Files
GridFire/docs/html/classgridfire_1_1_file_defined_engine_view.html
2025-07-01 11:40:58 -04:00

1399 lines
79 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: gridfire::FileDefinedEngineView Class Reference</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">&#160;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&amp;dn=expat.txt MIT */
var searchBox = new SearchBox("searchBox", "search/",'.html');
/* @license-end */
</script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;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&amp;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&amp;dn=expat.txt MIT */
$(function(){initNavTree('classgridfire_1_1_file_defined_engine_view.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="summary">
<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="#pri-types">Private Types</a> &#124;
<a href="#pri-methods">Private Member Functions</a> &#124;
<a href="#pri-attribs">Private Attributes</a> &#124;
<a href="classgridfire_1_1_file_defined_engine_view-members.html">List of all members</a> </div>
<div class="headertitle"><div class="title">gridfire::FileDefinedEngineView Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
</div><!--header-->
<div class="contents">
<p><code>#include &lt;<a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>&gt;</code></p>
<div class="dynheader">
Inheritance diagram for gridfire::FileDefinedEngineView:</div>
<div class="dyncontent">
<div class="center">
<img src="classgridfire_1_1_file_defined_engine_view.png" usemap="#gridfire::FileDefinedEngineView_map" alt=""/>
<map id="gridfire::FileDefinedEngineView_map" name="gridfire::FileDefinedEngineView_map">
<area href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations." alt="gridfire::DynamicEngine" shape="rect" coords="0,56,238,80"/>
<area href="classgridfire_1_1_engine_view.html" alt="gridfire::EngineView&lt; DynamicEngine &gt;" shape="rect" coords="248,56,486,80"/>
<area href="classgridfire_1_1_engine.html" title="Abstract base class for a reaction network engine." alt="gridfire::Engine" shape="rect" coords="0,0,238,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a8f2f64bab0f516ed2a6fd529912e0acd" id="r_a8f2f64bab0f516ed2a6fd529912e0acd"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a8f2f64bab0f516ed2a6fd529912e0acd">FileDefinedEngineView</a> (<a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;baseEngine, const std::string &amp;fileName, const <a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a> &amp;parser)</td></tr>
<tr class="separator:a8f2f64bab0f516ed2a6fd529912e0acd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a4c8b273c5cb3d470567c5691b68493a3" id="r_a4c8b273c5cb3d470567c5691b68493a3"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a4c8b273c5cb3d470567c5691b68493a3">getBaseEngine</a> () const override</td></tr>
<tr class="memdesc:a4c8b273c5cb3d470567c5691b68493a3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Access the underlying engine instance. <br /></td></tr>
<tr class="separator:a4c8b273c5cb3d470567c5691b68493a3"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8bb583e039b49608272997ed2d3387fa" id="r_a8bb583e039b49608272997ed2d3387fa"><td class="memItemLeft" align="right" valign="top">const std::vector&lt; fourdst::atomic::Species &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a8bb583e039b49608272997ed2d3387fa">getNetworkSpecies</a> () const override</td></tr>
<tr class="memdesc:a8bb583e039b49608272997ed2d3387fa"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the list of species in the network. <br /></td></tr>
<tr class="separator:a8bb583e039b49608272997ed2d3387fa"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a2c1d88b06568f9ea4c65e794d012ebfb" id="r_a2c1d88b06568f9ea4c65e794d012ebfb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a2c1d88b06568f9ea4c65e794d012ebfb">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:a2c1d88b06568f9ea4c65e794d012ebfb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the right-hand side (dY/dt) and energy generation. <br /></td></tr>
<tr class="separator:a2c1d88b06568f9ea4c65e794d012ebfb"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a48b2451f96b8f5511ffc4071519c0810" id="r_a48b2451f96b8f5511ffc4071519c0810"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a48b2451f96b8f5511ffc4071519c0810">generateJacobianMatrix</a> (const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) override</td></tr>
<tr class="memdesc:a48b2451f96b8f5511ffc4071519c0810"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate the Jacobian matrix for the current state. <br /></td></tr>
<tr class="separator:a48b2451f96b8f5511ffc4071519c0810"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0ef8804780d13bbfce0856237bb00470" id="r_a0ef8804780d13bbfce0856237bb00470"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0ef8804780d13bbfce0856237bb00470">getJacobianMatrixEntry</a> (const int i_defined, const int j_defined) const override</td></tr>
<tr class="memdesc:a0ef8804780d13bbfce0856237bb00470"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get an entry from the previously generated Jacobian matrix. <br /></td></tr>
<tr class="separator:a0ef8804780d13bbfce0856237bb00470"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a27a5163157cc15c4cb3b99a5d3564dbd" id="r_a27a5163157cc15c4cb3b99a5d3564dbd"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a27a5163157cc15c4cb3b99a5d3564dbd">generateStoichiometryMatrix</a> () override</td></tr>
<tr class="memdesc:a27a5163157cc15c4cb3b99a5d3564dbd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate the stoichiometry matrix for the network. <br /></td></tr>
