2025-07-24 11:10:45 -04:00
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
< html xmlns = "http://www.w3.org/1999/xhtml" lang = "en-US" >
< head >
< meta http-equiv = "Content-Type" content = "text/xhtml;charset=UTF-8" / >
< meta http-equiv = "X-UA-Compatible" content = "IE=11" / >
< meta name = "generator" content = "Doxygen 1.13.2" / >
< meta name = "viewport" content = "width=device-width, initial-scale=1" / >
< title > GridFire: src/lib/engine/views/engine_multiscale.cpp Source File< / title >
< link href = "tabs.css" rel = "stylesheet" type = "text/css" / >
< script type = "text/javascript" src = "jquery.js" > < / script >
< script type = "text/javascript" src = "dynsections.js" > < / script >
< script type = "text/javascript" src = "clipboard.js" > < / script >
< link href = "navtree.css" rel = "stylesheet" type = "text/css" / >
< script type = "text/javascript" src = "navtreedata.js" > < / script >
< script type = "text/javascript" src = "navtree.js" > < / script >
< script type = "text/javascript" src = "resize.js" > < / script >
< script type = "text/javascript" src = "cookie.js" > < / script >
< link href = "search/search.css" rel = "stylesheet" type = "text/css" / >
< script type = "text/javascript" src = "search/searchdata.js" > < / script >
< script type = "text/javascript" src = "search/search.js" > < / script >
< link href = "doxygen.css" rel = "stylesheet" type = "text/css" / >
< link href = "doxygen-awesome.css" rel = "stylesheet" type = "text/css" / >
< link href = "doxygen-awesome-sidebar-only.css" rel = "stylesheet" type = "text/css" / >
< / head >
< body >
< div id = "top" > <!-- do not remove this div, it is closed by doxygen! -->
< div id = "titlearea" >
< table cellspacing = "0" cellpadding = "0" >
< tbody >
< tr id = "projectrow" >
< td id = "projectalign" >
< div id = "projectname" > GridFire< span id = "projectnumber" >   0.0.1a< / span >
< / div >
< div id = "projectbrief" > General Purpose Nuclear Network< / div >
< / td >
< / tr >
< / tbody >
< / table >
< / div >
<!-- end header part -->
<!-- Generated by Doxygen 1.13.2 -->
< script type = "text/javascript" >
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699& dn=expat.txt MIT */
var searchBox = new SearchBox("searchBox", "search/",'.html');
/* @license-end */
< / script >
< script type = "text/javascript" >
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699& dn=expat.txt MIT */
$(function() { codefold.init(0); });
/* @license-end */
< / script >
< script type = "text/javascript" src = "menudata.js" > < / script >
< script type = "text/javascript" src = "menu.js" > < / script >
< script type = "text/javascript" >
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699& dn=expat.txt MIT */
$(function() {
initMenu('',true,false,'search.php','Search',true);
$(function() { init_search(); });
});
/* @license-end */
< / script >
< div id = "main-nav" > < / div >
< / div > <!-- top -->
< div id = "side-nav" class = "ui-resizable side-nav-resizable" >
< div id = "nav-tree" >
< div id = "nav-tree-contents" >
< div id = "nav-sync" class = "sync" > < / div >
< / div >
< / div >
< div id = "splitbar" style = "-moz-user-select:none;"
class="ui-resizable-handle">
< / div >
< / div >
< script type = "text/javascript" >
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699& dn=expat.txt MIT */
$(function(){initNavTree('engine__multiscale_8cpp_source.html',''); initResizable(true); });
/* @license-end */
< / script >
< div id = "doc-content" >
<!-- window showing the filter options -->
< div id = "MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
< / div >
<!-- iframe showing the search results (closed by default) -->
< div id = "MSearchResultsWindow" >
< div id = "MSearchResults" >
< div class = "SRPage" >
< div id = "SRIndex" >
< div id = "SRResults" > < / div >
< div class = "SRStatus" id = "Loading" > Loading...< / div >
< div class = "SRStatus" id = "Searching" > Searching...< / div >
< div class = "SRStatus" id = "NoMatches" > No Matches< / div >
< / div >
< / div >
< / div >
< / div >
< div class = "header" >
< div class = "headertitle" > < div class = "title" > engine_multiscale.cpp< / div > < / div >
< / div > <!-- header -->
< div class = "contents" >
< a href = "engine__multiscale_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__multiscale_8h.html" > gridfire/engine/views/engine_multiscale.h< / a > " < / span > < / div >
< div class = "line" > < a id = "l00002" name = "l00002" > < / a > < span class = "lineno" > 2< / span > < span class = "preprocessor" > #include " < a class = "code" href = "error__engine_8h.html" > gridfire/exceptions/error_engine.h< / a > " < / span > < / div >
< div class = "line" > < a id = "l00003" name = "l00003" > < / a > < span class = "lineno" > 3< / span > < / div >
< div class = "line" > < a id = "l00004" name = "l00004" > < / a > < span class = "lineno" > 4< / span > < span class = "preprocessor" > #include < stdexcept> < / span > < / div >
< div class = "line" > < a id = "l00005" name = "l00005" > < / a > < span class = "lineno" > 5< / span > < span class = "preprocessor" > #include < vector> < / span > < / div >
< div class = "line" > < a id = "l00006" name = "l00006" > < / a > < span class = "lineno" > 6< / span > < span class = "preprocessor" > #include < unordered_map> < / span > < / div >
< div class = "line" > < a id = "l00007" name = "l00007" > < / a > < span class = "lineno" > 7< / span > < span class = "preprocessor" > #include < unordered_set> < / span > < / div >
< div class = "line" > < a id = "l00008" name = "l00008" > < / a > < span class = "lineno" > 8< / span > < / div >
< div class = "line" > < a id = "l00009" name = "l00009" > < / a > < span class = "lineno" > 9< / span > < span class = "preprocessor" > #include < queue> < / span > < / div >
< div class = "line" > < a id = "l00010" name = "l00010" > < / a > < span class = "lineno" > 10< / span > < / div >
< div class = "line" > < a id = "l00011" name = "l00011" > < / a > < span class = "lineno" > 11< / span > < span class = "preprocessor" > #include < ranges> < / span > < / div >
< div class = "line" > < a id = "l00012" name = "l00012" > < / a > < span class = "lineno" > 12< / span > < span class = "preprocessor" > #include < algorithm> < / span > < / div >
< div class = "line" > < a id = "l00013" name = "l00013" > < / a > < span class = "lineno" > 13< / span > < / div >
< div class = "line" > < a id = "l00014" name = "l00014" > < / a > < span class = "lineno" > 14< / span > < span class = "preprocessor" > #include " quill/LogMacros.h" < / span > < / div >
< div class = "line" > < a id = "l00015" name = "l00015" > < / a > < span class = "lineno" > 15< / span > < span class = "preprocessor" > #include " quill/Logger.h" < / span > < / div >
< div class = "line" > < a id = "l00016" name = "l00016" > < / a > < span class = "lineno" > 16< / span > < / div >
< div class = "line" > < a id = "l00017" name = "l00017" > < / a > < span class = "lineno" > 17< / span > < span class = "keyword" > namespace < / span > {< / div >
< div class = "line" > < a id = "l00018" name = "l00018" > < / a > < span class = "lineno" > 18< / span > < span class = "keyword" > using namespace < / span > fourdst::atomic;< / div >
< div class = "line" > < a id = "l00019" name = "l00019" > < / a > < span class = "lineno" > 19< / span > std::vector< double> packCompositionToVector(< span class = "keyword" > const< / span > fourdst::composition::Composition& composition, < span class = "keyword" > const< / span > < a class = "code hl_class" href = "classgridfire_1_1_graph_engine.html" > gridfire::GraphEngine< / a > & engine) {< / div >
< div class = "line" > < a id = "l00020" name = "l00020" > < / a > < span class = "lineno" > 20< / span > std::vector< double> Y(engine.< a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767" > getNetworkSpecies< / a > ().size(), 0.0);< / div >
< div class = "line" > < a id = "l00021" name = "l00021" > < / a > < span class = "lineno" > 21< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & allSpecies = engine.< a class = "code hl_function" href = "classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767" > getNetworkSpecies< / a > ();< / div >
< div class = "line" > < a id = "l00022" name = "l00022" > < / a > < span class = "lineno" > 22< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < allSpecies.size(); ++i) {< / div >
< div class = "line" > < a id = "l00023" name = "l00023" > < / a > < span class = "lineno" > 23< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species = allSpecies[i];< / div >
< div class = "line" > < a id = "l00024" name = "l00024" > < / a > < span class = "lineno" > 24< / span > < span class = "keywordflow" > if< / span > (!composition.contains(species)) {< / div >
< div class = "line" > < a id = "l00025" name = "l00025" > < / a > < span class = "lineno" > 25< / span > Y[i] = 0.0; < span class = "comment" > // Species not in the composition, set to zero< / span > < / div >
< div class = "line" > < a id = "l00026" name = "l00026" > < / a > < span class = "lineno" > 26< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00027" name = "l00027" > < / a > < span class = "lineno" > 27< / span > Y[i] = composition.getMolarAbundance(species);< / div >
< div class = "line" > < a id = "l00028" name = "l00028" > < / a > < span class = "lineno" > 28< / span > }< / div >
< div class = "line" > < a id = "l00029" name = "l00029" > < / a > < span class = "lineno" > 29< / span > }< / div >
< div class = "line" > < a id = "l00030" name = "l00030" > < / a > < span class = "lineno" > 30< / span > < span class = "keywordflow" > return< / span > Y;< / div >
< div class = "line" > < a id = "l00031" name = "l00031" > < / a > < span class = "lineno" > 31< / span > }< / div >
< div class = "line" > < a id = "l00032" name = "l00032" > < / a > < span class = "lineno" > 32< / span > < / div >
< div class = "line" > < a id = "l00033" name = "l00033" > < / a > < span class = "lineno" > 33< / span > < span class = "keyword" > template< / span > < < span class = "keyword" > class< / span > T> < / div >
< div class = "line" > < a id = "l00034" name = "l00034" > < / a > < span class = "lineno" > 34< / span > < span class = "keywordtype" > void< / span > hash_combine(std::size_t& seed, < span class = "keyword" > const< / span > T& v) {< / div >
< div class = "line" > < a id = "l00035" name = "l00035" > < / a > < span class = "lineno" > 35< / span > std::hash< T> hashed;< / div >
< div class = "line" > < a id = "l00036" name = "l00036" > < / a > < span class = "lineno" > 36< / span > seed ^= hashed(v) + 0x9e3779b9 + (seed < < 6) + (seed > > 2);< / div >
< div class = "line" > < a id = "l00037" name = "l00037" > < / a > < span class = "lineno" > 37< / span > }< / div >
< div class = "line" > < a id = "l00038" name = "l00038" > < / a > < span class = "lineno" > 38< / span > < / div >
< div class = "line" > < a id = "l00039" name = "l00039" > < / a > < span class = "lineno" > 39< / span > std::vector< std::vector< size_t> > findConnectedComponentsBFS(< / div >
< div class = "line" > < a id = "l00040" name = "l00040" > < / a > < span class = "lineno" > 40< / span > < span class = "keyword" > const< / span > std::unordered_map< < span class = "keywordtype" > size_t< / span > , std::vector< size_t> > & graph,< / div >
< div class = "line" > < a id = "l00041" name = "l00041" > < / a > < span class = "lineno" > 41< / span > < span class = "keyword" > const< / span > std::vector< size_t> & nodes< / 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 > std::vector< std::vector< size_t> > components;< / div >
< div class = "line" > < a id = "l00044" name = "l00044" > < / a > < span class = "lineno" > 44< / span > std::unordered_set< size_t> visited;< / div >
< div class = "line" > < a id = "l00045" name = "l00045" > < / a > < span class = "lineno" > 45< / span > < / div >
< div class = "line" > < a id = "l00046" name = "l00046" > < / a > < span class = "lineno" > 46< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > & start_node : nodes) {< / div >
< div class = "line" > < a id = "l00047" name = "l00047" > < / a > < span class = "lineno" > 47< / span > < span class = "keywordflow" > if< / span > (visited.find(start_node) == visited.end()) {< / div >
< div class = "line" > < a id = "l00048" name = "l00048" > < / a > < span class = "lineno" > 48< / span > std::vector< size_t> current_component;< / div >
< div class = "line" > < a id = "l00049" name = "l00049" > < / a > < span class = "lineno" > 49< / span > std::queue< size_t> q;< / div >
< div class = "line" > < a id = "l00050" name = "l00050" > < / a > < span class = "lineno" > 50< / span > < / div >
< div class = "line" > < a id = "l00051" name = "l00051" > < / a > < span class = "lineno" > 51< / span > q.push(start_node);< / div >
< div class = "line" > < a id = "l00052" name = "l00052" > < / a > < span class = "lineno" > 52< / span > visited.insert(start_node);< / div >
< div class = "line" > < a id = "l00053" name = "l00053" > < / a > < span class = "lineno" > 53< / span > < / div >
< div class = "line" > < a id = "l00054" name = "l00054" > < / a > < span class = "lineno" > 54< / span > < span class = "keywordflow" > while< / span > (!q.empty()) {< / div >
< div class = "line" > < a id = "l00055" name = "l00055" > < / a > < span class = "lineno" > 55< / span > < span class = "keywordtype" > size_t< / span > u = q.front();< / div >
< div class = "line" > < a id = "l00056" name = "l00056" > < / a > < span class = "lineno" > 56< / span > q.pop();< / div >
< div class = "line" > < a id = "l00057" name = "l00057" > < / a > < span class = "lineno" > 57< / span > current_component.push_back(u);< / div >
< div class = "line" > < a id = "l00058" name = "l00058" > < / a > < span class = "lineno" > 58< / span > < / div >
< div class = "line" > < a id = "l00059" name = "l00059" > < / a > < span class = "lineno" > 59< / span > < span class = "keywordflow" > if< / span > (graph.count(u)) {< / div >
< div class = "line" > < a id = "l00060" name = "l00060" > < / a > < span class = "lineno" > 60< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & v : graph.at(u)) {< / div >
< div class = "line" > < a id = "l00061" name = "l00061" > < / a > < span class = "lineno" > 61< / span > < span class = "keywordflow" > if< / span > (visited.find(v) == visited.end()) {< / div >
< div class = "line" > < a id = "l00062" name = "l00062" > < / a > < span class = "lineno" > 62< / span > visited.insert(v);< / div >
< div class = "line" > < a id = "l00063" name = "l00063" > < / a > < span class = "lineno" > 63< / span > q.push(v);< / div >
< div class = "line" > < a id = "l00064" name = "l00064" > < / a > < span class = "lineno" > 64< / span > }< / div >
< div class = "line" > < a id = "l00065" name = "l00065" > < / a > < span class = "lineno" > 65< / span > }< / div >
< div class = "line" > < a id = "l00066" name = "l00066" > < / a > < span class = "lineno" > 66< / span > }< / div >
< div class = "line" > < a id = "l00067" name = "l00067" > < / a > < span class = "lineno" > 67< / span > }< / div >
< div class = "line" > < a id = "l00068" name = "l00068" > < / a > < span class = "lineno" > 68< / span > components.push_back(current_component);< / div >
< div class = "line" > < a id = "l00069" name = "l00069" > < / a > < span class = "lineno" > 69< / span > }< / div >
< div class = "line" > < a id = "l00070" name = "l00070" > < / a > < span class = "lineno" > 70< / span > }< / div >
< div class = "line" > < a id = "l00071" name = "l00071" > < / a > < span class = "lineno" > 71< / span > < span class = "keywordflow" > return< / span > components;< / div >
< div class = "line" > < a id = "l00072" name = "l00072" > < / a > < span class = "lineno" > 72< / span > }< / div >
< div class = "line" > < a id = "l00073" name = "l00073" > < / a > < span class = "lineno" > 73< / span > < / div >
< div class = "line" > < a id = "l00074" name = "l00074" > < / a > < span class = "lineno" > 74< / span > < span class = "keyword" > struct < / span > SpeciesSetIntersection {< / div >
< div class = "line" > < a id = "l00075" name = "l00075" > < / a > < span class = "lineno" > 75< / span > < span class = "keyword" > const< / span > Species species;< / div >
< div class = "line" > < a id = "l00076" name = "l00076" > < / a > < span class = "lineno" > 76< / span > std::size_t count;< / div >
< div class = "line" > < a id = "l00077" name = "l00077" > < / a > < span class = "lineno" > 77< / span > };< / div >
< div class = "line" > < a id = "l00078" name = "l00078" > < / a > < span class = "lineno" > 78< / span > < / div >
< div class = "line" > < a id = "l00079" name = "l00079" > < / a > < span class = "lineno" > 79< / span > std::expected< SpeciesSetIntersection, std::string> get_intersection_info (< / div >
< div class = "line" > < a id = "l00080" name = "l00080" > < / a > < span class = "lineno" > 80< / span > < span class = "keyword" > const< / span > std::unordered_set< Species> & setA,< / div >
< div class = "line" > < a id = "l00081" name = "l00081" > < / a > < span class = "lineno" > 81< / span > < span class = "keyword" > const< / span > std::unordered_set< Species> & setB< / div >
< div class = "line" > < a id = "l00082" name = "l00082" > < / a > < span class = "lineno" > 82< / span > ) {< / div >
< div class = "line" > < a id = "l00083" name = "l00083" > < / a > < span class = "lineno" > 83< / span > < span class = "comment" > // Iterate over the smaller of the two< / span > < / div >
< div class = "line" > < a id = "l00084" name = "l00084" > < / a > < span class = "lineno" > 84< / span > < span class = "keyword" > auto< / span > * outerSet = & setA;< / div >
< div class = "line" > < a id = "l00085" name = "l00085" > < / a > < span class = "lineno" > 85< / span > < span class = "keyword" > auto< / span > * innerSet = & setB;< / div >
< div class = "line" > < a id = "l00086" name = "l00086" > < / a > < span class = "lineno" > 86< / span > < span class = "keywordflow" > if< / span > (setA.size() > setB.size()) {< / div >
< div class = "line" > < a id = "l00087" name = "l00087" > < / a > < span class = "lineno" > 87< / span > outerSet = & setB;< / div >
< div class = "line" > < a id = "l00088" name = "l00088" > < / a > < span class = "lineno" > 88< / span > innerSet = & setA;< / div >
< div class = "line" > < a id = "l00089" name = "l00089" > < / a > < span class = "lineno" > 89< / span > }< / div >
< div class = "line" > < a id = "l00090" name = "l00090" > < / a > < span class = "lineno" > 90< / span > < / div >
< div class = "line" > < a id = "l00091" name = "l00091" > < / a > < span class = "lineno" > 91< / span > std::size_t matchCount = 0;< / div >
< div class = "line" > < a id = "l00092" name = "l00092" > < / a > < span class = "lineno" > 92< / span > < span class = "keyword" > const< / span > Species* firstMatch = < span class = "keyword" > nullptr< / span > ;< / div >
< div class = "line" > < a id = "l00093" name = "l00093" > < / a > < span class = "lineno" > 93< / span > < / div >
< div class = "line" > < a id = "l00094" name = "l00094" > < / a > < span class = "lineno" > 94< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > Species& sp : *outerSet) {< / div >
< div class = "line" > < a id = "l00095" name = "l00095" > < / a > < span class = "lineno" > 95< / span > < span class = "keywordflow" > if< / span > (innerSet-> contains(sp)) {< / div >
< div class = "line" > < a id = "l00096" name = "l00096" > < / a > < span class = "lineno" > 96< / span > < span class = "keywordflow" > if< / span > (matchCount == 0) {< / div >
< div class = "line" > < a id = "l00097" name = "l00097" > < / a > < span class = "lineno" > 97< / span > firstMatch = & sp;< / 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 > ++matchCount;< / div >
< div class = "line" > < a id = "l00100" name = "l00100" > < / a > < span class = "lineno" > 100< / span > < span class = "keywordflow" > if< / span > (matchCount > 1) {< / div >
< div class = "line" > < a id = "l00101" name = "l00101" > < / a > < span class = "lineno" > 101< / span > < span class = "keywordflow" > break< / span > ;< / div >
< div class = "line" > < a id = "l00102" name = "l00102" > < / a > < span class = "lineno" > 102< / span > }< / 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 > }< / div >
< div class = "line" > < a id = "l00105" name = "l00105" > < / a > < span class = "lineno" > 105< / span > < span class = "keywordflow" > if< / span > (!firstMatch) {< / div >
< div class = "line" > < a id = "l00106" name = "l00106" > < / a > < span class = "lineno" > 106< / span > < span class = "comment" > // No matches found< / span > < / div >
< div class = "line" > < a id = "l00107" name = "l00107" > < / a > < span class = "lineno" > 107< / span > < span class = "keywordflow" > return< / span > std::unexpected{< span class = "stringliteral" > " Intersection is empty" < / span > };< / div >
< div class = "line" > < a id = "l00108" name = "l00108" > < / a > < span class = "lineno" > 108< / span > }< / div >
< div class = "line" > < a id = "l00109" name = "l00109" > < / a > < span class = "lineno" > 109< / span > < span class = "keywordflow" > if< / span > (matchCount == 0) {< / div >
< div class = "line" > < a id = "l00110" name = "l00110" > < / a > < span class = "lineno" > 110< / span > < span class = "comment" > // No matches found< / span > < / div >
< div class = "line" > < a id = "l00111" name = "l00111" > < / a > < span class = "lineno" > 111< / span > < span class = "keywordflow" > return< / span > std::unexpected{< span class = "stringliteral" > " No intersection found" < / span > };< / div >
< div class = "line" > < a id = "l00112" name = "l00112" > < / a > < span class = "lineno" > 112< / span > }< / div >
< div class = "line" > < a id = "l00113" name = "l00113" > < / a > < span class = "lineno" > 113< / span > < / div >
< div class = "line" > < a id = "l00114" name = "l00114" > < / a > < span class = "lineno" > 114< / span > < span class = "comment" > // Return the first match and the count of matches< / span > < / div >
< div class = "line" > < a id = "l00115" name = "l00115" > < / a > < span class = "lineno" > 115< / span > < span class = "keywordflow" > return< / span > SpeciesSetIntersection{*firstMatch, matchCount};< / div >
< div class = "line" > < a id = "l00116" name = "l00116" > < / a > < span class = "lineno" > 116< / span > < / div >
< div class = "line" > < a id = "l00117" name = "l00117" > < / a > < span class = "lineno" > 117< / span > }< / 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 > < span class = "keywordtype" > bool< / span > has_distinct_reactant_and_product_species (< / div >
< div class = "line" > < a id = "l00120" name = "l00120" > < / a > < span class = "lineno" > 120< / span > < span class = "keyword" > const< / span > std::unordered_set< Species> & poolSpecies,< / div >
< div class = "line" > < a id = "l00121" name = "l00121" > < / a > < span class = "lineno" > 121< / span > < span class = "keyword" > const< / span > std::unordered_set< Species> & reactants,< / div >
< div class = "line" > < a id = "l00122" name = "l00122" > < / a > < span class = "lineno" > 122< / span > < span class = "keyword" > const< / span > std::unordered_set< Species> & products< / div >
< div class = "line" > < a id = "l00123" name = "l00123" > < / a > < span class = "lineno" > 123< / span > ) {< / div >
< div class = "line" > < a id = "l00124" name = "l00124" > < / a > < span class = "lineno" > 124< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > reactant_result = get_intersection_info(poolSpecies, reactants);< / div >
< div class = "line" > < a id = "l00125" name = "l00125" > < / a > < span class = "lineno" > 125< / span > < span class = "keywordflow" > if< / span > (!reactant_result) {< / div >
< div class = "line" > < a id = "l00126" name = "l00126" > < / a > < span class = "lineno" > 126< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > false< / span > ; < span class = "comment" > // No reactants found< / span > < / div >
< div class = "line" > < a id = "l00127" name = "l00127" > < / a > < span class = "lineno" > 127< / span > }< / div >
< div class = "line" > < a id = "l00128" name = "l00128" > < / a > < span class = "lineno" > 128< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > [reactantSample, reactantCount] = reactant_result.value();< / div >
< div class = "line" > < a id = "l00129" name = "l00129" > < / a > < span class = "lineno" > 129< / span > < / 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 > product_result = get_intersection_info(poolSpecies, products);< / div >
< div class = "line" > < a id = "l00131" name = "l00131" > < / a > < span class = "lineno" > 131< / span > < span class = "keywordflow" > if< / span > (!product_result) {< / div >
< div class = "line" > < a id = "l00132" name = "l00132" > < / a > < span class = "lineno" > 132< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > false< / span > ; < span class = "comment" > // No products found< / span > < / 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 > < / div >
< div class = "line" > < a id = "l00135" name = "l00135" > < / a > < span class = "lineno" > 135< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > [productSample, productCount] = product_result.value();< / div >
< div class = "line" > < a id = "l00136" name = "l00136" > < / a > < span class = "lineno" > 136< / span > < / div >
< div class = "line" > < a id = "l00137" name = "l00137" > < / a > < span class = "lineno" > 137< / span > < span class = "comment" > // If either side has ≥2 distinct matches, we can always pick< / span > < / div >
< div class = "line" > < a id = "l00138" name = "l00138" > < / a > < span class = "lineno" > 138< / span > < span class = "comment" > // one from each that differ.< / span > < / div >
< div class = "line" > < a id = "l00139" name = "l00139" > < / a > < span class = "lineno" > 139< / span > < span class = "keywordflow" > if< / span > (reactantCount > 1 || productCount > 1) {< / div >
< div class = "line" > < a id = "l00140" name = "l00140" > < / a > < span class = "lineno" > 140< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > true< / 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 > < / div >
< div class = "line" > < a id = "l00143" name = "l00143" > < / a > < span class = "lineno" > 143< / span > < span class = "comment" > // Exactly one match on each side → they must differ< / span > < / div >
< div class = "line" > < a id = "l00144" name = "l00144" > < / a > < span class = "lineno" > 144< / span > < span class = "keywordflow" > return< / span > reactantSample != productSample;< / div >
< div class = "line" > < a id = "l00145" name = "l00145" > < / a > < span class = "lineno" > 145< / span > }< / div >
< div class = "line" > < a id = "l00146" name = "l00146" > < / a > < span class = "lineno" > 146< / span > < / div >
< div class = "line" > < a id = "l00147" name = "l00147" > < / a > < span class = "lineno" > 147< / span > }< / div >
< div class = "line" > < a id = "l00148" name = "l00148" > < / a > < span class = "lineno" > 148< / span > < / div >
< div class = "line" > < a id = "l00149" name = "l00149" > < / a > < span class = "lineno" > 149< / span > < span class = "keyword" > namespace < / span > < a class = "code hl_namespace" href = "namespacegridfire.html" > gridfire< / a > {< / div >
< div class = "line" > < a id = "l00150" name = "l00150" > < / a > < span class = "lineno" > < a class = "line" href = "namespacegridfire.html#a8b632637f62614f509cde0e404a79054" > 150< / a > < / span > < span class = "keyword" > static< / span > < span class = "keywordtype" > int< / span > < a class = "code hl_variable" href = "namespacegridfire.html#a8b632637f62614f509cde0e404a79054" > s_operator_parens_called< / a > = 0;< / div >
< div class = "line" > < a id = "l00151" name = "l00151" > < / a > < span class = "lineno" > 151< / span > < span class = "keyword" > using < / span > fourdst::atomic::Species;< / div >
< div class = "line" > < a id = "l00152" name = "l00152" > < / a > < span class = "lineno" > 152< / span > < / div >
< div class = "foldopen" id = "foldopen00153" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00153" name = "l00153" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0df457c0f0f6f403a295335c84fd828f" > 153< / a > < / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0df457c0f0f6f403a295335c84fd828f" > MultiscalePartitioningEngineView::MultiscalePartitioningEngineView< / a > (< / div >
< div class = "line" > < a id = "l00154" name = "l00154" > < / a > < span class = "lineno" > 154< / span > < a class = "code hl_class" href = "classgridfire_1_1_graph_engine.html" > GraphEngine< / a > & baseEngine< / div >
< div class = "line" > < a id = "l00155" name = "l00155" > < / a > < span class = "lineno" > 155< / span > ) : < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > (baseEngine) {}< / div >
< / div >
< div class = "line" > < a id = "l00156" name = "l00156" > < / a > < span class = "lineno" > 156< / span > < / div >
< div class = "foldopen" id = "foldopen00157" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00157" name = "l00157" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a696f74f5135bbd62169b6577f92fee80" > 157< / a > < / span > < span class = "keyword" > const< / span > std::vector< Species> & < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a696f74f5135bbd62169b6577f92fee80" > MultiscalePartitioningEngineView::getNetworkSpecies< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00158" name = "l00158" > < / a > < span class = "lineno" > 158< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies();< / div >
< div class = "line" > < a id = "l00159" name = "l00159" > < / a > < span class = "lineno" > 159< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00160" name = "l00160" > < / a > < span class = "lineno" > 160< / span > < / div >
< div class = "foldopen" id = "foldopen00161" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00161" name = "l00161" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a716d7357e944e8394d8b8e0b5e7625eb" > 161< / 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_multiscale_partitioning_engine_view.html#a716d7357e944e8394d8b8e0b5e7625eb" > MultiscalePartitioningEngineView::calculateRHSAndEnergy< / a > (< / div >
< div class = "line" > < a id = "l00162" name = "l00162" > < / a > < span class = "lineno" > 162< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_full,< / div >
< div class = "line" > < a id = "l00163" name = "l00163" > < / a > < span class = "lineno" > 163< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00164" name = "l00164" > < / a > < span class = "lineno" > 164< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00165" name = "l00165" > < / a > < span class = "lineno" > 165< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00166" name = "l00166" > < / a > < span class = "lineno" > 166< / span > < span class = "keywordflow" > if< / span > (Y_full.size() != < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a696f74f5135bbd62169b6577f92fee80" > getNetworkSpecies< / a > ().size()) {< / div >
< div class = "line" > < a id = "l00167" name = "l00167" > < / a > < span class = "lineno" > 167< / span > LOG_ERROR(< / div >
< div class = "line" > < a id = "l00168" name = "l00168" > < / a > < span class = "lineno" > 168< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > ,< / div >
< div class = "line" > < a id = "l00169" name = "l00169" > < / a > < span class = "lineno" > 169< / span > < span class = "stringliteral" > " Y_full size ({}) does not match the number of species in the network ({})" < / span > ,< / div >
< div class = "line" > < a id = "l00170" name = "l00170" > < / a > < span class = "lineno" > 170< / span > Y_full.size(),< / div >
< div class = "line" > < a id = "l00171" name = "l00171" > < / a > < span class = "lineno" > 171< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a696f74f5135bbd62169b6577f92fee80" > getNetworkSpecies< / a > ().size()< / div >
< div class = "line" > < a id = "l00172" name = "l00172" > < / a > < span class = "lineno" > 172< / span > );< / div >
< div class = "line" > < a id = "l00173" name = "l00173" > < / a > < span class = "lineno" > 173< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " Y_full size does not match the number of species in the network. See logs for more details..." < / span > );< / div >
< div class = "line" > < a id = "l00174" name = "l00174" > < / a > < span class = "lineno" > 174< / span > }< / div >
< div class = "line" > < a id = "l00175" name = "l00175" > < / a > < span class = "lineno" > 175< / span > < / div >
< div class = "line" > < a id = "l00176" name = "l00176" > < / a > < span class = "lineno" > 176< / span > < span class = "comment" > // Check the cache to see if the network needs to be repartitioned. Note that the QSECacheKey manages binning of T9, rho, and Y_full to ensure that small changes (which would likely not result in a repartitioning) do not trigger a cache miss.< / span > < / div >
< div class = "line" > < a id = "l00177" name = "l00177" > < / a > < span class = "lineno" > 177< / span > < span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_q_s_e_cache_key.html" > QSECacheKey< / a > key(T9, rho, Y_full);< / div >
< div class = "line" > < a id = "l00178" name = "l00178" > < / a > < span class = "lineno" > 178< / span > < span class = "keywordflow" > if< / span > (! < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e" > m_qse_abundance_cache< / a > .contains(key)) {< / div >
< div class = "line" > < a id = "l00179" name = "l00179" > < / a > < span class = "lineno" > 179< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .miss(< a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505aafefea58639f78d7c750970bbad28420" > CacheStats::operators::CalculateRHSAndEnergy< / a > );< / div >
< div class = "line" > < a id = "l00180" name = "l00180" > < / a > < span class = "lineno" > 180< / span > LOG_ERROR(< / div >
< div class = "line" > < a id = "l00181" name = "l00181" > < / a > < span class = "lineno" > 181< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > ,< / div >
< div class = "line" > < a id = "l00182" name = "l00182" > < / a > < span class = "lineno" > 182< / span > < span class = "stringliteral" > " QSE abundance cache miss for T9 = {}, rho = {} (misses: {}, hits: {}). calculateRHSAndEnergy does not receive sufficient context to partition and stabilize the network. Throwing an error which should be caught by the caller and trigger a re-partition stage." < / span > ,< / div >
< div class = "line" > < a id = "l00183" name = "l00183" > < / a > < span class = "lineno" > 183< / span > T9,< / div >
< div class = "line" > < a id = "l00184" name = "l00184" > < / a > < span class = "lineno" > 184< / span > rho,< / div >
< div class = "line" > < a id = "l00185" name = "l00185" > < / a > < span class = "lineno" > 185< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .misses(),< / div >
< div class = "line" > < a id = "l00186" name = "l00186" > < / a > < span class = "lineno" > 186< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .hits()< / div >
< div class = "line" > < a id = "l00187" name = "l00187" > < / a > < span class = "lineno" > 187< / span > );< / div >
< div class = "line" > < a id = "l00188" name = "l00188" > < / a > < span class = "lineno" > 188< / span > < span class = "keywordflow" > return< / span > std::unexpected{< a class = "code hl_struct" href = "structgridfire_1_1expectations_1_1_stale_engine_error.html" > expectations::StaleEngineError< / a > (< a class = "code hl_enumvalue" href = "namespacegridfire_1_1expectations.html#aef568e2802c03adef56dbcb6511d66c7a109aa03c8823fcc0ab193b7e48664cbf" > expectations::StaleEngineErrorTypes::SYSTEM_RESIZED< / a > )};< / div >
< div class = "line" > < a id = "l00189" name = "l00189" > < / a > < span class = "lineno" > 189< / span > }< / div >
< div class = "line" > < a id = "l00190" name = "l00190" > < / a > < span class = "lineno" > 190< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .hit(< a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505aafefea58639f78d7c750970bbad28420" > CacheStats::operators::CalculateRHSAndEnergy< / a > );< / 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 > result = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .calculateRHSAndEnergy(Y_full, T9, rho);< / div >
< div class = "line" > < a id = "l00192" name = "l00192" > < / a > < span class = "lineno" > 192< / span > < span class = "keywordflow" > if< / span > (!result) {< / div >
< div class = "line" > < a id = "l00193" name = "l00193" > < / a > < span class = "lineno" > 193< / span > < span class = "keywordflow" > return< / span > std::unexpected{result.error()};< / div >
< div class = "line" > < a id = "l00194" name = "l00194" > < / a > < span class = "lineno" > 194< / span > }< / div >
< div class = "line" > < a id = "l00195" name = "l00195" > < / a > < span class = "lineno" > 195< / span > < span class = "keyword" > auto< / span > deriv = result.value();< / div >
< div class = "line" > < a id = "l00196" name = "l00196" > < / a > < span class = "lineno" > 196< / span > < / div >
< div class = "line" > < a id = "l00197" name = "l00197" > < / a > < span class = "lineno" > 197< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a53862719dd73f98bc69eecde090cf655" > m_algebraic_species_indices< / a > .size(); ++i) {< / div >
< div class = "line" > < a id = "l00198" name = "l00198" > < / a > < span class = "lineno" > 198< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > species_index = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a53862719dd73f98bc69eecde090cf655" > m_algebraic_species_indices< / a > [i];< / div >
< div class = "line" > < a id = "l00199" name = "l00199" > < / a > < span class = "lineno" > 199< / span > deriv.dydt[species_index] = 0.0; < span class = "comment" > // Fix the algebraic species to the equilibrium abundances we calculate.< / span > < / div >
< div class = "line" > < a id = "l00200" name = "l00200" > < / a > < span class = "lineno" > 200< / span > }< / div >
< div class = "line" > < a id = "l00201" name = "l00201" > < / a > < span class = "lineno" > 201< / span > < span class = "keywordflow" > return< / span > deriv;< / div >
< div class = "line" > < a id = "l00202" name = "l00202" > < / a > < span class = "lineno" > 202< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00203" name = "l00203" > < / a > < span class = "lineno" > 203< / span > < / div >
< div class = "foldopen" id = "foldopen00204" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00204" name = "l00204" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#acdf5ad8765290ea2b78170235aea391d" > 204< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#acdf5ad8765290ea2b78170235aea391d" > MultiscalePartitioningEngineView::generateJacobianMatrix< / a > (< / div >
< div class = "line" > < a id = "l00205" name = "l00205" > < / a > < span class = "lineno" > 205< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_full,< / div >
< div class = "line" > < a id = "l00206" name = "l00206" > < / a > < span class = "lineno" > 206< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00207" name = "l00207" > < / a > < span class = "lineno" > 207< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00208" name = "l00208" > < / a > < span class = "lineno" > 208< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00209" name = "l00209" > < / a > < span class = "lineno" > 209< / span > < span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_q_s_e_cache_key.html" > QSECacheKey< / a > key(T9, rho, Y_full);< / div >
< div class = "line" > < a id = "l00210" name = "l00210" > < / a > < span class = "lineno" > 210< / span > < span class = "keywordflow" > if< / span > (!< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e" > m_qse_abundance_cache< / a > .contains(key)) {< / div >
< div class = "line" > < a id = "l00211" name = "l00211" > < / a > < span class = "lineno" > 211< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .miss(< a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505a9e720102de6020a01552bc0e8935c566" > CacheStats::operators::GenerateJacobianMatrix< / a > );< / div >
< div class = "line" > < a id = "l00212" name = "l00212" > < / a > < span class = "lineno" > 212< / span > LOG_ERROR(< / div >
< div class = "line" > < a id = "l00213" name = "l00213" > < / a > < span class = "lineno" > 213< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > ,< / div >
< div class = "line" > < a id = "l00214" name = "l00214" > < / a > < span class = "lineno" > 214< / span > < span class = "stringliteral" > " QSE abundance cache miss for T9 = {}, rho = {} (misses: {}, hits: {}). generateJacobianMatrix does not receive sufficient context to partition and stabilize the network. Throwing an error which should be caught by the caller and trigger a re-partition stage." < / span > ,< / div >
< div class = "line" > < a id = "l00215" name = "l00215" > < / a > < span class = "lineno" > 215< / span > T9,< / div >
< div class = "line" > < a id = "l00216" name = "l00216" > < / a > < span class = "lineno" > 216< / span > rho,< / div >
< div class = "line" > < a id = "l00217" name = "l00217" > < / a > < span class = "lineno" > 217< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .misses(),< / div >
< div class = "line" > < a id = "l00218" name = "l00218" > < / a > < span class = "lineno" > 218< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .hits()< / div >
< div class = "line" > < a id = "l00219" name = "l00219" > < / a > < span class = "lineno" > 219< / span > );< / div >
< div class = "line" > < a id = "l00220" name = "l00220" > < / a > < span class = "lineno" > 220< / span > < span class = "keywordflow" > throw< / span > < a class = "code hl_class" href = "classgridfire_1_1exceptions_1_1_stale_engine_error.html" > exceptions::StaleEngineError< / a > (< span class = "stringliteral" > " QSE Cache Miss while lacking context for partitioning. This should be caught by the caller and trigger a re-partition stage." < / span > );< / div >
< div class = "line" > < a id = "l00221" name = "l00221" > < / a > < span class = "lineno" > 221< / span > }< / div >
< div class = "line" > < a id = "l00222" name = "l00222" > < / a > < span class = "lineno" > 222< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .hit(< a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505a9e720102de6020a01552bc0e8935c566" > CacheStats::operators::GenerateJacobianMatrix< / a > );< / div >
< div class = "line" > < a id = "l00223" name = "l00223" > < / a > < span class = "lineno" > 223< / span > < / div >
< div class = "line" > < a id = "l00224" name = "l00224" > < / a > < span class = "lineno" > 224< / span > < span class = "comment" > // TODO: Add sparsity pattern to this to prevent base engine from doing unnecessary work.< / span > < / div >
< div class = "line" > < a id = "l00225" name = "l00225" > < / a > < span class = "lineno" > 225< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .generateJacobianMatrix(Y_full, T9, rho);< / div >
< div class = "line" > < a id = "l00226" name = "l00226" > < / a > < span class = "lineno" > 226< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00227" name = "l00227" > < / a > < span class = "lineno" > 227< / span > < / div >
< div class = "foldopen" id = "foldopen00228" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00228" name = "l00228" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ac961484383e86d9712a424728e068633" > 228< / a > < / span > < span class = "keywordtype" > double< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ac961484383e86d9712a424728e068633" > MultiscalePartitioningEngineView::getJacobianMatrixEntry< / a > (< / div >
< div class = "line" > < a id = "l00229" name = "l00229" > < / a > < span class = "lineno" > 229< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > i_full,< / div >
< div class = "line" > < a id = "l00230" name = "l00230" > < / a > < span class = "lineno" > 230< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > j_full< / div >
< div class = "line" > < a id = "l00231" name = "l00231" > < / a > < span class = "lineno" > 231< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00232" name = "l00232" > < / a > < span class = "lineno" > 232< / span > < span class = "comment" > // // Check if the species we are differentiating with respect to is algebraic or dynamic. If it is algebraic we can reduce the work significantly...< / span > < / div >
< div class = "line" > < a id = "l00233" name = "l00233" > < / a > < span class = "lineno" > 233< / span > < span class = "comment" > // if (std::ranges::contains(m_algebraic_species_indices, j_full)) {< / span > < / div >
< div class = "line" > < a id = "l00234" name = "l00234" > < / a > < span class = "lineno" > 234< / span > < span class = "comment" > // const auto& species = m_baseEngine.getNetworkSpecies()[j_full];< / span > < / div >
