tboudreaux/GridFire
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

docs(docs): rebuilt for version v0.7.1_rc2

Browse Source
This commit is contained in:
Emily M. Boudreaux
2025-11-28 09:46:00 -05:00
parent 033c5a083d
commit a472dc5214
2480 changed files with 231104 additions and 76191 deletions
Download Patch File Download Diff File Expand all files Collapse all files

119
docs/html/namespacegridfire_1_1engine_1_1diagnostics.html
View File

@@ -3,18 +3,16 @@
<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="generator" content="Doxygen 1.9.8"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>GridFire: gridfire::engine::diagnostics Namespace 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="resize.js"></script>
<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>
@@ -29,7 +27,7 @@
<tbody>
<tr id="projectrow">
<td id="projectalign">
<div id="projectname">GridFire<span id="projectnumber">&#160;v0.7.0_rc2</span>
<div id="projectname">GridFire<span id="projectnumber">&#160;v0.7.1_rc2</span>
</div>
<div id="projectbrief">General Purpose Nuclear Network</div>
</td>
@@ -38,24 +36,19 @@
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.13.2 -->
<!-- Generated by Doxygen 1.9.8 -->
<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(); });
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
/* @license-end */
</script>
@@ -73,7 +66,7 @@ $(function() {
</div>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
$(function(){initNavTree('namespacegridfire_1_1engine_1_1diagnostics.html',''); initResizable(true); });
$(document).ready(function(){initNavTree('namespacegridfire_1_1engine_1_1diagnostics.html',''); initResizable(); });
/* @license-end */
</script>
<div id="doc-content">
@@ -107,16 +100,16 @@ $(function(){initNavTree('namespacegridfire_1_1engine_1_1diagnostics.html','');
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:ad792baf3c6720fce34a5161c0ade3fc4" id="r_ad792baf3c6720fce34a5161c0ade3fc4"><td class="memItemLeft" align="right" valign="top">std::optional&lt; nlohmann::json &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad792baf3c6720fce34a5161c0ade3fc4">report_limiting_species</a> (const <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html">DynamicEngine</a> &amp;engine, const std::vector&lt; double &gt; &amp;Y_full, const std::vector&lt; double &gt; &amp;E_full, double relTol, double absTol, size_t top_n=10, bool json=false)</td></tr>
<tr class="memitem:ad792baf3c6720fce34a5161c0ade3fc4" id="r_ad792baf3c6720fce34a5161c0ade3fc4"><td class="memItemLeft" align="right" valign="top">std::optional&lt; nlohmann::json &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire_1_1engine_1_1diagnostics.html#ad792baf3c6720fce34a5161c0ade3fc4">report_limiting_species</a> (const <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html">DynamicEngine</a> &amp;engine, const std::vector&lt; double &gt; &amp;Y_full, const std::vector&lt; double &gt; &amp;E_full, double relTol, double absTol, size_t top_n=10, bool json=false)</td></tr>
<tr class="memdesc:ad792baf3c6720fce34a5161c0ade3fc4"><td class="mdescLeft">&#160;</td><td class="mdescRight">Report the species that are limiting the accuracy of the integration. This is useful for identifying species that may be limiting the timestepping due to their high relative errors compared to the specified tolerances. <br /></td></tr>
<tr class="separator:ad792baf3c6720fce34a5161c0ade3fc4"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aac2570f6bc58b8825674f60f1634149b" id="r_aac2570f6bc58b8825674f60f1634149b"><td class="memItemLeft" align="right" valign="top">std::optional&lt; nlohmann::json &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aac2570f6bc58b8825674f60f1634149b">inspect_species_balance</a> (const <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html">DynamicEngine</a> &amp;engine, const std::string &amp;species_name, const fourdst::composition::Composition &amp;comp, double T9, double rho, bool json)</td></tr>
<tr class="memitem:aac2570f6bc58b8825674f60f1634149b" id="r_aac2570f6bc58b8825674f60f1634149b"><td class="memItemLeft" align="right" valign="top">std::optional&lt; nlohmann::json &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire_1_1engine_1_1diagnostics.html#aac2570f6bc58b8825674f60f1634149b">inspect_species_balance</a> (const <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html">DynamicEngine</a> &amp;engine, const std::string &amp;species_name, const fourdst::composition::Composition &amp;comp, double T9, double rho, bool json)</td></tr>
