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< a href = "engine__defined_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__defined_8h.html" > gridfire/engine/views/engine_defined.h< / a > " < / span > < / div >
< div class = "line" > < a id = "l00002" name = "l00002" > < / a > < span class = "lineno" > 2< / span > < / div >
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< div class = "line" > < a id = "l00003" name = "l00003" > < / a > < span class = "lineno" > 3< / span > < span class = "preprocessor" > #include < ranges> < / span > < / div >
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< div class = "line" > < a id = "l00004" name = "l00004" > < / a > < span class = "lineno" > 4< / span > < / div >
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< div class = "line" > < a id = "l00005" name = "l00005" > < / a > < span class = "lineno" > 5< / span > < span class = "preprocessor" > #include " quill/LogMacros.h" < / span > < / div >
< div class = "line" > < a id = "l00006" name = "l00006" > < / a > < span class = "lineno" > 6< / span > < / div >
< div class = "line" > < a id = "l00007" name = "l00007" > < / a > < span class = "lineno" > 7< / span > < span class = "preprocessor" > #include < string> < / span > < / div >
< div class = "line" > < a id = "l00008" name = "l00008" > < / a > < span class = "lineno" > 8< / span > < span class = "preprocessor" > #include < vector> < / span > < / div >
< div class = "line" > < a id = "l00009" name = "l00009" > < / a > < span class = "lineno" > 9< / span > < span class = "preprocessor" > #include < unordered_set> < / span > < / div >
< div class = "line" > < a id = "l00010" name = "l00010" > < / a > < span class = "lineno" > 10< / span > < span class = "preprocessor" > #include < stdexcept> < / span > < / div >
< div class = "line" > < a id = "l00011" name = "l00011" > < / a > < span class = "lineno" > 11< / span > < span class = "preprocessor" > #include < unordered_map> < / span > < / div >
< div class = "line" > < a id = "l00012" name = "l00012" > < / a > < span class = "lineno" > 12< / span > < span class = "preprocessor" > #include < utility> < / 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 = "keyword" > namespace < / span > < a class = "code hl_namespace" href = "namespacegridfire.html" > gridfire< / a > {< / div >
< div class = "line" > < a id = "l00015" name = "l00015" > < / a > < span class = "lineno" > 15< / span > < span class = "keyword" > using < / span > fourdst::atomic::Species;< / div >
< div class = "line" > < a id = "l00016" name = "l00016" > < / a > < span class = "lineno" > 16< / span > < / div >
< div class = "foldopen" id = "foldopen00017" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00017" name = "l00017" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a9b319b4a1bd5a08381ebb183daf72c92" > 17< / a > < / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a9b319b4a1bd5a08381ebb183daf72c92" > DefinedEngineView::DefinedEngineView< / a > (< span class = "keyword" > const< / span > std::vector< std::string> & peNames, < a class = "code hl_class" href = "classgridfire_1_1_dynamic_engine.html" > DynamicEngine< / a > & baseEngine) :< / div >
< div class = "line" > < a id = "l00018" name = "l00018" > < / a > < span class = "lineno" > 18< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > (baseEngine) {< / div >
< div class = "line" > < a id = "l00019" name = "l00019" > < / a > < span class = "lineno" > 19< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#adbc64284b5f5a3256867be46fa87c69e" > collect< / a > (peNames);< / div >
< div class = "line" > < a id = "l00020" name = "l00020" > < / a > < span class = "lineno" > 20< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00021" name = "l00021" > < / a > < span class = "lineno" > 21< / span > < / div >
< div class = "foldopen" id = "foldopen00022" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00022" name = "l00022" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a69b9a5812ad8bda13f956acd0da24484" > 22< / a > < / span > < span class = "keyword" > const< / span > < a class = "code hl_class" href = "classgridfire_1_1_dynamic_engine.html" > DynamicEngine< / a > & < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a69b9a5812ad8bda13f956acd0da24484" > DefinedEngineView::getBaseEngine< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00023" name = "l00023" > < / a > < span class = "lineno" > 23< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > ;< / div >
< div class = "line" > < a id = "l00024" name = "l00024" > < / a > < span class = "lineno" > 24< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00025" name = "l00025" > < / a > < span class = "lineno" > 25< / span > < / div >
< div class = "foldopen" id = "foldopen00026" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00026" name = "l00026" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a1a55f9748c45af6f13e16a6b6ceaa211" > 26< / a > < / span > < span class = "keyword" > const< / span > std::vector< Species> & < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a1a55f9748c45af6f13e16a6b6ceaa211" > DefinedEngineView::getNetworkSpecies< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00027" name = "l00027" > < / a > < span class = "lineno" > 27< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > ;< / div >
< div class = "line" > < a id = "l00028" name = "l00028" > < / a > < span class = "lineno" > 28< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00029" name = "l00029" > < / a > < span class = "lineno" > 29< / span > < / div >
< div class = "foldopen" id = "foldopen00030" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00030" name = "l00030" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d" > 30< / 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_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d" > DefinedEngineView::calculateRHSAndEnergy< / a > (< / div >
< div class = "line" > < a id = "l00031" name = "l00031" > < / a > < span class = "lineno" > 31< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_defined,< / div >
< div class = "line" > < a id = "l00032" name = "l00032" > < / a > < span class = "lineno" > 32< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00033" name = "l00033" > < / a > < span class = "lineno" > 33< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00034" name = "l00034" > < / a > < span class = "lineno" > 34< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00035" name = "l00035" > < / a > < span class = "lineno" > 35< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > validateNetworkState< / a > ();< / div >
< div class = "line" > < a id = "l00036" name = "l00036" > < / a > < span class = "lineno" > 36< / span > < / div >
< div class = "line" > < a id = "l00037" name = "l00037" > < / a > < span class = "lineno" > 37< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > Y_full = < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843" > mapViewToFull< / a > (Y_defined);< / div >
< div class = "line" > < a id = "l00038" name = "l00038" > < / a > < span class = "lineno" > 38< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > result = < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .calculateRHSAndEnergy(Y_full, T9, rho);< / div >
< div class = "line" > < a id = "l00039" name = "l00039" > < / a > < span class = "lineno" > 39< / span > < / div >
< div class = "line" > < a id = "l00040" name = "l00040" > < / a > < span class = "lineno" > 40< / span > < span class = "keywordflow" > if< / span > (!result) {< / div >
< div class = "line" > < a id = "l00041" name = "l00041" > < / a > < span class = "lineno" > 41< / span > < span class = "keywordflow" > return< / span > std::unexpected{result.error()};< / div >
< div class = "line" > < a id = "l00042" name = "l00042" > < / a > < span class = "lineno" > 42< / span > }< / div >
< div class = "line" > < a id = "l00043" name = "l00043" > < / a > < span class = "lineno" > 43< / span > < / div >
< div class = "line" > < a id = "l00044" name = "l00044" > < / a > < span class = "lineno" > 44< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > [dydt, nuclearEnergyGenerationRate] = result.value();< / div >
< div class = "line" > < a id = "l00045" name = "l00045" > < / a > < span class = "lineno" > 45< / span > < a class = "code hl_struct" href = "structgridfire_1_1_step_derivatives.html" > StepDerivatives< double> < / a > definedResults;< / div >
< div class = "line" > < a id = "l00046" name = "l00046" > < / a > < span class = "lineno" > 46< / span > definedResults.< a class = "code hl_variable" href = "structgridfire_1_1_step_derivatives.html#ab4aeb41be952c7b5844e1ee81fef9008" > nuclearEnergyGenerationRate< / a > = nuclearEnergyGenerationRate;< / div >
< div class = "line" > < a id = "l00047" name = "l00047" > < / a > < span class = "lineno" > 47< / span > definedResults.< a class = "code hl_variable" href = "structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d" > dydt< / a > = < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a2f59af6fb3516911de2a3e3ff0ed8873" > mapFullToView< / a > (dydt);< / div >
< div class = "line" > < a id = "l00048" name = "l00048" > < / a > < span class = "lineno" > 48< / span > < span class = "keywordflow" > return< / span > definedResults;< / div >
< div class = "line" > < a id = "l00049" name = "l00049" > < / a > < span class = "lineno" > 49< / span > }< / div >
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< / div >
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< div class = "line" > < a id = "l00050" name = "l00050" > < / a > < span class = "lineno" > 50< / span > < / div >
< div class = "foldopen" id = "foldopen00051" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00051" name = "l00051" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#ad25c722eaee1f28f8ed7b4d33a1f69ae" > 51< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#ad25c722eaee1f28f8ed7b4d33a1f69ae" > DefinedEngineView::generateJacobianMatrix< / a > (< / div >
< div class = "line" > < a id = "l00052" name = "l00052" > < / a > < span class = "lineno" > 52< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_dynamic,< / div >
< div class = "line" > < a id = "l00053" name = "l00053" > < / a > < span class = "lineno" > 53< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00054" name = "l00054" > < / a > < span class = "lineno" > 54< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00055" name = "l00055" > < / a > < span class = "lineno" > 55< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00056" name = "l00056" > < / a > < span class = "lineno" > 56< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > validateNetworkState< / a > ();< / div >
< div class = "line" > < a id = "l00057" name = "l00057" > < / a > < span class = "lineno" > 57< / span > < / div >
< div class = "line" > < a id = "l00058" name = "l00058" > < / a > < span class = "lineno" > 58< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > Y_full = < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843" > mapViewToFull< / a > (Y_dynamic);< / div >
< div class = "line" > < a id = "l00059" name = "l00059" > < / a > < span class = "lineno" > 59< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .generateJacobianMatrix(Y_full, T9, rho);< / div >
< div class = "line" > < a id = "l00060" name = "l00060" > < / a > < span class = "lineno" > 60< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00061" name = "l00061" > < / a > < span class = "lineno" > 61< / span > < / div >