< div class = "line" > < a id = "l00235" name = "l00235" > < / a > < span class = "lineno" > 235< / span > < span class = "comment" > // // If j is algebraic, we can return 0.0 since the Jacobian entry for algebraic species is always zero.< / span > < / div >
< div class = "line" > < a id = "l00236" name = "l00236" > < / a > < span class = "lineno" > 236< / span > < span class = "comment" > // return 0.0;< / span > < / div >
< div class = "line" > < a id = "l00237" name = "l00237" > < / a > < span class = "lineno" > 237< / span > < span class = "comment" > // }< / span > < / div >
< div class = "line" > < a id = "l00238" name = "l00238" > < / a > < span class = "lineno" > 238< / span > < span class = "comment" > // Otherwise we need to query the full jacobian< / span > < / div >
< div class = "line" > < a id = "l00239" name = "l00239" > < / a > < span class = "lineno" > 239< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getJacobianMatrixEntry(i_full, j_full);< / div >
< div class = "line" > < a id = "l00240" name = "l00240" > < / a > < span class = "lineno" > 240< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00241" name = "l00241" > < / a > < span class = "lineno" > 241< / span > < / div >
< div class = "foldopen" id = "foldopen00242" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00242" name = "l00242" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#abe76a46784b1ebc8ad67a9eec40d369a" > 242< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#abe76a46784b1ebc8ad67a9eec40d369a" > MultiscalePartitioningEngineView::generateStoichiometryMatrix< / a > () {< / div >
< div class = "line" > < a id = "l00243" name = "l00243" > < / a > < span class = "lineno" > 243< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .generateStoichiometryMatrix();< / div >
< div class = "line" > < a id = "l00244" name = "l00244" > < / a > < span class = "lineno" > 244< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00245" name = "l00245" > < / a > < span class = "lineno" > 245< / span > < / div >
< div class = "foldopen" id = "foldopen00246" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00246" name = "l00246" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a510b920dea726aef859ac1f6d051807e" > 246< / a > < / span > < span class = "keywordtype" > int< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a510b920dea726aef859ac1f6d051807e" > MultiscalePartitioningEngineView::getStoichiometryMatrixEntry< / a > (< / div >
< div class = "line" > < a id = "l00247" name = "l00247" > < / a > < span class = "lineno" > 247< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > speciesIndex,< / div >
< div class = "line" > < a id = "l00248" name = "l00248" > < / a > < span class = "lineno" > 248< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > int< / span > reactionIndex< / div >
< div class = "line" > < a id = "l00249" name = "l00249" > < / a > < span class = "lineno" > 249< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00250" name = "l00250" > < / a > < span class = "lineno" > 250< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getStoichiometryMatrixEntry(speciesIndex, reactionIndex);< / div >
< div class = "line" > < a id = "l00251" name = "l00251" > < / a > < span class = "lineno" > 251< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00252" name = "l00252" > < / a > < span class = "lineno" > 252< / span > < / div >
< div class = "foldopen" id = "foldopen00253" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00253" name = "l00253" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a79eb9c108d694a27ec913ed0143aa044" > 253< / a > < / span > < span class = "keywordtype" > double< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a79eb9c108d694a27ec913ed0143aa044" > MultiscalePartitioningEngineView::calculateMolarReactionFlow< / a > (< / div >
< div class = "line" > < a id = "l00254" name = "l00254" > < / a > < span class = "lineno" > 254< / 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 = "l00255" name = "l00255" > < / a > < span class = "lineno" > 255< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_full,< / div >
< div class = "line" > < a id = "l00256" name = "l00256" > < / a > < span class = "lineno" > 256< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00257" name = "l00257" > < / a > < span class = "lineno" > 257< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00258" name = "l00258" > < / a > < span class = "lineno" > 258< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00259" name = "l00259" > < / a > < span class = "lineno" > 259< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > key = < a class = "code hl_struct" href = "structgridfire_1_1_q_s_e_cache_key.html" > QSECacheKey< / a > (T9, rho, Y_full);< / div >
< div class = "line" > < a id = "l00260" name = "l00260" > < / a > < span class = "lineno" > 260< / span > < span class = "keywordflow" > if< / span > (!< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e" > m_qse_abundance_cache< / a > .contains(key)) {< / div >
< div class = "line" > < a id = "l00261" name = "l00261" > < / a > < span class = "lineno" > 261< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .miss(< a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505a03d2b9a7ab8b282118ff9e9e2e8c2894" > CacheStats::operators::CalculateMolarReactionFlow< / a > );< / div >
< div class = "line" > < a id = "l00262" name = "l00262" > < / a > < span class = "lineno" > 262< / span > LOG_ERROR(< / div >
< div class = "line" > < a id = "l00263" name = "l00263" > < / a > < span class = "lineno" > 263< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > ,< / div >
< div class = "line" > < a id = "l00264" name = "l00264" > < / a > < span class = "lineno" > 264< / span > < span class = "stringliteral" > " QSE abundance cache miss for T9 = {}, rho = {} (misses: {}, hits: {}). calculateMolarReactionFlow does not receive sufficient context to partition and stabilize the network. Throwing an error which should be caught by the caller and trigger a re-partition stage." < / span > ,< / div >
< div class = "line" > < a id = "l00265" name = "l00265" > < / a > < span class = "lineno" > 265< / span > T9,< / div >
< div class = "line" > < a id = "l00266" name = "l00266" > < / a > < span class = "lineno" > 266< / span > rho,< / div >
< div class = "line" > < a id = "l00267" name = "l00267" > < / a > < span class = "lineno" > 267< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .misses(),< / div >
< div class = "line" > < a id = "l00268" name = "l00268" > < / a > < span class = "lineno" > 268< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .hits()< / div >
< div class = "line" > < a id = "l00269" name = "l00269" > < / a > < span class = "lineno" > 269< / span > );< / div >
< div class = "line" > < a id = "l00270" name = "l00270" > < / a > < span class = "lineno" > 270< / span > < span class = "keywordflow" > throw< / span > < a class = "code hl_class" href = "classgridfire_1_1exceptions_1_1_stale_engine_error.html" > exceptions::StaleEngineError< / a > (< span class = "stringliteral" > " QSE Cache Miss while lacking context for partitioning. This should be caught by the caller and trigger a re-partition stage." < / 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 > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .hit(< a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505a03d2b9a7ab8b282118ff9e9e2e8c2894" > CacheStats::operators::CalculateMolarReactionFlow< / a > );< / div >
< div class = "line" > < a id = "l00273" name = "l00273" > < / a > < span class = "lineno" > 273< / span > std::vector< double> Y_algebraic = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e" > m_qse_abundance_cache< / a > .at(key);< / div >
< div class = "line" > < a id = "l00274" name = "l00274" > < / a > < span class = "lineno" > 274< / span > < / div >
< div class = "line" > < a id = "l00275" name = "l00275" > < / a > < span class = "lineno" > 275< / span > assert(Y_algebraic.size() == < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a53862719dd73f98bc69eecde090cf655" > m_algebraic_species_indices< / a > .size());< / div >
< div class = "line" > < a id = "l00276" name = "l00276" > < / a > < span class = "lineno" > 276< / span > < / div >
< div class = "line" > < a id = "l00277" name = "l00277" > < / a > < span class = "lineno" > 277< / span > < span class = "comment" > // Fix the algebraic species to the equilibrium abundances we calculate.< / span > < / div >
< div class = "line" > < a id = "l00278" name = "l00278" > < / a > < span class = "lineno" > 278< / span > std::vector< double> Y_mutable = Y_full;< / div >
< div class = "line" > < a id = "l00279" name = "l00279" > < / a > < span class = "lineno" > 279< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & [index, Yi] : std::views::zip(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a53862719dd73f98bc69eecde090cf655" > m_algebraic_species_indices< / a > , Y_algebraic)) {< / div >
< div class = "line" > < a id = "l00280" name = "l00280" > < / a > < span class = "lineno" > 280< / span > Y_mutable[index] = Yi;< / div >
< div class = "line" > < a id = "l00281" name = "l00281" > < / a > < span class = "lineno" > 281< / span > < / 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 > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .calculateMolarReactionFlow(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > , Y_mutable, T9, rho);< / 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_multiscale_partitioning_engine_view.html#ad751f2c1306895ee74a61f2071ca96eb" > 286< / 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_multiscale_partitioning_engine_view.html#ad751f2c1306895ee74a61f2071ca96eb" > MultiscalePartitioningEngineView::getNetworkReactions< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00287" name = "l00287" > < / a > < span class = "lineno" > 287< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkReactions();< / div >
< div class = "line" > < a id = "l00288" name = "l00288" > < / a > < span class = "lineno" > 288< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00289" name = "l00289" > < / a > < span class = "lineno" > 289< / span > < / div >
< div class = "foldopen" id = "foldopen00290" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00290" name = "l00290" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#acb5fa7f03cd89b8c1b6b9ffdf3abb12e" > 290< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#acb5fa7f03cd89b8c1b6b9ffdf3abb12e" > MultiscalePartitioningEngineView::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 = "l00291" name = "l00291" > < / a > < span class = "lineno" > 291< / span > LOG_CRITICAL(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " setNetworkReactions is not supported in MultiscalePartitioningEngineView. Did you mean to call this on the base engine?" < / span > );< / div >
< div class = "line" > < a id = "l00292" name = "l00292" > < / a > < span class = "lineno" > 292< / span > < span class = "keywordflow" > throw< / span > < a class = "code hl_class" href = "classgridfire_1_1exceptions_1_1_unable_to_set_network_reactions_error.html" > exceptions::UnableToSetNetworkReactionsError< / a > (< span class = "stringliteral" > " setNetworkReactions is not supported in MultiscalePartitioningEngineView. Did you mean to call this on the base engine?" < / span > );< / 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_multiscale_partitioning_engine_view.html#a560612347bbd5b7b380e990624d01105" > 295< / 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_multiscale_partitioning_engine_view.html#a560612347bbd5b7b380e990624d01105" > MultiscalePartitioningEngineView::getSpeciesTimescales< / a > (< / div >
< div class = "line" > < a id = "l00296" name = "l00296" > < / a > < span class = "lineno" > 296< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l00297" name = "l00297" > < / a > < span class = "lineno" > 297< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00298" name = "l00298" > < / a > < span class = "lineno" > 298< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00299" name = "l00299" > < / a > < span class = "lineno" > 299< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00300" name = "l00300" > < / a > < span class = "lineno" > 300< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > key = < a class = "code hl_struct" href = "structgridfire_1_1_q_s_e_cache_key.html" > QSECacheKey< / a > (T9, rho, Y);< / div >
< div class = "line" > < a id = "l00301" name = "l00301" > < / a > < span class = "lineno" > 301< / span > < span class = "keywordflow" > if< / span > (!< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e" > m_qse_abundance_cache< / a > .contains(key)) {< / div >
< div class = "line" > < a id = "l00302" name = "l00302" > < / a > < span class = "lineno" > 302< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .miss(< a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505a8fa91234134aca6058a27b9a926fdb8a" > CacheStats::operators::GetSpeciesTimescales< / a > );< / div >
< div class = "line" > < a id = "l00303" name = "l00303" > < / a > < span class = "lineno" > 303< / span > LOG_ERROR(< / div >
< div class = "line" > < a id = "l00304" name = "l00304" > < / a > < span class = "lineno" > 304< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > ,< / div >
< div class = "line" > < a id = "l00305" name = "l00305" > < / a > < span class = "lineno" > 305< / span > < span class = "stringliteral" > " QSE abundance cache miss for T9 = {}, rho = {} (misses: {}, hits: {}). getSpeciesTimescales does not receive sufficient context to partition and stabilize the network. Throwing an error which should be caught by the caller and trigger a re-partition stage." < / span > ,< / div >
< div class = "line" > < a id = "l00306" name = "l00306" > < / a > < span class = "lineno" > 306< / span > T9,< / div >
< div class = "line" > < a id = "l00307" name = "l00307" > < / a > < span class = "lineno" > 307< / span > rho,< / div >
< div class = "line" > < a id = "l00308" name = "l00308" > < / a > < span class = "lineno" > 308< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .misses(),< / div >
< div class = "line" > < a id = "l00309" name = "l00309" > < / a > < span class = "lineno" > 309< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .hits()< / div >
< div class = "line" > < a id = "l00310" name = "l00310" > < / a > < span class = "lineno" > 310< / span > );< / div >
< div class = "line" > < a id = "l00311" name = "l00311" > < / a > < span class = "lineno" > 311< / span > < span class = "keywordflow" > throw< / span > < a class = "code hl_class" href = "classgridfire_1_1exceptions_1_1_stale_engine_error.html" > exceptions::StaleEngineError< / a > (< span class = "stringliteral" > " QSE Cache Miss while lacking context for partitioning. This should be caught by the caller and trigger a re-partition stage." < / span > );< / div >
< div class = "line" > < a id = "l00312" name = "l00312" > < / a > < span class = "lineno" > 312< / span > }< / div >
< div class = "line" > < a id = "l00313" name = "l00313" > < / a > < span class = "lineno" > 313< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .hit(< a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505a8fa91234134aca6058a27b9a926fdb8a" > CacheStats::operators::GetSpeciesTimescales< / a > );< / div >
< div class = "line" > < a id = "l00314" name = "l00314" > < / a > < span class = "lineno" > 314< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > result = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getSpeciesTimescales(Y, T9, rho);< / div >
< div class = "line" > < a id = "l00315" name = "l00315" > < / a > < span class = "lineno" > 315< / span > < span class = "keywordflow" > if< / span > (!result) {< / div >
< div class = "line" > < a id = "l00316" name = "l00316" > < / a > < span class = "lineno" > 316< / span > < span class = "keywordflow" > return< / span > std::unexpected{result.error()};< / div >
< div class = "line" > < a id = "l00317" name = "l00317" > < / a > < span class = "lineno" > 317< / span > }< / div >
< div class = "line" > < a id = "l00318" name = "l00318" > < / a > < span class = "lineno" > 318< / span > std::unordered_map< Species, double> speciesTimescales = result.value();< / div >
< div class = "line" > < a id = "l00319" name = "l00319" > < / a > < span class = "lineno" > 319< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & algebraicSpecies : < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a4656c05b8235dbf4ec698b03a716a8c8" > m_algebraic_species< / a > ) {< / div >
< div class = "line" > < a id = "l00320" name = "l00320" > < / a > < span class = "lineno" > 320< / span > speciesTimescales[algebraicSpecies] = std::numeric_limits< double> ::infinity(); < span class = "comment" > // Algebraic species have infinite timescales.< / span > < / div >
< div class = "line" > < a id = "l00321" name = "l00321" > < / a > < span class = "lineno" > 321< / span > }< / div >
< div class = "line" > < a id = "l00322" name = "l00322" > < / a > < span class = "lineno" > 322< / span > < span class = "keywordflow" > return< / span > speciesTimescales;< / div >
< div class = "line" > < a id = "l00323" name = "l00323" > < / a > < span class = "lineno" > 323< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00324" name = "l00324" > < / a > < span class = "lineno" > 324< / span > < / div >
< div class = "line" > < a id = "l00325" name = "l00325" > < / a > < span class = "lineno" > 325< / 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 = "foldopen00326" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00326" name = "l00326" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa38c367ef3c74d012ccd10521cd5a727" > 326< / a > < / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa38c367ef3c74d012ccd10521cd5a727" > MultiscalePartitioningEngineView::getSpeciesDestructionTimescales< / a > (< / div >
< div class = "line" > < a id = "l00327" name = "l00327" > < / a > < span class = "lineno" > 327< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l00328" name = "l00328" > < / a > < span class = "lineno" > 328< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00329" name = "l00329" > < / a > < span class = "lineno" > 329< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00330" name = "l00330" > < / a > < span class = "lineno" > 330< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00331" name = "l00331" > < / a > < span class = "lineno" > 331< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > key = < a class = "code hl_struct" href = "structgridfire_1_1_q_s_e_cache_key.html" > QSECacheKey< / a > (T9, rho, Y);< / div >
< div class = "line" > < a id = "l00332" name = "l00332" > < / a > < span class = "lineno" > 332< / span > < span class = "keywordflow" > if< / span > (!< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e" > m_qse_abundance_cache< / a > .contains(key)) {< / div >
< div class = "line" > < a id = "l00333" name = "l00333" > < / a > < span class = "lineno" > 333< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .miss(< a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505a9ee18f2e987928cdb1afa7645a082061" > CacheStats::operators::GetSpeciesDestructionTimescales< / a > );< / div >
< div class = "line" > < a id = "l00334" name = "l00334" > < / a > < span class = "lineno" > 334< / span > LOG_ERROR(< / div >
< div class = "line" > < a id = "l00335" name = "l00335" > < / a > < span class = "lineno" > 335< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > ,< / div >
< div class = "line" > < a id = "l00336" name = "l00336" > < / a > < span class = "lineno" > 336< / span > < span class = "stringliteral" > " QSE abundance cache miss for T9 = {}, rho = {} (misses: {}, hits: {}). getSpeciesDestructionTimescales does not receive sufficient context to partition and stabilize the network. Throwing an error which should be caught by the caller and trigger a re-partition stage." < / span > ,< / div >
< div class = "line" > < a id = "l00337" name = "l00337" > < / a > < span class = "lineno" > 337< / span > T9,< / div >
< div class = "line" > < a id = "l00338" name = "l00338" > < / a > < span class = "lineno" > 338< / span > rho,< / div >
< div class = "line" > < a id = "l00339" name = "l00339" > < / a > < span class = "lineno" > 339< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .misses(),< / div >
< div class = "line" > < a id = "l00340" name = "l00340" > < / a > < span class = "lineno" > 340< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .hits()< / div >
< div class = "line" > < a id = "l00341" name = "l00341" > < / a > < span class = "lineno" > 341< / span > );< / div >
< div class = "line" > < a id = "l00342" name = "l00342" > < / a > < span class = "lineno" > 342< / span > < span class = "keywordflow" > throw< / span > < a class = "code hl_class" href = "classgridfire_1_1exceptions_1_1_stale_engine_error.html" > exceptions::StaleEngineError< / a > (< span class = "stringliteral" > " QSE Cache Miss while lacking context for partitioning. This should be caught by the caller and trigger a re-partition stage." < / 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_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > m_cacheStats< / a > .hit(< a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505a9ee18f2e987928cdb1afa7645a082061" > CacheStats::operators::GetSpeciesDestructionTimescales< / a > );< / div >
< div class = "line" > < a id = "l00345" name = "l00345" > < / a > < span class = "lineno" > 345< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > result = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getSpeciesDestructionTimescales(Y, T9, rho);< / div >
< div class = "line" > < a id = "l00346" name = "l00346" > < / a > < span class = "lineno" > 346< / span > < span class = "keywordflow" > if< / span > (!result) {< / div >
< div class = "line" > < a id = "l00347" name = "l00347" > < / a > < span class = "lineno" > 347< / span > < span class = "keywordflow" > return< / span > std::unexpected{result.error()};< / div >
< div class = "line" > < a id = "l00348" name = "l00348" > < / a > < span class = "lineno" > 348< / span > }< / div >
< div class = "line" > < a id = "l00349" name = "l00349" > < / a > < span class = "lineno" > 349< / span > std::unordered_map< Species, double> speciesDestructionTimescales = result.value();< / div >
< div class = "line" > < a id = "l00350" name = "l00350" > < / a > < span class = "lineno" > 350< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & algebraicSpecies : < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a4656c05b8235dbf4ec698b03a716a8c8" > m_algebraic_species< / a > ) {< / div >
< div class = "line" > < a id = "l00351" name = "l00351" > < / a > < span class = "lineno" > 351< / span > speciesDestructionTimescales[algebraicSpecies] = std::numeric_limits< double> ::infinity(); < span class = "comment" > // Algebraic species have infinite destruction timescales.< / span > < / div >
< div class = "line" > < a id = "l00352" name = "l00352" > < / a > < span class = "lineno" > 352< / span > }< / div >
< div class = "line" > < a id = "l00353" name = "l00353" > < / a > < span class = "lineno" > 353< / span > < span class = "keywordflow" > return< / span > speciesDestructionTimescales;< / div >
< div class = "line" > < a id = "l00354" name = "l00354" > < / a > < span class = "lineno" > 354< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00355" name = "l00355" > < / a > < span class = "lineno" > 355< / span > < / div >
< div class = "foldopen" id = "foldopen00356" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00356" name = "l00356" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a6bee75b5a6e508e6eebf83f0d48c50b8" > 356< / a > < / span > fourdst::composition::Composition < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a6bee75b5a6e508e6eebf83f0d48c50b8" > MultiscalePartitioningEngineView::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 = "l00357" name = "l00357" > < / a > < span class = "lineno" > 357< / span > < span class = "keyword" > const< / span > fourdst::composition::Composition baseUpdatedComposition = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .update(netIn);< / div >
< div class = "line" > < a id = "l00358" name = "l00358" > < / a > < span class = "lineno" > 358< / span > < span class = "keywordtype" > double< / span > T9 = netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a5be0f5195a5cd1dd177b9fc5ab83a7be" > temperature< / a > / 1.0e9; < span class = "comment" > // Convert temperature from Kelvin to T9 (T9 = T / 1e9)< / span > < / div >
< div class = "line" > < a id = "l00359" name = "l00359" > < / a > < span class = "lineno" > 359< / span > < / div >
< div class = "line" > < a id = "l00360" name = "l00360" > < / a > < span class = "lineno" > 360< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > preKey = < a class = "code hl_struct" href = "structgridfire_1_1_q_s_e_cache_key.html" > QSECacheKey< / a > (< / div >
< div class = "line" > < a id = "l00361" name = "l00361" > < / a > < span class = "lineno" > 361< / span > T9,< / div >
< div class = "line" > < a id = "l00362" name = "l00362" > < / a > < span class = "lineno" > 362< / span > netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577" > density< / a > ,< / div >
< div class = "line" > < a id = "l00363" name = "l00363" > < / a > < span class = "lineno" > 363< / span > packCompositionToVector(baseUpdatedComposition, < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > )< / div >
< div class = "line" > < a id = "l00364" name = "l00364" > < / a > < span class = "lineno" > 364< / span > );< / div >
< div class = "line" > < a id = "l00365" name = "l00365" > < / a > < span class = "lineno" > 365< / span > < span class = "keywordflow" > if< / span > (< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e" > m_qse_abundance_cache< / a > .contains(preKey)) {< / div >
< div class = "line" > < a id = "l00366" name = "l00366" > < / a > < span class = "lineno" > 366< / span > < span class = "keywordflow" > return< / span > baseUpdatedComposition;< / div >
< div class = "line" > < a id = "l00367" name = "l00367" > < / a > < span class = "lineno" > 367< / span > }< / div >
< div class = "line" > < a id = "l00368" name = "l00368" > < / a > < span class = "lineno" > 368< / span > < a class = "code hl_struct" href = "structgridfire_1_1_net_in.html" > NetIn< / a > baseUpdatedNetIn = netIn;< / div >
< div class = "line" > < a id = "l00369" name = "l00369" > < / a > < span class = "lineno" > 369< / span > baseUpdatedNetIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1" > composition< / a > = baseUpdatedComposition;< / div >
< div class = "line" > < a id = "l00370" name = "l00370" > < / a > < span class = "lineno" > 370< / span > < span class = "keyword" > const< / span > fourdst::composition::Composition equilibratedComposition = < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a4bc879246c6fbd8633b05052858df51d" > equilibrateNetwork< / a > (baseUpdatedNetIn);< / div >
< div class = "line" > < a id = "l00371" name = "l00371" > < / a > < span class = "lineno" > 371< / span > std::vector< double> Y_algebraic(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a53862719dd73f98bc69eecde090cf655" > m_algebraic_species_indices< / a > .size(), 0.0);< / div >
< div class = "line" > < a id = "l00372" name = "l00372" > < / a > < span class = "lineno" > 372< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a53862719dd73f98bc69eecde090cf655" > m_algebraic_species_indices< / a > .size(); ++i) {< / div >
< div class = "line" > < a id = "l00373" name = "l00373" > < / a > < span class = "lineno" > 373< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > species_index = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a53862719dd73f98bc69eecde090cf655" > m_algebraic_species_indices< / a > [i];< / div >
< div class = "line" > < a id = "l00374" name = "l00374" > < / a > < span class = "lineno" > 374< / span > Y_algebraic[i] = equilibratedComposition.getMolarAbundance(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies()[species_index]);< / div >
< div class = "line" > < a id = "l00375" name = "l00375" > < / a > < span class = "lineno" > 375< / span > }< / div >
< div class = "line" > < a id = "l00376" name = "l00376" > < / a > < span class = "lineno" > 376< / span > < / div >
< div class = "line" > < a id = "l00377" name = "l00377" > < / a > < span class = "lineno" > 377< / span > < span class = "comment" > // We store the algebraic abundances in the cache for both pre- and post-conditions to avoid recalculating them.< / span > < / div >
< div class = "line" > < a id = "l00378" name = "l00378" > < / a > < span class = "lineno" > 378< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e" > m_qse_abundance_cache< / a > [preKey] = Y_algebraic;< / div >
< div class = "line" > < a id = "l00379" name = "l00379" > < / a > < span class = "lineno" > 379< / span > < / div >
< div class = "line" > < a id = "l00380" name = "l00380" > < / a > < span class = "lineno" > 380< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > postKey = < a class = "code hl_struct" href = "structgridfire_1_1_q_s_e_cache_key.html" > QSECacheKey< / a > (< / div >
< div class = "line" > < a id = "l00381" name = "l00381" > < / a > < span class = "lineno" > 381< / span > T9,< / div >
< div class = "line" > < a id = "l00382" name = "l00382" > < / a > < span class = "lineno" > 382< / span > netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577" > density< / a > ,< / div >
< div class = "line" > < a id = "l00383" name = "l00383" > < / a > < span class = "lineno" > 383< / span > packCompositionToVector(equilibratedComposition, < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > )< / div >
< div class = "line" > < a id = "l00384" name = "l00384" > < / a > < span class = "lineno" > 384< / span > );< / div >
< div class = "line" > < a id = "l00385" name = "l00385" > < / a > < span class = "lineno" > 385< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e" > m_qse_abundance_cache< / a > [postKey] = Y_algebraic;< / div >
< div class = "line" > < a id = "l00386" name = "l00386" > < / a > < span class = "lineno" > 386< / span > < / div >
< div class = "line" > < a id = "l00387" name = "l00387" > < / a > < span class = "lineno" > 387< / span > < span class = "keywordflow" > return< / span > equilibratedComposition;< / div >
< div class = "line" > < a id = "l00388" name = "l00388" > < / a > < span class = "lineno" > 388< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00389" name = "l00389" > < / a > < span class = "lineno" > 389< / span > < / div >
< div class = "foldopen" id = "foldopen00390" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00390" name = "l00390" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ae7847959fc5af2b83f5446dd73567b46" > 390< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ae7847959fc5af2b83f5446dd73567b46" > MultiscalePartitioningEngineView::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 = "l00391" name = "l00391" > < / a > < span class = "lineno" > 391< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > key = < a class = "code hl_struct" href = "structgridfire_1_1_q_s_e_cache_key.html" > QSECacheKey< / a > (< / div >
< div class = "line" > < a id = "l00392" name = "l00392" > < / a > < span class = "lineno" > 392< / span > netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a5be0f5195a5cd1dd177b9fc5ab83a7be" > temperature< / a > ,< / div >
< div class = "line" > < a id = "l00393" name = "l00393" > < / a > < span class = "lineno" > 393< / span > netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577" > density< / a > ,< / div >
< div class = "line" > < a id = "l00394" name = "l00394" > < / a > < span class = "lineno" > 394< / span > packCompositionToVector(netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1" > composition< / a > , < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > )< / div >
< div class = "line" > < a id = "l00395" name = "l00395" > < / a > < span class = "lineno" > 395< / span > );< / div >
< div class = "line" > < a id = "l00396" name = "l00396" > < / a > < span class = "lineno" > 396< / span > < span class = "keywordflow" > if< / span > (< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e" > m_qse_abundance_cache< / a > .contains(key)) {< / div >
< div class = "line" > < a id = "l00397" name = "l00397" > < / a > < span class = "lineno" > 397< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .isStale(netIn); < span class = "comment" > // The cache hit indicates the engine is not stale for the given conditions.< / span > < / div >
< div class = "line" > < a id = "l00398" name = "l00398" > < / a > < span class = "lineno" > 398< / span > }< / div >
< div class = "line" > < a id = "l00399" name = "l00399" > < / a > < span class = "lineno" > 399< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > true< / span > ;< / div >
< div class = "line" > < a id = "l00400" name = "l00400" > < / a > < span class = "lineno" > 400< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00401" name = "l00401" > < / a > < span class = "lineno" > 401< / span > < / div >
< div class = "foldopen" id = "foldopen00402" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00402" name = "l00402" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1a0c0a0ade632eb10f0eecab828a059f" > 402< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1a0c0a0ade632eb10f0eecab828a059f" > MultiscalePartitioningEngineView::setScreeningModel< / a > (< / div >
< div class = "line" > < a id = "l00403" name = "l00403" > < / a > < span class = "lineno" > 403< / span > < 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 = "l00404" name = "l00404" > < / a > < span class = "lineno" > 404< / span > ) {< / div >
< div class = "line" > < a id = "l00405" name = "l00405" > < / a > < span class = "lineno" > 405< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .setScreeningModel(model);< / div >
< div class = "line" > < a id = "l00406" name = "l00406" > < / a > < span class = "lineno" > 406< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00407" name = "l00407" > < / a > < span class = "lineno" > 407< / span > < / div >
< div class = "foldopen" id = "foldopen00408" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00408" name = "l00408" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7bfb4e6fec2f337a1dea69e3d4f1fc82" > 408< / 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_multiscale_partitioning_engine_view.html#a7bfb4e6fec2f337a1dea69e3d4f1fc82" > MultiscalePartitioningEngineView::getScreeningModel< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00409" name = "l00409" > < / a > < span class = "lineno" > 409< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getScreeningModel();< / div >
< div class = "line" > < a id = "l00410" name = "l00410" > < / a > < span class = "lineno" > 410< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00411" name = "l00411" > < / a > < span class = "lineno" > 411< / span > < / div >
< div class = "foldopen" id = "foldopen00412" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00412" name = "l00412" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a22bd1f0e821ed415611d75bac67063d1" > 412< / 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_multiscale_partitioning_engine_view.html#a22bd1f0e821ed415611d75bac67063d1" > MultiscalePartitioningEngineView::getBaseEngine< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00413" name = "l00413" > < / a > < span class = "lineno" > 413< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > ;< / div >
< div class = "line" > < a id = "l00414" name = "l00414" > < / a > < span class = "lineno" > 414< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00415" name = "l00415" > < / a > < span class = "lineno" > 415< / span > < / div >
< div class = "foldopen" id = "foldopen00416" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00416" name = "l00416" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#af13e764c118a6cc51847384e9c70e05b" > 416< / a > < / span > std::vector< std::vector< size_t> > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#af13e764c118a6cc51847384e9c70e05b" > MultiscalePartitioningEngineView::analyzeTimescalePoolConnectivity< / a > (< / div >
< div class = "line" > < a id = "l00417" name = "l00417" > < / a > < span class = "lineno" > 417< / span > < span class = "keyword" > const< / span > std::vector< std::vector< size_t> > & timescale_pools,< / div >
< div class = "line" > < a id = "l00418" name = "l00418" > < / a > < span class = "lineno" > 418< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l00419" name = "l00419" > < / a > < span class = "lineno" > 419< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00420" name = "l00420" > < / a > < span class = "lineno" > 420< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00421" name = "l00421" > < / a > < span class = "lineno" > 421< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00422" name = "l00422" > < / a > < span class = "lineno" > 422< / span > std::vector< std::vector< size_t> > final_connected_pools;< / div >
< div class = "line" > < a id = "l00423" name = "l00423" > < / a > < span class = "lineno" > 423< / span > < / div >
< div class = "line" > < a id = "l00424" name = "l00424" > < / a > < span class = "lineno" > 424< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & pool : timescale_pools) {< / div >
< div class = "line" > < a id = "l00425" name = "l00425" > < / a > < span class = "lineno" > 425< / span > < span class = "keywordflow" > if< / span > (pool.empty()) {< / div >
< div class = "line" > < a id = "l00426" name = "l00426" > < / a > < span class = "lineno" > 426< / span > < span class = "keywordflow" > continue< / span > ; < span class = "comment" > // Skip empty pools< / span > < / div >
< div class = "line" > < a id = "l00427" name = "l00427" > < / a > < span class = "lineno" > 427< / span > }< / div >
< div class = "line" > < a id = "l00428" name = "l00428" > < / a > < span class = "lineno" > 428< / span > < / div >
< div class = "line" > < a id = "l00429" name = "l00429" > < / a > < span class = "lineno" > 429< / span > < span class = "comment" > // For each timescale pool, we need to analyze connectivity.< / span > < / div >
< div class = "line" > < a id = "l00430" name = "l00430" > < / a > < span class = "lineno" > 430< / span > < span class = "keyword" > auto< / span > connectivity_graph = < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aae0865e361dfeb23984d70409fdd9f39" > buildConnectivityGraph< / a > (pool);< / div >
< div class = "line" > < a id = "l00431" name = "l00431" > < / a > < span class = "lineno" > 431< / span > < span class = "keyword" > auto< / span > components = findConnectedComponentsBFS(connectivity_graph, pool);< / div >
< div class = "line" > < a id = "l00432" name = "l00432" > < / a > < span class = "lineno" > 432< / span > final_connected_pools.insert(final_connected_pools.end(), components.begin(), components.end());< / div >
< div class = "line" > < a id = "l00433" name = "l00433" > < / a > < span class = "lineno" > 433< / span > }< / div >
< div class = "line" > < a id = "l00434" name = "l00434" > < / a > < span class = "lineno" > 434< / span > < span class = "keywordflow" > return< / span > final_connected_pools;< / div >
< div class = "line" > < a id = "l00435" name = "l00435" > < / a > < span class = "lineno" > 435< / span > < / div >
< div class = "line" > < a id = "l00436" name = "l00436" > < / a > < span class = "lineno" > 436< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00437" name = "l00437" > < / a > < span class = "lineno" > 437< / span > < / div >
< div class = "foldopen" id = "foldopen00438" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00438" name = "l00438" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d26945df5395b9317552a3989c42d1c" > 438< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d26945df5395b9317552a3989c42d1c" > MultiscalePartitioningEngineView::partitionNetwork< / a > (< / div >
< div class = "line" > < a id = "l00439" name = "l00439" > < / a > < span class = "lineno" > 439< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l00440" name = "l00440" > < / a > < span class = "lineno" > 440< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00441" name = "l00441" > < / a > < span class = "lineno" > 441< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00442" name = "l00442" > < / a > < span class = "lineno" > 442< / span > ) {< / div >
< div class = "line" > < a id = "l00443" name = "l00443" > < / a > < span class = "lineno" > 443< / span > < span class = "comment" > // --- Step 0. Clear previous state ---< / span > < / div >
< div class = "line" > < a id = "l00444" name = "l00444" > < / a > < span class = "lineno" > 444< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Partitioning network..." < / span > );< / div >
< div class = "line" > < a id = "l00445" name = "l00445" > < / a > < span class = "lineno" > 445< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Clearing previous state..." < / span > );< / div >
< div class = "line" > < a id = "l00446" name = "l00446" > < / a > < span class = "lineno" > 446< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b4aa04a1e641204e4fd82361b0e39c6" > m_qse_groups< / a > .clear();< / div >
< div class = "line" > < a id = "l00447" name = "l00447" > < / a > < span class = "lineno" > 447< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aec6126b5c4a397d090790d7b75f9f70f" > m_dynamic_species< / a > .clear();< / div >
< div class = "line" > < a id = "l00448" name = "l00448" > < / a > < span class = "lineno" > 448< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a38b4f0373c3bd81503889650c0bb69bb" > m_dynamic_species_indices< / a > .clear();< / div >
< div class = "line" > < a id = "l00449" name = "l00449" > < / a > < span class = "lineno" > 449< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a4656c05b8235dbf4ec698b03a716a8c8" > m_algebraic_species< / a > .clear();< / div >
< div class = "line" > < a id = "l00450" name = "l00450" > < / a > < span class = "lineno" > 450< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a53862719dd73f98bc69eecde090cf655" > m_algebraic_species_indices< / a > .clear();< / div >
< div class = "line" > < a id = "l00451" name = "l00451" > < / a > < span class = "lineno" > 451< / span > < / div >
< div class = "line" > < a id = "l00452" name = "l00452" > < / a > < span class = "lineno" > 452< / span > < span class = "comment" > // --- Step 1. Identify distinct timescale regions ---< / span > < / div >
< div class = "line" > < a id = "l00453" name = "l00453" > < / a > < span class = "lineno" > 453< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Identifying fast reactions..." < / span > );< / div >
< div class = "line" > < a id = "l00454" name = "l00454" > < / a > < span class = "lineno" > 454< / span > < span class = "keyword" > const< / span > std::vector< std::vector< size_t> > timescale_pools = < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ad4d29ee55f89384807616d1068797067" > partitionByTimescale< / a > (Y, T9, rho);< / div >
< div class = "line" > < a id = "l00455" name = "l00455" > < / a > < span class = "lineno" > 455< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Found {} timescale pools." < / span > , timescale_pools.size());< / div >
< div class = "line" > < a id = "l00456" name = "l00456" > < / a > < span class = "lineno" > 456< / span > < / div >
< div class = "line" > < a id = "l00457" name = "l00457" > < / a > < span class = "lineno" > 457< / span > < span class = "comment" > // --- Step 2. Select the mean slowest pool as the base dynamical group ---< / span > < / div >
< div class = "line" > < a id = "l00458" name = "l00458" > < / a > < span class = "lineno" > 458< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Identifying mean slowest pool..." < / span > );< / div >
< div class = "line" > < a id = "l00459" name = "l00459" > < / a > < span class = "lineno" > 459< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > mean_slowest_pool_index = < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a54ca8004fbd8d6d3ea6f67efeb5dbc8d" > identifyMeanSlowestPool< / a > (timescale_pools, Y, T9, rho);< / div >
< div class = "line" > < a id = "l00460" name = "l00460" > < / a > < span class = "lineno" > 460< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Mean slowest pool index: {}" < / span > , mean_slowest_pool_index);< / div >
< div class = "line" > < a id = "l00461" name = "l00461" > < / a > < span class = "lineno" > 461< / span > < / div >
< div class = "line" > < a id = "l00462" name = "l00462" > < / a > < span class = "lineno" > 462< / span > < span class = "comment" > // --- Step 3. Push the slowest pool into the dynamic species list ---< / span > < / div >
