863" > < / a > < span class = "lineno" > 863< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00864" name = "l00864" > < / a > < span class = "lineno" > 864< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00865" name = "l00865" > < / a > < span class = "lineno" > 865< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00866" name = "l00866" > < / a > < span class = "lineno" > 866< / span > < span class = "keyword" > auto< / span > [dydt, _] = < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9" > calculateAllDerivatives< double> < / a > (Y, T9, rho);< / div >
< div class = "line" > < a id = "l00867" name = "l00867" > < / a > < span class = "lineno" > 867< / span > std::unordered_map< fourdst::atomic::Species, double> speciesDestructionTimescales;< / div >
< div class = "line" > < a id = "l00868" name = "l00868" > < / a > < span class = "lineno" > 868< / span > speciesDestructionTimescales.reserve(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size());< / div >
< div class = "line" > < a id = "l00869" name = "l00869" > < / a > < span class = "lineno" > 869< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > ) {< / div >
< div class = "line" > < a id = "l00870" name = "l00870" > < / a > < span class = "lineno" > 870< / span > < span class = "keywordtype" > double< / span > netDestructionFlow = 0.0;< / div >
< div class = "line" > < a id = "l00871" name = "l00871" > < / a > < span class = "lineno" > 871< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > ) {< / div >
< div class = "line" > < a id = "l00872" name = "l00872" > < / a > < span class = "lineno" > 872< / span > < span class = "keywordflow" > if< / span > (< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .stoichiometry(species) < 0) {< / div >
< div class = "line" > < a id = "l00873" name = "l00873" > < / a > < span class = "lineno" > 873< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > flow = < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f" > calculateMolarReactionFlow< double> < / a > (< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > , Y, T9, rho);< / div >
< div class = "line" > < a id = "l00874" name = "l00874" > < / a > < span class = "lineno" > 874< / span > netDestructionFlow += flow;< / div >
< div class = "line" > < a id = "l00875" name = "l00875" > < / a > < span class = "lineno" > 875< / span > }< / div >
< div class = "line" > < a id = "l00876" name = "l00876" > < / a > < span class = "lineno" > 876< / span > }< / div >
< div class = "line" > < a id = "l00877" name = "l00877" > < / a > < span class = "lineno" > 877< / span > < span class = "keywordtype" > double< / span > timescale = std::numeric_limits< double> ::infinity();< / div >
< div class = "line" > < a id = "l00878" name = "l00878" > < / a > < span class = "lineno" > 878< / span > < span class = "keywordflow" > if< / span > (netDestructionFlow != 0.0) {< / div >
< div class = "line" > < a id = "l00879" name = "l00879" > < / a > < span class = "lineno" > 879< / span > timescale = Y[< a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda" > getSpeciesIndex< / a > (species)] / netDestructionFlow;< / div >
< div class = "line" > < a id = "l00880" name = "l00880" > < / a > < span class = "lineno" > 880< / span > }< / div >
< div class = "line" > < a id = "l00881" name = "l00881" > < / a > < span class = "lineno" > 881< / span > speciesDestructionTimescales.emplace(species, timescale);< / div >
< div class = "line" > < a id = "l00882" name = "l00882" > < / a > < span class = "lineno" > 882< / span > }< / div >
< div class = "line" > < a id = "l00883" name = "l00883" > < / a > < span class = "lineno" > 883< / span > < span class = "keywordflow" > return< / span > speciesDestructionTimescales;< / div >
< div class = "line" > < a id = "l00884" name = "l00884" > < / a > < span class = "lineno" > 884< / span > }< / div >
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< / div >
2025-07-30 15:12:46 -04:00
< div class = "line" > < a id = "l00885" name = "l00885" > < / a > < span class = "lineno" > 885< / span > < / div >
< div class = "foldopen" id = "foldopen00886" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00886" name = "l00886" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a5ac7cff23e70bd07ba7e510b753e2ab6" > 886< / a > < / span > fourdst::composition::Composition < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a5ac7cff23e70bd07ba7e510b753e2ab6" > GraphEngine::update< / a > (< span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_net_in.html" > NetIn< / a > & netIn) {< / div >
< div class = "line" > < a id = "l00887" name = "l00887" > < / a > < span class = "lineno" > 887< / span > fourdst::composition::Composition baseUpdatedComposition = netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1" > composition< / a > ;< / div >
< div class = "line" > < a id = "l00888" name = "l00888" > < / a > < span class = "lineno" > 888< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > ) {< / div >
< div class = "line" > < a id = "l00889" name = "l00889" > < / a > < span class = "lineno" > 889< / span > < span class = "keywordflow" > if< / span > (!netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1" > composition< / a > .contains(species)) {< / div >
< div class = "line" > < a id = "l00890" name = "l00890" > < / a > < span class = "lineno" > 890< / span > baseUpdatedComposition.registerSpecies(species);< / div >
< div class = "line" > < a id = "l00891" name = "l00891" > < / a > < span class = "lineno" > 891< / span > baseUpdatedComposition.setMassFraction(species, 0.0);< / div >
< div class = "line" > < a id = "l00892" name = "l00892" > < / a > < span class = "lineno" > 892< / span > }< / div >
< div class = "line" > < a id = "l00893" name = "l00893" > < / a > < span class = "lineno" > 893< / span > }< / div >
< div class = "line" > < a id = "l00894" name = "l00894" > < / a > < span class = "lineno" > 894< / span > baseUpdatedComposition.finalize(< span class = "keyword" > false< / span > );< / div >
< div class = "line" > < a id = "l00895" name = "l00895" > < / a > < span class = "lineno" > 895< / span > < span class = "keywordflow" > return< / span > baseUpdatedComposition;< / div >
< div class = "line" > < a id = "l00896" name = "l00896" > < / a > < span class = "lineno" > 896< / span > }< / div >
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< / div >
2025-07-30 15:12:46 -04:00
< div class = "line" > < a id = "l00897" name = "l00897" > < / a > < span class = "lineno" > 897< / span > < / div >
< div class = "foldopen" id = "foldopen00898" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00898" name = "l00898" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#af04a9f8a629d6f6c58c477af0f1ab9e5" > 898< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#af04a9f8a629d6f6c58c477af0f1ab9e5" > GraphEngine::isStale< / a > (< span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_net_in.html" > NetIn< / a > & netIn) {< / div >
< div class = "line" > < a id = "l00899" name = "l00899" > < / a > < span class = "lineno" > 899< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > false< / span > ;< / div >
< div class = "line" > < a id = "l00900" name = "l00900" > < / a > < span class = "lineno" > 900< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00901" name = "l00901" > < / a > < span class = "lineno" > 901< / span > < / div >
< div class = "foldopen" id = "foldopen00902" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00902" name = "l00902" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889" > 902< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889" > GraphEngine::recordADTape< / a > () {< / div >
< div class = "line" > < a id = "l00903" name = "l00903" > < / a > < span class = "lineno" > 903< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Recording AD tape for the RHS calculation..." < / span > );< / div >
< div class = "line" > < a id = "l00904" name = "l00904" > < / a > < span class = "lineno" > 904< / span > < / div >
< div class = "line" > < a id = "l00905" name = "l00905" > < / a > < span class = "lineno" > 905< / span > < span class = "comment" > // Task 1: Set dimensions and initialize the matrix< / span > < / div >
< div class = "line" > < a id = "l00906" name = "l00906" > < / a > < span class = "lineno" > 906< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > numSpecies = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size();< / div >
< div class = "line" > < a id = "l00907" name = "l00907" > < / a > < span class = "lineno" > 907< / span > < span class = "keywordflow" > if< / span > (numSpecies == 0) {< / div >
< div class = "line" > < a id = "l00908" name = "l00908" > < / a > < span class = "lineno" > 908< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Cannot record AD tape: No species in the network." < / span > );< / div >
< div class = "line" > < a id = "l00909" name = "l00909" > < / a > < span class = "lineno" > 909< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00910" name = "l00910" > < / a > < span class = "lineno" > 910< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " Cannot record AD tape: No species in the network." < / span > );< / div >
< div class = "line" > < a id = "l00911" name = "l00911" > < / a > < span class = "lineno" > 911< / span > }< / div >
< div class = "line" > < a id = "l00912" name = "l00912" > < / a > < span class = "lineno" > 912< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > numADInputs = numSpecies + 2; < span class = "comment" > // Note here that by not letting T9 and rho be independent variables, we are constraining the network to a constant temperature and density during each evaluation.< / span > < / div >
< div class = "line" > < a id = "l00913" name = "l00913" > < / a > < span class = "lineno" > 913< / span > < / div >
< div class = "line" > < a id = "l00914" name = "l00914" > < / a > < span class = "lineno" > 914< / span > < span class = "comment" > // --- CppAD Tape Recording ---< / span > < / div >
< div class = "line" > < a id = "l00915" name = "l00915" > < / a > < span class = "lineno" > 915< / span > < span class = "comment" > // 1. Declare independent variable (adY)< / span > < / div >
< div class = "line" > < a id = "l00916" name = "l00916" > < / a > < span class = "lineno" > 916< / span > < span class = "comment" > // We also initialize the dummy variable for tape recording (these tell CppAD what the derivative chain looks like).< / span > < / div >
< div class = "line" > < a id = "l00917" name = "l00917" > < / a > < span class = "lineno" > 917< / span > < span class = "comment" > // Their numeric values are irrelevant except for in so far as they avoid numerical instabilities.< / span > < / div >
< div class = "line" > < a id = "l00918" name = "l00918" > < / a > < span class = "lineno" > 918< / span > < / div >
< div class = "line" > < a id = "l00919" name = "l00919" > < / a > < span class = "lineno" > 919< / span > < span class = "comment" > // Distribute total mass fraction uniformly between species in the dummy variable space< / span > < / div >
< div class = "line" > < a id = "l00920" name = "l00920" > < / a > < span class = "lineno" > 920< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > uniformMassFraction = < span class = "keyword" > static_cast< < / span > CppAD::AD< double> < span class = "keyword" > > < / span > (1.0 / < span class = "keyword" > static_cast< < / span > < span class = "keywordtype" > double< / span > < span class = "keyword" > > < / span > (numSpecies));< / div >