<tr class="separator:a27a5163157cc15c4cb3b99a5d3564dbd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a9da9224f5c99a5068f3d8cbf066e4693" id="r_a9da9224f5c99a5068f3d8cbf066e4693"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a9da9224f5c99a5068f3d8cbf066e4693">getStoichiometryMatrixEntry</a> (const int speciesIndex_defined, const int reactionIndex_defined) const override</td></tr>
<tr class="memdesc:a9da9224f5c99a5068f3d8cbf066e4693"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get an entry from the stoichiometry matrix. <br /></td></tr>
<tr class="separator:a9da9224f5c99a5068f3d8cbf066e4693"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac371fb66fd0a76a04df204c9dd9a05ef" id="r_ac371fb66fd0a76a04df204c9dd9a05ef"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ac371fb66fd0a76a04df204c9dd9a05ef">calculateMolarReactionFlow</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;reaction, const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:ac371fb66fd0a76a04df204c9dd9a05ef"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the molar reaction flow for a given reaction. <br /></td></tr>
<tr class="separator:ac371fb66fd0a76a04df204c9dd9a05ef"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5bbea17b69cc8f81bc251a04f4435a0c" id="r_a5bbea17b69cc8f81bc251a04f4435a0c"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a5bbea17b69cc8f81bc251a04f4435a0c">getNetworkReactions</a> () const override</td></tr>
<tr class="memdesc:a5bbea17b69cc8f81bc251a04f4435a0c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the set of logical reactions in the network. <br /></td></tr>
<tr class="separator:a5bbea17b69cc8f81bc251a04f4435a0c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ace3c6ea4841318c08695973ab3dcddc6" id="r_ace3c6ea4841318c08695973ab3dcddc6"><td class="memItemLeft" align="right" valign="top">std::unordered_map&lt; fourdst::atomic::Species, double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ace3c6ea4841318c08695973ab3dcddc6">getSpeciesTimescales</a> (const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:ace3c6ea4841318c08695973ab3dcddc6"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute timescales for all species in the network. <br /></td></tr>
<tr class="separator:ace3c6ea4841318c08695973ab3dcddc6"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ace3568eadaba69e7357b4386c5ca3eb0" id="r_ace3568eadaba69e7357b4386c5ca3eb0"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ace3568eadaba69e7357b4386c5ca3eb0">update</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) override</td></tr>
<tr class="separator:ace3568eadaba69e7357b4386c5ca3eb0"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a92f14da849e99d07c1ff1347addb9263" id="r_a92f14da849e99d07c1ff1347addb9263"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a92f14da849e99d07c1ff1347addb9263">setNetworkFile</a> (const std::string &amp;fileName)</td></tr>
<tr class="separator:a92f14da849e99d07c1ff1347addb9263"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad96bbee6d3d37b50d9236a975ef704c0" id="r_ad96bbee6d3d37b50d9236a975ef704c0"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad96bbee6d3d37b50d9236a975ef704c0">setScreeningModel</a> (<a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> model) override</td></tr>
<tr class="separator:ad96bbee6d3d37b50d9236a975ef704c0"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:adbc50f397445f92b810d80cf329b8626" id="r_adbc50f397445f92b810d80cf329b8626"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#adbc50f397445f92b810d80cf329b8626">getScreeningModel</a> () const override</td></tr>
<tr class="separator:adbc50f397445f92b810d80cf329b8626"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pub_methods_classgridfire_1_1_engine"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td></tr>
<tr class="memitem:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine" id="r_a2e7970bed2100699f226f4141d5db037"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a> ()=default</td></tr>
<tr class="memdesc:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor. <br /></td></tr>
<tr class="separator:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pub_methods_classgridfire_1_1_engine_view"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine_view')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView&lt; DynamicEngine &gt;</a></td></tr>
<tr class="memitem:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view" id="r_a994660f2d553f3a123512dc5eb421e74"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a> ()=default</td></tr>
<tr class="memdesc:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor. <br /></td></tr>
<tr class="separator:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-types" name="pri-types"></a>
Private Types</h2></td></tr>
<tr class="memitem:a63f8f85e75ecaab6fa39d48d7a846187" id="r_a63f8f85e75ecaab6fa39d48d7a846187"><td class="memItemLeft" align="right" valign="top">using&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a63f8f85e75ecaab6fa39d48d7a846187">Config</a> = fourdst::config::Config</td></tr>
<tr class="separator:a63f8f85e75ecaab6fa39d48d7a846187"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:acbb1a9bcb775e6d50de512a333afed08" id="r_acbb1a9bcb775e6d50de512a333afed08"><td class="memItemLeft" align="right" valign="top">using&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#acbb1a9bcb775e6d50de512a333afed08">LogManager</a> = fourdst::logging::LogManager</td></tr>
<tr class="separator:acbb1a9bcb775e6d50de512a333afed08"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:a3b5162b7be35405285ef9f825ec2663b" id="r_a3b5162b7be35405285ef9f825ec2663b"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a3b5162b7be35405285ef9f825ec2663b">buildFromFile</a> (const std::string &amp;fileName)</td></tr>