< div class = "line" > < a id = "l00463" name = "l00463" > < / a > < span class = "lineno" > 463< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a38b4f0373c3bd81503889650c0bb69bb" > m_dynamic_species_indices< / a > = timescale_pools[mean_slowest_pool_index];< / div >
< div class = "line" > < a id = "l00464" name = "l00464" > < / a > < span class = "lineno" > 464< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & index : < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a38b4f0373c3bd81503889650c0bb69bb" > m_dynamic_species_indices< / a > ) {< / div >
< div class = "line" > < a id = "l00465" name = "l00465" > < / a > < span class = "lineno" > 465< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aec6126b5c4a397d090790d7b75f9f70f" > m_dynamic_species< / a > .push_back(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies()[index]);< / div >
< div class = "line" > < a id = "l00466" name = "l00466" > < / a > < span class = "lineno" > 466< / span > }< / div >
< div class = "line" > < a id = "l00467" name = "l00467" > < / a > < span class = "lineno" > 467< / span > < / div >
< div class = "line" > < a id = "l00468" name = "l00468" > < / a > < span class = "lineno" > 468< / span > < span class = "comment" > // --- Step 4. Pack Candidate QSE Groups ---< / span > < / div >
< div class = "line" > < a id = "l00469" name = "l00469" > < / a > < span class = "lineno" > 469< / span > std::vector< std::vector< size_t> > candidate_pools;< / div >
< div class = "line" > < a id = "l00470" name = "l00470" > < / a > < span class = "lineno" > 470< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < timescale_pools.size(); ++i) {< / div >
< div class = "line" > < a id = "l00471" name = "l00471" > < / a > < span class = "lineno" > 471< / span > < span class = "keywordflow" > if< / span > (i == mean_slowest_pool_index) < span class = "keywordflow" > continue< / span > ; < span class = "comment" > // Skip the slowest pool< / span > < / div >
< div class = "line" > < a id = "l00472" name = "l00472" > < / a > < span class = "lineno" > 472< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Group {} with {} species identified for potential QSE." < / span > , i, timescale_pools[i].size());< / div >
< div class = "line" > < a id = "l00473" name = "l00473" > < / a > < span class = "lineno" > 473< / span > candidate_pools.push_back(timescale_pools[i]);< / div >
< div class = "line" > < a id = "l00474" name = "l00474" > < / a > < span class = "lineno" > 474< / span > }< / div >
< div class = "line" > < a id = "l00475" name = "l00475" > < / a > < span class = "lineno" > 475< / span > < / div >
< div class = "line" > < a id = "l00476" name = "l00476" > < / a > < span class = "lineno" > 476< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Preforming connectivity analysis on timescale pools..." < / span > );< / div >
< div class = "line" > < a id = "l00477" name = "l00477" > < / a > < span class = "lineno" > 477< / span > < span class = "keyword" > const< / span > std::vector< std::vector< size_t> > connected_pools = < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#af13e764c118a6cc51847384e9c70e05b" > analyzeTimescalePoolConnectivity< / a > (candidate_pools, Y, T9, rho);< / div >
< div class = "line" > < a id = "l00478" name = "l00478" > < / a > < span class = "lineno" > 478< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Found {} connected pools (compared to {} timescale pools) for QSE analysis." < / span > , connected_pools.size(), timescale_pools.size());< / div >
< div class = "line" > < a id = "l00479" name = "l00479" > < / a > < span class = "lineno" > 479< / span > < / div >
< div class = "line" > < a id = "l00480" name = "l00480" > < / a > < span class = "lineno" > 480< / span > < / div >
< div class = "line" > < a id = "l00481" name = "l00481" > < / a > < span class = "lineno" > 481< / span > < span class = "comment" > // --- Step 5. Identify potential seed species for each candidate pool ---< / span > < / div >
< div class = "line" > < a id = "l00482" name = "l00482" > < / a > < span class = "lineno" > 482< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Identifying potential seed species for candidate pools..." < / span > );< / div >
< div class = "line" > < a id = "l00483" name = "l00483" > < / a > < span class = "lineno" > 483< / span > < span class = "keyword" > const< / span > std::vector< QSEGroup> candidate_groups = < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ac206840057bac65b7f7738e6dfd1047a" > constructCandidateGroups< / a > (connected_pools, Y, T9, rho);< / div >
< div class = "line" > < a id = "l00484" name = "l00484" > < / a > < span class = "lineno" > 484< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Found {} candidate QSE groups for further analysis" < / span > , candidate_groups.size());< / div >
< div class = "line" > < a id = "l00485" name = "l00485" > < / a > < span class = "lineno" > 485< / span > < / div >
< div class = "line" > < a id = "l00486" name = "l00486" > < / a > < span class = "lineno" > 486< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Validating candidate groups with flux analysis..." < / span > );< / div >
< div class = "line" > < a id = "l00487" name = "l00487" > < / a > < span class = "lineno" > 487< / span > < span class = "keyword" > const< / span > std::vector< QSEGroup> validated_groups = < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa55ed182301d216264daae3e6dfd8917" > validateGroupsWithFluxAnalysis< / a > (candidate_groups, Y, T9, rho);< / div >
< div class = "line" > < a id = "l00488" name = "l00488" > < / a > < span class = "lineno" > 488< / span > LOG_TRACE_L1(< / div >
< div class = "line" > < a id = "l00489" name = "l00489" > < / a > < span class = "lineno" > 489< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > ,< / div >
< div class = "line" > < a id = "l00490" name = "l00490" > < / a > < span class = "lineno" > 490< / span > < span class = "stringliteral" > " Validated {} group(s) QSE groups. {}" < / span > ,< / div >
< div class = "line" > < a id = "l00491" name = "l00491" > < / a > < span class = "lineno" > 491< / span > validated_groups.size(),< / div >
< div class = "line" > < a id = "l00492" name = "l00492" > < / a > < span class = "lineno" > 492< / span > [& ]() -> std::string {< / div >
< div class = "line" > < a id = "l00493" name = "l00493" > < / a > < span class = "lineno" > 493< / span > std::stringstream ss;< / div >
< div class = "line" > < a id = "l00494" name = "l00494" > < / a > < span class = "lineno" > 494< / span > int count = 0;< / div >
< div class = "line" > < a id = "l00495" name = "l00495" > < / a > < span class = "lineno" > 495< / span > for (const auto& group : validated_groups) {< / div >
< div class = "line" > < a id = "l00496" name = "l00496" > < / a > < span class = "lineno" > 496< / span > ss < < < span class = "stringliteral" > " Group " < / span > < < count + 1;< / div >
< div class = "line" > < a id = "l00497" name = "l00497" > < / a > < span class = "lineno" > 497< / span > if (group.is_in_equilibrium) {< / div >
< div class = "line" > < a id = "l00498" name = "l00498" > < / a > < span class = "lineno" > 498< / span > ss < < < span class = "stringliteral" > " is in equilibrium" < / span > ;< / div >
< div class = "line" > < a id = "l00499" name = "l00499" > < / a > < span class = "lineno" > 499< / span > } else {< / div >
< div class = "line" > < a id = "l00500" name = "l00500" > < / a > < span class = "lineno" > 500< / span > ss < < < span class = "stringliteral" > " is not in equilibrium" < / span > ;< / div >
< div class = "line" > < a id = "l00501" name = "l00501" > < / a > < span class = "lineno" > 501< / span > }< / div >
< div class = "line" > < a id = "l00502" name = "l00502" > < / a > < span class = "lineno" > 502< / span > if (count < validated_groups.size() - 1) {< / div >
< div class = "line" > < a id = "l00503" name = "l00503" > < / a > < span class = "lineno" > 503< / span > ss < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l00504" name = "l00504" > < / a > < span class = "lineno" > 504< / span > }< / div >
< div class = "line" > < a id = "l00505" name = "l00505" > < / a > < span class = "lineno" > 505< / span > count++;< / div >
< div class = "line" > < a id = "l00506" name = "l00506" > < / a > < span class = "lineno" > 506< / span > }< / div >
< div class = "line" > < a id = "l00507" name = "l00507" > < / a > < span class = "lineno" > 507< / span > < span class = "keywordflow" > return< / span > ss.str();< / div >
< div class = "line" > < a id = "l00508" name = "l00508" > < / a > < span class = "lineno" > 508< / span > }()< / div >
< div class = "line" > < a id = "l00509" name = "l00509" > < / a > < span class = "lineno" > 509< / span > );< / div >
< div class = "line" > < a id = "l00510" name = "l00510" > < / a > < span class = "lineno" > 510< / span > < / div >
< div class = "line" > < a id = "l00511" name = "l00511" > < / a > < span class = "lineno" > 511< / span > m_qse_groups = std::move(validated_groups);< / div >
< div class = "line" > < a id = "l00512" name = "l00512" > < / a > < span class = "lineno" > 512< / span > LOG_TRACE_L1(m_logger, < span class = "stringliteral" > " Identified {} QSE groups." < / span > , m_qse_groups.size());< / div >
< div class = "line" > < a id = "l00513" name = "l00513" > < / a > < span class = "lineno" > 513< / span > < / div >
< div class = "line" > < a id = "l00514" name = "l00514" > < / a > < span class = "lineno" > 514< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & group : m_qse_groups) {< / div >
< div class = "line" > < a id = "l00515" name = "l00515" > < / a > < span class = "lineno" > 515< / span > < span class = "comment" > // Add algebraic species to the algebraic set< / span > < / div >
< div class = "line" > < a id = "l00516" name = "l00516" > < / a > < span class = "lineno" > 516< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & index : group.algebraic_indices) {< / div >
< div class = "line" > < a id = "l00517" name = "l00517" > < / a > < span class = "lineno" > 517< / span > < span class = "keywordflow" > if< / span > (std::ranges::find(m_algebraic_species_indices, index) == m_algebraic_species_indices.end()) {< / div >
< div class = "line" > < a id = "l00518" name = "l00518" > < / a > < span class = "lineno" > 518< / span > m_algebraic_species.push_back(m_baseEngine.getNetworkSpecies()[index]);< / div >
< div class = "line" > < a id = "l00519" name = "l00519" > < / a > < span class = "lineno" > 519< / span > m_algebraic_species_indices.push_back(index);< / div >
< div class = "line" > < a id = "l00520" name = "l00520" > < / a > < span class = "lineno" > 520< / span > < / div >
< div class = "line" > < a id = "l00521" name = "l00521" > < / a > < span class = "lineno" > 521< / span > }< / div >
< div class = "line" > < a id = "l00522" name = "l00522" > < / a > < span class = "lineno" > 522< / span > }< / div >
< div class = "line" > < a id = "l00523" name = "l00523" > < / a > < span class = "lineno" > 523< / span > }< / div >
< div class = "line" > < a id = "l00524" name = "l00524" > < / a > < span class = "lineno" > 524< / span > < / div >
< div class = "line" > < a id = "l00525" name = "l00525" > < / a > < span class = "lineno" > 525< / span > LOG_INFO(< / div >
< div class = "line" > < a id = "l00526" name = "l00526" > < / a > < span class = "lineno" > 526< / span > m_logger,< / div >
< div class = "line" > < a id = "l00527" name = "l00527" > < / a > < span class = "lineno" > 527< / span > < span class = "stringliteral" > " Partitioning complete. Found {} dynamic species, {} algebraic (QSE) species ({}) spread over {} QSE group{}." < / span > ,< / div >
< div class = "line" > < a id = "l00528" name = "l00528" > < / a > < span class = "lineno" > 528< / span > m_dynamic_species.size(),< / div >
< div class = "line" > < a id = "l00529" name = "l00529" > < / a > < span class = "lineno" > 529< / span > m_algebraic_species.size(),< / div >
< div class = "line" > < a id = "l00530" name = "l00530" > < / a > < span class = "lineno" > 530< / span > [& ]() -> std::string {< / div >
< div class = "line" > < a id = "l00531" name = "l00531" > < / a > < span class = "lineno" > 531< / span > std::stringstream ss;< / div >
< div class = "line" > < a id = "l00532" name = "l00532" > < / a > < span class = "lineno" > 532< / span > size_t count = 0;< / div >
< div class = "line" > < a id = "l00533" name = "l00533" > < / a > < span class = "lineno" > 533< / span > for (const auto& species : m_algebraic_species) {< / div >
< div class = "line" > < a id = "l00534" name = "l00534" > < / a > < span class = "lineno" > 534< / span > ss < < species.name();< / div >
< div class = "line" > < a id = "l00535" name = "l00535" > < / a > < span class = "lineno" > 535< / span > if (m_algebraic_species.size() > 1 & & count < m_algebraic_species.size() - 1) {< / div >
< div class = "line" > < a id = "l00536" name = "l00536" > < / a > < span class = "lineno" > 536< / span > ss < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l00537" name = "l00537" > < / a > < span class = "lineno" > 537< / span > }< / div >
< div class = "line" > < a id = "l00538" name = "l00538" > < / a > < span class = "lineno" > 538< / span > count++;< / div >
< div class = "line" > < a id = "l00539" name = "l00539" > < / a > < span class = "lineno" > 539< / span > }< / div >
< div class = "line" > < a id = "l00540" name = "l00540" > < / a > < span class = "lineno" > 540< / span > < span class = "keywordflow" > return< / span > ss.str();< / div >
< div class = "line" > < a id = "l00541" name = "l00541" > < / a > < span class = "lineno" > 541< / span > }(),< / div >
< div class = "line" > < a id = "l00542" name = "l00542" > < / a > < span class = "lineno" > 542< / span > m_qse_groups.size(),< / div >
< div class = "line" > < a id = "l00543" name = "l00543" > < / a > < span class = "lineno" > 543< / span > m_qse_groups.size() == 1 ? < span class = "stringliteral" > " " < / span > : < span class = "stringliteral" > " s" < / span > < / div >
< div class = "line" > < a id = "l00544" name = "l00544" > < / a > < span class = "lineno" > 544< / span > );< / div >
< div class = "line" > < a id = "l00545" name = "l00545" > < / a > < span class = "lineno" > 545< / span > < / div >
< div class = "line" > < a id = "l00546" name = "l00546" > < / a > < span class = "lineno" > 546< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00547" name = "l00547" > < / a > < span class = "lineno" > 547< / span > < / div >
< div class = "foldopen" id = "foldopen00548" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00548" name = "l00548" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a98b11ffe498846f5a3a72f08504346b7" > 548< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d26945df5395b9317552a3989c42d1c" > MultiscalePartitioningEngineView::partitionNetwork< / a > (< / div >
< div class = "line" > < a id = "l00549" name = "l00549" > < / a > < span class = "lineno" > 549< / span > < 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 = "l00550" name = "l00550" > < / a > < span class = "lineno" > 550< / span > ) {< / div >
< div class = "line" > < a id = "l00551" name = "l00551" > < / a > < span class = "lineno" > 551< / span > < span class = "keyword" > const< / span > std::vector< double> Y = packCompositionToVector(netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1" > composition< / a > , < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > );< / div >
< div class = "line" > < a id = "l00552" name = "l00552" > < / a > < span class = "lineno" > 552< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9 = netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a5be0f5195a5cd1dd177b9fc5ab83a7be" > temperature< / a > / 1e9; < span class = "comment" > // Convert temperature from Kelvin to T9 (T9 = T / 1e9)< / span > < / div >
< div class = "line" > < a id = "l00553" name = "l00553" > < / a > < span class = "lineno" > 553< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho = netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577" > density< / a > ; < span class = "comment" > // Density in g/cm^3< / span > < / div >
< div class = "line" > < a id = "l00554" name = "l00554" > < / a > < span class = "lineno" > 554< / span > < / div >
< div class = "line" > < a id = "l00555" name = "l00555" > < / a > < span class = "lineno" > 555< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d26945df5395b9317552a3989c42d1c" > partitionNetwork< / a > (Y, T9, rho);< / div >
< div class = "line" > < a id = "l00556" name = "l00556" > < / a > < span class = "lineno" > 556< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00557" name = "l00557" > < / a > < span class = "lineno" > 557< / span > < / div >
< div class = "foldopen" id = "foldopen00558" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00558" name = "l00558" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#acff59a15abac30eee16e9fa7b355fb18" > 558< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#acff59a15abac30eee16e9fa7b355fb18" > MultiscalePartitioningEngineView::exportToDot< / a > (< / div >
< div class = "line" > < a id = "l00559" name = "l00559" > < / a > < span class = "lineno" > 559< / span > < span class = "keyword" > const< / span > std::string & filename,< / div >
< div class = "line" > < a id = "l00560" name = "l00560" > < / a > < span class = "lineno" > 560< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l00561" name = "l00561" > < / a > < span class = "lineno" > 561< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00562" name = "l00562" > < / a > < span class = "lineno" > 562< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00563" name = "l00563" > < / a > < span class = "lineno" > 563< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00564" name = "l00564" > < / a > < span class = "lineno" > 564< / span > std::ofstream dotFile(filename);< / div >
< div class = "line" > < a id = "l00565" name = "l00565" > < / a > < span class = "lineno" > 565< / span > < span class = "keywordflow" > if< / span > (!dotFile.is_open()) {< / div >
< div class = "line" > < a id = "l00566" name = "l00566" > < / a > < span class = "lineno" > 566< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Failed to open file for writing: {}" < / span > , filename);< / div >
< div class = "line" > < a id = "l00567" name = "l00567" > < / a > < span class = "lineno" > 567< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(< span class = "stringliteral" > " Failed to open file for writing: " < / span > + filename);< / div >
< div class = "line" > < a id = "l00568" name = "l00568" > < / a > < span class = "lineno" > 568< / span > }< / div >
< div class = "line" > < a id = "l00569" name = "l00569" > < / a > < span class = "lineno" > 569< / span > < / div >
< div class = "line" > < a id = "l00570" name = "l00570" > < / a > < span class = "lineno" > 570< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & all_species = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies();< / div >
< div class = "line" > < a id = "l00571" name = "l00571" > < / a > < span class = "lineno" > 571< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & all_reactions = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkReactions();< / div >
< div class = "line" > < a id = "l00572" name = "l00572" > < / a > < span class = "lineno" > 572< / span > < / div >
< div class = "line" > < a id = "l00573" name = "l00573" > < / a > < span class = "lineno" > 573< / span > < span class = "comment" > // --- 1. Pre-computation and Categorization ---< / span > < / div >
< div class = "line" > < a id = "l00574" name = "l00574" > < / a > < span class = "lineno" > 574< / span > < / div >
< div class = "line" > < a id = "l00575" name = "l00575" > < / a > < span class = "lineno" > 575< / span > < span class = "comment" > // Categorize species into algebraic, seed, and core dynamic< / span > < / div >
< div class = "line" > < a id = "l00576" name = "l00576" > < / a > < span class = "lineno" > 576< / span > std::unordered_set< size_t> algebraic_indices;< / div >
< div class = "line" > < a id = "l00577" name = "l00577" > < / a > < span class = "lineno" > 577< / span > std::unordered_set< size_t> seed_indices;< / div >
< div class = "line" > < a id = "l00578" name = "l00578" > < / a > < span class = "lineno" > 578< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & group : < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b4aa04a1e641204e4fd82361b0e39c6" > m_qse_groups< / a > ) {< / div >
< div class = "line" > < a id = "l00579" name = "l00579" > < / a > < span class = "lineno" > 579< / span > < span class = "keywordflow" > if< / span > (group.is_in_equilibrium) {< / div >
< div class = "line" > < a id = "l00580" name = "l00580" > < / a > < span class = "lineno" > 580< / span > algebraic_indices.insert(group.algebraic_indices.begin(), group.algebraic_indices.end());< / div >
< div class = "line" > < a id = "l00581" name = "l00581" > < / a > < span class = "lineno" > 581< / span > seed_indices.insert(group.seed_indices.begin(), group.seed_indices.end());< / div >
< div class = "line" > < a id = "l00582" name = "l00582" > < / a > < span class = "lineno" > 582< / span > }< / div >
< div class = "line" > < a id = "l00583" name = "l00583" > < / a > < span class = "lineno" > 583< / span > }< / div >
< div class = "line" > < a id = "l00584" name = "l00584" > < / a > < span class = "lineno" > 584< / span > < / div >
< div class = "line" > < a id = "l00585" name = "l00585" > < / a > < span class = "lineno" > 585< / span > < span class = "comment" > // Calculate reaction flows and find min/max for logarithmic scaling of transparency< / span > < / div >
< div class = "line" > < a id = "l00586" name = "l00586" > < / a > < span class = "lineno" > 586< / span > std::vector< double> reaction_flows;< / div >
< div class = "line" > < a id = "l00587" name = "l00587" > < / a > < span class = "lineno" > 587< / span > reaction_flows.reserve(all_reactions.size());< / div >
< div class = "line" > < a id = "l00588" name = "l00588" > < / a > < span class = "lineno" > 588< / span > < span class = "keywordtype" > double< / span > min_log_flow = std::numeric_limits< double> ::max();< / div >
< div class = "line" > < a id = "l00589" name = "l00589" > < / a > < span class = "lineno" > 589< / span > < span class = "keywordtype" > double< / span > max_log_flow = std::numeric_limits< double> ::lowest();< / div >
< div class = "line" > < a id = "l00590" name = "l00590" > < / a > < span class = "lineno" > 590< / span > < / div >
< div class = "line" > < a id = "l00591" name = "l00591" > < / a > < span class = "lineno" > 591< / 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 > : all_reactions) {< / div >
< div class = "line" > < a id = "l00592" name = "l00592" > < / a > < span class = "lineno" > 592< / span > < span class = "keywordtype" > double< / span > flow = std::abs(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .calculateMolarReactionFlow(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > , Y, T9, rho));< / div >
< div class = "line" > < a id = "l00593" name = "l00593" > < / a > < span class = "lineno" > 593< / span > reaction_flows.push_back(flow);< / div >
< div class = "line" > < a id = "l00594" name = "l00594" > < / a > < span class = "lineno" > 594< / span > < span class = "keywordflow" > if< / span > (flow > 1e-99) { < span class = "comment" > // Avoid log(0)< / span > < / div >
< div class = "line" > < a id = "l00595" name = "l00595" > < / a > < span class = "lineno" > 595< / span > < span class = "keywordtype" > double< / span > log_flow = std::log10(flow);< / div >
< div class = "line" > < a id = "l00596" name = "l00596" > < / a > < span class = "lineno" > 596< / span > min_log_flow = std::min(min_log_flow, log_flow);< / div >
< div class = "line" > < a id = "l00597" name = "l00597" > < / a > < span class = "lineno" > 597< / span > max_log_flow = std::max(max_log_flow, log_flow);< / div >
< div class = "line" > < a id = "l00598" name = "l00598" > < / a > < span class = "lineno" > 598< / span > }< / div >
< div class = "line" > < a id = "l00599" name = "l00599" > < / a > < span class = "lineno" > 599< / span > }< / div >
< div class = "line" > < a id = "l00600" name = "l00600" > < / a > < span class = "lineno" > 600< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > log_flow_range = (max_log_flow > min_log_flow) ? (max_log_flow - min_log_flow) : 1.0;< / div >
< div class = "line" > < a id = "l00601" name = "l00601" > < / a > < span class = "lineno" > 601< / span > < / div >
< div class = "line" > < a id = "l00602" name = "l00602" > < / a > < span class = "lineno" > 602< / span > < span class = "comment" > // --- 2. Write DOT file content ---< / span > < / div >
< div class = "line" > < a id = "l00603" name = "l00603" > < / a > < span class = "lineno" > 603< / span > < / div >
< div class = "line" > < a id = "l00604" name = "l00604" > < / a > < span class = "lineno" > 604< / span > dotFile < < < span class = "stringliteral" > " digraph PartitionedNetwork {\n" < / span > ;< / div >
< div class = "line" > < a id = "l00605" name = "l00605" > < / a > < span class = "lineno" > 605< / span > dotFile < < < span class = "stringliteral" > " graph [rankdir=TB, splines=true, overlap=false, bgcolor=\" #f8fafc\" , label=\" Multiscale Partitioned Network View\" , fontname=\" Helvetica\" , fontsize=16, labeljust=l];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00606" name = "l00606" > < / a > < span class = "lineno" > 606< / span > dotFile < < < span class = "stringliteral" > " node [shape=circle, style=filled, fontname=\" Helvetica\" , width=0.8, fixedsize=true];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00607" name = "l00607" > < / a > < span class = "lineno" > 607< / span > dotFile < < < span class = "stringliteral" > " edge [fontname=\" Helvetica\" , fontsize=10];\n\n" < / span > ;< / div >
< div class = "line" > < a id = "l00608" name = "l00608" > < / a > < span class = "lineno" > 608< / span > < / div >
< div class = "line" > < a id = "l00609" name = "l00609" > < / a > < span class = "lineno" > 609< / span > < span class = "comment" > // --- Node Definitions ---< / span > < / div >
< div class = "line" > < a id = "l00610" name = "l00610" > < / a > < span class = "lineno" > 610< / span > < span class = "comment" > // Define all species nodes first, so they can be referenced by clusters and ranks later.< / span > < / div >
< div class = "line" > < a id = "l00611" name = "l00611" > < / a > < span class = "lineno" > 611< / span > dotFile < < < span class = "stringliteral" > " // --- Species Nodes Definitions ---\n" < / span > ;< / div >
< div class = "line" > < a id = "l00612" name = "l00612" > < / a > < span class = "lineno" > 612< / span > std::map< int, std::vector< std::string> > species_by_mass;< / div >
< div class = "line" > < a id = "l00613" name = "l00613" > < / a > < span class = "lineno" > 613< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < all_species.size(); ++i) {< / div >
< div class = "line" > < a id = "l00614" name = "l00614" > < / a > < span class = "lineno" > 614< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species = all_species[i];< / div >
< div class = "line" > < a id = "l00615" name = "l00615" > < / a > < span class = "lineno" > 615< / span > std::string fillcolor = < span class = "stringliteral" > " #f1f5f9" < / span > ; < span class = "comment" > // Default: Other/Uninvolved< / span > < / div >
< div class = "line" > < a id = "l00616" name = "l00616" > < / a > < span class = "lineno" > 616< / span > < / div >
< div class = "line" > < a id = "l00617" name = "l00617" > < / a > < span class = "lineno" > 617< / span > < span class = "comment" > // Determine color based on category. A species can be a seed and also in the core dynamic group.< / span > < / div >
< div class = "line" > < a id = "l00618" name = "l00618" > < / a > < span class = "lineno" > 618< / span > < span class = "comment" > // The more specific category (algebraic, then seed) takes precedence.< / span > < / div >
< div class = "line" > < a id = "l00619" name = "l00619" > < / a > < span class = "lineno" > 619< / span > < span class = "keywordflow" > if< / span > (algebraic_indices.contains(i)) {< / div >
< div class = "line" > < a id = "l00620" name = "l00620" > < / a > < span class = "lineno" > 620< / span > fillcolor = < span class = "stringliteral" > " #e0f2fe" < / span > ; < span class = "comment" > // Light Blue: Algebraic (in QSE)< / span > < / div >
< div class = "line" > < a id = "l00621" name = "l00621" > < / a > < span class = "lineno" > 621< / span > } < span class = "keywordflow" > else< / span > < span class = "keywordflow" > if< / span > (seed_indices.contains(i)) {< / div >
< div class = "line" > < a id = "l00622" name = "l00622" > < / a > < span class = "lineno" > 622< / span > fillcolor = < span class = "stringliteral" > " #a7f3d0" < / span > ; < span class = "comment" > // Light Green: Seed (Dynamic, feeds a QSE group)< / span > < / div >
< div class = "line" > < a id = "l00623" name = "l00623" > < / a > < span class = "lineno" > 623< / span > } < span class = "keywordflow" > else< / span > < span class = "keywordflow" > if< / span > (std::ranges::contains(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a38b4f0373c3bd81503889650c0bb69bb" > m_dynamic_species_indices< / a > , i)) {< / div >
< div class = "line" > < a id = "l00624" name = "l00624" > < / a > < span class = "lineno" > 624< / span > fillcolor = < span class = "stringliteral" > " #dcfce7" < / span > ; < span class = "comment" > // Pale Green: Core Dynamic< / span > < / div >
< div class = "line" > < a id = "l00625" name = "l00625" > < / a > < span class = "lineno" > 625< / span > }< / div >
< div class = "line" > < a id = "l00626" name = "l00626" > < / a > < span class = "lineno" > 626< / span > dotFile < < < span class = "stringliteral" > " \" " < / span > < < species.name() < < < span class = "stringliteral" > " \" [label=\" " < / span > < < species.name() < < < span class = "stringliteral" > " \" , fillcolor=\" " < / span > < < fillcolor < < < span class = "stringliteral" > " \" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00627" name = "l00627" > < / a > < span class = "lineno" > 627< / span > < / div >
< div class = "line" > < a id = "l00628" name = "l00628" > < / a > < span class = "lineno" > 628< / span > < span class = "comment" > // Group species by mass number for ranked layout.< / span > < / div >
< div class = "line" > < a id = "l00629" name = "l00629" > < / a > < span class = "lineno" > 629< / span > < span class = "comment" > // If species.a() returns incorrect values (e.g., 0 for many species), they will be grouped together here.< / span > < / div >
< div class = "line" > < a id = "l00630" name = "l00630" > < / a > < span class = "lineno" > 630< / span > species_by_mass[species.a()].push_back(std::string(species.name()));< / div >
< div class = "line" > < a id = "l00631" name = "l00631" > < / a > < span class = "lineno" > 631< / span > }< / div >
< div class = "line" > < a id = "l00632" name = "l00632" > < / a > < span class = "lineno" > 632< / span > dotFile < < < span class = "stringliteral" > " \n" < / span > ;< / div >
< div class = "line" > < a id = "l00633" name = "l00633" > < / a > < span class = "lineno" > 633< / span > < / div >
< div class = "line" > < a id = "l00634" name = "l00634" > < / a > < span class = "lineno" > 634< / span > < span class = "comment" > // --- Layout and Ranking ---< / span > < / div >
< div class = "line" > < a id = "l00635" name = "l00635" > < / a > < span class = "lineno" > 635< / span > < span class = "comment" > // Enforce a top-down layout based on mass number.< / span > < / div >
< div class = "line" > < a id = "l00636" name = "l00636" > < / a > < span class = "lineno" > 636< / span > dotFile < < < span class = "stringliteral" > " // --- Layout using Ranks ---\n" < / span > ;< / div >
< div class = "line" > < a id = "l00637" name = "l00637" > < / a > < span class = "lineno" > 637< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species_list: species_by_mass | std::views::values) {< / div >
< div class = "line" > < a id = "l00638" name = "l00638" > < / a > < span class = "lineno" > 638< / span > dotFile < < < span class = "stringliteral" > " { rank=same; " < / span > ;< / div >
< div class = "line" > < a id = "l00639" name = "l00639" > < / a > < span class = "lineno" > 639< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & name : species_list) {< / div >
< div class = "line" > < a id = "l00640" name = "l00640" > < / a > < span class = "lineno" > 640< / span > dotFile < < < span class = "stringliteral" > " \" " < / span > < < name < < < span class = "stringliteral" > " \" ; " < / span > ;< / div >
< div class = "line" > < a id = "l00641" name = "l00641" > < / a > < span class = "lineno" > 641< / span > }< / div >
< div class = "line" > < a id = "l00642" name = "l00642" > < / a > < span class = "lineno" > 642< / span > dotFile < < < span class = "stringliteral" > " }\n" < / span > ;< / div >
< div class = "line" > < a id = "l00643" name = "l00643" > < / a > < span class = "lineno" > 643< / span > }< / div >
< div class = "line" > < a id = "l00644" name = "l00644" > < / a > < span class = "lineno" > 644< / span > dotFile < < < span class = "stringliteral" > " \n" < / span > ;< / div >
< div class = "line" > < a id = "l00645" name = "l00645" > < / a > < span class = "lineno" > 645< / span > < / div >
< div class = "line" > < a id = "l00646" name = "l00646" > < / a > < span class = "lineno" > 646< / span > < span class = "comment" > // Chain by mass to get top down ordering< / span > < / div >
< div class = "line" > < a id = "l00647" name = "l00647" > < / a > < span class = "lineno" > 647< / span > dotFile < < < span class = "stringliteral" > " // --- Chain by Mass ---\n" < / span > ;< / div >
< div class = "line" > < a id = "l00648" name = "l00648" > < / a > < span class = "lineno" > 648< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & [mass, species_list] : species_by_mass) {< / div >
< div class = "line" > < a id = "l00649" name = "l00649" > < / a > < span class = "lineno" > 649< / span > < span class = "comment" > // Find the next largest mass in the species list< / span > < / div >
< div class = "line" > < a id = "l00650" name = "l00650" > < / a > < span class = "lineno" > 650< / span > < span class = "keywordtype" > int< / span > minLargestMass = std::numeric_limits< int> ::max();< / div >
< div class = "line" > < a id = "l00651" name = "l00651" > < / a > < span class = "lineno" > 651< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & next_mass: species_by_mass | std::views::keys) {< / div >
< div class = "line" > < a id = "l00652" name = "l00652" > < / a > < span class = "lineno" > 652< / span > < span class = "keywordflow" > if< / span > (next_mass > mass & & next_mass < minLargestMass) {< / div >
< div class = "line" > < a id = "l00653" name = "l00653" > < / a > < span class = "lineno" > 653< / span > minLargestMass = next_mass;< / div >
< div class = "line" > < a id = "l00654" name = "l00654" > < / a > < span class = "lineno" > 654< / span > }< / div >
< div class = "line" > < a id = "l00655" name = "l00655" > < / a > < span class = "lineno" > 655< / span > }< / div >
< div class = "line" > < a id = "l00656" name = "l00656" > < / a > < span class = "lineno" > 656< / span > < span class = "keywordflow" > if< / span > (minLargestMass != std::numeric_limits< int> ::max()) {< / div >
< div class = "line" > < a id = "l00657" name = "l00657" > < / a > < span class = "lineno" > 657< / span > < span class = "comment" > // Connect the current mass to the next largest mass< / span > < / div >
< div class = "line" > < a id = "l00658" name = "l00658" > < / a > < span class = "lineno" > 658< / span > dotFile < < < span class = "stringliteral" > " \" " < / span > < < species_list[0] < < < span class = "stringliteral" > " \" -> \" " < / span > < < species_by_mass[minLargestMass][0] < < < span class = "stringliteral" > " \" [style=invis];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00659" name = "l00659" > < / a > < span class = "lineno" > 659< / span > }< / div >
< div class = "line" > < a id = "l00660" name = "l00660" > < / a > < span class = "lineno" > 660< / span > }< / div >
< div class = "line" > < a id = "l00661" name = "l00661" > < / a > < span class = "lineno" > 661< / span > < / div >
< div class = "line" > < a id = "l00662" name = "l00662" > < / a > < span class = "lineno" > 662< / span > < span class = "comment" > // --- QSE Group Clusters ---< / span > < / div >
< div class = "line" > < a id = "l00663" name = "l00663" > < / a > < span class = "lineno" > 663< / span > < span class = "comment" > // Draw a prominent box around the algebraic species of each valid QSE group.< / span > < / div >
< div class = "line" > < a id = "l00664" name = "l00664" > < / a > < span class = "lineno" > 664< / span > dotFile < < < span class = "stringliteral" > " // --- QSE Group Clusters ---\n" < / span > ;< / div >
< div class = "line" > < a id = "l00665" name = "l00665" > < / a > < span class = "lineno" > 665< / span > < span class = "keywordtype" > int< / span > group_counter = 0;< / div >
< div class = "line" > < a id = "l00666" name = "l00666" > < / a > < span class = "lineno" > 666< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & group : < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b4aa04a1e641204e4fd82361b0e39c6" > m_qse_groups< / a > ) {< / div >
< div class = "line" > < a id = "l00667" name = "l00667" > < / a > < span class = "lineno" > 667< / span > < span class = "keywordflow" > if< / span > (!group.is_in_equilibrium || group.algebraic_indices.empty()) {< / div >
< div class = "line" > < a id = "l00668" name = "l00668" > < / a > < span class = "lineno" > 668< / span > < span class = "keywordflow" > continue< / span > ;< / div >
< div class = "line" > < a id = "l00669" name = "l00669" > < / a > < span class = "lineno" > 669< / span > }< / div >
< div class = "line" > < a id = "l00670" name = "l00670" > < / a > < span class = "lineno" > 670< / span > dotFile < < < span class = "stringliteral" > " subgraph cluster_qse_" < / span > < < group_counter++ < < < span class = "stringliteral" > " {\n" < / span > ;< / div >
< div class = "line" > < a id = "l00671" name = "l00671" > < / a > < span class = "lineno" > 671< / span > dotFile < < < span class = "stringliteral" > " label = \" QSE Group " < / span > < < group_counter < < < span class = "stringliteral" > " \" ;\n" < / span > ;< / div >
< div class = "line" > < a id = "l00672" name = "l00672" > < / a > < span class = "lineno" > 672< / span > dotFile < < < span class = "stringliteral" > " style = \" filled,rounded\" ;\n" < / span > ;< / div >
< div class = "line" > < a id = "l00673" name = "l00673" > < / a > < span class = "lineno" > 673< / span > dotFile < < < span class = "stringliteral" > " color = \" #38bdf8\" ;\n" < / span > ; < span class = "comment" > // A bright, visible blue for the border< / span > < / div >
< div class = "line" > < a id = "l00674" name = "l00674" > < / a > < span class = "lineno" > 674< / span > dotFile < < < span class = "stringliteral" > " penwidth = 2.0;\n" < / span > ; < span class = "comment" > // Thicker border< / span > < / div >
< div class = "line" > < a id = "l00675" name = "l00675" > < / a > < span class = "lineno" > 675< / span > dotFile < < < span class = "stringliteral" > " bgcolor = \" #f0f9ff80\" ;\n" < / span > ; < span class = "comment" > // Light blue fill with transparency< / span > < / div >
< div class = "line" > < a id = "l00676" name = "l00676" > < / a > < span class = "lineno" > 676< / span > dotFile < < < span class = "stringliteral" > " subgraph cluster_seed_" < / span > < < group_counter < < < span class = "stringliteral" > " {\n" < / span > ;< / div >
< div class = "line" > < a id = "l00677" name = "l00677" > < / a > < span class = "lineno" > 677< / span > dotFile < < < span class = "stringliteral" > " label = \" Seed Species\" ;\n" < / span > ;< / div >
< div class = "line" > < a id = "l00678" name = "l00678" > < / a > < span class = "lineno" > 678< / span > dotFile < < < span class = "stringliteral" > " style = \" filled,rounded\" ;\n" < / span > ;< / div >
< div class = "line" > < a id = "l00679" name = "l00679" > < / a > < span class = "lineno" > 679< / span > dotFile < < < span class = "stringliteral" > " color = \" #a7f3d0\" ;\n" < / span > ; < span class = "comment" > // Light green for seed species< / span > < / div >
< div class = "line" > < a id = "l00680" name = "l00680" > < / a > < span class = "lineno" > 680< / span > dotFile < < < span class = "stringliteral" > " penwidth = 1.5;\n" < / span > ; < span class = "comment" > // Thinner border for seed cluster< / span > < / div >
< div class = "line" > < a id = "l00681" name = "l00681" > < / a > < span class = "lineno" > 681< / span > std::vector< std::string> seed_node_ids;< / div >
< div class = "line" > < a id = "l00682" name = "l00682" > < / a > < span class = "lineno" > 682< / span > seed_node_ids.reserve(group.seed_indices.size());< / div >
< div class = "line" > < a id = "l00683" name = "l00683" > < / a > < span class = "lineno" > 683< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > species_idx : group.seed_indices) {< / div >
< div class = "line" > < a id = "l00684" name = "l00684" > < / a > < span class = "lineno" > 684< / span > std::stringstream ss;< / div >
< div class = "line" > < a id = "l00685" name = "l00685" > < / a > < span class = "lineno" > 685< / span > ss < < < span class = "stringliteral" > " node_" < / span > < < group_counter < < < span class = "stringliteral" > " _seed_" < / span > < < species_idx;< / div >
< div class = "line" > < a id = "l00686" name = "l00686" > < / a > < span class = "lineno" > 686< / span > dotFile < < < span class = "stringliteral" > " " < / span > < < ss.str() < < < span class = "stringliteral" > " [label=\" " < / span > < < all_species[species_idx].name() < < < span class = "stringliteral" > " \" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00687" name = "l00687" > < / a > < span class = "lineno" > 687< / span > seed_node_ids.push_back(ss.str());< / div >
< div class = "line" > < a id = "l00688" name = "l00688" > < / a > < span class = "lineno" > 688< / span > }< / div >
< div class = "line" > < a id = "l00689" name = "l00689" > < / a > < span class = "lineno" > 689< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < seed_node_ids.size() - 1; ++i) {< / div >
< div class = "line" > < a id = "l00690" name = "l00690" > < / a > < span class = "lineno" > 690< / span > dotFile < < < span class = "stringliteral" > " " < / span > < < seed_node_ids[i] < < < span class = "stringliteral" > " -> " < / span > < < seed_node_ids[i + 1] < < < span class = "stringliteral" > " [style=invis];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00691" name = "l00691" > < / a > < span class = "lineno" > 691< / span > }< / div >
< div class = "line" > < a id = "l00692" name = "l00692" > < / a > < span class = "lineno" > 692< / span > dotFile < < < span class = "stringliteral" > " }\n" < / span > ;< / div >
< div class = "line" > < a id = "l00693" name = "l00693" > < / a > < span class = "lineno" > 693< / span > dotFile < < < span class = "stringliteral" > " subgraph cluster_algebraic_" < / span > < < group_counter < < < span class = "stringliteral" > " {\n" < / span > ;< / div >
< div class = "line" > < a id = "l00694" name = "l00694" > < / a > < span class = "lineno" > 694< / span > dotFile < < < span class = "stringliteral" > " label = \" Algebraic Species\" ;\n" < / span > ;< / div >
< div class = "line" > < a id = "l00695" name = "l00695" > < / a > < span class = "lineno" > 695< / span > dotFile < < < span class = "stringliteral" > " style = \" filled,rounded\" ;\n" < / span > ;< / div >
< div class = "line" > < a id = "l00696" name = "l00696" > < / a > < span class = "lineno" > 696< / span > dotFile < < < span class = "stringliteral" > " color = \" #e0f2fe\" ;\n" < / span > ; < span class = "comment" > // Light blue for algebraic species< / span > < / div >
< div class = "line" > < a id = "l00697" name = "l00697" > < / a > < span class = "lineno" > 697< / span > dotFile < < < span class = "stringliteral" > " penwidth = 1.5;\n" < / span > ; < span class = "comment" > // Thinner border for algebraic cluster< / span > < / div >
< div class = "line" > < a id = "l00698" name = "l00698" > < / a > < span class = "lineno" > 698< / span > std::vector< std::string> algebraic_node_ids;< / div >
< div class = "line" > < a id = "l00699" name = "l00699" > < / a > < span class = "lineno" > 699< / span > algebraic_node_ids.reserve(group.algebraic_indices.size());< / div >