< div class = "foldopen" id = "foldopen00062" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00062" name = "l00062" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a273b175049f5ce7b9208e931ad139e1b" > 62< / a > < / span > < span class = "keywordtype" > double< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a273b175049f5ce7b9208e931ad139e1b" > DefinedEngineView::getJacobianMatrixEntry< / a > (< / div >
< div class = "line" > < a id = "l00063" name = "l00063" > < / a > < span class = "lineno" > 63< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > i_defined,< / div >
< div class = "line" > < a id = "l00064" name = "l00064" > < / a > < span class = "lineno" > 64< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > j_defined< / div >
< div class = "line" > < a id = "l00065" name = "l00065" > < / a > < span class = "lineno" > 65< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00066" name = "l00066" > < / a > < span class = "lineno" > 66< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > validateNetworkState< / a > ();< / div >
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< div class = "line" > < a id = "l00067" name = "l00067" > < / a > < span class = "lineno" > 67< / span > < / div >
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< div class = "line" > < a id = "l00068" name = "l00068" > < / a > < span class = "lineno" > 68< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > i_full = < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#af6fb8c3c7894b505bd81d15f012f154a" > mapViewToFullSpeciesIndex< / a > (i_defined);< / div >
< div class = "line" > < a id = "l00069" name = "l00069" > < / a > < span class = "lineno" > 69< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > j_full = < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#af6fb8c3c7894b505bd81d15f012f154a" > mapViewToFullSpeciesIndex< / a > (j_defined);< / div >
2025-07-01 11:40:58 -04:00
< div class = "line" > < a id = "l00070" name = "l00070" > < / a > < span class = "lineno" > 70< / span > < / div >
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< div class = "line" > < a id = "l00071" name = "l00071" > < / a > < span class = "lineno" > 71< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .getJacobianMatrixEntry(i_full, j_full);< / div >
2025-07-01 11:40:58 -04:00
< div class = "line" > < a id = "l00072" name = "l00072" > < / a > < span class = "lineno" > 72< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00073" name = "l00073" > < / a > < span class = "lineno" > 73< / span > < / div >
< div class = "foldopen" id = "foldopen00074" data-start = "{" data-end = "}" >
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< div class = "line" > < a id = "l00074" name = "l00074" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#ad07221be49ae1b5133c5b987dafac3b6" > 74< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#ad07221be49ae1b5133c5b987dafac3b6" > DefinedEngineView::generateStoichiometryMatrix< / a > () {< / div >
< div class = "line" > < a id = "l00075" name = "l00075" > < / a > < span class = "lineno" > 75< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > validateNetworkState< / a > ();< / div >
< div class = "line" > < a id = "l00076" name = "l00076" > < / a > < span class = "lineno" > 76< / span > < / div >
< div class = "line" > < a id = "l00077" name = "l00077" > < / a > < span class = "lineno" > 77< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .generateStoichiometryMatrix();< / div >
< div class = "line" > < a id = "l00078" name = "l00078" > < / a > < span class = "lineno" > 78< / span > }< / div >
< / div >
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< div class = "line" > < a id = "l00079" name = "l00079" > < / a > < span class = "lineno" > 79< / span > < / div >
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< div class = "foldopen" id = "foldopen00080" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00080" name = "l00080" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#afa2820971397114d788730cc33feefe2" > 80< / a > < / span > < span class = "keywordtype" > int< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#afa2820971397114d788730cc33feefe2" > DefinedEngineView::getStoichiometryMatrixEntry< / a > (< / div >
< div class = "line" > < a id = "l00081" name = "l00081" > < / a > < span class = "lineno" > 81< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > speciesIndex_defined,< / div >
< div class = "line" > < a id = "l00082" name = "l00082" > < / a > < span class = "lineno" > 82< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > reactionIndex_defined< / div >
< div class = "line" > < a id = "l00083" name = "l00083" > < / a > < span class = "lineno" > 83< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00084" name = "l00084" > < / a > < span class = "lineno" > 84< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > validateNetworkState< / a > ();< / div >
< div class = "line" > < a id = "l00085" name = "l00085" > < / a > < span class = "lineno" > 85< / span > < / div >
< div class = "line" > < a id = "l00086" name = "l00086" > < / a > < span class = "lineno" > 86< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > i_full = < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#af6fb8c3c7894b505bd81d15f012f154a" > mapViewToFullSpeciesIndex< / a > (speciesIndex_defined);< / div >
< div class = "line" > < a id = "l00087" name = "l00087" > < / a > < span class = "lineno" > 87< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > j_full = < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#aadf373d69a22fcd171a6c251466d53d1" > mapViewToFullReactionIndex< / a > (reactionIndex_defined);< / div >
< div class = "line" > < a id = "l00088" name = "l00088" > < / a > < span class = "lineno" > 88< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .getStoichiometryMatrixEntry(i_full, j_full);< / div >
< div class = "line" > < a id = "l00089" name = "l00089" > < / a > < span class = "lineno" > 89< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00090" name = "l00090" > < / a > < span class = "lineno" > 90< / span > < / div >
< div class = "foldopen" id = "foldopen00091" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00091" name = "l00091" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032" > 91< / a > < / span > < span class = "keywordtype" > double< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032" > DefinedEngineView::calculateMolarReactionFlow< / a > (< / div >
< div class = "line" > < a id = "l00092" name = "l00092" > < / a > < span class = "lineno" > 92< / 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 = "l00093" name = "l00093" > < / a > < span class = "lineno" > 93< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_defined,< / div >
< div class = "line" > < a id = "l00094" name = "l00094" > < / a > < span class = "lineno" > 94< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00095" name = "l00095" > < / a > < span class = "lineno" > 95< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00096" name = "l00096" > < / a > < span class = "lineno" > 96< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00097" name = "l00097" > < / a > < span class = "lineno" > 97< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > validateNetworkState< / a > ();< / div >
< div class = "line" > < a id = "l00098" name = "l00098" > < / a > < span class = "lineno" > 98< / span > < / div >
< div class = "line" > < a id = "l00099" name = "l00099" > < / a > < span class = "lineno" > 99< / span > < span class = "keywordflow" > if< / span > (!< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965" > m_activeReactions< / a > .contains(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > )) {< / div >
< div class = "line" > < a id = "l00100" name = "l00100" > < / a > < span class = "lineno" > 100< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Reaction ' {}' is not part of the active reactions in the DefinedEngineView." < / span > , < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id());< / div >
< div class = "line" > < a id = "l00101" name = "l00101" > < / a > < span class = "lineno" > 101< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00102" name = "l00102" > < / a > < span class = "lineno" > 102< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " Reaction not found in active reactions: " < / span > + std::string(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id()));< / div >
< div class = "line" > < a id = "l00103" name = "l00103" > < / a > < span class = "lineno" > 103< / span > }< / div >
< div class = "line" > < a id = "l00104" name = "l00104" > < / a > < span class = "lineno" > 104< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > Y_full = < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843" > mapViewToFull< / a > (Y_defined);< / div >
< div class = "line" > < a id = "l00105" name = "l00105" > < / a > < span class = "lineno" > 105< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .calculateMolarReactionFlow(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > , Y_full, T9, rho);< / div >
2025-07-01 11:40:58 -04:00
< div class = "line" > < a id = "l00106" name = "l00106" > < / a > < span class = "lineno" > 106< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00107" name = "l00107" > < / a > < span class = "lineno" > 107< / span > < / div >
< div class = "foldopen" id = "foldopen00108" data-start = "{" data-end = "}" >
2025-07-24 11:10:45 -04:00
< div class = "line" > < a id = "l00108" name = "l00108" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#ae03b4f9afac03d4011a4d7cf0423535d" > 108< / 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_defined_engine_view.html#ae03b4f9afac03d4011a4d7cf0423535d" > DefinedEngineView::getNetworkReactions< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00109" name = "l00109" > < / a > < span class = "lineno" > 109< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > validateNetworkState< / a > ();< / div >
< div class = "line" > < a id = "l00110" name = "l00110" > < / a > < span class = "lineno" > 110< / span > < / div >
< div class = "line" > < a id = "l00111" name = "l00111" > < / a > < span class = "lineno" > 111< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965" > m_activeReactions< / a > ;< / div >
< div class = "line" > < a id = "l00112" name = "l00112" > < / a > < span class = "lineno" > 112< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00113" name = "l00113" > < / a > < span class = "lineno" > 113< / span > < / div >
< div class = "foldopen" id = "foldopen00114" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00114" name = "l00114" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a9736edfb7c9148b60de30d50c0d3530d" > 114< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a9736edfb7c9148b60de30d50c0d3530d" > DefinedEngineView::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 = "l00115" name = "l00115" > < / a > < span class = "lineno" > 115< / span > std::vector< std::string> peNames;< / 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 > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > : reactions) {< / div >
< div class = "line" > < a id = "l00117" name = "l00117" > < / a > < span class = "lineno" > 117< / span > peNames.push_back(std::string(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id()));< / 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 > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#adbc64284b5f5a3256867be46fa87c69e" > collect< / a > (peNames);< / div >
< div class = "line" > < a id = "l00120" name = "l00120" > < / a > < span class = "lineno" > 120< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00121" name = "l00121" > < / a > < span class = "lineno" > 121< / span > < / div >