<tr class="separator:a3b5162b7be35405285ef9f825ec2663b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a51ba09ff01fdcac1125d42f276c9a0a7" id="r_a51ba09ff01fdcac1125d42f276c9a0a7"><td class="memItemLeft" align="right" valign="top">std::vector&lt; size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a51ba09ff01fdcac1125d42f276c9a0a7">constructSpeciesIndexMap</a> () const</td></tr>
<tr class="memdesc:a51ba09ff01fdcac1125d42f276c9a0a7"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructs the species index map. <br /></td></tr>
<tr class="separator:a51ba09ff01fdcac1125d42f276c9a0a7"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aebb3f3548f8781506f31580706810a4e" id="r_aebb3f3548f8781506f31580706810a4e"><td class="memItemLeft" align="right" valign="top">std::vector&lt; size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aebb3f3548f8781506f31580706810a4e">constructReactionIndexMap</a> () const</td></tr>
<tr class="memdesc:aebb3f3548f8781506f31580706810a4e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructs the reaction index map. <br /></td></tr>
<tr class="separator:aebb3f3548f8781506f31580706810a4e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac231044e37e0962f664f8465e1ccb022" id="r_ac231044e37e0962f664f8465e1ccb022"><td class="memItemLeft" align="right" valign="top">std::vector&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ac231044e37e0962f664f8465e1ccb022">mapViewToFull</a> (const std::vector&lt; double &gt; &amp;culled) const</td></tr>
<tr class="memdesc:ac231044e37e0962f664f8465e1ccb022"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps a vector of culled abundances to a vector of full abundances. <br /></td></tr>
<tr class="separator:ac231044e37e0962f664f8465e1ccb022"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a97e5ee4651dbe6754678fe96e4702fee" id="r_a97e5ee4651dbe6754678fe96e4702fee"><td class="memItemLeft" align="right" valign="top">std::vector&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a97e5ee4651dbe6754678fe96e4702fee">mapFullToView</a> (const std::vector&lt; double &gt; &amp;full) const</td></tr>
<tr class="memdesc:a97e5ee4651dbe6754678fe96e4702fee"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps a vector of full abundances to a vector of culled abundances. <br /></td></tr>
<tr class="separator:a97e5ee4651dbe6754678fe96e4702fee"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf" id="r_a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf">mapViewToFullSpeciesIndex</a> (size_t culledSpeciesIndex) const</td></tr>
<tr class="memdesc:a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps a culled species index to a full species index. <br /></td></tr>
<tr class="separator:a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae7d6f0ff9076d59d1245c047bbd1bdb9" id="r_ae7d6f0ff9076d59d1245c047bbd1bdb9"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ae7d6f0ff9076d59d1245c047bbd1bdb9">mapViewToFullReactionIndex</a> (size_t culledReactionIndex) const</td></tr>
<tr class="memdesc:ae7d6f0ff9076d59d1245c047bbd1bdb9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps a culled reaction index to a full reaction index. <br /></td></tr>
<tr class="separator:ae7d6f0ff9076d59d1245c047bbd1bdb9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae3f99002ab2c56a5bcdec00839f8628f" id="r_ae3f99002ab2c56a5bcdec00839f8628f"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ae3f99002ab2c56a5bcdec00839f8628f">validateNetworkState</a> () const</td></tr>
<tr class="separator:ae3f99002ab2c56a5bcdec00839f8628f"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
Private Attributes</h2></td></tr>
<tr class="memitem:a7a80966c023ae722239491af58609362" id="r_a7a80966c023ae722239491af58609362"><td class="memItemLeft" align="right" valign="top"><a class="el" href="#a63f8f85e75ecaab6fa39d48d7a846187">Config</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a7a80966c023ae722239491af58609362">m_config</a> = Config::getInstance()</td></tr>
<tr class="separator:a7a80966c023ae722239491af58609362"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a9d93633ed4ab68de94b7274f879a0432" id="r_a9d93633ed4ab68de94b7274f879a0432"><td class="memItemLeft" align="right" valign="top">quill::Logger *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a9d93633ed4ab68de94b7274f879a0432">m_logger</a> = LogManager::getInstance().getLogger(&quot;log&quot;)</td></tr>
<tr class="separator:a9d93633ed4ab68de94b7274f879a0432"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad8454c98fa9a4bb45dc81059bc51fc81" id="r_ad8454c98fa9a4bb45dc81059bc51fc81"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad8454c98fa9a4bb45dc81059bc51fc81">m_baseEngine</a></td></tr>
<tr class="separator:ad8454c98fa9a4bb45dc81059bc51fc81"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1b343998b93955025a589b2b4541e33b" id="r_a1b343998b93955025a589b2b4541e33b"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a1b343998b93955025a589b2b4541e33b">m_fileName</a></td></tr>
<tr class="memdesc:a1b343998b93955025a589b2b4541e33b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Name of the file defining the reaction set considered by the engine view. <br /></td></tr>
<tr class="separator:a1b343998b93955025a589b2b4541e33b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0a9b07176cb93b54c677b6ce71fda500" id="r_a0a9b07176cb93b54c677b6ce71fda500"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0a9b07176cb93b54c677b6ce71fda500">m_parser</a></td></tr>
<tr class="memdesc:a0a9b07176cb93b54c677b6ce71fda500"><td class="mdescLeft">&#160;</td><td class="mdescRight">Parser for the network file. <br /></td></tr>
<tr class="separator:a0a9b07176cb93b54c677b6ce71fda500"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a299a0c61aa4f26029c770013c9feff5e" id="r_a299a0c61aa4f26029c770013c9feff5e"><td class="memItemLeft" align="right" valign="top">std::vector&lt; fourdst::atomic::Species &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a299a0c61aa4f26029c770013c9feff5e">m_activeSpecies</a></td></tr>
