1416 lines
272 KiB
HTML
1416 lines
272 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/engine_graph.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__graph_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_graph.cpp</div></div>
|
|
</div><!--header-->
|
|
<div class="contents">
|
|
<a href="engine__graph_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="preprocessor">#include "<a class="code" href="engine__graph_8h.html">gridfire/engine/engine_graph.h</a>"</span></div>
|
|
<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span><span class="preprocessor">#include "<a class="code" href="reaction_8h.html">gridfire/reaction/reaction.h</a>"</span></div>
|
|
<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="preprocessor">#include "<a class="code" href="network_8h.html">gridfire/network.h</a>"</span></div>
|
|
<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span><span class="preprocessor">#include "<a class="code" href="screening__types_8h.html">gridfire/screening/screening_types.h</a>"</span></div>
|
|
<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span><span class="preprocessor">#include "<a class="code" href="priming_8h.html">gridfire/engine/procedures/priming.h</a>"</span></div>
|
|
<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="preprocessor">#include "<a class="code" href="partition__ground_8h.html">gridfire/partition/partition_ground.h</a>"</span></div>
|
|
<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span><span class="preprocessor">#include "<a class="code" href="construction_8h.html">gridfire/engine/procedures/construction.h</a>"</span></div>
|
|
<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 "fourdst/composition/species.h"</span></div>
|
|
<div class="line"><a id="l00010" name="l00010"></a><span class="lineno"> 10</span><span class="preprocessor">#include "fourdst/composition/atomicSpecies.h"</span></div>
|
|
<div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span> </div>
|
|
<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span><span class="preprocessor">#include "quill/LogMacros.h"</span></div>
|
|
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span> </div>
|
|
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="preprocessor">#include <cstdint></span></div>
|
|
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include <iostream></span></div>
|
|
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="preprocessor">#include <set></span></div>
|
|
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="preprocessor">#include <stdexcept></span></div>
|
|
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#include <string></span></div>
|
|
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span><span class="preprocessor">#include <string_view></span></div>
|
|
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span><span class="preprocessor">#include <unordered_map></span></div>
|
|
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span><span class="preprocessor">#include <utility></span></div>
|
|
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span><span class="preprocessor">#include <vector></span></div>
|
|
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span><span class="preprocessor">#include <fstream></span></div>
|
|
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span><span class="preprocessor">#include <ranges></span></div>
|
|
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span> </div>
|
|
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span><span class="preprocessor">#include <boost/numeric/odeint.hpp></span></div>
|
|
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> </div>
|
|
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span><span class="preprocessor">#include "cppad/cppad.hpp"</span></div>
|
|
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span><span class="preprocessor">#include "cppad/utility/sparse_rc.hpp"</span></div>
|
|
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span><span class="preprocessor">#include "cppad/utility/sparse_rcv.hpp"</span></div>
|
|
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span> </div>
|
|
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> </div>
|
|
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacegridfire.html">gridfire</a> {</div>
|
|
<div class="foldopen" id="foldopen00034" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5"> 34</a></span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5">GraphEngine::GraphEngine</a>(</div>
|
|
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> <span class="keyword">const</span> fourdst::composition::Composition &composition,</div>
|
|
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a> buildDepth</div>
|
|
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> ): <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5">GraphEngine</a>(composition, <a class="code hl_namespace" href="namespacegridfire_1_1partition.html">partition</a>::GroundStatePartitionFunction(), buildDepth) {}</div>
|
|
</div>
|
|
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> </div>
|
|
<div class="foldopen" id="foldopen00039" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a39d9838ed40bea71ee6c552bb5969026"> 39</a></span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5">GraphEngine::GraphEngine</a>(</div>
|
|
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> <span class="keyword">const</span> fourdst::composition::Composition &composition,</div>
|
|
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1partition_1_1_partition_function.html">partition::PartitionFunction</a>& partitionFunction,</div>
|
|
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a> buildDepth) :</div>
|
|
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>(<a class="code hl_function" href="namespacegridfire.html#aedddb89e400a6111f69bfe0c3fd4214e">build_reaclib_nuclear_network</a>(composition, buildDepth, false)),</div>
|
|
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01">m_depth</a>(buildDepth),</div>
|
|
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e">m_partitionFunction</a>(partitionFunction.clone())</div>
|
|
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> {</div>
|
|
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">syncInternalMaps</a>();</div>
|
|
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> </div>
|
|
<div class="foldopen" id="foldopen00050" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a1e7e851dfa21d41c2dc533ba56fc4c7b"> 50</a></span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5">GraphEngine::GraphEngine</a>(</div>
|
|
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &reactions</div>
|
|
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> ) :</div>
|
|
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>(reactions) {</div>
|
|
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">syncInternalMaps</a>();</div>
|
|
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> </div>
|
|
<div class="foldopen" id="foldopen00057" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#aaed3743a52246b0f7bf03995e1c12081"> 57</a></span> std::expected<StepDerivatives<double>, <a class="code hl_struct" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a>> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aaed3743a52246b0f7bf03995e1c12081">GraphEngine::calculateRHSAndEnergy</a>(</div>
|
|
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> <span class="keyword">const</span> std::vector<double> &Y,</div>
|
|
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
|
|
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
|
|
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> <span class="keywordflow">if</span> (<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de">m_usePrecomputation</a>) {</div>
|
|
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> std::vector<double> bare_rates;</div>
|
|
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> std::vector<double> bare_reverse_rates;</div>
|
|
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> bare_rates.reserve(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size());</div>
|
|
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> bare_reverse_rates.reserve(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size());</div>
|
|
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> </div>
|
|
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> <span class="comment">// TODO: Add cache to this</span></div>
|
|
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>: <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
|
|
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> bare_rates.push_back(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.calculate_rate(T9));</div>
|
|
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> bare_reverse_rates.push_back(<a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28">calculateReverseRate</a>(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>, T9));</div>
|
|
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> }</div>
|
|
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> </div>
|
|
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> <span class="comment">// --- The public facing interface can always use the precomputed version since taping is done internally ---</span></div>
|
|
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> <span class="keywordflow">return</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a97f98706b51fbe0d167ed81ffe58c438">calculateAllDerivativesUsingPrecomputation</a>(Y, bare_rates, bare_reverse_rates, T9, rho);</div>
|
|
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> } <span class="keywordflow">else</span> {</div>
|
|
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> <span class="keywordflow">return</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives<double></a>(Y, T9, rho);</div>
|
|
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> }</div>
|
|
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> </div>
|
|
<div class="foldopen" id="foldopen00081" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f"> 81</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">GraphEngine::syncInternalMaps</a>() {</div>
|
|
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> LOG_INFO(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Synchronizing internal maps for REACLIB graph network (serif::network::GraphNetwork)..."</span>);</div>
|
|
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa">collectNetworkSpecies</a>();</div>
|
|
<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567">populateReactionIDMap</a>();</div>
|
|
<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391">populateSpeciesToIndexMap</a>();</div>
|
|
<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a29b338630c959449c15881935ac30746">collectAtomicReverseRateAtomicBases</a>();</div>
|
|
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38">generateStoichiometryMatrix</a>();</div>
|
|
<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a8d0c0bd54a2908cff62dae7af0c149b5">reserveJacobianMatrix</a>();</div>
|
|
<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889">recordADTape</a>();</div>
|
|
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> </div>
|
|
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> n = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a>.Domain();</div>
|
|
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> m = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a>.Range();</div>
|
|
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> </div>
|
|
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> <span class="keyword">const</span> std::vector<bool> select_domain(n, <span class="keyword">true</span>);</div>
|
|
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> <span class="keyword">const</span> std::vector<bool> select_range(m, <span class="keyword">true</span>);</div>
|
|
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> </div>
|
|
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a>.subgraph_sparsity(select_domain, select_range, <span class="keyword">false</span>, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a19b2eea0e8d05ac90f9fd7120bdc6e06">m_full_jacobian_sparsity_pattern</a>);</div>
|
|
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a250cc6350dc052fbdfdf9a02066e7891">m_jac_work</a>.clear();</div>
|
|
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> </div>
|
|
<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd">precomputeNetwork</a>();</div>
|
|
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> LOG_INFO(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Internal maps synchronized. Network contains {} species and {} reactions."</span>,</div>
|
|
<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size(), <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size());</div>
|
|
<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> </div>
|
|
<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> <span class="comment">// --- Network Graph Construction Methods ---</span></div>
|
|
<div class="foldopen" id="foldopen00106" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa"> 106</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa">GraphEngine::collectNetworkSpecies</a>() {</div>
|
|
<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.clear();</div>
|
|
<div class="line"><a id="l00108" name="l00108"></a><span class="lineno"> 108</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.clear();</div>
|
|
<div class="line"><a id="l00109" name="l00109"></a><span class="lineno"> 109</span> </div>
|
|
<div class="line"><a id="l00110" name="l00110"></a><span class="lineno"> 110</span> std::set<std::string_view> uniqueSpeciesNames;</div>
|
|
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> </div>
|
|
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>: <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
|
|
<div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& reactant: <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants()) {</div>
|
|
<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span> uniqueSpeciesNames.insert(reactant.name());</div>
|
|
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> }</div>
|
|
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& product: <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products()) {</div>
|
|
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> uniqueSpeciesNames.insert(product.name());</div>
|
|
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> }</div>
|
|
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> }</div>
|
|
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span> </div>
|
|
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& name: uniqueSpeciesNames) {</div>
|
|
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> <span class="keyword">auto</span> it = fourdst::atomic::species.find(std::string(name));</div>
|
|
<div class="line"><a id="l00123" name="l00123"></a><span class="lineno"> 123</span> <span class="keywordflow">if</span> (it != fourdst::atomic::species.end()) {</div>
|
|
<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.push_back(it->second);</div>
|
|
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.insert({name, it->second});</div>
|
|
<div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</span> } <span class="keywordflow">else</span> {</div>
|
|
<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Species '{}' not found in global atomic species database."</span>, name);</div>
|
|
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>->flush_log();</div>
|
|
<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Species not found in global atomic species database: "</span> + std::string(name));</div>
|
|
<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> }</div>
|
|
<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> }</div>
|
|
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> </div>
|
|
<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> </div>
|
|
<div class="foldopen" id="foldopen00135" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567"> 135</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567">GraphEngine::populateReactionIDMap</a>() {</div>
|
|
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Populating reaction ID map for REACLIB graph network (serif::network::GraphNetwork)..."</span>);</div>
|
|
<div class="line"><a id="l00137" name="l00137"></a><span class="lineno"> 137</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">m_reactionIDMap</a>.clear();</div>
|
|
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> <span class="keywordflow">for</span> (<span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>: <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
|
|
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">m_reactionIDMap</a>.emplace(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id(), &<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>);</div>
|
|
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> }</div>
|
|
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Populated {} reactions in the reaction ID map."</span>, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">m_reactionIDMap</a>.size());</div>
|
|
<div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span> </div>
|
|
<div class="foldopen" id="foldopen00144" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391"> 144</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391">GraphEngine::populateSpeciesToIndexMap</a>() {</div>
|
|
<div class="line"><a id="l00145" name="l00145"></a><span class="lineno"> 145</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a>.clear();</div>
|
|
<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"> 146</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size(); ++i) {</div>
|
|
<div class="line"><a id="l00147" name="l00147"></a><span class="lineno"> 147</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a>.insert({<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>[i], i});</div>
|
|
<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"> 148</span> }</div>
|
|
<div class="line"><a id="l00149" name="l00149"></a><span class="lineno"> 149</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00150" name="l00150"></a><span class="lineno"> 150</span> </div>
|
|
<div class="foldopen" id="foldopen00151" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00151" name="l00151"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a8d0c0bd54a2908cff62dae7af0c149b5"> 151</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a8d0c0bd54a2908cff62dae7af0c149b5">GraphEngine::reserveJacobianMatrix</a>()<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00152" name="l00152"></a><span class="lineno"> 152</span> <span class="comment">// The implementation of this function (and others) constrains this nuclear network to a constant temperature and density during</span></div>
|
|
<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</span> <span class="comment">// each evaluation.</span></div>
|
|
<div class="line"><a id="l00154" name="l00154"></a><span class="lineno"> 154</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> numSpecies = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size();</div>
|
|
<div class="line"><a id="l00155" name="l00155"></a><span class="lineno"> 155</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.clear();</div>
|
|
<div class="line"><a id="l00156" name="l00156"></a><span class="lineno"> 156</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.resize(numSpecies, numSpecies, <span class="keyword">false</span>); <span class="comment">// Sparse matrix, no initial values</span></div>
|
|
<div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</span> LOG_TRACE_L2(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Jacobian matrix resized to {} rows and {} columns."</span>,</div>
|
|
<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"> 158</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.size1(), <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.size2());</div>
|
|
<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> </div>
|
|
<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span> <span class="comment">// --- Basic Accessors and Queries ---</span></div>
|
|
<div class="foldopen" id="foldopen00162" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00162" name="l00162"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767"> 162</a></span> <span class="keyword">const</span> std::vector<fourdst::atomic::Species>& <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767">GraphEngine::getNetworkSpecies</a>()<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00163" name="l00163"></a><span class="lineno"> 163</span> <span class="comment">// Returns a constant reference to the vector of unique species in the network.</span></div>
|
|
<div class="line"><a id="l00164" name="l00164"></a><span class="lineno"> 164</span> LOG_TRACE_L3(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Providing access to network species vector. Size: {}."</span>, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size());</div>
|
|
<div class="line"><a id="l00165" name="l00165"></a><span class="lineno"> 165</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>;</div>
|
|
<div class="line"><a id="l00166" name="l00166"></a><span class="lineno"> 166</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00167" name="l00167"></a><span class="lineno"> 167</span> </div>
|
|
<div class="foldopen" id="foldopen00168" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00168" name="l00168"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da"> 168</a></span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a>& <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da">GraphEngine::getNetworkReactions</a>()<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00169" name="l00169"></a><span class="lineno"> 169</span> <span class="comment">// Returns a constant reference to the set of reactions in the network.</span></div>
|
|
<div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> LOG_TRACE_L3(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Providing access to network reactions set. Size: {}."</span>, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size());</div>
|
|
<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>;</div>
|
|
<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span> </div>
|
|
<div class="foldopen" id="foldopen00174" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00174" name="l00174"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a371ba0881d6903ddb2d586faa61805d0"> 174</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a371ba0881d6903ddb2d586faa61805d0">GraphEngine::setNetworkReactions</a>(<span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &reactions) {</div>
|
|
<div class="line"><a id="l00175" name="l00175"></a><span class="lineno"> 175</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a> = reactions;</div>
|
|
<div class="line"><a id="l00176" name="l00176"></a><span class="lineno"> 176</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">syncInternalMaps</a>();</div>
|
|
<div class="line"><a id="l00177" name="l00177"></a><span class="lineno"> 177</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00178" name="l00178"></a><span class="lineno"> 178</span> </div>
|
|
<div class="foldopen" id="foldopen00179" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00179" name="l00179"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b"> 179</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b">GraphEngine::involvesSpecies</a>(<span class="keyword">const</span> fourdst::atomic::Species& species)<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00180" name="l00180"></a><span class="lineno"> 180</span> <span class="comment">// Checks if a given species is present in the network's species map for efficient lookup.</span></div>
|
|
<div class="line"><a id="l00181" name="l00181"></a><span class="lineno"> 181</span> <span class="keyword">const</span> <span class="keywordtype">bool</span> found = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.contains(species.name());</div>
|
|
<div class="line"><a id="l00182" name="l00182"></a><span class="lineno"> 182</span> LOG_DEBUG(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Checking if species '{}' is involved in the network: {}."</span>, species.name(), found ? <span class="stringliteral">"Yes"</span> : <span class="stringliteral">"No"</span>);</div>
|
|
<div class="line"><a id="l00183" name="l00183"></a><span class="lineno"> 183</span> <span class="keywordflow">return</span> found;</div>
|
|
<div class="line"><a id="l00184" name="l00184"></a><span class="lineno"> 184</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00185" name="l00185"></a><span class="lineno"> 185</span> </div>
|
|
<div class="line"><a id="l00186" name="l00186"></a><span class="lineno"> 186</span> <span class="comment">// --- Validation Methods ---</span></div>
|
|
<div class="foldopen" id="foldopen00187" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00187" name="l00187"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be"> 187</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be">GraphEngine::validateConservation</a>()<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00188" name="l00188"></a><span class="lineno"> 188</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Validating mass (A) and charge (Z) conservation across all reactions in the network."</span>);</div>
|
|
<div class="line"><a id="l00189" name="l00189"></a><span class="lineno"> 189</span> </div>
|
|
<div class="line"><a id="l00190" name="l00190"></a><span class="lineno"> 190</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a> : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
|
|
<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span> uint64_t totalReactantA = 0;</div>
|
|
<div class="line"><a id="l00192" name="l00192"></a><span class="lineno"> 192</span> uint64_t totalReactantZ = 0;</div>
|
|
<div class="line"><a id="l00193" name="l00193"></a><span class="lineno"> 193</span> uint64_t totalProductA = 0;</div>
|
|
<div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> uint64_t totalProductZ = 0;</div>
|
|
<div class="line"><a id="l00195" name="l00195"></a><span class="lineno"> 195</span> </div>
|
|
<div class="line"><a id="l00196" name="l00196"></a><span class="lineno"> 196</span> <span class="comment">// Calculate total A and Z for reactants</span></div>
|
|
<div class="line"><a id="l00197" name="l00197"></a><span class="lineno"> 197</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& reactant : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants()) {</div>
|
|
<div class="line"><a id="l00198" name="l00198"></a><span class="lineno"> 198</span> <span class="keyword">auto</span> it = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.find(reactant.name());</div>