< div class = "line" > < a id = "l00700" name = "l00700" > < / a > < span class = "lineno" > 700< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > species_idx : group.algebraic_indices) {< / div >
< div class = "line" > < a id = "l00701" name = "l00701" > < / a > < span class = "lineno" > 701< / span > std::stringstream ss;< / div >
< div class = "line" > < a id = "l00702" name = "l00702" > < / a > < span class = "lineno" > 702< / span > ss < < < span class = "stringliteral" > " node_" < / span > < < group_counter < < < span class = "stringliteral" > " _algebraic_" < / span > < < species_idx;< / div >
< div class = "line" > < a id = "l00703" name = "l00703" > < / a > < span class = "lineno" > 703< / span > dotFile < < < span class = "stringliteral" > " " < / span > < < ss.str() < < < span class = "stringliteral" > " [label=\" " < / span > < < all_species[species_idx].name() < < < span class = "stringliteral" > " \" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00704" name = "l00704" > < / a > < span class = "lineno" > 704< / span > algebraic_node_ids.push_back(ss.str());< / div >
< div class = "line" > < a id = "l00705" name = "l00705" > < / a > < span class = "lineno" > 705< / span > }< / div >
< div class = "line" > < a id = "l00706" name = "l00706" > < / a > < span class = "lineno" > 706< / span > < span class = "comment" > // Make invisible edges between algebraic indices to keep them in top-down order< / span > < / div >
< div class = "line" > < a id = "l00707" name = "l00707" > < / a > < span class = "lineno" > 707< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < algebraic_node_ids.size() - 1; ++i) {< / div >
< div class = "line" > < a id = "l00708" name = "l00708" > < / a > < span class = "lineno" > 708< / span > dotFile < < < span class = "stringliteral" > " " < / span > < < algebraic_node_ids[i] < < < span class = "stringliteral" > " -> " < / span > < < algebraic_node_ids[i + 1] < < < span class = "stringliteral" > " [style=invis];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00709" name = "l00709" > < / a > < span class = "lineno" > 709< / span > }< / div >
< div class = "line" > < a id = "l00710" name = "l00710" > < / a > < span class = "lineno" > 710< / span > dotFile < < < span class = "stringliteral" > " }\n" < / span > ;< / div >
< div class = "line" > < a id = "l00711" name = "l00711" > < / a > < span class = "lineno" > 711< / span > dotFile < < < span class = "stringliteral" > " }\n" < / span > ;< / div >
< div class = "line" > < a id = "l00712" name = "l00712" > < / a > < span class = "lineno" > 712< / span > }< / div >
< div class = "line" > < a id = "l00713" name = "l00713" > < / a > < span class = "lineno" > 713< / span > dotFile < < < span class = "stringliteral" > " \n" < / span > ;< / div >
< div class = "line" > < a id = "l00714" name = "l00714" > < / a > < span class = "lineno" > 714< / span > < / div >
< div class = "line" > < a id = "l00715" name = "l00715" > < / a > < span class = "lineno" > 715< / span > < / div >
< div class = "line" > < a id = "l00716" name = "l00716" > < / a > < span class = "lineno" > 716< / span > < span class = "comment" > // --- Legend ---< / span > < / div >
< div class = "line" > < a id = "l00717" name = "l00717" > < / a > < span class = "lineno" > 717< / span > < span class = "comment" > // Add a legend to explain colors and conventions.< / span > < / div >
< div class = "line" > < a id = "l00718" name = "l00718" > < / a > < span class = "lineno" > 718< / span > dotFile < < < span class = "stringliteral" > " // --- Legend ---\n" < / span > ;< / div >
< div class = "line" > < a id = "l00719" name = "l00719" > < / a > < span class = "lineno" > 719< / span > dotFile < < < span class = "stringliteral" > " subgraph cluster_legend {\n" < / span > ;< / div >
< div class = "line" > < a id = "l00720" name = "l00720" > < / a > < span class = "lineno" > 720< / span > dotFile < < < span class = "stringliteral" > " rank = sink" < / span > ; < span class = "comment" > // Try to push the legend to the bottom< / span > < / div >
< div class = "line" > < a id = "l00721" name = "l00721" > < / a > < span class = "lineno" > 721< / span > dotFile < < < span class = "stringliteral" > " label = \" Legend\" ;\n" < / span > ;< / div >
< div class = "line" > < a id = "l00722" name = "l00722" > < / a > < span class = "lineno" > 722< / span > dotFile < < < span class = "stringliteral" > " bgcolor = \" #ffffff\" ;\n" < / span > ;< / div >
< div class = "line" > < a id = "l00723" name = "l00723" > < / a > < span class = "lineno" > 723< / span > dotFile < < < span class = "stringliteral" > " color = \" #e2e8f0\" ;\n" < / span > ;< / div >
< div class = "line" > < a id = "l00724" name = "l00724" > < / a > < span class = "lineno" > 724< / span > dotFile < < < span class = "stringliteral" > " node [shape=box, style=filled, fontname=\" Helvetica\" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00725" name = "l00725" > < / a > < span class = "lineno" > 725< / span > dotFile < < < span class = "stringliteral" > " key_core [label=\" Core Dynamic\" , fillcolor=\" #dcfce7\" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00726" name = "l00726" > < / a > < span class = "lineno" > 726< / span > dotFile < < < span class = "stringliteral" > " key_seed [label=\" Seed (Dynamic)\" , fillcolor=\" #a7f3d0\" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00727" name = "l00727" > < / a > < span class = "lineno" > 727< / span > dotFile < < < span class = "stringliteral" > " key_qse [label=\" Algebraic (QSE)\" , fillcolor=\" #e0f2fe\" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00728" name = "l00728" > < / a > < span class = "lineno" > 728< / span > dotFile < < < span class = "stringliteral" > " key_other [label=\" Other\" , fillcolor=\" #f1f5f9\" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00729" name = "l00729" > < / a > < span class = "lineno" > 729< / span > dotFile < < < span class = "stringliteral" > " key_info [label=\" Edge Opacity ~ log(Reaction Flow)\" , shape=plaintext];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00730" name = "l00730" > < / a > < span class = "lineno" > 730< / span > dotFile < < < span class = "stringliteral" > " " < / span > ;< span class = "comment" > // Use invisible edges to stack legend items vertically< / span > < / div >
< div class = "line" > < a id = "l00731" name = "l00731" > < / a > < span class = "lineno" > 731< / span > dotFile < < < span class = "stringliteral" > " key_core -> key_seed -> key_qse -> key_other -> key_info [style=invis];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00732" name = "l00732" > < / a > < span class = "lineno" > 732< / span > dotFile < < < span class = "stringliteral" > " }\n\n" < / span > ;< / div >
< div class = "line" > < a id = "l00733" name = "l00733" > < / a > < span class = "lineno" > 733< / span > < / div >
< div class = "line" > < a id = "l00734" name = "l00734" > < / a > < span class = "lineno" > 734< / span > < span class = "comment" > // --- Reaction Edges ---< / span > < / div >
< div class = "line" > < a id = "l00735" name = "l00735" > < / a > < span class = "lineno" > 735< / span > < span class = "comment" > // Draw edges with transparency scaled by the log of the molar reaction flow.< / span > < / div >
< div class = "line" > < a id = "l00736" name = "l00736" > < / a > < span class = "lineno" > 736< / span > dotFile < < < span class = "stringliteral" > " // --- Reaction Edges ---\n" < / span > ;< / div >
< div class = "line" > < a id = "l00737" name = "l00737" > < / a > < span class = "lineno" > 737< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < all_reactions.size(); ++i) {< / div >
< div class = "line" > < a id = "l00738" name = "l00738" > < / a > < span class = "lineno" > 738< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > = all_reactions[i];< / div >
< div class = "line" > < a id = "l00739" name = "l00739" > < / a > < span class = "lineno" > 739< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > flow = reaction_flows[i];< / div >
< div class = "line" > < a id = "l00740" name = "l00740" > < / a > < span class = "lineno" > 740< / span > < / div >
< div class = "line" > < a id = "l00741" name = "l00741" > < / a > < span class = "lineno" > 741< / span > < span class = "keywordflow" > if< / span > (flow < 1e-99) < span class = "keywordflow" > continue< / span > ; < span class = "comment" > // Don' t draw edges for negligible flows< / span > < / div >
< div class = "line" > < a id = "l00742" name = "l00742" > < / a > < span class = "lineno" > 742< / span > < / div >
< div class = "line" > < a id = "l00743" name = "l00743" > < / a > < span class = "lineno" > 743< / span > < span class = "keywordtype" > double< / span > log_flow_val = std::log10(flow);< / div >
< div class = "line" > < a id = "l00744" name = "l00744" > < / a > < span class = "lineno" > 744< / span > < span class = "keywordtype" > double< / span > norm_alpha = (log_flow_val - min_log_flow) / log_flow_range;< / div >
< div class = "line" > < a id = "l00745" name = "l00745" > < / a > < span class = "lineno" > 745< / span > < span class = "keywordtype" > int< / span > alpha_val = 0x30 + < span class = "keyword" > static_cast< < / span > < span class = "keywordtype" > int< / span > < span class = "keyword" > > < / span > (norm_alpha * (0xFF - 0x30)); < span class = "comment" > // Scale from ~20% to 100% opacity< / span > < / div >
< div class = "line" > < a id = "l00746" name = "l00746" > < / a > < span class = "lineno" > 746< / span > alpha_val = std::clamp(alpha_val, 0x00, 0xFF);< / div >
< div class = "line" > < a id = "l00747" name = "l00747" > < / a > < span class = "lineno" > 747< / span > < / div >
< div class = "line" > < a id = "l00748" name = "l00748" > < / a > < span class = "lineno" > 748< / span > std::stringstream alpha_hex;< / div >
< div class = "line" > < a id = "l00749" name = "l00749" > < / a > < span class = "lineno" > 749< / span > alpha_hex < < std::setw(2) < < std::setfill(< span class = "charliteral" > ' 0' < / span > ) < < std::hex < < alpha_val;< / div >
< div class = "line" > < a id = "l00750" name = "l00750" > < / a > < span class = "lineno" > 750< / span > std::string edge_color = < span class = "stringliteral" > " #475569" < / span > + alpha_hex.str();< / div >
< div class = "line" > < a id = "l00751" name = "l00751" > < / a > < span class = "lineno" > 751< / span > < / div >
< div class = "line" > < a id = "l00752" name = "l00752" > < / a > < span class = "lineno" > 752< / span > std::string reactionNodeId = < span class = "stringliteral" > " reaction_" < / span > + std::string(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id());< / div >
< div class = "line" > < a id = "l00753" name = "l00753" > < / a > < span class = "lineno" > 753< / span > dotFile < < < span class = "stringliteral" > " \" " < / span > < < reactionNodeId < < < span class = "stringliteral" > " \" [shape=point, fillcolor=black, width=0.05, height=0.05];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00754" name = "l00754" > < / a > < span class = "lineno" > 754< / 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 = "l00755" name = "l00755" > < / a > < span class = "lineno" > 755< / span > dotFile < < < span class = "stringliteral" > " \" " < / span > < < reactant.name() < < < span class = "stringliteral" > " \" -> \" " < / span > < < reactionNodeId < < < span class = "stringliteral" > " \" [color=\" " < / span > < < edge_color < < < span class = "stringliteral" > " \" , arrowhead=none];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00756" name = "l00756" > < / a > < span class = "lineno" > 756< / span > }< / div >
< div class = "line" > < a id = "l00757" name = "l00757" > < / a > < span class = "lineno" > 757< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & product : < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products()) {< / div >
< div class = "line" > < a id = "l00758" name = "l00758" > < / a > < span class = "lineno" > 758< / span > dotFile < < < span class = "stringliteral" > " \" " < / span > < < reactionNodeId < < < span class = "stringliteral" > " \" -> \" " < / span > < < product.name() < < < span class = "stringliteral" > " \" [color=\" " < / span > < < edge_color < < < span class = "stringliteral" > " \" ];\n" < / span > ;< / div >
< div class = "line" > < a id = "l00759" name = "l00759" > < / a > < span class = "lineno" > 759< / span > }< / div >
< div class = "line" > < a id = "l00760" name = "l00760" > < / a > < span class = "lineno" > 760< / span > dotFile < < < span class = "stringliteral" > " \n" < / span > ;< / div >
< div class = "line" > < a id = "l00761" name = "l00761" > < / a > < span class = "lineno" > 761< / span > }< / div >
< div class = "line" > < a id = "l00762" name = "l00762" > < / a > < span class = "lineno" > 762< / span > < / div >
< div class = "line" > < a id = "l00763" name = "l00763" > < / a > < span class = "lineno" > 763< / span > dotFile < < < span class = "stringliteral" > " }\n" < / span > ;< / div >
< div class = "line" > < a id = "l00764" name = "l00764" > < / a > < span class = "lineno" > 764< / span > dotFile.close();< / div >
< div class = "line" > < a id = "l00765" name = "l00765" > < / a > < span class = "lineno" > 765< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00766" name = "l00766" > < / a > < span class = "lineno" > 766< / span > < / div >
< div class = "line" > < a id = "l00767" name = "l00767" > < / a > < span class = "lineno" > 767< / span > < / div >
< div class = "foldopen" id = "foldopen00768" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00768" name = "l00768" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aada497e8df74a295fdf5df7d7cdf64e0" > 768< / a > < / span > std::vector< double> < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aada497e8df74a295fdf5df7d7cdf64e0" > MultiscalePartitioningEngineView::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 = "l00769" name = "l00769" > < / a > < span class = "lineno" > 769< / span > std::vector< double> Y(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aec6126b5c4a397d090790d7b75f9f70f" > m_dynamic_species< / a > .size(), 0.0); < span class = "comment" > // Initialize with zeros< / span > < / div >
< div class = "line" > < a id = "l00770" name = "l00770" > < / a > < span class = "lineno" > 770< / 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 = "l00771" name = "l00771" > < / a > < span class = "lineno" > 771< / span > Y[< a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a91d32b7197fcb27ee697d5bfde960f3f" > 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 = "l00772" name = "l00772" > < / a > < span class = "lineno" > 772< / span > }< / div >
< div class = "line" > < a id = "l00773" name = "l00773" > < / a > < span class = "lineno" > 773< / span > < span class = "keywordflow" > return< / span > Y; < span class = "comment" > // Return the vector of molar abundances< / span > < / div >
< div class = "line" > < a id = "l00774" name = "l00774" > < / a > < span class = "lineno" > 774< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00775" name = "l00775" > < / a > < span class = "lineno" > 775< / span > < / div >
< div class = "foldopen" id = "foldopen00776" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00776" name = "l00776" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c82e4e082d1c82b1b090ac9847c7c5e" > 776< / a > < / span > std::vector< Species> < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c82e4e082d1c82b1b090ac9847c7c5e" > MultiscalePartitioningEngineView::getFastSpecies< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00777" name = "l00777" > < / a > < span class = "lineno" > 777< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & all_species = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies();< / div >
< div class = "line" > < a id = "l00778" name = "l00778" > < / a > < span class = "lineno" > 778< / span > std::vector< Species> fast_species;< / div >
< div class = "line" > < a id = "l00779" name = "l00779" > < / a > < span class = "lineno" > 779< / span > fast_species.reserve(all_species.size() - < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aec6126b5c4a397d090790d7b75f9f70f" > m_dynamic_species< / a > .size());< / div >
< div class = "line" > < a id = "l00780" name = "l00780" > < / a > < span class = "lineno" > 780< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species : all_species) {< / div >
< div class = "line" > < a id = "l00781" name = "l00781" > < / a > < span class = "lineno" > 781< / span > < span class = "keyword" > auto< / span > it = std::ranges::find(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aec6126b5c4a397d090790d7b75f9f70f" > m_dynamic_species< / a > , species);< / div >
< div class = "line" > < a id = "l00782" name = "l00782" > < / a > < span class = "lineno" > 782< / span > < span class = "keywordflow" > if< / span > (it == < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aec6126b5c4a397d090790d7b75f9f70f" > m_dynamic_species< / a > .end()) {< / div >
< div class = "line" > < a id = "l00783" name = "l00783" > < / a > < span class = "lineno" > 783< / span > fast_species.push_back(species);< / div >
< div class = "line" > < a id = "l00784" name = "l00784" > < / a > < span class = "lineno" > 784< / span > }< / div >
< div class = "line" > < a id = "l00785" name = "l00785" > < / a > < span class = "lineno" > 785< / span > }< / div >
< div class = "line" > < a id = "l00786" name = "l00786" > < / a > < span class = "lineno" > 786< / span > < span class = "keywordflow" > return< / span > fast_species;< / div >
< div class = "line" > < a id = "l00787" name = "l00787" > < / a > < span class = "lineno" > 787< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00788" name = "l00788" > < / a > < span class = "lineno" > 788< / span > < / div >
< div class = "foldopen" id = "foldopen00789" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00789" name = "l00789" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1e04e8cb8c84b1bd033ac599accf0888" > 789< / a > < / span > < span class = "keyword" > const< / span > std::vector< Species> & < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1e04e8cb8c84b1bd033ac599accf0888" > MultiscalePartitioningEngineView::getDynamicSpecies< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00790" name = "l00790" > < / a > < span class = "lineno" > 790< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aec6126b5c4a397d090790d7b75f9f70f" > m_dynamic_species< / a > ;< / div >
< div class = "line" > < a id = "l00791" name = "l00791" > < / a > < span class = "lineno" > 791< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00792" name = "l00792" > < / a > < span class = "lineno" > 792< / span > < / div >
< div class = "foldopen" id = "foldopen00793" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00793" name = "l00793" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a05730ced13ac5331060ca011f0da6235" > 793< / 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_multiscale_partitioning_engine_view.html#a05730ced13ac5331060ca011f0da6235" > MultiscalePartitioningEngineView::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 = "l00794" name = "l00794" > < / a > < span class = "lineno" > 794< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .primeEngine(netIn);< / div >
< div class = "line" > < a id = "l00795" name = "l00795" > < / a > < span class = "lineno" > 795< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00796" name = "l00796" > < / a > < span class = "lineno" > 796< / span > < / div >
< div class = "foldopen" id = "foldopen00797" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00797" name = "l00797" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a4bc879246c6fbd8633b05052858df51d" > 797< / a > < / span > fourdst::composition::Composition < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a4bc879246c6fbd8633b05052858df51d" > MultiscalePartitioningEngineView::equilibrateNetwork< / a > (< / div >
< div class = "line" > < a id = "l00798" name = "l00798" > < / a > < span class = "lineno" > 798< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l00799" name = "l00799" > < / a > < span class = "lineno" > 799< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00800" name = "l00800" > < / a > < span class = "lineno" > 800< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00801" name = "l00801" > < / a > < span class = "lineno" > 801< / span > ) {< / div >
< div class = "line" > < a id = "l00802" name = "l00802" > < / a > < span class = "lineno" > 802< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d26945df5395b9317552a3989c42d1c" > partitionNetwork< / a > (Y, T9, rho);< / div >
< div class = "line" > < a id = "l00803" name = "l00803" > < / a > < span class = "lineno" > 803< / span > < span class = "keyword" > const< / span > std::vector< double> Y_equilibrated = < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c5fcb8e3396d74359fd601554c9ffa9" > solveQSEAbundances< / a > (Y, T9, rho);< / div >
< div class = "line" > < a id = "l00804" name = "l00804" > < / a > < span class = "lineno" > 804< / span > fourdst::composition::Composition composition;< / div >
< div class = "line" > < a id = "l00805" name = "l00805" > < / a > < span class = "lineno" > 805< / span > < / div >
< div class = "line" > < a id = "l00806" name = "l00806" > < / a > < span class = "lineno" > 806< / span > std::vector< std::string> symbols;< / div >
< div class = "line" > < a id = "l00807" name = "l00807" > < / a > < span class = "lineno" > 807< / span > symbols.reserve(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies().size());< / div >
< div class = "line" > < a id = "l00808" name = "l00808" > < / a > < span class = "lineno" > 808< / 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_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies()) {< / div >
< div class = "line" > < a id = "l00809" name = "l00809" > < / a > < span class = "lineno" > 809< / span > symbols.emplace_back(species.name());< / div >
< div class = "line" > < a id = "l00810" name = "l00810" > < / a > < span class = "lineno" > 810< / span > }< / div >
< div class = "line" > < a id = "l00811" name = "l00811" > < / a > < span class = "lineno" > 811< / span > composition.registerSymbol(symbols);< / div >
< div class = "line" > < a id = "l00812" name = "l00812" > < / a > < span class = "lineno" > 812< / span > < / div >
< div class = "line" > < a id = "l00813" name = "l00813" > < / a > < span class = "lineno" > 813< / span > std::vector< double> X;< / div >
< div class = "line" > < a id = "l00814" name = "l00814" > < / a > < span class = "lineno" > 814< / span > X.reserve(Y_equilibrated.size());< / div >
< div class = "line" > < a id = "l00815" name = "l00815" > < / a > < span class = "lineno" > 815< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < Y_equilibrated.size(); ++i) {< / div >
< div class = "line" > < a id = "l00816" name = "l00816" > < / a > < span class = "lineno" > 816< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > molarMass = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies()[i].mass();< / div >
< div class = "line" > < a id = "l00817" name = "l00817" > < / a > < span class = "lineno" > 817< / span > X.push_back(Y_equilibrated[i] * molarMass); < span class = "comment" > // Convert from molar abundance to mass fraction< / span > < / div >
< div class = "line" > < a id = "l00818" name = "l00818" > < / a > < span class = "lineno" > 818< / span > }< / div >
< div class = "line" > < a id = "l00819" name = "l00819" > < / a > < span class = "lineno" > 819< / span > < / div >
< div class = "line" > < a id = "l00820" name = "l00820" > < / a > < span class = "lineno" > 820< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < Y_equilibrated.size(); ++i) {< / div >
< div class = "line" > < a id = "l00821" name = "l00821" > < / a > < span class = "lineno" > 821< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies()[i];< / div >
< div class = "line" > < a id = "l00822" name = "l00822" > < / a > < span class = "lineno" > 822< / span > < span class = "keywordflow" > if< / span > (X[i] < 0.0 & & std::abs(X[i]) < 1e-20) {< / div >
< div class = "line" > < a id = "l00823" name = "l00823" > < / a > < span class = "lineno" > 823< / span > composition.setMassFraction(std::string(species.name()), 0.0); < span class = "comment" > // Avoid negative mass fractions< / span > < / div >
< div class = "line" > < a id = "l00824" name = "l00824" > < / a > < span class = "lineno" > 824< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00825" name = "l00825" > < / a > < span class = "lineno" > 825< / span > composition.setMassFraction(std::string(species.name()), X[i]);< / div >
< div class = "line" > < a id = "l00826" name = "l00826" > < / a > < span class = "lineno" > 826< / span > }< / div >
< div class = "line" > < a id = "l00827" name = "l00827" > < / a > < span class = "lineno" > 827< / span > }< / div >
< div class = "line" > < a id = "l00828" name = "l00828" > < / a > < span class = "lineno" > 828< / span > < / div >
< div class = "line" > < a id = "l00829" name = "l00829" > < / a > < span class = "lineno" > 829< / span > composition.finalize(< span class = "keyword" > true< / span > );< / div >
< div class = "line" > < a id = "l00830" name = "l00830" > < / a > < span class = "lineno" > 830< / span > < / div >
< div class = "line" > < a id = "l00831" name = "l00831" > < / a > < span class = "lineno" > 831< / span > < span class = "keywordflow" > return< / span > composition;< / div >
< div class = "line" > < a id = "l00832" name = "l00832" > < / a > < span class = "lineno" > 832< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00833" name = "l00833" > < / a > < span class = "lineno" > 833< / span > < / div >
< div class = "foldopen" id = "foldopen00834" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00834" name = "l00834" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b17f94386882ea1524147782b7a1ddc" > 834< / a > < / span > fourdst::composition::Composition < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a4bc879246c6fbd8633b05052858df51d" > MultiscalePartitioningEngineView::equilibrateNetwork< / a > (< / div >
< div class = "line" > < a id = "l00835" name = "l00835" > < / a > < span class = "lineno" > 835< / span > < 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 = "l00836" name = "l00836" > < / a > < span class = "lineno" > 836< / span > ) {< / div >
< div class = "line" > < a id = "l00837" name = "l00837" > < / a > < span class = "lineno" > 837< / span > < span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_priming_report.html" > PrimingReport< / a > primingReport = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .primeEngine(netIn);< / div >
< div class = "line" > < a id = "l00838" name = "l00838" > < / a > < span class = "lineno" > 838< / span > < span class = "keyword" > const< / span > std::vector< double> Y = packCompositionToVector(primingReport.< a class = "code hl_variable" href = "structgridfire_1_1_priming_report.html#a15032fd3354bd8fb383e13929bbd0ceb" > primedComposition< / a > , < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > );< / div >
< div class = "line" > < a id = "l00839" name = "l00839" > < / a > < span class = "lineno" > 839< / span > < / div >
< div class = "line" > < a id = "l00840" name = "l00840" > < / a > < span class = "lineno" > 840< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9 = netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a5be0f5195a5cd1dd177b9fc5ab83a7be" > temperature< / a > / 1e9; < span class = "comment" > // Convert temperature from Kelvin to T9 (T9 = T / 1e9)< / span > < / div >
< div class = "line" > < a id = "l00841" name = "l00841" > < / a > < span class = "lineno" > 841< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho = netIn.< a class = "code hl_variable" href = "structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577" > density< / a > ; < span class = "comment" > // Density in g/cm^3< / span > < / div >
< div class = "line" > < a id = "l00842" name = "l00842" > < / a > < span class = "lineno" > 842< / span > < / div >
< div class = "line" > < a id = "l00843" name = "l00843" > < / a > < span class = "lineno" > 843< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a4bc879246c6fbd8633b05052858df51d" > equilibrateNetwork< / a > (Y, T9, rho);< / div >
< div class = "line" > < a id = "l00844" name = "l00844" > < / a > < span class = "lineno" > 844< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00845" name = "l00845" > < / a > < span class = "lineno" > 845< / span > < / div >
< div class = "foldopen" id = "foldopen00846" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00846" name = "l00846" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a91d32b7197fcb27ee697d5bfde960f3f" > 846< / a > < / span > < span class = "keywordtype" > int< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a91d32b7197fcb27ee697d5bfde960f3f" > MultiscalePartitioningEngineView::getSpeciesIndex< / a > (< span class = "keyword" > const< / span > fourdst::atomic::Species & species)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00847" name = "l00847" > < / a > < span class = "lineno" > 847< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getSpeciesIndex(species);< / div >
< div class = "line" > < a id = "l00848" name = "l00848" > < / a > < span class = "lineno" > 848< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00849" name = "l00849" > < / a > < span class = "lineno" > 849< / span > < / div >
< div class = "foldopen" id = "foldopen00850" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l00850" name = "l00850" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ad4d29ee55f89384807616d1068797067" > 850< / a > < / span > std::vector< std::vector< size_t> > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ad4d29ee55f89384807616d1068797067" > MultiscalePartitioningEngineView::partitionByTimescale< / a > (< / div >
< div class = "line" > < a id = "l00851" name = "l00851" > < / a > < span class = "lineno" > 851< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_full,< / div >
< div class = "line" > < a id = "l00852" name = "l00852" > < / a > < span class = "lineno" > 852< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l00853" name = "l00853" > < / a > < span class = "lineno" > 853< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l00854" name = "l00854" > < / a > < span class = "lineno" > 854< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l00855" name = "l00855" > < / a > < span class = "lineno" > 855< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Partitioning by timescale..." < / span > );< / div >
< div class = "line" > < a id = "l00856" name = "l00856" > < / a > < span class = "lineno" > 856< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > result= < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getSpeciesDestructionTimescales(Y_full, T9, rho);< / div >
< div class = "line" > < a id = "l00857" name = "l00857" > < / a > < span class = "lineno" > 857< / span > < span class = "keywordflow" > if< / span > (!result) {< / div >
< div class = "line" > < a id = "l00858" name = "l00858" > < / a > < span class = "lineno" > 858< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Failed to get species timescales due to stale engine state" < / span > );< / div >
< div class = "line" > < a id = "l00859" name = "l00859" > < / a > < span class = "lineno" > 859< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l00860" name = "l00860" > < / a > < span class = "lineno" > 860< / span > < span class = "keywordflow" > throw< / span > < a class = "code hl_class" href = "classgridfire_1_1exceptions_1_1_stale_engine_error.html" > exceptions::StaleEngineError< / a > (< span class = "stringliteral" > " Failed to get species timescales due to stale engine state" < / span > );< / div >
< div class = "line" > < a id = "l00861" name = "l00861" > < / a > < span class = "lineno" > 861< / span > }< / div >
< div class = "line" > < a id = "l00862" name = "l00862" > < / a > < span class = "lineno" > 862< / span > std::unordered_map< Species, double> all_timescales = result.value();< / div >
< div class = "line" > < a id = "l00863" name = "l00863" > < / a > < span class = "lineno" > 863< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & all_species = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies();< / div >
< div class = "line" > < a id = "l00864" name = "l00864" > < / a > < span class = "lineno" > 864< / span > < / div >
< div class = "line" > < a id = "l00865" name = "l00865" > < / a > < span class = "lineno" > 865< / span > std::vector< std::pair< double, size_t> > sorted_timescales;< / div >
< div class = "line" > < a id = "l00866" name = "l00866" > < / a > < span class = "lineno" > 866< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < all_species.size(); ++i) {< / div >
< div class = "line" > < a id = "l00867" name = "l00867" > < / a > < span class = "lineno" > 867< / span > < span class = "keywordtype" > double< / span > timescale = all_timescales.at(all_species[i]);< / div >
< div class = "line" > < a id = "l00868" name = "l00868" > < / a > < span class = "lineno" > 868< / span > < span class = "keywordflow" > if< / span > (std::isfinite(timescale) & & timescale > 0) {< / div >
< div class = "line" > < a id = "l00869" name = "l00869" > < / a > < span class = "lineno" > 869< / span > sorted_timescales.push_back({timescale, i});< / div >
< div class = "line" > < a id = "l00870" name = "l00870" > < / a > < span class = "lineno" > 870< / span > }< / div >
< div class = "line" > < a id = "l00871" name = "l00871" > < / a > < span class = "lineno" > 871< / span > }< / div >
< div class = "line" > < a id = "l00872" name = "l00872" > < / a > < span class = "lineno" > 872< / span > < / div >
< div class = "line" > < a id = "l00873" name = "l00873" > < / a > < span class = "lineno" > 873< / span > std::ranges::sort(< / div >
< div class = "line" > < a id = "l00874" name = "l00874" > < / a > < span class = "lineno" > 874< / span > sorted_timescales,< / div >
< div class = "line" > < a id = "l00875" name = "l00875" > < / a > < span class = "lineno" > 875< / span > [](< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & a, < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & b)< / div >
< div class = "line" > < a id = "l00876" name = "l00876" > < / a > < span class = "lineno" > 876< / span > {< / div >
< div class = "line" > < a id = "l00877" name = "l00877" > < / a > < span class = "lineno" > 877< / span > < span class = "keywordflow" > return< / span > a.first > b.first;< / div >
< div class = "line" > < a id = "l00878" name = "l00878" > < / a > < span class = "lineno" > 878< / span > }< / div >
< div class = "line" > < a id = "l00879" name = "l00879" > < / a > < span class = "lineno" > 879< / span > );< / div >
< div class = "line" > < a id = "l00880" name = "l00880" > < / a > < span class = "lineno" > 880< / span > < / div >
< div class = "line" > < a id = "l00881" name = "l00881" > < / a > < span class = "lineno" > 881< / span > std::vector< std::vector< size_t> > final_pools;< / div >
< div class = "line" > < a id = "l00882" name = "l00882" > < / a > < span class = "lineno" > 882< / span > < span class = "keywordflow" > if< / span > (sorted_timescales.empty()) {< / div >
< div class = "line" > < a id = "l00883" name = "l00883" > < / a > < span class = "lineno" > 883< / span > < span class = "keywordflow" > return< / span > final_pools;< / div >
< div class = "line" > < a id = "l00884" name = "l00884" > < / a > < span class = "lineno" > 884< / span > }< / div >
< div class = "line" > < a id = "l00885" name = "l00885" > < / a > < span class = "lineno" > 885< / span > < / div >
< div class = "line" > < a id = "l00886" name = "l00886" > < / a > < span class = "lineno" > 886< / span > < span class = "keyword" > constexpr< / span > < span class = "keywordtype" > double< / span > ABSOLUTE_QSE_TIMESCALE_THRESHOLD = 3.156e7; < span class = "comment" > // Absolute threshold for QSE timescale (1 yr)< / span > < / div >
< div class = "line" > < a id = "l00887" name = "l00887" > < / a > < span class = "lineno" > 887< / span > < span class = "keyword" > constexpr< / span > < span class = "keywordtype" > double< / span > MIN_GAP_THRESHOLD = 2.0; < span class = "comment" > // Require a 2 order of magnitude gap< / span > < / div >
< div class = "line" > < a id = "l00888" name = "l00888" > < / a > < span class = "lineno" > 888< / span > < / div >
< div class = "line" > < a id = "l00889" name = "l00889" > < / a > < span class = "lineno" > 889< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Found {} species with finite timescales." < / span > , sorted_timescales.size());< / div >
< div class = "line" > < a id = "l00890" name = "l00890" > < / a > < span class = "lineno" > 890< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Absolute QSE timescale threshold: {} seconds ({} years)." < / span > ,< / div >
< div class = "line" > < a id = "l00891" name = "l00891" > < / a > < span class = "lineno" > 891< / span > ABSOLUTE_QSE_TIMESCALE_THRESHOLD, ABSOLUTE_QSE_TIMESCALE_THRESHOLD / 3.156e7);< / div >
< div class = "line" > < a id = "l00892" name = "l00892" > < / a > < span class = "lineno" > 892< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Minimum gap threshold: {} orders of magnitude." < / span > , MIN_GAP_THRESHOLD);< / div >
< div class = "line" > < a id = "l00893" name = "l00893" > < / a > < span class = "lineno" > 893< / span > < / div >
< div class = "line" > < a id = "l00894" name = "l00894" > < / a > < span class = "lineno" > 894< / span > std::vector< size_t> dynamic_pool_indices;< / div >
< div class = "line" > < a id = "l00895" name = "l00895" > < / a > < span class = "lineno" > 895< / span > std::vector< std::pair< double, size_t> > fast_candidates;< / div >
< div class = "line" > < a id = "l00896" name = "l00896" > < / a > < span class = "lineno" > 896< / span > < / div >
< div class = "line" > < a id = "l00897" name = "l00897" > < / a > < span class = "lineno" > 897< / span > < span class = "comment" > // 1. First Pass: Absolute Timescale Cutoff< / span > < / div >
< div class = "line" > < a id = "l00898" name = "l00898" > < / a > < span class = "lineno" > 898< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & ts_pair : sorted_timescales) {< / div >
< div class = "line" > < a id = "l00899" name = "l00899" > < / a > < span class = "lineno" > 899< / span > < span class = "keywordflow" > if< / span > (ts_pair.first > ABSOLUTE_QSE_TIMESCALE_THRESHOLD) {< / div >
< div class = "line" > < a id = "l00900" name = "l00900" > < / a > < span class = "lineno" > 900< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Species {} with timescale {} is considered dynamic (slower than qse timescale threshold)." < / span > ,< / div >
< div class = "line" > < a id = "l00901" name = "l00901" > < / a > < span class = "lineno" > 901< / span > all_species[ts_pair.second].name(), ts_pair.first);< / div >
< div class = "line" > < a id = "l00902" name = "l00902" > < / a > < span class = "lineno" > 902< / span > dynamic_pool_indices.push_back(ts_pair.second);< / div >
< div class = "line" > < a id = "l00903" name = "l00903" > < / a > < span class = "lineno" > 903< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l00904" name = "l00904" > < / a > < span class = "lineno" > 904< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Species {} with timescale {} is a candidate fast species (faster than qse timescale threshold)." < / span > ,< / div >
< div class = "line" > < a id = "l00905" name = "l00905" > < / a > < span class = "lineno" > 905< / span > all_species[ts_pair.second].name(), ts_pair.first);< / div >
< div class = "line" > < a id = "l00906" name = "l00906" > < / a > < span class = "lineno" > 906< / span > fast_candidates.push_back(ts_pair);< / div >
< div class = "line" > < a id = "l00907" name = "l00907" > < / a > < span class = "lineno" > 907< / span > }< / div >
< div class = "line" > < a id = "l00908" name = "l00908" > < / a > < span class = "lineno" > 908< / span > }< / div >
< div class = "line" > < a id = "l00909" name = "l00909" > < / a > < span class = "lineno" > 909< / span > < / div >
< div class = "line" > < a id = "l00910" name = "l00910" > < / a > < span class = "lineno" > 910< / span > < span class = "keywordflow" > if< / span > (!dynamic_pool_indices.empty()) {< / div >
< div class = "line" > < a id = "l00911" name = "l00911" > < / a > < span class = "lineno" > 911< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Found {} dynamic species (slower than QSE timescale threshold)." < / span > , dynamic_pool_indices.size());< / div >
< div class = "line" > < a id = "l00912" name = "l00912" > < / a > < span class = "lineno" > 912< / span > final_pools.push_back(dynamic_pool_indices);< / div >
< div class = "line" > < a id = "l00913" name = "l00913" > < / a > < span class = "lineno" > 913< / span > }< / div >
< div class = "line" > < a id = "l00914" name = "l00914" > < / a > < span class = "lineno" > 914< / span > < / div >
< div class = "line" > < a id = "l00915" name = "l00915" > < / a > < span class = "lineno" > 915< / span > < span class = "keywordflow" > if< / span > (fast_candidates.empty()) {< / div >
< div class = "line" > < a id = "l00916" name = "l00916" > < / a > < span class = "lineno" > 916< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " No fast candidates found." < / span > );< / div >
< div class = "line" > < a id = "l00917" name = "l00917" > < / a > < span class = "lineno" > 917< / span > < span class = "keywordflow" > return< / span > final_pools;< / div >
< div class = "line" > < a id = "l00918" name = "l00918" > < / a > < span class = "lineno" > 918< / span > }< / div >
< div class = "line" > < a id = "l00919" name = "l00919" > < / a > < span class = "lineno" > 919< / span > < / div >
< div class = "line" > < a id = "l00920" name = "l00920" > < / a > < span class = "lineno" > 920< / span > < span class = "comment" > // 2. Second Pass: Gap Detection on the remaining " fast" candidates< / span > < / div >
< div class = "line" > < a id = "l00921" name = "l00921" > < / a > < span class = "lineno" > 921< / span > std::vector< size_t> split_points;< / div >
< div class = "line" > < a id = "l00922" name = "l00922" > < / a > < span class = "lineno" > 922< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < fast_candidates.size() - 1; ++i) {< / div >
< div class = "line" > < a id = "l00923" name = "l00923" > < / a > < span class = "lineno" > 923< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > t1 = fast_candidates[i].first;< / div >
< div class = "line" > < a id = "l00924" name = "l00924" > < / a > < span class = "lineno" > 924< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > t2 = fast_candidates[i+1].first;< / div >
< div class = "line" > < a id = "l00925" name = "l00925" > < / a > < span class = "lineno" > 925< / span > < span class = "keywordflow" > if< / span > (std::log10(t1) - std::log10(t2) > MIN_GAP_THRESHOLD) {< / div >
< div class = "line" > < a id = "l00926" name = "l00926" > < / a > < span class = "lineno" > 926< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Detected gap between species {} (timescale {:0.2E}) and {} (timescale {:0.2E})." < / span > ,< / div >
< div class = "line" > < a id = "l00927" name = "l00927" > < / a > < span class = "lineno" > 927< / span > all_species[fast_candidates[i].second].name(), t1,< / div >
< div class = "line" > < a id = "l00928" name = "l00928" > < / a > < span class = "lineno" > 928< / span > all_species[fast_candidates[i+1].second].name(), t2);< / div >
< div class = "line" > < a id = "l00929" name = "l00929" > < / a > < span class = "lineno" > 929< / span > split_points.push_back(i + 1);< / div >
< div class = "line" > < a id = "l00930" name = "l00930" > < / a > < span class = "lineno" > 930< / span > }< / div >
< div class = "line" > < a id = "l00931" name = "l00931" > < / a > < span class = "lineno" > 931< / span > }< / div >
< div class = "line" > < a id = "l00932" name = "l00932" > < / a > < span class = "lineno" > 932< / span > < / div >
< div class = "line" > < a id = "l00933" name = "l00933" > < / a > < span class = "lineno" > 933< / span > < span class = "keywordtype" > size_t< / span > last_split = 0;< / div >
< div class = "line" > < a id = "l00934" name = "l00934" > < / a > < span class = "lineno" > 934< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > split : split_points) {< / div >
< div class = "line" > < a id = "l00935" name = "l00935" > < / a > < span class = "lineno" > 935< / span > std::vector< size_t> pool;< / div >
< div class = "line" > < a id = "l00936" name = "l00936" > < / a > < span class = "lineno" > 936< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = last_split; i < split; ++i) {< / div >