<tr class="memdesc:a299a0c61aa4f26029c770013c9feff5e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Active species in the defined engine. <br /></td></tr>
<tr class="separator:a299a0c61aa4f26029c770013c9feff5e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae012da2b1f6169cb13e6075a73353ab2" id="r_ae012da2b1f6169cb13e6075a73353ab2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ae012da2b1f6169cb13e6075a73353ab2">m_activeReactions</a></td></tr>
<tr class="memdesc:ae012da2b1f6169cb13e6075a73353ab2"><td class="mdescLeft">&#160;</td><td class="mdescRight">Active reactions in the defined engine. <br /></td></tr>
<tr class="separator:ae012da2b1f6169cb13e6075a73353ab2"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aebd4a1a584f2784f1df3d503645be03b" id="r_aebd4a1a584f2784f1df3d503645be03b"><td class="memItemLeft" align="right" valign="top">std::vector&lt; size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aebd4a1a584f2784f1df3d503645be03b">m_speciesIndexMap</a></td></tr>
<tr class="memdesc:aebd4a1a584f2784f1df3d503645be03b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps indices of active species to indices in the full network. <br /></td></tr>
<tr class="separator:aebd4a1a584f2784f1df3d503645be03b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af0a77a4749a15aae87bdecfccbd1736e" id="r_af0a77a4749a15aae87bdecfccbd1736e"><td class="memItemLeft" align="right" valign="top">std::vector&lt; size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#af0a77a4749a15aae87bdecfccbd1736e">m_reactionIndexMap</a></td></tr>
<tr class="memdesc:af0a77a4749a15aae87bdecfccbd1736e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps indices of active reactions to indices in the full network. <br /></td></tr>
<tr class="separator:af0a77a4749a15aae87bdecfccbd1736e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a6e421bc748933be31bed9ff53f12b595" id="r_a6e421bc748933be31bed9ff53f12b595"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a6e421bc748933be31bed9ff53f12b595">m_isStale</a> = true</td></tr>
<tr class="separator:a6e421bc748933be31bed9ff53f12b595"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00016">16</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
<a id="a63f8f85e75ecaab6fa39d48d7a846187" name="a63f8f85e75ecaab6fa39d48d7a846187"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a63f8f85e75ecaab6fa39d48d7a846187">&#9670;&#160;</a></span>Config</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">using <a class="el" href="#a63f8f85e75ecaab6fa39d48d7a846187">gridfire::FileDefinedEngineView::Config</a> = fourdst::config::Config</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00071">71</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
<a id="acbb1a9bcb775e6d50de512a333afed08" name="acbb1a9bcb775e6d50de512a333afed08"></a>
<h2 class="memtitle"><span class="permalink"><a href="#acbb1a9bcb775e6d50de512a333afed08">&#9670;&#160;</a></span>LogManager</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">using <a class="el" href="#acbb1a9bcb775e6d50de512a333afed08">gridfire::FileDefinedEngineView::LogManager</a> = fourdst::logging::LogManager</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00072">72</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
<h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
<a id="a8f2f64bab0f516ed2a6fd529912e0acd" name="a8f2f64bab0f516ed2a6fd529912e0acd"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a8f2f64bab0f516ed2a6fd529912e0acd">&#9670;&#160;</a></span>FileDefinedEngineView()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">gridfire::FileDefinedEngineView::FileDefinedEngineView </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;</td> <td class="paramname"><span class="paramname"><em>baseEngine</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::string &amp;</td> <td class="paramname"><span class="paramname"><em>fileName</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a> &amp;</td> <td class="paramname"><span class="paramname"><em>parser</em></span>&#160;)</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel explicit">explicit</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00008">8</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a id="a3b5162b7be35405285ef9f825ec2663b" name="a3b5162b7be35405285ef9f825ec2663b"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a3b5162b7be35405285ef9f825ec2663b">&#9670;&#160;</a></span>buildFromFile()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void gridfire::FileDefinedEngineView::buildFromFile </td>
<td>(</td>
<td class="paramtype">const std::string &amp;</td> <td class="paramname"><span class="paramname"><em>fileName</em></span></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00208">208</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="ac371fb66fd0a76a04df204c9dd9a05ef" name="ac371fb66fd0a76a04df204c9dd9a05ef"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ac371fb66fd0a76a04df204c9dd9a05ef">&#9670;&#160;</a></span>calculateMolarReactionFlow()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">double gridfire::FileDefinedEngineView::calculateMolarReactionFlow </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;</td> <td class="paramname"><span class="paramname"><em>reaction</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Calculate the molar reaction flow for a given reaction. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">reaction</td><td>The reaction for which to calculate the flow. </td></tr>
<tr><td class="paramname">Y</td><td>Vector of current abundances. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Molar flow rate for the reaction (e.g., mol/g/s).</dd></dl>