|
|
<div class="line"><a id="l00199" name="l00199"></a><span class="lineno"> 199</span> <span class="keywordflow">if</span> (it != <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.end()) {</div>
|
|
<div class="line"><a id="l00200" name="l00200"></a><span class="lineno"> 200</span> totalReactantA += it->second.a();</div>
|
|
<div class="line"><a id="l00201" name="l00201"></a><span class="lineno"> 201</span> totalReactantZ += it->second.z();</div>
|
|
<div class="line"><a id="l00202" name="l00202"></a><span class="lineno"> 202</span> } <span class="keywordflow">else</span> {</div>
|
|
<div class="line"><a id="l00203" name="l00203"></a><span class="lineno"> 203</span> <span class="comment">// This scenario indicates a severe data integrity issue:</span></div>
|
|
<div class="line"><a id="l00204" name="l00204"></a><span class="lineno"> 204</span> <span class="comment">// a reactant is part of a reaction but not in the network's species map.</span></div>
|
|
<div class="line"><a id="l00205" name="l00205"></a><span class="lineno"> 205</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"CRITICAL ERROR: Reactant species '{}' in reaction '{}' not found in network species map during conservation validation."</span>,</div>
|
|
<div class="line"><a id="l00206" name="l00206"></a><span class="lineno"> 206</span> reactant.name(), <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id());</div>
|
|
<div class="line"><a id="l00207" name="l00207"></a><span class="lineno"> 207</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
|
|
<div class="line"><a id="l00208" name="l00208"></a><span class="lineno"> 208</span> }</div>
|
|
<div class="line"><a id="l00209" name="l00209"></a><span class="lineno"> 209</span> }</div>
|
|
<div class="line"><a id="l00210" name="l00210"></a><span class="lineno"> 210</span> </div>
|
|
<div class="line"><a id="l00211" name="l00211"></a><span class="lineno"> 211</span> <span class="comment">// Calculate total A and Z for products</span></div>
|
|
<div class="line"><a id="l00212" name="l00212"></a><span class="lineno"> 212</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& product : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products()) {</div>
|
|
<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</span> <span class="keyword">auto</span> it = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.find(product.name());</div>
|
|
<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span> <span class="keywordflow">if</span> (it != <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.end()) {</div>
|
|
<div class="line"><a id="l00215" name="l00215"></a><span class="lineno"> 215</span> totalProductA += it->second.a();</div>
|
|
<div class="line"><a id="l00216" name="l00216"></a><span class="lineno"> 216</span> totalProductZ += it->second.z();</div>
|
|
<div class="line"><a id="l00217" name="l00217"></a><span class="lineno"> 217</span> } <span class="keywordflow">else</span> {</div>
|
|
<div class="line"><a id="l00218" name="l00218"></a><span class="lineno"> 218</span> <span class="comment">// Similar critical error for product species</span></div>
|
|
<div class="line"><a id="l00219" name="l00219"></a><span class="lineno"> 219</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"CRITICAL ERROR: Product species '{}' in reaction '{}' not found in network species map during conservation validation."</span>,</div>
|
|
<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span> product.name(), <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id());</div>
|
|
<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"> 221</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
|
|
<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> }</div>
|
|
<div class="line"><a id="l00223" name="l00223"></a><span class="lineno"> 223</span> }</div>
|
|
<div class="line"><a id="l00224" name="l00224"></a><span class="lineno"> 224</span> </div>
|
|
<div class="line"><a id="l00225" name="l00225"></a><span class="lineno"> 225</span> <span class="comment">// Compare totals for conservation</span></div>
|
|
<div class="line"><a id="l00226" name="l00226"></a><span class="lineno"> 226</span> <span class="keywordflow">if</span> (totalReactantA != totalProductA) {</div>
|
|
<div class="line"><a id="l00227" name="l00227"></a><span class="lineno"> 227</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Mass number (A) not conserved for reaction '{}': Reactants A={} vs Products A={}."</span>,</div>
|
|
<div class="line"><a id="l00228" name="l00228"></a><span class="lineno"> 228</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id(), totalReactantA, totalProductA);</div>
|
|
<div class="line"><a id="l00229" name="l00229"></a><span class="lineno"> 229</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
|
|
<div class="line"><a id="l00230" name="l00230"></a><span class="lineno"> 230</span> }</div>
|
|
<div class="line"><a id="l00231" name="l00231"></a><span class="lineno"> 231</span> <span class="keywordflow">if</span> (totalReactantZ != totalProductZ) {</div>
|
|
<div class="line"><a id="l00232" name="l00232"></a><span class="lineno"> 232</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Atomic number (Z) not conserved for reaction '{}': Reactants Z={} vs Products Z={}."</span>,</div>
|
|
<div class="line"><a id="l00233" name="l00233"></a><span class="lineno"> 233</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id(), totalReactantZ, totalProductZ);</div>
|
|
<div class="line"><a id="l00234" name="l00234"></a><span class="lineno"> 234</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
|
|
<div class="line"><a id="l00235" name="l00235"></a><span class="lineno"> 235</span> }</div>
|
|
<div class="line"><a id="l00236" name="l00236"></a><span class="lineno"> 236</span> }</div>
|
|
<div class="line"><a id="l00237" name="l00237"></a><span class="lineno"> 237</span> </div>
|
|
<div class="line"><a id="l00238" name="l00238"></a><span class="lineno"> 238</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Mass (A) and charge (Z) conservation validated successfully for all reactions."</span>);</div>
|
|
<div class="line"><a id="l00239" name="l00239"></a><span class="lineno"> 239</span> <span class="keywordflow">return</span> <span class="keyword">true</span>; <span class="comment">// All reactions passed the conservation check</span></div>
|
|
<div class="line"><a id="l00240" name="l00240"></a><span class="lineno"> 240</span> }</div>
|
|
</div>
|
|
<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_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28"> 242</a></span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28">GraphEngine::calculateReverseRate</a>(</div>
|
|
<div class="line"><a id="l00243" name="l00243"></a><span class="lineno"> 243</span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>,</div>
|
|
<div class="line"><a id="l00244" name="l00244"></a><span class="lineno"> 244</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9</div>
|
|
<div class="line"><a id="l00245" name="l00245"></a><span class="lineno"> 245</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00246" name="l00246"></a><span class="lineno"> 246</span> <span class="keywordflow">if</span> (!<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc">m_useReverseReactions</a>) {</div>
|
|
<div class="line"><a id="l00247" name="l00247"></a><span class="lineno"> 247</span> LOG_TRACE_L3_LIMIT_EVERY_N(std::numeric_limits<int>::max(), <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Reverse reactions are disabled. Returning 0.0 for reverse rate of reaction '{}'."</span>, <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id());</div>
|
|
<div class="line"><a id="l00248" name="l00248"></a><span class="lineno"> 248</span> <span class="keywordflow">return</span> 0.0; <span class="comment">// If reverse reactions are not used, return 0.0</span></div>
|
|
<div class="line"><a id="l00249" name="l00249"></a><span class="lineno"> 249</span> }</div>
|
|
<div class="line"><a id="l00250" name="l00250"></a><span class="lineno"> 250</span> <span class="keyword">const</span> <span class="keywordtype">double</span> temp = T9 * 1e9; <span class="comment">// Convert T9 to Kelvin</span></div>
|
|
<div class="line"><a id="l00251" name="l00251"></a><span class="lineno"> 251</span> </div>
|
|
<div class="line"><a id="l00252" name="l00252"></a><span class="lineno"> 252</span> <span class="comment">// In debug builds we check the units on kB to ensure it is in erg/K. This is removed in release builds to avoid overhead. (Note assert is a no-op in release builds)</span></div>
|
|
<div class="line"><a id="l00253" name="l00253"></a><span class="lineno"> 253</span> assert(Constants::getInstance().get(<span class="stringliteral">"kB"</span>).unit == <span class="stringliteral">"erg / K"</span>);</div>
|
|
<div class="line"><a id="l00254" name="l00254"></a><span class="lineno"> 254</span> </div>
|
|
<div class="line"><a id="l00255" name="l00255"></a><span class="lineno"> 255</span> <span class="keyword">const</span> <span class="keywordtype">double</span> kBMeV = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">m_constants</a>.kB * 624151; <span class="comment">// Convert kB to MeV/K NOTE: This relies on the fact that m_constants.kB is in erg/K!</span></div>
|
|
<div class="line"><a id="l00256" name="l00256"></a><span class="lineno"> 256</span> <span class="keyword">const</span> <span class="keywordtype">double</span> expFactor = std::exp(-<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.qValue() / (kBMeV * temp));</div>
|
|
<div class="line"><a id="l00257" name="l00257"></a><span class="lineno"> 257</span> <span class="keywordtype">double</span> reverseRate = 0.0;</div>
|
|
<div class="line"><a id="l00258" name="l00258"></a><span class="lineno"> 258</span> <span class="keyword">const</span> <span class="keywordtype">double</span> forwardRate = <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.calculate_rate(T9);</div>
|
|
<div class="line"><a id="l00259" name="l00259"></a><span class="lineno"> 259</span> </div>
|
|
<div class="line"><a id="l00260" name="l00260"></a><span class="lineno"> 260</span> <span class="keywordflow">if</span> (<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants().size() == 2 && <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products().size() == 2) {</div>
|
|
<div class="line"><a id="l00261" name="l00261"></a><span class="lineno"> 261</span> reverseRate = <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755">calculateReverseRateTwoBody</a>(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>, T9, forwardRate, expFactor);</div>
|
|
<div class="line"><a id="l00262" name="l00262"></a><span class="lineno"> 262</span> } <span class="keywordflow">else</span> {</div>
|
|
<div class="line"><a id="l00263" name="l00263"></a><span class="lineno"> 263</span> LOG_WARNING_LIMIT_EVERY_N(1000000, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Reverse rate calculation for reactions with more than two reactants or products is not implemented (reaction id {})."</span>, <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.peName());</div>
|
|
<div class="line"><a id="l00264" name="l00264"></a><span class="lineno"> 264</span> }</div>
|
|
<div class="line"><a id="l00265" name="l00265"></a><span class="lineno"> 265</span> LOG_TRACE_L2_LIMIT_EVERY_N(1000, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Calculated reverse rate for reaction '{}': {:.3E} at T9={:.3E}."</span>, <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id(), reverseRate, T9);</div>
|
|
<div class="line"><a id="l00266" name="l00266"></a><span class="lineno"> 266</span> <span class="keywordflow">return</span> reverseRate;</div>
|
|
<div class="line"><a id="l00267" name="l00267"></a><span class="lineno"> 267</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00268" name="l00268"></a><span class="lineno"> 268</span> </div>
|
|
<div class="foldopen" id="foldopen00269" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00269" name="l00269"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755"> 269</a></span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755">GraphEngine::calculateReverseRateTwoBody</a>(</div>
|
|
<div class="line"><a id="l00270" name="l00270"></a><span class="lineno"> 270</span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>,</div>
|
|
<div class="line"><a id="l00271" name="l00271"></a><span class="lineno"> 271</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
|
|
<div class="line"><a id="l00272" name="l00272"></a><span class="lineno"> 272</span> <span class="keyword">const</span> <span class="keywordtype">double</span> forwardRate,</div>
|
|
<div class="line"><a id="l00273" name="l00273"></a><span class="lineno"> 273</span> <span class="keyword">const</span> <span class="keywordtype">double</span> expFactor</div>
|
|
<div class="line"><a id="l00274" name="l00274"></a><span class="lineno"> 274</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00275" name="l00275"></a><span class="lineno"> 275</span> std::vector<double> reactantPartitionFunctions;</div>
|
|
<div class="line"><a id="l00276" name="l00276"></a><span class="lineno"> 276</span> std::vector<double> productPartitionFunctions;</div>
|
|
<div class="line"><a id="l00277" name="l00277"></a><span class="lineno"> 277</span> </div>
|
|
<div class="line"><a id="l00278" name="l00278"></a><span class="lineno"> 278</span> reactantPartitionFunctions.reserve(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants().size());</div>
|
|
<div class="line"><a id="l00279" name="l00279"></a><span class="lineno"> 279</span> productPartitionFunctions.reserve(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products().size());</div>
|
|
<div class="line"><a id="l00280" name="l00280"></a><span class="lineno"> 280</span> </div>
|
|
<div class="line"><a id="l00281" name="l00281"></a><span class="lineno"> 281</span> std::unordered_map<fourdst::atomic::Species, int> reactantMultiplicity;</div>
|
|
<div class="line"><a id="l00282" name="l00282"></a><span class="lineno"> 282</span> std::unordered_map<fourdst::atomic::Species, int> productMultiplicity;</div>
|
|
<div class="line"><a id="l00283" name="l00283"></a><span class="lineno"> 283</span> </div>
|
|
<div class="line"><a id="l00284" name="l00284"></a><span class="lineno"> 284</span> reactantMultiplicity.reserve(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants().size());</div>
|
|
<div class="line"><a id="l00285" name="l00285"></a><span class="lineno"> 285</span> productMultiplicity.reserve(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products().size());</div>
|
|
<div class="line"><a id="l00286" name="l00286"></a><span class="lineno"> 286</span> </div>
|
|
<div class="line"><a id="l00287" name="l00287"></a><span class="lineno"> 287</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& reactant : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants()) {</div>
|
|
<div class="line"><a id="l00288" name="l00288"></a><span class="lineno"> 288</span> reactantMultiplicity[reactant] += 1;</div>
|
|
<div class="line"><a id="l00289" name="l00289"></a><span class="lineno"> 289</span> }</div>
|
|
<div class="line"><a id="l00290" name="l00290"></a><span class="lineno"> 290</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& product : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products()) {</div>
|
|
<div class="line"><a id="l00291" name="l00291"></a><span class="lineno"> 291</span> productMultiplicity[product] += 1;</div>
|
|
<div class="line"><a id="l00292" name="l00292"></a><span class="lineno"> 292</span> }</div>
|
|
<div class="line"><a id="l00293" name="l00293"></a><span class="lineno"> 293</span> <span class="keywordtype">double</span> reactantSymmetryFactor = 1.0;</div>
|
|
<div class="line"><a id="l00294" name="l00294"></a><span class="lineno"> 294</span> <span class="keywordtype">double</span> productSymmetryFactor = 1.0;</div>
|
|
<div class="line"><a id="l00295" name="l00295"></a><span class="lineno"> 295</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& count : reactantMultiplicity | std::views::values) {</div>
|
|
<div class="line"><a id="l00296" name="l00296"></a><span class="lineno"> 296</span> reactantSymmetryFactor *= std::tgamma(count + 1);</div>
|
|
<div class="line"><a id="l00297" name="l00297"></a><span class="lineno"> 297</span> }</div>
|
|
<div class="line"><a id="l00298" name="l00298"></a><span class="lineno"> 298</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& count : productMultiplicity | std::views::values) {</div>
|
|
<div class="line"><a id="l00299" name="l00299"></a><span class="lineno"> 299</span> productSymmetryFactor *= std::tgamma(count + 1);</div>
|
|
<div class="line"><a id="l00300" name="l00300"></a><span class="lineno"> 300</span> }</div>
|
|
<div class="line"><a id="l00301" name="l00301"></a><span class="lineno"> 301</span> <span class="keyword">const</span> <span class="keywordtype">double</span> symmetryFactor = reactantSymmetryFactor / productSymmetryFactor;</div>
|
|
<div class="line"><a id="l00302" name="l00302"></a><span class="lineno"> 302</span> </div>
|
|
<div class="line"><a id="l00303" name="l00303"></a><span class="lineno"> 303</span> <span class="comment">// Accumulate mass terms</span></div>
|
|
<div class="line"><a id="l00304" name="l00304"></a><span class="lineno"> 304</span> <span class="keyword">auto</span> mass_op = [](<span class="keywordtype">double</span> acc, <span class="keyword">const</span> <span class="keyword">auto</span>& species) { <span class="keywordflow">return</span> acc * species.a(); };</div>
|
|
<div class="line"><a id="l00305" name="l00305"></a><span class="lineno"> 305</span> <span class="keyword">const</span> <span class="keywordtype">double</span> massNumerator = std::accumulate(</div>
|
|
<div class="line"><a id="l00306" name="l00306"></a><span class="lineno"> 306</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants().begin(),</div>
|
|
<div class="line"><a id="l00307" name="l00307"></a><span class="lineno"> 307</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants().end(),</div>
|
|
<div class="line"><a id="l00308" name="l00308"></a><span class="lineno"> 308</span> 1.0,</div>
|
|
<div class="line"><a id="l00309" name="l00309"></a><span class="lineno"> 309</span> mass_op</div>
|
|
<div class="line"><a id="l00310" name="l00310"></a><span class="lineno"> 310</span> );</div>
|
|
<div class="line"><a id="l00311" name="l00311"></a><span class="lineno"> 311</span> <span class="keyword">const</span> <span class="keywordtype">double</span> massDenominator = std::accumulate(</div>
|
|
<div class="line"><a id="l00312" name="l00312"></a><span class="lineno"> 312</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products().begin(),</div>
|
|
<div class="line"><a id="l00313" name="l00313"></a><span class="lineno"> 313</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products().end(),</div>
|
|
<div class="line"><a id="l00314" name="l00314"></a><span class="lineno"> 314</span> 1.0,</div>
|
|
<div class="line"><a id="l00315" name="l00315"></a><span class="lineno"> 315</span> mass_op</div>
|
|
<div class="line"><a id="l00316" name="l00316"></a><span class="lineno"> 316</span> );</div>
|
|
<div class="line"><a id="l00317" name="l00317"></a><span class="lineno"> 317</span> </div>
|
|
<div class="line"><a id="l00318" name="l00318"></a><span class="lineno"> 318</span> <span class="comment">// Accumulate partition functions</span></div>
|
|
<div class="line"><a id="l00319" name="l00319"></a><span class="lineno"> 319</span> <span class="keyword">auto</span> pf_op = [&](<span class="keywordtype">double</span> acc, <span class="keyword">const</span> <span class="keyword">auto</span>& species) {</div>
|
|
<div class="line"><a id="l00320" name="l00320"></a><span class="lineno"> 320</span> <span class="keywordflow">return</span> acc * <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e">m_partitionFunction</a>->evaluate(species.z(), species.a(), T9);</div>
|
|
<div class="line"><a id="l00321" name="l00321"></a><span class="lineno"> 321</span> };</div>
|
|
<div class="line"><a id="l00322" name="l00322"></a><span class="lineno"> 322</span> <span class="keyword">const</span> <span class="keywordtype">double</span> partitionFunctionNumerator = std::accumulate(</div>
|
|
<div class="line"><a id="l00323" name="l00323"></a><span class="lineno"> 323</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants().begin(),</div>
|
|
<div class="line"><a id="l00324" name="l00324"></a><span class="lineno"> 324</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants().end(),</div>
|
|
<div class="line"><a id="l00325" name="l00325"></a><span class="lineno"> 325</span> 1.0,</div>
|
|
<div class="line"><a id="l00326" name="l00326"></a><span class="lineno"> 326</span> pf_op</div>
|
|
<div class="line"><a id="l00327" name="l00327"></a><span class="lineno"> 327</span> );</div>
|
|
<div class="line"><a id="l00328" name="l00328"></a><span class="lineno"> 328</span> <span class="keyword">const</span> <span class="keywordtype">double</span> partitionFunctionDenominator = std::accumulate(</div>
|
|
<div class="line"><a id="l00329" name="l00329"></a><span class="lineno"> 329</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products().begin(),</div>
|
|
<div class="line"><a id="l00330" name="l00330"></a><span class="lineno"> 330</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products().end(),</div>
|
|
<div class="line"><a id="l00331" name="l00331"></a><span class="lineno"> 331</span> 1.0,</div>
|
|
<div class="line"><a id="l00332" name="l00332"></a><span class="lineno"> 332</span> pf_op</div>
|
|
<div class="line"><a id="l00333" name="l00333"></a><span class="lineno"> 333</span> );</div>
|
|
<div class="line"><a id="l00334" name="l00334"></a><span class="lineno"> 334</span> </div>
|
|
<div class="line"><a id="l00335" name="l00335"></a><span class="lineno"> 335</span> <span class="keyword">const</span> <span class="keywordtype">double</span> CT = std::pow(massNumerator/massDenominator, 1.5) *</div>
|
|
<div class="line"><a id="l00336" name="l00336"></a><span class="lineno"> 336</span> (partitionFunctionNumerator/partitionFunctionDenominator);</div>
|
|
<div class="line"><a id="l00337" name="l00337"></a><span class="lineno"> 337</span> </div>
|
|
<div class="line"><a id="l00338" name="l00338"></a><span class="lineno"> 338</span> <span class="keyword">const</span> <span class="keywordtype">double</span> reverseRate = forwardRate * symmetryFactor * CT * expFactor;</div>
|
|
<div class="line"><a id="l00339" name="l00339"></a><span class="lineno"> 339</span> <span class="keywordflow">if</span> (!std::isfinite(reverseRate)) {</div>
|
|
<div class="line"><a id="l00340" name="l00340"></a><span class="lineno"> 340</span> <span class="keywordflow">return</span> 0.0; <span class="comment">// If the reverse rate is not finite, return 0.0</span></div>
|
|
<div class="line"><a id="l00341" name="l00341"></a><span class="lineno"> 341</span> }</div>
|
|
<div class="line"><a id="l00342" name="l00342"></a><span class="lineno"> 342</span> <span class="keywordflow">return</span> reverseRate; <span class="comment">// Return the calculated reverse rate</span></div>
|
|
<div class="line"><a id="l00343" name="l00343"></a><span class="lineno"> 343</span> </div>
|
|
<div class="line"><a id="l00344" name="l00344"></a><span class="lineno"> 344</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00345" name="l00345"></a><span class="lineno"> 345</span> </div>
|
|
<div class="foldopen" id="foldopen00346" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00346" name="l00346"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#af28950c5af3a92eb03a1a64ed0f913e7"> 346</a></span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af28950c5af3a92eb03a1a64ed0f913e7">GraphEngine::calculateReverseRateTwoBodyDerivative</a>(</div>
|
|
<div class="line"><a id="l00347" name="l00347"></a><span class="lineno"> 347</span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>,</div>
|
|
<div class="line"><a id="l00348" name="l00348"></a><span class="lineno"> 348</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
|
|
<div class="line"><a id="l00349" name="l00349"></a><span class="lineno"> 349</span> <span class="keyword">const</span> <span class="keywordtype">double</span> reverseRate</div>
|
|
<div class="line"><a id="l00350" name="l00350"></a><span class="lineno"> 350</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00351" name="l00351"></a><span class="lineno"> 351</span> <span class="keywordflow">if</span> (!<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc">m_useReverseReactions</a>) {</div>
|
|
<div class="line"><a id="l00352" name="l00352"></a><span class="lineno"> 352</span> LOG_TRACE_L3_LIMIT_EVERY_N(std::numeric_limits<int>::max(), <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Reverse reactions are disabled. Returning 0.0 for reverse rate of reaction '{}'."</span>, <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id());</div>
|
|
<div class="line"><a id="l00353" name="l00353"></a><span class="lineno"> 353</span> <span class="keywordflow">return</span> 0.0; <span class="comment">// If reverse reactions are not used, return 0.0</span></div>
|
|
<div class="line"><a id="l00354" name="l00354"></a><span class="lineno"> 354</span> }</div>
|
|
<div class="line"><a id="l00355" name="l00355"></a><span class="lineno"> 355</span> <span class="keyword">const</span> <span class="keywordtype">double</span> d_log_kFwd = <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.calculate_forward_rate_log_derivative(T9);</div>
|
|
<div class="line"><a id="l00356" name="l00356"></a><span class="lineno"> 356</span> </div>
|
|
<div class="line"><a id="l00357" name="l00357"></a><span class="lineno"> 357</span> <span class="keyword">auto</span> log_deriv_pf_op = [&](<span class="keywordtype">double</span> acc, <span class="keyword">const</span> <span class="keyword">auto</span>& species) {</div>
|
|
<div class="line"><a id="l00358" name="l00358"></a><span class="lineno"> 358</span> <span class="keyword">const</span> <span class="keywordtype">double</span> g = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e">m_partitionFunction</a>->evaluate(species.z(), species.a(), T9);</div>
|
|
<div class="line"><a id="l00359" name="l00359"></a><span class="lineno"> 359</span> <span class="keyword">const</span> <span class="keywordtype">double</span> dg_dT = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e">m_partitionFunction</a>->evaluateDerivative(species.z(), species.a(), T9);</div>
|
|
<div class="line"><a id="l00360" name="l00360"></a><span class="lineno"> 360</span> <span class="keywordflow">return</span> (g == 0.0) ? acc : acc + (dg_dT / g);</div>
|
|
<div class="line"><a id="l00361" name="l00361"></a><span class="lineno"> 361</span> };</div>
|
|
<div class="line"><a id="l00362" name="l00362"></a><span class="lineno"> 362</span> </div>
|
|