< div class = "foldopen" id = "foldopen00122" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00122" name = "l00122" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#ac8daafabbc76f4b6811bede241a03d72" > 122< / a > < / span > std::expected< std::unordered_map< 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_defined_engine_view.html#ac8daafabbc76f4b6811bede241a03d72" > DefinedEngineView::getSpeciesTimescales< / a > (< / div >
< div class = "line" > < a id = "l00123" name = "l00123" > < / a > < span class = "lineno" > 123< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_defined,< / div >
< div class = "line" > < a id = "l00124" name = "l00124" > < / a > < span class = "lineno" > 124< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00125" name = "l00125" > < / a > < span class = "lineno" > 125< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00126" name = "l00126" > < / a > < span class = "lineno" > 126< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00127" name = "l00127" > < / a > < span class = "lineno" > 127< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > validateNetworkState< / a > ();< / div >
< div class = "line" > < a id = "l00128" name = "l00128" > < / a > < span class = "lineno" > 128< / span > < / div >
< div class = "line" > < a id = "l00129" name = "l00129" > < / a > < span class = "lineno" > 129< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > Y_full = < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843" > mapViewToFull< / a > (Y_defined);< / div >
< div class = "line" > < a id = "l00130" name = "l00130" > < / a > < span class = "lineno" > 130< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > result = < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .getSpeciesTimescales(Y_full, T9, rho);< / div >
< div class = "line" > < a id = "l00131" name = "l00131" > < / a > < span class = "lineno" > 131< / span > < span class = "keywordflow" > if< / span > (!result) {< / div >
< div class = "line" > < a id = "l00132" name = "l00132" > < / a > < span class = "lineno" > 132< / span > < span class = "keywordflow" > return< / span > std::unexpected{result.error()};< / div >
< div class = "line" > < a id = "l00133" name = "l00133" > < / a > < span class = "lineno" > 133< / span > }< / div >
< div class = "line" > < a id = "l00134" name = "l00134" > < / a > < span class = "lineno" > 134< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & fullTimescales = result.value();< / div >
< div class = "line" > < a id = "l00135" name = "l00135" > < / a > < span class = "lineno" > 135< / span > < / div >
< div class = "line" > < a id = "l00136" name = "l00136" > < / a > < span class = "lineno" > 136< / span > std::unordered_map< Species, double> definedTimescales;< / div >
< div class = "line" > < a id = "l00137" name = "l00137" > < / a > < span class = "lineno" > 137< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & active_species : < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > ) {< / div >
< div class = "line" > < a id = "l00138" name = "l00138" > < / a > < span class = "lineno" > 138< / span > < span class = "keywordflow" > if< / span > (fullTimescales.contains(active_species)) {< / div >
< div class = "line" > < a id = "l00139" name = "l00139" > < / a > < span class = "lineno" > 139< / span > definedTimescales[active_species] = fullTimescales.at(active_species);< / 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 > }< / div >
< div class = "line" > < a id = "l00142" name = "l00142" > < / a > < span class = "lineno" > 142< / span > < span class = "keywordflow" > return< / span > definedTimescales;< / div >
< div class = "line" > < a id = "l00143" name = "l00143" > < / a > < span class = "lineno" > 143< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00144" name = "l00144" > < / a > < span class = "lineno" > 144< / span > < / div >
< div class = "line" > < a id = "l00145" name = "l00145" > < / a > < span class = "lineno" > 145< / 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 > > < / div >
< div class = "foldopen" id = "foldopen00146" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00146" name = "l00146" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a3d58e36ed8a6a0d82bb65e91090f7491" > 146< / a > < / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a3d58e36ed8a6a0d82bb65e91090f7491" > DefinedEngineView::getSpeciesDestructionTimescales< / a > (< / div >
< div class = "line" > < a id = "l00147" name = "l00147" > < / a > < span class = "lineno" > 147< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_defined,< / div >
< div class = "line" > < a id = "l00148" name = "l00148" > < / a > < span class = "lineno" > 148< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00149" name = "l00149" > < / a > < span class = "lineno" > 149< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00150" name = "l00150" > < / a > < span class = "lineno" > 150< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00151" name = "l00151" > < / a > < span class = "lineno" > 151< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > validateNetworkState< / a > ();< / div >
< div class = "line" > < a id = "l00152" name = "l00152" > < / a > < span class = "lineno" > 152< / span > < / div >
< div class = "line" > < a id = "l00153" name = "l00153" > < / a > < span class = "lineno" > 153< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > Y_full = < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843" > mapViewToFull< / a > (Y_defined);< / div >
< div class = "line" > < a id = "l00154" name = "l00154" > < / a > < span class = "lineno" > 154< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > result = < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .getSpeciesDestructionTimescales(Y_full, T9, rho);< / div >
< div class = "line" > < a id = "l00155" name = "l00155" > < / a > < span class = "lineno" > 155< / span > < / div >
< div class = "line" > < a id = "l00156" name = "l00156" > < / a > < span class = "lineno" > 156< / span > < span class = "keywordflow" > if< / span > (!result) {< / div >
< div class = "line" > < a id = "l00157" name = "l00157" > < / a > < span class = "lineno" > 157< / span > < span class = "keywordflow" > return< / span > std::unexpected{result.error()};< / div >
< div class = "line" > < a id = "l00158" name = "l00158" > < / a > < span class = "lineno" > 158< / span > }< / div >
< div class = "line" > < a id = "l00159" name = "l00159" > < / a > < span class = "lineno" > 159< / span > < / div >
< div class = "line" > < a id = "l00160" name = "l00160" > < / a > < span class = "lineno" > 160< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & destructionTimescales = result.value();< / div >
< div class = "line" > < a id = "l00161" name = "l00161" > < / a > < span class = "lineno" > 161< / span > < / div >
< div class = "line" > < a id = "l00162" name = "l00162" > < / a > < span class = "lineno" > 162< / span > std::unordered_map< Species, double> definedTimescales;< / div >
< div class = "line" > < a id = "l00163" name = "l00163" > < / a > < span class = "lineno" > 163< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & active_species : < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > ) {< / div >
< div class = "line" > < a id = "l00164" name = "l00164" > < / a > < span class = "lineno" > 164< / span > < span class = "keywordflow" > if< / span > (destructionTimescales.contains(active_species)) {< / div >
< div class = "line" > < a id = "l00165" name = "l00165" > < / a > < span class = "lineno" > 165< / span > definedTimescales[active_species] = destructionTimescales.at(active_species);< / div >
< div class = "line" > < a id = "l00166" name = "l00166" > < / a > < span class = "lineno" > 166< / span > }< / div >
< div class = "line" > < a id = "l00167" name = "l00167" > < / a > < span class = "lineno" > 167< / span > }< / div >
< div class = "line" > < a id = "l00168" name = "l00168" > < / a > < span class = "lineno" > 168< / span > < span class = "keywordflow" > return< / span > definedTimescales;< / div >
< div class = "line" > < a id = "l00169" name = "l00169" > < / a > < span class = "lineno" > 169< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00170" name = "l00170" > < / a > < span class = "lineno" > 170< / span > < / div >
< div class = "foldopen" id = "foldopen00171" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00171" name = "l00171" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#ae5762f395caea5381ec177507816b5ae" > 171< / a > < / span > fourdst::composition::Composition < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#ae5762f395caea5381ec177507816b5ae" > DefinedEngineView::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 = "l00172" name = "l00172" > < / a > < span class = "lineno" > 172< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .update(netIn);< / div >
< div class = "line" > < a id = "l00173" name = "l00173" > < / a > < span class = "lineno" > 173< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00174" name = "l00174" > < / a > < span class = "lineno" > 174< / span > < / div >
< div class = "foldopen" id = "foldopen00175" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00175" name = "l00175" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a7d9e738dd28efb4d6127de7379169c87" > 175< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a7d9e738dd28efb4d6127de7379169c87" > DefinedEngineView::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 = "l00176" name = "l00176" > < / a > < span class = "lineno" > 176< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .isStale(netIn);< / div >
< div class = "line" > < a id = "l00177" name = "l00177" > < / a > < span class = "lineno" > 177< / span > }< / div >
< / div >
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< div class = "line" > < a id = "l00178" name = "l00178" > < / a > < span class = "lineno" > 178< / span > < / div >
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< div class = "line" > < a id = "l00179" name = "l00179" > < / a > < span class = "lineno" > 179< / span > < / div >
< div class = "foldopen" id = "foldopen00180" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00180" name = "l00180" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#abf2da57c83c3c4c635cb301f53088258" > 180< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#abf2da57c83c3c4c635cb301f53088258" > DefinedEngineView::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 = "l00181" name = "l00181" > < / a > < span class = "lineno" > 181< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .setScreeningModel(model);< / div >
< div class = "line" > < a id = "l00182" name = "l00182" > < / a > < span class = "lineno" > 182< / span > }< / div >
< / div >
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< div class = "line" > < a id = "l00183" name = "l00183" > < / a > < span class = "lineno" > 183< / span > < / div >
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< div class = "foldopen" id = "foldopen00184" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00184" name = "l00184" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a3c657b82a0117118a4bb0ce7f624ae0c" > 184< / 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_defined_engine_view.html#a3c657b82a0117118a4bb0ce7f624ae0c" > DefinedEngineView::getScreeningModel< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00185" name = "l00185" > < / a > < span class = "lineno" > 185< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .getScreeningModel();< / div >
< div class = "line" > < a id = "l00186" name = "l00186" > < / a > < span class = "lineno" > 186< / span > }< / div >
< / div >
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< div class = "line" > < a id = "l00187" name = "l00187" > < / a > < span class = "lineno" > 187< / span > < / div >