< div class = "line" > < a id = "l00937" name = "l00937" > < / a > < span class = "lineno" > 937< / span > pool.push_back(fast_candidates[i].second);< / div >
< div class = "line" > < a id = "l00938" name = "l00938" > < / a > < span class = "lineno" > 938< / span > }< / div >
< div class = "line" > < a id = "l00939" name = "l00939" > < / a > < span class = "lineno" > 939< / span > final_pools.push_back(pool);< / div >
< div class = "line" > < a id = "l00940" name = "l00940" > < / a > < span class = "lineno" > 940< / span > last_split = split;< / div >
< div class = "line" > < a id = "l00941" name = "l00941" > < / a > < span class = "lineno" > 941< / span > }< / div >
< div class = "line" > < a id = "l00942" name = "l00942" > < / a > < span class = "lineno" > 942< / span > < / div >
< div class = "line" > < a id = "l00943" name = "l00943" > < / a > < span class = "lineno" > 943< / span > std::vector< size_t> final_fast_pool;< / div >
< div class = "line" > < a id = "l00944" name = "l00944" > < / a > < span class = "lineno" > 944< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = last_split; i < fast_candidates.size(); ++i) {< / div >
< div class = "line" > < a id = "l00945" name = "l00945" > < / a > < span class = "lineno" > 945< / span > final_fast_pool.push_back(fast_candidates[i].second);< / div >
< div class = "line" > < a id = "l00946" name = "l00946" > < / a > < span class = "lineno" > 946< / span > }< / div >
< div class = "line" > < a id = "l00947" name = "l00947" > < / a > < span class = "lineno" > 947< / span > final_pools.push_back(final_fast_pool);< / div >
< div class = "line" > < a id = "l00948" name = "l00948" > < / a > < span class = "lineno" > 948< / span > < / div >
< div class = "line" > < a id = "l00949" name = "l00949" > < / a > < span class = "lineno" > 949< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Final partitioned pools: {}" < / span > ,< / div >
< div class = "line" > < a id = "l00950" name = "l00950" > < / a > < span class = "lineno" > 950< / span > [& ]() -> std::string {< / div >
< div class = "line" > < a id = "l00951" name = "l00951" > < / a > < span class = "lineno" > 951< / span > std::stringstream ss;< / div >
< div class = "line" > < a id = "l00952" name = "l00952" > < / a > < span class = "lineno" > 952< / span > < span class = "keywordtype" > int< / span > oc = 0;< / div >
< div class = "line" > < a id = "l00953" name = "l00953" > < / a > < span class = "lineno" > 953< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & pool : final_pools) {< / div >
< div class = "line" > < a id = "l00954" name = "l00954" > < / a > < span class = "lineno" > 954< / span > ss < < < span class = "stringliteral" > " [" < / span > ;< / div >
< div class = "line" > < a id = "l00955" name = "l00955" > < / a > < span class = "lineno" > 955< / span > < span class = "keywordtype" > int< / span > ic = 0;< / div >
< div class = "line" > < a id = "l00956" name = "l00956" > < / a > < span class = "lineno" > 956< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & idx : pool) {< / div >
< div class = "line" > < a id = "l00957" name = "l00957" > < / a > < span class = "lineno" > 957< / span > ss < < all_species[idx].name();< / div >
< div class = "line" > < a id = "l00958" name = "l00958" > < / a > < span class = "lineno" > 958< / span > < span class = "keywordflow" > if< / span > (ic < pool.size() - 1) {< / div >
< div class = "line" > < a id = "l00959" name = "l00959" > < / a > < span class = "lineno" > 959< / span > ss < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l00960" name = "l00960" > < / a > < span class = "lineno" > 960< / span > }< / div >
< div class = "line" > < a id = "l00961" name = "l00961" > < / a > < span class = "lineno" > 961< / span > ic++;< / div >
< div class = "line" > < a id = "l00962" name = "l00962" > < / a > < span class = "lineno" > 962< / span > }< / div >
< div class = "line" > < a id = "l00963" name = "l00963" > < / a > < span class = "lineno" > 963< / span > ss < < < span class = "stringliteral" > " ]" < / span > ;< / div >
< div class = "line" > < a id = "l00964" name = "l00964" > < / a > < span class = "lineno" > 964< / span > < span class = "keywordflow" > if< / span > (oc < final_pools.size() - 1) {< / div >
< div class = "line" > < a id = "l00965" name = "l00965" > < / a > < span class = "lineno" > 965< / span > ss < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l00966" name = "l00966" > < / a > < span class = "lineno" > 966< / span > }< / div >
< div class = "line" > < a id = "l00967" name = "l00967" > < / a > < span class = "lineno" > 967< / span > oc++;< / div >
< div class = "line" > < a id = "l00968" name = "l00968" > < / a > < span class = "lineno" > 968< / span > }< / div >
< div class = "line" > < a id = "l00969" name = "l00969" > < / a > < span class = "lineno" > 969< / span > < span class = "keywordflow" > return< / span > ss.str();< / div >
< div class = "line" > < a id = "l00970" name = "l00970" > < / a > < span class = "lineno" > 970< / span > }());< / div >
< div class = "line" > < a id = "l00971" name = "l00971" > < / a > < span class = "lineno" > 971< / span > < span class = "keywordflow" > return< / span > final_pools;< / div >
< div class = "line" > < a id = "l00972" name = "l00972" > < / a > < span class = "lineno" > 972< / span > < / div >
< div class = "line" > < a id = "l00973" name = "l00973" > < / a > < span class = "lineno" > 973< / span > }< / div >
< / div >
< div class = "line" > < a id = "l00974" name = "l00974" > < / a > < span class = "lineno" > 974< / span > < / div >
< div class = "line" > < a id = "l00975" name = "l00975" > < / a > < span class = "lineno" > 975< / span > < span class = "comment" > // std::unordered_map< size_t, std::vector< size_t> > MultiscalePartitioningEngineView::buildConnectivityGraph(< / span > < / div >
< div class = "line" > < a id = "l00976" name = "l00976" > < / a > < span class = "lineno" > 976< / span > < span class = "comment" > // const std::unordered_set< size_t> & fast_reaction_indices< / span > < / div >
< div class = "line" > < a id = "l00977" name = "l00977" > < / a > < span class = "lineno" > 977< / span > < span class = "comment" > // ) const {< / span > < / div >
< div class = "line" > < a id = "l00978" name = "l00978" > < / a > < span class = "lineno" > 978< / span > < span class = "comment" > // const auto& all_reactions = m_baseEngine.getNetworkReactions();< / span > < / div >
< div class = "line" > < a id = "l00979" name = "l00979" > < / a > < span class = "lineno" > 979< / span > < span class = "comment" > // std::unordered_map< size_t, std::vector< size_t> > connectivity;< / span > < / div >
< div class = "line" > < a id = "l00980" name = "l00980" > < / a > < span class = "lineno" > 980< / span > < span class = "comment" > // for (const size_t reaction_idx : fast_reaction_indices) {< / span > < / div >
< div class = "line" > < a id = "l00981" name = "l00981" > < / a > < span class = "lineno" > 981< / span > < span class = "comment" > // const auto& reaction = all_reactions[reaction_idx];< / span > < / div >
< div class = "line" > < a id = "l00982" name = "l00982" > < / a > < span class = "lineno" > 982< / span > < span class = "comment" > // const auto& reactants = reaction.reactants();< / span > < / div >
< div class = "line" > < a id = "l00983" name = "l00983" > < / a > < span class = "lineno" > 983< / span > < span class = "comment" > // const auto& products = reaction.products();< / span > < / div >
< div class = "line" > < a id = "l00984" name = "l00984" > < / a > < span class = "lineno" > 984< / span > < span class = "comment" > //< / span > < / div >
< div class = "line" > < a id = "l00985" name = "l00985" > < / a > < span class = "lineno" > 985< / span > < span class = "comment" > // // For each fast reaction, create edges between all reactants and all products.< / span > < / div >
< div class = "line" > < a id = "l00986" name = "l00986" > < / a > < span class = "lineno" > 986< / span > < span class = "comment" > // // This represents that nucleons can flow quickly between these species.< / span > < / div >
< div class = "line" > < a id = "l00987" name = "l00987" > < / a > < span class = "lineno" > 987< / span > < span class = "comment" > // for (const auto& reactant : reactants) {< / span > < / div >
< div class = "line" > < a id = "l00988" name = "l00988" > < / a > < span class = "lineno" > 988< / span > < span class = "comment" > // const size_t reactant_idx = m_baseEngine.getSpeciesIndex(reactant);< / span > < / div >
< div class = "line" > < a id = "l00989" name = "l00989" > < / a > < span class = "lineno" > 989< / span > < span class = "comment" > // for (const auto& product : products) {< / span > < / div >
< div class = "line" > < a id = "l00990" name = "l00990" > < / a > < span class = "lineno" > 990< / span > < span class = "comment" > // const size_t product_idx = m_baseEngine.getSpeciesIndex(product);< / span > < / div >
< div class = "line" > < a id = "l00991" name = "l00991" > < / a > < span class = "lineno" > 991< / span > < span class = "comment" > //< / span > < / div >
< div class = "line" > < a id = "l00992" name = "l00992" > < / a > < span class = "lineno" > 992< / span > < span class = "comment" > // // Add a two-way edge to the adjacency list.< / span > < / div >
< div class = "line" > < a id = "l00993" name = "l00993" > < / a > < span class = "lineno" > 993< / span > < span class = "comment" > // connectivity[reactant_idx].push_back(product_idx);< / span > < / div >
< div class = "line" > < a id = "l00994" name = "l00994" > < / a > < span class = "lineno" > 994< / span > < span class = "comment" > // connectivity[product_idx].push_back(reactant_idx);< / span > < / div >
< div class = "line" > < a id = "l00995" name = "l00995" > < / a > < span class = "lineno" > 995< / span > < span class = "comment" > // }< / span > < / div >
< div class = "line" > < a id = "l00996" name = "l00996" > < / a > < span class = "lineno" > 996< / span > < span class = "comment" > // }< / span > < / div >
< div class = "line" > < a id = "l00997" name = "l00997" > < / a > < span class = "lineno" > 997< / span > < span class = "comment" > // }< / span > < / div >
< div class = "line" > < a id = "l00998" name = "l00998" > < / a > < span class = "lineno" > 998< / span > < span class = "comment" > // return connectivity;< / span > < / div >
< div class = "line" > < a id = "l00999" name = "l00999" > < / a > < span class = "lineno" > 999< / span > < span class = "comment" > // }< / span > < / div >
< div class = "line" > < a id = "l01000" name = "l01000" > < / a > < span class = "lineno" > 1000< / span > < / div >
< div class = "line" > < a id = "l01001" name = "l01001" > < / a > < span class = "lineno" > 1001< / span > std::vector< MultiscalePartitioningEngineView::QSEGroup> < / div >
< div class = "foldopen" id = "foldopen01002" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01002" name = "l01002" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa55ed182301d216264daae3e6dfd8917" > 1002< / a > < / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa55ed182301d216264daae3e6dfd8917" > MultiscalePartitioningEngineView::validateGroupsWithFluxAnalysis< / a > (< / div >
< div class = "line" > < a id = "l01003" name = "l01003" > < / a > < span class = "lineno" > 1003< / span > < span class = "keyword" > const< / span > std::vector< QSEGroup> & candidate_groups,< / div >
< div class = "line" > < a id = "l01004" name = "l01004" > < / a > < span class = "lineno" > 1004< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l01005" name = "l01005" > < / a > < span class = "lineno" > 1005< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9, < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l01006" name = "l01006" > < / a > < span class = "lineno" > 1006< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01007" name = "l01007" > < / a > < span class = "lineno" > 1007< / span > < span class = "keyword" > constexpr< / span > < span class = "keywordtype" > double< / span > FLUX_RATIO_THRESHOLD = 100;< / div >
< div class = "line" > < a id = "l01008" name = "l01008" > < / a > < span class = "lineno" > 1008< / span > std::vector< QSEGroup> validated_groups = candidate_groups;< / div >
< div class = "line" > < a id = "l01009" name = "l01009" > < / a > < span class = "lineno" > 1009< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > auto< / span > & group : validated_groups) {< / div >
< div class = "line" > < a id = "l01010" name = "l01010" > < / a > < span class = "lineno" > 1010< / span > < span class = "keywordtype" > double< / span > internal_flux = 0.0;< / div >
< div class = "line" > < a id = "l01011" name = "l01011" > < / a > < span class = "lineno" > 1011< / span > < span class = "keywordtype" > double< / span > external_flux = 0.0;< / div >
< div class = "line" > < a id = "l01012" name = "l01012" > < / a > < span class = "lineno" > 1012< / span > < / div >
< div class = "line" > < a id = "l01013" name = "l01013" > < / a > < span class = "lineno" > 1013< / span > < span class = "keyword" > const< / span > std::unordered_set< size_t> group_members(< / div >
< div class = "line" > < a id = "l01014" name = "l01014" > < / a > < span class = "lineno" > 1014< / span > group.species_indices.begin(),< / div >
< div class = "line" > < a id = "l01015" name = "l01015" > < / a > < span class = "lineno" > 1015< / span > group.species_indices.end()< / div >
< div class = "line" > < a id = "l01016" name = "l01016" > < / a > < span class = "lineno" > 1016< / span > );< / div >
< div class = "line" > < a id = "l01017" name = "l01017" > < / a > < span class = "lineno" > 1017< / span > < / div >
< div class = "line" > < a id = "l01018" name = "l01018" > < / a > < span class = "lineno" > 1018< / 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_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkReactions()) {< / div >
< div class = "line" > < a id = "l01019" name = "l01019" > < / a > < span class = "lineno" > 1019< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > flow = std::abs(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .calculateMolarReactionFlow(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > , Y, T9, rho));< / div >
< div class = "line" > < a id = "l01020" name = "l01020" > < / a > < span class = "lineno" > 1020< / span > < span class = "keywordflow" > if< / span > (flow == 0.0) {< / div >
< div class = "line" > < a id = "l01021" name = "l01021" > < / a > < span class = "lineno" > 1021< / span > < span class = "keywordflow" > continue< / span > ; < span class = "comment" > // Skip reactions with zero flow< / span > < / div >
< div class = "line" > < a id = "l01022" name = "l01022" > < / a > < span class = "lineno" > 1022< / span > }< / div >
< div class = "line" > < a id = "l01023" name = "l01023" > < / a > < span class = "lineno" > 1023< / span > < span class = "keywordtype" > bool< / span > has_internal_reactant = < span class = "keyword" > false< / span > ;< / div >
< div class = "line" > < a id = "l01024" name = "l01024" > < / a > < span class = "lineno" > 1024< / span > < span class = "keywordtype" > bool< / span > has_external_reactant = < span class = "keyword" > false< / span > ;< / div >
< div class = "line" > < a id = "l01025" name = "l01025" > < / a > < span class = "lineno" > 1025< / span > < / div >
< div class = "line" > < a id = "l01026" name = "l01026" > < / a > < span class = "lineno" > 1026< / 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 = "l01027" name = "l01027" > < / a > < span class = "lineno" > 1027< / span > < span class = "keywordflow" > if< / span > (group_members.contains(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getSpeciesIndex(reactant))) {< / div >
< div class = "line" > < a id = "l01028" name = "l01028" > < / a > < span class = "lineno" > 1028< / span > has_internal_reactant = < span class = "keyword" > true< / span > ;< / div >
< div class = "line" > < a id = "l01029" name = "l01029" > < / a > < span class = "lineno" > 1029< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l01030" name = "l01030" > < / a > < span class = "lineno" > 1030< / span > has_external_reactant = < span class = "keyword" > true< / span > ;< / div >
< div class = "line" > < a id = "l01031" name = "l01031" > < / a > < span class = "lineno" > 1031< / span > }< / div >
< div class = "line" > < a id = "l01032" name = "l01032" > < / a > < span class = "lineno" > 1032< / span > }< / div >
< div class = "line" > < a id = "l01033" name = "l01033" > < / a > < span class = "lineno" > 1033< / span > < / div >
< div class = "line" > < a id = "l01034" name = "l01034" > < / a > < span class = "lineno" > 1034< / span > < span class = "keywordtype" > bool< / span > has_internal_product = < span class = "keyword" > false< / span > ;< / div >
< div class = "line" > < a id = "l01035" name = "l01035" > < / a > < span class = "lineno" > 1035< / span > < span class = "keywordtype" > bool< / span > has_external_product = < span class = "keyword" > false< / span > ;< / div >
< div class = "line" > < a id = "l01036" name = "l01036" > < / a > < span class = "lineno" > 1036< / span > < / div >
< div class = "line" > < a id = "l01037" name = "l01037" > < / a > < span class = "lineno" > 1037< / span > < 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 = "l01038" name = "l01038" > < / a > < span class = "lineno" > 1038< / span > < span class = "keywordflow" > if< / span > (group_members.contains(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getSpeciesIndex(product))) {< / div >
< div class = "line" > < a id = "l01039" name = "l01039" > < / a > < span class = "lineno" > 1039< / span > has_internal_product = < span class = "keyword" > true< / span > ;< / div >
< div class = "line" > < a id = "l01040" name = "l01040" > < / a > < span class = "lineno" > 1040< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l01041" name = "l01041" > < / a > < span class = "lineno" > 1041< / span > has_external_product = < span class = "keyword" > true< / span > ;< / div >
< div class = "line" > < a id = "l01042" name = "l01042" > < / a > < span class = "lineno" > 1042< / span > }< / div >
< div class = "line" > < a id = "l01043" name = "l01043" > < / a > < span class = "lineno" > 1043< / span > }< / div >
< div class = "line" > < a id = "l01044" name = "l01044" > < / a > < span class = "lineno" > 1044< / span > < / div >
< div class = "line" > < a id = "l01045" name = "l01045" > < / a > < span class = "lineno" > 1045< / span > < span class = "comment" > // Classify the reaction based on its participants< / span > < / div >
< div class = "line" > < a id = "l01046" name = "l01046" > < / a > < span class = "lineno" > 1046< / span > < span class = "keywordflow" > if< / span > ((has_internal_reactant & & has_internal_product) & & !(has_external_reactant || has_external_product)) {< / div >
< div class = "line" > < a id = "l01047" name = "l01047" > < / a > < span class = "lineno" > 1047< / span > LOG_TRACE_L3(< / div >
< div class = "line" > < a id = "l01048" name = "l01048" > < / a > < span class = "lineno" > 1048< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > ,< / div >
< div class = "line" > < a id = "l01049" name = "l01049" > < / a > < span class = "lineno" > 1049< / span > < span class = "stringliteral" > " Reaction {} is internal to the group containing {} and contributes to internal flux by {}" < / span > ,< / div >
< div class = "line" > < a id = "l01050" name = "l01050" > < / a > < span class = "lineno" > 1050< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id(),< / div >
< div class = "line" > < a id = "l01051" name = "l01051" > < / a > < span class = "lineno" > 1051< / span > [& ]() -> std::string {< / div >
< div class = "line" > < a id = "l01052" name = "l01052" > < / a > < span class = "lineno" > 1052< / span > std::stringstream ss;< / div >
< div class = "line" > < a id = "l01053" name = "l01053" > < / a > < span class = "lineno" > 1053< / span > int count = 0;< / div >
< div class = "line" > < a id = "l01054" name = "l01054" > < / a > < span class = "lineno" > 1054< / span > for (const auto& idx : group.algebraic_indices) {< / div >
< div class = "line" > < a id = "l01055" name = "l01055" > < / a > < span class = "lineno" > 1055< / span > ss < < m_baseEngine.getNetworkSpecies()[idx].name();< / div >
< div class = "line" > < a id = "l01056" name = "l01056" > < / a > < span class = "lineno" > 1056< / span > if (count < group.species_indices.size() - 1) {< / div >
< div class = "line" > < a id = "l01057" name = "l01057" > < / a > < span class = "lineno" > 1057< / span > ss < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l01058" name = "l01058" > < / a > < span class = "lineno" > 1058< / span > }< / div >
< div class = "line" > < a id = "l01059" name = "l01059" > < / a > < span class = "lineno" > 1059< / span > count++;< / div >
< div class = "line" > < a id = "l01060" name = "l01060" > < / a > < span class = "lineno" > 1060< / span > }< / div >
< div class = "line" > < a id = "l01061" name = "l01061" > < / a > < span class = "lineno" > 1061< / span > < span class = "keywordflow" > return< / span > ss.str();< / div >
< div class = "line" > < a id = "l01062" name = "l01062" > < / a > < span class = "lineno" > 1062< / span > }(),< / div >
< div class = "line" > < a id = "l01063" name = "l01063" > < / a > < span class = "lineno" > 1063< / span > flow< / div >
< div class = "line" > < a id = "l01064" name = "l01064" > < / a > < span class = "lineno" > 1064< / span > );< / div >
< div class = "line" > < a id = "l01065" name = "l01065" > < / a > < span class = "lineno" > 1065< / span > internal_flux += flow; < span class = "comment" > // Internal flux within the group< / span > < / div >
< div class = "line" > < a id = "l01066" name = "l01066" > < / a > < span class = "lineno" > 1066< / span > } < span class = "keywordflow" > else< / span > < span class = "keywordflow" > if< / span > ((has_internal_reactant || has_internal_product) & & (has_external_reactant || has_external_product)) {< / div >
< div class = "line" > < a id = "l01067" name = "l01067" > < / a > < span class = "lineno" > 1067< / span > LOG_TRACE_L3(< / div >
< div class = "line" > < a id = "l01068" name = "l01068" > < / a > < span class = "lineno" > 1068< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > ,< / div >
< div class = "line" > < a id = "l01069" name = "l01069" > < / a > < span class = "lineno" > 1069< / span > < span class = "stringliteral" > " Reaction {} is external to the group containing {} and contributes to external flux by {}" < / span > ,< / div >
< div class = "line" > < a id = "l01070" name = "l01070" > < / a > < span class = "lineno" > 1070< / span > < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id(),< / div >
< div class = "line" > < a id = "l01071" name = "l01071" > < / a > < span class = "lineno" > 1071< / span > [& ]() -> std::string {< / div >
< div class = "line" > < a id = "l01072" name = "l01072" > < / a > < span class = "lineno" > 1072< / span > std::stringstream ss;< / div >
< div class = "line" > < a id = "l01073" name = "l01073" > < / a > < span class = "lineno" > 1073< / span > int count = 0;< / div >
< div class = "line" > < a id = "l01074" name = "l01074" > < / a > < span class = "lineno" > 1074< / span > for (const auto& idx : group.algebraic_indices) {< / div >
< div class = "line" > < a id = "l01075" name = "l01075" > < / a > < span class = "lineno" > 1075< / span > ss < < m_baseEngine.getNetworkSpecies()[idx].name();< / div >
< div class = "line" > < a id = "l01076" name = "l01076" > < / a > < span class = "lineno" > 1076< / span > if (count < group.species_indices.size() - 1) {< / div >
< div class = "line" > < a id = "l01077" name = "l01077" > < / a > < span class = "lineno" > 1077< / span > ss < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l01078" name = "l01078" > < / a > < span class = "lineno" > 1078< / span > }< / div >
< div class = "line" > < a id = "l01079" name = "l01079" > < / a > < span class = "lineno" > 1079< / span > count++;< / div >
< div class = "line" > < a id = "l01080" name = "l01080" > < / a > < span class = "lineno" > 1080< / span > }< / div >
< div class = "line" > < a id = "l01081" name = "l01081" > < / a > < span class = "lineno" > 1081< / span > < span class = "keywordflow" > return< / span > ss.str();< / div >
< div class = "line" > < a id = "l01082" name = "l01082" > < / a > < span class = "lineno" > 1082< / span > }(),< / div >
< div class = "line" > < a id = "l01083" name = "l01083" > < / a > < span class = "lineno" > 1083< / span > flow< / div >
< div class = "line" > < a id = "l01084" name = "l01084" > < / a > < span class = "lineno" > 1084< / span > );< / div >
< div class = "line" > < a id = "l01085" name = "l01085" > < / a > < span class = "lineno" > 1085< / span > external_flux += flow; < span class = "comment" > // External flux to/from the group< / span > < / div >
< div class = "line" > < a id = "l01086" name = "l01086" > < / a > < span class = "lineno" > 1086< / span > }< / div >
< div class = "line" > < a id = "l01087" name = "l01087" > < / a > < span class = "lineno" > 1087< / span > < span class = "comment" > // otherwise the reaction is fully decoupled from the QSE group and can be ignored.< / span > < / div >
< div class = "line" > < a id = "l01088" name = "l01088" > < / a > < span class = "lineno" > 1088< / span > }< / div >
< div class = "line" > < a id = "l01089" name = "l01089" > < / a > < span class = "lineno" > 1089< / span > < span class = "keywordflow" > if< / span > (internal_flux > FLUX_RATIO_THRESHOLD * external_flux) {< / div >
< div class = "line" > < a id = "l01090" name = "l01090" > < / a > < span class = "lineno" > 1090< / span > LOG_TRACE_L1(< / div >
< div class = "line" > < a id = "l01091" name = "l01091" > < / a > < span class = "lineno" > 1091< / span > m_logger,< / div >
< div class = "line" > < a id = "l01092" name = "l01092" > < / a > < span class = "lineno" > 1092< / span > < span class = "stringliteral" > " Group containing {} is in equilibrium: internal flux = {}, external flux = {}, ratio = {}" < / span > ,< / div >
< div class = "line" > < a id = "l01093" name = "l01093" > < / a > < span class = "lineno" > 1093< / span > [& ]() -> std::string {< / div >
< div class = "line" > < a id = "l01094" name = "l01094" > < / a > < span class = "lineno" > 1094< / span > std::stringstream ss;< / div >
< div class = "line" > < a id = "l01095" name = "l01095" > < / a > < span class = "lineno" > 1095< / span > < span class = "keywordtype" > int< / span > count = 0;< / div >
< div class = "line" > < a id = "l01096" name = "l01096" > < / a > < span class = "lineno" > 1096< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & idx : group.algebraic_indices) {< / div >
< div class = "line" > < a id = "l01097" name = "l01097" > < / a > < span class = "lineno" > 1097< / span > ss < < m_baseEngine.getNetworkSpecies()[idx].name();< / div >
< div class = "line" > < a id = "l01098" name = "l01098" > < / a > < span class = "lineno" > 1098< / span > < span class = "keywordflow" > if< / span > (count < group.species_indices.size() - 1) {< / div >
< div class = "line" > < a id = "l01099" name = "l01099" > < / a > < span class = "lineno" > 1099< / span > ss < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l01100" name = "l01100" > < / a > < span class = "lineno" > 1100< / span > }< / div >
< div class = "line" > < a id = "l01101" name = "l01101" > < / a > < span class = "lineno" > 1101< / span > count++;< / div >
< div class = "line" > < a id = "l01102" name = "l01102" > < / a > < span class = "lineno" > 1102< / span > }< / div >
< div class = "line" > < a id = "l01103" name = "l01103" > < / a > < span class = "lineno" > 1103< / span > < span class = "keywordflow" > return< / span > ss.str();< / div >
< div class = "line" > < a id = "l01104" name = "l01104" > < / a > < span class = "lineno" > 1104< / span > }(),< / div >
< div class = "line" > < a id = "l01105" name = "l01105" > < / a > < span class = "lineno" > 1105< / span > internal_flux,< / div >
< div class = "line" > < a id = "l01106" name = "l01106" > < / a > < span class = "lineno" > 1106< / span > external_flux,< / div >
< div class = "line" > < a id = "l01107" name = "l01107" > < / a > < span class = "lineno" > 1107< / span > internal_flux / external_flux< / div >
< div class = "line" > < a id = "l01108" name = "l01108" > < / a > < span class = "lineno" > 1108< / span > );< / div >
< div class = "line" > < a id = "l01109" name = "l01109" > < / a > < span class = "lineno" > 1109< / span > group.is_in_equilibrium = < span class = "keyword" > true< / span > ; < span class = "comment" > // This group is in equilibrium if internal flux is significantly larger than external flux.< / span > < / div >
< div class = "line" > < a id = "l01110" name = "l01110" > < / a > < span class = "lineno" > 1110< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l01111" name = "l01111" > < / a > < span class = "lineno" > 1111< / span > LOG_TRACE_L1(< / div >
< div class = "line" > < a id = "l01112" name = "l01112" > < / a > < span class = "lineno" > 1112< / span > m_logger,< / div >
< div class = "line" > < a id = "l01113" name = "l01113" > < / a > < span class = "lineno" > 1113< / span > < span class = "stringliteral" > " Group containing {} is NOT in equilibrium: internal flux = {}, external flux = {}, ratio = {}" < / span > ,< / div >
< div class = "line" > < a id = "l01114" name = "l01114" > < / a > < span class = "lineno" > 1114< / span > [& ]() -> std::string {< / div >
< div class = "line" > < a id = "l01115" name = "l01115" > < / a > < span class = "lineno" > 1115< / span > std::stringstream ss;< / div >
< div class = "line" > < a id = "l01116" name = "l01116" > < / a > < span class = "lineno" > 1116< / span > < span class = "keywordtype" > int< / span > count = 0;< / div >
< div class = "line" > < a id = "l01117" name = "l01117" > < / a > < span class = "lineno" > 1117< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & idx : group.algebraic_indices) {< / div >
< div class = "line" > < a id = "l01118" name = "l01118" > < / a > < span class = "lineno" > 1118< / span > ss < < m_baseEngine.getNetworkSpecies()[idx].name();< / div >
< div class = "line" > < a id = "l01119" name = "l01119" > < / a > < span class = "lineno" > 1119< / span > < span class = "keywordflow" > if< / span > (count < group.species_indices.size() - 1) {< / div >
< div class = "line" > < a id = "l01120" name = "l01120" > < / a > < span class = "lineno" > 1120< / span > ss < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l01121" name = "l01121" > < / a > < span class = "lineno" > 1121< / span > }< / div >
< div class = "line" > < a id = "l01122" name = "l01122" > < / a > < span class = "lineno" > 1122< / span > count++;< / div >
< div class = "line" > < a id = "l01123" name = "l01123" > < / a > < span class = "lineno" > 1123< / span > }< / div >
< div class = "line" > < a id = "l01124" name = "l01124" > < / a > < span class = "lineno" > 1124< / span > < span class = "keywordflow" > return< / span > ss.str();< / div >
< div class = "line" > < a id = "l01125" name = "l01125" > < / a > < span class = "lineno" > 1125< / span > }(),< / div >
< div class = "line" > < a id = "l01126" name = "l01126" > < / a > < span class = "lineno" > 1126< / span > internal_flux,< / div >
< div class = "line" > < a id = "l01127" name = "l01127" > < / a > < span class = "lineno" > 1127< / span > external_flux,< / div >
< div class = "line" > < a id = "l01128" name = "l01128" > < / a > < span class = "lineno" > 1128< / span > internal_flux / external_flux< / div >
< div class = "line" > < a id = "l01129" name = "l01129" > < / a > < span class = "lineno" > 1129< / span > );< / div >
< div class = "line" > < a id = "l01130" name = "l01130" > < / a > < span class = "lineno" > 1130< / span > group.is_in_equilibrium = < span class = "keyword" > false< / span > ;< / div >
< div class = "line" > < a id = "l01131" name = "l01131" > < / a > < span class = "lineno" > 1131< / span > }< / div >
< div class = "line" > < a id = "l01132" name = "l01132" > < / a > < span class = "lineno" > 1132< / span > }< / div >
< div class = "line" > < a id = "l01133" name = "l01133" > < / a > < span class = "lineno" > 1133< / span > < span class = "keywordflow" > return< / span > validated_groups;< / div >
< div class = "line" > < a id = "l01134" name = "l01134" > < / a > < span class = "lineno" > 1134< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01135" name = "l01135" > < / a > < span class = "lineno" > 1135< / span > < / div >
< div class = "foldopen" id = "foldopen01136" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01136" name = "l01136" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c5fcb8e3396d74359fd601554c9ffa9" > 1136< / a > < / span > std::vector< double> < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c5fcb8e3396d74359fd601554c9ffa9" > MultiscalePartitioningEngineView::solveQSEAbundances< / a > (< / div >
< div class = "line" > < a id = "l01137" name = "l01137" > < / a > < span class = "lineno" > 1137< / span > < span class = "keyword" > const< / span > std::vector< double> & Y_full,< / div >
< div class = "line" > < a id = "l01138" name = "l01138" > < / a > < span class = "lineno" > 1138< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l01139" name = "l01139" > < / a > < span class = "lineno" > 1139< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l01140" name = "l01140" > < / a > < span class = "lineno" > 1140< / span > ) {< / div >
< div class = "line" > < a id = "l01141" name = "l01141" > < / a > < span class = "lineno" > 1141< / span > LOG_TRACE_L1(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Solving for QSE abundances..." < / span > );< / div >
< div class = "line" > < a id = "l01142" name = "l01142" > < / a > < span class = "lineno" > 1142< / span > < span class = "keyword" > auto< / span > Y_out = Y_full;< / div >
< div class = "line" > < a id = "l01143" name = "l01143" > < / a > < span class = "lineno" > 1143< / span > < / div >
< div class = "line" > < a id = "l01144" name = "l01144" > < / a > < span class = "lineno" > 1144< / span > < / div >
< div class = "line" > < a id = "l01145" name = "l01145" > < / a > < span class = "lineno" > 1145< / span > < span class = "comment" > // Sort by timescale to solve fastest QSE groups first (these can seed slower groups)< / span > < / div >
< div class = "line" > < a id = "l01146" name = "l01146" > < / a > < span class = "lineno" > 1146< / span > std::ranges::sort(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b4aa04a1e641204e4fd82361b0e39c6" > m_qse_groups< / a > , [](< span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html" > QSEGroup< / a > & a, < span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html" > QSEGroup< / a > & b) {< / div >
< div class = "line" > < a id = "l01147" name = "l01147" > < / a > < span class = "lineno" > 1147< / span > < span class = "keywordflow" > return< / span > a.< a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a66e6677638af72e4db75f5518dc867f9" > mean_timescale< / a > < b.< a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a66e6677638af72e4db75f5518dc867f9" > mean_timescale< / a > ;< / div >
< div class = "line" > < a id = "l01148" name = "l01148" > < / a > < span class = "lineno" > 1148< / span > });< / div >
< div class = "line" > < a id = "l01149" name = "l01149" > < / a > < span class = "lineno" > 1149< / span > < / div >
< div class = "line" > < a id = "l01150" name = "l01150" > < / a > < span class = "lineno" > 1150< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & [species_indices, is_in_equilibrium, algebraic_indices, seed_indices, mean_timescale] : < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b4aa04a1e641204e4fd82361b0e39c6" > m_qse_groups< / a > ) {< / div >
< div class = "line" > < a id = "l01151" name = "l01151" > < / a > < span class = "lineno" > 1151< / span > < span class = "keywordflow" > if< / span > (!is_in_equilibrium || species_indices.empty()) {< / div >
< div class = "line" > < a id = "l01152" name = "l01152" > < / a > < span class = "lineno" > 1152< / span > LOG_TRACE_L1(< / div >
< div class = "line" > < a id = "l01153" name = "l01153" > < / a > < span class = "lineno" > 1153< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > ,< / div >
< div class = "line" > < a id = "l01154" name = "l01154" > < / a > < span class = "lineno" > 1154< / span > < span class = "stringliteral" > " Skipping QSE group with {} species ({} algebraic ({}), {} seeds ({})) as it is not in equilibrium." < / span > ,< / div >
< div class = "line" > < a id = "l01155" name = "l01155" > < / a > < span class = "lineno" > 1155< / span > species_indices.size(),< / div >
< div class = "line" > < a id = "l01156" name = "l01156" > < / a > < span class = "lineno" > 1156< / span > algebraic_indices.size(),< / div >
< div class = "line" > < a id = "l01157" name = "l01157" > < / a > < span class = "lineno" > 1157< / span > [& ]() -> std::string {< / div >
< div class = "line" > < a id = "l01158" name = "l01158" > < / a > < span class = "lineno" > 1158< / span > std::ostringstream os;< / div >
< div class = "line" > < a id = "l01159" name = "l01159" > < / a > < span class = "lineno" > 1159< / span > int count = 0;< / div >
< div class = "line" > < a id = "l01160" name = "l01160" > < / a > < span class = "lineno" > 1160< / span > for (const auto& idx : algebraic_indices) {< / div >
< div class = "line" > < a id = "l01161" name = "l01161" > < / a > < span class = "lineno" > 1161< / span > os < < m_baseEngine.getNetworkSpecies()[idx].name();< / div >
< div class = "line" > < a id = "l01162" name = "l01162" > < / a > < span class = "lineno" > 1162< / span > if (count < algebraic_indices.size() - 1) {< / div >
< div class = "line" > < a id = "l01163" name = "l01163" > < / a > < span class = "lineno" > 1163< / span > os < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l01164" name = "l01164" > < / a > < span class = "lineno" > 1164< / span > }< / div >
< div class = "line" > < a id = "l01165" name = "l01165" > < / a > < span class = "lineno" > 1165< / span > count++;< / div >
< div class = "line" > < a id = "l01166" name = "l01166" > < / a > < span class = "lineno" > 1166< / span > }< / div >
< div class = "line" > < a id = "l01167" name = "l01167" > < / a > < span class = "lineno" > 1167< / span > < span class = "keywordflow" > return< / span > os.str();< / div >
< div class = "line" > < a id = "l01168" name = "l01168" > < / a > < span class = "lineno" > 1168< / span > }(),< / div >
< div class = "line" > < a id = "l01169" name = "l01169" > < / a > < span class = "lineno" > 1169< / span > seed_indices.size(),< / div >
< div class = "line" > < a id = "l01170" name = "l01170" > < / a > < span class = "lineno" > 1170< / span > [& ]() -> std::string {< / div >
< div class = "line" > < a id = "l01171" name = "l01171" > < / a > < span class = "lineno" > 1171< / span > std::ostringstream os;< / div >
< div class = "line" > < a id = "l01172" name = "l01172" > < / a > < span class = "lineno" > 1172< / span > < span class = "keywordtype" > int< / span > count = 0;< / div >
< div class = "line" > < a id = "l01173" name = "l01173" > < / a > < span class = "lineno" > 1173< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & idx : seed_indices) {< / div >
< div class = "line" > < a id = "l01174" name = "l01174" > < / a > < span class = "lineno" > 1174< / span > os < < < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies()[idx].name();< / div >
< div class = "line" > < a id = "l01175" name = "l01175" > < / a > < span class = "lineno" > 1175< / span > < span class = "keywordflow" > if< / span > (count < seed_indices.size() - 1) {< / div >
< div class = "line" > < a id = "l01176" name = "l01176" > < / a > < span class = "lineno" > 1176< / span > os < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l01177" name = "l01177" > < / a > < span class = "lineno" > 1177< / span > }< / div >
< div class = "line" > < a id = "l01178" name = "l01178" > < / a > < span class = "lineno" > 1178< / span > count++;< / div >
< div class = "line" > < a id = "l01179" name = "l01179" > < / a > < span class = "lineno" > 1179< / span > }< / div >
< div class = "line" > < a id = "l01180" name = "l01180" > < / a > < span class = "lineno" > 1180< / span > < span class = "keywordflow" > return< / span > os.str();< / div >
< div class = "line" > < a id = "l01181" name = "l01181" > < / a > < span class = "lineno" > 1181< / span > }()< / div >
< div class = "line" > < a id = "l01182" name = "l01182" > < / a > < span class = "lineno" > 1182< / span > );< / div >
< div class = "line" > < a id = "l01183" name = "l01183" > < / a > < span class = "lineno" > 1183< / span > < span class = "keywordflow" > continue< / span > ;< / div >
< div class = "line" > < a id = "l01184" name = "l01184" > < / a > < span class = "lineno" > 1184< / span > }< / div >
< div class = "line" > < a id = "l01185" name = "l01185" > < / a > < span class = "lineno" > 1185< / span > < / div >
< div class = "line" > < a id = "l01186" name = "l01186" > < / a > < span class = "lineno" > 1186< / span > LOG_TRACE_L1(< / div >
< div class = "line" > < a id = "l01187" name = "l01187" > < / a > < span class = "lineno" > 1187< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > ,< / div >
< div class = "line" > < a id = "l01188" name = "l01188" > < / a > < span class = "lineno" > 1188< / span > < span class = "stringliteral" > " Solving for QSE abundances for group with {} species ([{}] algebraic, [{}] seeds)." < / span > ,< / div >
< div class = "line" > < a id = "l01189" name = "l01189" > < / a > < span class = "lineno" > 1189< / span > species_indices.size(),< / div >
< div class = "line" > < a id = "l01190" name = "l01190" > < / a > < span class = "lineno" > 1190< / span > [& ]() -> std::string {< / div >
< div class = "line" > < a id = "l01191" name = "l01191" > < / a > < span class = "lineno" > 1191< / span > std::stringstream ss;< / div >
< div class = "line" > < a id = "l01192" name = "l01192" > < / a > < span class = "lineno" > 1192< / span > int count = 0;< / div >
< div class = "line" > < a id = "l01193" name = "l01193" > < / a > < span class = "lineno" > 1193< / span > for (const auto& idx : algebraic_indices) {< / div >
< div class = "line" > < a id = "l01194" name = "l01194" > < / a > < span class = "lineno" > 1194< / span > ss < < m_baseEngine.getNetworkSpecies()[idx].name();< / div >
< div class = "line" > < a id = "l01195" name = "l01195" > < / a > < span class = "lineno" > 1195< / span > if (count < algebraic_indices.size() - 1) {< / div >
< div class = "line" > < a id = "l01196" name = "l01196" > < / a > < span class = "lineno" > 1196< / span > ss < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l01197" name = "l01197" > < / a > < span class = "lineno" > 1197< / span > }< / div >
< div class = "line" > < a id = "l01198" name = "l01198" > < / a > < span class = "lineno" > 1198< / span > count++;< / div >
< div class = "line" > < a id = "l01199" name = "l01199" > < / a > < span class = "lineno" > 1199< / span > }< / div >
< div class = "line" > < a id = "l01200" name = "l01200" > < / a > < span class = "lineno" > 1200< / span > < span class = "keywordflow" > return< / span > ss.str();< / div >
< div class = "line" > < a id = "l01201" name = "l01201" > < / a > < span class = "lineno" > 1201< / span > }(),< / div >
< div class = "line" > < a id = "l01202" name = "l01202" > < / a > < span class = "lineno" > 1202< / span > [& ]() -> std::string {< / div >
< div class = "line" > < a id = "l01203" name = "l01203" > < / a > < span class = "lineno" > 1203< / span > std::stringstream ss;< / div >
< div class = "line" > < a id = "l01204" name = "l01204" > < / a > < span class = "lineno" > 1204< / span > < span class = "keywordtype" > int< / span > count = 0;< / div >
< div class = "line" > < a id = "l01205" name = "l01205" > < / a > < span class = "lineno" > 1205< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & idx : seed_indices) {< / div >
< div class = "line" > < a id = "l01206" name = "l01206" > < / a > < span class = "lineno" > 1206< / span > ss < < m_baseEngine.getNetworkSpecies()[idx].name();< / div >
< div class = "line" > < a id = "l01207" name = "l01207" > < / a > < span class = "lineno" > 1207< / span > < span class = "keywordflow" > if< / span > (count < seed_indices.size() - 1) {< / div >
< div class = "line" > < a id = "l01208" name = "l01208" > < / a > < span class = "lineno" > 1208< / span > ss < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l01209" name = "l01209" > < / a > < span class = "lineno" > 1209< / span > }< / div >
< div class = "line" > < a id = "l01210" name = "l01210" > < / a > < span class = "lineno" > 1210< / span > count++;< / div >