<p>This method computes the net rate at which the given reaction proceeds under the current state. </p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00085">85</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="a2c1d88b06568f9ea4c65e794d012ebfb" name="a2c1d88b06568f9ea4c65e794d012ebfb"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a2c1d88b06568f9ea4c65e794d012ebfb">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt; gridfire::FileDefinedEngineView::calculateRHSAndEnergy </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Calculate the right-hand side (dY/dt) and energy generation. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">Y</td><td>Vector of current abundances for all species. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives&lt;double&gt;</a> containing dY/dt and energy generation rate.</dd></dl>
<p>This function must be implemented by derived classes to compute the time derivatives of all species and the specific nuclear energy generation rate for the current state. </p>
<p>Implements <a class="el" href="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">gridfire::Engine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00029">29</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="aebb3f3548f8781506f31580706810a4e" name="aebb3f3548f8781506f31580706810a4e"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aebb3f3548f8781506f31580706810a4e">&#9670;&#160;</a></span>constructReactionIndexMap()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::vector&lt; size_t &gt; gridfire::FileDefinedEngineView::constructReactionIndexMap </td>
<td>(</td>
<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Constructs the reaction index map. </p>
<dl class="section return"><dt>Returns</dt><dd>A vector mapping culled reaction indices to full reaction indices.</dd></dl>
<p>This method creates a map from the indices of the active reactions to the indices of the corresponding reactions in the full network.</p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00176">176</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="a51ba09ff01fdcac1125d42f276c9a0a7" name="a51ba09ff01fdcac1125d42f276c9a0a7"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a51ba09ff01fdcac1125d42f276c9a0a7">&#9670;&#160;</a></span>constructSpeciesIndexMap()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::vector&lt; size_t &gt; gridfire::FileDefinedEngineView::constructSpeciesIndexMap </td>
<td>(</td>
<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Constructs the species index map. </p>
<dl class="section return"><dt>Returns</dt><dd>A vector mapping culled species indices to full species indices.</dd></dl>
<p>This method creates a map from the indices of the active species to the indices of the corresponding species in the full network.</p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00147">147</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="a48b2451f96b8f5511ffc4071519c0810" name="a48b2451f96b8f5511ffc4071519c0810"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a48b2451f96b8f5511ffc4071519c0810">&#9670;&#160;</a></span>generateJacobianMatrix()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void gridfire::FileDefinedEngineView::generateJacobianMatrix </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;)</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Generate the Jacobian matrix for the current state. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">Y</td><td>Vector of current abundances. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3.</td></tr>
</table>
</dd>
</dl>
<p>This method must compute and store the Jacobian matrix (∂(dY/dt)_i/∂Y_j) for the current state. The matrix can then be accessed via <a class="el" href="#a0ef8804780d13bbfce0856237bb00470" title="Get an entry from the previously generated Jacobian matrix.">getJacobianMatrixEntry()</a>. </p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00045">45</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="a27a5163157cc15c4cb3b99a5d3564dbd" name="a27a5163157cc15c4cb3b99a5d3564dbd"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a27a5163157cc15c4cb3b99a5d3564dbd">&#9670;&#160;</a></span>generateStoichiometryMatrix()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void gridfire::FileDefinedEngineView::generateStoichiometryMatrix </td>
<td>(</td>
<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Generate the stoichiometry matrix for the network. </p>
<p>This method must compute and store the stoichiometry matrix, which encodes the net change of each species in each reaction. </p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00068">68</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="a4c8b273c5cb3d470567c5691b68493a3" name="a4c8b273c5cb3d470567c5691b68493a3"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a4c8b273c5cb3d470567c5691b68493a3">&#9670;&#160;</a></span>getBaseEngine()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">const <a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp; gridfire::FileDefinedEngineView::getBaseEngine </td>
<td>(</td>
<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Access the underlying engine instance. </p>
<dl class="section return"><dt>Returns</dt><dd>Const reference to the underlying engine.</dd></dl>
<p>This method must be implemented by derived classes to provide access to the base engine. The returned reference should remain valid for the lifetime of the <a class="el" href="classgridfire_1_1_engine_view.html" title="Abstract base class for a &quot;view&quot; of a reaction network engine.">EngineView</a>.</p>
<p>Example: </p><div class="fragment"><div class="line"><span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>&amp; engine = myView.getBaseEngine();</div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><div class="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00121">engine_abstract.h:121</a></div></div>