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< div class = "foldopen" id = "foldopen00188" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00188" name = "l00188" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3" > 188< / a > < / span > < span class = "keywordtype" > int< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3" > DefinedEngineView::getSpeciesIndex< / a > (< span class = "keyword" > const< / span > Species & species)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00189" name = "l00189" > < / a > < span class = "lineno" > 189< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > validateNetworkState< / a > ();< / div >
< div class = "line" > < a id = "l00190" name = "l00190" > < / a > < span class = "lineno" > 190< / span > < / div >
< div class = "line" > < a id = "l00191" name = "l00191" > < / a > < span class = "lineno" > 191< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > it = std::ranges::find(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > , species);< / div >
< div class = "line" > < a id = "l00192" name = "l00192" > < / a > < span class = "lineno" > 192< / span > < span class = "keywordflow" > if< / span > (it != < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > .end()) {< / div >
< div class = "line" > < a id = "l00193" name = "l00193" > < / a > < span class = "lineno" > 193< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > static_cast< < / span > < span class = "keywordtype" > int< / span > < span class = "keyword" > > < / span > (std::distance(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > .begin(), it));< / div >
< div class = "line" > < a id = "l00194" name = "l00194" > < / a > < span class = "lineno" > 194< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00195" name = "l00195" > < / a > < span class = "lineno" > 195< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Species ' {}' not found in active species list." < / span > , species.name());< / div >
< div class = "line" > < a id = "l00196" name = "l00196" > < / a > < span class = "lineno" > 196< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00197" name = "l00197" > < / a > < span class = "lineno" > 197< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " Species not found in active species list: " < / span > + std::string(species.name()));< / div >
< div class = "line" > < a id = "l00198" name = "l00198" > < / a > < span class = "lineno" > 198< / span > }< / div >
< div class = "line" > < a id = "l00199" name = "l00199" > < / a > < span class = "lineno" > 199< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00200" name = "l00200" > < / a > < span class = "lineno" > 200< / span > < / div >
< div class = "foldopen" id = "foldopen00201" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00201" name = "l00201" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a72789c1c3379594b65b560da50192de2" > 201< / a > < / span > std::vector< double> < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a72789c1c3379594b65b560da50192de2" > DefinedEngineView::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 = "l00202" name = "l00202" > < / a > < span class = "lineno" > 202< / span > std::vector< double> Y(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > .size(), 0.0); < span class = "comment" > // Initialize with zeros< / span > < / div >
< div class = "line" > < a id = "l00203" name = "l00203" > < / a > < span class = "lineno" > 203< / 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 = "l00204" name = "l00204" > < / a > < span class = "lineno" > 204< / span > < span class = "keyword" > auto< / span > it = std::ranges::find(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > , entry.isotope());< / div >
< div class = "line" > < a id = "l00205" name = "l00205" > < / a > < span class = "lineno" > 205< / span > < span class = "keywordflow" > if< / span > (it != < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > .end()) {< / div >
< div class = "line" > < a id = "l00206" name = "l00206" > < / a > < span class = "lineno" > 206< / span > Y[< a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3" > 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 = "l00207" name = "l00207" > < / a > < span class = "lineno" > 207< / 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 > < span class = "keywordflow" > return< / span > Y; < span class = "comment" > // Return the vector of molar abundances< / span > < / div >
< div class = "line" > < a id = "l00210" name = "l00210" > < / a > < span class = "lineno" > 210< / span > }< / div >
< / div >
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< div class = "line" > < a id = "l00211" name = "l00211" > < / a > < span class = "lineno" > 211< / span > < / div >
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< div class = "foldopen" id = "foldopen00212" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00212" name = "l00212" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a13033abd3b44904f98b58c93e22da460" > 212< / 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_defined_engine_view.html#a13033abd3b44904f98b58c93e22da460" > DefinedEngineView::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 = "l00213" name = "l00213" > < / a > < span class = "lineno" > 213< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .primeEngine(netIn);< / div >
< div class = "line" > < a id = "l00214" name = "l00214" > < / a > < span class = "lineno" > 214< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00215" name = "l00215" > < / a > < span class = "lineno" > 215< / span > < / div >
< div class = "foldopen" id = "foldopen00216" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00216" name = "l00216" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a9ea4812bc697fe43f8aded14f8aa0985" > 216< / a > < / span > std::vector< size_t> < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a9ea4812bc697fe43f8aded14f8aa0985" > DefinedEngineView::constructSpeciesIndexMap< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00217" name = "l00217" > < / a > < span class = "lineno" > 217< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Constructing species index map for DefinedEngineView..." < / span > );< / div >
< div class = "line" > < a id = "l00218" name = "l00218" > < / a > < span class = "lineno" > 218< / span > std::unordered_map< Species, size_t> fullSpeciesReverseMap;< / div >
< div class = "line" > < a id = "l00219" name = "l00219" > < / a > < span class = "lineno" > 219< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & fullSpeciesList = < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .getNetworkSpecies();< / div >
< div class = "line" > < a id = "l00220" name = "l00220" > < / a > < span class = "lineno" > 220< / span > < / div >
< div class = "line" > < a id = "l00221" name = "l00221" > < / a > < span class = "lineno" > 221< / span > fullSpeciesReverseMap.reserve(fullSpeciesList.size());< / 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 > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < fullSpeciesList.size(); ++i) {< / div >
< div class = "line" > < a id = "l00224" name = "l00224" > < / a > < span class = "lineno" > 224< / span > fullSpeciesReverseMap[fullSpeciesList[i]] = i;< / div >
< div class = "line" > < a id = "l00225" name = "l00225" > < / a > < span class = "lineno" > 225< / span > }< / div >
< div class = "line" > < a id = "l00226" name = "l00226" > < / a > < span class = "lineno" > 226< / span > < / div >
< div class = "line" > < a id = "l00227" name = "l00227" > < / a > < span class = "lineno" > 227< / span > std::vector< size_t> speciesIndexMap;< / div >
< div class = "line" > < a id = "l00228" name = "l00228" > < / a > < span class = "lineno" > 228< / span > speciesIndexMap.reserve(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > .size());< / div >
< div class = "line" > < a id = "l00229" name = "l00229" > < / a > < span class = "lineno" > 229< / span > < / div >
< div class = "line" > < a id = "l00230" name = "l00230" > < / a > < span class = "lineno" > 230< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & active_species : < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > ) {< / div >
< div class = "line" > < a id = "l00231" name = "l00231" > < / a > < span class = "lineno" > 231< / span > < span class = "keyword" > auto< / span > it = fullSpeciesReverseMap.find(active_species);< / div >
< div class = "line" > < a id = "l00232" name = "l00232" > < / a > < span class = "lineno" > 232< / span > < span class = "keywordflow" > if< / span > (it != fullSpeciesReverseMap.end()) {< / div >
< div class = "line" > < a id = "l00233" name = "l00233" > < / a > < span class = "lineno" > 233< / span > speciesIndexMap.push_back(it-> second);< / div >
< div class = "line" > < a id = "l00234" name = "l00234" > < / a > < span class = "lineno" > 234< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00235" name = "l00235" > < / a > < span class = "lineno" > 235< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Species ' {}' not found in full species map." < / span > , active_species.name());< / div >
< div class = "line" > < a id = "l00236" name = "l00236" > < / a > < span class = "lineno" > 236< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00237" name = "l00237" > < / a > < span class = "lineno" > 237< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " Species not found in full species map: " < / span > + std::string(active_species.name()));< / div >
< div class = "line" > < a id = "l00238" name = "l00238" > < / a > < span class = "lineno" > 238< / span > }< / div >
< div class = "line" > < a id = "l00239" name = "l00239" > < / a > < span class = "lineno" > 239< / span > }< / div >
< div class = "line" > < a id = "l00240" name = "l00240" > < / a > < span class = "lineno" > 240< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Species index map constructed with {} entries." < / span > , speciesIndexMap.size());< / div >
< div class = "line" > < a id = "l00241" name = "l00241" > < / a > < span class = "lineno" > 241< / span > < span class = "keywordflow" > return< / span > speciesIndexMap;< / div >
< div class = "line" > < a id = "l00242" name = "l00242" > < / a > < span class = "lineno" > 242< / span > < / div >
< div class = "line" > < a id = "l00243" name = "l00243" > < / a > < span class = "lineno" > 243< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00244" name = "l00244" > < / a > < span class = "lineno" > 244< / span > < / div >
< div class = "foldopen" id = "foldopen00245" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00245" name = "l00245" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#ab2514984afaaf8590c28ab71943fbe68" > 245< / a > < / span > std::vector< size_t> < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#ab2514984afaaf8590c28ab71943fbe68" > DefinedEngineView::constructReactionIndexMap< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00246" name = "l00246" > < / a > < span class = "lineno" > 246< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Constructing reaction index map for DefinedEngineView..." < / span > );< / div >
< div class = "line" > < a id = "l00247" name = "l00247" > < / a > < span class = "lineno" > 247< / span > < / div >
< div class = "line" > < a id = "l00248" name = "l00248" > < / a > < span class = "lineno" > 248< / span > < span class = "comment" > // --- Step 1: Create a reverse map using the reaction' s unique ID as the key. ---< / span > < / div >
< div class = "line" > < a id = "l00249" name = "l00249" > < / a > < span class = "lineno" > 249< / span > std::unordered_map< std::string_view, size_t> fullReactionReverseMap;< / div >