<div class="line"><a id="l00363" name="l00363"></a><span class="lineno"> 363</span> <span class="keyword">const</span> <span class="keywordtype">double</span> reactant_log_derivative_sum = std::accumulate(</div>
|
|
<div class="line"><a id="l00364" name="l00364"></a><span class="lineno"> 364</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants().begin(),</div>
|
|
<div class="line"><a id="l00365" name="l00365"></a><span class="lineno"> 365</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants().end(),</div>
|
|
<div class="line"><a id="l00366" name="l00366"></a><span class="lineno"> 366</span> 0.0,</div>
|
|
<div class="line"><a id="l00367" name="l00367"></a><span class="lineno"> 367</span> log_deriv_pf_op</div>
|
|
<div class="line"><a id="l00368" name="l00368"></a><span class="lineno"> 368</span> );</div>
|
|
<div class="line"><a id="l00369" name="l00369"></a><span class="lineno"> 369</span> </div>
|
|
<div class="line"><a id="l00370" name="l00370"></a><span class="lineno"> 370</span> <span class="keyword">const</span> <span class="keywordtype">double</span> product_log_derivative_sum = std::accumulate(</div>
|
|
<div class="line"><a id="l00371" name="l00371"></a><span class="lineno"> 371</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products().begin(),</div>
|
|
<div class="line"><a id="l00372" name="l00372"></a><span class="lineno"> 372</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products().end(),</div>
|
|
<div class="line"><a id="l00373" name="l00373"></a><span class="lineno"> 373</span> 0.0,</div>
|
|
<div class="line"><a id="l00374" name="l00374"></a><span class="lineno"> 374</span> log_deriv_pf_op</div>
|
|
<div class="line"><a id="l00375" name="l00375"></a><span class="lineno"> 375</span> );</div>
|
|
<div class="line"><a id="l00376" name="l00376"></a><span class="lineno"> 376</span> </div>
|
|
<div class="line"><a id="l00377" name="l00377"></a><span class="lineno"> 377</span> <span class="keyword">const</span> <span class="keywordtype">double</span> d_log_C = reactant_log_derivative_sum - product_log_derivative_sum;</div>
|
|
<div class="line"><a id="l00378" name="l00378"></a><span class="lineno"> 378</span> </div>
|
|
<div class="line"><a id="l00379" name="l00379"></a><span class="lineno"> 379</span> <span class="keyword">const</span> <span class="keywordtype">double</span> d_log_exp = <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.qValue() / (<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">m_constants</a>.kB * T9 * T9);</div>
|
|
<div class="line"><a id="l00380" name="l00380"></a><span class="lineno"> 380</span> </div>
|
|
<div class="line"><a id="l00381" name="l00381"></a><span class="lineno"> 381</span> <span class="keyword">const</span> <span class="keywordtype">double</span> log_total_derivative = d_log_kFwd + d_log_C + d_log_exp;</div>
|
|
<div class="line"><a id="l00382" name="l00382"></a><span class="lineno"> 382</span> </div>
|
|
<div class="line"><a id="l00383" name="l00383"></a><span class="lineno"> 383</span> <span class="keywordflow">return</span> reverseRate * log_total_derivative; <span class="comment">// Return the derivative of the reverse rate with respect to T9</span></div>
|
|
<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> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00386" name="l00386"></a><span class="lineno"> 386</span> </div>
|
|
<div class="foldopen" id="foldopen00387" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00387" name="l00387"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#ae7a210d9ab13ad5fb0c612f027acabd0"> 387</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#ae7a210d9ab13ad5fb0c612f027acabd0">GraphEngine::isUsingReverseReactions</a>()<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00388" name="l00388"></a><span class="lineno"> 388</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc">m_useReverseReactions</a>;</div>
|
|
<div class="line"><a id="l00389" name="l00389"></a><span class="lineno"> 389</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00390" name="l00390"></a><span class="lineno"> 390</span> </div>
|
|
<div class="foldopen" id="foldopen00391" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00391" name="l00391"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197"> 391</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197">GraphEngine::setUseReverseReactions</a>(<span class="keyword">const</span> <span class="keywordtype">bool</span> useReverse) {</div>
|
|
<div class="line"><a id="l00392" name="l00392"></a><span class="lineno"> 392</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc">m_useReverseReactions</a> = useReverse;</div>
|
|
<div class="line"><a id="l00393" name="l00393"></a><span class="lineno"> 393</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00394" name="l00394"></a><span class="lineno"> 394</span> </div>
|
|
<div class="foldopen" id="foldopen00395" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00395" name="l00395"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda"> 395</a></span> <span class="keywordtype">int</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda">GraphEngine::getSpeciesIndex</a>(<span class="keyword">const</span> fourdst::atomic::Species &species)<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00396" name="l00396"></a><span class="lineno"> 396</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a>.at(species); <span class="comment">// Returns the index of the species in the stoichiometry matrix</span></div>
|
|
<div class="line"><a id="l00397" name="l00397"></a><span class="lineno"> 397</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00398" name="l00398"></a><span class="lineno"> 398</span> </div>
|
|
<div class="foldopen" id="foldopen00399" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00399" name="l00399"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a27f3a928e1f6bbe7e847cffed6db729f"> 399</a></span> std::vector<double> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a27f3a928e1f6bbe7e847cffed6db729f">GraphEngine::mapNetInToMolarAbundanceVector</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a> &netIn)<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00400" name="l00400"></a><span class="lineno"> 400</span> std::vector<double> Y(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size(), 0.0); <span class="comment">// Initialize with zeros</span></div>
|
|
<div class="line"><a id="l00401" name="l00401"></a><span class="lineno"> 401</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& [symbol, entry] : netIn.<a class="code hl_variable" href="structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1">composition</a>) {</div>
|
|
<div class="line"><a id="l00402" name="l00402"></a><span class="lineno"> 402</span> Y[<a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda">getSpeciesIndex</a>(entry.isotope())] = netIn.<a class="code hl_variable" href="structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1">composition</a>.getMolarAbundance(symbol); <span class="comment">// Map species to their molar abundance</span></div>
|
|
<div class="line"><a id="l00403" name="l00403"></a><span class="lineno"> 403</span> }</div>
|
|
<div class="line"><a id="l00404" name="l00404"></a><span class="lineno"> 404</span> <span class="keywordflow">return</span> Y; <span class="comment">// Return the vector of molar abundances</span></div>
|
|
<div class="line"><a id="l00405" name="l00405"></a><span class="lineno"> 405</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00406" name="l00406"></a><span class="lineno"> 406</span> </div>
|
|
<div class="foldopen" id="foldopen00407" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00407" name="l00407"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#ae7a371be61ab09b3fa4a93f05bd44e5e"> 407</a></span> <a class="code hl_struct" href="structgridfire_1_1_priming_report.html">PrimingReport</a> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#ae7a371be61ab09b3fa4a93f05bd44e5e">GraphEngine::primeEngine</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a> &netIn) {</div>
|
|
<div class="line"><a id="l00408" name="l00408"></a><span class="lineno"> 408</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a> fullNetIn;</div>
|
|
<div class="line"><a id="l00409" name="l00409"></a><span class="lineno"> 409</span> fourdst::composition::Composition composition;</div>
|
|
<div class="line"><a id="l00410" name="l00410"></a><span class="lineno"> 410</span> </div>
|
|
<div class="line"><a id="l00411" name="l00411"></a><span class="lineno"> 411</span> std::vector<std::string> symbols;</div>
|
|
<div class="line"><a id="l00412" name="l00412"></a><span class="lineno"> 412</span> symbols.reserve(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size());</div>
|
|
<div class="line"><a id="l00413" name="l00413"></a><span class="lineno"> 413</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span> &symbol: <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>) {</div>
|
|
<div class="line"><a id="l00414" name="l00414"></a><span class="lineno"> 414</span> symbols.emplace_back(symbol.name());</div>
|
|
<div class="line"><a id="l00415" name="l00415"></a><span class="lineno"> 415</span> }</div>
|
|
<div class="line"><a id="l00416" name="l00416"></a><span class="lineno"> 416</span> composition.registerSymbol(symbols);</div>
|
|
<div class="line"><a id="l00417" name="l00417"></a><span class="lineno"> 417</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& [symbol, entry] : netIn.<a class="code hl_variable" href="structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1">composition</a>) {</div>
|
|
<div class="line"><a id="l00418" name="l00418"></a><span class="lineno"> 418</span> <span class="keywordflow">if</span> (<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a>.contains(symbol)) {</div>
|
|
<div class="line"><a id="l00419" name="l00419"></a><span class="lineno"> 419</span> composition.setMassFraction(symbol, entry.mass_fraction());</div>
|
|
<div class="line"><a id="l00420" name="l00420"></a><span class="lineno"> 420</span> } <span class="keywordflow">else</span> {</div>
|
|
<div class="line"><a id="l00421" name="l00421"></a><span class="lineno"> 421</span> composition.setMassFraction(symbol, 0.0);</div>
|
|
<div class="line"><a id="l00422" name="l00422"></a><span class="lineno"> 422</span> }</div>
|
|
<div class="line"><a id="l00423" name="l00423"></a><span class="lineno"> 423</span> }</div>
|
|
<div class="line"><a id="l00424" name="l00424"></a><span class="lineno"> 424</span> composition.finalize(<span class="keyword">true</span>);</div>
|
|
<div class="line"><a id="l00425" name="l00425"></a><span class="lineno"> 425</span> fullNetIn.<a class="code hl_variable" href="structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1">composition</a> = composition;</div>
|
|
<div class="line"><a id="l00426" name="l00426"></a><span class="lineno"> 426</span> fullNetIn.<a class="code hl_variable" href="structgridfire_1_1_net_in.html#a5be0f5195a5cd1dd177b9fc5ab83a7be">temperature</a> = netIn.<a class="code hl_variable" href="structgridfire_1_1_net_in.html#a5be0f5195a5cd1dd177b9fc5ab83a7be">temperature</a>;</div>
|
|
<div class="line"><a id="l00427" name="l00427"></a><span class="lineno"> 427</span> fullNetIn.<a class="code hl_variable" href="structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577">density</a> = netIn.<a class="code hl_variable" href="structgridfire_1_1_net_in.html#a06f0dff9f8927b7cf2da3004c8fa1577">density</a>;</div>
|
|
<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="keyword">auto</span> primingReport = <a class="code hl_function" href="namespacegridfire.html#acd0bfdfbce4e84af102d62ff8a797c9f">primeNetwork</a>(fullNetIn, *<span class="keyword">this</span>);</div>
|
|
<div class="line"><a id="l00430" name="l00430"></a><span class="lineno"> 430</span> </div>
|
|
<div class="line"><a id="l00431" name="l00431"></a><span class="lineno"> 431</span> <span class="keywordflow">return</span> primingReport;</div>
|
|
<div class="line"><a id="l00432" name="l00432"></a><span class="lineno"> 432</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00433" name="l00433"></a><span class="lineno"> 433</span> </div>
|
|
<div class="foldopen" id="foldopen00434" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00434" name="l00434"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a166a5f4349580f9aa0b930afec73fcc4"> 434</a></span> <a class="code hl_typedef" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a166a5f4349580f9aa0b930afec73fcc4">GraphEngine::getDepth</a>()<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00435" name="l00435"></a><span class="lineno"> 435</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01">m_depth</a>;</div>
|
|
<div class="line"><a id="l00436" name="l00436"></a><span class="lineno"> 436</span> }</div>
|
|
</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_graph_engine.html#ad9d6c70ace5cbbf7f3aa7b31fce39490"> 438</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#ad9d6c70ace5cbbf7f3aa7b31fce39490">GraphEngine::rebuild</a>(<span class="keyword">const</span> fourdst::composition::Composition& comp, <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a> depth) {</div>
|
|
<div class="line"><a id="l00439" name="l00439"></a><span class="lineno"> 439</span> <span class="keywordflow">if</span> (depth != <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01">m_depth</a>) {</div>
|
|
<div class="line"><a id="l00440" name="l00440"></a><span class="lineno"> 440</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01">m_depth</a> = depth;</div>
|
|
<div class="line"><a id="l00441" name="l00441"></a><span class="lineno"> 441</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a> = <a class="code hl_function" href="namespacegridfire.html#aedddb89e400a6111f69bfe0c3fd4214e">build_reaclib_nuclear_network</a>(comp, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01">m_depth</a>, <span class="keyword">false</span>);</div>
|
|
<div class="line"><a id="l00442" name="l00442"></a><span class="lineno"> 442</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">syncInternalMaps</a>(); <span class="comment">// Resync internal maps after changing the depth</span></div>
|
|
<div class="line"><a id="l00443" name="l00443"></a><span class="lineno"> 443</span> } <span class="keywordflow">else</span> {</div>
|
|
<div class="line"><a id="l00444" name="l00444"></a><span class="lineno"> 444</span> LOG_DEBUG(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Rebuild requested with the same depth. No changes made to the network."</span>);</div>
|
|
<div class="line"><a id="l00445" name="l00445"></a><span class="lineno"> 445</span> }</div>
|
|
<div class="line"><a id="l00446" name="l00446"></a><span class="lineno"> 446</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00447" name="l00447"></a><span class="lineno"> 447</span> </div>
|
|
<div class="foldopen" id="foldopen00448" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00448" name="l00448"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a97f98706b51fbe0d167ed81ffe58c438"> 448</a></span> <a class="code hl_struct" href="structgridfire_1_1_step_derivatives.html">StepDerivatives<double></a> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a97f98706b51fbe0d167ed81ffe58c438">GraphEngine::calculateAllDerivativesUsingPrecomputation</a>(</div>
|
|
<div class="line"><a id="l00449" name="l00449"></a><span class="lineno"> 449</span> <span class="keyword">const</span> std::vector<double> &Y_in,</div>
|
|
<div class="line"><a id="l00450" name="l00450"></a><span class="lineno"> 450</span> <span class="keyword">const</span> std::vector<double> &bare_rates,</div>
|
|
<div class="line"><a id="l00451" name="l00451"></a><span class="lineno"> 451</span> <span class="keyword">const</span> std::vector<double> &bare_reverse_rates,</div>
|
|
<div class="line"><a id="l00452" name="l00452"></a><span class="lineno"> 452</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
|
|
<div class="line"><a id="l00453" name="l00453"></a><span class="lineno"> 453</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
|
|
<div class="line"><a id="l00454" name="l00454"></a><span class="lineno"> 454</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00455" name="l00455"></a><span class="lineno"> 455</span> <span class="comment">// --- Calculate screening factors ---</span></div>
|
|
<div class="line"><a id="l00456" name="l00456"></a><span class="lineno"> 456</span> <span class="keyword">const</span> std::vector<double> screeningFactors = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#af17cf3762abac3efcab9a8e87c961210">m_screeningModel</a>->calculateScreeningFactors(</div>
|
|
<div class="line"><a id="l00457" name="l00457"></a><span class="lineno"> 457</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>,</div>
|
|
<div class="line"><a id="l00458" name="l00458"></a><span class="lineno"> 458</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>,</div>
|
|
<div class="line"><a id="l00459" name="l00459"></a><span class="lineno"> 459</span> Y_in,</div>
|
|
<div class="line"><a id="l00460" name="l00460"></a><span class="lineno"> 460</span> T9,</div>
|
|
<div class="line"><a id="l00461" name="l00461"></a><span class="lineno"> 461</span> rho</div>
|
|
<div class="line"><a id="l00462" name="l00462"></a><span class="lineno"> 462</span> );</div>
|
|
<div class="line"><a id="l00463" name="l00463"></a><span class="lineno"> 463</span> </div>
|
|
<div class="line"><a id="l00464" name="l00464"></a><span class="lineno"> 464</span> <span class="comment">// --- Optimized loop ---</span></div>
|
|
<div class="line"><a id="l00465" name="l00465"></a><span class="lineno"> 465</span> std::vector<double> molarReactionFlows;</div>
|
|
<div class="line"><a id="l00466" name="l00466"></a><span class="lineno"> 466</span> molarReactionFlows.reserve(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>.size());</div>
|
|
<div class="line"><a id="l00467" name="l00467"></a><span class="lineno"> 467</span> </div>
|
|
<div class="line"><a id="l00468" name="l00468"></a><span class="lineno"> 468</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& precomp : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>) {</div>
|
|
<div class="line"><a id="l00469" name="l00469"></a><span class="lineno"> 469</span> <span class="keywordtype">double</span> forwardAbundanceProduct = 1.0;</div>
|
|
<div class="line"><a id="l00470" name="l00470"></a><span class="lineno"> 470</span> <span class="comment">// bool below_threshold = false;</span></div>
|
|
<div class="line"><a id="l00471" name="l00471"></a><span class="lineno"> 471</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < precomp.unique_reactant_indices.size(); ++i) {</div>
|
|
<div class="line"><a id="l00472" name="l00472"></a><span class="lineno"> 472</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> reactantIndex = precomp.unique_reactant_indices[i];</div>
|
|
<div class="line"><a id="l00473" name="l00473"></a><span class="lineno"> 473</span> <span class="keyword">const</span> <span class="keywordtype">int</span> power = precomp.reactant_powers[i];</div>
|
|
<div class="line"><a id="l00474" name="l00474"></a><span class="lineno"> 474</span> <span class="comment">// const double abundance = Y_in[reactantIndex];</span></div>
|
|
<div class="line"><a id="l00475" name="l00475"></a><span class="lineno"> 475</span> <span class="comment">// if (abundance < MIN_ABUNDANCE_THRESHOLD) {</span></div>
|
|
<div class="line"><a id="l00476" name="l00476"></a><span class="lineno"> 476</span> <span class="comment">// below_threshold = true;</span></div>
|
|
<div class="line"><a id="l00477" name="l00477"></a><span class="lineno"> 477</span> <span class="comment">// break;</span></div>
|
|
<div class="line"><a id="l00478" name="l00478"></a><span class="lineno"> 478</span> <span class="comment">// }</span></div>
|
|
<div class="line"><a id="l00479" name="l00479"></a><span class="lineno"> 479</span> </div>
|
|
<div class="line"><a id="l00480" name="l00480"></a><span class="lineno"> 480</span> forwardAbundanceProduct *= std::pow(Y_in[reactantIndex], power);</div>
|
|
<div class="line"><a id="l00481" name="l00481"></a><span class="lineno"> 481</span> }</div>
|
|
<div class="line"><a id="l00482" name="l00482"></a><span class="lineno"> 482</span> <span class="comment">// if (below_threshold) {</span></div>
|
|
<div class="line"><a id="l00483" name="l00483"></a><span class="lineno"> 483</span> <span class="comment">// molarReactionFlows.push_back(0.0);</span></div>
|
|
<div class="line"><a id="l00484" name="l00484"></a><span class="lineno"> 484</span> <span class="comment">// continue; // Skip this reaction if any reactant is below the abundance threshold</span></div>
|
|
<div class="line"><a id="l00485" name="l00485"></a><span class="lineno"> 485</span> <span class="comment">// }</span></div>
|
|
<div class="line"><a id="l00486" name="l00486"></a><span class="lineno"> 486</span> </div>
|
|
<div class="line"><a id="l00487" name="l00487"></a><span class="lineno"> 487</span> <span class="keyword">const</span> <span class="keywordtype">double</span> bare_rate = bare_rates[precomp.reaction_index];</div>
|
|
<div class="line"><a id="l00488" name="l00488"></a><span class="lineno"> 488</span> <span class="keyword">const</span> <span class="keywordtype">double</span> screeningFactor = screeningFactors[precomp.reaction_index];</div>
|
|
<div class="line"><a id="l00489" name="l00489"></a><span class="lineno"> 489</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> numReactants = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>[precomp.reaction_index].reactants().size();</div>
|
|
<div class="line"><a id="l00490" name="l00490"></a><span class="lineno"> 490</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> numProducts = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>[precomp.reaction_index].products().size();</div>
|
|
<div class="line"><a id="l00491" name="l00491"></a><span class="lineno"> 491</span> </div>
|
|
<div class="line"><a id="l00492" name="l00492"></a><span class="lineno"> 492</span> <span class="keyword">const</span> <span class="keywordtype">double</span> forwardMolarReactionFlow =</div>
|
|
<div class="line"><a id="l00493" name="l00493"></a><span class="lineno"> 493</span> screeningFactor *</div>
|
|
<div class="line"><a id="l00494" name="l00494"></a><span class="lineno"> 494</span> bare_rate *</div>
|
|
<div class="line"><a id="l00495" name="l00495"></a><span class="lineno"> 495</span> precomp.symmetry_factor *</div>
|
|
<div class="line"><a id="l00496" name="l00496"></a><span class="lineno"> 496</span> forwardAbundanceProduct *</div>
|
|
<div class="line"><a id="l00497" name="l00497"></a><span class="lineno"> 497</span> std::pow(rho, numReactants > 1 ? numReactants - 1 : 0.0);</div>
|
|
<div class="line"><a id="l00498" name="l00498"></a><span class="lineno"> 498</span> </div>
|
|
<div class="line"><a id="l00499" name="l00499"></a><span class="lineno"> 499</span> <span class="keywordtype">double</span> reverseMolarReactionFlow = 0.0;</div>
|
|
<div class="line"><a id="l00500" name="l00500"></a><span class="lineno"> 500</span> <span class="keywordflow">if</span> (precomp.reverse_symmetry_factor != 0.0 and <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc">m_useReverseReactions</a>) {</div>
|
|
<div class="line"><a id="l00501" name="l00501"></a><span class="lineno"> 501</span> <span class="keyword">const</span> <span class="keywordtype">double</span> bare_reverse_rate = bare_reverse_rates[precomp.reaction_index];</div>
|
|
<div class="line"><a id="l00502" name="l00502"></a><span class="lineno"> 502</span> <span class="keywordtype">double</span> reverseAbundanceProduct = 1.0;</div>
|
|
<div class="line"><a id="l00503" name="l00503"></a><span class="lineno"> 503</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < precomp.unique_product_indices.size(); ++i) {</div>
|
|
<div class="line"><a id="l00504" name="l00504"></a><span class="lineno"> 504</span> reverseAbundanceProduct *= std::pow(Y_in[precomp.unique_product_indices[i]], precomp.product_powers[i]);</div>
|
|
<div class="line"><a id="l00505" name="l00505"></a><span class="lineno"> 505</span> }</div>
|
|
<div class="line"><a id="l00506" name="l00506"></a><span class="lineno"> 506</span> reverseMolarReactionFlow = screeningFactor *</div>
|
|
<div class="line"><a id="l00507" name="l00507"></a><span class="lineno"> 507</span> bare_reverse_rate *</div>
|
|
<div class="line"><a id="l00508" name="l00508"></a><span class="lineno"> 508</span> precomp.reverse_symmetry_factor *</div>
|
|
<div class="line"><a id="l00509" name="l00509"></a><span class="lineno"> 509</span> reverseAbundanceProduct *</div>
|
|
<div class="line"><a id="l00510" name="l00510"></a><span class="lineno"> 510</span> std::pow(rho, numProducts > 1 ? numProducts - 1 : 0.0);</div>
|
|
<div class="line"><a id="l00511" name="l00511"></a><span class="lineno"> 511</span> }</div>
|
|
<div class="line"><a id="l00512" name="l00512"></a><span class="lineno"> 512</span> </div>
|
|
<div class="line"><a id="l00513" name="l00513"></a><span class="lineno"> 513</span> molarReactionFlows.push_back(forwardMolarReactionFlow - reverseMolarReactionFlow);</div>
|
|
<div class="line"><a id="l00514" name="l00514"></a><span class="lineno"> 514</span> </div>
|
|
<div class="line"><a id="l00515" name="l00515"></a><span class="lineno"> 515</span> }</div>
|
|
<div class="line"><a id="l00516" name="l00516"></a><span class="lineno"> 516</span> </div>
|
|
<div class="line"><a id="l00517" name="l00517"></a><span class="lineno"> 517</span> <span class="comment">// --- Assemble molar abundance derivatives ---</span></div>
|
|
<div class="line"><a id="l00518" name="l00518"></a><span class="lineno"> 518</span> <a class="code hl_struct" href="structgridfire_1_1_step_derivatives.html">StepDerivatives<double></a> result;</div>
|
|
<div class="line"><a id="l00519" name="l00519"></a><span class="lineno"> 519</span> result.<a class="code hl_variable" href="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d">dydt</a>.assign(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size(), 0.0); <span class="comment">// Initialize derivatives to zero</span></div>
|
|
<div class="line"><a id="l00520" name="l00520"></a><span class="lineno"> 520</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j < <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>.size(); ++j) {</div>
|
|
<div class="line"><a id="l00521" name="l00521"></a><span class="lineno"> 521</span> <span class="keyword">const</span> <span class="keyword">auto</span>& precomp = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>[j];</div>
|
|
<div class="line"><a id="l00522" name="l00522"></a><span class="lineno"> 522</span> <span class="keyword">const</span> <span class="keywordtype">double</span> R_j = molarReactionFlows[j];</div>
|
|
<div class="line"><a id="l00523" name="l00523"></a><span class="lineno"> 523</span> </div>
|
|
<div class="line"><a id="l00524" name="l00524"></a><span class="lineno"> 524</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < precomp.affected_species_indices.size(); ++i) {</div>