</div><!-- fragment -->
<p>Implements <a class="el" href="classgridfire_1_1_engine_view.html#ad294227f8b5cf6d970c349eabf5447a6">gridfire::EngineView&lt; DynamicEngine &gt;</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00021">21</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="a0ef8804780d13bbfce0856237bb00470" name="a0ef8804780d13bbfce0856237bb00470"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a0ef8804780d13bbfce0856237bb00470">&#9670;&#160;</a></span>getJacobianMatrixEntry()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">double gridfire::FileDefinedEngineView::getJacobianMatrixEntry </td>
<td>(</td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>i</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>j</em></span>&#160;) const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Get an entry from the previously generated Jacobian matrix. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">i</td><td>Row index (species index). </td></tr>
<tr><td class="paramname">j</td><td>Column index (species index). </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Value of the Jacobian matrix at (i, j).</dd></dl>
<p>The Jacobian must have been generated by <a class="el" href="#a48b2451f96b8f5511ffc4071519c0810" title="Generate the Jacobian matrix for the current state.">generateJacobianMatrix()</a> before calling this. </p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00056">56</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="a5bbea17b69cc8f81bc251a04f4435a0c" name="a5bbea17b69cc8f81bc251a04f4435a0c"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a5bbea17b69cc8f81bc251a04f4435a0c">&#9670;&#160;</a></span>getNetworkReactions()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp; gridfire::FileDefinedEngineView::getNetworkReactions </td>
<td>(</td>
<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Get the set of logical reactions in the network. </p>
<dl class="section return"><dt>Returns</dt><dd>Reference to the LogicalReactionSet containing all reactions. </dd></dl>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00102">102</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="a8bb583e039b49608272997ed2d3387fa" name="a8bb583e039b49608272997ed2d3387fa"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a8bb583e039b49608272997ed2d3387fa">&#9670;&#160;</a></span>getNetworkSpecies()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">const std::vector&lt; Species &gt; &amp; gridfire::FileDefinedEngineView::getNetworkSpecies </td>
<td>(</td>
<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Get the list of species in the network. </p>
<dl class="section return"><dt>Returns</dt><dd>Vector of Species objects representing all network species. </dd></dl>
<p>Implements <a class="el" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">gridfire::Engine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00025">25</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="adbc50f397445f92b810d80cf329b8626" name="adbc50f397445f92b810d80cf329b8626"></a>
<h2 class="memtitle"><span class="permalink"><a href="#adbc50f397445f92b810d80cf329b8626">&#9670;&#160;</a></span>getScreeningModel()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> gridfire::FileDefinedEngineView::getScreeningModel </td>
<td>(</td>
<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00143">143</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="ace3c6ea4841318c08695973ab3dcddc6" name="ace3c6ea4841318c08695973ab3dcddc6"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ace3c6ea4841318c08695973ab3dcddc6">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::unordered_map&lt; Species, double &gt; gridfire::FileDefinedEngineView::getSpeciesTimescales </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Compute timescales for all species in the network. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">Y</td><td>Vector of current abundances. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Map from Species to their characteristic timescales (s).</dd></dl>
<p>This method estimates the timescale for abundance change of each species, which can be used for timestep control, diagnostics, and reaction network culling. </p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00108">108</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="a9da9224f5c99a5068f3d8cbf066e4693" name="a9da9224f5c99a5068f3d8cbf066e4693"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a9da9224f5c99a5068f3d8cbf066e4693">&#9670;&#160;</a></span>getStoichiometryMatrixEntry()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">int gridfire::FileDefinedEngineView::getStoichiometryMatrixEntry </td>
<td>(</td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>speciesIndex</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>reactionIndex</em></span>&#160;) const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Get an entry from the stoichiometry matrix. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">speciesIndex</td><td>Index of the species. </td></tr>
<tr><td class="paramname">reactionIndex</td><td>Index of the reaction. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Stoichiometric coefficient for the species in the reaction.</dd></dl>