< div class = "line" > < a id = "l00921" name = "l00921" > < / a > < span class = "lineno" > 921< / span > std::vector< CppAD::AD< double> > adInput(numADInputs, uniformMassFraction);< / div >
< div class = "line" > < a id = "l00922" name = "l00922" > < / a > < span class = "lineno" > 922< / span > adInput[numSpecies] = 1.0; < span class = "comment" > // Dummy T9< / span > < / div >
< div class = "line" > < a id = "l00923" name = "l00923" > < / a > < span class = "lineno" > 923< / span > adInput[numSpecies + 1] = 1.0; < span class = "comment" > // Dummy rho< / span > < / div >
< div class = "line" > < a id = "l00924" name = "l00924" > < / a > < span class = "lineno" > 924< / span > < / div >
< div class = "line" > < a id = "l00925" name = "l00925" > < / a > < span class = "lineno" > 925< / span > < span class = "comment" > // 3. Declare independent variables (what CppAD will differentiate wrt.)< / span > < / div >
< div class = "line" > < a id = "l00926" name = "l00926" > < / a > < span class = "lineno" > 926< / span > < span class = "comment" > // This also beings the tape recording process.< / span > < / div >
< div class = "line" > < a id = "l00927" name = "l00927" > < / a > < span class = "lineno" > 927< / span > CppAD::Independent(adInput);< / div >
< div class = "line" > < a id = "l00928" name = "l00928" > < / a > < span class = "lineno" > 928< / span > < / div >
< div class = "line" > < a id = "l00929" name = "l00929" > < / a > < span class = "lineno" > 929< / span > std::vector< CppAD::AD< double> > adY(numSpecies);< / div >
< div class = "line" > < a id = "l00930" name = "l00930" > < / a > < span class = "lineno" > 930< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < numSpecies; ++i) {< / div >
< div class = "line" > < a id = "l00931" name = "l00931" > < / a > < span class = "lineno" > 931< / span > adY[i] = adInput[i];< / div >
< div class = "line" > < a id = "l00932" name = "l00932" > < / a > < span class = "lineno" > 932< / span > }< / div >
< div class = "line" > < a id = "l00933" name = "l00933" > < / a > < span class = "lineno" > 933< / span > < span class = "keyword" > const< / span > CppAD::AD< double> adT9 = adInput[numSpecies];< / div >
< div class = "line" > < a id = "l00934" name = "l00934" > < / a > < span class = "lineno" > 934< / span > < span class = "keyword" > const< / span > CppAD::AD< double> adRho = adInput[numSpecies + 1];< / div >
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< div class = "line" > < a id = "l00935" name = "l00935" > < / a > < span class = "lineno" > 935< / span > < / div >
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< div class = "line" > < a id = "l00936" name = "l00936" > < / a > < span class = "lineno" > 936< / span > < / div >
< div class = "line" > < a id = "l00937" name = "l00937" > < / a > < span class = "lineno" > 937< / span > < span class = "comment" > // 5. Call the actual templated function< / span > < / div >
< div class = "line" > < a id = "l00938" name = "l00938" > < / a > < span class = "lineno" > 938< / span > < span class = "comment" > // We let T9 and rho be constant, so we pass them as fixed values.< / span > < / div >
< div class = "line" > < a id = "l00939" name = "l00939" > < / a > < span class = "lineno" > 939< / span > < span class = "keyword" > auto< / span > [dydt, nuclearEnergyGenerationRate] = < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9" > calculateAllDerivatives< CppAD::AD< double> < / a > > (adY, adT9, adRho);< / div >
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< div class = "line" > < a id = "l00940" name = "l00940" > < / a > < span class = "lineno" > 940< / span > < / div >
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< div class = "line" > < a id = "l00941" name = "l00941" > < / a > < span class = "lineno" > 941< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876" > m_rhsADFun< / a > .Dependent(adInput, dydt);< / div >
< div class = "line" > < a id = "l00942" name = "l00942" > < / a > < span class = "lineno" > 942< / span > < / div >
< div class = "line" > < a id = "l00943" name = "l00943" > < / a > < span class = "lineno" > 943< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " AD tape recorded successfully for the RHS calculation. Number of independent variables: {}." < / span > ,< / div >
< div class = "line" > < a id = "l00944" name = "l00944" > < / a > < span class = "lineno" > 944< / span > adInput.size());< / div >
< div class = "line" > < a id = "l00945" name = "l00945" > < / a > < span class = "lineno" > 945< / span > }< / div >
< / div >
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< div class = "line" > < a id = "l00946" name = "l00946" > < / a > < span class = "lineno" > 946< / span > < / div >
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< div class = "foldopen" id = "foldopen00947" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00947" name = "l00947" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a29b338630c959449c15881935ac30746" > 947< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a29b338630c959449c15881935ac30746" > GraphEngine::collectAtomicReverseRateAtomicBases< / a > () {< / div >
< div class = "line" > < a id = "l00948" name = "l00948" > < / a > < span class = "lineno" > 948< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a816797b1d656d416844489692af44cf6" > m_atomicReverseRates< / a > .clear();< / div >
< div class = "line" > < a id = "l00949" name = "l00949" > < / a > < span class = "lineno" > 949< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a816797b1d656d416844489692af44cf6" > m_atomicReverseRates< / a > .reserve(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > .size());< / div >
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< div class = "line" > < a id = "l00950" name = "l00950" > < / a > < span class = "lineno" > 950< / span > < / div >
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< div class = "line" > < a id = "l00951" name = "l00951" > < / a > < span class = "lineno" > 951< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > : < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > ) {< / div >
< div class = "line" > < a id = "l00952" name = "l00952" > < / a > < span class = "lineno" > 952< / span > < span class = "keywordflow" > if< / span > (< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .qValue() != 0.0) {< / div >
< div class = "line" > < a id = "l00953" name = "l00953" > < / a > < span class = "lineno" > 953< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a816797b1d656d416844489692af44cf6" > m_atomicReverseRates< / a > .push_back(std::make_unique< AtomicReverseRate> (< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > , *< span class = "keyword" > this< / span > ));< / div >
< div class = "line" > < a id = "l00954" name = "l00954" > < / a > < span class = "lineno" > 954< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00955" name = "l00955" > < / a > < span class = "lineno" > 955< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a816797b1d656d416844489692af44cf6" > m_atomicReverseRates< / a > .push_back(< span class = "keyword" > nullptr< / span > );< / div >
< div class = "line" > < a id = "l00956" name = "l00956" > < / a > < span class = "lineno" > 956< / span > }< / div >
< div class = "line" > < a id = "l00957" name = "l00957" > < / a > < span class = "lineno" > 957< / span > }< / div >
< div class = "line" > < a id = "l00958" name = "l00958" > < / a > < span class = "lineno" > 958< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00959" name = "l00959" > < / a > < span class = "lineno" > 959< / span > < / div >
< div class = "foldopen" id = "foldopen00960" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00960" name = "l00960" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd" > 960< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd" > GraphEngine::precomputeNetwork< / a > () {< / div >
< div class = "line" > < a id = "l00961" name = "l00961" > < / a > < span class = "lineno" > 961< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > m_logger< / a > , < span class = "stringliteral" > " Pre-computing constant components of GraphNetwork state..." < / span > );< / div >
< div class = "line" > < a id = "l00962" name = "l00962" > < / a > < span class = "lineno" > 962< / span > < / div >
< div class = "line" > < a id = "l00963" name = "l00963" > < / a > < span class = "lineno" > 963< / span > < span class = "comment" > // --- Reverse map for fast species lookups ---< / span > < / div >
< div class = "line" > < a id = "l00964" name = "l00964" > < / a > < span class = "lineno" > 964< / span > std::unordered_map< fourdst::atomic::Species, size_t> speciesIndexMap;< / div >
< div class = "line" > < a id = "l00965" name = "l00965" > < / a > < span class = "lineno" > 965< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > .size(); ++i) {< / div >
< div class = "line" > < a id = "l00966" name = "l00966" > < / a > < span class = "lineno" > 966< / span > speciesIndexMap[< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > m_networkSpecies< / a > [i]] = i;< / div >
< div class = "line" > < a id = "l00967" name = "l00967" > < / a > < span class = "lineno" > 967< / span > }< / div >
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< div class = "line" > < a id = "l00968" name = "l00968" > < / a > < span class = "lineno" > 968< / span > < / div >
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< div class = "line" > < a id = "l00969" name = "l00969" > < / a > < span class = "lineno" > 969< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3" > m_precomputedReactions< / a > .clear();< / div >
< div class = "line" > < a id = "l00970" name = "l00970" > < / a > < span class = "lineno" > 970< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3" > m_precomputedReactions< / a > .reserve(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > .size());< / div >
< div class = "line" > < a id = "l00971" name = "l00971" > < / a > < span class = "lineno" > 971< / span > < / div >
< div class = "line" > < a id = "l00972" name = "l00972" > < / a > < span class = "lineno" > 972< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > .size(); ++i) {< / div >
< div class = "line" > < a id = "l00973" name = "l00973" > < / a > < span class = "lineno" > 973< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > m_reactions< / a > [i];< / div >
< div class = "line" > < a id = "l00974" name = "l00974" > < / a > < span class = "lineno" > 974< / span > < a class = "code hl_struct" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html" > PrecomputedReaction< / a > precomp;< / div >
< div class = "line" > < a id = "l00975" name = "l00975" > < / a > < span class = "lineno" > 975< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a93635f6940d3534e949f402503c3d497" > reaction_index< / a > = i;< / div >
< div class = "line" > < a id = "l00976" name = "l00976" > < / a > < span class = "lineno" > 976< / span > < / div >
< div class = "line" > < a id = "l00977" name = "l00977" > < / a > < span class = "lineno" > 977< / span > < span class = "comment" > // --- Precompute forward reaction information ---< / span > < / div >
< div class = "line" > < a id = "l00978" name = "l00978" > < / a > < span class = "lineno" > 978< / span > < span class = "comment" > // Count occurrences for each reactant to determine powers and symmetry< / span > < / div >