|
|
<div class="line"><a id="l00525" name="l00525"></a><span class="lineno"> 525</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> speciesIndex = precomp.affected_species_indices[i];</div>
|
|
<div class="line"><a id="l00526" name="l00526"></a><span class="lineno"> 526</span> <span class="keyword">const</span> <span class="keywordtype">int</span> stoichiometricCoefficient = precomp.stoichiometric_coefficients[i];</div>
|
|
<div class="line"><a id="l00527" name="l00527"></a><span class="lineno"> 527</span> </div>
|
|
<div class="line"><a id="l00528" name="l00528"></a><span class="lineno"> 528</span> <span class="comment">// Update the derivative for this species</span></div>
|
|
<div class="line"><a id="l00529" name="l00529"></a><span class="lineno"> 529</span> result.<a class="code hl_variable" href="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d">dydt</a>[speciesIndex] += <span class="keyword">static_cast<</span><span class="keywordtype">double</span><span class="keyword">></span>(stoichiometricCoefficient) * R_j;</div>
|
|
<div class="line"><a id="l00530" name="l00530"></a><span class="lineno"> 530</span> }</div>
|
|
<div class="line"><a id="l00531" name="l00531"></a><span class="lineno"> 531</span> }</div>
|
|
<div class="line"><a id="l00532" name="l00532"></a><span class="lineno"> 532</span> </div>
|
|
<div class="line"><a id="l00533" name="l00533"></a><span class="lineno"> 533</span> <span class="comment">// --- Calculate the nuclear energy generation rate ---</span></div>
|
|
<div class="line"><a id="l00534" name="l00534"></a><span class="lineno"> 534</span> <span class="keywordtype">double</span> massProductionRate = 0.0; <span class="comment">// [mol][s^-1]</span></div>
|
|
<div class="line"><a id="l00535" name="l00535"></a><span class="lineno"> 535</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size(); ++i) {</div>
|
|
<div class="line"><a id="l00536" name="l00536"></a><span class="lineno"> 536</span> <span class="keyword">const</span> <span class="keyword">auto</span>& species = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>[i];</div>
|
|
<div class="line"><a id="l00537" name="l00537"></a><span class="lineno"> 537</span> massProductionRate += result.<a class="code hl_variable" href="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d">dydt</a>[i] * species.mass() * <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">m_constants</a>.u;</div>
|
|
<div class="line"><a id="l00538" name="l00538"></a><span class="lineno"> 538</span> }</div>
|
|
<div class="line"><a id="l00539" name="l00539"></a><span class="lineno"> 539</span> result.<a class="code hl_variable" href="structgridfire_1_1_step_derivatives.html#ab4aeb41be952c7b5844e1ee81fef9008">nuclearEnergyGenerationRate</a> = -massProductionRate * <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">m_constants</a>.Na * <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">m_constants</a>.c * <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">m_constants</a>.c; <span class="comment">// [erg][s^-1][g^-1]</span></div>
|
|
<div class="line"><a id="l00540" name="l00540"></a><span class="lineno"> 540</span> <span class="keywordflow">return</span> result;</div>
|
|
<div class="line"><a id="l00541" name="l00541"></a><span class="lineno"> 541</span> </div>
|
|
<div class="line"><a id="l00542" name="l00542"></a><span class="lineno"> 542</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00543" name="l00543"></a><span class="lineno"> 543</span> </div>
|
|
<div class="line"><a id="l00544" name="l00544"></a><span class="lineno"> 544</span> <span class="comment">// --- Generate Stoichiometry Matrix ---</span></div>
|
|
<div class="foldopen" id="foldopen00545" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00545" name="l00545"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38"> 545</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38">GraphEngine::generateStoichiometryMatrix</a>() {</div>
|
|
<div class="line"><a id="l00546" name="l00546"></a><span class="lineno"> 546</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Generating stoichiometry matrix..."</span>);</div>
|
|
<div class="line"><a id="l00547" name="l00547"></a><span class="lineno"> 547</span> </div>
|
|
<div class="line"><a id="l00548" name="l00548"></a><span class="lineno"> 548</span> <span class="comment">// Task 1: Set dimensions and initialize the matrix</span></div>
|
|
<div class="line"><a id="l00549" name="l00549"></a><span class="lineno"> 549</span> <span class="keywordtype">size_t</span> numSpecies = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size();</div>
|
|
<div class="line"><a id="l00550" name="l00550"></a><span class="lineno"> 550</span> <span class="keywordtype">size_t</span> numReactions = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size();</div>
|
|
<div class="line"><a id="l00551" name="l00551"></a><span class="lineno"> 551</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a>.resize(numSpecies, numReactions, <span class="keyword">false</span>);</div>
|
|
<div class="line"><a id="l00552" name="l00552"></a><span class="lineno"> 552</span> </div>
|
|
<div class="line"><a id="l00553" name="l00553"></a><span class="lineno"> 553</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Stoichiometry matrix initialized with dimensions: {} rows (species) x {} columns (reactions)."</span>,</div>
|
|
<div class="line"><a id="l00554" name="l00554"></a><span class="lineno"> 554</span> numSpecies, numReactions);</div>
|
|
<div class="line"><a id="l00555" name="l00555"></a><span class="lineno"> 555</span> </div>
|
|
<div class="line"><a id="l00556" name="l00556"></a><span class="lineno"> 556</span> <span class="comment">// Task 2: Populate the stoichiometry matrix</span></div>
|
|
<div class="line"><a id="l00557" name="l00557"></a><span class="lineno"> 557</span> <span class="comment">// Iterate through all reactions, assign them a column index, and fill in their stoichiometric coefficients.</span></div>
|
|
<div class="line"><a id="l00558" name="l00558"></a><span class="lineno"> 558</span> <span class="keywordtype">size_t</span> reactionColumnIndex = 0;</div>
|
|
<div class="line"><a id="l00559" name="l00559"></a><span class="lineno"> 559</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a> : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
|
|
<div class="line"><a id="l00560" name="l00560"></a><span class="lineno"> 560</span> <span class="comment">// Get the net stoichiometry for the current reaction</span></div>
|
|
<div class="line"><a id="l00561" name="l00561"></a><span class="lineno"> 561</span> std::unordered_map<fourdst::atomic::Species, int> netStoichiometry = <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.stoichiometry();</div>
|
|
<div class="line"><a id="l00562" name="l00562"></a><span class="lineno"> 562</span> </div>
|
|
<div class="line"><a id="l00563" name="l00563"></a><span class="lineno"> 563</span> <span class="comment">// Iterate through the species and their coefficients in the stoichiometry map</span></div>
|
|
<div class="line"><a id="l00564" name="l00564"></a><span class="lineno"> 564</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& [species, coefficient] : netStoichiometry) {</div>
|
|
<div class="line"><a id="l00565" name="l00565"></a><span class="lineno"> 565</span> <span class="comment">// Find the row index for this species</span></div>
|
|
<div class="line"><a id="l00566" name="l00566"></a><span class="lineno"> 566</span> <span class="keyword">auto</span> it = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a>.find(species);</div>
|
|
<div class="line"><a id="l00567" name="l00567"></a><span class="lineno"> 567</span> <span class="keywordflow">if</span> (it != <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a>.end()) {</div>
|
|
<div class="line"><a id="l00568" name="l00568"></a><span class="lineno"> 568</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> speciesRowIndex = it->second;</div>
|
|
<div class="line"><a id="l00569" name="l00569"></a><span class="lineno"> 569</span> <span class="comment">// Set the matrix element. Boost.uBLAS handles sparse insertion.</span></div>
|
|
<div class="line"><a id="l00570" name="l00570"></a><span class="lineno"> 570</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a>(speciesRowIndex, reactionColumnIndex) = coefficient;</div>
|
|
<div class="line"><a id="l00571" name="l00571"></a><span class="lineno"> 571</span> } <span class="keywordflow">else</span> {</div>
|
|
<div class="line"><a id="l00572" name="l00572"></a><span class="lineno"> 572</span> <span class="comment">// This scenario should ideally not happen if m_networkSpeciesMap and m_speciesToIndexMap are correctly synced</span></div>
|
|
<div class="line"><a id="l00573" name="l00573"></a><span class="lineno"> 573</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"CRITICAL ERROR: Species '{}' from reaction '{}' stoichiometry not found in species to index map."</span>,</div>
|
|
<div class="line"><a id="l00574" name="l00574"></a><span class="lineno"> 574</span> species.name(), <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id());</div>
|
|
<div class="line"><a id="l00575" name="l00575"></a><span class="lineno"> 575</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a> -> flush_log();</div>
|
|
<div class="line"><a id="l00576" name="l00576"></a><span class="lineno"> 576</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Species not found in species to index map: "</span> + std::string(species.name()));</div>
|
|
<div class="line"><a id="l00577" name="l00577"></a><span class="lineno"> 577</span> }</div>
|
|
<div class="line"><a id="l00578" name="l00578"></a><span class="lineno"> 578</span> }</div>
|
|
<div class="line"><a id="l00579" name="l00579"></a><span class="lineno"> 579</span> reactionColumnIndex++; <span class="comment">// Move to the next column for the next reaction</span></div>
|
|
<div class="line"><a id="l00580" name="l00580"></a><span class="lineno"> 580</span> }</div>
|
|
<div class="line"><a id="l00581" name="l00581"></a><span class="lineno"> 581</span> </div>
|
|
<div class="line"><a id="l00582" name="l00582"></a><span class="lineno"> 582</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Stoichiometry matrix population complete. Number of non-zero elements: {}."</span>,</div>
|
|
<div class="line"><a id="l00583" name="l00583"></a><span class="lineno"> 583</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a>.nnz()); <span class="comment">// Assuming nnz() exists for compressed_matrix</span></div>
|
|
<div class="line"><a id="l00584" name="l00584"></a><span class="lineno"> 584</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00585" name="l00585"></a><span class="lineno"> 585</span> </div>
|
|
<div class="foldopen" id="foldopen00586" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00586" name="l00586"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#aaf4d54e4b774ab8ec8eabec006579d31"> 586</a></span> <a class="code hl_struct" href="structgridfire_1_1_step_derivatives.html">StepDerivatives<double></a> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">GraphEngine::calculateAllDerivatives</a>(</div>
|
|
<div class="line"><a id="l00587" name="l00587"></a><span class="lineno"> 587</span> <span class="keyword">const</span> std::vector<double> &Y_in,</div>
|
|
<div class="line"><a id="l00588" name="l00588"></a><span class="lineno"> 588</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
|
|
<div class="line"><a id="l00589" name="l00589"></a><span class="lineno"> 589</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
|
|
<div class="line"><a id="l00590" name="l00590"></a><span class="lineno"> 590</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00591" name="l00591"></a><span class="lineno"> 591</span> <span class="keywordflow">return</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives<double></a>(Y_in, T9, rho);</div>
|
|
<div class="line"><a id="l00592" name="l00592"></a><span class="lineno"> 592</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00593" name="l00593"></a><span class="lineno"> 593</span> </div>
|
|
<div class="foldopen" id="foldopen00594" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00594" name="l00594"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a71a3d1181b90c3becdc5d9a3da05b9c9"> 594</a></span> <a class="code hl_struct" href="structgridfire_1_1_step_derivatives.html">StepDerivatives<ADDouble></a> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">GraphEngine::calculateAllDerivatives</a>(</div>
|
|
<div class="line"><a id="l00595" name="l00595"></a><span class="lineno"> 595</span> <span class="keyword">const</span> std::vector<ADDouble> &Y_in,</div>
|
|
<div class="line"><a id="l00596" name="l00596"></a><span class="lineno"> 596</span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc">ADDouble</a> &T9,</div>
|
|
<div class="line"><a id="l00597" name="l00597"></a><span class="lineno"> 597</span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc">ADDouble</a> &rho</div>
|
|
<div class="line"><a id="l00598" name="l00598"></a><span class="lineno"> 598</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00599" name="l00599"></a><span class="lineno"> 599</span> <span class="keywordflow">return</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives<ADDouble></a>(Y_in, T9, rho);</div>
|
|
<div class="line"><a id="l00600" name="l00600"></a><span class="lineno"> 600</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00601" name="l00601"></a><span class="lineno"> 601</span> </div>
|
|
<div class="foldopen" id="foldopen00602" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00602" name="l00602"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f"> 602</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f">GraphEngine::setScreeningModel</a>(<span class="keyword">const</span> <a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> model) {</div>
|
|
<div class="line"><a id="l00603" name="l00603"></a><span class="lineno"> 603</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#af17cf3762abac3efcab9a8e87c961210">m_screeningModel</a> = <a class="code hl_function" href="namespacegridfire_1_1screening.html#a6ca8556d27ac373e176f5b23437c416e">screening::selectScreeningModel</a>(model);</div>
|
|
<div class="line"><a id="l00604" name="l00604"></a><span class="lineno"> 604</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a52edc3e88f1e8fc497e1e63972d63c80">m_screeningType</a> = model;</div>
|
|
<div class="line"><a id="l00605" name="l00605"></a><span class="lineno"> 605</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00606" name="l00606"></a><span class="lineno"> 606</span> </div>
|
|
<div class="foldopen" id="foldopen00607" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00607" name="l00607"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a"> 607</a></span> <a class="code hl_enumeration" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a">GraphEngine::getScreeningModel</a>()<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00608" name="l00608"></a><span class="lineno"> 608</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a52edc3e88f1e8fc497e1e63972d63c80">m_screeningType</a>;</div>
|
|
<div class="line"><a id="l00609" name="l00609"></a><span class="lineno"> 609</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00610" name="l00610"></a><span class="lineno"> 610</span> </div>
|
|
<div class="foldopen" id="foldopen00611" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00611" name="l00611"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1"> 611</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1">GraphEngine::setPrecomputation</a>(<span class="keyword">const</span> <span class="keywordtype">bool</span> precompute) {</div>
|
|
<div class="line"><a id="l00612" name="l00612"></a><span class="lineno"> 612</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de">m_usePrecomputation</a> = precompute;</div>
|
|
<div class="line"><a id="l00613" name="l00613"></a><span class="lineno"> 613</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00614" name="l00614"></a><span class="lineno"> 614</span> </div>
|
|
<div class="foldopen" id="foldopen00615" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00615" name="l00615"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f"> 615</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f">GraphEngine::isPrecomputationEnabled</a>()<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00616" name="l00616"></a><span class="lineno"> 616</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de">m_usePrecomputation</a>;</div>
|
|
<div class="line"><a id="l00617" name="l00617"></a><span class="lineno"> 617</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00618" name="l00618"></a><span class="lineno"> 618</span> </div>
|
|
<div class="foldopen" id="foldopen00619" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00619" name="l00619"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#add98ece49ec5c538bddf3cc77004fe44"> 619</a></span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1partition_1_1_partition_function.html">partition::PartitionFunction</a> & <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#add98ece49ec5c538bddf3cc77004fe44">GraphEngine::getPartitionFunction</a>()<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00620" name="l00620"></a><span class="lineno"> 620</span> <span class="keywordflow">return</span> *<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e">m_partitionFunction</a>;</div>
|
|
<div class="line"><a id="l00621" name="l00621"></a><span class="lineno"> 621</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00622" name="l00622"></a><span class="lineno"> 622</span> </div>
|
|
<div class="foldopen" id="foldopen00623" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00623" name="l00623"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f"> 623</a></span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">GraphEngine::calculateMolarReactionFlow</a>(</div>
|
|
<div class="line"><a id="l00624" name="l00624"></a><span class="lineno"> 624</span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>,</div>
|
|
<div class="line"><a id="l00625" name="l00625"></a><span class="lineno"> 625</span> <span class="keyword">const</span> std::vector<double> &Y,</div>
|
|
<div class="line"><a id="l00626" name="l00626"></a><span class="lineno"> 626</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
|
|
<div class="line"><a id="l00627" name="l00627"></a><span class="lineno"> 627</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
|
|
<div class="line"><a id="l00628" name="l00628"></a><span class="lineno"> 628</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00629" name="l00629"></a><span class="lineno"> 629</span> <span class="keywordflow">return</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">calculateMolarReactionFlow<double></a>(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>, Y, T9, rho);</div>
|
|
<div class="line"><a id="l00630" name="l00630"></a><span class="lineno"> 630</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00631" name="l00631"></a><span class="lineno"> 631</span> </div>
|
|
<div class="foldopen" id="foldopen00632" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00632" name="l00632"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119"> 632</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119">GraphEngine::generateJacobianMatrix</a>(</div>
|
|
<div class="line"><a id="l00633" name="l00633"></a><span class="lineno"> 633</span> <span class="keyword">const</span> std::vector<double> &Y_dynamic,</div>
|
|
<div class="line"><a id="l00634" name="l00634"></a><span class="lineno"> 634</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
|
|
<div class="line"><a id="l00635" name="l00635"></a><span class="lineno"> 635</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
|
|
<div class="line"><a id="l00636" name="l00636"></a><span class="lineno"> 636</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00637" name="l00637"></a><span class="lineno"> 637</span> </div>
|
|
<div class="line"><a id="l00638" name="l00638"></a><span class="lineno"> 638</span> LOG_TRACE_L1_LIMIT_EVERY_N(1000, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Generating jacobian matrix for T9={}, rho={}.."</span>, T9, rho);</div>
|
|
<div class="line"><a id="l00639" name="l00639"></a><span class="lineno"> 639</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> numSpecies = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size();</div>
|
|
<div class="line"><a id="l00640" name="l00640"></a><span class="lineno"> 640</span> </div>
|
|
<div class="line"><a id="l00641" name="l00641"></a><span class="lineno"> 641</span> <span class="comment">// 1. Pack the input variables into a vector for CppAD</span></div>
|
|
<div class="line"><a id="l00642" name="l00642"></a><span class="lineno"> 642</span> std::vector<double> adInput(numSpecies + 2, 0.0); <span class="comment">// +2 for T9 and rho</span></div>
|
|
<div class="line"><a id="l00643" name="l00643"></a><span class="lineno"> 643</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < numSpecies; ++i) {</div>
|
|
<div class="line"><a id="l00644" name="l00644"></a><span class="lineno"> 644</span> adInput[i] = std::max(Y_dynamic[i], 1e-99); <span class="comment">// regularize the jacobian...</span></div>
|
|
<div class="line"><a id="l00645" name="l00645"></a><span class="lineno"> 645</span> }</div>
|
|
<div class="line"><a id="l00646" name="l00646"></a><span class="lineno"> 646</span> adInput[numSpecies] = T9; <span class="comment">// T9</span></div>
|
|
<div class="line"><a id="l00647" name="l00647"></a><span class="lineno"> 647</span> adInput[numSpecies + 1] = rho; <span class="comment">// rho</span></div>
|
|
<div class="line"><a id="l00648" name="l00648"></a><span class="lineno"> 648</span> </div>
|
|
<div class="line"><a id="l00649" name="l00649"></a><span class="lineno"> 649</span> <span class="comment">// 2. Calculate the full jacobian</span></div>
|
|
<div class="line"><a id="l00650" name="l00650"></a><span class="lineno"> 650</span> <span class="keyword">const</span> std::vector<double> dotY = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a>.Jacobian(adInput);</div>
|
|
<div class="line"><a id="l00651" name="l00651"></a><span class="lineno"> 651</span> </div>
|
|
<div class="line"><a id="l00652" name="l00652"></a><span class="lineno"> 652</span> <span class="comment">// 3. Pack jacobian vector into sparse matrix</span></div>
|
|
<div class="line"><a id="l00653" name="l00653"></a><span class="lineno"> 653</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.clear();</div>
|
|
<div class="line"><a id="l00654" name="l00654"></a><span class="lineno"> 654</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < numSpecies; ++i) {</div>
|
|
<div class="line"><a id="l00655" name="l00655"></a><span class="lineno"> 655</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j < numSpecies; ++j) {</div>
|
|
<div class="line"><a id="l00656" name="l00656"></a><span class="lineno"> 656</span> <span class="keyword">const</span> <span class="keywordtype">double</span> value = dotY[i * (numSpecies + 2) + j];</div>
|
|
<div class="line"><a id="l00657" name="l00657"></a><span class="lineno"> 657</span> <span class="keywordflow">if</span> (std::abs(value) > <a class="code hl_variable" href="namespacegridfire.html#ae01b1738df1921db565bcbd68dd6cf64">MIN_JACOBIAN_THRESHOLD</a> || i == j) { <span class="comment">// Always keep diagonal elements to avoid pathological stiffness</span></div>
|
|
<div class="line"><a id="l00658" name="l00658"></a><span class="lineno"> 658</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>(i, j) = value;</div>
|
|
<div class="line"><a id="l00659" name="l00659"></a><span class="lineno"> 659</span> }</div>
|
|
<div class="line"><a id="l00660" name="l00660"></a><span class="lineno"> 660</span> }</div>
|
|
<div class="line"><a id="l00661" name="l00661"></a><span class="lineno"> 661</span> }</div>
|
|
<div class="line"><a id="l00662" name="l00662"></a><span class="lineno"> 662</span> LOG_TRACE_L1_LIMIT_EVERY_N(1000, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Jacobian matrix generated with dimensions: {} rows x {} columns."</span>, <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.size1(), <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.size2());</div>
|
|
<div class="line"><a id="l00663" name="l00663"></a><span class="lineno"> 663</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00664" name="l00664"></a><span class="lineno"> 664</span> </div>
|
|
<div class="foldopen" id="foldopen00665" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00665" name="l00665"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a9687eef88c97eeb7f8680acb230f8ac1"> 665</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119">GraphEngine::generateJacobianMatrix</a>(</div>
|
|
<div class="line"><a id="l00666" name="l00666"></a><span class="lineno"> 666</span> <span class="keyword">const</span> std::vector<double> &Y_dynamic,</div>
|
|
<div class="line"><a id="l00667" name="l00667"></a><span class="lineno"> 667</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
|
|
<div class="line"><a id="l00668" name="l00668"></a><span class="lineno"> 668</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho,</div>
|
|
<div class="line"><a id="l00669" name="l00669"></a><span class="lineno"> 669</span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire.html#a898dfe22579e649935645cbd6f073178">SparsityPattern</a> &sparsityPattern</div>
|
|
<div class="line"><a id="l00670" name="l00670"></a><span class="lineno"> 670</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00671" name="l00671"></a><span class="lineno"> 671</span> <span class="comment">// --- Pack the input variables into a vector for CppAD ---</span></div>
|
|
<div class="line"><a id="l00672" name="l00672"></a><span class="lineno"> 672</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> numSpecies = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size();</div>
|
|
<div class="line"><a id="l00673" name="l00673"></a><span class="lineno"> 673</span> std::vector<double> x(numSpecies + 2, 0.0);</div>
|
|
<div class="line"><a id="l00674" name="l00674"></a><span class="lineno"> 674</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < numSpecies; ++i) {</div>
|
|
<div class="line"><a id="l00675" name="l00675"></a><span class="lineno"> 675</span> x[i] = Y_dynamic[i];</div>
|
|
<div class="line"><a id="l00676" name="l00676"></a><span class="lineno"> 676</span> }</div>
|
|
<div class="line"><a id="l00677" name="l00677"></a><span class="lineno"> 677</span> x[numSpecies] = T9;</div>
|
|
<div class="line"><a id="l00678" name="l00678"></a><span class="lineno"> 678</span> x[numSpecies + 1] = rho;</div>
|
|
<div class="line"><a id="l00679" name="l00679"></a><span class="lineno"> 679</span> </div>
|
|