< div class = "line" > < a id = "l00250" name = "l00250" > < / a > < span class = "lineno" > 250< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & fullReactionSet = < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .getNetworkReactions();< / div >
< div class = "line" > < a id = "l00251" name = "l00251" > < / a > < span class = "lineno" > 251< / span > fullReactionReverseMap.reserve(fullReactionSet.size());< / div >
< div class = "line" > < a id = "l00252" name = "l00252" > < / a > < span class = "lineno" > 252< / span > < / div >
< div class = "line" > < a id = "l00253" name = "l00253" > < / a > < span class = "lineno" > 253< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i_full = 0; i_full < fullReactionSet.size(); ++i_full) {< / div >
< div class = "line" > < a id = "l00254" name = "l00254" > < / a > < span class = "lineno" > 254< / span > fullReactionReverseMap[fullReactionSet[i_full].id()] = i_full;< / div >
< div class = "line" > < a id = "l00255" name = "l00255" > < / a > < span class = "lineno" > 255< / span > }< / div >
< div class = "line" > < a id = "l00256" name = "l00256" > < / a > < span class = "lineno" > 256< / span > < / div >
< div class = "line" > < a id = "l00257" name = "l00257" > < / a > < span class = "lineno" > 257< / span > < span class = "comment" > // --- Step 2: Build the final index map using the active reaction set. ---< / span > < / div >
< div class = "line" > < a id = "l00258" name = "l00258" > < / a > < span class = "lineno" > 258< / span > std::vector< size_t> reactionIndexMap;< / div >
< div class = "line" > < a id = "l00259" name = "l00259" > < / a > < span class = "lineno" > 259< / span > reactionIndexMap.reserve(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965" > m_activeReactions< / a > .size());< / div >
< div class = "line" > < a id = "l00260" name = "l00260" > < / a > < span class = "lineno" > 260< / span > < / div >
< div class = "line" > < a id = "l00261" name = "l00261" > < / a > < span class = "lineno" > 261< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & active_reaction_ptr : < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965" > m_activeReactions< / a > ) {< / div >
< div class = "line" > < a id = "l00262" name = "l00262" > < / a > < span class = "lineno" > 262< / span > < span class = "keyword" > auto< / span > it = fullReactionReverseMap.find(active_reaction_ptr.id());< / div >
< div class = "line" > < a id = "l00263" name = "l00263" > < / a > < span class = "lineno" > 263< / span > < / div >
< div class = "line" > < a id = "l00264" name = "l00264" > < / a > < span class = "lineno" > 264< / span > < span class = "keywordflow" > if< / span > (it != fullReactionReverseMap.end()) {< / div >
< div class = "line" > < a id = "l00265" name = "l00265" > < / a > < span class = "lineno" > 265< / span > reactionIndexMap.push_back(it-> second);< / div >
< div class = "line" > < a id = "l00266" name = "l00266" > < / a > < span class = "lineno" > 266< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00267" name = "l00267" > < / a > < span class = "lineno" > 267< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Active reaction ' {}' not found in base engine during reaction index map construction." < / span > , active_reaction_ptr.id());< / div >
< div class = "line" > < a id = "l00268" name = "l00268" > < / a > < span class = "lineno" > 268< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00269" name = "l00269" > < / a > < span class = "lineno" > 269< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " Mismatch between active reactions and base engine." < / span > );< / div >
< div class = "line" > < a id = "l00270" name = "l00270" > < / a > < span class = "lineno" > 270< / span > }< / div >
< div class = "line" > < a id = "l00271" name = "l00271" > < / a > < span class = "lineno" > 271< / span > }< / div >
< div class = "line" > < a id = "l00272" name = "l00272" > < / a > < span class = "lineno" > 272< / span > < / div >
< div class = "line" > < a id = "l00273" name = "l00273" > < / a > < span class = "lineno" > 273< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Reaction index map constructed with {} entries." < / span > , reactionIndexMap.size());< / div >
< div class = "line" > < a id = "l00274" name = "l00274" > < / a > < span class = "lineno" > 274< / span > < span class = "keywordflow" > return< / span > reactionIndexMap;< / div >
< div class = "line" > < a id = "l00275" name = "l00275" > < / a > < span class = "lineno" > 275< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00276" name = "l00276" > < / a > < span class = "lineno" > 276< / span > < / div >
< div class = "foldopen" id = "foldopen00277" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00277" name = "l00277" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843" > 277< / a > < / span > std::vector< double> < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843" > DefinedEngineView::mapViewToFull< / a > (< span class = "keyword" > const< / span > std::vector< double> & culled)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00278" name = "l00278" > < / a > < span class = "lineno" > 278< / span > std::vector< double> full(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .getNetworkSpecies().size(), 0.0);< / div >
< div class = "line" > < a id = "l00279" name = "l00279" > < / a > < span class = "lineno" > 279< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i_culled = 0; i_culled < culled.size(); ++i_culled) {< / div >
< div class = "line" > < a id = "l00280" name = "l00280" > < / a > < span class = "lineno" > 280< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > i_full = < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e" > m_speciesIndexMap< / a > [i_culled];< / div >
< div class = "line" > < a id = "l00281" name = "l00281" > < / a > < span class = "lineno" > 281< / span > full[i_full] += culled[i_culled];< / div >
< div class = "line" > < a id = "l00282" name = "l00282" > < / a > < span class = "lineno" > 282< / span > }< / div >
< div class = "line" > < a id = "l00283" name = "l00283" > < / a > < span class = "lineno" > 283< / span > < span class = "keywordflow" > return< / span > full;< / div >
< div class = "line" > < a id = "l00284" name = "l00284" > < / a > < span class = "lineno" > 284< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00285" name = "l00285" > < / a > < span class = "lineno" > 285< / span > < / div >
< div class = "foldopen" id = "foldopen00286" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00286" name = "l00286" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a2f59af6fb3516911de2a3e3ff0ed8873" > 286< / a > < / span > std::vector< double> < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a2f59af6fb3516911de2a3e3ff0ed8873" > DefinedEngineView::mapFullToView< / a > (< span class = "keyword" > const< / span > std::vector< double> & full)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00287" name = "l00287" > < / a > < span class = "lineno" > 287< / span > std::vector< double> culled(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > .size(), 0.0);< / div >
< div class = "line" > < a id = "l00288" name = "l00288" > < / a > < span class = "lineno" > 288< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i_culled = 0; i_culled < < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > .size(); ++i_culled) {< / div >
< div class = "line" > < a id = "l00289" name = "l00289" > < / a > < span class = "lineno" > 289< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > i_full = < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e" > m_speciesIndexMap< / a > [i_culled];< / div >
< div class = "line" > < a id = "l00290" name = "l00290" > < / a > < span class = "lineno" > 290< / span > culled[i_culled] = full[i_full];< / div >
< div class = "line" > < a id = "l00291" name = "l00291" > < / a > < span class = "lineno" > 291< / span > }< / div >
< div class = "line" > < a id = "l00292" name = "l00292" > < / a > < span class = "lineno" > 292< / span > < span class = "keywordflow" > return< / span > culled;< / div >
< div class = "line" > < a id = "l00293" name = "l00293" > < / a > < span class = "lineno" > 293< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00294" name = "l00294" > < / a > < span class = "lineno" > 294< / span > < / div >
< div class = "foldopen" id = "foldopen00295" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00295" name = "l00295" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#af6fb8c3c7894b505bd81d15f012f154a" > 295< / a > < / span > < span class = "keywordtype" > size_t< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#af6fb8c3c7894b505bd81d15f012f154a" > DefinedEngineView::mapViewToFullSpeciesIndex< / a > (< span class = "keywordtype" > size_t< / span > culledSpeciesIndex)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00296" name = "l00296" > < / a > < span class = "lineno" > 296< / span > < span class = "keywordflow" > if< / span > (culledSpeciesIndex < 0 || culledSpeciesIndex > = < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e" > m_speciesIndexMap< / a > .size()) {< / div >
< div class = "line" > < a id = "l00297" name = "l00297" > < / a > < span class = "lineno" > 297< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Defined index {} is out of bounds for species index map of size {}." < / span > , culledSpeciesIndex, < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e" > m_speciesIndexMap< / a > .size());< / div >
< div class = "line" > < a id = "l00298" name = "l00298" > < / a > < span class = "lineno" > 298< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00299" name = "l00299" > < / a > < span class = "lineno" > 299< / span > < span class = "keywordflow" > throw< / span > std::out_of_range(< span class = "stringliteral" > " Defined index " < / span > + std::to_string(culledSpeciesIndex) + < span class = "stringliteral" > " is out of bounds for species index map of size " < / span > + std::to_string(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e" > m_speciesIndexMap< / a > .size()) + < span class = "stringliteral" > " ." < / span > );< / 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 = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e" > m_speciesIndexMap< / a > [culledSpeciesIndex];< / div >
< div class = "line" > < a id = "l00302" name = "l00302" > < / a > < span class = "lineno" > 302< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00303" name = "l00303" > < / a > < span class = "lineno" > 303< / span > < / div >
< div class = "foldopen" id = "foldopen00304" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00304" name = "l00304" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#aadf373d69a22fcd171a6c251466d53d1" > 304< / a > < / span > < span class = "keywordtype" > size_t< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#aadf373d69a22fcd171a6c251466d53d1" > DefinedEngineView::mapViewToFullReactionIndex< / a > (< span class = "keywordtype" > size_t< / span > culledReactionIndex)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00305" name = "l00305" > < / a > < span class = "lineno" > 305< / span > < span class = "keywordflow" > if< / span > (culledReactionIndex < 0 || culledReactionIndex > = < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd" > m_reactionIndexMap< / a > .size()) {< / div >
< div class = "line" > < a id = "l00306" name = "l00306" > < / a > < span class = "lineno" > 306< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Defined index {} is out of bounds for reaction index map of size {}." < / span > , culledReactionIndex, < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd" > m_reactionIndexMap< / a > .size());< / div >