< div class = "line" > < a id = "l01211" name = "l01211" > < / a > < span class = "lineno" > 1211< / span > }< / div >
< div class = "line" > < a id = "l01212" name = "l01212" > < / a > < span class = "lineno" > 1212< / span > < span class = "keywordflow" > return< / span > ss.str();< / div >
< div class = "line" > < a id = "l01213" name = "l01213" > < / a > < span class = "lineno" > 1213< / span > }()< / div >
< div class = "line" > < a id = "l01214" name = "l01214" > < / a > < span class = "lineno" > 1214< / span > );< / div >
< div class = "line" > < a id = "l01215" name = "l01215" > < / a > < span class = "lineno" > 1215< / span > < / div >
< div class = "line" > < a id = "l01216" name = "l01216" > < / a > < span class = "lineno" > 1216< / span > std::vector< size_t> qse_solve_indices;< / div >
< div class = "line" > < a id = "l01217" name = "l01217" > < / a > < span class = "lineno" > 1217< / span > std::vector< size_t> seed_indices_vec;< / div >
< div class = "line" > < a id = "l01218" name = "l01218" > < / a > < span class = "lineno" > 1218< / span > < / div >
< div class = "line" > < a id = "l01219" name = "l01219" > < / a > < span class = "lineno" > 1219< / span > seed_indices_vec.reserve(species_indices.size());< / div >
< div class = "line" > < a id = "l01220" name = "l01220" > < / a > < span class = "lineno" > 1220< / span > qse_solve_indices.reserve(species_indices.size());< / div >
< div class = "line" > < a id = "l01221" name = "l01221" > < / a > < span class = "lineno" > 1221< / span > < / div >
< div class = "line" > < a id = "l01222" name = "l01222" > < / a > < span class = "lineno" > 1222< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > seed_idx : seed_indices) {< / div >
< div class = "line" > < a id = "l01223" name = "l01223" > < / a > < span class = "lineno" > 1223< / span > seed_indices_vec.emplace_back(seed_idx);< / div >
< div class = "line" > < a id = "l01224" name = "l01224" > < / a > < span class = "lineno" > 1224< / span > }< / div >
< div class = "line" > < a id = "l01225" name = "l01225" > < / a > < span class = "lineno" > 1225< / span > < / div >
< div class = "line" > < a id = "l01226" name = "l01226" > < / a > < span class = "lineno" > 1226< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > algebraic_idx : algebraic_indices) {< / div >
< div class = "line" > < a id = "l01227" name = "l01227" > < / a > < span class = "lineno" > 1227< / span > qse_solve_indices.emplace_back(algebraic_idx);< / div >
< div class = "line" > < a id = "l01228" name = "l01228" > < / a > < span class = "lineno" > 1228< / span > }< / div >
< div class = "line" > < a id = "l01229" name = "l01229" > < / a > < span class = "lineno" > 1229< / span > < / div >
< div class = "line" > < a id = "l01230" name = "l01230" > < / a > < span class = "lineno" > 1230< / span > < span class = "keywordflow" > if< / span > (qse_solve_indices.empty()) < span class = "keywordflow" > continue< / span > ;< / div >
< div class = "line" > < a id = "l01231" name = "l01231" > < / a > < span class = "lineno" > 1231< / span > < / div >
< div class = "line" > < a id = "l01232" name = "l01232" > < / a > < span class = "lineno" > 1232< / span > Eigen::VectorXd Y_scale(qse_solve_indices.size());< / div >
< div class = "line" > < a id = "l01233" name = "l01233" > < / a > < span class = "lineno" > 1233< / span > Eigen::VectorXd v_initial(qse_solve_indices.size());< / div >
< div class = "line" > < a id = "l01234" name = "l01234" > < / a > < span class = "lineno" > 1234< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < qse_solve_indices.size(); ++i) {< / div >
< div class = "line" > < a id = "l01235" name = "l01235" > < / a > < span class = "lineno" > 1235< / span > < span class = "keyword" > constexpr< / span > < span class = "keywordtype" > double< / span > abundance_floor = 1.0e-15;< / div >
< div class = "line" > < a id = "l01236" name = "l01236" > < / a > < span class = "lineno" > 1236< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > initial_abundance = Y_full[qse_solve_indices[i]];< / div >
< div class = "line" > < a id = "l01237" name = "l01237" > < / a > < span class = "lineno" > 1237< / span > Y_scale(i) = std::max(initial_abundance, abundance_floor);< / div >
< div class = "line" > < a id = "l01238" name = "l01238" > < / a > < span class = "lineno" > 1238< / span > v_initial(i) = std::asinh(initial_abundance / Y_scale(i)); < span class = "comment" > // Scale the initial abundances using asinh< / span > < / div >
< div class = "line" > < a id = "l01239" name = "l01239" > < / a > < span class = "lineno" > 1239< / span > }< / div >
< div class = "line" > < a id = "l01240" name = "l01240" > < / a > < span class = "lineno" > 1240< / span > < / div >
< div class = "line" > < a id = "l01241" name = "l01241" > < / a > < span class = "lineno" > 1241< / span > EigenFunctor functor(*< span class = "keyword" > this< / span > , qse_solve_indices, Y_full, T9, rho, Y_scale);< / div >
< div class = "line" > < a id = "l01242" name = "l01242" > < / a > < span class = "lineno" > 1242< / span > Eigen::LevenbergMarquardt lm(functor);< / div >
< div class = "line" > < a id = "l01243" name = "l01243" > < / a > < span class = "lineno" > 1243< / span > lm.parameters.ftol = 1.0e-10;< / div >
< div class = "line" > < a id = "l01244" name = "l01244" > < / a > < span class = "lineno" > 1244< / span > lm.parameters.xtol = 1.0e-10;< / div >
< div class = "line" > < a id = "l01245" name = "l01245" > < / a > < span class = "lineno" > 1245< / span > < / div >
< div class = "line" > < a id = "l01246" name = "l01246" > < / a > < span class = "lineno" > 1246< / span > LOG_TRACE_L1(m_logger, < span class = "stringliteral" > " Minimizing functor..." < / span > );< / div >
< div class = "line" > < a id = "l01247" name = "l01247" > < / a > < span class = "lineno" > 1247< / span > Eigen::LevenbergMarquardtSpace::Status status = lm.minimize(v_initial);< / div >
< div class = "line" > < a id = "l01248" name = "l01248" > < / a > < span class = "lineno" > 1248< / span > < / div >
< div class = "line" > < a id = "l01249" name = "l01249" > < / a > < span class = "lineno" > 1249< / span > < span class = "keywordflow" > if< / span > (status < = 0 || status > = 4) {< / div >
< div class = "line" > < a id = "l01250" name = "l01250" > < / a > < span class = "lineno" > 1250< / span > std::stringstream msg;< / div >
< div class = "line" > < a id = "l01251" name = "l01251" > < / a > < span class = "lineno" > 1251< / span > msg < < < span class = "stringliteral" > " QSE solver failed with status: " < / span > < < status < < < span class = "stringliteral" > " for group with seed " < / span > ;< / div >
< div class = "line" > < a id = "l01252" name = "l01252" > < / a > < span class = "lineno" > 1252< / span > < span class = "keywordflow" > if< / span > (seed_indices.size() == 1) {< / div >
< div class = "line" > < a id = "l01253" name = "l01253" > < / a > < span class = "lineno" > 1253< / span > msg < < < span class = "stringliteral" > " nucleus " < / span > < < m_baseEngine.getNetworkSpecies()[seed_indices_vec[0]].name();< / div >
< div class = "line" > < a id = "l01254" name = "l01254" > < / a > < span class = "lineno" > 1254< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l01255" name = "l01255" > < / a > < span class = "lineno" > 1255< / span > msg < < < span class = "stringliteral" > " nuclei " < / span > ;< / div >
< div class = "line" > < a id = "l01256" name = "l01256" > < / a > < span class = "lineno" > 1256< / span > < span class = "comment" > // TODO: Refactor nice list printing into utility function somewhere< / span > < / div >
< div class = "line" > < a id = "l01257" name = "l01257" > < / a > < span class = "lineno" > 1257< / span > < span class = "keywordtype" > size_t< / span > counter = 0;< / div >
< div class = "line" > < a id = "l01258" name = "l01258" > < / a > < span class = "lineno" > 1258< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & seed_idx : seed_indices) {< / div >
< div class = "line" > < a id = "l01259" name = "l01259" > < / a > < span class = "lineno" > 1259< / span > msg < < m_baseEngine.getNetworkSpecies()[seed_idx].name();< / div >
< div class = "line" > < a id = "l01260" name = "l01260" > < / a > < span class = "lineno" > 1260< / span > < span class = "keywordflow" > if< / span > (counter < seed_indices.size() - 2) {< / div >
< div class = "line" > < a id = "l01261" name = "l01261" > < / a > < span class = "lineno" > 1261< / span > msg < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l01262" name = "l01262" > < / a > < span class = "lineno" > 1262< / span > } < span class = "keywordflow" > else< / span > < span class = "keywordflow" > if< / span > (counter == seed_indices.size() - 2) {< / div >
< div class = "line" > < a id = "l01263" name = "l01263" > < / a > < span class = "lineno" > 1263< / span > < span class = "keywordflow" > if< / span > (seed_indices.size() < 2) {< / div >
< div class = "line" > < a id = "l01264" name = "l01264" > < / a > < span class = "lineno" > 1264< / span > msg < < < span class = "stringliteral" > " and " < / span > ;< / div >
< div class = "line" > < a id = "l01265" name = "l01265" > < / a > < span class = "lineno" > 1265< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l01266" name = "l01266" > < / a > < span class = "lineno" > 1266< / span > msg < < < span class = "stringliteral" > " , and " < / span > ;< / div >
< div class = "line" > < a id = "l01267" name = "l01267" > < / a > < span class = "lineno" > 1267< / span > }< / div >
< div class = "line" > < a id = "l01268" name = "l01268" > < / a > < span class = "lineno" > 1268< / span > }< / div >
< div class = "line" > < a id = "l01269" name = "l01269" > < / a > < span class = "lineno" > 1269< / span > ++counter;< / div >
< div class = "line" > < a id = "l01270" name = "l01270" > < / a > < span class = "lineno" > 1270< / span > }< / div >
< div class = "line" > < a id = "l01271" name = "l01271" > < / a > < span class = "lineno" > 1271< / span > }< / div >
< div class = "line" > < a id = "l01272" name = "l01272" > < / a > < span class = "lineno" > 1272< / span > < span class = "keywordflow" > throw< / span > std::runtime_error(msg.str());< / div >
< div class = "line" > < a id = "l01273" name = "l01273" > < / a > < span class = "lineno" > 1273< / span > }< / div >
< div class = "line" > < a id = "l01274" name = "l01274" > < / a > < span class = "lineno" > 1274< / span > LOG_TRACE_L1(m_logger, < span class = "stringliteral" > " Minimization succeeded!" < / span > );< / div >
< div class = "line" > < a id = "l01275" name = "l01275" > < / a > < span class = "lineno" > 1275< / span > Eigen::VectorXd Y_final_qse = Y_scale.array() * v_initial.array().sinh(); < span class = "comment" > // Convert back to physical abundances using asinh scaling< / span > < / div >
< div class = "line" > < a id = "l01276" name = "l01276" > < / a > < span class = "lineno" > 1276< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < qse_solve_indices.size(); ++i) {< / div >
< div class = "line" > < a id = "l01277" name = "l01277" > < / a > < span class = "lineno" > 1277< / span > LOG_TRACE_L1(< / div >
< div class = "line" > < a id = "l01278" name = "l01278" > < / a > < span class = "lineno" > 1278< / span > m_logger,< / div >
< div class = "line" > < a id = "l01279" name = "l01279" > < / a > < span class = "lineno" > 1279< / span > < span class = "stringliteral" > " Species {} (index {}) started with abundance {} and ended with {}." < / span > ,< / div >
< div class = "line" > < a id = "l01280" name = "l01280" > < / a > < span class = "lineno" > 1280< / span > m_baseEngine.getNetworkSpecies()[qse_solve_indices[i]].name(),< / div >
< div class = "line" > < a id = "l01281" name = "l01281" > < / a > < span class = "lineno" > 1281< / span > qse_solve_indices[i],< / div >
< div class = "line" > < a id = "l01282" name = "l01282" > < / a > < span class = "lineno" > 1282< / span > Y_full[qse_solve_indices[i]],< / div >
< div class = "line" > < a id = "l01283" name = "l01283" > < / a > < span class = "lineno" > 1283< / span > Y_final_qse(i)< / div >
< div class = "line" > < a id = "l01284" name = "l01284" > < / a > < span class = "lineno" > 1284< / span > );< / div >
< div class = "line" > < a id = "l01285" name = "l01285" > < / a > < span class = "lineno" > 1285< / span > Y_out[qse_solve_indices[i]] = Y_final_qse(i);< / div >
< div class = "line" > < a id = "l01286" name = "l01286" > < / a > < span class = "lineno" > 1286< / span > }< / div >
< div class = "line" > < a id = "l01287" name = "l01287" > < / a > < span class = "lineno" > 1287< / span > }< / div >
< div class = "line" > < a id = "l01288" name = "l01288" > < / a > < span class = "lineno" > 1288< / span > < span class = "keywordflow" > return< / span > Y_out;< / div >
< div class = "line" > < a id = "l01289" name = "l01289" > < / a > < span class = "lineno" > 1289< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01290" name = "l01290" > < / a > < span class = "lineno" > 1290< / span > < / div >
< div class = "foldopen" id = "foldopen01291" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01291" name = "l01291" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a54ca8004fbd8d6d3ea6f67efeb5dbc8d" > 1291< / a > < / span > < span class = "keywordtype" > size_t< / span > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a54ca8004fbd8d6d3ea6f67efeb5dbc8d" > MultiscalePartitioningEngineView::identifyMeanSlowestPool< / a > (< / div >
< div class = "line" > < a id = "l01292" name = "l01292" > < / a > < span class = "lineno" > 1292< / span > < span class = "keyword" > const< / span > std::vector< std::vector< size_t> > & pools,< / div >
< div class = "line" > < a id = "l01293" name = "l01293" > < / a > < span class = "lineno" > 1293< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l01294" name = "l01294" > < / a > < span class = "lineno" > 1294< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l01295" name = "l01295" > < / a > < span class = "lineno" > 1295< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l01296" name = "l01296" > < / a > < span class = "lineno" > 1296< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01297" name = "l01297" > < / a > < span class = "lineno" > 1297< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & result = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getSpeciesDestructionTimescales(Y, T9, rho);< / div >
< div class = "line" > < a id = "l01298" name = "l01298" > < / a > < span class = "lineno" > 1298< / span > < span class = "keywordflow" > if< / span > (!result) {< / div >
< div class = "line" > < a id = "l01299" name = "l01299" > < / a > < span class = "lineno" > 1299< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Failed to get species timescales due to stale engine state" < / span > );< / div >
< div class = "line" > < a id = "l01300" name = "l01300" > < / a > < span class = "lineno" > 1300< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l01301" name = "l01301" > < / a > < span class = "lineno" > 1301< / span > < span class = "keywordflow" > throw< / span > < a class = "code hl_class" href = "classgridfire_1_1exceptions_1_1_stale_engine_error.html" > exceptions::StaleEngineError< / a > (< span class = "stringliteral" > " Failed to get species timescales due to stale engine state" < / span > );< / div >
< div class = "line" > < a id = "l01302" name = "l01302" > < / a > < span class = "lineno" > 1302< / span > }< / div >
< div class = "line" > < a id = "l01303" name = "l01303" > < / a > < span class = "lineno" > 1303< / span > < span class = "keyword" > const< / span > std::unordered_map< Species, double> all_timescales = result.value();< / div >
< div class = "line" > < a id = "l01304" name = "l01304" > < / a > < span class = "lineno" > 1304< / span > < / div >
< div class = "line" > < a id = "l01305" name = "l01305" > < / a > < span class = "lineno" > 1305< / span > < / div >
< div class = "line" > < a id = "l01306" name = "l01306" > < / a > < span class = "lineno" > 1306< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & all_species = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies();< / div >
< div class = "line" > < a id = "l01307" name = "l01307" > < / a > < span class = "lineno" > 1307< / span > < / div >
< div class = "line" > < a id = "l01308" name = "l01308" > < / a > < span class = "lineno" > 1308< / span > < span class = "keywordtype" > size_t< / span > slowest_pool_index = 0; < span class = "comment" > // Default to the first pool if no valid pool is found< / span > < / div >
< div class = "line" > < a id = "l01309" name = "l01309" > < / a > < span class = "lineno" > 1309< / span > < span class = "keywordtype" > double< / span > slowest_mean_timescale = std::numeric_limits< double> ::min();< / div >
< div class = "line" > < a id = "l01310" name = "l01310" > < / a > < span class = "lineno" > 1310< / span > < span class = "keywordtype" > size_t< / span > count = 0;< / div >
< div class = "line" > < a id = "l01311" name = "l01311" > < / a > < span class = "lineno" > 1311< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & pool : pools) {< / div >
< div class = "line" > < a id = "l01312" name = "l01312" > < / a > < span class = "lineno" > 1312< / span > < span class = "keywordtype" > double< / span > mean_timescale = 0.0;< / div >
< div class = "line" > < a id = "l01313" name = "l01313" > < / a > < span class = "lineno" > 1313< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species_idx : pool) {< / div >
< div class = "line" > < a id = "l01314" name = "l01314" > < / a > < span class = "lineno" > 1314< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > timescale = all_timescales.at(all_species[species_idx]);< / div >
< div class = "line" > < a id = "l01315" name = "l01315" > < / a > < span class = "lineno" > 1315< / span > mean_timescale += timescale;< / div >
< div class = "line" > < a id = "l01316" name = "l01316" > < / a > < span class = "lineno" > 1316< / span > }< / div >
< div class = "line" > < a id = "l01317" name = "l01317" > < / a > < span class = "lineno" > 1317< / span > mean_timescale = mean_timescale / pool.size();< / div >
< div class = "line" > < a id = "l01318" name = "l01318" > < / a > < span class = "lineno" > 1318< / span > < span class = "keywordflow" > if< / span > (std::isinf(mean_timescale)) {< / div >
< div class = "line" > < a id = "l01319" name = "l01319" > < / a > < span class = "lineno" > 1319< / span > LOG_CRITICAL(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Encountered infinite mean timescale for pool {} with species: {}" < / span > ,< / div >
< div class = "line" > < a id = "l01320" name = "l01320" > < / a > < span class = "lineno" > 1320< / span > count, [& ]() -> std::string {< / div >
< div class = "line" > < a id = "l01321" name = "l01321" > < / a > < span class = "lineno" > 1321< / span > std::stringstream ss;< / div >
< div class = "line" > < a id = "l01322" name = "l01322" > < / a > < span class = "lineno" > 1322< / span > < span class = "keywordtype" > size_t< / span > iCount = 0;< / div >
< div class = "line" > < a id = "l01323" name = "l01323" > < / a > < span class = "lineno" > 1323< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & idx : pool) {< / div >
< div class = "line" > < a id = "l01324" name = "l01324" > < / a > < span class = "lineno" > 1324< / span > ss < < all_species[idx].name() < < < span class = "stringliteral" > " : " < / span > < < all_timescales.at(all_species[idx]);< / div >
< div class = "line" > < a id = "l01325" name = "l01325" > < / a > < span class = "lineno" > 1325< / span > < span class = "keywordflow" > if< / span > (iCount < pool.size() - 1) {< / div >
< div class = "line" > < a id = "l01326" name = "l01326" > < / a > < span class = "lineno" > 1326< / span > ss < < < span class = "stringliteral" > " , " < / span > ;< / div >
< div class = "line" > < a id = "l01327" name = "l01327" > < / a > < span class = "lineno" > 1327< / span > }< / div >
< div class = "line" > < a id = "l01328" name = "l01328" > < / a > < span class = "lineno" > 1328< / span > iCount++;< / div >
< div class = "line" > < a id = "l01329" name = "l01329" > < / a > < span class = "lineno" > 1329< / span > }< / div >
< div class = "line" > < a id = "l01330" name = "l01330" > < / a > < span class = "lineno" > 1330< / span > < span class = "keywordflow" > return< / span > ss.str();< / div >
< div class = "line" > < a id = "l01331" name = "l01331" > < / a > < span class = "lineno" > 1331< / span > }()< / div >
< div class = "line" > < a id = "l01332" name = "l01332" > < / a > < span class = "lineno" > 1332< / span > );< / div >
< div class = "line" > < a id = "l01333" name = "l01333" > < / a > < span class = "lineno" > 1333< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l01334" name = "l01334" > < / a > < span class = "lineno" > 1334< / span > < span class = "keywordflow" > throw< / span > std::logic_error(< span class = "stringliteral" > " Encountered infinite mean destruction timescale for a pool while identifying the mean slowest pool set, indicating a potential issue with species timescales. Check log file for more details on specific pool composition..." < / span > );< / div >
< div class = "line" > < a id = "l01335" name = "l01335" > < / a > < span class = "lineno" > 1335< / span > }< / div >
< div class = "line" > < a id = "l01336" name = "l01336" > < / a > < span class = "lineno" > 1336< / span > < span class = "keywordflow" > if< / span > (mean_timescale > slowest_mean_timescale) {< / div >
< div class = "line" > < a id = "l01337" name = "l01337" > < / a > < span class = "lineno" > 1337< / span > slowest_mean_timescale = mean_timescale;< / div >
< div class = "line" > < a id = "l01338" name = "l01338" > < / a > < span class = "lineno" > 1338< / span > slowest_pool_index = & pool - & pools[0]; < span class = "comment" > // Get the index of the pool< / span > < / div >
< div class = "line" > < a id = "l01339" name = "l01339" > < / a > < span class = "lineno" > 1339< / span > }< / div >
< div class = "line" > < a id = "l01340" name = "l01340" > < / a > < span class = "lineno" > 1340< / span > }< / div >
< div class = "line" > < a id = "l01341" name = "l01341" > < / a > < span class = "lineno" > 1341< / span > < span class = "keywordflow" > return< / span > slowest_pool_index;< / div >
< div class = "line" > < a id = "l01342" name = "l01342" > < / a > < span class = "lineno" > 1342< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01343" name = "l01343" > < / a > < span class = "lineno" > 1343< / span > < / div >
< div class = "foldopen" id = "foldopen01344" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01344" name = "l01344" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ae3875c61dc916c0982ed122c2e272d94" > 1344< / a > < / span > std::unordered_map< size_t, std::vector< size_t> > < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aae0865e361dfeb23984d70409fdd9f39" > MultiscalePartitioningEngineView::buildConnectivityGraph< / a > (< / div >
< div class = "line" > < a id = "l01345" name = "l01345" > < / a > < span class = "lineno" > 1345< / span > < span class = "keyword" > const< / span > std::vector< size_t> & species_pool< / div >
< div class = "line" > < a id = "l01346" name = "l01346" > < / a > < span class = "lineno" > 1346< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01347" name = "l01347" > < / a > < span class = "lineno" > 1347< / span > std::unordered_map< size_t, std::vector< size_t> > connectivity_graph;< / div >
< div class = "line" > < a id = "l01348" name = "l01348" > < / a > < span class = "lineno" > 1348< / span > < span class = "keyword" > const< / span > std::set< size_t> pool_set(species_pool.begin(), species_pool.end());< / div >
< div class = "line" > < a id = "l01349" name = "l01349" > < / a > < span class = "lineno" > 1349< / span > < span class = "keyword" > const< / span > std::unordered_set< Species> pool_species = [& ]() -> std::unordered_set< Species> {< / div >
< div class = "line" > < a id = "l01350" name = "l01350" > < / a > < span class = "lineno" > 1350< / span > std::unordered_set< Species> result;< / div >
< div class = "line" > < a id = "l01351" name = "l01351" > < / a > < span class = "lineno" > 1351< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species_idx : species_pool) {< / div >
< div class = "line" > < a id = "l01352" name = "l01352" > < / a > < span class = "lineno" > 1352< / span > Species species = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies()[species_idx];< / div >
< div class = "line" > < a id = "l01353" name = "l01353" > < / a > < span class = "lineno" > 1353< / span > result.insert(species);< / div >
< div class = "line" > < a id = "l01354" name = "l01354" > < / a > < span class = "lineno" > 1354< / span > }< / div >
< div class = "line" > < a id = "l01355" name = "l01355" > < / a > < span class = "lineno" > 1355< / span > < span class = "keywordflow" > return< / span > result;< / div >
< div class = "line" > < a id = "l01356" name = "l01356" > < / a > < span class = "lineno" > 1356< / span > }();< / div >
< div class = "line" > < a id = "l01357" name = "l01357" > < / a > < span class = "lineno" > 1357< / span > < / div >
< div class = "line" > < a id = "l01358" name = "l01358" > < / a > < span class = "lineno" > 1358< / span > std::map< size_t, std::vector< reaction::LogicalReaction*> > speciesReactionMap;< / div >
< div class = "line" > < a id = "l01359" name = "l01359" > < / a > < span class = "lineno" > 1359< / span > std::vector< const reaction::LogicalReaction*> candidate_reactions;< / div >
< div class = "line" > < a id = "l01360" name = "l01360" > < / a > < span class = "lineno" > 1360< / span > < / div >
< div class = "line" > < a id = "l01361" name = "l01361" > < / a > < span class = "lineno" > 1361< / span > < span class = "keyword" > auto< / span > getSpeciesIdx = [& ](< span class = "keyword" > const< / span > std::vector< Species> & species) -> std::vector< size_t> {< / div >
< div class = "line" > < a id = "l01362" name = "l01362" > < / a > < span class = "lineno" > 1362< / span > std::vector< size_t> result;< / div >
< div class = "line" > < a id = "l01363" name = "l01363" > < / a > < span class = "lineno" > 1363< / span > result.reserve(species.size());< / div >
< div class = "line" > < a id = "l01364" name = "l01364" > < / a > < span class = "lineno" > 1364< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & s : species) {< / div >
< div class = "line" > < a id = "l01365" name = "l01365" > < / a > < span class = "lineno" > 1365< / span > < span class = "keywordtype" > size_t< / span > idx = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getSpeciesIndex(s);< / div >
< div class = "line" > < a id = "l01366" name = "l01366" > < / a > < span class = "lineno" > 1366< / span > result.push_back(idx);< / div >
< div class = "line" > < a id = "l01367" name = "l01367" > < / a > < span class = "lineno" > 1367< / span > }< / div >
< div class = "line" > < a id = "l01368" name = "l01368" > < / a > < span class = "lineno" > 1368< / span > < span class = "keywordflow" > return< / span > result;< / div >
< div class = "line" > < a id = "l01369" name = "l01369" > < / a > < span class = "lineno" > 1369< / span > };< / div >
< div class = "line" > < a id = "l01370" name = "l01370" > < / a > < span class = "lineno" > 1370< / span > < / div >
< div class = "line" > < a id = "l01371" name = "l01371" > < / a > < span class = "lineno" > 1371< / 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_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkReactions()) {< / div >
< div class = "line" > < a id = "l01372" name = "l01372" > < / a > < span class = "lineno" > 1372< / span > < span class = "keyword" > const< / span > std::vector< Species> & reactants = < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .reactants();< / div >
< div class = "line" > < a id = "l01373" name = "l01373" > < / a > < span class = "lineno" > 1373< / span > < span class = "keyword" > const< / span > std::vector< Species> & products = < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .products();< / div >
< div class = "line" > < a id = "l01374" name = "l01374" > < / a > < span class = "lineno" > 1374< / span > < / div >
< div class = "line" > < a id = "l01375" name = "l01375" > < / a > < span class = "lineno" > 1375< / span > std::unordered_set< Species> reactant_set(reactants.begin(), reactants.end());< / div >
< div class = "line" > < a id = "l01376" name = "l01376" > < / a > < span class = "lineno" > 1376< / span > std::unordered_set< Species> product_set(products.begin(), products.end());< / div >
< div class = "line" > < a id = "l01377" name = "l01377" > < / a > < span class = "lineno" > 1377< / span > < / div >
< div class = "line" > < a id = "l01378" name = "l01378" > < / a > < span class = "lineno" > 1378< / span > < span class = "comment" > // Only consider reactions where at least one distinct reactant and product are in the pool< / span > < / div >
< div class = "line" > < a id = "l01379" name = "l01379" > < / a > < span class = "lineno" > 1379< / span > < span class = "keywordflow" > if< / span > (has_distinct_reactant_and_product_species(pool_species, reactant_set, product_set)) {< / div >
< div class = "line" > < a id = "l01380" name = "l01380" > < / a > < span class = "lineno" > 1380< / span > std::vector< size_t> involvedIDs = getSpeciesIdx(reactants);< / div >
< div class = "line" > < a id = "l01381" name = "l01381" > < / a > < span class = "lineno" > 1381< / span > std::vector< size_t> involvedProducts = getSpeciesIdx(products);< / div >
< div class = "line" > < a id = "l01382" name = "l01382" > < / a > < span class = "lineno" > 1382< / span > involvedIDs.insert(involvedIDs.end(), involvedProducts.begin(), involvedProducts.end());< / div >
< div class = "line" > < a id = "l01383" name = "l01383" > < / a > < span class = "lineno" > 1383< / span > std::set< size_t> involvedSet(involvedIDs.begin(), involvedIDs.end());< / div >
< div class = "line" > < a id = "l01384" name = "l01384" > < / a > < span class = "lineno" > 1384< / span > < / div >
< div class = "line" > < a id = "l01385" name = "l01385" > < / a > < span class = "lineno" > 1385< / span > std::vector< size_t> intersection;< / div >
< div class = "line" > < a id = "l01386" name = "l01386" > < / a > < span class = "lineno" > 1386< / span > intersection.reserve(involvedSet.size());< / div >
< div class = "line" > < a id = "l01387" name = "l01387" > < / a > < span class = "lineno" > 1387< / span > < / div >
< div class = "line" > < a id = "l01388" name = "l01388" > < / a > < span class = "lineno" > 1388< / span > std::ranges::set_intersection(pool_set, involvedSet, std::back_inserter(intersection));< / div >
< div class = "line" > < a id = "l01389" name = "l01389" > < / a > < span class = "lineno" > 1389< / span > < / div >
< div class = "line" > < a id = "l01390" name = "l01390" > < / a > < span class = "lineno" > 1390< / span > < span class = "comment" > // Add clique< / span > < / div >
< div class = "line" > < a id = "l01391" name = "l01391" > < / a > < span class = "lineno" > 1391< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > & u : intersection) {< / div >
< div class = "line" > < a id = "l01392" name = "l01392" > < / a > < span class = "lineno" > 1392< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keywordtype" > size_t< / span > & v : intersection) {< / div >
< div class = "line" > < a id = "l01393" name = "l01393" > < / a > < span class = "lineno" > 1393< / span > < span class = "keywordflow" > if< / span > (u != v) { < span class = "comment" > // Avoid self-loops< / span > < / div >
< div class = "line" > < a id = "l01394" name = "l01394" > < / a > < span class = "lineno" > 1394< / span > connectivity_graph[u].push_back(v);< / div >
< div class = "line" > < a id = "l01395" name = "l01395" > < / a > < span class = "lineno" > 1395< / span > }< / div >
< div class = "line" > < a id = "l01396" name = "l01396" > < / a > < span class = "lineno" > 1396< / span > }< / div >
< div class = "line" > < a id = "l01397" name = "l01397" > < / a > < span class = "lineno" > 1397< / span > }< / div >
< div class = "line" > < a id = "l01398" name = "l01398" > < / a > < span class = "lineno" > 1398< / span > }< / div >
< div class = "line" > < a id = "l01399" name = "l01399" > < / a > < span class = "lineno" > 1399< / span > }< / div >
< div class = "line" > < a id = "l01400" name = "l01400" > < / a > < span class = "lineno" > 1400< / span > < / div >
< div class = "line" > < a id = "l01401" name = "l01401" > < / a > < span class = "lineno" > 1401< / span > < / div >
< div class = "line" > < a id = "l01402" name = "l01402" > < / a > < span class = "lineno" > 1402< / span > < span class = "keywordflow" > return< / span > connectivity_graph;< / div >
< div class = "line" > < a id = "l01403" name = "l01403" > < / a > < span class = "lineno" > 1403< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01404" name = "l01404" > < / a > < span class = "lineno" > 1404< / span > < / div >
< div class = "foldopen" id = "foldopen01405" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01405" name = "l01405" > < / a > < span class = "lineno" > < a class = "line" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ac206840057bac65b7f7738e6dfd1047a" > 1405< / a > < / span > std::vector< MultiscalePartitioningEngineView::QSEGroup> < a class = "code hl_function" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ac206840057bac65b7f7738e6dfd1047a" > MultiscalePartitioningEngineView::constructCandidateGroups< / a > (< / div >
< div class = "line" > < a id = "l01406" name = "l01406" > < / a > < span class = "lineno" > 1406< / span > < span class = "keyword" > const< / span > std::vector< std::vector< size_t> > & candidate_pools,< / div >
< div class = "line" > < a id = "l01407" name = "l01407" > < / a > < span class = "lineno" > 1407< / span > < span class = "keyword" > const< / span > std::vector< double> & Y,< / div >
< div class = "line" > < a id = "l01408" name = "l01408" > < / a > < span class = "lineno" > 1408< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9, < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho< / div >
< div class = "line" > < a id = "l01409" name = "l01409" > < / a > < span class = "lineno" > 1409< / span > )< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01410" name = "l01410" > < / a > < span class = "lineno" > 1410< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & all_species = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkSpecies();< / div >
< div class = "line" > < a id = "l01411" name = "l01411" > < / a > < span class = "lineno" > 1411< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & all_reactions = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getNetworkReactions();< / div >
< div class = "line" > < a id = "l01412" name = "l01412" > < / a > < span class = "lineno" > 1412< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & result = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getSpeciesDestructionTimescales(Y, T9, rho);< / div >
< div class = "line" > < a id = "l01413" name = "l01413" > < / a > < span class = "lineno" > 1413< / span > < span class = "keywordflow" > if< / span > (!result) {< / div >
< div class = "line" > < a id = "l01414" name = "l01414" > < / a > < span class = "lineno" > 1414< / span > LOG_ERROR(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Failed to get species timescales due to stale engine state" < / span > );< / div >
< div class = "line" > < a id = "l01415" name = "l01415" > < / a > < span class = "lineno" > 1415< / span > < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > -> flush_log();< / div >
< div class = "line" > < a id = "l01416" name = "l01416" > < / a > < span class = "lineno" > 1416< / span > < span class = "keywordflow" > throw< / span > < a class = "code hl_class" href = "classgridfire_1_1exceptions_1_1_stale_engine_error.html" > exceptions::StaleEngineError< / a > (< span class = "stringliteral" > " Failed to get species timescales due to stale engine state" < / span > );< / div >
< div class = "line" > < a id = "l01417" name = "l01417" > < / a > < span class = "lineno" > 1417< / span > }< / div >
< div class = "line" > < a id = "l01418" name = "l01418" > < / a > < span class = "lineno" > 1418< / span > < span class = "keyword" > const< / span > std::unordered_map< Species, double> destruction_timescales = result.value();< / div >
< div class = "line" > < a id = "l01419" name = "l01419" > < / a > < span class = "lineno" > 1419< / span > < / div >
< div class = "line" > < a id = "l01420" name = "l01420" > < / a > < span class = "lineno" > 1420< / span > std::vector< QSEGroup> candidate_groups;< / div >
< div class = "line" > < a id = "l01421" name = "l01421" > < / a > < span class = "lineno" > 1421< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & pool : candidate_pools) {< / div >
< div class = "line" > < a id = "l01422" name = "l01422" > < / a > < span class = "lineno" > 1422< / span > < span class = "keywordflow" > if< / span > (pool.empty()) < span class = "keywordflow" > continue< / span > ; < span class = "comment" > // Skip empty pools< / span > < / div >
< div class = "line" > < a id = "l01423" name = "l01423" > < / a > < span class = "lineno" > 1423< / span > < / div >
< div class = "line" > < a id = "l01424" name = "l01424" > < / a > < span class = "lineno" > 1424< / span > < span class = "comment" > // For each pool first identify all topological bridge connections< / span > < / div >
< div class = "line" > < a id = "l01425" name = "l01425" > < / a > < span class = "lineno" > 1425< / span > std::vector< std::pair< reaction::LogicalReaction, double> > bridge_reactions;< / div >
< div class = "line" > < a id = "l01426" name = "l01426" > < / a > < span class = "lineno" > 1426< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species_idx : pool) {< / div >
< div class = "line" > < a id = "l01427" name = "l01427" > < / a > < span class = "lineno" > 1427< / span > Species ash = all_species[species_idx];< / div >
< div class = "line" > < a id = "l01428" name = "l01428" > < / a > < span class = "lineno" > 1428< / 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 > : all_reactions) {< / div >
< div class = "line" > < a id = "l01429" name = "l01429" > < / a > < span class = "lineno" > 1429< / span > < span class = "keywordflow" > if< / span > (< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .contains(ash)) {< / div >
< div class = "line" > < a id = "l01430" name = "l01430" > < / a > < span class = "lineno" > 1430< / span > < span class = "comment" > // Check to make sure there is at least one reactant that is not in the pool< / span > < / div >
< div class = "line" > < a id = "l01431" name = "l01431" > < / a > < span class = "lineno" > 1431< / span > < span class = "comment" > // This lets seed nuclei bring mass into the QSE group.< / span > < / div >
< div class = "line" > < a id = "l01432" name = "l01432" > < / a > < span class = "lineno" > 1432< / span > < span class = "keywordtype" > bool< / span > has_external_reactant = < span class = "keyword" > false< / span > ;< / div >
< div class = "line" > < a id = "l01433" name = "l01433" > < / a > < span class = "lineno" > 1433< / 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 = "l01434" name = "l01434" > < / a > < span class = "lineno" > 1434< / span > < span class = "keywordflow" > if< / span > (std::ranges::find(pool, < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getSpeciesIndex(reactant)) == pool.end()) {< / div >
< div class = "line" > < a id = "l01435" name = "l01435" > < / a > < span class = "lineno" > 1435< / span > has_external_reactant = < span class = "keyword" > true< / span > ;< / div >
< div class = "line" > < a id = "l01436" name = "l01436" > < / a > < span class = "lineno" > 1436< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Found external reactant {} in reaction {} for species {}." < / span > , reactant.name(), < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id(), ash.name());< / div >
< div class = "line" > < a id = "l01437" name = "l01437" > < / a > < span class = "lineno" > 1437< / span > < span class = "keywordflow" > break< / span > ; < span class = "comment" > // Found an external reactant, no need to check further< / span > < / div >
< div class = "line" > < a id = "l01438" name = "l01438" > < / a > < span class = "lineno" > 1438< / span > }< / div >
< div class = "line" > < a id = "l01439" name = "l01439" > < / a > < span class = "lineno" > 1439< / span > }< / div >
< div class = "line" > < a id = "l01440" name = "l01440" > < / a > < span class = "lineno" > 1440< / span > < span class = "keywordflow" > if< / span > (has_external_reactant) {< / div >
< div class = "line" > < a id = "l01441" name = "l01441" > < / a > < span class = "lineno" > 1441< / span > < span class = "keywordtype" > double< / span > flow = std::abs(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .calculateMolarReactionFlow(< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > , Y, T9, rho));< / div >
< div class = "line" > < a id = "l01442" name = "l01442" > < / a > < span class = "lineno" > 1442< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Found bridge reaction {} with flow {} for species {}." < / span > , < a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > .id(), flow, ash.name());< / div >
< div class = "line" > < a id = "l01443" name = "l01443" > < / a > < span class = "lineno" > 1443< / span > bridge_reactions.push_back({< a class = "code hl_namespace" href = "namespacegridfire_1_1reaction.html" > reaction< / a > , flow});< / div >
< div class = "line" > < a id = "l01444" name = "l01444" > < / a > < span class = "lineno" > 1444< / span > }< / div >
< div class = "line" > < a id = "l01445" name = "l01445" > < / a > < span class = "lineno" > 1445< / span > }< / div >
< div class = "line" > < a id = "l01446" name = "l01446" > < / a > < span class = "lineno" > 1446< / span > }< / div >
< div class = "line" > < a id = "l01447" name = "l01447" > < / a > < span class = "lineno" > 1447< / span > }< / div >
< div class = "line" > < a id = "l01448" name = "l01448" > < / a > < span class = "lineno" > 1448< / span > std::ranges::sort(< / div >
< div class = "line" > < a id = "l01449" name = "l01449" > < / a > < span class = "lineno" > 1449< / span > bridge_reactions,< / div >
< div class = "line" > < a id = "l01450" name = "l01450" > < / a > < span class = "lineno" > 1450< / span > [](< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & a, < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & b) {< / div >
< div class = "line" > < a id = "l01451" name = "l01451" > < / a > < span class = "lineno" > 1451< / span > < span class = "keywordflow" > return< / span > a.second > b.second; < span class = "comment" > // Sort by flow in descending order< / span > < / div >
< div class = "line" > < a id = "l01452" name = "l01452" > < / a > < span class = "lineno" > 1452< / span > });< / div >
< div class = "line" > < a id = "l01453" name = "l01453" > < / a > < span class = "lineno" > 1453< / span > < / div >
< div class = "line" > < a id = "l01454" name = "l01454" > < / a > < span class = "lineno" > 1454< / span > < span class = "keyword" > constexpr< / span > < span class = "keywordtype" > double< / span > MIN_GAP_THRESHOLD = 1; < span class = "comment" > // Minimum logarithmic molar flow gap threshold for bridge reactions< / span > < / div >
< div class = "line" > < a id = "l01455" name = "l01455" > < / a > < span class = "lineno" > 1455< / span > std::vector< size_t> split_points;< / div >
< div class = "line" > < a id = "l01456" name = "l01456" > < / a > < span class = "lineno" > 1456< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < bridge_reactions.size() - 1; ++i) {< / div >
< div class = "line" > < a id = "l01457" name = "l01457" > < / a > < span class = "lineno" > 1457< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > f1 = bridge_reactions[i].second;< / div >
< div class = "line" > < a id = "l01458" name = "l01458" > < / a > < span class = "lineno" > 1458< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > f2 = bridge_reactions[i + 1].second;< / div >
< div class = "line" > < a id = "l01459" name = "l01459" > < / a > < span class = "lineno" > 1459< / span > < span class = "keywordflow" > if< / span > (std::log10(f1) - std::log10(f2) > MIN_GAP_THRESHOLD) {< / div >
< div class = "line" > < a id = "l01460" name = "l01460" > < / a > < span class = "lineno" > 1460< / span > LOG_TRACE_L3(< a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > m_logger< / a > , < span class = "stringliteral" > " Detected gap between bridge reactions with flows {} and {}." < / span > , f1, f2);< / div >