<div class="line"><a id="l00680" name="l00680"></a><span class="lineno"> 680</span> <span class="comment">// --- Convert into CppAD Sparsity pattern ---</span></div>
|
|
<div class="line"><a id="l00681" name="l00681"></a><span class="lineno"> 681</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> nnz = sparsityPattern.size(); <span class="comment">// Number of non-zero entries in the sparsity pattern</span></div>
|
|
<div class="line"><a id="l00682" name="l00682"></a><span class="lineno"> 682</span> std::vector<size_t> row_indices(nnz);</div>
|
|
<div class="line"><a id="l00683" name="l00683"></a><span class="lineno"> 683</span> std::vector<size_t> col_indices(nnz);</div>
|
|
<div class="line"><a id="l00684" name="l00684"></a><span class="lineno"> 684</span> </div>
|
|
<div class="line"><a id="l00685" name="l00685"></a><span class="lineno"> 685</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> k = 0; k < nnz; ++k) {</div>
|
|
<div class="line"><a id="l00686" name="l00686"></a><span class="lineno"> 686</span> row_indices[k] = sparsityPattern[k].first;</div>
|
|
<div class="line"><a id="l00687" name="l00687"></a><span class="lineno"> 687</span> col_indices[k] = sparsityPattern[k].second;</div>
|
|
<div class="line"><a id="l00688" name="l00688"></a><span class="lineno"> 688</span> }</div>
|
|
<div class="line"><a id="l00689" name="l00689"></a><span class="lineno"> 689</span> </div>
|
|
<div class="line"><a id="l00690" name="l00690"></a><span class="lineno"> 690</span> std::vector<double> values(nnz);</div>
|
|
<div class="line"><a id="l00691" name="l00691"></a><span class="lineno"> 691</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> num_rows_jac = numSpecies;</div>
|
|
<div class="line"><a id="l00692" name="l00692"></a><span class="lineno"> 692</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> num_cols_jac = numSpecies + 2; <span class="comment">// +2 for T9 and rho</span></div>
|
|
<div class="line"><a id="l00693" name="l00693"></a><span class="lineno"> 693</span> </div>
|
|
<div class="line"><a id="l00694" name="l00694"></a><span class="lineno"> 694</span> CppAD::sparse_rc<std::vector<size_t>> CppAD_sparsity_pattern(num_rows_jac, num_cols_jac, nnz);</div>
|
|
<div class="line"><a id="l00695" name="l00695"></a><span class="lineno"> 695</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> k = 0; k < nnz; ++k) {</div>
|
|
<div class="line"><a id="l00696" name="l00696"></a><span class="lineno"> 696</span> CppAD_sparsity_pattern.set(k, sparsityPattern[k].first, sparsityPattern[k].second);</div>
|
|
<div class="line"><a id="l00697" name="l00697"></a><span class="lineno"> 697</span> }</div>
|
|
<div class="line"><a id="l00698" name="l00698"></a><span class="lineno"> 698</span> </div>
|
|
<div class="line"><a id="l00699" name="l00699"></a><span class="lineno"> 699</span> CppAD::sparse_rcv<std::vector<size_t>, std::vector<double>> jac_subset(CppAD_sparsity_pattern);</div>
|
|
<div class="line"><a id="l00700" name="l00700"></a><span class="lineno"> 700</span> </div>
|
|
<div class="line"><a id="l00701" name="l00701"></a><span class="lineno"> 701</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a>.sparse_jac_rev(</div>
|
|
<div class="line"><a id="l00702" name="l00702"></a><span class="lineno"> 702</span> x,</div>
|
|
<div class="line"><a id="l00703" name="l00703"></a><span class="lineno"> 703</span> jac_subset, <span class="comment">// Sparse Jacobian output</span></div>
|
|
<div class="line"><a id="l00704" name="l00704"></a><span class="lineno"> 704</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a19b2eea0e8d05ac90f9fd7120bdc6e06">m_full_jacobian_sparsity_pattern</a>,</div>
|
|
<div class="line"><a id="l00705" name="l00705"></a><span class="lineno"> 705</span> <span class="stringliteral">"cppad"</span>,</div>
|
|
<div class="line"><a id="l00706" name="l00706"></a><span class="lineno"> 706</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a250cc6350dc052fbdfdf9a02066e7891">m_jac_work</a> <span class="comment">// Work vector for CppAD</span></div>
|
|
<div class="line"><a id="l00707" name="l00707"></a><span class="lineno"> 707</span> );</div>
|
|
<div class="line"><a id="l00708" name="l00708"></a><span class="lineno"> 708</span> </div>
|
|
<div class="line"><a id="l00709" name="l00709"></a><span class="lineno"> 709</span> <span class="comment">// --- Convert the sparse Jacobian back to the Boost uBLAS format ---</span></div>
|
|
<div class="line"><a id="l00710" name="l00710"></a><span class="lineno"> 710</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>.clear();</div>
|
|
<div class="line"><a id="l00711" name="l00711"></a><span class="lineno"> 711</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> k = 0; k < nnz; ++k) {</div>
|
|
<div class="line"><a id="l00712" name="l00712"></a><span class="lineno"> 712</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> row = jac_subset.row()[k];</div>
|
|
<div class="line"><a id="l00713" name="l00713"></a><span class="lineno"> 713</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> col = jac_subset.col()[k];</div>
|
|
<div class="line"><a id="l00714" name="l00714"></a><span class="lineno"> 714</span> <span class="keyword">const</span> <span class="keywordtype">double</span> value = jac_subset.val()[k];</div>
|
|
<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="keywordflow">if</span> (std::abs(value) > <a class="code hl_variable" href="namespacegridfire.html#ae01b1738df1921db565bcbd68dd6cf64">MIN_JACOBIAN_THRESHOLD</a>) {</div>
|
|
<div class="line"><a id="l00717" name="l00717"></a><span class="lineno"> 717</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>(row, col) = value; <span class="comment">// Insert into the sparse matrix</span></div>
|
|
<div class="line"><a id="l00718" name="l00718"></a><span class="lineno"> 718</span> }</div>
|
|
<div class="line"><a id="l00719" name="l00719"></a><span class="lineno"> 719</span> }</div>
|
|
<div class="line"><a id="l00720" name="l00720"></a><span class="lineno"> 720</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00721" name="l00721"></a><span class="lineno"> 721</span> </div>
|
|
<div class="foldopen" id="foldopen00722" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00722" name="l00722"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c"> 722</a></span> <span class="keywordtype">double</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c">GraphEngine::getJacobianMatrixEntry</a>(<span class="keyword">const</span> <span class="keywordtype">int</span> i, <span class="keyword">const</span> <span class="keywordtype">int</span> j)<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00723" name="l00723"></a><span class="lineno"> 723</span> <span class="comment">// LOG_TRACE_L3(m_logger, "Getting jacobian matrix entry for {},{} = {}", i, j, m_jacobianMatrix(i, j));</span></div>
|
|
<div class="line"><a id="l00724" name="l00724"></a><span class="lineno"> 724</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a>(i, j);</div>
|
|
<div class="line"><a id="l00725" name="l00725"></a><span class="lineno"> 725</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00726" name="l00726"></a><span class="lineno"> 726</span> </div>
|
|
<div class="foldopen" id="foldopen00727" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00727" name="l00727"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9"> 727</a></span> std::unordered_map<fourdst::atomic::Species, int> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9">GraphEngine::getNetReactionStoichiometry</a>(</div>
|
|
<div class="line"><a id="l00728" name="l00728"></a><span class="lineno"> 728</span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a></div>
|
|
<div class="line"><a id="l00729" name="l00729"></a><span class="lineno"> 729</span> ) {</div>
|
|
<div class="line"><a id="l00730" name="l00730"></a><span class="lineno"> 730</span> <span class="keywordflow">return</span> <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.stoichiometry();</div>
|
|
<div class="line"><a id="l00731" name="l00731"></a><span class="lineno"> 731</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00732" name="l00732"></a><span class="lineno"> 732</span> </div>
|
|
<div class="foldopen" id="foldopen00733" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00733" name="l00733"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152"> 733</a></span> <span class="keywordtype">int</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152">GraphEngine::getStoichiometryMatrixEntry</a>(</div>
|
|
<div class="line"><a id="l00734" name="l00734"></a><span class="lineno"> 734</span> <span class="keyword">const</span> <span class="keywordtype">int</span> speciesIndex,</div>
|
|
<div class="line"><a id="l00735" name="l00735"></a><span class="lineno"> 735</span> <span class="keyword">const</span> <span class="keywordtype">int</span> reactionIndex</div>
|
|
<div class="line"><a id="l00736" name="l00736"></a><span class="lineno"> 736</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00737" name="l00737"></a><span class="lineno"> 737</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a>(speciesIndex, reactionIndex);</div>
|
|
<div class="line"><a id="l00738" name="l00738"></a><span class="lineno"> 738</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00739" name="l00739"></a><span class="lineno"> 739</span> </div>
|
|
<div class="foldopen" id="foldopen00740" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00740" name="l00740"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929"> 740</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929">GraphEngine::exportToDot</a>(<span class="keyword">const</span> std::string &filename)<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00741" name="l00741"></a><span class="lineno"> 741</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Exporting network graph to DOT file: {}"</span>, filename);</div>
|
|
<div class="line"><a id="l00742" name="l00742"></a><span class="lineno"> 742</span> </div>
|
|
<div class="line"><a id="l00743" name="l00743"></a><span class="lineno"> 743</span> std::ofstream dotFile(filename);</div>
|
|
<div class="line"><a id="l00744" name="l00744"></a><span class="lineno"> 744</span> <span class="keywordflow">if</span> (!dotFile.is_open()) {</div>
|
|
<div class="line"><a id="l00745" name="l00745"></a><span class="lineno"> 745</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Failed to open file for writing: {}"</span>, filename);</div>
|
|
<div class="line"><a id="l00746" name="l00746"></a><span class="lineno"> 746</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>->flush_log();</div>
|
|
<div class="line"><a id="l00747" name="l00747"></a><span class="lineno"> 747</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Failed to open file for writing: "</span> + filename);</div>
|
|
<div class="line"><a id="l00748" name="l00748"></a><span class="lineno"> 748</span> }</div>
|
|
<div class="line"><a id="l00749" name="l00749"></a><span class="lineno"> 749</span> </div>
|
|
<div class="line"><a id="l00750" name="l00750"></a><span class="lineno"> 750</span> dotFile << <span class="stringliteral">"digraph NuclearReactionNetwork {\n"</span>;</div>
|
|
<div class="line"><a id="l00751" name="l00751"></a><span class="lineno"> 751</span> dotFile << <span class="stringliteral">" graph [rankdir=LR, splines=true, overlap=false, bgcolor=\"#f0f0f0\"];\n"</span>;</div>
|
|
<div class="line"><a id="l00752" name="l00752"></a><span class="lineno"> 752</span> dotFile << <span class="stringliteral">" node [shape=circle, style=filled, fillcolor=\"#a7c7e7\", fontname=\"Helvetica\"];\n"</span>;</div>
|
|
<div class="line"><a id="l00753" name="l00753"></a><span class="lineno"> 753</span> dotFile << <span class="stringliteral">" edge [fontname=\"Helvetica\", fontsize=10];\n\n"</span>;</div>
|
|
<div class="line"><a id="l00754" name="l00754"></a><span class="lineno"> 754</span> </div>
|
|
<div class="line"><a id="l00755" name="l00755"></a><span class="lineno"> 755</span> <span class="comment">// 1. Define all species as nodes</span></div>
|
|
<div class="line"><a id="l00756" name="l00756"></a><span class="lineno"> 756</span> dotFile << <span class="stringliteral">" // --- Species Nodes ---\n"</span>;</div>
|
|
<div class="line"><a id="l00757" name="l00757"></a><span class="lineno"> 757</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& species : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>) {</div>
|
|
<div class="line"><a id="l00758" name="l00758"></a><span class="lineno"> 758</span> dotFile << <span class="stringliteral">" \""</span> << species.name() << <span class="stringliteral">"\" [label=\""</span> << species.name() << <span class="stringliteral">"\"];\n"</span>;</div>
|
|
<div class="line"><a id="l00759" name="l00759"></a><span class="lineno"> 759</span> }</div>
|
|
<div class="line"><a id="l00760" name="l00760"></a><span class="lineno"> 760</span> dotFile << <span class="stringliteral">"\n"</span>;</div>
|
|
<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> <span class="comment">// 2. Define all reactions as intermediate nodes and connect them</span></div>
|
|
<div class="line"><a id="l00763" name="l00763"></a><span class="lineno"> 763</span> dotFile << <span class="stringliteral">" // --- Reaction Edges ---\n"</span>;</div>
|
|
<div class="line"><a id="l00764" name="l00764"></a><span class="lineno"> 764</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a> : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
|
|
<div class="line"><a id="l00765" name="l00765"></a><span class="lineno"> 765</span> <span class="comment">// Create a unique ID for the reaction node</span></div>
|
|
<div class="line"><a id="l00766" name="l00766"></a><span class="lineno"> 766</span> std::string reactionNodeId = <span class="stringliteral">"reaction_"</span> + std::string(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id());</div>
|
|
<div class="line"><a id="l00767" name="l00767"></a><span class="lineno"> 767</span> </div>
|
|
<div class="line"><a id="l00768" name="l00768"></a><span class="lineno"> 768</span> <span class="comment">// Define the reaction node (small, black dot)</span></div>
|
|
<div class="line"><a id="l00769" name="l00769"></a><span class="lineno"> 769</span> dotFile << <span class="stringliteral">" \""</span> << reactionNodeId << <span class="stringliteral">"\" [shape=point, fillcolor=black, width=0.1, height=0.1, label=\"\"];\n"</span>;</div>
|
|
<div class="line"><a id="l00770" name="l00770"></a><span class="lineno"> 770</span> </div>
|
|
<div class="line"><a id="l00771" name="l00771"></a><span class="lineno"> 771</span> <span class="comment">// Draw edges from reactants to the reaction node</span></div>
|
|
<div class="line"><a id="l00772" name="l00772"></a><span class="lineno"> 772</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& reactant : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants()) {</div>
|
|
<div class="line"><a id="l00773" name="l00773"></a><span class="lineno"> 773</span> dotFile << <span class="stringliteral">" \""</span> << reactant.name() << <span class="stringliteral">"\" -> \""</span> << reactionNodeId << <span class="stringliteral">"\";\n"</span>;</div>
|
|
<div class="line"><a id="l00774" name="l00774"></a><span class="lineno"> 774</span> }</div>
|
|
<div class="line"><a id="l00775" name="l00775"></a><span class="lineno"> 775</span> </div>
|
|
<div class="line"><a id="l00776" name="l00776"></a><span class="lineno"> 776</span> <span class="comment">// Draw edges from the reaction node to products</span></div>
|
|
<div class="line"><a id="l00777" name="l00777"></a><span class="lineno"> 777</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& product : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products()) {</div>
|
|
<div class="line"><a id="l00778" name="l00778"></a><span class="lineno"> 778</span> dotFile << <span class="stringliteral">" \""</span> << reactionNodeId << <span class="stringliteral">"\" -> \""</span> << product.name() << <span class="stringliteral">"\" [label=\""</span> << <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.qValue() << <span class="stringliteral">" MeV\"];\n"</span>;</div>
|
|
<div class="line"><a id="l00779" name="l00779"></a><span class="lineno"> 779</span> }</div>
|
|
<div class="line"><a id="l00780" name="l00780"></a><span class="lineno"> 780</span> dotFile << <span class="stringliteral">"\n"</span>;</div>
|
|
<div class="line"><a id="l00781" name="l00781"></a><span class="lineno"> 781</span> }</div>
|
|
<div class="line"><a id="l00782" name="l00782"></a><span class="lineno"> 782</span> </div>
|
|
<div class="line"><a id="l00783" name="l00783"></a><span class="lineno"> 783</span> dotFile << <span class="stringliteral">"}\n"</span>;</div>
|
|
<div class="line"><a id="l00784" name="l00784"></a><span class="lineno"> 784</span> dotFile.close();</div>
|
|
<div class="line"><a id="l00785" name="l00785"></a><span class="lineno"> 785</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Successfully exported network to {}"</span>, filename);</div>
|
|
<div class="line"><a id="l00786" name="l00786"></a><span class="lineno"> 786</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00787" name="l00787"></a><span class="lineno"> 787</span> </div>
|
|
<div class="foldopen" id="foldopen00788" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00788" name="l00788"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95"> 788</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95">GraphEngine::exportToCSV</a>(<span class="keyword">const</span> std::string &filename)<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00789" name="l00789"></a><span class="lineno"> 789</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Exporting network graph to CSV file: {}"</span>, filename);</div>
|
|
<div class="line"><a id="l00790" name="l00790"></a><span class="lineno"> 790</span> </div>
|
|
<div class="line"><a id="l00791" name="l00791"></a><span class="lineno"> 791</span> std::ofstream csvFile(filename, std::ios::out | std::ios::trunc);</div>
|
|
<div class="line"><a id="l00792" name="l00792"></a><span class="lineno"> 792</span> <span class="keywordflow">if</span> (!csvFile.is_open()) {</div>
|
|
<div class="line"><a id="l00793" name="l00793"></a><span class="lineno"> 793</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Failed to open file for writing: {}"</span>, filename);</div>
|
|
<div class="line"><a id="l00794" name="l00794"></a><span class="lineno"> 794</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>->flush_log();</div>
|
|
<div class="line"><a id="l00795" name="l00795"></a><span class="lineno"> 795</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Failed to open file for writing: "</span> + filename);</div>
|
|
<div class="line"><a id="l00796" name="l00796"></a><span class="lineno"> 796</span> }</div>
|
|
<div class="line"><a id="l00797" name="l00797"></a><span class="lineno"> 797</span> csvFile << <span class="stringliteral">"Reaction;Reactants;Products;Q-value;sources;rates\n"</span>;</div>
|
|
<div class="line"><a id="l00798" name="l00798"></a><span class="lineno"> 798</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a> : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
|
|
<div class="line"><a id="l00799" name="l00799"></a><span class="lineno"> 799</span> <span class="comment">// Dynamic cast to REACLIBReaction to access specific properties</span></div>
|
|
<div class="line"><a id="l00800" name="l00800"></a><span class="lineno"> 800</span> csvFile << <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.id() << <span class="stringliteral">";"</span>;</div>
|
|
<div class="line"><a id="l00801" name="l00801"></a><span class="lineno"> 801</span> <span class="comment">// Reactants</span></div>
|
|
<div class="line"><a id="l00802" name="l00802"></a><span class="lineno"> 802</span> <span class="keywordtype">size_t</span> count = 0;</div>
|
|
<div class="line"><a id="l00803" name="l00803"></a><span class="lineno"> 803</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& reactant : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants()) {</div>
|
|
<div class="line"><a id="l00804" name="l00804"></a><span class="lineno"> 804</span> csvFile << reactant.name();</div>
|
|
<div class="line"><a id="l00805" name="l00805"></a><span class="lineno"> 805</span> <span class="keywordflow">if</span> (++count < <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants().size()) {</div>
|
|
<div class="line"><a id="l00806" name="l00806"></a><span class="lineno"> 806</span> csvFile << <span class="stringliteral">","</span>;</div>
|
|
<div class="line"><a id="l00807" name="l00807"></a><span class="lineno"> 807</span> }</div>
|
|
<div class="line"><a id="l00808" name="l00808"></a><span class="lineno"> 808</span> }</div>
|
|
<div class="line"><a id="l00809" name="l00809"></a><span class="lineno"> 809</span> csvFile << <span class="stringliteral">";"</span>;</div>
|
|
<div class="line"><a id="l00810" name="l00810"></a><span class="lineno"> 810</span> count = 0;</div>
|
|
<div class="line"><a id="l00811" name="l00811"></a><span class="lineno"> 811</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& product : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products()) {</div>
|
|
<div class="line"><a id="l00812" name="l00812"></a><span class="lineno"> 812</span> csvFile << product.name();</div>
|
|
<div class="line"><a id="l00813" name="l00813"></a><span class="lineno"> 813</span> <span class="keywordflow">if</span> (++count < <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products().size()) {</div>
|
|
<div class="line"><a id="l00814" name="l00814"></a><span class="lineno"> 814</span> csvFile << <span class="stringliteral">","</span>;</div>
|
|
<div class="line"><a id="l00815" name="l00815"></a><span class="lineno"> 815</span> }</div>
|
|
<div class="line"><a id="l00816" name="l00816"></a><span class="lineno"> 816</span> }</div>
|
|
<div class="line"><a id="l00817" name="l00817"></a><span class="lineno"> 817</span> csvFile << <span class="stringliteral">";"</span> << <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.qValue() << <span class="stringliteral">";"</span>;</div>
|
|
<div class="line"><a id="l00818" name="l00818"></a><span class="lineno"> 818</span> <span class="comment">// Reaction coefficients</span></div>
|
|
<div class="line"><a id="l00819" name="l00819"></a><span class="lineno"> 819</span> <span class="keyword">auto</span> sources = <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.sources();</div>
|
|
<div class="line"><a id="l00820" name="l00820"></a><span class="lineno"> 820</span> count = 0;</div>
|
|
<div class="line"><a id="l00821" name="l00821"></a><span class="lineno"> 821</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& source : sources) {</div>
|
|
<div class="line"><a id="l00822" name="l00822"></a><span class="lineno"> 822</span> csvFile << source;</div>
|
|
<div class="line"><a id="l00823" name="l00823"></a><span class="lineno"> 823</span> <span class="keywordflow">if</span> (++count < sources.size()) {</div>
|
|
<div class="line"><a id="l00824" name="l00824"></a><span class="lineno"> 824</span> csvFile << <span class="stringliteral">","</span>;</div>
|
|
<div class="line"><a id="l00825" name="l00825"></a><span class="lineno"> 825</span> }</div>
|
|
<div class="line"><a id="l00826" name="l00826"></a><span class="lineno"> 826</span> }</div>
|
|
<div class="line"><a id="l00827" name="l00827"></a><span class="lineno"> 827</span> csvFile << <span class="stringliteral">";"</span>;</div>
|
|
<div class="line"><a id="l00828" name="l00828"></a><span class="lineno"> 828</span> <span class="comment">// Reaction coefficients</span></div>
|
|
<div class="line"><a id="l00829" name="l00829"></a><span class="lineno"> 829</span> count = 0;</div>
|
|
<div class="line"><a id="l00830" name="l00830"></a><span class="lineno"> 830</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& rates : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>) {</div>
|
|
<div class="line"><a id="l00831" name="l00831"></a><span class="lineno"> 831</span> csvFile << rates;</div>
|
|
<div class="line"><a id="l00832" name="l00832"></a><span class="lineno"> 832</span> <span class="keywordflow">if</span> (++count < <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.size()) {</div>
|
|
<div class="line"><a id="l00833" name="l00833"></a><span class="lineno"> 833</span> csvFile << <span class="stringliteral">","</span>;</div>
|
|
<div class="line"><a id="l00834" name="l00834"></a><span class="lineno"> 834</span> }</div>
|
|
<div class="line"><a id="l00835" name="l00835"></a><span class="lineno"> 835</span> }</div>
|
|
<div class="line"><a id="l00836" name="l00836"></a><span class="lineno"> 836</span> csvFile << <span class="stringliteral">"\n"</span>;</div>
|
|
<div class="line"><a id="l00837" name="l00837"></a><span class="lineno"> 837</span> }</div>
|
|
<div class="line"><a id="l00838" name="l00838"></a><span class="lineno"> 838</span> csvFile.close();</div>
|
|
<div class="line"><a id="l00839" name="l00839"></a><span class="lineno"> 839</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Successfully exported network graph to {}"</span>, filename);</div>
|
|
<div class="line"><a id="l00840" name="l00840"></a><span class="lineno"> 840</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00841" name="l00841"></a><span class="lineno"> 841</span> </div>
|
|
<div class="foldopen" id="foldopen00842" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00842" name="l00842"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a65f9f33cddb0bbd1da7c9d0cff23d581"> 842</a></span> std::expected<std::unordered_map<fourdst::atomic::Species, double>, <a class="code hl_struct" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a>> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a65f9f33cddb0bbd1da7c9d0cff23d581">GraphEngine::getSpeciesTimescales</a>(</div>
|
|
<div class="line"><a id="l00843" name="l00843"></a><span class="lineno"> 843</span> <span class="keyword">const</span> std::vector<double> &Y,</div>
|
|
<div class="line"><a id="l00844" name="l00844"></a><span class="lineno"> 844</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
|
|
<div class="line"><a id="l00845" name="l00845"></a><span class="lineno"> 845</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
|
|
<div class="line"><a id="l00846" name="l00846"></a><span class="lineno"> 846</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00847" name="l00847"></a><span class="lineno"> 847</span> <span class="keyword">auto</span> [dydt, _] = <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives<double></a>(Y, T9, rho);</div>
|
|
<div class="line"><a id="l00848" name="l00848"></a><span class="lineno"> 848</span> std::unordered_map<fourdst::atomic::Species, double> speciesTimescales;</div>
|
|
<div class="line"><a id="l00849" name="l00849"></a><span class="lineno"> 849</span> speciesTimescales.reserve(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size());</div>
|
|