< div class = "line" > < a id = "l00307" name = "l00307" > < / a > < span class = "lineno" > 307< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00308" name = "l00308" > < / a > < span class = "lineno" > 308< / span > < span class = "keywordflow" > throw< / span > std::out_of_range(< span class = "stringliteral" > " Defined index " < / span > + std::to_string(culledReactionIndex) + < span class = "stringliteral" > " is out of bounds for reaction index map of size " < / span > + std::to_string(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd" > m_reactionIndexMap< / a > .size()) + < span class = "stringliteral" > " ." < / span > );< / div >
< div class = "line" > < a id = "l00309" name = "l00309" > < / a > < span class = "lineno" > 309< / span > }< / div >
< div class = "line" > < a id = "l00310" name = "l00310" > < / a > < span class = "lineno" > 310< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd" > m_reactionIndexMap< / a > [culledReactionIndex];< / div >
< div class = "line" > < a id = "l00311" name = "l00311" > < / a > < span class = "lineno" > 311< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00312" name = "l00312" > < / a > < span class = "lineno" > 312< / span > < / div >
< div class = "foldopen" id = "foldopen00313" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00313" name = "l00313" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > 313< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > DefinedEngineView::validateNetworkState< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00314" name = "l00314" > < / a > < span class = "lineno" > 314< / span > < span class = "keywordflow" > if< / span > (< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a217d541f3fa777b1552f652fbb520382" > m_isStale< / a > ) {< / div >
< div class = "line" > < a id = "l00315" name = "l00315" > < / a > < span class = "lineno" > 315< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " DefinedEngineView is stale. Please call update() with a valid NetIn object." < / span > );< / div >
< div class = "line" > < a id = "l00316" name = "l00316" > < / a > < span class = "lineno" > 316< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00317" name = "l00317" > < / a > < span class = "lineno" > 317< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " DefinedEngineView is stale. Please call update() with a valid NetIn object." < / span > );< / div >
< div class = "line" > < a id = "l00318" name = "l00318" > < / a > < span class = "lineno" > 318< / span > }< / div >
< div class = "line" > < a id = "l00319" name = "l00319" > < / a > < span class = "lineno" > 319< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00320" name = "l00320" > < / a > < span class = "lineno" > 320< / span > < / div >
< div class = "foldopen" id = "foldopen00321" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00321" name = "l00321" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_defined_engine_view.html#adbc64284b5f5a3256867be46fa87c69e" > 321< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#adbc64284b5f5a3256867be46fa87c69e" > DefinedEngineView::collect< / a > (< span class = "keyword" > const< / span > std::vector< std::string> & peNames) {< / div >
< div class = "line" > < a id = "l00322" name = "l00322" > < / a > < span class = "lineno" > 322< / span > std::unordered_set< Species> seenSpecies;< / div >
< div class = "line" > < a id = "l00323" name = "l00323" > < / a > < span class = "lineno" > 323< / span > < / div >
< div class = "line" > < a id = "l00324" name = "l00324" > < / a > < span class = "lineno" > 324< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & fullNetworkReactionSet = < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > m_baseEngine< / a > .getNetworkReactions();< / div >
< div class = "line" > < a id = "l00325" name = "l00325" > < / a > < span class = "lineno" > 325< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & peName : peNames) {< / div >
< div class = "line" > < a id = "l00326" name = "l00326" > < / a > < span class = "lineno" > 326< / span > < span class = "keywordflow" > if< / span > (!fullNetworkReactionSet.contains(peName)) {< / div >
< div class = "line" > < a id = "l00327" name = "l00327" > < / a > < span class = "lineno" > 327< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Reaction with name ' {}' not found in the base engine' s network reactions. Aborting..." < / span > , peName);< / div >
< div class = "line" > < a id = "l00328" name = "l00328" > < / a > < span class = "lineno" > 328< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00329" name = "l00329" > < / a > < span class = "lineno" > 329< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " Reaction with name ' " < / span > + std::string(peName) + < span class = "stringliteral" > " ' not found in the base engine' s network reactions." < / span > );< / div >
< div class = "line" > < a id = "l00330" name = "l00330" > < / a > < span class = "lineno" > 330< / span > }< / div >
< div class = "line" > < a id = "l00331" name = "l00331" > < / a > < span class = "lineno" > 331< / span > < span class = "keyword" > auto< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > = fullNetworkReactionSet[peName];< / div >
< div class = "line" > < a id = "l00332" name = "l00332" > < / a > < span class = "lineno" > 332< / 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 = "l00333" name = "l00333" > < / a > < span class = "lineno" > 333< / span > < span class = "keywordflow" > if< / span > (!seenSpecies.contains(reactant)) {< / div >
< div class = "line" > < a id = "l00334" name = "l00334" > < / a > < span class = "lineno" > 334< / span > seenSpecies.insert(reactant);< / div >
< div class = "line" > < a id = "l00335" name = "l00335" > < / a > < span class = "lineno" > 335< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > .push_back(reactant);< / div >
< div class = "line" > < a id = "l00336" name = "l00336" > < / a > < span class = "lineno" > 336< / span > }< / 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 = "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 = "l00339" name = "l00339" > < / a > < span class = "lineno" > 339< / span > < span class = "keywordflow" > if< / span > (!seenSpecies.contains(product)) {< / div >
< div class = "line" > < a id = "l00340" name = "l00340" > < / a > < span class = "lineno" > 340< / span > seenSpecies.insert(product);< / div >
< div class = "line" > < a id = "l00341" name = "l00341" > < / a > < span class = "lineno" > 341< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > .push_back(product);< / div >
< div class = "line" > < a id = "l00342" name = "l00342" > < / a > < span class = "lineno" > 342< / 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 > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965" > m_activeReactions< / a > .add_reaction(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > );< / div >
< div class = "line" > < a id = "l00345" name = "l00345" > < / a > < span class = "lineno" > 345< / span > }< / div >
< div class = "line" > < a id = "l00346" name = "l00346" > < / a > < span class = "lineno" > 346< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " DefinedEngineView built with {} active species and {} active reactions." < / span > , < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > .size(), < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965" > m_activeReactions< / a > .size());< / div >
< div class = "line" > < a id = "l00347" name = "l00347" > < / a > < span class = "lineno" > 347< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Active species: {}" < / span > , [< span class = "keyword" > this< / span > ]() -> std::string {< / div >
< div class = "line" > < a id = "l00348" name = "l00348" > < / a > < span class = "lineno" > 348< / span > std::string result;< / div >
< div class = "line" > < a id = "l00349" name = "l00349" > < / a > < span class = "lineno" > 349< / 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_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > m_activeSpecies< / a > ) {< / div >
< div class = "line" > < a id = "l00350" name = "l00350" > < / a > < span class = "lineno" > 350< / span > result += std::string(species.name()) + < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l00351" name = "l00351" > < / a > < span class = "lineno" > 351< / span > }< / div >
< div class = "line" > < a id = "l00352" name = "l00352" > < / a > < span class = "lineno" > 352< / span > < span class = "keywordflow" > if< / span > (!result.empty()) {< / div >
< div class = "line" > < a id = "l00353" name = "l00353" > < / a > < span class = "lineno" > 353< / span > result.pop_back(); < span class = "comment" > // Remove last space< / span > < / div >
< div class = "line" > < a id = "l00354" name = "l00354" > < / a > < span class = "lineno" > 354< / span > result.pop_back(); < span class = "comment" > // Remove last comma< / span > < / div >
< div class = "line" > < a id = "l00355" name = "l00355" > < / a > < span class = "lineno" > 355< / span > }< / div >
< div class = "line" > < a id = "l00356" name = "l00356" > < / a > < span class = "lineno" > 356< / span > < span class = "keywordflow" > return< / span > result;< / div >
< div class = "line" > < a id = "l00357" name = "l00357" > < / a > < span class = "lineno" > 357< / span > }());< / div >
< div class = "line" > < a id = "l00358" name = "l00358" > < / a > < span class = "lineno" > 358< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > m_logger< / a > , < span class = "stringliteral" > " Active reactions: {}" < / span > , [< span class = "keyword" > this< / span > ]() -> std::string {< / div >
< div class = "line" > < a id = "l00359" name = "l00359" > < / a > < span class = "lineno" > 359< / span > std::string result;< / div >
< div class = "line" > < a id = "l00360" name = "l00360" > < / a > < span class = "lineno" > 360< / 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_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965" > m_activeReactions< / a > ) {< / div >
< div class = "line" > < a id = "l00361" name = "l00361" > < / a > < span class = "lineno" > 361< / span > result += std::string(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id()) + < span class = "stringliteral" > " , " < / 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 = "keywordflow" > if< / span > (!result.empty()) {< / div >
< div class = "line" > < a id = "l00364" name = "l00364" > < / a > < span class = "lineno" > 364< / span > result.pop_back(); < span class = "comment" > // Remove last space< / span > < / div >
< div class = "line" > < a id = "l00365" name = "l00365" > < / a > < span class = "lineno" > 365< / span > result.pop_back(); < span class = "comment" > // Remove last comma< / span > < / div >
< div class = "line" > < a id = "l00366" name = "l00366" > < / a > < span class = "lineno" > 366< / span > }< / div >
< div class = "line" > < a id = "l00367" name = "l00367" > < / a > < span class = "lineno" > 367< / span > < span class = "keywordflow" > return< / span > result;< / 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 > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e" > m_speciesIndexMap< / a > = < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a9ea4812bc697fe43f8aded14f8aa0985" > constructSpeciesIndexMap< / a > ();< / div >
< div class = "line" > < a id = "l00370" name = "l00370" > < / a > < span class = "lineno" > 370< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd" > m_reactionIndexMap< / a > = < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#ab2514984afaaf8590c28ab71943fbe68" > constructReactionIndexMap< / a > ();< / div >