< div class = "line" > < a id = "l00979" name = "l00979" > < / a > < span class = "lineno" > 979< / span > std::unordered_map< size_t, int> reactantCounts;< / div >
< div class = "line" > < a id = "l00980" name = "l00980" > < / a > < span class = "lineno" > 980< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & reactant: < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants()) {< / div >
< div class = "line" > < a id = "l00981" name = "l00981" > < / a > < span class = "lineno" > 981< / span > < span class = "keywordtype" > size_t< / span > reactantIndex = speciesIndexMap.at(reactant);< / div >
< div class = "line" > < a id = "l00982" name = "l00982" > < / a > < span class = "lineno" > 982< / span > reactantCounts[reactantIndex]++;< / div >
< div class = "line" > < a id = "l00983" name = "l00983" > < / a > < span class = "lineno" > 983< / span > }< / div >
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< div class = "line" > < a id = "l00984" name = "l00984" > < / a > < span class = "lineno" > 984< / span > < / div >
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< div class = "line" > < a id = "l00985" name = "l00985" > < / a > < span class = "lineno" > 985< / span > < span class = "keywordtype" > double< / span > symmetryDenominator = 1.0;< / div >
< div class = "line" > < a id = "l00986" name = "l00986" > < / a > < span class = "lineno" > 986< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & [index, count] : reactantCounts) {< / div >
< div class = "line" > < a id = "l00987" name = "l00987" > < / a > < span class = "lineno" > 987< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a510e380116e2e6d9158cf00fedac2666" > unique_reactant_indices< / a > .push_back(index);< / div >
< div class = "line" > < a id = "l00988" name = "l00988" > < / a > < span class = "lineno" > 988< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a03d596c88289e21e7bd18711e3a1f275" > reactant_powers< / a > .push_back(count);< / div >
< div class = "line" > < a id = "l00989" name = "l00989" > < / a > < span class = "lineno" > 989< / span > < / div >
< div class = "line" > < a id = "l00990" name = "l00990" > < / a > < span class = "lineno" > 990< / span > symmetryDenominator *= std::tgamma(count + 1);< / div >
< div class = "line" > < a id = "l00991" name = "l00991" > < / a > < span class = "lineno" > 991< / span > }< / div >
< div class = "line" > < a id = "l00992" name = "l00992" > < / a > < span class = "lineno" > 992< / span > < / div >
< div class = "line" > < a id = "l00993" name = "l00993" > < / a > < span class = "lineno" > 993< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#ac42504e868c0b9fd9ac9a405ea739f0e" > symmetry_factor< / a > = 1.0/symmetryDenominator;< / div >
< div class = "line" > < a id = "l00994" name = "l00994" > < / a > < span class = "lineno" > 994< / span > < / div >
< div class = "line" > < a id = "l00995" name = "l00995" > < / a > < span class = "lineno" > 995< / span > < span class = "comment" > // --- Precompute reverse reaction information ---< / span > < / div >
< div class = "line" > < a id = "l00996" name = "l00996" > < / a > < span class = "lineno" > 996< / span > < span class = "keywordflow" > if< / span > (< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .qValue() != 0.0) {< / div >
< div class = "line" > < a id = "l00997" name = "l00997" > < / a > < span class = "lineno" > 997< / span > std::unordered_map< size_t, int> productCounts;< / div >
< div class = "line" > < a id = "l00998" name = "l00998" > < / a > < span class = "lineno" > 998< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & product : < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products()) {< / div >
< div class = "line" > < a id = "l00999" name = "l00999" > < / a > < span class = "lineno" > 999< / span > productCounts[speciesIndexMap.at(product)]++;< / div >
< div class = "line" > < a id = "l01000" name = "l01000" > < / a > < span class = "lineno" > 1000< / span > }< / div >
< div class = "line" > < a id = "l01001" name = "l01001" > < / a > < span class = "lineno" > 1001< / span > < span class = "keywordtype" > double< / span > reverseSymmetryDenominator = 1.0;< / div >
< div class = "line" > < a id = "l01002" name = "l01002" > < / a > < span class = "lineno" > 1002< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & [index, count] : productCounts) {< / div >
< div class = "line" > < a id = "l01003" name = "l01003" > < / a > < span class = "lineno" > 1003< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a9974f944a2cf5179baabebe09d60cf18" > unique_product_indices< / a > .push_back(index);< / div >
< div class = "line" > < a id = "l01004" name = "l01004" > < / a > < span class = "lineno" > 1004< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3ce63aa3ad88568f4eb0d3ca2414209f" > product_powers< / a > .push_back(count);< / div >
< div class = "line" > < a id = "l01005" name = "l01005" > < / a > < span class = "lineno" > 1005< / span > reverseSymmetryDenominator *= std::tgamma(count + 1);< / div >
< div class = "line" > < a id = "l01006" name = "l01006" > < / a > < span class = "lineno" > 1006< / span > }< / div >
< div class = "line" > < a id = "l01007" name = "l01007" > < / a > < span class = "lineno" > 1007< / span > < / div >
< div class = "line" > < a id = "l01008" name = "l01008" > < / a > < span class = "lineno" > 1008< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a6bcfe2230dd54b088180d34389266b07" > reverse_symmetry_factor< / a > = 1.0/reverseSymmetryDenominator;< / div >
< div class = "line" > < a id = "l01009" name = "l01009" > < / a > < span class = "lineno" > 1009< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l01010" name = "l01010" > < / a > < span class = "lineno" > 1010< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a9974f944a2cf5179baabebe09d60cf18" > unique_product_indices< / a > .clear();< / div >
< div class = "line" > < a id = "l01011" name = "l01011" > < / a > < span class = "lineno" > 1011< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3ce63aa3ad88568f4eb0d3ca2414209f" > product_powers< / a > .clear();< / div >
< div class = "line" > < a id = "l01012" name = "l01012" > < / a > < span class = "lineno" > 1012< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a6bcfe2230dd54b088180d34389266b07" > reverse_symmetry_factor< / a > = 0.0; < span class = "comment" > // No reverse reaction for Q = 0 reactions< / span > < / div >
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< div class = "line" > < a id = "l01013" name = "l01013" > < / a > < span class = "lineno" > 1013< / span > }< / div >
< div class = "line" > < a id = "l01014" name = "l01014" > < / a > < span class = "lineno" > 1014< / span > < / div >
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< div class = "line" > < a id = "l01015" name = "l01015" > < / a > < span class = "lineno" > 1015< / span > < span class = "comment" > // --- Precompute stoichiometry information ---< / span > < / div >
< div class = "line" > < a id = "l01016" name = "l01016" > < / a > < span class = "lineno" > 1016< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > stoichiometryMap = < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .stoichiometry();< / div >
< div class = "line" > < a id = "l01017" name = "l01017" > < / a > < span class = "lineno" > 1017< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3e2e67e532970738d20491ea56b170f3" > affected_species_indices< / a > .reserve(stoichiometryMap.size());< / div >
< div class = "line" > < a id = "l01018" name = "l01018" > < / a > < span class = "lineno" > 1018< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a7a7e9167b19e339e0d69544b9c00e79c" > stoichiometric_coefficients< / a > .reserve(stoichiometryMap.size());< / div >
< div class = "line" > < a id = "l01019" name = "l01019" > < / a > < span class = "lineno" > 1019< / span > < / div >
< div class = "line" > < a id = "l01020" name = "l01020" > < / a > < span class = "lineno" > 1020< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & [species, coeff] : stoichiometryMap) {< / div >
< div class = "line" > < a id = "l01021" name = "l01021" > < / a > < span class = "lineno" > 1021< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3e2e67e532970738d20491ea56b170f3" > affected_species_indices< / a > .push_back(speciesIndexMap.at(species));< / div >
< div class = "line" > < a id = "l01022" name = "l01022" > < / a > < span class = "lineno" > 1022< / span > precomp.< a class = "code hl_variable" href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a7a7e9167b19e339e0d69544b9c00e79c" > stoichiometric_coefficients< / a > .push_back(coeff);< / div >
< div class = "line" > < a id = "l01023" name = "l01023" > < / a > < span class = "lineno" > 1023< / span > }< / div >
< div class = "line" > < a id = "l01024" name = "l01024" > < / a > < span class = "lineno" > 1024< / span > < / div >
< div class = "line" > < a id = "l01025" name = "l01025" > < / a > < span class = "lineno" > 1025< / span > < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3" > m_precomputedReactions< / a > .push_back(std::move(precomp));< / div >
< div class = "line" > < a id = "l01026" name = "l01026" > < / a > < span class = "lineno" > 1026< / span > }< / div >
< div class = "line" > < a id = "l01027" name = "l01027" > < / a > < span class = "lineno" > 1027< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01028" name = "l01028" > < / a > < span class = "lineno" > 1028< / span > < / div >
< div class = "foldopen" id = "foldopen01029" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01029" name = "l01029" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#ad9b8dd0e8ba9c7745e33acc9a649d2e0" > 1029< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#ad9b8dd0e8ba9c7745e33acc9a649d2e0" > GraphEngine::AtomicReverseRate::forward< / a > (< / div >
< div class = "line" > < a id = "l01030" name = "l01030" > < / a > < span class = "lineno" > 1030< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > p,< / div >
< div class = "line" > < a id = "l01031" name = "l01031" > < / a > < span class = "lineno" > 1031< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > q,< / div >
< div class = "line" > < a id = "l01032" name = "l01032" > < / a > < span class = "lineno" > 1032< / span > < span class = "keyword" > const< / span > CppAD::vector< bool> & vx,< / div >
< div class = "line" > < a id = "l01033" name = "l01033" > < / a > < span class = "lineno" > 1033< / span > CppAD::vector< bool> & vy,< / div >
< div class = "line" > < a id = "l01034" name = "l01034" > < / a > < span class = "lineno" > 1034< / span > < span class = "keyword" > const< / span > CppAD::vector< double> & tx,< / div >
< div class = "line" > < a id = "l01035" name = "l01035" > < / a > < span class = "lineno" > 1035< / span > CppAD::vector< double> & ty< / div >
< div class = "line" > < a id = "l01036" name = "l01036" > < / a > < span class = "lineno" > 1036< / span > ) {< / div >
< div class = "line" > < a id = "l01037" name = "l01037" > < / a > < span class = "lineno" > 1037< / span > < / div >
< div class = "line" > < a id = "l01038" name = "l01038" > < / a > < span class = "lineno" > 1038< / span > < span class = "keywordflow" > if< / span > ( p != 0) { < span class = "keywordflow" > return< / span > < span class = "keyword" > false< / span > ; }< / div >