<div class="line"><a id="l00850" name="l00850"></a><span class="lineno"> 850</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size(); ++i) {</div>
|
|
<div class="line"><a id="l00851" name="l00851"></a><span class="lineno"> 851</span> <span class="keywordtype">double</span> timescale = std::numeric_limits<double>::infinity();</div>
|
|
<div class="line"><a id="l00852" name="l00852"></a><span class="lineno"> 852</span> <span class="keyword">const</span> <span class="keyword">auto</span> species = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>[i];</div>
|
|
<div class="line"><a id="l00853" name="l00853"></a><span class="lineno"> 853</span> <span class="keywordflow">if</span> (std::abs(dydt[i]) > 0.0) {</div>
|
|
<div class="line"><a id="l00854" name="l00854"></a><span class="lineno"> 854</span> timescale = std::abs(Y[i] / dydt[i]);</div>
|
|
<div class="line"><a id="l00855" name="l00855"></a><span class="lineno"> 855</span> }</div>
|
|
<div class="line"><a id="l00856" name="l00856"></a><span class="lineno"> 856</span> speciesTimescales.emplace(species, timescale);</div>
|
|
<div class="line"><a id="l00857" name="l00857"></a><span class="lineno"> 857</span> }</div>
|
|
<div class="line"><a id="l00858" name="l00858"></a><span class="lineno"> 858</span> <span class="keywordflow">return</span> speciesTimescales;</div>
|
|
<div class="line"><a id="l00859" name="l00859"></a><span class="lineno"> 859</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00860" name="l00860"></a><span class="lineno"> 860</span> </div>
|
|
<div class="foldopen" id="foldopen00861" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00861" name="l00861"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#aef8f6bde24d27345067b71084330c7da"> 861</a></span> std::expected<std::unordered_map<fourdst::atomic::Species, double>, <a class="code hl_struct" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a>> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#aef8f6bde24d27345067b71084330c7da">GraphEngine::getSpeciesDestructionTimescales</a>(</div>
|
|
<div class="line"><a id="l00862" name="l00862"></a><span class="lineno"> 862</span> <span class="keyword">const</span> std::vector<double> &Y,</div>
|
|
<div class="line"><a id="l00863" name="l00863"></a><span class="lineno"> 863</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9,</div>
|
|
<div class="line"><a id="l00864" name="l00864"></a><span class="lineno"> 864</span> <span class="keyword">const</span> <span class="keywordtype">double</span> rho</div>
|
|
<div class="line"><a id="l00865" name="l00865"></a><span class="lineno"> 865</span> )<span class="keyword"> const </span>{</div>
|
|
<div class="line"><a id="l00866" name="l00866"></a><span class="lineno"> 866</span> <span class="keyword">auto</span> [dydt, _] = <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives<double></a>(Y, T9, rho);</div>
|
|
<div class="line"><a id="l00867" name="l00867"></a><span class="lineno"> 867</span> std::unordered_map<fourdst::atomic::Species, double> speciesDestructionTimescales;</div>
|
|
<div class="line"><a id="l00868" name="l00868"></a><span class="lineno"> 868</span> speciesDestructionTimescales.reserve(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size());</div>
|
|
<div class="line"><a id="l00869" name="l00869"></a><span class="lineno"> 869</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& species : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>) {</div>
|
|
<div class="line"><a id="l00870" name="l00870"></a><span class="lineno"> 870</span> <span class="keywordtype">double</span> netDestructionFlow = 0.0;</div>
|
|
<div class="line"><a id="l00871" name="l00871"></a><span class="lineno"> 871</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a> : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
|
|
<div class="line"><a id="l00872" name="l00872"></a><span class="lineno"> 872</span> <span class="keywordflow">if</span> (<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.stoichiometry(species) < 0) {</div>
|
|
<div class="line"><a id="l00873" name="l00873"></a><span class="lineno"> 873</span> <span class="keyword">const</span> <span class="keywordtype">double</span> flow = <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">calculateMolarReactionFlow<double></a>(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>, Y, T9, rho);</div>
|
|
<div class="line"><a id="l00874" name="l00874"></a><span class="lineno"> 874</span> netDestructionFlow += flow;</div>
|
|
<div class="line"><a id="l00875" name="l00875"></a><span class="lineno"> 875</span> }</div>
|
|
<div class="line"><a id="l00876" name="l00876"></a><span class="lineno"> 876</span> }</div>
|
|
<div class="line"><a id="l00877" name="l00877"></a><span class="lineno"> 877</span> <span class="keywordtype">double</span> timescale = std::numeric_limits<double>::infinity();</div>
|
|
<div class="line"><a id="l00878" name="l00878"></a><span class="lineno"> 878</span> <span class="keywordflow">if</span> (netDestructionFlow != 0.0) {</div>
|
|
<div class="line"><a id="l00879" name="l00879"></a><span class="lineno"> 879</span> timescale = Y[<a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda">getSpeciesIndex</a>(species)] / netDestructionFlow;</div>
|
|
<div class="line"><a id="l00880" name="l00880"></a><span class="lineno"> 880</span> }</div>
|
|
<div class="line"><a id="l00881" name="l00881"></a><span class="lineno"> 881</span> speciesDestructionTimescales.emplace(species, timescale);</div>
|
|
<div class="line"><a id="l00882" name="l00882"></a><span class="lineno"> 882</span> }</div>
|
|
<div class="line"><a id="l00883" name="l00883"></a><span class="lineno"> 883</span> <span class="keywordflow">return</span> speciesDestructionTimescales;</div>
|
|
<div class="line"><a id="l00884" name="l00884"></a><span class="lineno"> 884</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00885" name="l00885"></a><span class="lineno"> 885</span> </div>
|
|
<div class="foldopen" id="foldopen00886" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00886" name="l00886"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a5ac7cff23e70bd07ba7e510b753e2ab6"> 886</a></span> fourdst::composition::Composition <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a5ac7cff23e70bd07ba7e510b753e2ab6">GraphEngine::update</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a> &netIn) {</div>
|
|
<div class="line"><a id="l00887" name="l00887"></a><span class="lineno"> 887</span> fourdst::composition::Composition baseUpdatedComposition = netIn.<a class="code hl_variable" href="structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1">composition</a>;</div>
|
|
<div class="line"><a id="l00888" name="l00888"></a><span class="lineno"> 888</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& species : <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>) {</div>
|
|
<div class="line"><a id="l00889" name="l00889"></a><span class="lineno"> 889</span> <span class="keywordflow">if</span> (!netIn.<a class="code hl_variable" href="structgridfire_1_1_net_in.html#a13058f4929e72c1187abbebcddb8aed1">composition</a>.contains(species)) {</div>
|
|
<div class="line"><a id="l00890" name="l00890"></a><span class="lineno"> 890</span> baseUpdatedComposition.registerSpecies(species);</div>
|
|
<div class="line"><a id="l00891" name="l00891"></a><span class="lineno"> 891</span> baseUpdatedComposition.setMassFraction(species, 0.0);</div>
|
|
<div class="line"><a id="l00892" name="l00892"></a><span class="lineno"> 892</span> }</div>
|
|
<div class="line"><a id="l00893" name="l00893"></a><span class="lineno"> 893</span> }</div>
|
|
<div class="line"><a id="l00894" name="l00894"></a><span class="lineno"> 894</span> baseUpdatedComposition.finalize(<span class="keyword">false</span>);</div>
|
|
<div class="line"><a id="l00895" name="l00895"></a><span class="lineno"> 895</span> <span class="keywordflow">return</span> baseUpdatedComposition;</div>
|
|
<div class="line"><a id="l00896" name="l00896"></a><span class="lineno"> 896</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00897" name="l00897"></a><span class="lineno"> 897</span> </div>
|
|
<div class="foldopen" id="foldopen00898" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00898" name="l00898"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#af04a9f8a629d6f6c58c477af0f1ab9e5"> 898</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af04a9f8a629d6f6c58c477af0f1ab9e5">GraphEngine::isStale</a>(<span class="keyword">const</span> <a class="code hl_struct" href="structgridfire_1_1_net_in.html">NetIn</a> &netIn) {</div>
|
|
<div class="line"><a id="l00899" name="l00899"></a><span class="lineno"> 899</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
|
|
<div class="line"><a id="l00900" name="l00900"></a><span class="lineno"> 900</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00901" name="l00901"></a><span class="lineno"> 901</span> </div>
|
|
<div class="foldopen" id="foldopen00902" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00902" name="l00902"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889"> 902</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889">GraphEngine::recordADTape</a>() {</div>
|
|
<div class="line"><a id="l00903" name="l00903"></a><span class="lineno"> 903</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Recording AD tape for the RHS calculation..."</span>);</div>
|
|
<div class="line"><a id="l00904" name="l00904"></a><span class="lineno"> 904</span> </div>
|
|
<div class="line"><a id="l00905" name="l00905"></a><span class="lineno"> 905</span> <span class="comment">// Task 1: Set dimensions and initialize the matrix</span></div>
|
|
<div class="line"><a id="l00906" name="l00906"></a><span class="lineno"> 906</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> numSpecies = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size();</div>
|
|
<div class="line"><a id="l00907" name="l00907"></a><span class="lineno"> 907</span> <span class="keywordflow">if</span> (numSpecies == 0) {</div>
|
|
<div class="line"><a id="l00908" name="l00908"></a><span class="lineno"> 908</span> LOG_ERROR(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Cannot record AD tape: No species in the network."</span>);</div>
|
|
<div class="line"><a id="l00909" name="l00909"></a><span class="lineno"> 909</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>->flush_log();</div>
|
|
<div class="line"><a id="l00910" name="l00910"></a><span class="lineno"> 910</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Cannot record AD tape: No species in the network."</span>);</div>
|
|
<div class="line"><a id="l00911" name="l00911"></a><span class="lineno"> 911</span> }</div>
|
|
<div class="line"><a id="l00912" name="l00912"></a><span class="lineno"> 912</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> numADInputs = numSpecies + 2; <span class="comment">// Note here that by not letting T9 and rho be independent variables, we are constraining the network to a constant temperature and density during each evaluation.</span></div>
|
|
<div class="line"><a id="l00913" name="l00913"></a><span class="lineno"> 913</span> </div>
|
|
<div class="line"><a id="l00914" name="l00914"></a><span class="lineno"> 914</span> <span class="comment">// --- CppAD Tape Recording ---</span></div>
|
|
<div class="line"><a id="l00915" name="l00915"></a><span class="lineno"> 915</span> <span class="comment">// 1. Declare independent variable (adY)</span></div>
|
|
<div class="line"><a id="l00916" name="l00916"></a><span class="lineno"> 916</span> <span class="comment">// We also initialize the dummy variable for tape recording (these tell CppAD what the derivative chain looks like).</span></div>
|
|
<div class="line"><a id="l00917" name="l00917"></a><span class="lineno"> 917</span> <span class="comment">// Their numeric values are irrelevant except for in so far as they avoid numerical instabilities.</span></div>
|
|
<div class="line"><a id="l00918" name="l00918"></a><span class="lineno"> 918</span> </div>
|
|
<div class="line"><a id="l00919" name="l00919"></a><span class="lineno"> 919</span> <span class="comment">// Distribute total mass fraction uniformly between species in the dummy variable space</span></div>
|
|
<div class="line"><a id="l00920" name="l00920"></a><span class="lineno"> 920</span> <span class="keyword">const</span> <span class="keyword">auto</span> uniformMassFraction = <span class="keyword">static_cast<</span>CppAD::AD<double><span class="keyword">></span>(1.0 / <span class="keyword">static_cast<</span><span class="keywordtype">double</span><span class="keyword">></span>(numSpecies));</div>
|
|
<div class="line"><a id="l00921" name="l00921"></a><span class="lineno"> 921</span> std::vector<CppAD::AD<double>> adInput(numADInputs, uniformMassFraction);</div>
|
|
<div class="line"><a id="l00922" name="l00922"></a><span class="lineno"> 922</span> adInput[numSpecies] = 1.0; <span class="comment">// Dummy T9</span></div>
|
|
<div class="line"><a id="l00923" name="l00923"></a><span class="lineno"> 923</span> adInput[numSpecies + 1] = 1.0; <span class="comment">// Dummy rho</span></div>
|
|
<div class="line"><a id="l00924" name="l00924"></a><span class="lineno"> 924</span> </div>
|
|
<div class="line"><a id="l00925" name="l00925"></a><span class="lineno"> 925</span> <span class="comment">// 3. Declare independent variables (what CppAD will differentiate wrt.)</span></div>
|
|
<div class="line"><a id="l00926" name="l00926"></a><span class="lineno"> 926</span> <span class="comment">// This also beings the tape recording process.</span></div>
|
|
<div class="line"><a id="l00927" name="l00927"></a><span class="lineno"> 927</span> CppAD::Independent(adInput);</div>
|
|
<div class="line"><a id="l00928" name="l00928"></a><span class="lineno"> 928</span> </div>
|
|
<div class="line"><a id="l00929" name="l00929"></a><span class="lineno"> 929</span> std::vector<CppAD::AD<double>> adY(numSpecies);</div>
|
|
<div class="line"><a id="l00930" name="l00930"></a><span class="lineno"> 930</span> <span class="keywordflow">for</span>(<span class="keywordtype">size_t</span> i = 0; i < numSpecies; ++i) {</div>
|
|
<div class="line"><a id="l00931" name="l00931"></a><span class="lineno"> 931</span> adY[i] = adInput[i];</div>
|
|
<div class="line"><a id="l00932" name="l00932"></a><span class="lineno"> 932</span> }</div>
|
|
<div class="line"><a id="l00933" name="l00933"></a><span class="lineno"> 933</span> <span class="keyword">const</span> CppAD::AD<double> adT9 = adInput[numSpecies];</div>
|
|
<div class="line"><a id="l00934" name="l00934"></a><span class="lineno"> 934</span> <span class="keyword">const</span> CppAD::AD<double> adRho = adInput[numSpecies + 1];</div>
|
|
<div class="line"><a id="l00935" name="l00935"></a><span class="lineno"> 935</span> </div>
|
|
<div class="line"><a id="l00936" name="l00936"></a><span class="lineno"> 936</span> </div>
|
|
<div class="line"><a id="l00937" name="l00937"></a><span class="lineno"> 937</span> <span class="comment">// 5. Call the actual templated function</span></div>
|
|
<div class="line"><a id="l00938" name="l00938"></a><span class="lineno"> 938</span> <span class="comment">// We let T9 and rho be constant, so we pass them as fixed values.</span></div>
|
|
<div class="line"><a id="l00939" name="l00939"></a><span class="lineno"> 939</span> <span class="keyword">auto</span> [dydt, nuclearEnergyGenerationRate] = <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives<CppAD::AD<double></a>>(adY, adT9, adRho);</div>
|
|
<div class="line"><a id="l00940" name="l00940"></a><span class="lineno"> 940</span> </div>
|
|
<div class="line"><a id="l00941" name="l00941"></a><span class="lineno"> 941</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a>.Dependent(adInput, dydt);</div>
|
|
<div class="line"><a id="l00942" name="l00942"></a><span class="lineno"> 942</span> </div>
|
|
<div class="line"><a id="l00943" name="l00943"></a><span class="lineno"> 943</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"AD tape recorded successfully for the RHS calculation. Number of independent variables: {}."</span>,</div>
|
|
<div class="line"><a id="l00944" name="l00944"></a><span class="lineno"> 944</span> adInput.size());</div>
|
|
<div class="line"><a id="l00945" name="l00945"></a><span class="lineno"> 945</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00946" name="l00946"></a><span class="lineno"> 946</span> </div>
|
|
<div class="foldopen" id="foldopen00947" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00947" name="l00947"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a29b338630c959449c15881935ac30746"> 947</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a29b338630c959449c15881935ac30746">GraphEngine::collectAtomicReverseRateAtomicBases</a>() {</div>
|
|
<div class="line"><a id="l00948" name="l00948"></a><span class="lineno"> 948</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a816797b1d656d416844489692af44cf6">m_atomicReverseRates</a>.clear();</div>
|
|
<div class="line"><a id="l00949" name="l00949"></a><span class="lineno"> 949</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a816797b1d656d416844489692af44cf6">m_atomicReverseRates</a>.reserve(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size());</div>
|
|
<div class="line"><a id="l00950" name="l00950"></a><span class="lineno"> 950</span> </div>
|
|
<div class="line"><a id="l00951" name="l00951"></a><span class="lineno"> 951</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>: <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>) {</div>
|
|
<div class="line"><a id="l00952" name="l00952"></a><span class="lineno"> 952</span> <span class="keywordflow">if</span> (<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.qValue() != 0.0) {</div>
|
|
<div class="line"><a id="l00953" name="l00953"></a><span class="lineno"> 953</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a816797b1d656d416844489692af44cf6">m_atomicReverseRates</a>.push_back(std::make_unique<AtomicReverseRate>(<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>, *<span class="keyword">this</span>));</div>
|
|
<div class="line"><a id="l00954" name="l00954"></a><span class="lineno"> 954</span> } <span class="keywordflow">else</span> {</div>
|
|
<div class="line"><a id="l00955" name="l00955"></a><span class="lineno"> 955</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a816797b1d656d416844489692af44cf6">m_atomicReverseRates</a>.push_back(<span class="keyword">nullptr</span>);</div>
|
|
<div class="line"><a id="l00956" name="l00956"></a><span class="lineno"> 956</span> }</div>
|
|
<div class="line"><a id="l00957" name="l00957"></a><span class="lineno"> 957</span> }</div>
|
|
<div class="line"><a id="l00958" name="l00958"></a><span class="lineno"> 958</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l00959" name="l00959"></a><span class="lineno"> 959</span> </div>
|
|
<div class="foldopen" id="foldopen00960" data-start="{" data-end="}">
|
|
<div class="line"><a id="l00960" name="l00960"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd"> 960</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd">GraphEngine::precomputeNetwork</a>() {</div>
|
|
<div class="line"><a id="l00961" name="l00961"></a><span class="lineno"> 961</span> LOG_TRACE_L1(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a>, <span class="stringliteral">"Pre-computing constant components of GraphNetwork state..."</span>);</div>
|
|
<div class="line"><a id="l00962" name="l00962"></a><span class="lineno"> 962</span> </div>
|
|
<div class="line"><a id="l00963" name="l00963"></a><span class="lineno"> 963</span> <span class="comment">// --- Reverse map for fast species lookups ---</span></div>
|
|
<div class="line"><a id="l00964" name="l00964"></a><span class="lineno"> 964</span> std::unordered_map<fourdst::atomic::Species, size_t> speciesIndexMap;</div>
|
|
<div class="line"><a id="l00965" name="l00965"></a><span class="lineno"> 965</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>.size(); ++i) {</div>
|
|
<div class="line"><a id="l00966" name="l00966"></a><span class="lineno"> 966</span> speciesIndexMap[<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a>[i]] = i;</div>
|
|
<div class="line"><a id="l00967" name="l00967"></a><span class="lineno"> 967</span> }</div>
|
|
<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> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>.clear();</div>
|
|
<div class="line"><a id="l00970" name="l00970"></a><span class="lineno"> 970</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>.reserve(<a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size());</div>
|
|
<div class="line"><a id="l00971" name="l00971"></a><span class="lineno"> 971</span> </div>
|
|
<div class="line"><a id="l00972" name="l00972"></a><span class="lineno"> 972</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>.size(); ++i) {</div>
|
|
<div class="line"><a id="l00973" name="l00973"></a><span class="lineno"> 973</span> <span class="keyword">const</span> <span class="keyword">auto</span>& <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a> = <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a>[i];</div>
|
|
<div class="line"><a id="l00974" name="l00974"></a><span class="lineno"> 974</span> <a class="code hl_struct" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html">PrecomputedReaction</a> precomp;</div>
|
|
<div class="line"><a id="l00975" name="l00975"></a><span class="lineno"> 975</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a93635f6940d3534e949f402503c3d497">reaction_index</a> = i;</div>
|
|
<div class="line"><a id="l00976" name="l00976"></a><span class="lineno"> 976</span> </div>
|
|
<div class="line"><a id="l00977" name="l00977"></a><span class="lineno"> 977</span> <span class="comment">// --- Precompute forward reaction information ---</span></div>
|
|
<div class="line"><a id="l00978" name="l00978"></a><span class="lineno"> 978</span> <span class="comment">// Count occurrences for each reactant to determine powers and symmetry</span></div>
|
|
<div class="line"><a id="l00979" name="l00979"></a><span class="lineno"> 979</span> std::unordered_map<size_t, int> reactantCounts;</div>
|
|
<div class="line"><a id="l00980" name="l00980"></a><span class="lineno"> 980</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& reactant: <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.reactants()) {</div>
|
|
<div class="line"><a id="l00981" name="l00981"></a><span class="lineno"> 981</span> <span class="keywordtype">size_t</span> reactantIndex = speciesIndexMap.at(reactant);</div>
|
|
<div class="line"><a id="l00982" name="l00982"></a><span class="lineno"> 982</span> reactantCounts[reactantIndex]++;</div>
|
|
<div class="line"><a id="l00983" name="l00983"></a><span class="lineno"> 983</span> }</div>
|
|
<div class="line"><a id="l00984" name="l00984"></a><span class="lineno"> 984</span> </div>
|
|
<div class="line"><a id="l00985" name="l00985"></a><span class="lineno"> 985</span> <span class="keywordtype">double</span> symmetryDenominator = 1.0;</div>
|
|
<div class="line"><a id="l00986" name="l00986"></a><span class="lineno"> 986</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& [index, count] : reactantCounts) {</div>
|
|
<div class="line"><a id="l00987" name="l00987"></a><span class="lineno"> 987</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a510e380116e2e6d9158cf00fedac2666">unique_reactant_indices</a>.push_back(index);</div>
|
|
<div class="line"><a id="l00988" name="l00988"></a><span class="lineno"> 988</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a03d596c88289e21e7bd18711e3a1f275">reactant_powers</a>.push_back(count);</div>
|
|
<div class="line"><a id="l00989" name="l00989"></a><span class="lineno"> 989</span> </div>
|
|
<div class="line"><a id="l00990" name="l00990"></a><span class="lineno"> 990</span> symmetryDenominator *= std::tgamma(count + 1);</div>
|
|
<div class="line"><a id="l00991" name="l00991"></a><span class="lineno"> 991</span> }</div>
|
|
<div class="line"><a id="l00992" name="l00992"></a><span class="lineno"> 992</span> </div>
|
|
<div class="line"><a id="l00993" name="l00993"></a><span class="lineno"> 993</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#ac42504e868c0b9fd9ac9a405ea739f0e">symmetry_factor</a> = 1.0/symmetryDenominator;</div>
|
|
<div class="line"><a id="l00994" name="l00994"></a><span class="lineno"> 994</span> </div>
|
|
<div class="line"><a id="l00995" name="l00995"></a><span class="lineno"> 995</span> <span class="comment">// --- Precompute reverse reaction information ---</span></div>
|
|
<div class="line"><a id="l00996" name="l00996"></a><span class="lineno"> 996</span> <span class="keywordflow">if</span> (<a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.qValue() != 0.0) {</div>
|
|
<div class="line"><a id="l00997" name="l00997"></a><span class="lineno"> 997</span> std::unordered_map<size_t, int> productCounts;</div>
|
|
<div class="line"><a id="l00998" name="l00998"></a><span class="lineno"> 998</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& product : <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.products()) {</div>
|
|
<div class="line"><a id="l00999" name="l00999"></a><span class="lineno"> 999</span> productCounts[speciesIndexMap.at(product)]++;</div>
|
|
<div class="line"><a id="l01000" name="l01000"></a><span class="lineno"> 1000</span> }</div>
|
|
<div class="line"><a id="l01001" name="l01001"></a><span class="lineno"> 1001</span> <span class="keywordtype">double</span> reverseSymmetryDenominator = 1.0;</div>
|
|
<div class="line"><a id="l01002" name="l01002"></a><span class="lineno"> 1002</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& [index, count] : productCounts) {</div>
|
|
<div class="line"><a id="l01003" name="l01003"></a><span class="lineno"> 1003</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a9974f944a2cf5179baabebe09d60cf18">unique_product_indices</a>.push_back(index);</div>
|
|
<div class="line"><a id="l01004" name="l01004"></a><span class="lineno"> 1004</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3ce63aa3ad88568f4eb0d3ca2414209f">product_powers</a>.push_back(count);</div>
|
|
<div class="line"><a id="l01005" name="l01005"></a><span class="lineno"> 1005</span> reverseSymmetryDenominator *= std::tgamma(count + 1);</div>
|
|
<div class="line"><a id="l01006" name="l01006"></a><span class="lineno"> 1006</span> }</div>
|
|
<div class="line"><a id="l01007" name="l01007"></a><span class="lineno"> 1007</span> </div>
|
|
<div class="line"><a id="l01008" name="l01008"></a><span class="lineno"> 1008</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a6bcfe2230dd54b088180d34389266b07">reverse_symmetry_factor</a> = 1.0/reverseSymmetryDenominator;</div>
|
|
<div class="line"><a id="l01009" name="l01009"></a><span class="lineno"> 1009</span> } <span class="keywordflow">else</span> {</div>
|
|
<div class="line"><a id="l01010" name="l01010"></a><span class="lineno"> 1010</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a9974f944a2cf5179baabebe09d60cf18">unique_product_indices</a>.clear();</div>