< div class = "line" > < a id = "l00371" name = "l00371" > < / a > < span class = "lineno" > 371< / span > < a class = "code hl_variable" href = "classgridfire_1_1_defined_engine_view.html#a217d541f3fa777b1552f652fbb520382" > m_isStale< / a > = < span class = "keyword" > false< / span > ;< / div >
< div class = "line" > < a id = "l00372" name = "l00372" > < / a > < span class = "lineno" > 372< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00373" name = "l00373" > < / a > < span class = "lineno" > 373< / span > < / div >
< div class = "line" > < a id = "l00374" name = "l00374" > < / a > < span class = "lineno" > 374< / span > < / div >
< div class = "line" > < a id = "l00378" name = "l00378" > < / a > < span class = "lineno" > 378< / span > < / div >
< div class = "foldopen" id = "foldopen00379" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00379" name = "l00379" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_file_defined_engine_view.html#a8f2f64bab0f516ed2a6fd529912e0acd" > 379< / a > < / span > < a class = "code hl_function" href = "classgridfire_1_1_file_defined_engine_view.html#a8f2f64bab0f516ed2a6fd529912e0acd" > FileDefinedEngineView::FileDefinedEngineView< / a > (< / div >
< div class = "line" > < a id = "l00380" name = "l00380" > < / a > < span class = "lineno" > 380< / span > < a class = "code hl_class" href = "classgridfire_1_1_dynamic_engine.html" > DynamicEngine< / a > & baseEngine,< / div >
< div class = "line" > < a id = "l00381" name = "l00381" > < / a > < span class = "lineno" > 381< / span > < span class = "keyword" > const< / span > std::string & fileName,< / div >
< div class = "line" > < a id = "l00382" name = "l00382" > < / a > < span class = "lineno" > 382< / span > < span class = "keyword" > const< / span > < a class = "code hl_class" href = "classgridfire_1_1io_1_1_network_file_parser.html" > io::NetworkFileParser< / a > & parser< / div >
< div class = "line" > < a id = "l00383" name = "l00383" > < / a > < span class = "lineno" > 383< / span > ):< / div >
< div class = "line" > < a id = "l00384" name = "l00384" > < / a > < span class = "lineno" > 384< / span > < a class = "code hl_function" href = "classgridfire_1_1_defined_engine_view.html#a9b319b4a1bd5a08381ebb183daf72c92" > DefinedEngineView< / a > (parser.parse(fileName), baseEngine),< / div >
< div class = "line" > < a id = "l00385" name = "l00385" > < / a > < span class = "lineno" > 385< / span > < a class = "code hl_variable" href = "classgridfire_1_1_file_defined_engine_view.html#a1b343998b93955025a589b2b4541e33b" > m_fileName< / a > (fileName),< / div >
< div class = "line" > < a id = "l00386" name = "l00386" > < / a > < span class = "lineno" > 386< / span > < a class = "code hl_variable" href = "classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500" > m_parser< / a > (parser) {}< / div >
< / div >
< div class = "line" > < a id = "l00387" name = "l00387" > < / a > < span class = "lineno" > 387< / span > }< / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a13033abd3b44904f98b58c93e22da460" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a13033abd3b44904f98b58c93e22da460" > gridfire::DefinedEngineView::primeEngine< / a > < / div > < div class = "ttdeci" > PrimingReport primeEngine(const NetIn & netIn) override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00212" > engine_defined.cpp:212< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a142725470f96cba3edb48a29f1264032" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032" > gridfire::DefinedEngineView::calculateMolarReactionFlow< / a > < / div > < div class = "ttdeci" > double calculateMolarReactionFlow(const reaction::Reaction & reaction, const std::vector< double > & Y_defined, const double T9, const double rho) const override< / div > < div class = "ttdoc" > Calculates the molar reaction flow for a given reaction in the active network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00091" > engine_defined.cpp:91< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a1a55f9748c45af6f13e16a6b6ceaa211" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a1a55f9748c45af6f13e16a6b6ceaa211" > gridfire::DefinedEngineView::getNetworkSpecies< / a > < / div > < div class = "ttdeci" > const std::vector< fourdst::atomic::Species > & getNetworkSpecies() const override< / div > < div class = "ttdoc" > Gets the list of active species in the network defined by the file.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00026" > engine_defined.cpp:26< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a217d541f3fa777b1552f652fbb520382" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a217d541f3fa777b1552f652fbb520382" > gridfire::DefinedEngineView::m_isStale< / a > < / div > < div class = "ttdeci" > bool m_isStale< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__defined_8h_source.html#l00177" > engine_defined.h:177< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a273b175049f5ce7b9208e931ad139e1b" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a273b175049f5ce7b9208e931ad139e1b" > gridfire::DefinedEngineView::getJacobianMatrixEntry< / a > < / div > < div class = "ttdeci" > double getJacobianMatrixEntry(const int i_defined, const int j_defined) const override< / div > < div class = "ttdoc" > Gets an entry from the Jacobian matrix for the active species.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00062" > engine_defined.cpp:62< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a2f59af6fb3516911de2a3e3ff0ed8873" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a2f59af6fb3516911de2a3e3ff0ed8873" > gridfire::DefinedEngineView::mapFullToView< / a > < / div > < div class = "ttdeci" > std::vector< double > mapFullToView(const std::vector< double > & full) const< / div > < div class = "ttdoc" > Maps a vector of full abundances to a vector of culled abundances.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00286" > engine_defined.cpp:286< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a373d4a83f30527a1bfaf1d74ad14c965" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a373d4a83f30527a1bfaf1d74ad14c965" > gridfire::DefinedEngineView::m_activeReactions< / a > < / div > < div class = "ttdeci" > reaction::LogicalReactionSet m_activeReactions< / div > < div class = "ttdoc" > Maps indices of active species to indices in the full network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__defined_8h_source.html#l00184" > engine_defined.h:184< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a3c657b82a0117118a4bb0ce7f624ae0c" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a3c657b82a0117118a4bb0ce7f624ae0c" > gridfire::DefinedEngineView::getScreeningModel< / a > < / div > < div class = "ttdeci" > screening::ScreeningType getScreeningModel() const override< / div > < div class = "ttdoc" > Gets the screening model from the base engine.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00184" > engine_defined.cpp:184< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a3d58e36ed8a6a0d82bb65e91090f7491" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a3d58e36ed8a6a0d82bb65e91090f7491" > gridfire::DefinedEngineView::getSpeciesDestructionTimescales< / a > < / div > < div class = "ttdeci" > std::expected< std::unordered_map< fourdst::atomic::Species, double > , expectations::StaleEngineError > getSpeciesDestructionTimescales(const std::vector< double > & Y_defined, const double T9, const double rho) const override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00146" > engine_defined.cpp:146< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a4b0d71367cb1d4c06bcd01251bbeb60d" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d" > gridfire::DefinedEngineView::calculateRHSAndEnergy< / a > < / div > < div class = "ttdeci" > std::expected< StepDerivatives< double > , expectations::StaleEngineError > calculateRHSAndEnergy(const std::vector< double > & Y_defined, const double T9, const double rho) const override< / div > < div class = "ttdoc" > Calculates the right-hand side (dY/dt) and energy generation for the active species.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00030" > engine_defined.cpp:30< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a4f4aa847ee80ad430de9b1cfdda6b4e3" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a4f4aa847ee80ad430de9b1cfdda6b4e3" > gridfire::DefinedEngineView::m_logger< / a > < / div > < div class = "ttdeci" > quill::Logger * m_logger< / div > < div class = "ttdoc" > Active species in the defined engine.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__defined_8h_source.html#l00180" > engine_defined.h:180< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a56bd041c2fc7fe4f1371c38c8c0443e0" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a56bd041c2fc7fe4f1371c38c8c0443e0" > gridfire::DefinedEngineView::validateNetworkState< / a > < / div > < div class = "ttdeci" > void validateNetworkState() const< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00313" > engine_defined.cpp:313< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a626ab005bfa08b201518c13627e1f843" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a626ab005bfa08b201518c13627e1f843" > gridfire::DefinedEngineView::mapViewToFull< / a > < / div > < div class = "ttdeci" > std::vector< double > mapViewToFull(const std::vector< double > & defined) const< / div > < div class = "ttdoc" > Maps a vector of culled abundances to a vector of full abundances.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00277" > engine_defined.cpp:277< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a64e9c79a36d529e1b296fe5786e57aae" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a64e9c79a36d529e1b296fe5786e57aae" > gridfire::DefinedEngineView::m_activeSpecies< / a > < / div > < div class = "ttdeci" > std::vector< fourdst::atomic::Species > m_activeSpecies< / div > < div class = "ttdoc" > Active reactions in the defined engine.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__defined_8h_source.html#l00182" > engine_defined.h:182< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a69b9a5812ad8bda13f956acd0da24484" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a69b9a5812ad8bda13f956acd0da24484" > gridfire::DefinedEngineView::getBaseEngine< / a > < / div > < div class = "ttdeci" > const DynamicEngine & getBaseEngine() const override< / div > < div class = "ttdoc" > Access the underlying engine instance.