<tr class="memdesc:aac2570f6bc58b8825674f60f1634149b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Inspect the production and destruction balance of a specific species in the reaction network. This function analyzes the reactions that create and destroy the specified species, providing insights into potential imbalances that may affect the accuracy of the simulation. <br /></td></tr>
<tr class="separator:aac2570f6bc58b8825674f60f1634149b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8a42702b787f12988ae8fc7e1e6d8186" id="r_a8a42702b787f12988ae8fc7e1e6d8186"><td class="memItemLeft" align="right" valign="top">std::optional&lt; nlohmann::json &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a8a42702b787f12988ae8fc7e1e6d8186">inspect_jacobian_stiffness</a> (const <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html">DynamicEngine</a> &amp;engine, const fourdst::composition::Composition &amp;comp, double T9, double rho, bool json)</td></tr>
<tr class="memitem:a8a42702b787f12988ae8fc7e1e6d8186" id="r_a8a42702b787f12988ae8fc7e1e6d8186"><td class="memItemLeft" align="right" valign="top">std::optional&lt; nlohmann::json &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire_1_1engine_1_1diagnostics.html#a8a42702b787f12988ae8fc7e1e6d8186">inspect_jacobian_stiffness</a> (const <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html">DynamicEngine</a> &amp;engine, const fourdst::composition::Composition &amp;comp, double T9, double rho, bool json)</td></tr>
<tr class="memdesc:a8a42702b787f12988ae8fc7e1e6d8186"><td class="mdescLeft">&#160;</td><td class="mdescRight">Inspect the stiffness of the Jacobian matrix for the reaction network at the given temperature and density. This function evaluates the diagonal and off-diagonal elements of the Jacobian to identify potential numerical issues related to stiffness. <br /></td></tr>
<tr class="separator:a8a42702b787f12988ae8fc7e1e6d8186"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab247fdf00c23cf857d9131a3462d41ae" id="r_ab247fdf00c23cf857d9131a3462d41ae"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ab247fdf00c23cf857d9131a3462d41ae">save_jacobian_to_file</a> (const <a class="el" href="classgridfire_1_1engine_1_1_network_jacobian.html">NetworkJacobian</a> &amp;jacobian, const std::string &amp;filename)</td></tr>
<tr class="memitem:ab247fdf00c23cf857d9131a3462d41ae" id="r_ab247fdf00c23cf857d9131a3462d41ae"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacegridfire_1_1engine_1_1diagnostics.html#ab247fdf00c23cf857d9131a3462d41ae">save_jacobian_to_file</a> (const <a class="el" href="classgridfire_1_1engine_1_1NetworkJacobian.html">NetworkJacobian</a> &amp;jacobian, const std::string &amp;filename)</td></tr>
<tr class="memdesc:ab247fdf00c23cf857d9131a3462d41ae"><td class="mdescLeft">&#160;</td><td class="mdescRight">Save the Jacobian matrix to a file for external analysis. <br /></td></tr>
<tr class="separator:ab247fdf00c23cf857d9131a3462d41ae"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
@@ -130,27 +123,37 @@ Functions</h2></td></tr>
<tr>
<td class="memname">std::optional&lt; nlohmann::json &gt; gridfire::engine::diagnostics::inspect_jacobian_stiffness </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html">DynamicEngine</a> &amp;</td> <td class="paramname"><span class="paramname"><em>engine</em></span>, </td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html">DynamicEngine</a> &amp;&#160;</td>
<td class="paramname"><em>engine</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const fourdst::composition::Composition &amp;</td> <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
<td class="paramtype">const fourdst::composition::Composition &amp;&#160;</td>
<td class="paramname"><em>comp</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
<td class="paramtype">double&#160;</td>
<td class="paramname"><em>T9</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>, </td>
<td class="paramtype">double&#160;</td>
<td class="paramname"><em>rho</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool</td> <td class="paramname"><span class="paramname"><em>json</em></span>&#160;)</td>