< div class = "line" > < a id = "l01039" name = "l01039" > < / a > < span class = "lineno" > 1039< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9 = tx[0];< / div >
< div class = "line" > < a id = "l01040" name = "l01040" > < / a > < span class = "lineno" > 1040< / span > < / div >
< div class = "line" > < a id = "l01041" name = "l01041" > < / a > < span class = "lineno" > 1041< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > reverseRate = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a75d355a0bef27217165644affd0cca4d" > m_engine< / a > .calculateReverseRate(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a98ed8b450f7868f55e8362a848a4710d" > m_reaction< / a > , T9);< / div >
< div class = "line" > < a id = "l01042" name = "l01042" > < / a > < span class = "lineno" > 1042< / span > < span class = "comment" > // std::cout < < m_reaction.peName() < < " reverseRate: " < < reverseRate < < " at T9: " < < T9 < < " \n" ;< / span > < / div >
< div class = "line" > < a id = "l01043" name = "l01043" > < / a > < span class = "lineno" > 1043< / span > ty[0] = reverseRate; < span class = "comment" > // Store the reverse rate in the output vector< / span > < / div >
< div class = "line" > < a id = "l01044" name = "l01044" > < / a > < span class = "lineno" > 1044< / span > < / div >
< div class = "line" > < a id = "l01045" name = "l01045" > < / a > < span class = "lineno" > 1045< / span > < span class = "keywordflow" > if< / span > (vx.size() > 0) {< / div >
< div class = "line" > < a id = "l01046" name = "l01046" > < / a > < span class = "lineno" > 1046< / span > vy[0] = vx[0];< / div >
< div class = "line" > < a id = "l01047" name = "l01047" > < / a > < span class = "lineno" > 1047< / span > }< / div >
< div class = "line" > < a id = "l01048" name = "l01048" > < / a > < span class = "lineno" > 1048< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > true< / span > ;< / div >
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< div class = "line" > < a id = "l01049" name = "l01049" > < / a > < span class = "lineno" > 1049< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01050" name = "l01050" > < / a > < span class = "lineno" > 1050< / span > < / div >
< div class = "foldopen" id = "foldopen01051" data-start = "{" data-end = "}" >
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< div class = "line" > < a id = "l01051" name = "l01051" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a4e8ff268c4377599c8798c7929ec2d5e" > 1051< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a4e8ff268c4377599c8798c7929ec2d5e" > GraphEngine::AtomicReverseRate::reverse< / a > (< / div >
< div class = "line" > < a id = "l01052" name = "l01052" > < / a > < span class = "lineno" > 1052< / span > < span class = "keywordtype" > size_t< / span > q,< / div >
< div class = "line" > < a id = "l01053" name = "l01053" > < / a > < span class = "lineno" > 1053< / span > < span class = "keyword" > const< / span > CppAD::vector< double> & tx,< / div >
< div class = "line" > < a id = "l01054" name = "l01054" > < / a > < span class = "lineno" > 1054< / span > < span class = "keyword" > const< / span > CppAD::vector< double> & ty,< / div >
< div class = "line" > < a id = "l01055" name = "l01055" > < / a > < span class = "lineno" > 1055< / span > CppAD::vector< double> & px,< / div >
< div class = "line" > < a id = "l01056" name = "l01056" > < / a > < span class = "lineno" > 1056< / span > < span class = "keyword" > const< / span > CppAD::vector< double> & py< / div >
< div class = "line" > < a id = "l01057" name = "l01057" > < / a > < span class = "lineno" > 1057< / span > ) {< / div >
< div class = "line" > < a id = "l01058" name = "l01058" > < / a > < span class = "lineno" > 1058< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9 = tx[0];< / div >
< div class = "line" > < a id = "l01059" name = "l01059" > < / a > < span class = "lineno" > 1059< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > reverseRate = ty[0];< / div >
< div class = "line" > < a id = "l01060" name = "l01060" > < / a > < span class = "lineno" > 1060< / span > < / div >
< div class = "line" > < a id = "l01061" name = "l01061" > < / a > < span class = "lineno" > 1061< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > derivative = < a class = "code hl_variable" href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a75d355a0bef27217165644affd0cca4d" > m_engine< / a > .calculateReverseRateTwoBodyDerivative(< a class = "code hl_variable" href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a98ed8b450f7868f55e8362a848a4710d" > m_reaction< / a > , T9, reverseRate);< / div >
< div class = "line" > < a id = "l01062" name = "l01062" > < / a > < span class = "lineno" > 1062< / span > < span class = "comment" > // std::cout < < m_reaction.peName() < < " reverseRate Derivative: " < < derivative < < " \n" ;< / span > < / div >
< div class = "line" > < a id = "l01063" name = "l01063" > < / a > < span class = "lineno" > 1063< / span > < / div >
< div class = "line" > < a id = "l01064" name = "l01064" > < / a > < span class = "lineno" > 1064< / span > px[0] = py[0] * derivative; < span class = "comment" > // Return the derivative of the reverse rate with respect to T9< / span > < / div >
< div class = "line" > < a id = "l01065" name = "l01065" > < / a > < span class = "lineno" > 1065< / span > < / div >
< div class = "line" > < a id = "l01066" name = "l01066" > < / a > < span class = "lineno" > 1066< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > true< / span > ;< / div >
< div class = "line" > < a id = "l01067" name = "l01067" > < / a > < span class = "lineno" > 1067< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l01068" name = "l01068" > < / a > < span class = "lineno" > 1068< / span > < / div >
< div class = "foldopen" id = "foldopen01069" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01069" name = "l01069" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#aec41632c2a362be33a1f7ff04204cbf4" > 1069< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#aec41632c2a362be33a1f7ff04204cbf4" > GraphEngine::AtomicReverseRate::for_sparse_jac< / a > (< / div >
< div class = "line" > < a id = "l01070" name = "l01070" > < / a > < span class = "lineno" > 1070< / span > < span class = "keywordtype" > size_t< / span > q,< / div >
< div class = "line" > < a id = "l01071" name = "l01071" > < / a > < span class = "lineno" > 1071< / span > < span class = "keyword" > const< / span > CppAD::vector< std::set< size_t> > & r,< / div >
< div class = "line" > < a id = "l01072" name = "l01072" > < / a > < span class = "lineno" > 1072< / span > CppAD::vector< std::set< size_t> > & s< / div >
< div class = "line" > < a id = "l01073" name = "l01073" > < / a > < span class = "lineno" > 1073< / span > ) {< / div >
< div class = "line" > < a id = "l01074" name = "l01074" > < / a > < span class = "lineno" > 1074< / span > s[0] = r[0];< / div >
< div class = "line" > < a id = "l01075" name = "l01075" > < / a > < span class = "lineno" > 1075< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > true< / span > ;< / div >
< div class = "line" > < a id = "l01076" name = "l01076" > < / a > < span class = "lineno" > 1076< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l01077" name = "l01077" > < / a > < span class = "lineno" > 1077< / span > < / div >
< div class = "foldopen" id = "foldopen01078" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01078" name = "l01078" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a881d4daf2b973d523548cd8d4021bdc4" > 1078< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a881d4daf2b973d523548cd8d4021bdc4" > GraphEngine::AtomicReverseRate::rev_sparse_jac< / a > (< / div >
< div class = "line" > < a id = "l01079" name = "l01079" > < / a > < span class = "lineno" > 1079< / span > < span class = "keywordtype" > size_t< / span > q,< / div >
< div class = "line" > < a id = "l01080" name = "l01080" > < / a > < span class = "lineno" > 1080< / span > < span class = "keyword" > const< / span > CppAD::vector< std::set< size_t> > & rt,< / div >
< div class = "line" > < a id = "l01081" name = "l01081" > < / a > < span class = "lineno" > 1081< / span > CppAD::vector< std::set< size_t> > & st< / div >
< div class = "line" > < a id = "l01082" name = "l01082" > < / a > < span class = "lineno" > 1082< / span > ) {< / div >
< div class = "line" > < a id = "l01083" name = "l01083" > < / a > < span class = "lineno" > 1083< / span > st[0] = rt[0];< / div >
< div class = "line" > < a id = "l01084" name = "l01084" > < / a > < span class = "lineno" > 1084< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > true< / span > ;< / div >
< div class = "line" > < a id = "l01085" name = "l01085" > < / a > < span class = "lineno" > 1085< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l01086" name = "l01086" > < / a > < span class = "lineno" > 1086< / span > }< / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_1_1_atomic_reverse_rate_html_a4e8ff268c4377599c8798c7929ec2d5e" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a4e8ff268c4377599c8798c7929ec2d5e" > gridfire::GraphEngine::AtomicReverseRate::reverse< / a > < / div > < div class = "ttdeci" > bool reverse(size_t q, const CppAD::vector< double > & tx, const CppAD::vector< double > & ty, CppAD::vector< double > & px, const CppAD::vector< double > & py) override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01051" > engine_graph.cpp:1051< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_1_1_atomic_reverse_rate_html_a75d355a0bef27217165644affd0cca4d" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a75d355a0bef27217165644affd0cca4d" > gridfire::GraphEngine::AtomicReverseRate::m_engine< / a > < / div > < div class = "ttdeci" > const GraphEngine & m_engine< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00444" > engine_graph.h:444< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_1_1_atomic_reverse_rate_html_a881d4daf2b973d523548cd8d4021bdc4" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a881d4daf2b973d523548cd8d4021bdc4" > gridfire::GraphEngine::AtomicReverseRate::rev_sparse_jac< / a > < / div > < div class = "ttdeci" > bool rev_sparse_jac(size_t q, const CppAD::vector< std::set< size_t > > & rt, CppAD::vector< std::set< size_t > > & st) override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01078" > engine_graph.cpp:1078< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_1_1_atomic_reverse_rate_html_a98ed8b450f7868f55e8362a848a4710d" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a98ed8b450f7868f55e8362a848a4710d" > gridfire::GraphEngine::AtomicReverseRate::m_reaction< / a > < / div > < div class = "ttdeci" > const reaction::Reaction & m_reaction< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00443" > engine_graph.h:443< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_1_1_atomic_reverse_rate_html_ad9b8dd0e8ba9c7745e33acc9a649d2e0" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#ad9b8dd0e8ba9c7745e33acc9a649d2e0" > gridfire::GraphEngine::AtomicReverseRate::forward< / a > < / div > < div class = "ttdeci" > bool forward(size_t p, size_t q, const CppAD::vector< bool > & vx, CppAD::vector< bool > & vy, const CppAD::vector< double > & tx, CppAD::vector< double > & ty) override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01029" > engine_graph.cpp:1029< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_1_1_atomic_reverse_rate_html_aec41632c2a362be33a1f7ff04204cbf4" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#aec41632c2a362be33a1f7ff04204cbf4" > gridfire::GraphEngine::AtomicReverseRate::for_sparse_jac< / a > < / div > < div class = "ttdeci" > bool for_sparse_jac(size_t q, const CppAD::vector< std::set< size_t > > & r, CppAD::vector< std::set< size_t > > & s) override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01069" > engine_graph.cpp:1069< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a015f8975701f028c29835d3a9794e00f" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f" > gridfire::GraphEngine::isPrecomputationEnabled< / a > < / div > < div class = "ttdeci" > bool isPrecomputationEnabled() const< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00615" > engine_graph.cpp:615< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a01fc9fd5d576b66d07360d05e821c755" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755" > gridfire::GraphEngine::calculateReverseRateTwoBody< / a > < / div > < div class = "ttdeci" > double calculateReverseRateTwoBody(const reaction::Reaction & reaction, const double T9, const double forwardRate, const double expFactor) const< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00269" > engine_graph.cpp:269< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a0b7b85f824e1021ae6e56b644db53b28" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28" > gridfire::GraphEngine::calculateReverseRate< / a > < / div > < div class = "ttdeci" > double calculateReverseRate(const reaction::Reaction & reaction, double T9) const< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00242" > engine_graph.cpp:242< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a0ed390f3e598ebba4e245ac90bb78767" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767" > gridfire::GraphEngine::getNetworkSpecies< / a > < / div > < div class = "ttdeci" > const std::vector< fourdst::atomic::Species > & getNetworkSpecies() const override< / div > < div class = "ttdoc" > Gets the list of species in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00162" > engine_graph.cpp:162< / a > < / div > < / div >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a10c01bc20ae668c2857efb2a1783098e" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e" > gridfire::GraphEngine::m_constants< / a > < / div > < div class = "ttdeci" > constants m_constants< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00450" > engine_graph.h:450< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a166a5f4349580f9aa0b930afec73fcc4" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a166a5f4349580f9aa0b930afec73fcc4" > gridfire::GraphEngine::getDepth< / a > < / div > < div class = "ttdeci" > BuildDepthType getDepth() const override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00434" > engine_graph.cpp:434< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a191cff35402d3c97c82c5c966a39d0de" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de" > gridfire::GraphEngine::m_usePrecomputation< / a > < / div > < div class = "ttdeci" > bool m_usePrecomputation< / div > < div class = "ttdoc" > Flag to enable or disable using precomputed reactions for efficiency. Mathematically,...< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00471" > engine_graph.h:471< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a19b2eea0e8d05ac90f9fd7120bdc6e06" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a19b2eea0e8d05ac90f9fd7120bdc6e06" > gridfire::GraphEngine::m_full_jacobian_sparsity_pattern< / a > < / div > < div class = "ttdeci" > CppAD::sparse_rc< std::vector< size_t > > m_full_jacobian_sparsity_pattern< / div > < div class = "ttdoc" > Full sparsity pattern for the Jacobian matrix.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00464" > engine_graph.h:464< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a250cc6350dc052fbdfdf9a02066e7891" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a250cc6350dc052fbdfdf9a02066e7891" > gridfire::GraphEngine::m_jac_work< / a > < / div > < div class = "ttdeci" > CppAD::sparse_jac_work m_jac_work< / div > < div class = "ttdoc" > Work object for sparse Jacobian calculations.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00463" > engine_graph.h:463< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a26602e1b3c610780a47b5a6511d6d567" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567" > gridfire::GraphEngine::populateReactionIDMap< / a > < / div > < div class = "ttdeci" > void populateReactionIDMap()< / div > < div class = "ttdoc" > Populates the reaction ID map.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00135" > engine_graph.cpp:135< / a > < / div > < / div >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a27f3a928e1f6bbe7e847cffed6db729f" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a27f3a928e1f6bbe7e847cffed6db729f" > gridfire::GraphEngine::mapNetInToMolarAbundanceVector< / a > < / div > < div class = "ttdeci" > std::vector< double > mapNetInToMolarAbundanceVector(const NetIn & netIn) const override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00399" > engine_graph.cpp:399< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a29b338630c959449c15881935ac30746" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a29b338630c959449c15881935ac30746" > gridfire::GraphEngine::collectAtomicReverseRateAtomicBases< / a > < / div > < div class = "ttdeci" > void collectAtomicReverseRateAtomicBases()< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00947" > engine_graph.cpp:947< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a2e22b111f6d00ecc9e3804a71f1ce876" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876" > gridfire::GraphEngine::m_rhsADFun< / a > < / div > < div class = "ttdeci" > CppAD::ADFun< double > m_rhsADFun< / div > < div class = "ttdoc" > CppAD function for the right-hand side of the ODE.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00462" > engine_graph.h:462< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a2f1718c89d4aaad028102724d18fa910" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910" > gridfire::GraphEngine::m_jacobianMatrix< / a > < / div > < div class = "ttdeci" > boost::numeric::ublas::compressed_matrix< double > m_jacobianMatrix< / div > < div class = "ttdoc" > Jacobian matrix (species x species).< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00461" > engine_graph.h:461< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a303e6093591cde91430f866a04a8be7c" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c" > gridfire::GraphEngine::getJacobianMatrixEntry< / a > < / div > < div class = "ttdeci" > double getJacobianMatrixEntry(const int i, const int j) const override< / div > < div class = "ttdoc" > Gets an entry from the previously generated Jacobian matrix.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00722" > engine_graph.cpp:722< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a30e09ed0bce6aa5fc89beaa316a7b827" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827" > gridfire::GraphEngine::m_networkSpeciesMap< / a > < / div > < div class = "ttdeci" > std::unordered_map< std::string_view, fourdst::atomic::Species > m_networkSpeciesMap< / div > < div class = "ttdoc" > Map from species name to Species object.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00456" > engine_graph.h:456< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a32d3efbf4c3d5158f87c0c732cdc26dc" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc" > gridfire::GraphEngine::m_useReverseReactions< / a > < / div > < div class = "ttdeci" > bool m_useReverseReactions< / div > < div class = "ttdoc" > Flag to enable or disable reverse reactions. If false, only forward reactions are considered.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00473" > engine_graph.h:473< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a3621f36d77ea8c738ad7de6e5b35ca3e" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e" > gridfire::GraphEngine::m_partitionFunction< / a > < / div > < div class = "ttdeci" > std::unique_ptr< partition::PartitionFunction > m_partitionFunction< / div > < div class = "ttdoc" > Partition function for the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00478" > engine_graph.h:478< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a371ba0881d6903ddb2d586faa61805d0" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a371ba0881d6903ddb2d586faa61805d0" > gridfire::GraphEngine::setNetworkReactions< / a > < / div > < div class = "ttdeci" > void setNetworkReactions(const reaction::LogicalReactionSet & reactions) override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00174" > engine_graph.cpp:174< / a > < / div > < / div >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a409991d527ea4d4b05d1af907fe5d197" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197" > gridfire::GraphEngine::setUseReverseReactions< / a > < / div > < div class = "ttdeci" > void setUseReverseReactions(bool useReverse)< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00391" > engine_graph.cpp:391< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a47202c43342b96480070874bffce1391" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391" > gridfire::GraphEngine::populateSpeciesToIndexMap< / a > < / div > < div class = "ttdeci" > void populateSpeciesToIndexMap()< / div > < div class = "ttdoc" > Populates the species-to-index map.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00144" > engine_graph.cpp:144< / a > < / div > < / div >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a483979fc154adc88d029b3b672066d53" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53" > gridfire::GraphEngine::m_logger< / a > < / div > < div class = "ttdeci" > quill::Logger * m_logger< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00448" > engine_graph.h:448< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a52edc3e88f1e8fc497e1e63972d63c80" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a52edc3e88f1e8fc497e1e63972d63c80" > gridfire::GraphEngine::m_screeningType< / a > < / div > < div class = "ttdeci" > screening::ScreeningType m_screeningType< / div > < div class = "ttdoc" > Screening type for the reaction network. Default to no screening.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00468" > engine_graph.h:468< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a5ac7cff23e70bd07ba7e510b753e2ab6" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a5ac7cff23e70bd07ba7e510b753e2ab6" > gridfire::GraphEngine::update< / a > < / div > < div class = "ttdeci" > fourdst::composition::Composition update(const NetIn & netIn) override< / div > < div class = "ttdoc" > Update the internal state of the engine.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00886" > engine_graph.cpp:886< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a5d431d5385b1219ba29689eb29601ea3" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3" > gridfire::GraphEngine::m_precomputedReactions< / a > < / div > < div class = "ttdeci" > std::vector< PrecomputedReaction > m_precomputedReactions< / div > < div class = "ttdoc" > Precomputed reactions for efficiency.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00477" > engine_graph.h:477< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a5d6cc63b99b467c2a976d1fbaaa1dfa3" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3" > gridfire::GraphEngine::m_reactionIDMap< / a > < / div > < div class = "ttdeci" > std::unordered_map< std::string_view, reaction::Reaction * > m_reactionIDMap< / div > < div class = "ttdoc" > Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a ...< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00453" > engine_graph.h:453< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a65f9f33cddb0bbd1da7c9d0cff23d581" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a65f9f33cddb0bbd1da7c9d0cff23d581" > gridfire::GraphEngine::getSpeciesTimescales< / a > < / div > < div class = "ttdeci" > std::expected< std::unordered_map< fourdst::atomic::Species, double > , expectations::StaleEngineError > getSpeciesTimescales(const std::vector< double > & Y, double T9, double rho) const override< / div > < div class = "ttdoc" > Computes timescales for all species in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00842" > engine_graph.cpp:842< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a697f2004e0d02c59e83c7890742d7c9a" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a" > gridfire::GraphEngine::getScreeningModel< / a > < / div > < div class = "ttdeci" > screening::ScreeningType getScreeningModel() const override< / div > < div class = "ttdoc" > Get the current electron screening model.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00607" > engine_graph.cpp:607< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a6b5feaf788bade212b7c8df7ac8c8152" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152" > gridfire::GraphEngine::getStoichiometryMatrixEntry< / a > < / div > < div class = "ttdeci" > int getStoichiometryMatrixEntry(const int speciesIndex, const int reactionIndex) const override< / div > < div class = "ttdoc" > Gets an entry from the stoichiometry matrix.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00733" > engine_graph.cpp:733< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a6c5410878496abc349ba30b691cdf0f1" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1" > gridfire::GraphEngine::setPrecomputation< / a > < / div > < div class = "ttdeci" > void setPrecomputation(bool precompute)< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00611" > engine_graph.cpp:611< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a80c73690d5af247ff9f2ba8b00abce01" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01" > gridfire::GraphEngine::m_depth< / a > < / div > < div class = "ttdeci" > BuildDepthType m_depth< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00475" > engine_graph.h:475< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a8110e687844f921438bb517e1d8ce62f" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f" > gridfire::GraphEngine::setScreeningModel< / a > < / div > < div class = "ttdeci" > void setScreeningModel(screening::ScreeningType) override< / div > < div class = "ttdoc" > Set the electron screening model.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00602" > engine_graph.cpp:602< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a816797b1d656d416844489692af44cf6" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a816797b1d656d416844489692af44cf6" > gridfire::GraphEngine::m_atomicReverseRates< / a > < / div > < div class = "ttdeci" > std::vector< std::unique_ptr< AtomicReverseRate > > m_atomicReverseRates< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00466" > engine_graph.h:466< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a832e2fe066381811a3e0464806ff5e95" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95" > gridfire::GraphEngine::exportToCSV< / a > < / div > < div class = "ttdeci" > void exportToCSV(const std::string & filename) const< / div > < div class = "ttdoc" > Exports the network to a CSV file for analysis.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00788" > engine_graph.cpp:788< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a8c29d8bbde407e913be5eb77efb2c0c9" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9" > gridfire::GraphEngine::getNetReactionStoichiometry< / a > < / div > < div class = "ttdeci" > static std::unordered_map< fourdst::atomic::Species, int > getNetReactionStoichiometry(const reaction::Reaction & reaction)< / div > < div class = "ttdoc" > Gets the net stoichiometry for a given reaction.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00727" > engine_graph.cpp:727< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a8d0c0bd54a2908cff62dae7af0c149b5" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a8d0c0bd54a2908cff62dae7af0c149b5" > gridfire::GraphEngine::reserveJacobianMatrix< / a > < / div > < div class = "ttdeci" > void reserveJacobianMatrix() const< / div > < div class = "ttdoc" > Reserves space for the Jacobian matrix.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00151" > engine_graph.cpp:151< / a > < / div > < / div >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a914f6abc61805cddaebcb8f3cf470dda" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda" > gridfire::GraphEngine::getSpeciesIndex< / a > < / div > < div class = "ttdeci" > int getSpeciesIndex(const fourdst::atomic::Species & species) const override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00395" > engine_graph.cpp:395< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a9245642b741f215e52861d00e756fb3f" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f" > gridfire::GraphEngine::calculateMolarReactionFlow< / a > < / div > < div class = "ttdeci" > double calculateMolarReactionFlow(const reaction::Reaction & reaction, const std::vector< double > & Y, const double T9, const double rho) const override< / div > < div class = "ttdoc" > Calculates the molar reaction flow for a given reaction.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00623" > engine_graph.cpp:623< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a92644bc333bff69c5685be4552ca12fd" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd" > gridfire::GraphEngine::precomputeNetwork< / a > < / div > < div class = "ttdeci" > void precomputeNetwork()< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00960" > engine_graph.cpp:960< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a92d26068ba139e47d335f5fe9e2814cc" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc" > gridfire::GraphEngine::m_networkSpecies< / a > < / div > < div class = "ttdeci" > std::vector< fourdst::atomic::Species > m_networkSpecies< / div > < div class = "ttdoc" > Vector of unique species in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00455" > engine_graph.h:455< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a95563f6bc86007d9ee053a0f1e15b889" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889" > gridfire::GraphEngine::recordADTape< / a > < / div > < div class = "ttdeci" > void recordADTape()< / div > < div class = "ttdoc" > Records the AD tape for the right-hand side of the ODE.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00902" > engine_graph.cpp:902< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a97f98706b51fbe0d167ed81ffe58c438" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a97f98706b51fbe0d167ed81ffe58c438" > gridfire::GraphEngine::calculateAllDerivativesUsingPrecomputation< / a > < / div > < div class = "ttdeci" > StepDerivatives< double > calculateAllDerivativesUsingPrecomputation(const std::vector< double > & Y_in, const std::vector< double > & bare_rates, const std::vector< double > & bare_reverse_rates, double T9, double rho) const< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00448" > engine_graph.cpp:448< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_aa6202cee0c3c481eda77cc9a91bc126b" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b" > gridfire::GraphEngine::involvesSpecies< / a > < / div > < div class = "ttdeci" > bool involvesSpecies(const fourdst::atomic::Species & species) const< / div > < div class = "ttdoc" > Checks if a given species is involved in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00179" > engine_graph.cpp:179< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_aaed3743a52246b0f7bf03995e1c12081" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#aaed3743a52246b0f7bf03995e1c12081" > gridfire::GraphEngine::calculateRHSAndEnergy< / a > < / div > < div class = "ttdeci" > std::expected< StepDerivatives< double > , expectations::StaleEngineError > calculateRHSAndEnergy(const std::vector< double > & Y, const double T9, const double rho) const override< / div > < div class = "ttdoc" > Calculates the right-hand side (dY/dt) and energy generation rate.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00057" > engine_graph.cpp:57< / a > < / div > < / div >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_acb7c4f5108b0efeae48ad15598e808c3" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3" > gridfire::GraphEngine::m_reactions< / a > < / div > < div class = "ttdeci" > reaction::LogicalReactionSet m_reactions< / div > < div class = "ttdoc" > Set of REACLIB reactions in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00452" > engine_graph.h:452< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_acdce8d87e23a2cd1504bc9472e538c0f" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f" > gridfire::GraphEngine::syncInternalMaps< / a > < / div > < div class = "ttdeci" > void syncInternalMaps()< / div > < div class = "ttdoc" > Synchronizes the internal maps.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00081" > engine_graph.cpp:81< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_acf4cfccea20f5cb31c9886bf233a28be" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be" > gridfire::GraphEngine::validateConservation< / a > < / div > < div class = "ttdeci" > bool validateConservation() const< / div > < div class = "ttdoc" > Validates mass and charge conservation across all reactions.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00187" > engine_graph.cpp:187< / a > < / div > < / div >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_ad049a295e2bb0f3e97b76d5742875119" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119" > gridfire::GraphEngine::generateJacobianMatrix< / a > < / div > < div class = "ttdeci" > void generateJacobianMatrix(const std::vector< double > & Y_dynamic, const double T9, const double rho) const override< / div > < div class = "ttdoc" > Generates the Jacobian matrix for the current state.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00632" > engine_graph.cpp:632< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_ad1cb5fd32efc37668e2d9ecf0c72ad24" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24" > gridfire::GraphEngine::m_stoichiometryMatrix< / a > < / div > < div class = "ttdeci" > boost::numeric::ublas::compressed_matrix< int > m_stoichiometryMatrix< / div > < div class = "ttdoc" > Stoichiometry matrix (species x reactions).< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00459" > engine_graph.h:459< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_ad45650d10fc5dff1673ae3f806d067da" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da" > gridfire::GraphEngine::getNetworkReactions< / a > < / div > < div class = "ttdeci" > const reaction::LogicalReactionSet & getNetworkReactions() const override< / div > < div class = "ttdoc" > Gets the set of logical reactions in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00168" > engine_graph.cpp:168< / a > < / div > < / div >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_ad8237c252145a75092202d00f5e1ddf7" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7" > gridfire::GraphEngine::m_speciesToIndexMap< / a > < / div > < div class = "ttdeci" > std::unordered_map< fourdst::atomic::Species, size_t > m_speciesToIndexMap< / div > < div class = "ttdoc" > Map from species to their index in the stoichiometry matrix.