< div class = "line" > < a id = "l01461" name = "l01461" > < / a > < span class = "lineno" > 1461< / span > split_points.push_back(i + 1);< / div >
< div class = "line" > < a id = "l01462" name = "l01462" > < / a > < span class = "lineno" > 1462< / span > }< / div >
< div class = "line" > < a id = "l01463" name = "l01463" > < / a > < span class = "lineno" > 1463< / span > }< / div >
< div class = "line" > < a id = "l01464" name = "l01464" > < / a > < span class = "lineno" > 1464< / span > < / div >
< div class = "line" > < a id = "l01465" name = "l01465" > < / a > < span class = "lineno" > 1465< / span > < span class = "keywordflow" > if< / span > (split_points.empty()) { < span class = "comment" > // If no split points were found, we consider the whole set of bridge reactions as one group.< / span > < / div >
< div class = "line" > < a id = "l01466" name = "l01466" > < / a > < span class = "lineno" > 1466< / span > split_points.push_back(bridge_reactions.size() - 1);< / div >
< div class = "line" > < a id = "l01467" name = "l01467" > < / a > < span class = "lineno" > 1467< / span > }< / div >
< div class = "line" > < a id = "l01468" name = "l01468" > < / a > < span class = "lineno" > 1468< / span > < / div >
< div class = "line" > < a id = "l01469" name = "l01469" > < / a > < span class = "lineno" > 1469< / span > std::vector< size_t> seed_indices;< / div >
< div class = "line" > < a id = "l01470" name = "l01470" > < / a > < span class = "lineno" > 1470< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < bridge_reactions.size(); ++i) {< / div >
< div class = "line" > < a id = "l01471" name = "l01471" > < / a > < span class = "lineno" > 1471< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & fuel : bridge_reactions[i].first.reactants()) {< / div >
< div class = "line" > < a id = "l01472" name = "l01472" > < / a > < span class = "lineno" > 1472< / span > < span class = "keywordtype" > size_t< / span > fuel_idx = < a class = "code hl_variable" href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > m_baseEngine< / a > .getSpeciesIndex(fuel);< / div >
< div class = "line" > < a id = "l01473" name = "l01473" > < / a > < span class = "lineno" > 1473< / span > < span class = "comment" > // Only add the fuel if it is not already in the pool< / span > < / div >
< div class = "line" > < a id = "l01474" name = "l01474" > < / a > < span class = "lineno" > 1474< / span > < span class = "keywordflow" > if< / span > (std::ranges::find(pool, fuel_idx) == pool.end()) {< / div >
< div class = "line" > < a id = "l01475" name = "l01475" > < / a > < span class = "lineno" > 1475< / span > seed_indices.push_back(fuel_idx);< / div >
< div class = "line" > < a id = "l01476" name = "l01476" > < / a > < span class = "lineno" > 1476< / span > }< / div >
< div class = "line" > < a id = "l01477" name = "l01477" > < / a > < span class = "lineno" > 1477< / span > }< / div >
< div class = "line" > < a id = "l01478" name = "l01478" > < / a > < span class = "lineno" > 1478< / span > }< / div >
< div class = "line" > < a id = "l01479" name = "l01479" > < / a > < span class = "lineno" > 1479< / span > std::set< size_t> all_indices(pool.begin(), pool.end());< / div >
< div class = "line" > < a id = "l01480" name = "l01480" > < / a > < span class = "lineno" > 1480< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & seed_idx : seed_indices) {< / div >
< div class = "line" > < a id = "l01481" name = "l01481" > < / a > < span class = "lineno" > 1481< / span > all_indices.insert(seed_idx);< / div >
< div class = "line" > < a id = "l01482" name = "l01482" > < / a > < span class = "lineno" > 1482< / span > }< / div >
< div class = "line" > < a id = "l01483" name = "l01483" > < / a > < span class = "lineno" > 1483< / span > < span class = "keyword" > const< / span > std::set< size_t> poolSet(pool.begin(), pool.end());< / div >
< div class = "line" > < a id = "l01484" name = "l01484" > < / a > < span class = "lineno" > 1484< / span > < span class = "keyword" > const< / span > std::set< size_t> seedSet(seed_indices.begin(), seed_indices.end());< / div >
< div class = "line" > < a id = "l01485" name = "l01485" > < / a > < span class = "lineno" > 1485< / span > < / div >
< div class = "line" > < a id = "l01486" name = "l01486" > < / a > < span class = "lineno" > 1486< / span > < span class = "keywordtype" > double< / span > mean_timescale = 0.0;< / div >
< div class = "line" > < a id = "l01487" name = "l01487" > < / a > < span class = "lineno" > 1487< / span > < span class = "keywordflow" > for< / span > (< span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & pool_idx : poolSet) {< / div >
< div class = "line" > < a id = "l01488" name = "l01488" > < / a > < span class = "lineno" > 1488< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & species = all_species[pool_idx];< / div >
< div class = "line" > < a id = "l01489" name = "l01489" > < / a > < span class = "lineno" > 1489< / span > < span class = "keywordflow" > if< / span > (destruction_timescales.contains(species)) {< / div >
< div class = "line" > < a id = "l01490" name = "l01490" > < / a > < span class = "lineno" > 1490< / span > mean_timescale += std::min(destruction_timescales.at(species), species.halfLife()); < span class = "comment" > // Use the minimum of destruction timescale and half-life< / span > < / div >
< div class = "line" > < a id = "l01491" name = "l01491" > < / a > < span class = "lineno" > 1491< / span > } < span class = "keywordflow" > else< / span > {< / div >
< div class = "line" > < a id = "l01492" name = "l01492" > < / a > < span class = "lineno" > 1492< / span > mean_timescale += species.halfLife();< / div >
< div class = "line" > < a id = "l01493" name = "l01493" > < / a > < span class = "lineno" > 1493< / span > }< / div >
< div class = "line" > < a id = "l01494" name = "l01494" > < / a > < span class = "lineno" > 1494< / span > }< / div >
< div class = "line" > < a id = "l01495" name = "l01495" > < / a > < span class = "lineno" > 1495< / span > mean_timescale /= poolSet.size();< / div >
< div class = "line" > < a id = "l01496" name = "l01496" > < / a > < span class = "lineno" > 1496< / span > < a class = "code hl_struct" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html" > QSEGroup< / a > qse_group(all_indices, < span class = "keyword" > false< / span > , poolSet, seedSet, mean_timescale);< / div >
< div class = "line" > < a id = "l01497" name = "l01497" > < / a > < span class = "lineno" > 1497< / span > candidate_groups.push_back(qse_group);< / div >
< div class = "line" > < a id = "l01498" name = "l01498" > < / a > < span class = "lineno" > 1498< / span > }< / div >
< div class = "line" > < a id = "l01499" name = "l01499" > < / a > < span class = "lineno" > 1499< / span > < span class = "keywordflow" > return< / span > candidate_groups;< / div >
< div class = "line" > < a id = "l01500" name = "l01500" > < / a > < span class = "lineno" > 1500< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01501" name = "l01501" > < / a > < span class = "lineno" > 1501< / span > < / div >
< div class = "line" > < a id = "l01502" name = "l01502" > < / a > < span class = "lineno" > 1502< / span > < / div >
< div class = "foldopen" id = "foldopen01503" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01503" name = "l01503" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#ad7bd060a3eaaaefab0c31e60dcdb5f28" > 1503< / a > < / span > < span class = "keywordtype" > int< / span > < a class = "code hl_function" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#ad7bd060a3eaaaefab0c31e60dcdb5f28" > MultiscalePartitioningEngineView::EigenFunctor::operator()< / a > (< span class = "keyword" > const< / span > < a class = "code hl_typedef" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a3ebf684b36e98da38d8ee6f0be4f91e2" > InputType< / a > & v_qse, < a class = "code hl_typedef" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4d597d16bd9f982d44512d5a6beddae0" > OutputType< / a > & f_qse)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01504" name = "l01504" > < / a > < span class = "lineno" > 1504< / span > < a class = "code hl_variable" href = "namespacegridfire.html#a8b632637f62614f509cde0e404a79054" > s_operator_parens_called< / a > ++;< / div >
< div class = "line" > < a id = "l01505" name = "l01505" > < / a > < span class = "lineno" > 1505< / span > std::vector< double> y_trial = < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a3bc901d2d8234d1f61e94d0fe0777f7d" > m_Y_full_initial< / a > ;< / div >
< div class = "line" > < a id = "l01506" name = "l01506" > < / a > < span class = "lineno" > 1506< / span > Eigen::VectorXd y_qse = < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a8dd40205db7aef439b6f04289ca5dfd5" > m_Y_scale< / a > .array() * v_qse.array().sinh(); < span class = "comment" > // Convert to physical abundances using asinh scaling< / span > < / div >
< div class = "line" > < a id = "l01507" name = "l01507" > < / a > < span class = "lineno" > 1507< / span > < / div >
< div class = "line" > < a id = "l01508" name = "l01508" > < / a > < span class = "lineno" > 1508< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > .size(); ++i) {< / div >
< div class = "line" > < a id = "l01509" name = "l01509" > < / a > < span class = "lineno" > 1509< / span > y_trial[< a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > [i]] = y_qse(i);< / div >
< div class = "line" > < a id = "l01510" name = "l01510" > < / a > < span class = "lineno" > 1510< / span > }< / div >
< div class = "line" > < a id = "l01511" name = "l01511" > < / a > < span class = "lineno" > 1511< / span > < / div >
< div class = "line" > < a id = "l01512" name = "l01512" > < / a > < span class = "lineno" > 1512< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > result = < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#af2acc70592e5545f9e8f0a33e10ffdc7" > m_view< / a > -> getBaseEngine().calculateRHSAndEnergy(y_trial, < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a7f65ed75e9dca9b6e1160ad297e07678" > m_T9< / a > , < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4dc013f4fb9d93b38ef601741dbe4d4c" > m_rho< / a > );< / div >
< div class = "line" > < a id = "l01513" name = "l01513" > < / a > < span class = "lineno" > 1513< / span > < span class = "keywordflow" > if< / span > (!result) {< / div >
< div class = "line" > < a id = "l01514" name = "l01514" > < / a > < span class = "lineno" > 1514< / span > < span class = "keywordflow" > throw< / span > < a class = "code hl_class" href = "classgridfire_1_1exceptions_1_1_stale_engine_error.html" > exceptions::StaleEngineError< / a > (< span class = "stringliteral" > " Failed to calculate RHS and energy due to stale engine state" < / span > );< / div >
< div class = "line" > < a id = "l01515" name = "l01515" > < / a > < span class = "lineno" > 1515< / span > }< / div >
< div class = "line" > < a id = "l01516" name = "l01516" > < / a > < span class = "lineno" > 1516< / span > < span class = "keyword" > const< / span > < span class = "keyword" > auto< / span > & [dydt, nuclearEnergyGenerationRate] = result.value();< / div >
< div class = "line" > < a id = "l01517" name = "l01517" > < / a > < span class = "lineno" > 1517< / span > f_qse.resize(< a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > .size());< / div >
< div class = "line" > < a id = "l01518" name = "l01518" > < / a > < span class = "lineno" > 1518< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > .size(); ++i) {< / div >
< div class = "line" > < a id = "l01519" name = "l01519" > < / a > < span class = "lineno" > 1519< / span > f_qse(i) = dydt[< a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > [i]];< / div >
< div class = "line" > < a id = "l01520" name = "l01520" > < / a > < span class = "lineno" > 1520< / span > }< / div >
< div class = "line" > < a id = "l01521" name = "l01521" > < / a > < span class = "lineno" > 1521< / span > < / div >
< div class = "line" > < a id = "l01522" name = "l01522" > < / a > < span class = "lineno" > 1522< / span > < span class = "keywordflow" > return< / span > 0; < span class = "comment" > // Success< / span > < / div >
< div class = "line" > < a id = "l01523" name = "l01523" > < / a > < span class = "lineno" > 1523< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01524" name = "l01524" > < / a > < span class = "lineno" > 1524< / span > < / div >
< div class = "foldopen" id = "foldopen01525" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01525" name = "l01525" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#aa65aec7175a56a31887b8b8fca5434bc" > 1525< / a > < / span > < span class = "keywordtype" > int< / span > < a class = "code hl_function" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#aa65aec7175a56a31887b8b8fca5434bc" > MultiscalePartitioningEngineView::EigenFunctor::df< / a > (< span class = "keyword" > const< / span > < a class = "code hl_typedef" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a3ebf684b36e98da38d8ee6f0be4f91e2" > InputType< / a > & v_qse, < a class = "code hl_typedef" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#ad7353c20a6eac2ac0d9d13791577080d" > JacobianType< / a > & J_qse)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01526" name = "l01526" > < / a > < span class = "lineno" > 1526< / span > std::vector< double> y_trial = < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a3bc901d2d8234d1f61e94d0fe0777f7d" > m_Y_full_initial< / a > ;< / div >
< div class = "line" > < a id = "l01527" name = "l01527" > < / a > < span class = "lineno" > 1527< / span > Eigen::VectorXd y_qse = < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a8dd40205db7aef439b6f04289ca5dfd5" > m_Y_scale< / a > .array() * v_qse.array().sinh(); < span class = "comment" > // Convert to physical abundances using asinh scaling< / span > < / div >
< div class = "line" > < a id = "l01528" name = "l01528" > < / a > < span class = "lineno" > 1528< / span > < / div >
< div class = "line" > < a id = "l01529" name = "l01529" > < / a > < span class = "lineno" > 1529< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > .size(); ++i) {< / div >
< div class = "line" > < a id = "l01530" name = "l01530" > < / a > < span class = "lineno" > 1530< / span > y_trial[< a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > [i]] = y_qse(i);< / div >
< div class = "line" > < a id = "l01531" name = "l01531" > < / a > < span class = "lineno" > 1531< / span > }< / div >
< div class = "line" > < a id = "l01532" name = "l01532" > < / a > < span class = "lineno" > 1532< / span > < / div >
< div class = "line" > < a id = "l01533" name = "l01533" > < / a > < span class = "lineno" > 1533< / span > < span class = "comment" > // TODO: Think about if the jacobian matrix should be mutable so that generateJacobianMatrix can be const< / span > < / div >
< div class = "line" > < a id = "l01534" name = "l01534" > < / a > < span class = "lineno" > 1534< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#af2acc70592e5545f9e8f0a33e10ffdc7" > m_view< / a > -> getBaseEngine().generateJacobianMatrix(y_trial, < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a7f65ed75e9dca9b6e1160ad297e07678" > m_T9< / a > , < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4dc013f4fb9d93b38ef601741dbe4d4c" > m_rho< / a > );< / div >
< div class = "line" > < a id = "l01535" name = "l01535" > < / a > < span class = "lineno" > 1535< / span > < / div >
< div class = "line" > < a id = "l01536" name = "l01536" > < / a > < span class = "lineno" > 1536< / span > < span class = "comment" > // TODO: Think very carefully about the indices here.< / span > < / div >
< div class = "line" > < a id = "l01537" name = "l01537" > < / a > < span class = "lineno" > 1537< / span > J_qse.resize(< a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > .size(), < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > .size());< / div >
< div class = "line" > < a id = "l01538" name = "l01538" > < / a > < span class = "lineno" > 1538< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > i = 0; i < < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > .size(); ++i) {< / div >
< div class = "line" > < a id = "l01539" name = "l01539" > < / a > < span class = "lineno" > 1539< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > size_t< / span > j = 0; j < < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > .size(); ++j) {< / div >
< div class = "line" > < a id = "l01540" name = "l01540" > < / a > < span class = "lineno" > 1540< / span > J_qse(i, j) = < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#af2acc70592e5545f9e8f0a33e10ffdc7" > m_view< / a > -> getBaseEngine().getJacobianMatrixEntry(< / div >
< div class = "line" > < a id = "l01541" name = "l01541" > < / a > < span class = "lineno" > 1541< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > [i],< / div >
< div class = "line" > < a id = "l01542" name = "l01542" > < / a > < span class = "lineno" > 1542< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > m_qse_solve_indices< / a > [j]< / div >
< div class = "line" > < a id = "l01543" name = "l01543" > < / a > < span class = "lineno" > 1543< / span > );< / div >
< div class = "line" > < a id = "l01544" name = "l01544" > < / a > < span class = "lineno" > 1544< / span > }< / div >
< div class = "line" > < a id = "l01545" name = "l01545" > < / a > < span class = "lineno" > 1545< / span > }< / div >
< div class = "line" > < a id = "l01546" name = "l01546" > < / a > < span class = "lineno" > 1546< / span > < / div >
< div class = "line" > < a id = "l01547" name = "l01547" > < / a > < span class = "lineno" > 1547< / span > < span class = "comment" > // Chain rule for asinh scaling:< / span > < / div >
< div class = "line" > < a id = "l01548" name = "l01548" > < / a > < span class = "lineno" > 1548< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > long< / span > j = 0; j < J_qse.cols(); ++j) {< / div >
< div class = "line" > < a id = "l01549" name = "l01549" > < / a > < span class = "lineno" > 1549< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > dY_dv = < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a8dd40205db7aef439b6f04289ca5dfd5" > m_Y_scale< / a > (j) * std::cosh(v_qse(j));< / div >
< div class = "line" > < a id = "l01550" name = "l01550" > < / a > < span class = "lineno" > 1550< / span > J_qse.col(j) *= dY_dv; < span class = "comment" > // Scale the column by the derivative of the asinh scaling< / span > < / div >
< div class = "line" > < a id = "l01551" name = "l01551" > < / a > < span class = "lineno" > 1551< / span > }< / div >
< div class = "line" > < a id = "l01552" name = "l01552" > < / a > < span class = "lineno" > 1552< / span > < span class = "keywordflow" > return< / span > 0; < span class = "comment" > // Success< / span > < / div >
< div class = "line" > < a id = "l01553" name = "l01553" > < / a > < span class = "lineno" > 1553< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01554" name = "l01554" > < / a > < span class = "lineno" > 1554< / span > < / div >
< div class = "line" > < a id = "l01555" name = "l01555" > < / a > < span class = "lineno" > 1555< / span > < / div >
< div class = "foldopen" id = "foldopen01556" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01556" name = "l01556" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_q_s_e_cache_key.html#a3078528fc69b8e687448d3108a216c03" > 1556< / a > < / span > < a class = "code hl_function" href = "structgridfire_1_1_q_s_e_cache_key.html#a3078528fc69b8e687448d3108a216c03" > QSECacheKey::QSECacheKey< / a > (< / div >
< div class = "line" > < a id = "l01557" name = "l01557" > < / a > < span class = "lineno" > 1557< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > T9,< / div >
< div class = "line" > < a id = "l01558" name = "l01558" > < / a > < span class = "lineno" > 1558< / span > < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > rho,< / div >
< div class = "line" > < a id = "l01559" name = "l01559" > < / a > < span class = "lineno" > 1559< / span > < span class = "keyword" > const< / span > std::vector< double> & Y< / div >
< div class = "line" > < a id = "l01560" name = "l01560" > < / a > < span class = "lineno" > 1560< / span > ) :< / div >
< div class = "line" > < a id = "l01561" name = "l01561" > < / a > < span class = "lineno" > 1561< / span > < a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#a2ab20b15ab7f9da15c36989e8d9a2bc7" > m_T9< / a > (T9),< / div >
< div class = "line" > < a id = "l01562" name = "l01562" > < / a > < span class = "lineno" > 1562< / span > < a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#abb0d1c5b8c88ae2edbc1f8d3b8759f63" > m_rho< / a > (rho),< / div >
< div class = "line" > < a id = "l01563" name = "l01563" > < / a > < span class = "lineno" > 1563< / span > < a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#afa8f157d3dd3505276294815357b028a" > m_Y< / a > (Y) {< / div >
< div class = "line" > < a id = "l01564" name = "l01564" > < / a > < span class = "lineno" > 1564< / span > < a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#ab860b40d4ccb3c16a962d96bc767ff05" > m_hash< / a > = < a class = "code hl_function" href = "structgridfire_1_1_q_s_e_cache_key.html#a99772155522bf6cbe08313565444a39d" > hash< / a > ();< / div >
< div class = "line" > < a id = "l01565" name = "l01565" > < / a > < span class = "lineno" > 1565< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01566" name = "l01566" > < / a > < span class = "lineno" > 1566< / span > < / div >
< div class = "foldopen" id = "foldopen01567" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01567" name = "l01567" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_q_s_e_cache_key.html#a99772155522bf6cbe08313565444a39d" > 1567< / a > < / span > < span class = "keywordtype" > size_t< / span > < a class = "code hl_function" href = "structgridfire_1_1_q_s_e_cache_key.html#a99772155522bf6cbe08313565444a39d" > QSECacheKey::hash< / a > ()< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01568" name = "l01568" > < / a > < span class = "lineno" > 1568< / span > std::size_t seed = 0;< / div >
< div class = "line" > < a id = "l01569" name = "l01569" > < / a > < span class = "lineno" > 1569< / span > < / div >
< div class = "line" > < a id = "l01570" name = "l01570" > < / a > < span class = "lineno" > 1570< / span > hash_combine(seed, < a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#afa8f157d3dd3505276294815357b028a" > m_Y< / a > .size());< / div >
< div class = "line" > < a id = "l01571" name = "l01571" > < / a > < span class = "lineno" > 1571< / span > < / div >
< div class = "line" > < a id = "l01572" name = "l01572" > < / a > < span class = "lineno" > 1572< / span > hash_combine(seed, < a class = "code hl_function" href = "structgridfire_1_1_q_s_e_cache_key.html#ac7e043ac0254936602c37a7e6a1391b3" > bin< / a > (< a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#a2ab20b15ab7f9da15c36989e8d9a2bc7" > m_T9< / a > , < a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#a711acccecadd93495fd08c81838be2d8" > m_cacheConfig< / a > .T9_tol));< / div >
< div class = "line" > < a id = "l01573" name = "l01573" > < / a > < span class = "lineno" > 1573< / span > hash_combine(seed, < a class = "code hl_function" href = "structgridfire_1_1_q_s_e_cache_key.html#ac7e043ac0254936602c37a7e6a1391b3" > bin< / a > (< a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#abb0d1c5b8c88ae2edbc1f8d3b8759f63" > m_rho< / a > , < a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#a711acccecadd93495fd08c81838be2d8" > m_cacheConfig< / a > .rho_tol));< / div >
< div class = "line" > < a id = "l01574" name = "l01574" > < / a > < span class = "lineno" > 1574< / span > < / div >
< div class = "line" > < a id = "l01575" name = "l01575" > < / a > < span class = "lineno" > 1575< / span > < span class = "keywordflow" > for< / span > (< span class = "keywordtype" > double< / span > Yi : < a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#afa8f157d3dd3505276294815357b028a" > m_Y< / a > ) {< / div >
< div class = "line" > < a id = "l01576" name = "l01576" > < / a > < span class = "lineno" > 1576< / span > < span class = "keywordflow" > if< / span > (Yi < 0.0 & & std::abs(Yi) < 1e-20) {< / div >
< div class = "line" > < a id = "l01577" name = "l01577" > < / a > < span class = "lineno" > 1577< / span > Yi = 0.0; < span class = "comment" > // Avoid negative abundances< / span > < / div >
< div class = "line" > < a id = "l01578" name = "l01578" > < / a > < span class = "lineno" > 1578< / span > } < span class = "keywordflow" > else< / span > < span class = "keywordflow" > if< / span > (Yi < 0.0 & & std::abs(Yi) > = 1e-20) {< / div >
< div class = "line" > < a id = "l01579" name = "l01579" > < / a > < span class = "lineno" > 1579< / span > < span class = "keywordflow" > throw< / span > std::invalid_argument(< span class = "stringliteral" > " Yi should be positive for valid hashing (expected Yi > 0, received " < / span > + std::to_string(Yi) + < span class = "stringliteral" > " )" < / span > );< / div >
< div class = "line" > < a id = "l01580" name = "l01580" > < / a > < span class = "lineno" > 1580< / span > }< / div >
< div class = "line" > < a id = "l01581" name = "l01581" > < / a > < span class = "lineno" > 1581< / span > hash_combine(seed, < a class = "code hl_function" href = "structgridfire_1_1_q_s_e_cache_key.html#ac7e043ac0254936602c37a7e6a1391b3" > bin< / a > (Yi, < a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#a711acccecadd93495fd08c81838be2d8" > m_cacheConfig< / a > .Yi_tol));< / div >
< div class = "line" > < a id = "l01582" name = "l01582" > < / a > < span class = "lineno" > 1582< / span > }< / div >
< div class = "line" > < a id = "l01583" name = "l01583" > < / a > < span class = "lineno" > 1583< / span > < / div >
< div class = "line" > < a id = "l01584" name = "l01584" > < / a > < span class = "lineno" > 1584< / span > < span class = "keywordflow" > return< / span > seed;< / div >
< div class = "line" > < a id = "l01585" name = "l01585" > < / a > < span class = "lineno" > 1585< / span > < / div >
< div class = "line" > < a id = "l01586" name = "l01586" > < / a > < span class = "lineno" > 1586< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01587" name = "l01587" > < / a > < span class = "lineno" > 1587< / span > < / div >
< div class = "foldopen" id = "foldopen01588" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01588" name = "l01588" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_q_s_e_cache_key.html#ac7e043ac0254936602c37a7e6a1391b3" > 1588< / a > < / span > < span class = "keywordtype" > long< / span > < a class = "code hl_function" href = "structgridfire_1_1_q_s_e_cache_key.html#ac7e043ac0254936602c37a7e6a1391b3" > QSECacheKey::bin< / a > (< span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > value, < span class = "keyword" > const< / span > < span class = "keywordtype" > double< / span > tol) {< / div >
< div class = "line" > < a id = "l01589" name = "l01589" > < / a > < span class = "lineno" > 1589< / span > < span class = "keywordflow" > return< / span > < span class = "keyword" > static_cast< < / span > < span class = "keywordtype" > long< / span > < span class = "keyword" > > < / span > (std::floor(value / tol));< / div >
< div class = "line" > < a id = "l01590" name = "l01590" > < / a > < span class = "lineno" > 1590< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01591" name = "l01591" > < / a > < span class = "lineno" > 1591< / span > < / div >
< div class = "foldopen" id = "foldopen01592" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01592" name = "l01592" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_q_s_e_cache_key.html#acfd92321fda5bc0ed1d2e803cbae6a81" > 1592< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "structgridfire_1_1_q_s_e_cache_key.html#acfd92321fda5bc0ed1d2e803cbae6a81" > QSECacheKey::operator==< / a > (< span class = "keyword" > const< / span > < a class = "code hl_function" href = "structgridfire_1_1_q_s_e_cache_key.html#a3078528fc69b8e687448d3108a216c03" > QSECacheKey< / a > & other)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01593" name = "l01593" > < / a > < span class = "lineno" > 1593< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#ab860b40d4ccb3c16a962d96bc767ff05" > m_hash< / a > == other.< a class = "code hl_variable" href = "structgridfire_1_1_q_s_e_cache_key.html#ab860b40d4ccb3c16a962d96bc767ff05" > m_hash< / a > ;< / div >
< div class = "line" > < a id = "l01594" name = "l01594" > < / a > < span class = "lineno" > 1594< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01595" name = "l01595" > < / a > < span class = "lineno" > 1595< / span > < / div >
< div class = "foldopen" id = "foldopen01596" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01596" name = "l01596" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a82c2256254ca88e141672891e5228f88" > 1596< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a82c2256254ca88e141672891e5228f88" > MultiscalePartitioningEngineView::QSEGroup::operator==< / a > (< span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html" > QSEGroup< / a > & other)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01597" name = "l01597" > < / a > < span class = "lineno" > 1597< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a66e6677638af72e4db75f5518dc867f9" > mean_timescale< / a > == other.< a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a66e6677638af72e4db75f5518dc867f9" > mean_timescale< / a > ;< / div >
< div class = "line" > < a id = "l01598" name = "l01598" > < / a > < span class = "lineno" > 1598< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01599" name = "l01599" > < / a > < span class = "lineno" > 1599< / span > < / div >
< div class = "foldopen" id = "foldopen01600" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01600" name = "l01600" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a2d09ce96d0d7cfe8f0aeb01f22f07a06" > 1600< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a2d09ce96d0d7cfe8f0aeb01f22f07a06" > MultiscalePartitioningEngineView::QSEGroup::operator< < / a > (< span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html" > QSEGroup< / a > & other)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01601" name = "l01601" > < / a > < span class = "lineno" > 1601< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a66e6677638af72e4db75f5518dc867f9" > mean_timescale< / a > < other.< a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a66e6677638af72e4db75f5518dc867f9" > mean_timescale< / a > ;< / div >
< div class = "line" > < a id = "l01602" name = "l01602" > < / a > < span class = "lineno" > 1602< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01603" name = "l01603" > < / a > < span class = "lineno" > 1603< / span > < / div >
< div class = "foldopen" id = "foldopen01604" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01604" name = "l01604" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a77d5ebb3b85649bddab09e5ee7fac50a" > 1604< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a77d5ebb3b85649bddab09e5ee7fac50a" > MultiscalePartitioningEngineView::QSEGroup::operator> < / a > (< span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html" > QSEGroup< / a > & other)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01605" name = "l01605" > < / a > < span class = "lineno" > 1605< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a66e6677638af72e4db75f5518dc867f9" > mean_timescale< / a > > other.< a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a66e6677638af72e4db75f5518dc867f9" > mean_timescale< / a > ;< / div >
< div class = "line" > < a id = "l01606" name = "l01606" > < / a > < span class = "lineno" > 1606< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01607" name = "l01607" > < / a > < span class = "lineno" > 1607< / span > < / div >
< div class = "foldopen" id = "foldopen01608" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01608" name = "l01608" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#ac81f994476d580a92686e7f84b726c2a" > 1608< / a > < / span > < span class = "keywordtype" > bool< / span > < a class = "code hl_function" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#ac81f994476d580a92686e7f84b726c2a" > MultiscalePartitioningEngineView::QSEGroup::operator!=< / a > (< span class = "keyword" > const< / span > < a class = "code hl_struct" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html" > QSEGroup< / a > & other)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01609" name = "l01609" > < / a > < span class = "lineno" > 1609< / span > < span class = "keywordflow" > return< / span > !(*< span class = "keyword" > this< / span > == other);< / div >
< div class = "line" > < a id = "l01610" name = "l01610" > < / a > < span class = "lineno" > 1610< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01611" name = "l01611" > < / a > < span class = "lineno" > 1611< / span > < / div >
< div class = "foldopen" id = "foldopen01612" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01612" name = "l01612" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#a5eb642e161ffb5500ccc1e412849ee5e" > 1612< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#a5eb642e161ffb5500ccc1e412849ee5e" > MultiscalePartitioningEngineView::CacheStats::hit< / a > (< span class = "keyword" > const< / span > < a class = "code hl_enumeration" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505" > operators< / a > op) {< / div >
< div class = "line" > < a id = "l01613" name = "l01613" > < / a > < span class = "lineno" > 1613< / span > < span class = "keywordflow" > if< / span > (op == < a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505ab1c94ca2fbc3e78fc30069c8d0f01680" > operators::All< / a > ) {< / div >
< div class = "line" > < a id = "l01614" name = "l01614" > < / a > < span class = "lineno" > 1614< / span > < span class = "keywordflow" > throw< / span > std::invalid_argument(< span class = "stringliteral" > " Cannot use ' ALL' as an operator for a hit" < / span > );< / div >
< div class = "line" > < a id = "l01615" name = "l01615" > < / a > < span class = "lineno" > 1615< / span > }< / div >
< div class = "line" > < a id = "l01616" name = "l01616" > < / a > < span class = "lineno" > 1616< / span > < / div >
< div class = "line" > < a id = "l01617" name = "l01617" > < / a > < span class = "lineno" > 1617< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#a0c3bd8d5918e344657227a09cd7e39a5" > m_hit< / a > ++;< / div >
< div class = "line" > < a id = "l01618" name = "l01618" > < / a > < span class = "lineno" > 1618< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac18229250c4c160aada96e19325faa29" > m_operatorHits< / a > [op]++;< / div >
< div class = "line" > < a id = "l01619" name = "l01619" > < / a > < span class = "lineno" > 1619< / span > }< / div >
< / div >
< div class = "foldopen" id = "foldopen01620" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01620" name = "l01620" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac55fb580dd4b9763cefe4612555b03f3" > 1620< / a > < / span > < span class = "keywordtype" > void< / span > < a class = "code hl_function" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac55fb580dd4b9763cefe4612555b03f3" > MultiscalePartitioningEngineView::CacheStats::miss< / a > (< span class = "keyword" > const< / span > < a class = "code hl_enumeration" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505" > operators< / a > op) {< / div >
< div class = "line" > < a id = "l01621" name = "l01621" > < / a > < span class = "lineno" > 1621< / span > < span class = "keywordflow" > if< / span > (op == < a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505ab1c94ca2fbc3e78fc30069c8d0f01680" > operators::All< / a > ) {< / div >
< div class = "line" > < a id = "l01622" name = "l01622" > < / a > < span class = "lineno" > 1622< / span > < span class = "keywordflow" > throw< / span > std::invalid_argument(< span class = "stringliteral" > " Cannot use ' ALL' as an operator for a miss" < / span > );< / div >
< div class = "line" > < a id = "l01623" name = "l01623" > < / a > < span class = "lineno" > 1623< / span > }< / div >
< div class = "line" > < a id = "l01624" name = "l01624" > < / a > < span class = "lineno" > 1624< / span > < / div >
< div class = "line" > < a id = "l01625" name = "l01625" > < / a > < span class = "lineno" > 1625< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#a73ca615753553f4a85160bd9f166da5b" > m_miss< / a > ++;< / div >
< div class = "line" > < a id = "l01626" name = "l01626" > < / a > < span class = "lineno" > 1626< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#afc5299ebf09f9b208f65619012902b77" > m_operatorMisses< / a > [op]++;< / div >
< div class = "line" > < a id = "l01627" name = "l01627" > < / a > < span class = "lineno" > 1627< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01628" name = "l01628" > < / a > < span class = "lineno" > 1628< / span > < / div >
< div class = "foldopen" id = "foldopen01629" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01629" name = "l01629" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#aaf8b925a169a732c14f4451a33451f51" > 1629< / a > < / span > < span class = "keywordtype" > size_t< / span > < a class = "code hl_function" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#aaf8b925a169a732c14f4451a33451f51" > MultiscalePartitioningEngineView::CacheStats::hits< / a > (< span class = "keyword" > const< / span > < a class = "code hl_enumeration" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505" > operators< / a > op)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01630" name = "l01630" > < / a > < span class = "lineno" > 1630< / span > < span class = "keywordflow" > if< / span > (op == < a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505ab1c94ca2fbc3e78fc30069c8d0f01680" > operators::All< / a > ) {< / div >
< div class = "line" > < a id = "l01631" name = "l01631" > < / a > < span class = "lineno" > 1631< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#a0c3bd8d5918e344657227a09cd7e39a5" > m_hit< / a > ;< / div >
< div class = "line" > < a id = "l01632" name = "l01632" > < / a > < span class = "lineno" > 1632< / span > }< / div >
< div class = "line" > < a id = "l01633" name = "l01633" > < / a > < span class = "lineno" > 1633< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac18229250c4c160aada96e19325faa29" > m_operatorHits< / a > .at(op);< / div >
< div class = "line" > < a id = "l01634" name = "l01634" > < / a > < span class = "lineno" > 1634< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01635" name = "l01635" > < / a > < span class = "lineno" > 1635< / span > < / div >
< div class = "foldopen" id = "foldopen01636" data-start = "{" data-end = "}" >
< div class = "line" > < a id = "l01636" name = "l01636" > < / a > < span class = "lineno" > < a class = "line" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#a5df4f2c27e9eaa781c972a8c9b595787" > 1636< / a > < / span > < span class = "keywordtype" > size_t< / span > < a class = "code hl_function" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#a5df4f2c27e9eaa781c972a8c9b595787" > MultiscalePartitioningEngineView::CacheStats::misses< / a > (< span class = "keyword" > const< / span > < a class = "code hl_enumeration" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505" > operators< / a > op)< span class = "keyword" > const < / span > {< / div >
< div class = "line" > < a id = "l01637" name = "l01637" > < / a > < span class = "lineno" > 1637< / span > < span class = "keywordflow" > if< / span > (op == < a class = "code hl_enumvalue" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505ab1c94ca2fbc3e78fc30069c8d0f01680" > operators::All< / a > ) {< / div >
< div class = "line" > < a id = "l01638" name = "l01638" > < / a > < span class = "lineno" > 1638< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#a73ca615753553f4a85160bd9f166da5b" > m_miss< / a > ;< / div >
< div class = "line" > < a id = "l01639" name = "l01639" > < / a > < span class = "lineno" > 1639< / span > }< / div >
< div class = "line" > < a id = "l01640" name = "l01640" > < / a > < span class = "lineno" > 1640< / span > < span class = "keywordflow" > return< / span > < a class = "code hl_variable" href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#afc5299ebf09f9b208f65619012902b77" > m_operatorMisses< / a > .at(op);< / div >
< div class = "line" > < a id = "l01641" name = "l01641" > < / a > < span class = "lineno" > 1641< / span > }< / div >
< / div >
< div class = "line" > < a id = "l01642" name = "l01642" > < / a > < span class = "lineno" > 1642< / span > < / div >
< div class = "line" > < a id = "l01643" name = "l01643" > < / a > < span class = "lineno" > 1643< / span > }< / 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 >
2025-07-30 15:12:46 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html" > gridfire::GraphEngine< / a > < / div > < div class = "ttdoc" > A reaction network engine that uses a graph-based representation.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8h_source.html#l00100" > engine_graph.h:100< / a > < / div > < / div >
2025-07-24 11:10:45 -04:00