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00022" > engine_defined.cpp:22< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a6e3243a8a8bcdce3282a8f82c5f98195" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a6e3243a8a8bcdce3282a8f82c5f98195" > gridfire::DefinedEngineView::m_baseEngine< / a > < / div > < div class = "ttdeci" > DynamicEngine & m_baseEngine< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__defined_8h_source.html#l00178" > engine_defined.h:178< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a72789c1c3379594b65b560da50192de2" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a72789c1c3379594b65b560da50192de2" > gridfire::DefinedEngineView::mapNetInToMolarAbundanceVector< / a > < / div > < div class = "ttdeci" > std::vector< double > mapNetInToMolarAbundanceVector(const NetIn & netIn) const override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00201" > engine_defined.cpp:201< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a7d9e738dd28efb4d6127de7379169c87" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a7d9e738dd28efb4d6127de7379169c87" > gridfire::DefinedEngineView::isStale< / a > < / div > < div class = "ttdeci" > bool isStale(const NetIn & netIn) override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00175" > engine_defined.cpp:175< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a9736edfb7c9148b60de30d50c0d3530d" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a9736edfb7c9148b60de30d50c0d3530d" > gridfire::DefinedEngineView::setNetworkReactions< / a > < / div > < div class = "ttdeci" > void setNetworkReactions(const reaction::LogicalReactionSet & reactions) override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00114" > engine_defined.cpp:114< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a9b319b4a1bd5a08381ebb183daf72c92" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a9b319b4a1bd5a08381ebb183daf72c92" > gridfire::DefinedEngineView::DefinedEngineView< / a > < / div > < div class = "ttdeci" > DefinedEngineView(const std::vector< std::string > & peNames, DynamicEngine & baseEngine)< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00017" > engine_defined.cpp:17< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_a9ea4812bc697fe43f8aded14f8aa0985" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#a9ea4812bc697fe43f8aded14f8aa0985" > gridfire::DefinedEngineView::constructSpeciesIndexMap< / a > < / div > < div class = "ttdeci" > std::vector< size_t > constructSpeciesIndexMap() const< / div > < div class = "ttdoc" > Constructs the species index map.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00216" > engine_defined.cpp:216< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_aadf373d69a22fcd171a6c251466d53d1" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#aadf373d69a22fcd171a6c251466d53d1" > gridfire::DefinedEngineView::mapViewToFullReactionIndex< / a > < / div > < div class = "ttdeci" > size_t mapViewToFullReactionIndex(size_t definedReactionIndex) const< / div > < div class = "ttdoc" > Maps a culled reaction index to a full reaction index.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00304" > engine_defined.cpp:304< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_ab2514984afaaf8590c28ab71943fbe68" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#ab2514984afaaf8590c28ab71943fbe68" > gridfire::DefinedEngineView::constructReactionIndexMap< / a > < / div > < div class = "ttdeci" > std::vector< size_t > constructReactionIndexMap() const< / div > < div class = "ttdoc" > Constructs the reaction index map.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00245" > engine_defined.cpp:245< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_abf2da57c83c3c4c635cb301f53088258" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#abf2da57c83c3c4c635cb301f53088258" > gridfire::DefinedEngineView::setScreeningModel< / a > < / div > < div class = "ttdeci" > void setScreeningModel(screening::ScreeningType model) override< / div > < div class = "ttdoc" > Sets the screening model for the base engine.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00180" > engine_defined.cpp:180< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_abfee22688617ffe91c69be93049c89b3" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3" > gridfire::DefinedEngineView::getSpeciesIndex< / a > < / div > < div class = "ttdeci" > int getSpeciesIndex(const fourdst::atomic::Species & species) const override< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00188" > engine_defined.cpp:188< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_ac8daafabbc76f4b6811bede241a03d72" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#ac8daafabbc76f4b6811bede241a03d72" > gridfire::DefinedEngineView::getSpeciesTimescales< / a > < / div > < div class = "ttdeci" > std::expected< std::unordered_map< fourdst::atomic::Species, double > , expectations::StaleEngineError > getSpeciesTimescales(const std::vector< double > & Y_defined, const double T9, const double rho) const override< / div > < div class = "ttdoc" > Computes timescales for all active species in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00122" > engine_defined.cpp:122< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_acc4976262e208d1dd2185ebccbdd275e" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#acc4976262e208d1dd2185ebccbdd275e" > gridfire::DefinedEngineView::m_speciesIndexMap< / a > < / div > < div class = "ttdeci" > std::vector< size_t > m_speciesIndexMap< / div > < div class = "ttdoc" > Maps indices of active reactions to indices in the full network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__defined_8h_source.html#l00187" > engine_defined.h:187< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_ad07221be49ae1b5133c5b987dafac3b6" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#ad07221be49ae1b5133c5b987dafac3b6" > gridfire::DefinedEngineView::generateStoichiometryMatrix< / a > < / div > < div class = "ttdeci" > void generateStoichiometryMatrix() override< / div > < div class = "ttdoc" > Generates the stoichiometry matrix for the active reactions and species.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00074" > engine_defined.cpp:74< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_ad25c722eaee1f28f8ed7b4d33a1f69ae" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#ad25c722eaee1f28f8ed7b4d33a1f69ae" > gridfire::DefinedEngineView::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 active species.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00051" > engine_defined.cpp:51< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_adbc64284b5f5a3256867be46fa87c69e" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#adbc64284b5f5a3256867be46fa87c69e" > gridfire::DefinedEngineView::collect< / a > < / div > < div class = "ttdeci" > void collect(const std::vector< std::string > & peNames)< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00321" > engine_defined.cpp:321< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_ae03b4f9afac03d4011a4d7cf0423535d" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#ae03b4f9afac03d4011a4d7cf0423535d" > gridfire::DefinedEngineView::getNetworkReactions< / a > < / div > < div class = "ttdeci" > const reaction::LogicalReactionSet & getNetworkReactions() const override< / div > < div class = "ttdoc" > Gets the set of active logical reactions in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00108" > engine_defined.cpp:108< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_ae5762f395caea5381ec177507816b5ae" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#ae5762f395caea5381ec177507816b5ae" > gridfire::DefinedEngineView::update< / a > < / div > < div class = "ttdeci" > fourdst::composition::Composition update(const NetIn & netIn) override< / div > < div class = "ttdoc" > Updates the engine view if it is marked as stale.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00171" > engine_defined.cpp:171< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_af6fb8c3c7894b505bd81d15f012f154a" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#af6fb8c3c7894b505bd81d15f012f154a" > gridfire::DefinedEngineView::mapViewToFullSpeciesIndex< / a > < / div > < div class = "ttdeci" > size_t mapViewToFullSpeciesIndex(size_t definedSpeciesIndex) const< / div > < div class = "ttdoc" > Maps a culled species index to a full species index.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00295" > engine_defined.cpp:295< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_afa2820971397114d788730cc33feefe2" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#afa2820971397114d788730cc33feefe2" > gridfire::DefinedEngineView::getStoichiometryMatrixEntry< / a > < / div > < div class = "ttdeci" > int getStoichiometryMatrixEntry(const int speciesIndex_defined, const int reactionIndex_defined) const override< / div > < div class = "ttdoc" > Gets an entry from the stoichiometry matrix for the active species and reactions.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00080" > engine_defined.cpp:80< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_defined_engine_view_html_affda6d60651c53ee02532806104671bd" > < div class = "ttname" > < a href = "classgridfire_1_1_defined_engine_view.html#affda6d60651c53ee02532806104671bd" > gridfire::DefinedEngineView::m_reactionIndexMap< / a > < / div > < div class = "ttdeci" > std::vector< size_t > m_reactionIndexMap< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__defined_8h_source.html#l00189" > engine_defined.h:189< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_dynamic_engine_html" > < div class = "ttname" > < a href = "classgridfire_1_1_dynamic_engine.html" > gridfire::DynamicEngine< / a > < / div > < div class = "ttdoc" > Abstract class for engines supporting Jacobian and stoichiometry operations.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__abstract_8h_source.html#l00130" > engine_abstract.h:130< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_file_defined_engine_view_html_a0a9b07176cb93b54c677b6ce71fda500" > < div class = "ttname" > < a href = "classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500" > gridfire::FileDefinedEngineView::m_parser< / a > < / div > < div class = "ttdeci" > const io::NetworkFileParser & m_parser< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__defined_8h_source.html#l00275" > engine_defined.h:275< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_file_defined_engine_view_html_a1b343998b93955025a589b2b4541e33b" > < div class = "ttname" > < a href = "classgridfire_1_1_file_defined_engine_view.html#a1b343998b93955025a589b2b4541e33b" > gridfire::FileDefinedEngineView::m_fileName< / a > < / div > < div class = "ttdeci" > std::string m_fileName< / div > < div class = "ttdoc" > Parser for the network file.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__defined_8h_source.html#l00273" > engine_defined.h:273< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_file_defined_engine_view_html_a8f2f64bab0f516ed2a6fd529912e0acd" > < div class = "ttname" > < a href = "classgridfire_1_1_file_defined_engine_view.html#a8f2f64bab0f516ed2a6fd529912e0acd" > gridfire::FileDefinedEngineView::FileDefinedEngineView< / a > < / div > < div class = "ttdeci" > FileDefinedEngineView(DynamicEngine & baseEngine, const std::string & fileName, const io::NetworkFileParser & parser)< / div > < div class = "ttdoc" > FileDefinedEngineView Implementation ///.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00379" > engine_defined.cpp:379< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1io_1_1_network_file_parser_html" > < div class = "ttname" > < a href = "classgridfire_1_1io_1_1_network_file_parser.html" > gridfire::io::NetworkFileParser< / a > < / div > < div class = "ttdoc" > An abstract base class for network file parsers.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "network__file_8h_source.html#l00022" > network_file.h:22< / a > < / div > < / div >
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< 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 >
< div class = "ttc" id = "aengine__defined_8h_html" > < div class = "ttname" > < a href = "engine__defined_8h.html" > engine_defined.h< / a > < / div > < / div >
< 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 >
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< 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_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 >
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< 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 >
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< 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 >
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< 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_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 >
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