<p>The stoichiometry matrix must have been generated by <a class="el" href="#a27a5163157cc15c4cb3b99a5d3564dbd" title="Generate the stoichiometry matrix for the network.">generateStoichiometryMatrix()</a>. </p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00074">74</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="a97e5ee4651dbe6754678fe96e4702fee" name="a97e5ee4651dbe6754678fe96e4702fee"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a97e5ee4651dbe6754678fe96e4702fee">&#9670;&#160;</a></span>mapFullToView()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::vector&lt; double &gt; gridfire::FileDefinedEngineView::mapFullToView </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>full</em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Maps a vector of full abundances to a vector of culled abundances. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">full</td><td>A vector of abundances for the full network. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>A vector of abundances for the active species, with the abundances of the active species copied from the full vector. </dd></dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00276">276</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="ac231044e37e0962f664f8465e1ccb022" name="ac231044e37e0962f664f8465e1ccb022"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ac231044e37e0962f664f8465e1ccb022">&#9670;&#160;</a></span>mapViewToFull()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::vector&lt; double &gt; gridfire::FileDefinedEngineView::mapViewToFull </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>culled</em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Maps a vector of culled abundances to a vector of full abundances. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">culled</td><td>A vector of abundances for the active species. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>A vector of abundances for the full network, with the abundances of the active species copied from the culled vector. </dd></dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00267">267</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="ae7d6f0ff9076d59d1245c047bbd1bdb9" name="ae7d6f0ff9076d59d1245c047bbd1bdb9"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ae7d6f0ff9076d59d1245c047bbd1bdb9">&#9670;&#160;</a></span>mapViewToFullReactionIndex()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">size_t gridfire::FileDefinedEngineView::mapViewToFullReactionIndex </td>
<td>(</td>
<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>culledReactionIndex</em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Maps a culled reaction index to a full reaction index. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">culledReactionIndex</td><td>The index of the reaction in the culled reaction list. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>The index of the corresponding reaction in the full network.</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::out_of_range</td><td>If the culled index is out of bounds for the reaction index map. </td></tr>
</table>
</dd>
</dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00294">294</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf" name="a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf">&#9670;&#160;</a></span>mapViewToFullSpeciesIndex()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">size_t gridfire::FileDefinedEngineView::mapViewToFullSpeciesIndex </td>
<td>(</td>
<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>culledSpeciesIndex</em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Maps a culled species index to a full species index. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">culledSpeciesIndex</td><td>The index of the species in the culled species list. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>The index of the corresponding species in the full network.</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::out_of_range</td><td>If the culled index is out of bounds for the species index map. </td></tr>
</table>
</dd>
</dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00285">285</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="a92f14da849e99d07c1ff1347addb9263" name="a92f14da849e99d07c1ff1347addb9263"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a92f14da849e99d07c1ff1347addb9263">&#9670;&#160;</a></span>setNetworkFile()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void gridfire::FileDefinedEngineView::setNetworkFile </td>
<td>(</td>
<td class="paramtype">const std::string &amp;</td> <td class="paramname"><span class="paramname"><em>fileName</em></span></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00133">133</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="ad96bbee6d3d37b50d9236a975ef704c0" name="ad96bbee6d3d37b50d9236a975ef704c0"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ad96bbee6d3d37b50d9236a975ef704c0">&#9670;&#160;</a></span>setScreeningModel()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void gridfire::FileDefinedEngineView::setScreeningModel </td>
<td>(</td>
<td class="paramtype"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a></td> <td class="paramname"><span class="paramname"><em>model</em></span></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00139">139</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="ace3568eadaba69e7357b4386c5ca3eb0" name="ace3568eadaba69e7357b4386c5ca3eb0"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ace3568eadaba69e7357b4386c5ca3eb0">&#9670;&#160;</a></span>update()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void gridfire::FileDefinedEngineView::update </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td> <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00127">127</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="ae3f99002ab2c56a5bcdec00839f8628f" name="ae3f99002ab2c56a5bcdec00839f8628f"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ae3f99002ab2c56a5bcdec00839f8628f">&#9670;&#160;</a></span>validateNetworkState()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void gridfire::FileDefinedEngineView::validateNetworkState </td>
<td>(</td>
<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00303">303</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<h2 class="groupheader">Member Data Documentation</h2>