< div class = "ttc" id = "aclassgridfire_1_1_graph_engine_html_a0ed390f3e598ebba4e245ac90bb78767" > < div class = "ttname" > < a href = "classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767" > gridfire::GraphEngine::getNetworkSpecies< / a > < / div > < div class = "ttdeci" > const std::vector< fourdst::atomic::Species > & getNetworkSpecies() const override< / div > < div class = "ttdoc" > Gets the list of species in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__graph_8cpp_source.html#l00162" > engine_graph.cpp:162< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a0437c51f94bf834a11adf481b2afad93" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0437c51f94bf834a11adf481b2afad93" > gridfire::MultiscalePartitioningEngineView::m_baseEngine< / a > < / div > < div class = "ttdeci" > GraphEngine & m_baseEngine< / div > < div class = "ttdoc" > The base engine to which this view delegates calculations.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00914" > engine_multiscale.h:914< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a05730ced13ac5331060ca011f0da6235" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a05730ced13ac5331060ca011f0da6235" > gridfire::MultiscalePartitioningEngineView::primeEngine< / a > < / div > < div class = "ttdeci" > PrimingReport primeEngine(const NetIn & netIn) override< / div > < div class = "ttdoc" > Primes the engine with a specific species.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00793" > engine_multiscale.cpp:793< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a0df457c0f0f6f403a295335c84fd828f" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a0df457c0f0f6f403a295335c84fd828f" > gridfire::MultiscalePartitioningEngineView::MultiscalePartitioningEngineView< / a > < / div > < div class = "ttdeci" > MultiscalePartitioningEngineView(GraphEngine & baseEngine)< / div > < div class = "ttdoc" > Constructs a MultiscalePartitioningEngineView.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00153" > engine_multiscale.cpp:153< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a1a0c0a0ade632eb10f0eecab828a059f" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1a0c0a0ade632eb10f0eecab828a059f" > gridfire::MultiscalePartitioningEngineView::setScreeningModel< / a > < / div > < div class = "ttdeci" > void setScreeningModel(screening::ScreeningType model) override< / div > < div class = "ttdoc" > Sets the electron screening model.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00402" > engine_multiscale.cpp:402< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a1b4aa04a1e641204e4fd82361b0e39c6" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1b4aa04a1e641204e4fd82361b0e39c6" > gridfire::MultiscalePartitioningEngineView::m_qse_groups< / a > < / div > < div class = "ttdeci" > std::vector< QSEGroup > m_qse_groups< / div > < div class = "ttdoc" > The list of identified equilibrium groups.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00918" > engine_multiscale.h:918< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a1e04e8cb8c84b1bd033ac599accf0888" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a1e04e8cb8c84b1bd033ac599accf0888" > gridfire::MultiscalePartitioningEngineView::getDynamicSpecies< / a > < / div > < div class = "ttdeci" > const std::vector< fourdst::atomic::Species > & getDynamicSpecies() const< / div > < div class = "ttdoc" > Gets the dynamic species in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00789" > engine_multiscale.cpp:789< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a22bd1f0e821ed415611d75bac67063d1" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a22bd1f0e821ed415611d75bac67063d1" > gridfire::MultiscalePartitioningEngineView::getBaseEngine< / a > < / div > < div class = "ttdeci" > const DynamicEngine & getBaseEngine() const override< / div > < div class = "ttdoc" > Gets the base engine.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00412" > engine_multiscale.cpp:412< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a38b4f0373c3bd81503889650c0bb69bb" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a38b4f0373c3bd81503889650c0bb69bb" > gridfire::MultiscalePartitioningEngineView::m_dynamic_species_indices< / a > < / div > < div class = "ttdeci" > std::vector< size_t > m_dynamic_species_indices< / div > < div class = "ttdoc" > Indices mapping the dynamic species back to the base engine' s full species list.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00926" > engine_multiscale.h:926< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a3c5fcb8e3396d74359fd601554c9ffa9" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c5fcb8e3396d74359fd601554c9ffa9" > gridfire::MultiscalePartitioningEngineView::solveQSEAbundances< / a > < / div > < div class = "ttdeci" > std::vector< double > solveQSEAbundances(const std::vector< double > & Y_full, double T9, double rho)< / div > < div class = "ttdoc" > Solves for the QSE abundances of the algebraic species in a given state.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01136" > engine_multiscale.cpp:1136< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a3c82e4e082d1c82b1b090ac9847c7c5e" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c82e4e082d1c82b1b090ac9847c7c5e" > gridfire::MultiscalePartitioningEngineView::getFastSpecies< / a > < / div > < div class = "ttdeci" > std::vector< fourdst::atomic::Species > getFastSpecies() const< / div > < div class = "ttdoc" > Gets the fast species in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00776" > engine_multiscale.cpp:776< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a4656c05b8235dbf4ec698b03a716a8c8" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a4656c05b8235dbf4ec698b03a716a8c8" > gridfire::MultiscalePartitioningEngineView::m_algebraic_species< / a > < / div > < div class = "ttdeci" > std::vector< fourdst::atomic::Species > m_algebraic_species< / div > < div class = "ttdoc" > Species that are treated as algebraic (in QSE) in the QSE groups.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00930" > engine_multiscale.h:930< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a4bc879246c6fbd8633b05052858df51d" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a4bc879246c6fbd8633b05052858df51d" > gridfire::MultiscalePartitioningEngineView::equilibrateNetwork< / a > < / div > < div class = "ttdeci" > fourdst::composition::Composition equilibrateNetwork(const std::vector< double > & Y, double T9, double rho)< / div > < div class = "ttdoc" > Equilibrates the network by partitioning and solving for QSE abundances.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00797" > engine_multiscale.cpp:797< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a510b920dea726aef859ac1f6d051807e" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a510b920dea726aef859ac1f6d051807e" > gridfire::MultiscalePartitioningEngineView::getStoichiometryMatrixEntry< / a > < / div > < div class = "ttdeci" > int getStoichiometryMatrixEntry(int speciesIndex, int reactionIndex) const override< / div > < div class = "ttdoc" > Gets an entry from the stoichiometry matrix.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00246" > engine_multiscale.cpp:246< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a53862719dd73f98bc69eecde090cf655" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a53862719dd73f98bc69eecde090cf655" > gridfire::MultiscalePartitioningEngineView::m_algebraic_species_indices< / a > < / div > < div class = "ttdeci" > std::vector< size_t > m_algebraic_species_indices< / div > < div class = "ttdoc" > Indices of algebraic species in the full network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00934" > engine_multiscale.h:934< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a54ca8004fbd8d6d3ea6f67efeb5dbc8d" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a54ca8004fbd8d6d3ea6f67efeb5dbc8d" > gridfire::MultiscalePartitioningEngineView::identifyMeanSlowestPool< / a > < / div > < div class = "ttdeci" > size_t identifyMeanSlowestPool(const std::vector< std::vector< size_t > > & pools, const std::vector< double > & Y, double T9, double rho) const< / div > < div class = "ttdoc" > Identifies the pool with the slowest mean timescale.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01291" > engine_multiscale.cpp:1291< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a560612347bbd5b7b380e990624d01105" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a560612347bbd5b7b380e990624d01105" > gridfire::MultiscalePartitioningEngineView::getSpeciesTimescales< / a > < / div > < div class = "ttdeci" > std::expected< std::unordered_map< fourdst::atomic::Species, double > , expectations::StaleEngineError > getSpeciesTimescales(const std::vector< double > & Y, double T9, double rho) const override< / div > < div class = "ttdoc" > Computes timescales for all species in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00295" > engine_multiscale.cpp:295< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a696f74f5135bbd62169b6577f92fee80" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a696f74f5135bbd62169b6577f92fee80" > gridfire::MultiscalePartitioningEngineView::getNetworkSpecies< / a > < / div > < div class = "ttdeci" > const std::vector< fourdst::atomic::Species > & getNetworkSpecies() const override< / div > < div class = "ttdoc" > Gets the list of species in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00157" > engine_multiscale.cpp:157< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a6bee75b5a6e508e6eebf83f0d48c50b8" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a6bee75b5a6e508e6eebf83f0d48c50b8" > gridfire::MultiscalePartitioningEngineView::update< / a > < / div > < div class = "ttdeci" > fourdst::composition::Composition update(const NetIn & netIn) override< / div > < div class = "ttdoc" > Updates the internal state of the engine, performing partitioning and QSE equilibration.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00356" > engine_multiscale.cpp:356< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a707e46d2f72993c206210f81b35b884e" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a707e46d2f72993c206210f81b35b884e" > gridfire::MultiscalePartitioningEngineView::m_qse_abundance_cache< / a > < / div > < div class = "ttdeci" > std::unordered_map< QSECacheKey, std::vector< double > > m_qse_abundance_cache< / div > < div class = "ttdoc" > Cache for QSE abundances based on T9, rho, and Y.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00953" > engine_multiscale.h:953< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a716d7357e944e8394d8b8e0b5e7625eb" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a716d7357e944e8394d8b8e0b5e7625eb" > gridfire::MultiscalePartitioningEngineView::calculateRHSAndEnergy< / a > < / div > < div class = "ttdeci" > std::expected< StepDerivatives< double > , expectations::StaleEngineError > calculateRHSAndEnergy(const std::vector< double > & Y_full, double T9, double rho) const override< / div > < div class = "ttdoc" > Calculates the right-hand side (dY/dt) and energy generation.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00161" > engine_multiscale.cpp:161< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a79eb9c108d694a27ec913ed0143aa044" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a79eb9c108d694a27ec913ed0143aa044" > gridfire::MultiscalePartitioningEngineView::calculateMolarReactionFlow< / a > < / div > < div class = "ttdeci" > double calculateMolarReactionFlow(const reaction::Reaction & reaction, const std::vector< double > & Y_full, double T9, double rho) const override< / div > < div class = "ttdoc" > Calculates the molar reaction flow for a given reaction.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00253" > engine_multiscale.cpp:253< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a7bfb4e6fec2f337a1dea69e3d4f1fc82" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7bfb4e6fec2f337a1dea69e3d4f1fc82" > gridfire::MultiscalePartitioningEngineView::getScreeningModel< / a > < / div > < div class = "ttdeci" > screening::ScreeningType getScreeningModel() const override< / div > < div class = "ttdoc" > Gets the current electron screening model.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00408" > engine_multiscale.cpp:408< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a7d26945df5395b9317552a3989c42d1c" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d26945df5395b9317552a3989c42d1c" > gridfire::MultiscalePartitioningEngineView::partitionNetwork< / a > < / div > < div class = "ttdeci" > void partitionNetwork(const std::vector< double > & Y, double T9, double rho)< / div > < div class = "ttdoc" > Partitions the network into dynamic and algebraic (QSE) groups based on timescales.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00438" > engine_multiscale.cpp:438< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a7d357c775dcbb253a4001d172805380a" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a7d357c775dcbb253a4001d172805380a" > gridfire::MultiscalePartitioningEngineView::m_logger< / a > < / div > < div class = "ttdeci" > quill::Logger * m_logger< / div > < div class = "ttdoc" > Logger instance for logging messages.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00910" > engine_multiscale.h:910< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a91d32b7197fcb27ee697d5bfde960f3f" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#a91d32b7197fcb27ee697d5bfde960f3f" > gridfire::MultiscalePartitioningEngineView::getSpeciesIndex< / a > < / div > < div class = "ttdeci" > int getSpeciesIndex(const fourdst::atomic::Species & species) const override< / div > < div class = "ttdoc" > Gets the index of a species in the full network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00846" > engine_multiscale.cpp:846< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_aa38c367ef3c74d012ccd10521cd5a727" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa38c367ef3c74d012ccd10521cd5a727" > gridfire::MultiscalePartitioningEngineView::getSpeciesDestructionTimescales< / a > < / div > < div class = "ttdeci" > std::expected< std::unordered_map< fourdst::atomic::Species, double > , expectations::StaleEngineError > getSpeciesDestructionTimescales(const std::vector< double > & Y, double T9, double rho) const override< / div > < div class = "ttdoc" > Computes destruction timescales for all species in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00326" > engine_multiscale.cpp:326< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_aa55ed182301d216264daae3e6dfd8917" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa55ed182301d216264daae3e6dfd8917" > gridfire::MultiscalePartitioningEngineView::validateGroupsWithFluxAnalysis< / a > < / div > < div class = "ttdeci" > std::vector< QSEGroup > validateGroupsWithFluxAnalysis(const std::vector< QSEGroup > & candidate_groups, const std::vector< double > & Y, double T9, double rho) const< / div > < div class = "ttdoc" > Validates candidate QSE groups using flux analysis.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01002" > engine_multiscale.cpp:1002< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_aa81057b96cf46986151a5e8ef99a017a" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aa81057b96cf46986151a5e8ef99a017a" > gridfire::MultiscalePartitioningEngineView::m_cacheStats< / a > < / div > < div class = "ttdeci" > CacheStats m_cacheStats< / div > < div class = "ttdoc" > Statistics for the QSE abundance cache.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00957" > engine_multiscale.h:957< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_aada497e8df74a295fdf5df7d7cdf64e0" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aada497e8df74a295fdf5df7d7cdf64e0" > gridfire::MultiscalePartitioningEngineView::mapNetInToMolarAbundanceVector< / a > < / div > < div class = "ttdeci" > std::vector< double > mapNetInToMolarAbundanceVector(const NetIn & netIn) const override< / div > < div class = "ttdoc" > Maps a NetIn struct to a molar abundance vector for the full network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00768" > engine_multiscale.cpp:768< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_aae0865e361dfeb23984d70409fdd9f39" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aae0865e361dfeb23984d70409fdd9f39" > gridfire::MultiscalePartitioningEngineView::buildConnectivityGraph< / a > < / div > < div class = "ttdeci" > std::unordered_map< size_t, std::vector< size_t > > buildConnectivityGraph(const std::unordered_set< size_t > & fast_reaction_indices) const< / div > < div class = "ttdoc" > Builds a connectivity graph from a set of fast reaction indices.< / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_abe76a46784b1ebc8ad67a9eec40d369a" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#abe76a46784b1ebc8ad67a9eec40d369a" > gridfire::MultiscalePartitioningEngineView::generateStoichiometryMatrix< / a > < / div > < div class = "ttdeci" > void generateStoichiometryMatrix() override< / div > < div class = "ttdoc" > Generates the stoichiometry matrix for the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00242" > engine_multiscale.cpp:242< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_ac206840057bac65b7f7738e6dfd1047a" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ac206840057bac65b7f7738e6dfd1047a" > gridfire::MultiscalePartitioningEngineView::constructCandidateGroups< / a > < / div > < div class = "ttdeci" > std::vector< QSEGroup > constructCandidateGroups(const std::vector< std::vector< size_t > > & candidate_pools, const std::vector< double > & Y, double T9, double rho) const< / div > < div class = "ttdoc" > Constructs candidate QSE groups from connected timescale pools.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01405" > engine_multiscale.cpp:1405< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_ac961484383e86d9712a424728e068633" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ac961484383e86d9712a424728e068633" > gridfire::MultiscalePartitioningEngineView::getJacobianMatrixEntry< / a > < / div > < div class = "ttdeci" > double getJacobianMatrixEntry(int i_full, int j_full) const override< / div > < div class = "ttdoc" > Gets an entry from the previously generated Jacobian matrix.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00228" > engine_multiscale.cpp:228< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_acb5fa7f03cd89b8c1b6b9ffdf3abb12e" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#acb5fa7f03cd89b8c1b6b9ffdf3abb12e" > gridfire::MultiscalePartitioningEngineView::setNetworkReactions< / a > < / div > < div class = "ttdeci" > void setNetworkReactions(const reaction::LogicalReactionSet & reactions) override< / div > < div class = "ttdoc" > Sets the set of logical reactions in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00290" > engine_multiscale.cpp:290< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_acdf5ad8765290ea2b78170235aea391d" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#acdf5ad8765290ea2b78170235aea391d" > gridfire::MultiscalePartitioningEngineView::generateJacobianMatrix< / a > < / div > < div class = "ttdeci" > void generateJacobianMatrix(const std::vector< double > & Y_full, double T9, double rho) const override< / div > < div class = "ttdoc" > Generates the Jacobian matrix for the current state.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00204" > engine_multiscale.cpp:204< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_acff59a15abac30eee16e9fa7b355fb18" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#acff59a15abac30eee16e9fa7b355fb18" > gridfire::MultiscalePartitioningEngineView::exportToDot< / a > < / div > < div class = "ttdeci" > void exportToDot(const std::string & filename, const std::vector< double > & Y, const double T9, const double rho) const< / div > < div class = "ttdoc" > Exports the network to a DOT file for visualization.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00558" > engine_multiscale.cpp:558< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_ad4d29ee55f89384807616d1068797067" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ad4d29ee55f89384807616d1068797067" > gridfire::MultiscalePartitioningEngineView::partitionByTimescale< / a > < / div > < div class = "ttdeci" > std::vector< std::vector< size_t > > partitionByTimescale(const std::vector< double > & Y_full, double T9, double rho) const< / div > < div class = "ttdoc" > Partitions the network by timescale.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00850" > engine_multiscale.cpp:850< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_ad751f2c1306895ee74a61f2071ca96eb" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ad751f2c1306895ee74a61f2071ca96eb" > gridfire::MultiscalePartitioningEngineView::getNetworkReactions< / a > < / div > < div class = "ttdeci" > const reaction::LogicalReactionSet & getNetworkReactions() const override< / div > < div class = "ttdoc" > Gets the set of logical reactions in the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00286" > engine_multiscale.cpp:286< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_ae7847959fc5af2b83f5446dd73567b46" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#ae7847959fc5af2b83f5446dd73567b46" > gridfire::MultiscalePartitioningEngineView::isStale< / a > < / div > < div class = "ttdeci" > bool isStale(const NetIn & netIn) override< / div > < div class = "ttdoc" > Checks if the engine' s internal state is stale relative to the provided conditions.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00390" > engine_multiscale.cpp:390< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_aec6126b5c4a397d090790d7b75f9f70f" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#aec6126b5c4a397d090790d7b75f9f70f" > gridfire::MultiscalePartitioningEngineView::m_dynamic_species< / a > < / div > < div class = "ttdeci" > std::vector< fourdst::atomic::Species > m_dynamic_species< / div > < div class = "ttdoc" > The simplified set of species presented to the solver (the " slow" species).< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00922" > engine_multiscale.h:922< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1_multiscale_partitioning_engine_view_html_af13e764c118a6cc51847384e9c70e05b" > < div class = "ttname" > < a href = "classgridfire_1_1_multiscale_partitioning_engine_view.html#af13e764c118a6cc51847384e9c70e05b" > gridfire::MultiscalePartitioningEngineView::analyzeTimescalePoolConnectivity< / a > < / div > < div class = "ttdeci" > std::vector< std::vector< size_t > > analyzeTimescalePoolConnectivity(const std::vector< std::vector< size_t > > & timescale_pools, const std::vector< double > & Y, double T9, double rho) const< / div > < div class = "ttdoc" > Analyzes the connectivity of timescale pools.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00416" > engine_multiscale.cpp:416< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1exceptions_1_1_stale_engine_error_html" > < div class = "ttname" > < a href = "classgridfire_1_1exceptions_1_1_stale_engine_error.html" > gridfire::exceptions::StaleEngineError< / a > < / div > < div class = "ttdef" > < b > Definition< / b > < a href = "error__engine_8h_source.html#l00062" > error_engine.h:62< / a > < / div > < / div >
< div class = "ttc" id = "aclassgridfire_1_1exceptions_1_1_unable_to_set_network_reactions_error_html" > < div class = "ttname" > < a href = "classgridfire_1_1exceptions_1_1_unable_to_set_network_reactions_error.html" > gridfire::exceptions::UnableToSetNetworkReactionsError< / a > < / div > < div class = "ttdef" > < b > Definition< / b > < a href = "error__engine_8h_source.html#l00099" > error_engine.h:99< / a > < / div > < / div >
< 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__multiscale_8h_html" > < div class = "ttname" > < a href = "engine__multiscale_8h.html" > engine_multiscale.h< / a > < / div > < / div >
< div class = "ttc" id = "aerror__engine_8h_html" > < div class = "ttname" > < a href = "error__engine_8h.html" > error_engine.h< / a > < / div > < / div >
< div class = "ttc" id = "anamespacegridfire_1_1expectations_html_aef568e2802c03adef56dbcb6511d66c7a109aa03c8823fcc0ab193b7e48664cbf" > < div class = "ttname" > < a href = "namespacegridfire_1_1expectations.html#aef568e2802c03adef56dbcb6511d66c7a109aa03c8823fcc0ab193b7e48664cbf" > gridfire::expectations::StaleEngineErrorTypes::SYSTEM_RESIZED< / a > < / div > < div class = "ttdeci" > @ SYSTEM_RESIZED< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "expected__engine_8h_source.html#l00014" > expected_engine.h:14< / 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 >
< 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 >
< 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 >
< 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 >
< div class = "ttc" id = "anamespacegridfire_html_a8b632637f62614f509cde0e404a79054" > < div class = "ttname" > < a href = "namespacegridfire.html#a8b632637f62614f509cde0e404a79054" > gridfire::s_operator_parens_called< / a > < / div > < div class = "ttdeci" > static int s_operator_parens_called< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l00150" > engine_multiscale.cpp:150< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_a0c3bd8d5918e344657227a09cd7e39a5" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#a0c3bd8d5918e344657227a09cd7e39a5" > gridfire::MultiscalePartitioningEngineView::CacheStats::m_hit< / a > < / div > < div class = "ttdeci" > size_t m_hit< / div > < div class = "ttdoc" > Total number of cache hits.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00848" > engine_multiscale.h:848< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_a5df4f2c27e9eaa781c972a8c9b595787" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#a5df4f2c27e9eaa781c972a8c9b595787" > gridfire::MultiscalePartitioningEngineView::CacheStats::misses< / a > < / div > < div class = "ttdeci" > size_t misses(const operators op=operators::All) const< / div > < div class = "ttdoc" > Gets the number of misses for a specific operator or all operators.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01636" > engine_multiscale.cpp:1636< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_a5eb642e161ffb5500ccc1e412849ee5e" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#a5eb642e161ffb5500ccc1e412849ee5e" > gridfire::MultiscalePartitioningEngineView::CacheStats::hit< / a > < / div > < div class = "ttdeci" > void hit(const operators op=operators::Other)< / div > < div class = "ttdoc" > Increments the hit counter for a given operator.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01612" > engine_multiscale.cpp:1612< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_a73ca615753553f4a85160bd9f166da5b" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#a73ca615753553f4a85160bd9f166da5b" > gridfire::MultiscalePartitioningEngineView::CacheStats::m_miss< / a > < / div > < div class = "ttdeci" > size_t m_miss< / div > < div class = "ttdoc" > Total number of cache misses.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00852" > engine_multiscale.h:852< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_aaf8b925a169a732c14f4451a33451f51" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#aaf8b925a169a732c14f4451a33451f51" > gridfire::MultiscalePartitioningEngineView::CacheStats::hits< / a > < / div > < div class = "ttdeci" > size_t hits(const operators op=operators::All) const< / div > < div class = "ttdoc" > Gets the number of hits for a specific operator or all operators.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01629" > engine_multiscale.cpp:1629< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_ac18229250c4c160aada96e19325faa29" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac18229250c4c160aada96e19325faa29" > gridfire::MultiscalePartitioningEngineView::CacheStats::m_operatorHits< / a > < / div > < div class = "ttdeci" > std::map< operators,size_t > m_operatorHits< / div > < div class = "ttdoc" > Map from operators to the number of cache hits for that operator.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00857" > engine_multiscale.h:857< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_ac558e59f790508a5e8522c412be5b505" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505" > gridfire::MultiscalePartitioningEngineView::CacheStats::operators< / a > < / div > < div class = "ttdeci" > operators< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00823" > engine_multiscale.h:823< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_ac558e59f790508a5e8522c412be5b505a03d2b9a7ab8b282118ff9e9e2e8c2894" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505a03d2b9a7ab8b282118ff9e9e2e8c2894" > gridfire::MultiscalePartitioningEngineView::CacheStats::operators::CalculateMolarReactionFlow< / a > < / div > < div class = "ttdeci" > @ CalculateMolarReactionFlow< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00826" > engine_multiscale.h:826< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_ac558e59f790508a5e8522c412be5b505a8fa91234134aca6058a27b9a926fdb8a" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505a8fa91234134aca6058a27b9a926fdb8a" > gridfire::MultiscalePartitioningEngineView::CacheStats::operators::GetSpeciesTimescales< / a > < / div > < div class = "ttdeci" > @ GetSpeciesTimescales< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00827" > engine_multiscale.h:827< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_ac558e59f790508a5e8522c412be5b505a9e720102de6020a01552bc0e8935c566" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505a9e720102de6020a01552bc0e8935c566" > gridfire::MultiscalePartitioningEngineView::CacheStats::operators::GenerateJacobianMatrix< / a > < / div > < div class = "ttdeci" > @ GenerateJacobianMatrix< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00825" > engine_multiscale.h:825< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_ac558e59f790508a5e8522c412be5b505a9ee18f2e987928cdb1afa7645a082061" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505a9ee18f2e987928cdb1afa7645a082061" > gridfire::MultiscalePartitioningEngineView::CacheStats::operators::GetSpeciesDestructionTimescales< / a > < / div > < div class = "ttdeci" > @ GetSpeciesDestructionTimescales< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00828" > engine_multiscale.h:828< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_ac558e59f790508a5e8522c412be5b505aafefea58639f78d7c750970bbad28420" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505aafefea58639f78d7c750970bbad28420" > gridfire::MultiscalePartitioningEngineView::CacheStats::operators::CalculateRHSAndEnergy< / a > < / div > < div class = "ttdeci" > @ CalculateRHSAndEnergy< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00824" > engine_multiscale.h:824< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_ac558e59f790508a5e8522c412be5b505ab1c94ca2fbc3e78fc30069c8d0f01680" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac558e59f790508a5e8522c412be5b505ab1c94ca2fbc3e78fc30069c8d0f01680" > gridfire::MultiscalePartitioningEngineView::CacheStats::operators::All< / a > < / div > < div class = "ttdeci" > @ All< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00830" > engine_multiscale.h:830< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_ac55fb580dd4b9763cefe4612555b03f3" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#ac55fb580dd4b9763cefe4612555b03f3" > gridfire::MultiscalePartitioningEngineView::CacheStats::miss< / a > < / div > < div class = "ttdeci" > void miss(const operators op=operators::Other)< / div > < div class = "ttdoc" > Increments the miss counter for a given operator.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01620" > engine_multiscale.cpp:1620< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats_html_afc5299ebf09f9b208f65619012902b77" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_cache_stats.html#afc5299ebf09f9b208f65619012902b77" > gridfire::MultiscalePartitioningEngineView::CacheStats::m_operatorMisses< / a > < / div > < div class = "ttdeci" > std::map< operators,size_t > m_operatorMisses< / div > < div class = "ttdoc" > Map from operators to the number of cache misses for that operator.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00869" > engine_multiscale.h:869< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor_html_a3bc901d2d8234d1f61e94d0fe0777f7d" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a3bc901d2d8234d1f61e94d0fe0777f7d" > gridfire::MultiscalePartitioningEngineView::EigenFunctor::m_Y_full_initial< / a > < / div > < div class = "ttdeci" > const std::vector< double > & m_Y_full_initial< / div > < div class = "ttdoc" > Initial abundances of all species in the full network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00749" > engine_multiscale.h:749< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor_html_a3ebf684b36e98da38d8ee6f0be4f91e2" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a3ebf684b36e98da38d8ee6f0be4f91e2" > gridfire::MultiscalePartitioningEngineView::EigenFunctor::InputType< / a > < / div > < div class = "ttdeci" > Eigen::Matrix< double, Eigen::Dynamic, 1 > InputType< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00730" > engine_multiscale.h:730< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor_html_a4d597d16bd9f982d44512d5a6beddae0" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4d597d16bd9f982d44512d5a6beddae0" > gridfire::MultiscalePartitioningEngineView::EigenFunctor::OutputType< / a > < / div > < div class = "ttdeci" > Eigen::Matrix< double, Eigen::Dynamic, 1 > OutputType< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00731" > engine_multiscale.h:731< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor_html_a4dc013f4fb9d93b38ef601741dbe4d4c" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4dc013f4fb9d93b38ef601741dbe4d4c" > gridfire::MultiscalePartitioningEngineView::EigenFunctor::m_rho< / a > < / div > < div class = "ttdeci" > const double m_rho< / div > < div class = "ttdoc" > Density in g/cm^3.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00757" > engine_multiscale.h:757< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor_html_a4eb11e99dc2a7e038d815bf7c6bd0be8" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a4eb11e99dc2a7e038d815bf7c6bd0be8" > gridfire::MultiscalePartitioningEngineView::EigenFunctor::m_qse_solve_indices< / a > < / div > < div class = "ttdeci" > const std::vector< size_t > & m_qse_solve_indices< / div > < div class = "ttdoc" > Indices of the species to solve for in the QSE group.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00745" > engine_multiscale.h:745< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor_html_a7f65ed75e9dca9b6e1160ad297e07678" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a7f65ed75e9dca9b6e1160ad297e07678" > gridfire::MultiscalePartitioningEngineView::EigenFunctor::m_T9< / a > < / div > < div class = "ttdeci" > const double m_T9< / div > < div class = "ttdoc" > Temperature in units of 10^9 K.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00753" > engine_multiscale.h:753< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor_html_a8dd40205db7aef439b6f04289ca5dfd5" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#a8dd40205db7aef439b6f04289ca5dfd5" > gridfire::MultiscalePartitioningEngineView::EigenFunctor::m_Y_scale< / a > < / div > < div class = "ttdeci" > const Eigen::VectorXd & m_Y_scale< / div > < div class = "ttdoc" > Scaling factors for the species abundances, used to improve solver stability.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00761" > engine_multiscale.h:761< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor_html_aa65aec7175a56a31887b8b8fca5434bc" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#aa65aec7175a56a31887b8b8fca5434bc" > gridfire::MultiscalePartitioningEngineView::EigenFunctor::df< / a > < / div > < div class = "ttdeci" > int df(const InputType & v_qse, JacobianType & J_qse) const< / div > < div class = "ttdoc" > Evaluates the Jacobian of the functor, J_qse = d(f_qse)/d(v_qse).< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01525" > engine_multiscale.cpp:1525< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor_html_ad7353c20a6eac2ac0d9d13791577080d" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#ad7353c20a6eac2ac0d9d13791577080d" > gridfire::MultiscalePartitioningEngineView::EigenFunctor::JacobianType< / a > < / div > < div class = "ttdeci" > Eigen::Matrix< double, Eigen::Dynamic, Eigen::Dynamic > JacobianType< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00732" > engine_multiscale.h:732< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor_html_ad7bd060a3eaaaefab0c31e60dcdb5f28" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#ad7bd060a3eaaaefab0c31e60dcdb5f28" > gridfire::MultiscalePartitioningEngineView::EigenFunctor::operator()< / a > < / div > < div class = "ttdeci" > int operator()(const InputType & v_qse, OutputType & f_qse) const< / div > < div class = "ttdoc" > Evaluates the functor' s residual vector f_qse = dY_alg/dt.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01503" > engine_multiscale.cpp:1503< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor_html_af2acc70592e5545f9e8f0a33e10ffdc7" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_eigen_functor.html#af2acc70592e5545f9e8f0a33e10ffdc7" > gridfire::MultiscalePartitioningEngineView::EigenFunctor::m_view< / a > < / div > < div class = "ttdeci" > MultiscalePartitioningEngineView * m_view< / div > < div class = "ttdoc" > Pointer to the MultiscalePartitioningEngineView instance.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00741" > engine_multiscale.h:741< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group_html" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html" > gridfire::MultiscalePartitioningEngineView::QSEGroup< / a > < / div > < div class = "ttdoc" > Struct representing a QSE group.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00677" > engine_multiscale.h:677< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group_html_a2d09ce96d0d7cfe8f0aeb01f22f07a06" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a2d09ce96d0d7cfe8f0aeb01f22f07a06" > gridfire::MultiscalePartitioningEngineView::QSEGroup::operator< < / a > < / div > < div class = "ttdeci" > bool operator< (const QSEGroup & other) const< / div > < div class = "ttdoc" > Less-than operator for QSEGroup, used for sorting.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01600" > engine_multiscale.cpp:1600< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group_html_a66e6677638af72e4db75f5518dc867f9" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a66e6677638af72e4db75f5518dc867f9" > gridfire::MultiscalePartitioningEngineView::QSEGroup::mean_timescale< / a > < / div > < div class = "ttdeci" > double mean_timescale< / div > < div class = "ttdoc" > Mean timescale of the group.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00682" > engine_multiscale.h:682< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group_html_a77d5ebb3b85649bddab09e5ee7fac50a" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a77d5ebb3b85649bddab09e5ee7fac50a" > gridfire::MultiscalePartitioningEngineView::QSEGroup::operator> < / a > < / div > < div class = "ttdeci" > bool operator> (const QSEGroup & other) const< / div > < div class = "ttdoc" > Greater-than operator for QSEGroup.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01604" > engine_multiscale.cpp:1604< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group_html_a82c2256254ca88e141672891e5228f88" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a82c2256254ca88e141672891e5228f88" > gridfire::MultiscalePartitioningEngineView::QSEGroup::operator==< / a > < / div > < div class = "ttdeci" > bool operator==(const QSEGroup & other) const< / div > < div class = "ttdoc" > Equality operator for QSEGroup.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01596" > engine_multiscale.cpp:1596< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group_html_ac81f994476d580a92686e7f84b726c2a" > < div class = "ttname" > < a href = "structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#ac81f994476d580a92686e7f84b726c2a" > gridfire::MultiscalePartitioningEngineView::QSEGroup::operator!=< / a > < / div > < div class = "ttdeci" > bool operator!=(const QSEGroup & other) const< / div > < div class = "ttdoc" > Inequality operator for QSEGroup.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01608" > engine_multiscale.cpp:1608< / a > < / div > < / div >
< 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 >
< div class = "ttc" id = "astructgridfire_1_1_net_in_html_a06f0dff9f8927b7cf2da3004c8fa1577" > < div class = "ttname" > < a href = "structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577" > gridfire::NetIn::density< / a > < / div > < div class = "ttdeci" > double density< / div > < div class = "ttdoc" > Density in g/cm^3.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "network_8h_source.html#l00058" > network.h:58< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_net_in_html_a13058f4929e72c1187abbebcddb8aed1" > < div class = "ttname" > < a href = "structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1" > gridfire::NetIn::composition< / a > < / div > < div class = "ttdeci" > fourdst::composition::Composition composition< / div > < div class = "ttdoc" > Composition of the network.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "network_8h_source.html#l00054" > network.h:54< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_net_in_html_a5be0f5195a5cd1dd177b9fc5ab83a7be" > < div class = "ttname" > < a href = "structgridfire_1_1_net_in.html#a5be0f5195a5cd1dd177b9fc5ab83a7be" > gridfire::NetIn::temperature< / a > < / div > < div class = "ttdeci" > double temperature< / div > < div class = "ttdoc" > Temperature in Kelvin.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "network_8h_source.html#l00057" > network.h:57< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_priming_report_html" > < div class = "ttname" > < a href = "structgridfire_1_1_priming_report.html" > gridfire::PrimingReport< / a > < / div > < div class = "ttdoc" > Captures the result of a network priming operation.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "reporting_8h_source.html#l00067" > reporting.h:67< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_priming_report_html_a15032fd3354bd8fb383e13929bbd0ceb" > < div class = "ttname" > < a href = "structgridfire_1_1_priming_report.html#a15032fd3354bd8fb383e13929bbd0ceb" > gridfire::PrimingReport::primedComposition< / a > < / div > < div class = "ttdeci" > fourdst::composition::Composition primedComposition< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "reporting_8h_source.html#l00069" > reporting.h:69< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_q_s_e_cache_key_html" > < div class = "ttname" > < a href = "structgridfire_1_1_q_s_e_cache_key.html" > gridfire::QSECacheKey< / a > < / div > < div class = "ttdoc" > Key struct for the QSE abundance cache.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00047" > engine_multiscale.h:47< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_q_s_e_cache_key_html_a2ab20b15ab7f9da15c36989e8d9a2bc7" > < div class = "ttname" > < a href = "structgridfire_1_1_q_s_e_cache_key.html#a2ab20b15ab7f9da15c36989e8d9a2bc7" > gridfire::QSECacheKey::m_T9< / a > < / div > < div class = "ttdeci" > double m_T9< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00048" > engine_multiscale.h:48< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_q_s_e_cache_key_html_a3078528fc69b8e687448d3108a216c03" > < div class = "ttname" > < a href = "structgridfire_1_1_q_s_e_cache_key.html#a3078528fc69b8e687448d3108a216c03" > gridfire::QSECacheKey::QSECacheKey< / a > < / div > < div class = "ttdeci" > QSECacheKey(const double T9, const double rho, const std::vector< double > & Y)< / div > < div class = "ttdoc" > Constructs a QSECacheKey.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01556" > engine_multiscale.cpp:1556< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_q_s_e_cache_key_html_a711acccecadd93495fd08c81838be2d8" > < div class = "ttname" > < a href = "structgridfire_1_1_q_s_e_cache_key.html#a711acccecadd93495fd08c81838be2d8" > gridfire::QSECacheKey::m_cacheConfig< / a > < / div > < div class = "ttdeci" > QSECacheConfig m_cacheConfig< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00055" > engine_multiscale.h:55< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_q_s_e_cache_key_html_a99772155522bf6cbe08313565444a39d" > < div class = "ttname" > < a href = "structgridfire_1_1_q_s_e_cache_key.html#a99772155522bf6cbe08313565444a39d" > gridfire::QSECacheKey::hash< / a > < / div > < div class = "ttdeci" > size_t hash() const< / div > < div class = "ttdoc" > Computes the hash value for this key.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01567" > engine_multiscale.cpp:1567< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_q_s_e_cache_key_html_ab860b40d4ccb3c16a962d96bc767ff05" > < div class = "ttname" > < a href = "structgridfire_1_1_q_s_e_cache_key.html#ab860b40d4ccb3c16a962d96bc767ff05" > gridfire::QSECacheKey::m_hash< / a > < / div > < div class = "ttdeci" > std::size_t m_hash< / div > < div class = "ttdoc" > Precomputed hash value for this key.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00052" > engine_multiscale.h:52< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_q_s_e_cache_key_html_abb0d1c5b8c88ae2edbc1f8d3b8759f63" > < div class = "ttname" > < a href = "structgridfire_1_1_q_s_e_cache_key.html#abb0d1c5b8c88ae2edbc1f8d3b8759f63" > gridfire::QSECacheKey::m_rho< / a > < / div > < div class = "ttdeci" > double m_rho< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00049" > engine_multiscale.h:49< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_q_s_e_cache_key_html_ac7e043ac0254936602c37a7e6a1391b3" > < div class = "ttname" > < a href = "structgridfire_1_1_q_s_e_cache_key.html#ac7e043ac0254936602c37a7e6a1391b3" > gridfire::QSECacheKey::bin< / a > < / div > < div class = "ttdeci" > static long bin(double value, double tol)< / div > < div class = "ttdoc" > Converts a value to a discrete bin based on a tolerance.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01588" > engine_multiscale.cpp:1588< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_q_s_e_cache_key_html_acfd92321fda5bc0ed1d2e803cbae6a81" > < div class = "ttname" > < a href = "structgridfire_1_1_q_s_e_cache_key.html#acfd92321fda5bc0ed1d2e803cbae6a81" > gridfire::QSECacheKey::operator==< / a > < / div > < div class = "ttdeci" > bool operator==(const QSECacheKey & other) const< / div > < div class = "ttdoc" > Equality operator for QSECacheKey.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "#l01592" > engine_multiscale.cpp:1592< / a > < / div > < / div >
< div class = "ttc" id = "astructgridfire_1_1_q_s_e_cache_key_html_afa8f157d3dd3505276294815357b028a" > < div class = "ttname" > < a href = "structgridfire_1_1_q_s_e_cache_key.html#afa8f157d3dd3505276294815357b028a" > gridfire::QSECacheKey::m_Y< / a > < / div > < div class = "ttdeci" > std::vector< double > m_Y< / div > < div class = "ttdoc" > Note that the ordering of Y must match the dynamic species indices in the view.< / div > < div class = "ttdef" > < b > Definition< / b > < a href = "engine__multiscale_8h_source.html#l00050" > engine_multiscale.h:50< / 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 >
< / div > <!-- fragment --> < / div > <!-- contents -->
< / div > <!-- doc - content -->
<!-- start footer part -->
< div id = "nav-path" class = "navpath" > <!-- id is needed for treeview function! -->
< ul >
< li class = "navelem" > < a class = "el" href = "dir_68267d1309a1af8e8297ef4c3efbcdba.html" > src< / a > < / li > < li class = "navelem" > < a class = "el" href = "dir_c85d3e3c5052e9ad9ce18c6863244a25.html" > lib< / a > < / li > < li class = "navelem" > < a class = "el" href = "dir_3cc0b3e3c66436f74054a789a4a47fbc.html" > engine< / a > < / li > < li class = "navelem" > < a class = "el" href = "dir_e87948a39c0c6c3f66d9f5f967ab86bd.html" > views< / a > < / li > < li class = "navelem" > < a class = "el" href = "engine__multiscale_8cpp.html" > engine_multiscale.cpp< / a > < / li >
< li class = "footer" > Generated by < a href = "https://www.doxygen.org/index.html" > < img class = "footer" src = "doxygen.svg" width = "104" height = "31" alt = "doxygen" / > < / a > 1.13.2 < / li >
< / ul >
< / div >
< / body >
< / html >