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00457" > engine_graph.h:457< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_ad9d6c70ace5cbbf7f3aa7b31fce39490" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#ad9d6c70ace5cbbf7f3aa7b31fce39490" > gridfire::GraphEngine::rebuild< / a > < / div > < div class = "ttdeci" > void rebuild(const fourdst::composition::Composition & comp, const BuildDepthType depth) override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00438" > engine_graph.cpp:438< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_adac8c7d62bae76e17fc060e86dadd929" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929" > gridfire::GraphEngine::exportToDot< / a > < / div > < div class = "ttdeci" > void exportToDot(const std::string & filename) const< / div > < div class = "ttdoc" > Exports the network to a DOT file for visualization.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00740" > engine_graph.cpp:740< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_add98ece49ec5c538bddf3cc77004fe44" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#add98ece49ec5c538bddf3cc77004fe44" > gridfire::GraphEngine::getPartitionFunction< / a > < / div > < div class = "ttdeci" > const partition::PartitionFunction & getPartitionFunction() const< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00619" > engine_graph.cpp:619< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_ae7a210d9ab13ad5fb0c612f027acabd0" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#ae7a210d9ab13ad5fb0c612f027acabd0" > gridfire::GraphEngine::isUsingReverseReactions< / a > < / div > < div class = "ttdeci" > bool isUsingReverseReactions() const< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00387" > engine_graph.cpp:387< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_ae7a371be61ab09b3fa4a93f05bd44e5e" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#ae7a371be61ab09b3fa4a93f05bd44e5e" > gridfire::GraphEngine::primeEngine< / a > < / div > < div class = "ttdeci" > PrimingReport primeEngine(const NetIn & netIn) override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00407" > engine_graph.cpp:407< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_aed726d36ee2b3796beff6067a1e4db38" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38" > gridfire::GraphEngine::generateStoichiometryMatrix< / a > < / div > < div class = "ttdeci" > void generateStoichiometryMatrix() override< / div > < div class = "ttdoc" > Generates the stoichiometry matrix for the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00545" > engine_graph.cpp:545< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_aedf42d83bfcc28313b6b6454034d2efa" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa" > gridfire::GraphEngine::collectNetworkSpecies< / a > < / div > < div class = "ttdeci" > void collectNetworkSpecies()< / div > < div class = "ttdoc" > Collects the unique species in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00106" > engine_graph.cpp:106< / a > < / div > < / div >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_aef8f6bde24d27345067b71084330c7da" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#aef8f6bde24d27345067b71084330c7da" > gridfire::GraphEngine::getSpeciesDestructionTimescales< / a > < / div > < div class = "ttdeci" > std::expected< std::unordered_map< fourdst::atomic::Species, double > , expectations::StaleEngineError > getSpeciesDestructionTimescales(const std::vector< double > & Y, double T9, double rho) const override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00861" > engine_graph.cpp:861< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_af04a9f8a629d6f6c58c477af0f1ab9e5" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#af04a9f8a629d6f6c58c477af0f1ab9e5" > gridfire::GraphEngine::isStale< / a > < / div > < div class = "ttdeci" > bool isStale(const NetIn & netIn) override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00898" > engine_graph.cpp:898< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_af17cf3762abac3efcab9a8e87c961210" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#af17cf3762abac3efcab9a8e87c961210" > gridfire::GraphEngine::m_screeningModel< / a > < / div > < div class = "ttdeci" > std::unique_ptr< screening::ScreeningModel > m_screeningModel< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00469" > engine_graph.h:469< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_af28950c5af3a92eb03a1a64ed0f913e7" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#af28950c5af3a92eb03a1a64ed0f913e7" > gridfire::GraphEngine::calculateReverseRateTwoBodyDerivative< / a > < / div > < div class = "ttdeci" > double calculateReverseRateTwoBodyDerivative(const reaction::Reaction & reaction, const double T9, const double reverseRate) const< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00346" > engine_graph.cpp:346< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_af41df9ce979b6410e12642cb093916c9" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9" > gridfire::GraphEngine::calculateAllDerivatives< / a > < / div > < div class = "ttdeci" > StepDerivatives< T > calculateAllDerivatives(const std::vector< T > & Y_in, T T9, T rho) const< / div > < div class = "ttdoc" > Calculates all derivatives (dY/dt) and the energy generation rate.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00715" > engine_graph.h:715< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_afad967546b611d9c005268760feb75d5" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5" > gridfire::GraphEngine::GraphEngine< / a > < / div > < div class = "ttdeci" > GraphEngine(const fourdst::composition::Composition & composition, const BuildDepthType=NetworkBuildDepth::Full)< / div > < div class = "ttdoc" > Constructs a GraphEngine from a composition.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00034" > engine_graph.cpp:34< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1partition_1_1_partition_function_html" > < div class = "ttname" > < a href = "classgridfire_1_1partition_1_1_partition_function.html" > gridfire::partition::PartitionFunction< / a > < / div > < div class = "ttdoc" > Abstract interface for evaluating nuclear partition functions.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "partition__abstract_8h_source.html#l00017" > partition_abstract.h:17< / a > < / div > < / div >
2025-07-01 11:40:51 -04:00
< div class = "ttc" id = "aclassgridfire_1_1reaction_1_1_reaction_html" > < div class = "ttname" > < a href = "classgridfire_1_1reaction_1_1_reaction.html" > gridfire::reaction::Reaction< / a > < / div > < div class = "ttdoc" > Represents a single nuclear reaction from a specific data source.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "reaction_8h_source.html#l00072" > reaction.h:72< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "aconstruction_8h_html" > < div class = "ttname" > < a href = "construction_8h.html" > construction.h< / a > < / div > < / div >
2025-07-01 07:24:18 -04:00
< div class = "ttc" id = "aengine__graph_8h_html" > < div class = "ttname" > < a href = "engine__graph_8h.html" > engine_graph.h< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "anamespacegridfire_1_1partition_html" > < div class = "ttname" > < a href = "namespacegridfire_1_1partition.html" > gridfire::partition< / a > < / div > < div class = "ttdef" > < b > Definition< / b > < a href = "partition__composite_8h_source.html#l00015" > partition_composite.h:15< / a > < / div > < / div >
2025-07-01 11:40:51 -04:00
< div class = "ttc" id = "anamespacegridfire_1_1reaction_html" > < div class = "ttname" > < a href = "namespacegridfire_1_1reaction.html" > gridfire::reaction< / a > < / div > < div class = "ttdef" > < b > Definition< / b > < a href = "reaction_8h_source.html#l00025" > reaction.h:25< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "anamespacegridfire_1_1reaction_html_aa86f08712565f278adacc7cd2361eb31" > < div class = "ttname" > < a href = "namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" > gridfire::reaction::LogicalReactionSet< / a > < / div > < div class = "ttdeci" > TemplatedReactionSet< LogicalReaction > LogicalReactionSet< / div > < div class = "ttdoc" > A set of logical reactions.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "reaction_8h_source.html#l00563" > reaction.h:563< / a > < / div > < / div >
2025-07-01 15:06:22 -04:00
< div class = "ttc" id = "anamespacegridfire_1_1screening_html_a6ca8556d27ac373e176f5b23437c416e" > < div class = "ttname" > < a href = "namespacegridfire_1_1screening.html#a6ca8556d27ac373e176f5b23437c416e" > gridfire::screening::selectScreeningModel< / a > < / div > < div class = "ttdeci" > std::unique_ptr< ScreeningModel > selectScreeningModel(ScreeningType type)< / div > < div class = "ttdoc" > A factory function to select and create a screening model.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "screening__types_8cpp_source.html#l00009" > screening_types.cpp:9< / a > < / div > < / div >
< div class = "ttc" id = "anamespacegridfire_1_1screening_html_aa82aafbc4f8c28d0a75b60798e3a7d25" > < div class = "ttname" > < a href = "namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25" > gridfire::screening::ScreeningType< / a > < / div > < div class = "ttdeci" > ScreeningType< / div > < div class = "ttdoc" > Enumerates the available plasma screening models.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "screening__types_8h_source.html#l00015" > screening_types.h:15< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "anamespacegridfire_html" > < div class = "ttname" > < a href = "namespacegridfire.html" > gridfire< / a > < / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__abstract_8h_source.html#l00031" > engine_abstract.h:31< / a > < / div > < / div >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "anamespacegridfire_html_a1121d0b2d005195333412559fa29d3cc" > < div class = "ttname" > < a href = "namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc" > gridfire::ADDouble< / a > < / div > < div class = "ttdeci" > CppAD::AD< double > ADDouble< / div > < div class = "ttdoc" > Alias for CppAD AD type for double precision.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00044" > engine_graph.h:44< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "anamespacegridfire_html_a3b1f70dc7ff5b501809330a97079e4f6" > < div class = "ttname" > < a href = "namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6" > gridfire::BuildDepthType< / a > < / div > < div class = "ttdeci" > std::variant< NetworkBuildDepth, int > BuildDepthType< / div > < div class = "ttdoc" > Variant specifying either a predefined NetworkBuildDepth or a custom integer depth.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "building_8h_source.html#l00037" > building.h:37< / a > < / div > < / div >
< div class = "ttc" id = "anamespacegridfire_html_a898dfe22579e649935645cbd6f073178" > < div class = "ttname" > < a href = "namespacegridfire.html#a898dfe22579e649935645cbd6f073178" > gridfire::SparsityPattern< / a > < / div > < div class = "ttdeci" > std::vector< std::pair< size_t, size_t > > SparsityPattern< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__abstract_8h_source.html#l00065" > engine_abstract.h:65< / a > < / div > < / div >