|
|
<div class="line"><a id="l01011" name="l01011"></a><span class="lineno"> 1011</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3ce63aa3ad88568f4eb0d3ca2414209f">product_powers</a>.clear();</div>
|
|
<div class="line"><a id="l01012" name="l01012"></a><span class="lineno"> 1012</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a6bcfe2230dd54b088180d34389266b07">reverse_symmetry_factor</a> = 0.0; <span class="comment">// No reverse reaction for Q = 0 reactions</span></div>
|
|
<div class="line"><a id="l01013" name="l01013"></a><span class="lineno"> 1013</span> }</div>
|
|
<div class="line"><a id="l01014" name="l01014"></a><span class="lineno"> 1014</span> </div>
|
|
<div class="line"><a id="l01015" name="l01015"></a><span class="lineno"> 1015</span> <span class="comment">// --- Precompute stoichiometry information ---</span></div>
|
|
<div class="line"><a id="l01016" name="l01016"></a><span class="lineno"> 1016</span> <span class="keyword">const</span> <span class="keyword">auto</span> stoichiometryMap = <a class="code hl_namespace" href="namespacegridfire_1_1reaction.html">reaction</a>.stoichiometry();</div>
|
|
<div class="line"><a id="l01017" name="l01017"></a><span class="lineno"> 1017</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3e2e67e532970738d20491ea56b170f3">affected_species_indices</a>.reserve(stoichiometryMap.size());</div>
|
|
<div class="line"><a id="l01018" name="l01018"></a><span class="lineno"> 1018</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a7a7e9167b19e339e0d69544b9c00e79c">stoichiometric_coefficients</a>.reserve(stoichiometryMap.size());</div>
|
|
<div class="line"><a id="l01019" name="l01019"></a><span class="lineno"> 1019</span> </div>
|
|
<div class="line"><a id="l01020" name="l01020"></a><span class="lineno"> 1020</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& [species, coeff] : stoichiometryMap) {</div>
|
|
<div class="line"><a id="l01021" name="l01021"></a><span class="lineno"> 1021</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3e2e67e532970738d20491ea56b170f3">affected_species_indices</a>.push_back(speciesIndexMap.at(species));</div>
|
|
<div class="line"><a id="l01022" name="l01022"></a><span class="lineno"> 1022</span> precomp.<a class="code hl_variable" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a7a7e9167b19e339e0d69544b9c00e79c">stoichiometric_coefficients</a>.push_back(coeff);</div>
|
|
<div class="line"><a id="l01023" name="l01023"></a><span class="lineno"> 1023</span> }</div>
|
|
<div class="line"><a id="l01024" name="l01024"></a><span class="lineno"> 1024</span> </div>
|
|
<div class="line"><a id="l01025" name="l01025"></a><span class="lineno"> 1025</span> <a class="code hl_variable" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">m_precomputedReactions</a>.push_back(std::move(precomp));</div>
|
|
<div class="line"><a id="l01026" name="l01026"></a><span class="lineno"> 1026</span> }</div>
|
|
<div class="line"><a id="l01027" name="l01027"></a><span class="lineno"> 1027</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l01028" name="l01028"></a><span class="lineno"> 1028</span> </div>
|
|
<div class="foldopen" id="foldopen01029" data-start="{" data-end="}">
|
|
<div class="line"><a id="l01029" name="l01029"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#ad9b8dd0e8ba9c7745e33acc9a649d2e0"> 1029</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#ad9b8dd0e8ba9c7745e33acc9a649d2e0">GraphEngine::AtomicReverseRate::forward</a>(</div>
|
|
<div class="line"><a id="l01030" name="l01030"></a><span class="lineno"> 1030</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> p,</div>
|
|
<div class="line"><a id="l01031" name="l01031"></a><span class="lineno"> 1031</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> q,</div>
|
|
<div class="line"><a id="l01032" name="l01032"></a><span class="lineno"> 1032</span> <span class="keyword">const</span> CppAD::vector<bool> &vx,</div>
|
|
<div class="line"><a id="l01033" name="l01033"></a><span class="lineno"> 1033</span> CppAD::vector<bool> &vy,</div>
|
|
<div class="line"><a id="l01034" name="l01034"></a><span class="lineno"> 1034</span> <span class="keyword">const</span> CppAD::vector<double> &tx,</div>
|
|
<div class="line"><a id="l01035" name="l01035"></a><span class="lineno"> 1035</span> CppAD::vector<double> &ty</div>
|
|
<div class="line"><a id="l01036" name="l01036"></a><span class="lineno"> 1036</span> ) {</div>
|
|
<div class="line"><a id="l01037" name="l01037"></a><span class="lineno"> 1037</span> </div>
|
|
<div class="line"><a id="l01038" name="l01038"></a><span class="lineno"> 1038</span> <span class="keywordflow">if</span> ( p != 0) { <span class="keywordflow">return</span> <span class="keyword">false</span>; }</div>
|
|
<div class="line"><a id="l01039" name="l01039"></a><span class="lineno"> 1039</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9 = tx[0];</div>
|
|
<div class="line"><a id="l01040" name="l01040"></a><span class="lineno"> 1040</span> </div>
|
|
<div class="line"><a id="l01041" name="l01041"></a><span class="lineno"> 1041</span> <span class="keyword">const</span> <span class="keywordtype">double</span> reverseRate = <a class="code hl_variable" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a75d355a0bef27217165644affd0cca4d">m_engine</a>.calculateReverseRate(<a class="code hl_variable" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a98ed8b450f7868f55e8362a848a4710d">m_reaction</a>, T9);</div>
|
|
<div class="line"><a id="l01042" name="l01042"></a><span class="lineno"> 1042</span> <span class="comment">// std::cout << m_reaction.peName() << " reverseRate: " << reverseRate << " at T9: " << T9 << "\n";</span></div>
|
|
<div class="line"><a id="l01043" name="l01043"></a><span class="lineno"> 1043</span> ty[0] = reverseRate; <span class="comment">// Store the reverse rate in the output vector</span></div>
|
|
<div class="line"><a id="l01044" name="l01044"></a><span class="lineno"> 1044</span> </div>
|
|
<div class="line"><a id="l01045" name="l01045"></a><span class="lineno"> 1045</span> <span class="keywordflow">if</span> (vx.size() > 0) {</div>
|
|
<div class="line"><a id="l01046" name="l01046"></a><span class="lineno"> 1046</span> vy[0] = vx[0];</div>
|
|
<div class="line"><a id="l01047" name="l01047"></a><span class="lineno"> 1047</span> }</div>
|
|
<div class="line"><a id="l01048" name="l01048"></a><span class="lineno"> 1048</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
|
|
<div class="line"><a id="l01049" name="l01049"></a><span class="lineno"> 1049</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l01050" name="l01050"></a><span class="lineno"> 1050</span> </div>
|
|
<div class="foldopen" id="foldopen01051" data-start="{" data-end="}">
|
|
<div class="line"><a id="l01051" name="l01051"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a4e8ff268c4377599c8798c7929ec2d5e"> 1051</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a4e8ff268c4377599c8798c7929ec2d5e">GraphEngine::AtomicReverseRate::reverse</a>(</div>
|
|
<div class="line"><a id="l01052" name="l01052"></a><span class="lineno"> 1052</span> <span class="keywordtype">size_t</span> q,</div>
|
|
<div class="line"><a id="l01053" name="l01053"></a><span class="lineno"> 1053</span> <span class="keyword">const</span> CppAD::vector<double> &tx,</div>
|
|
<div class="line"><a id="l01054" name="l01054"></a><span class="lineno"> 1054</span> <span class="keyword">const</span> CppAD::vector<double> &ty,</div>
|
|
<div class="line"><a id="l01055" name="l01055"></a><span class="lineno"> 1055</span> CppAD::vector<double> &px,</div>
|
|
<div class="line"><a id="l01056" name="l01056"></a><span class="lineno"> 1056</span> <span class="keyword">const</span> CppAD::vector<double> &py</div>
|
|
<div class="line"><a id="l01057" name="l01057"></a><span class="lineno"> 1057</span> ) {</div>
|
|
<div class="line"><a id="l01058" name="l01058"></a><span class="lineno"> 1058</span> <span class="keyword">const</span> <span class="keywordtype">double</span> T9 = tx[0];</div>
|
|
<div class="line"><a id="l01059" name="l01059"></a><span class="lineno"> 1059</span> <span class="keyword">const</span> <span class="keywordtype">double</span> reverseRate = ty[0];</div>
|
|
<div class="line"><a id="l01060" name="l01060"></a><span class="lineno"> 1060</span> </div>
|
|
<div class="line"><a id="l01061" name="l01061"></a><span class="lineno"> 1061</span> <span class="keyword">const</span> <span class="keywordtype">double</span> derivative = <a class="code hl_variable" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a75d355a0bef27217165644affd0cca4d">m_engine</a>.calculateReverseRateTwoBodyDerivative(<a class="code hl_variable" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a98ed8b450f7868f55e8362a848a4710d">m_reaction</a>, T9, reverseRate);</div>
|
|
<div class="line"><a id="l01062" name="l01062"></a><span class="lineno"> 1062</span> <span class="comment">// std::cout << m_reaction.peName() << " reverseRate Derivative: " << derivative << "\n";</span></div>
|
|
<div class="line"><a id="l01063" name="l01063"></a><span class="lineno"> 1063</span> </div>
|
|
<div class="line"><a id="l01064" name="l01064"></a><span class="lineno"> 1064</span> px[0] = py[0] * derivative; <span class="comment">// Return the derivative of the reverse rate with respect to T9</span></div>
|
|
<div class="line"><a id="l01065" name="l01065"></a><span class="lineno"> 1065</span> </div>
|
|
<div class="line"><a id="l01066" name="l01066"></a><span class="lineno"> 1066</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
|
|
<div class="line"><a id="l01067" name="l01067"></a><span class="lineno"> 1067</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l01068" name="l01068"></a><span class="lineno"> 1068</span> </div>
|
|
<div class="foldopen" id="foldopen01069" data-start="{" data-end="}">
|
|
<div class="line"><a id="l01069" name="l01069"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#aec41632c2a362be33a1f7ff04204cbf4"> 1069</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#aec41632c2a362be33a1f7ff04204cbf4">GraphEngine::AtomicReverseRate::for_sparse_jac</a>(</div>
|
|
<div class="line"><a id="l01070" name="l01070"></a><span class="lineno"> 1070</span> <span class="keywordtype">size_t</span> q,</div>
|
|
<div class="line"><a id="l01071" name="l01071"></a><span class="lineno"> 1071</span> <span class="keyword">const</span> CppAD::vector<std::set<size_t>> &r,</div>
|
|
<div class="line"><a id="l01072" name="l01072"></a><span class="lineno"> 1072</span> CppAD::vector<std::set<size_t>> &s</div>
|
|
<div class="line"><a id="l01073" name="l01073"></a><span class="lineno"> 1073</span> ) {</div>
|
|
<div class="line"><a id="l01074" name="l01074"></a><span class="lineno"> 1074</span> s[0] = r[0];</div>
|
|
<div class="line"><a id="l01075" name="l01075"></a><span class="lineno"> 1075</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
|
|
<div class="line"><a id="l01076" name="l01076"></a><span class="lineno"> 1076</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l01077" name="l01077"></a><span class="lineno"> 1077</span> </div>
|
|
<div class="foldopen" id="foldopen01078" data-start="{" data-end="}">
|
|
<div class="line"><a id="l01078" name="l01078"></a><span class="lineno"><a class="line" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a881d4daf2b973d523548cd8d4021bdc4"> 1078</a></span> <span class="keywordtype">bool</span> <a class="code hl_function" href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a881d4daf2b973d523548cd8d4021bdc4">GraphEngine::AtomicReverseRate::rev_sparse_jac</a>(</div>
|
|
<div class="line"><a id="l01079" name="l01079"></a><span class="lineno"> 1079</span> <span class="keywordtype">size_t</span> q,</div>
|
|
<div class="line"><a id="l01080" name="l01080"></a><span class="lineno"> 1080</span> <span class="keyword">const</span> CppAD::vector<std::set<size_t>> &rt,</div>
|
|
<div class="line"><a id="l01081" name="l01081"></a><span class="lineno"> 1081</span> CppAD::vector<std::set<size_t>> &st</div>
|
|
<div class="line"><a id="l01082" name="l01082"></a><span class="lineno"> 1082</span> ) {</div>
|
|
<div class="line"><a id="l01083" name="l01083"></a><span class="lineno"> 1083</span> st[0] = rt[0];</div>
|
|
<div class="line"><a id="l01084" name="l01084"></a><span class="lineno"> 1084</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
|
|
<div class="line"><a id="l01085" name="l01085"></a><span class="lineno"> 1085</span> }</div>
|
|
</div>
|
|
<div class="line"><a id="l01086" name="l01086"></a><span class="lineno"> 1086</span>}</div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_1_1_atomic_reverse_rate_html_a4e8ff268c4377599c8798c7929ec2d5e"><div class="ttname"><a href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a4e8ff268c4377599c8798c7929ec2d5e">gridfire::GraphEngine::AtomicReverseRate::reverse</a></div><div class="ttdeci">bool reverse(size_t q, const CppAD::vector< double > &tx, const CppAD::vector< double > &ty, CppAD::vector< double > &px, const CppAD::vector< double > &py) override</div><div class="ttdef"><b>Definition</b> <a href="#l01051">engine_graph.cpp:1051</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_1_1_atomic_reverse_rate_html_a75d355a0bef27217165644affd0cca4d"><div class="ttname"><a href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a75d355a0bef27217165644affd0cca4d">gridfire::GraphEngine::AtomicReverseRate::m_engine</a></div><div class="ttdeci">const GraphEngine & m_engine</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00444">engine_graph.h:444</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_1_1_atomic_reverse_rate_html_a881d4daf2b973d523548cd8d4021bdc4"><div class="ttname"><a href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a881d4daf2b973d523548cd8d4021bdc4">gridfire::GraphEngine::AtomicReverseRate::rev_sparse_jac</a></div><div class="ttdeci">bool rev_sparse_jac(size_t q, const CppAD::vector< std::set< size_t > > &rt, CppAD::vector< std::set< size_t > > &st) override</div><div class="ttdef"><b>Definition</b> <a href="#l01078">engine_graph.cpp:1078</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_1_1_atomic_reverse_rate_html_a98ed8b450f7868f55e8362a848a4710d"><div class="ttname"><a href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#a98ed8b450f7868f55e8362a848a4710d">gridfire::GraphEngine::AtomicReverseRate::m_reaction</a></div><div class="ttdeci">const reaction::Reaction & m_reaction</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00443">engine_graph.h:443</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_1_1_atomic_reverse_rate_html_ad9b8dd0e8ba9c7745e33acc9a649d2e0"><div class="ttname"><a href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#ad9b8dd0e8ba9c7745e33acc9a649d2e0">gridfire::GraphEngine::AtomicReverseRate::forward</a></div><div class="ttdeci">bool forward(size_t p, size_t q, const CppAD::vector< bool > &vx, CppAD::vector< bool > &vy, const CppAD::vector< double > &tx, CppAD::vector< double > &ty) override</div><div class="ttdef"><b>Definition</b> <a href="#l01029">engine_graph.cpp:1029</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_1_1_atomic_reverse_rate_html_aec41632c2a362be33a1f7ff04204cbf4"><div class="ttname"><a href="classgridfire_1_1_graph_engine_1_1_atomic_reverse_rate.html#aec41632c2a362be33a1f7ff04204cbf4">gridfire::GraphEngine::AtomicReverseRate::for_sparse_jac</a></div><div class="ttdeci">bool for_sparse_jac(size_t q, const CppAD::vector< std::set< size_t > > &r, CppAD::vector< std::set< size_t > > &s) override</div><div class="ttdef"><b>Definition</b> <a href="#l01069">engine_graph.cpp:1069</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a015f8975701f028c29835d3a9794e00f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f">gridfire::GraphEngine::isPrecomputationEnabled</a></div><div class="ttdeci">bool isPrecomputationEnabled() const</div><div class="ttdef"><b>Definition</b> <a href="#l00615">engine_graph.cpp:615</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a01fc9fd5d576b66d07360d05e821c755"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755">gridfire::GraphEngine::calculateReverseRateTwoBody</a></div><div class="ttdeci">double calculateReverseRateTwoBody(const reaction::Reaction &reaction, const double T9, const double forwardRate, const double expFactor) const</div><div class="ttdef"><b>Definition</b> <a href="#l00269">engine_graph.cpp:269</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a0b7b85f824e1021ae6e56b644db53b28"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28">gridfire::GraphEngine::calculateReverseRate</a></div><div class="ttdeci">double calculateReverseRate(const reaction::Reaction &reaction, double T9) const</div><div class="ttdef"><b>Definition</b> <a href="#l00242">engine_graph.cpp:242</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a0ed390f3e598ebba4e245ac90bb78767"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767">gridfire::GraphEngine::getNetworkSpecies</a></div><div class="ttdeci">const std::vector< fourdst::atomic::Species > & getNetworkSpecies() const override</div><div class="ttdoc">Gets the list of species in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00162">engine_graph.cpp:162</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a10c01bc20ae668c2857efb2a1783098e"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">gridfire::GraphEngine::m_constants</a></div><div class="ttdeci">constants m_constants</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00450">engine_graph.h:450</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a166a5f4349580f9aa0b930afec73fcc4"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a166a5f4349580f9aa0b930afec73fcc4">gridfire::GraphEngine::getDepth</a></div><div class="ttdeci">BuildDepthType getDepth() const override</div><div class="ttdef"><b>Definition</b> <a href="#l00434">engine_graph.cpp:434</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a191cff35402d3c97c82c5c966a39d0de"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de">gridfire::GraphEngine::m_usePrecomputation</a></div><div class="ttdeci">bool m_usePrecomputation</div><div class="ttdoc">Flag to enable or disable using precomputed reactions for efficiency. Mathematically,...</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00471">engine_graph.h:471</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a19b2eea0e8d05ac90f9fd7120bdc6e06"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a19b2eea0e8d05ac90f9fd7120bdc6e06">gridfire::GraphEngine::m_full_jacobian_sparsity_pattern</a></div><div class="ttdeci">CppAD::sparse_rc< std::vector< size_t > > m_full_jacobian_sparsity_pattern</div><div class="ttdoc">Full sparsity pattern for the Jacobian matrix.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00464">engine_graph.h:464</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a250cc6350dc052fbdfdf9a02066e7891"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a250cc6350dc052fbdfdf9a02066e7891">gridfire::GraphEngine::m_jac_work</a></div><div class="ttdeci">CppAD::sparse_jac_work m_jac_work</div><div class="ttdoc">Work object for sparse Jacobian calculations.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00463">engine_graph.h:463</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a26602e1b3c610780a47b5a6511d6d567"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567">gridfire::GraphEngine::populateReactionIDMap</a></div><div class="ttdeci">void populateReactionIDMap()</div><div class="ttdoc">Populates the reaction ID map.</div><div class="ttdef"><b>Definition</b> <a href="#l00135">engine_graph.cpp:135</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a27f3a928e1f6bbe7e847cffed6db729f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a27f3a928e1f6bbe7e847cffed6db729f">gridfire::GraphEngine::mapNetInToMolarAbundanceVector</a></div><div class="ttdeci">std::vector< double > mapNetInToMolarAbundanceVector(const NetIn &netIn) const override</div><div class="ttdef"><b>Definition</b> <a href="#l00399">engine_graph.cpp:399</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a29b338630c959449c15881935ac30746"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a29b338630c959449c15881935ac30746">gridfire::GraphEngine::collectAtomicReverseRateAtomicBases</a></div><div class="ttdeci">void collectAtomicReverseRateAtomicBases()</div><div class="ttdef"><b>Definition</b> <a href="#l00947">engine_graph.cpp:947</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a2e22b111f6d00ecc9e3804a71f1ce876"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">gridfire::GraphEngine::m_rhsADFun</a></div><div class="ttdeci">CppAD::ADFun< double > m_rhsADFun</div><div class="ttdoc">CppAD function for the right-hand side of the ODE.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00462">engine_graph.h:462</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a2f1718c89d4aaad028102724d18fa910"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">gridfire::GraphEngine::m_jacobianMatrix</a></div><div class="ttdeci">boost::numeric::ublas::compressed_matrix< double > m_jacobianMatrix</div><div class="ttdoc">Jacobian matrix (species x species).</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00461">engine_graph.h:461</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a303e6093591cde91430f866a04a8be7c"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a303e6093591cde91430f866a04a8be7c">gridfire::GraphEngine::getJacobianMatrixEntry</a></div><div class="ttdeci">double getJacobianMatrixEntry(const int i, const int j) const override</div><div class="ttdoc">Gets an entry from the previously generated Jacobian matrix.</div><div class="ttdef"><b>Definition</b> <a href="#l00722">engine_graph.cpp:722</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a30e09ed0bce6aa5fc89beaa316a7b827"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">gridfire::GraphEngine::m_networkSpeciesMap</a></div><div class="ttdeci">std::unordered_map< std::string_view, fourdst::atomic::Species > m_networkSpeciesMap</div><div class="ttdoc">Map from species name to Species object.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00456">engine_graph.h:456</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a32d3efbf4c3d5158f87c0c732cdc26dc"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a32d3efbf4c3d5158f87c0c732cdc26dc">gridfire::GraphEngine::m_useReverseReactions</a></div><div class="ttdeci">bool m_useReverseReactions</div><div class="ttdoc">Flag to enable or disable reverse reactions. If false, only forward reactions are considered.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00473">engine_graph.h:473</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a3621f36d77ea8c738ad7de6e5b35ca3e"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a3621f36d77ea8c738ad7de6e5b35ca3e">gridfire::GraphEngine::m_partitionFunction</a></div><div class="ttdeci">std::unique_ptr< partition::PartitionFunction > m_partitionFunction</div><div class="ttdoc">Partition function for the network.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00478">engine_graph.h:478</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a371ba0881d6903ddb2d586faa61805d0"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a371ba0881d6903ddb2d586faa61805d0">gridfire::GraphEngine::setNetworkReactions</a></div><div class="ttdeci">void setNetworkReactions(const reaction::LogicalReactionSet &reactions) override</div><div class="ttdef"><b>Definition</b> <a href="#l00174">engine_graph.cpp:174</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a409991d527ea4d4b05d1af907fe5d197"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197">gridfire::GraphEngine::setUseReverseReactions</a></div><div class="ttdeci">void setUseReverseReactions(bool useReverse)</div><div class="ttdef"><b>Definition</b> <a href="#l00391">engine_graph.cpp:391</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a47202c43342b96480070874bffce1391"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391">gridfire::GraphEngine::populateSpeciesToIndexMap</a></div><div class="ttdeci">void populateSpeciesToIndexMap()</div><div class="ttdoc">Populates the species-to-index map.</div><div class="ttdef"><b>Definition</b> <a href="#l00144">engine_graph.cpp:144</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a483979fc154adc88d029b3b672066d53"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">gridfire::GraphEngine::m_logger</a></div><div class="ttdeci">quill::Logger * m_logger</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00448">engine_graph.h:448</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a52edc3e88f1e8fc497e1e63972d63c80"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a52edc3e88f1e8fc497e1e63972d63c80">gridfire::GraphEngine::m_screeningType</a></div><div class="ttdeci">screening::ScreeningType m_screeningType</div><div class="ttdoc">Screening type for the reaction network. Default to no screening.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00468">engine_graph.h:468</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a5ac7cff23e70bd07ba7e510b753e2ab6"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a5ac7cff23e70bd07ba7e510b753e2ab6">gridfire::GraphEngine::update</a></div><div class="ttdeci">fourdst::composition::Composition update(const NetIn &netIn) override</div><div class="ttdoc">Update the internal state of the engine.</div><div class="ttdef"><b>Definition</b> <a href="#l00886">engine_graph.cpp:886</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a5d431d5385b1219ba29689eb29601ea3"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">gridfire::GraphEngine::m_precomputedReactions</a></div><div class="ttdeci">std::vector< PrecomputedReaction > m_precomputedReactions</div><div class="ttdoc">Precomputed reactions for efficiency.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00477">engine_graph.h:477</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a5d6cc63b99b467c2a976d1fbaaa1dfa3"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">gridfire::GraphEngine::m_reactionIDMap</a></div><div class="ttdeci">std::unordered_map< std::string_view, reaction::Reaction * > m_reactionIDMap</div><div class="ttdoc">Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a ...</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00453">engine_graph.h:453</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a65f9f33cddb0bbd1da7c9d0cff23d581"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a65f9f33cddb0bbd1da7c9d0cff23d581">gridfire::GraphEngine::getSpeciesTimescales</a></div><div class="ttdeci">std::expected< std::unordered_map< fourdst::atomic::Species, double >, expectations::StaleEngineError > getSpeciesTimescales(const std::vector< double > &Y, double T9, double rho) const override</div><div class="ttdoc">Computes timescales for all species in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00842">engine_graph.cpp:842</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a697f2004e0d02c59e83c7890742d7c9a"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a">gridfire::GraphEngine::getScreeningModel</a></div><div class="ttdeci">screening::ScreeningType getScreeningModel() const override</div><div class="ttdoc">Get the current electron screening model.