1959 lines
377 KiB
HTML
1959 lines
377 KiB
HTML
<!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>
|
|
<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>
|
|
<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>
|