< div class = "ttc" id = "anamespacegridfire_html_acd0bfdfbce4e84af102d62ff8a797c9f" > < div class = "ttname" > < a href = "namespacegridfire.html#acd0bfdfbce4e84af102d62ff8a797c9f" > gridfire::primeNetwork< / a > < / div > < div class = "ttdeci" > PrimingReport primeNetwork(const NetIn & , DynamicEngine & engine)< / div > < div class = "ttdoc" > Primes absent species in the network to their equilibrium abundances.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "priming_8cpp_source.html#l00039" > priming.cpp:39< / a > < / div > < / div >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "anamespacegridfire_html_ae01b1738df1921db565bcbd68dd6cf64" > < div class = "ttname" > < a href = "namespacegridfire.html#ae01b1738df1921db565bcbd68dd6cf64" > gridfire::MIN_JACOBIAN_THRESHOLD< / a > < / div > < div class = "ttdeci" > static constexpr double MIN_JACOBIAN_THRESHOLD< / div > < div class = "ttdoc" > Minimum value for Jacobian matrix entries.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00074" > engine_graph.h:74< / a > < / div > < / div >
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< div class = "ttc" id = "anamespacegridfire_html_aedddb89e400a6111f69bfe0c3fd4214e" > < div class = "ttname" > < a href = "namespacegridfire.html#aedddb89e400a6111f69bfe0c3fd4214e" > gridfire::build_reaclib_nuclear_network< / a > < / div > < div class = "ttdeci" > reaction::LogicalReactionSet build_reaclib_nuclear_network(const fourdst::composition::Composition & composition, BuildDepthType maxLayers=NetworkBuildDepth::Full, bool reverse=false)< / div > < div class = "ttdoc" > Builds a nuclear reaction network from the Reaclib library based on an initial composition.< / div > < / div >
2025-07-01 07:24:18 -04:00
< div class = "ttc" id = "anetwork_8h_html" > < div class = "ttname" > < a href = "network_8h.html" > network.h< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "apartition__ground_8h_html" > < div class = "ttname" > < a href = "partition__ground_8h.html" > partition_ground.h< / a > < / div > < / div >
< div class = "ttc" id = "apriming_8h_html" > < div class = "ttname" > < a href = "priming_8h.html" > priming.h< / a > < / div > < / div >
2025-07-01 07:24:18 -04:00
< div class = "ttc" id = "areaction_8h_html" > < div class = "ttname" > < a href = "reaction_8h.html" > reaction.h< / a > < / div > < div class = "ttdoc" > Defines classes for representing and managing nuclear reactions.< / div > < / div >
2025-07-01 11:40:51 -04:00
< div class = "ttc" id = "ascreening__types_8h_html" > < div class = "ttname" > < a href = "screening__types_8h.html" > screening_types.h< / a > < / div > < / div >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html" > < div class = "ttname" > < a href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html" > gridfire::GraphEngine::PrecomputedReaction< / a > < / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00384" > engine_graph.h:384< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a03d596c88289e21e7bd18711e3a1f275" > < div class = "ttname" > < a href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a03d596c88289e21e7bd18711e3a1f275" > gridfire::GraphEngine::PrecomputedReaction::reactant_powers< / a > < / div > < div class = "ttdeci" > std::vector< int > reactant_powers< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00388" > engine_graph.h:388< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a3ce63aa3ad88568f4eb0d3ca2414209f" > < div class = "ttname" > < a href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3ce63aa3ad88568f4eb0d3ca2414209f" > gridfire::GraphEngine::PrecomputedReaction::product_powers< / a > < / div > < div class = "ttdeci" > std::vector< int > product_powers< / div > < div class = "ttdoc" > Powers of each unique product in the reverse reaction.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00395" > engine_graph.h:395< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a3e2e67e532970738d20491ea56b170f3" > < div class = "ttname" > < a href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3e2e67e532970738d20491ea56b170f3" > gridfire::GraphEngine::PrecomputedReaction::affected_species_indices< / a > < / div > < div class = "ttdeci" > std::vector< size_t > affected_species_indices< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00390" > engine_graph.h:390< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a510e380116e2e6d9158cf00fedac2666" > < div class = "ttname" > < a href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a510e380116e2e6d9158cf00fedac2666" > gridfire::GraphEngine::PrecomputedReaction::unique_reactant_indices< / a > < / div > < div class = "ttdeci" > std::vector< size_t > unique_reactant_indices< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00387" > engine_graph.h:387< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a6bcfe2230dd54b088180d34389266b07" > < div class = "ttname" > < a href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a6bcfe2230dd54b088180d34389266b07" > gridfire::GraphEngine::PrecomputedReaction::reverse_symmetry_factor< / a > < / div > < div class = "ttdeci" > double reverse_symmetry_factor< / div > < div class = "ttdoc" > Symmetry factor for reverse reactions.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00396" > engine_graph.h:396< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a7a7e9167b19e339e0d69544b9c00e79c" > < div class = "ttname" > < a href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a7a7e9167b19e339e0d69544b9c00e79c" > gridfire::GraphEngine::PrecomputedReaction::stoichiometric_coefficients< / a > < / div > < div class = "ttdeci" > std::vector< int > stoichiometric_coefficients< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00391" > engine_graph.h:391< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a93635f6940d3534e949f402503c3d497" > < div class = "ttname" > < a href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a93635f6940d3534e949f402503c3d497" > gridfire::GraphEngine::PrecomputedReaction::reaction_index< / a > < / div > < div class = "ttdeci" > size_t reaction_index< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00386" > engine_graph.h:386< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a9974f944a2cf5179baabebe09d60cf18" > < div class = "ttname" > < a href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a9974f944a2cf5179baabebe09d60cf18" > gridfire::GraphEngine::PrecomputedReaction::unique_product_indices< / a > < / div > < div class = "ttdeci" > std::vector< size_t > unique_product_indices< / div > < div class = "ttdoc" > Unique product indices for reverse reactions.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00394" > engine_graph.h:394< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_ac42504e868c0b9fd9ac9a405ea739f0e" > < div class = "ttname" > < a href = "structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#ac42504e868c0b9fd9ac9a405ea739f0e" > gridfire::GraphEngine::PrecomputedReaction::symmetry_factor< / a > < / div > < div class = "ttdeci" > double symmetry_factor< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00389" > engine_graph.h:389< / a > < / div > < / div >
2025-07-01 11:40:51 -04:00
< div class = "ttc" id = "astructgridfire_1_1_net_in_html" > < div class = "ttname" > < a href = "structgridfire_1_1_net_in.html" > gridfire::NetIn< / a > < / div > < div class = "ttdef" > < b > Definition< / b > < a href = "network_8h_source.html#l00053" > network.h:53< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "astructgridfire_1_1_net_in_html_a06f0dff9f8927b7cf2da3004c8fa1577" > < div class = "ttname" > < a href = "structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577" > gridfire::NetIn::density< / a > < / div > < div class = "ttdeci" > double density< / div > < div class = "ttdoc" > Density in g/cm^3.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "network_8h_source.html#l00058" > network.h:58< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_net_in_html_a13058f4929e72c1187abbebcddb8aed1" > < div class = "ttname" > < a href = "structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1" > gridfire::NetIn::composition< / a > < / div > < div class = "ttdeci" > fourdst::composition::Composition composition< / div > < div class = "ttdoc" > Composition of the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "network_8h_source.html#l00054" > network.h:54< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_net_in_html_a5be0f5195a5cd1dd177b9fc5ab83a7be" > < div class = "ttname" > < a href = "structgridfire_1_1_net_in.html#a5be0f5195a5cd1dd177b9fc5ab83a7be" > gridfire::NetIn::temperature< / a > < / div > < div class = "ttdeci" > double temperature< / div > < div class = "ttdoc" > Temperature in Kelvin.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "network_8h_source.html#l00057" > network.h:57< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_priming_report_html" > < div class = "ttname" > < a href = "structgridfire_1_1_priming_report.html" > gridfire::PrimingReport< / a > < / div > < div class = "ttdoc" > Captures the result of a network priming operation.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "reporting_8h_source.html#l00067" > reporting.h:67< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_step_derivatives_html" > < div class = "ttname" > < a href = "structgridfire_1_1_step_derivatives.html" > gridfire::StepDerivatives< / a > < / div > < div class = "ttdoc" > Structure holding derivatives and energy generation for a network step.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__abstract_8h_source.html#l00060" > engine_abstract.h:60< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_step_derivatives_html_ab4aeb41be952c7b5844e1ee81fef9008" > < div class = "ttname" > < a href = "structgridfire_1_1_step_derivatives.html#ab4aeb41be952c7b5844e1ee81fef9008" > gridfire::StepDerivatives::nuclearEnergyGenerationRate< / a > < / div > < div class = "ttdeci" > T nuclearEnergyGenerationRate< / div > < div class = "ttdoc" > Specific energy generation rate (e.g., erg/g/s).< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__abstract_8h_source.html#l00062" > engine_abstract.h:62< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_step_derivatives_html_ae0de268b86c2404379409c4feae0b34d" > < div class = "ttname" > < a href = "structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d" > gridfire::StepDerivatives::dydt< / a > < / div > < div class = "ttdeci" > std::vector< T > dydt< / div > < div class = "ttdoc" > Derivatives of abundances (dY/dt for each species).< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__abstract_8h_source.html#l00061" > engine_abstract.h:61< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1expectations_1_1_stale_engine_error_html" > < div class = "ttname" > < a href = "structgridfire_1_1expectations_1_1_stale_engine_error.html" > gridfire::expectations::StaleEngineError< / a > < / div > < div class = "ttdef" > < b > Definition< / b > < a href = "expected__engine_8h_source.html#l00044" > expected_engine.h:44< / a > < / div > < / div >
2025-07-01 07:24:18 -04:00
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2025-07-01 07:24:18 -04:00
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