<a id="ae012da2b1f6169cb13e6075a73353ab2" name="ae012da2b1f6169cb13e6075a73353ab2"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ae012da2b1f6169cb13e6075a73353ab2">&#9670;&#160;</a></span>m_activeReactions</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> gridfire::FileDefinedEngineView::m_activeReactions</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Active reactions in the defined engine. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00081">81</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
<a id="a299a0c61aa4f26029c770013c9feff5e" name="a299a0c61aa4f26029c770013c9feff5e"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a299a0c61aa4f26029c770013c9feff5e">&#9670;&#160;</a></span>m_activeSpecies</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::vector&lt;fourdst::atomic::Species&gt; gridfire::FileDefinedEngineView::m_activeSpecies</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Active species in the defined engine. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00080">80</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
<a id="ad8454c98fa9a4bb45dc81059bc51fc81" name="ad8454c98fa9a4bb45dc81059bc51fc81"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ad8454c98fa9a4bb45dc81059bc51fc81">&#9670;&#160;</a></span>m_baseEngine</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>&amp; gridfire::FileDefinedEngineView::m_baseEngine</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00076">76</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
<a id="a7a80966c023ae722239491af58609362" name="a7a80966c023ae722239491af58609362"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a7a80966c023ae722239491af58609362">&#9670;&#160;</a></span>m_config</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="#a63f8f85e75ecaab6fa39d48d7a846187">Config</a>&amp; gridfire::FileDefinedEngineView::m_config = Config::getInstance()</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00073">73</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
<a id="a1b343998b93955025a589b2b4541e33b" name="a1b343998b93955025a589b2b4541e33b"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a1b343998b93955025a589b2b4541e33b">&#9670;&#160;</a></span>m_fileName</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::string gridfire::FileDefinedEngineView::m_fileName</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Name of the file defining the reaction set considered by the engine view. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00077">77</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
<a id="a6e421bc748933be31bed9ff53f12b595" name="a6e421bc748933be31bed9ff53f12b595"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a6e421bc748933be31bed9ff53f12b595">&#9670;&#160;</a></span>m_isStale</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">bool gridfire::FileDefinedEngineView::m_isStale = true</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00086">86</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
<a id="a9d93633ed4ab68de94b7274f879a0432" name="a9d93633ed4ab68de94b7274f879a0432"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a9d93633ed4ab68de94b7274f879a0432">&#9670;&#160;</a></span>m_logger</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">quill::Logger* gridfire::FileDefinedEngineView::m_logger = LogManager::getInstance().getLogger(&quot;log&quot;)</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00074">74</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
<a id="a0a9b07176cb93b54c677b6ce71fda500" name="a0a9b07176cb93b54c677b6ce71fda500"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a0a9b07176cb93b54c677b6ce71fda500">&#9670;&#160;</a></span>m_parser</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">const <a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a>&amp; gridfire::FileDefinedEngineView::m_parser</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Parser for the network file. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00078">78</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
<a id="af0a77a4749a15aae87bdecfccbd1736e" name="af0a77a4749a15aae87bdecfccbd1736e"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af0a77a4749a15aae87bdecfccbd1736e">&#9670;&#160;</a></span>m_reactionIndexMap</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::vector&lt;size_t&gt; gridfire::FileDefinedEngineView::m_reactionIndexMap</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Maps indices of active reactions to indices in the full network. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00084">84</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
<a id="aebd4a1a584f2784f1df3d503645be03b" name="aebd4a1a584f2784f1df3d503645be03b"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aebd4a1a584f2784f1df3d503645be03b">&#9670;&#160;</a></span>m_speciesIndexMap</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::vector&lt;size_t&gt; gridfire::FileDefinedEngineView::m_speciesIndexMap</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Maps indices of active species to indices in the full network. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00083">83</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
<hr/>The documentation for this class was generated from the following files:<ul>
<li>src/network/include/gridfire/engine/views/<a class="el" href="engine__defined_8h_source.html">engine_defined.h</a></li>
<li>src/network/lib/engine/views/<a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a></li>
</ul>
</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="namespacegridfire.html">gridfire</a></li><li class="navelem"><a class="el" href="classgridfire_1_1_file_defined_engine_view.html">FileDefinedEngineView</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>