</div><div class="ttdef"><b>Definition</b> <a href="#l00607">engine_graph.cpp:607</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a6b5feaf788bade212b7c8df7ac8c8152"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152">gridfire::GraphEngine::getStoichiometryMatrixEntry</a></div><div class="ttdeci">int getStoichiometryMatrixEntry(const int speciesIndex, const int reactionIndex) const override</div><div class="ttdoc">Gets an entry from the stoichiometry matrix.</div><div class="ttdef"><b>Definition</b> <a href="#l00733">engine_graph.cpp:733</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a6c5410878496abc349ba30b691cdf0f1"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1">gridfire::GraphEngine::setPrecomputation</a></div><div class="ttdeci">void setPrecomputation(bool precompute)</div><div class="ttdef"><b>Definition</b> <a href="#l00611">engine_graph.cpp:611</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a80c73690d5af247ff9f2ba8b00abce01"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a80c73690d5af247ff9f2ba8b00abce01">gridfire::GraphEngine::m_depth</a></div><div class="ttdeci">BuildDepthType m_depth</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00475">engine_graph.h:475</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a8110e687844f921438bb517e1d8ce62f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f">gridfire::GraphEngine::setScreeningModel</a></div><div class="ttdeci">void setScreeningModel(screening::ScreeningType) override</div><div class="ttdoc">Set the electron screening model.</div><div class="ttdef"><b>Definition</b> <a href="#l00602">engine_graph.cpp:602</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a816797b1d656d416844489692af44cf6"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a816797b1d656d416844489692af44cf6">gridfire::GraphEngine::m_atomicReverseRates</a></div><div class="ttdeci">std::vector< std::unique_ptr< AtomicReverseRate > > m_atomicReverseRates</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00466">engine_graph.h:466</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a832e2fe066381811a3e0464806ff5e95"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95">gridfire::GraphEngine::exportToCSV</a></div><div class="ttdeci">void exportToCSV(const std::string &filename) const</div><div class="ttdoc">Exports the network to a CSV file for analysis.</div><div class="ttdef"><b>Definition</b> <a href="#l00788">engine_graph.cpp:788</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a8c29d8bbde407e913be5eb77efb2c0c9"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9">gridfire::GraphEngine::getNetReactionStoichiometry</a></div><div class="ttdeci">static std::unordered_map< fourdst::atomic::Species, int > getNetReactionStoichiometry(const reaction::Reaction &reaction)</div><div class="ttdoc">Gets the net stoichiometry for a given reaction.</div><div class="ttdef"><b>Definition</b> <a href="#l00727">engine_graph.cpp:727</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a8d0c0bd54a2908cff62dae7af0c149b5"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a8d0c0bd54a2908cff62dae7af0c149b5">gridfire::GraphEngine::reserveJacobianMatrix</a></div><div class="ttdeci">void reserveJacobianMatrix() const</div><div class="ttdoc">Reserves space for the Jacobian matrix.</div><div class="ttdef"><b>Definition</b> <a href="#l00151">engine_graph.cpp:151</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a914f6abc61805cddaebcb8f3cf470dda"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a914f6abc61805cddaebcb8f3cf470dda">gridfire::GraphEngine::getSpeciesIndex</a></div><div class="ttdeci">int getSpeciesIndex(const fourdst::atomic::Species &species) const override</div><div class="ttdef"><b>Definition</b> <a href="#l00395">engine_graph.cpp:395</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a9245642b741f215e52861d00e756fb3f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">gridfire::GraphEngine::calculateMolarReactionFlow</a></div><div class="ttdeci">double calculateMolarReactionFlow(const reaction::Reaction &reaction, const std::vector< double > &Y, const double T9, const double rho) const override</div><div class="ttdoc">Calculates the molar reaction flow for a given reaction.</div><div class="ttdef"><b>Definition</b> <a href="#l00623">engine_graph.cpp:623</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a92644bc333bff69c5685be4552ca12fd"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a92644bc333bff69c5685be4552ca12fd">gridfire::GraphEngine::precomputeNetwork</a></div><div class="ttdeci">void precomputeNetwork()</div><div class="ttdef"><b>Definition</b> <a href="#l00960">engine_graph.cpp:960</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a92d26068ba139e47d335f5fe9e2814cc"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">gridfire::GraphEngine::m_networkSpecies</a></div><div class="ttdeci">std::vector< fourdst::atomic::Species > m_networkSpecies</div><div class="ttdoc">Vector of unique species in the network.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00455">engine_graph.h:455</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a95563f6bc86007d9ee053a0f1e15b889"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889">gridfire::GraphEngine::recordADTape</a></div><div class="ttdeci">void recordADTape()</div><div class="ttdoc">Records the AD tape for the right-hand side of the ODE.</div><div class="ttdef"><b>Definition</b> <a href="#l00902">engine_graph.cpp:902</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a97f98706b51fbe0d167ed81ffe58c438"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a97f98706b51fbe0d167ed81ffe58c438">gridfire::GraphEngine::calculateAllDerivativesUsingPrecomputation</a></div><div class="ttdeci">StepDerivatives< double > calculateAllDerivativesUsingPrecomputation(const std::vector< double > &Y_in, const std::vector< double > &bare_rates, const std::vector< double > &bare_reverse_rates, double T9, double rho) const</div><div class="ttdef"><b>Definition</b> <a href="#l00448">engine_graph.cpp:448</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_aa6202cee0c3c481eda77cc9a91bc126b"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b">gridfire::GraphEngine::involvesSpecies</a></div><div class="ttdeci">bool involvesSpecies(const fourdst::atomic::Species &species) const</div><div class="ttdoc">Checks if a given species is involved in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00179">engine_graph.cpp:179</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_aaed3743a52246b0f7bf03995e1c12081"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#aaed3743a52246b0f7bf03995e1c12081">gridfire::GraphEngine::calculateRHSAndEnergy</a></div><div class="ttdeci">std::expected< StepDerivatives< double >, expectations::StaleEngineError > calculateRHSAndEnergy(const std::vector< double > &Y, const double T9, const double rho) const override</div><div class="ttdoc">Calculates the right-hand side (dY/dt) and energy generation rate.</div><div class="ttdef"><b>Definition</b> <a href="#l00057">engine_graph.cpp:57</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_acb7c4f5108b0efeae48ad15598e808c3"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">gridfire::GraphEngine::m_reactions</a></div><div class="ttdeci">reaction::LogicalReactionSet m_reactions</div><div class="ttdoc">Set of REACLIB reactions in the network.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00452">engine_graph.h:452</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_acdce8d87e23a2cd1504bc9472e538c0f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">gridfire::GraphEngine::syncInternalMaps</a></div><div class="ttdeci">void syncInternalMaps()</div><div class="ttdoc">Synchronizes the internal maps.</div><div class="ttdef"><b>Definition</b> <a href="#l00081">engine_graph.cpp:81</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_acf4cfccea20f5cb31c9886bf233a28be"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be">gridfire::GraphEngine::validateConservation</a></div><div class="ttdeci">bool validateConservation() const</div><div class="ttdoc">Validates mass and charge conservation across all reactions.</div><div class="ttdef"><b>Definition</b> <a href="#l00187">engine_graph.cpp:187</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ad049a295e2bb0f3e97b76d5742875119"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119">gridfire::GraphEngine::generateJacobianMatrix</a></div><div class="ttdeci">void generateJacobianMatrix(const std::vector< double > &Y_dynamic, const double T9, const double rho) const override</div><div class="ttdoc">Generates the Jacobian matrix for the current state.</div><div class="ttdef"><b>Definition</b> <a href="#l00632">engine_graph.cpp:632</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ad1cb5fd32efc37668e2d9ecf0c72ad24"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">gridfire::GraphEngine::m_stoichiometryMatrix</a></div><div class="ttdeci">boost::numeric::ublas::compressed_matrix< int > m_stoichiometryMatrix</div><div class="ttdoc">Stoichiometry matrix (species x reactions).</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00459">engine_graph.h:459</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ad45650d10fc5dff1673ae3f806d067da"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da">gridfire::GraphEngine::getNetworkReactions</a></div><div class="ttdeci">const reaction::LogicalReactionSet & getNetworkReactions() const override</div><div class="ttdoc">Gets the set of logical reactions in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00168">engine_graph.cpp:168</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ad8237c252145a75092202d00f5e1ddf7"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">gridfire::GraphEngine::m_speciesToIndexMap</a></div><div class="ttdeci">std::unordered_map< fourdst::atomic::Species, size_t > m_speciesToIndexMap</div><div class="ttdoc">Map from species to their index in the stoichiometry matrix.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00457">engine_graph.h:457</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ad9d6c70ace5cbbf7f3aa7b31fce39490"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ad9d6c70ace5cbbf7f3aa7b31fce39490">gridfire::GraphEngine::rebuild</a></div><div class="ttdeci">void rebuild(const fourdst::composition::Composition &comp, const BuildDepthType depth) override</div><div class="ttdef"><b>Definition</b> <a href="#l00438">engine_graph.cpp:438</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_adac8c7d62bae76e17fc060e86dadd929"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929">gridfire::GraphEngine::exportToDot</a></div><div class="ttdeci">void exportToDot(const std::string &filename) const</div><div class="ttdoc">Exports the network to a DOT file for visualization.</div><div class="ttdef"><b>Definition</b> <a href="#l00740">engine_graph.cpp:740</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_add98ece49ec5c538bddf3cc77004fe44"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#add98ece49ec5c538bddf3cc77004fe44">gridfire::GraphEngine::getPartitionFunction</a></div><div class="ttdeci">const partition::PartitionFunction & getPartitionFunction() const</div><div class="ttdef"><b>Definition</b> <a href="#l00619">engine_graph.cpp:619</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ae7a210d9ab13ad5fb0c612f027acabd0"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ae7a210d9ab13ad5fb0c612f027acabd0">gridfire::GraphEngine::isUsingReverseReactions</a></div><div class="ttdeci">bool isUsingReverseReactions() const</div><div class="ttdef"><b>Definition</b> <a href="#l00387">engine_graph.cpp:387</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ae7a371be61ab09b3fa4a93f05bd44e5e"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ae7a371be61ab09b3fa4a93f05bd44e5e">gridfire::GraphEngine::primeEngine</a></div><div class="ttdeci">PrimingReport primeEngine(const NetIn &netIn) override</div><div class="ttdef"><b>Definition</b> <a href="#l00407">engine_graph.cpp:407</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_aed726d36ee2b3796beff6067a1e4db38"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#aed726d36ee2b3796beff6067a1e4db38">gridfire::GraphEngine::generateStoichiometryMatrix</a></div><div class="ttdeci">void generateStoichiometryMatrix() override</div><div class="ttdoc">Generates the stoichiometry matrix for the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00545">engine_graph.cpp:545</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_aedf42d83bfcc28313b6b6454034d2efa"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa">gridfire::GraphEngine::collectNetworkSpecies</a></div><div class="ttdeci">void collectNetworkSpecies()</div><div class="ttdoc">Collects the unique species in the network.</div><div class="ttdef"><b>Definition</b> <a href="#l00106">engine_graph.cpp:106</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_aef8f6bde24d27345067b71084330c7da"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#aef8f6bde24d27345067b71084330c7da">gridfire::GraphEngine::getSpeciesDestructionTimescales</a></div><div class="ttdeci">std::expected< std::unordered_map< fourdst::atomic::Species, double >, expectations::StaleEngineError > getSpeciesDestructionTimescales(const std::vector< double > &Y, double T9, double rho) const override</div><div class="ttdef"><b>Definition</b> <a href="#l00861">engine_graph.cpp:861</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_af04a9f8a629d6f6c58c477af0f1ab9e5"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#af04a9f8a629d6f6c58c477af0f1ab9e5">gridfire::GraphEngine::isStale</a></div><div class="ttdeci">bool isStale(const NetIn &netIn) override</div><div class="ttdef"><b>Definition</b> <a href="#l00898">engine_graph.cpp:898</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_af17cf3762abac3efcab9a8e87c961210"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#af17cf3762abac3efcab9a8e87c961210">gridfire::GraphEngine::m_screeningModel</a></div><div class="ttdeci">std::unique_ptr< screening::ScreeningModel > m_screeningModel</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00469">engine_graph.h:469</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_af28950c5af3a92eb03a1a64ed0f913e7"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#af28950c5af3a92eb03a1a64ed0f913e7">gridfire::GraphEngine::calculateReverseRateTwoBodyDerivative</a></div><div class="ttdeci">double calculateReverseRateTwoBodyDerivative(const reaction::Reaction &reaction, const double T9, const double reverseRate) const</div><div class="ttdef"><b>Definition</b> <a href="#l00346">engine_graph.cpp:346</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_af41df9ce979b6410e12642cb093916c9"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">gridfire::GraphEngine::calculateAllDerivatives</a></div><div class="ttdeci">StepDerivatives< T > calculateAllDerivatives(const std::vector< T > &Y_in, T T9, T rho) const</div><div class="ttdoc">Calculates all derivatives (dY/dt) and the energy generation rate.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00715">engine_graph.h:715</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_afad967546b611d9c005268760feb75d5"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#afad967546b611d9c005268760feb75d5">gridfire::GraphEngine::GraphEngine</a></div><div class="ttdeci">GraphEngine(const fourdst::composition::Composition &composition, const BuildDepthType=NetworkBuildDepth::Full)</div><div class="ttdoc">Constructs a GraphEngine from a composition.</div><div class="ttdef"><b>Definition</b> <a href="#l00034">engine_graph.cpp:34</a></div></div>
|
|
<div class="ttc" id="aclassgridfire_1_1partition_1_1_partition_function_html"><div class="ttname"><a href="classgridfire_1_1partition_1_1_partition_function.html">gridfire::partition::PartitionFunction</a></div><div class="ttdoc">Abstract interface for evaluating nuclear partition functions.</div><div class="ttdef"><b>Definition</b> <a href="partition__abstract_8h_source.html#l00017">partition_abstract.h:17</a></div></div>
|
|
<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="aconstruction_8h_html"><div class="ttname"><a href="construction_8h.html">construction.h</a></div></div>
|
|
<div class="ttc" id="aengine__graph_8h_html"><div class="ttname"><a href="engine__graph_8h.html">engine_graph.h</a></div></div>
|
|
<div class="ttc" id="anamespacegridfire_1_1partition_html"><div class="ttname"><a href="namespacegridfire_1_1partition.html">gridfire::partition</a></div><div class="ttdef"><b>Definition</b> <a href="partition__composite_8h_source.html#l00015">partition_composite.h:15</a></div></div>
|
|
<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_a6ca8556d27ac373e176f5b23437c416e"><div class="ttname"><a href="namespacegridfire_1_1screening.html#a6ca8556d27ac373e176f5b23437c416e">gridfire::screening::selectScreeningModel</a></div><div class="ttdeci">std::unique_ptr< ScreeningModel > selectScreeningModel(ScreeningType type)</div><div class="ttdoc">A factory function to select and create a screening model.</div><div class="ttdef"><b>Definition</b> <a href="screening__types_8cpp_source.html#l00009">screening_types.cpp:9</a></div></div>
|
|
<div class="ttc" id="anamespacegridfire_1_1screening_html_aa82aafbc4f8c28d0a75b60798e3a7d25"><div class="ttname"><a href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">gridfire::screening::ScreeningType</a></div><div class="ttdeci">ScreeningType</div><div class="ttdoc">Enumerates the available plasma screening models.</div><div class="ttdef"><b>Definition</b> <a href="screening__types_8h_source.html#l00015">screening_types.h:15</a></div></div>
|
|
<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_a1121d0b2d005195333412559fa29d3cc"><div class="ttname"><a href="namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc">gridfire::ADDouble</a></div><div class="ttdeci">CppAD::AD< double > ADDouble</div><div class="ttdoc">Alias for CppAD AD type for double precision.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00044">engine_graph.h:44</a></div></div>
|
|
<div class="ttc" id="anamespacegridfire_html_a3b1f70dc7ff5b501809330a97079e4f6"><div class="ttname"><a href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">gridfire::BuildDepthType</a></div><div class="ttdeci">std::variant< NetworkBuildDepth, int > BuildDepthType</div><div class="ttdoc">Variant specifying either a predefined NetworkBuildDepth or a custom integer depth.</div><div class="ttdef"><b>Definition</b> <a href="building_8h_source.html#l00037">building.h:37</a></div></div>
|
|
<div class="ttc" id="anamespacegridfire_html_a898dfe22579e649935645cbd6f073178"><div class="ttname"><a href="namespacegridfire.html#a898dfe22579e649935645cbd6f073178">gridfire::SparsityPattern</a></div><div class="ttdeci">std::vector< std::pair< size_t, size_t > > SparsityPattern</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00065">engine_abstract.h:65</a></div></div>
|
|
<div class="ttc" id="anamespacegridfire_html_acd0bfdfbce4e84af102d62ff8a797c9f"><div class="ttname"><a href="namespacegridfire.html#acd0bfdfbce4e84af102d62ff8a797c9f">gridfire::primeNetwork</a></div><div class="ttdeci">PrimingReport primeNetwork(const NetIn &, DynamicEngine &engine)</div><div class="ttdoc">Primes absent species in the network to their equilibrium abundances.</div><div class="ttdef"><b>Definition</b> <a href="priming_8cpp_source.html#l00039">priming.cpp:39</a></div></div>
|
|
<div class="ttc" id="anamespacegridfire_html_ae01b1738df1921db565bcbd68dd6cf64"><div class="ttname"><a href="namespacegridfire.html#ae01b1738df1921db565bcbd68dd6cf64">gridfire::MIN_JACOBIAN_THRESHOLD</a></div><div class="ttdeci">static constexpr double MIN_JACOBIAN_THRESHOLD</div><div class="ttdoc">Minimum value for Jacobian matrix entries.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00074">engine_graph.h:74</a></div></div>
|
|
<div class="ttc" id="anamespacegridfire_html_aedddb89e400a6111f69bfe0c3fd4214e"><div class="ttname"><a href="namespacegridfire.html#aedddb89e400a6111f69bfe0c3fd4214e">gridfire::build_reaclib_nuclear_network</a></div><div class="ttdeci">reaction::LogicalReactionSet build_reaclib_nuclear_network(const fourdst::composition::Composition &composition, BuildDepthType maxLayers=NetworkBuildDepth::Full, bool reverse=false)</div><div class="ttdoc">Builds a nuclear reaction network from the Reaclib library based on an initial composition.</div></div>
|
|
<div class="ttc" id="anetwork_8h_html"><div class="ttname"><a href="network_8h.html">network.h</a></div></div>
|
|
<div class="ttc" id="apartition__ground_8h_html"><div class="ttname"><a href="partition__ground_8h.html">partition_ground.h</a></div></div>
|
|
<div class="ttc" id="apriming_8h_html"><div class="ttname"><a href="priming_8h.html">priming.h</a></div></div>
|
|
<div class="ttc" id="areaction_8h_html"><div class="ttname"><a href="reaction_8h.html">reaction.h</a></div><div class="ttdoc">Defines classes for representing and managing nuclear reactions.</div></div>
|
|
<div class="ttc" id="ascreening__types_8h_html"><div class="ttname"><a href="screening__types_8h.html">screening_types.h</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html">gridfire::GraphEngine::PrecomputedReaction</a></div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00384">engine_graph.h:384</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a03d596c88289e21e7bd18711e3a1f275"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a03d596c88289e21e7bd18711e3a1f275">gridfire::GraphEngine::PrecomputedReaction::reactant_powers</a></div><div class="ttdeci">std::vector< int > reactant_powers</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00388">engine_graph.h:388</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a3ce63aa3ad88568f4eb0d3ca2414209f"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3ce63aa3ad88568f4eb0d3ca2414209f">gridfire::GraphEngine::PrecomputedReaction::product_powers</a></div><div class="ttdeci">std::vector< int > product_powers</div><div class="ttdoc">Powers of each unique product in the reverse reaction.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00395">engine_graph.h:395</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a3e2e67e532970738d20491ea56b170f3"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a3e2e67e532970738d20491ea56b170f3">gridfire::GraphEngine::PrecomputedReaction::affected_species_indices</a></div><div class="ttdeci">std::vector< size_t > affected_species_indices</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00390">engine_graph.h:390</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a510e380116e2e6d9158cf00fedac2666"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a510e380116e2e6d9158cf00fedac2666">gridfire::GraphEngine::PrecomputedReaction::unique_reactant_indices</a></div><div class="ttdeci">std::vector< size_t > unique_reactant_indices</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00387">engine_graph.h:387</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a6bcfe2230dd54b088180d34389266b07"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a6bcfe2230dd54b088180d34389266b07">gridfire::GraphEngine::PrecomputedReaction::reverse_symmetry_factor</a></div><div class="ttdeci">double reverse_symmetry_factor</div><div class="ttdoc">Symmetry factor for reverse reactions.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00396">engine_graph.h:396</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a7a7e9167b19e339e0d69544b9c00e79c"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a7a7e9167b19e339e0d69544b9c00e79c">gridfire::GraphEngine::PrecomputedReaction::stoichiometric_coefficients</a></div><div class="ttdeci">std::vector< int > stoichiometric_coefficients</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00391">engine_graph.h:391</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a93635f6940d3534e949f402503c3d497"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a93635f6940d3534e949f402503c3d497">gridfire::GraphEngine::PrecomputedReaction::reaction_index</a></div><div class="ttdeci">size_t reaction_index</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00386">engine_graph.h:386</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_a9974f944a2cf5179baabebe09d60cf18"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a9974f944a2cf5179baabebe09d60cf18">gridfire::GraphEngine::PrecomputedReaction::unique_product_indices</a></div><div class="ttdeci">std::vector< size_t > unique_product_indices</div><div class="ttdoc">Unique product indices for reverse reactions.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00394">engine_graph.h:394</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1_graph_engine_1_1_precomputed_reaction_html_ac42504e868c0b9fd9ac9a405ea739f0e"><div class="ttname"><a href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#ac42504e868c0b9fd9ac9a405ea739f0e">gridfire::GraphEngine::PrecomputedReaction::symmetry_factor</a></div><div class="ttdeci">double symmetry_factor</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00389">engine_graph.h:389</a></div></div>
|
|
<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_step_derivatives_html"><div class="ttname"><a href="structgridfire_1_1_step_derivatives.html">gridfire::StepDerivatives</a></div><div class="ttdoc">Structure holding derivatives and energy generation for a network step.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00060">engine_abstract.h:60</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1_step_derivatives_html_ab4aeb41be952c7b5844e1ee81fef9008"><div class="ttname"><a href="structgridfire_1_1_step_derivatives.html#ab4aeb41be952c7b5844e1ee81fef9008">gridfire::StepDerivatives::nuclearEnergyGenerationRate</a></div><div class="ttdeci">T nuclearEnergyGenerationRate</div><div class="ttdoc">Specific energy generation rate (e.g., erg/g/s).</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00062">engine_abstract.h:62</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1_step_derivatives_html_ae0de268b86c2404379409c4feae0b34d"><div class="ttname"><a href="structgridfire_1_1_step_derivatives.html#ae0de268b86c2404379409c4feae0b34d">gridfire::StepDerivatives::dydt</a></div><div class="ttdeci">std::vector< T > dydt</div><div class="ttdoc">Derivatives of abundances (dY/dt for each species).</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00061">engine_abstract.h:61</a></div></div>
|
|
<div class="ttc" id="astructgridfire_1_1expectations_1_1_stale_engine_error_html"><div class="ttname"><a href="structgridfire_1_1expectations_1_1_stale_engine_error.html">gridfire::expectations::StaleEngineError</a></div><div class="ttdef"><b>Definition</b> <a href="expected__engine_8h_source.html#l00044">expected_engine.h:44</a></div></div>
|
|
</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="engine__graph_8cpp.html">engine_graph.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>
|