<td class="paramtype">bool&#160;</td>
<td class="paramname"><em>json</em>&#160;</td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
@@ -158,7 +161,7 @@ Functions</h2></td></tr>
<p>Inspect the stiffness of the Jacobian matrix for the reaction network at the given temperature and density. This function evaluates the diagonal and off-diagonal elements of the Jacobian to identify potential numerical issues related to stiffness. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">engine</td><td>Constant reference to the <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> instance. </td></tr>
<tr><td class="paramname">engine</td><td>Constant reference to the <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> instance. </td></tr>
<tr><td class="paramname">comp</td><td>The current composition of the system as a fourdst::composition::Composition object. </td></tr>
<tr><td class="paramname">T9</td><td>The temperature in GK (10^9 K). </td></tr>
<tr><td class="paramname">rho</td><td>The density in g/cm^3. </td></tr>
@@ -179,32 +182,43 @@ Functions</h2></td></tr>
<tr>
<td class="memname">std::optional&lt; nlohmann::json &gt; gridfire::engine::diagnostics::inspect_species_balance </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html">DynamicEngine</a> &amp;</td> <td class="paramname"><span class="paramname"><em>engine</em></span>, </td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html">DynamicEngine</a> &amp;&#160;</td>
<td class="paramname"><em>engine</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::string &amp;</td> <td class="paramname"><span class="paramname"><em>species_name</em></span>, </td>
<td class="paramtype">const std::string &amp;&#160;</td>
<td class="paramname"><em>species_name</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const fourdst::composition::Composition &amp;</td> <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
<td class="paramtype">const fourdst::composition::Composition &amp;&#160;</td>
<td class="paramname"><em>comp</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
<td class="paramtype">double&#160;</td>
<td class="paramname"><em>T9</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>, </td>
<td class="paramtype">double&#160;</td>
<td class="paramname"><em>rho</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool</td> <td class="paramname"><span class="paramname"><em>json</em></span>&#160;)</td>
<td class="paramtype">bool&#160;</td>
<td class="paramname"><em>json</em>&#160;</td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
@@ -212,7 +226,7 @@ Functions</h2></td></tr>
<p>Inspect the production and destruction balance of a specific species in the reaction network. This function analyzes the reactions that create and destroy the specified species, providing insights into potential imbalances that may affect the accuracy of the simulation. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">engine</td><td>Constant reference to the <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> instance. </td></tr>
<tr><td class="paramname">engine</td><td>Constant reference to the <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> instance. </td></tr>
<tr><td class="paramname">species_name</td><td>The name of the species to inspect. </td></tr>
<tr><td class="paramname">comp</td><td>The current composition of the system as a fourdst::composition::Composition object. </td></tr>
<tr><td class="paramname">T9</td><td>The temperature in GK (10^9 K). </td></tr>
@@ -234,37 +248,49 @@ Functions</h2></td></tr>
<tr>
<td class="memname">std::optional&lt; nlohmann::json &gt; gridfire::engine::diagnostics::report_limiting_species </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html">DynamicEngine</a> &amp;</td> <td class="paramname"><span class="paramname"><em>engine</em></span>, </td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html">DynamicEngine</a> &amp;&#160;</td>
<td class="paramname"><em>engine</em>, </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_full</em></span>, </td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;&#160;</td>
<td class="paramname"><em>Y_full</em>, </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>E_full</em></span>, </td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;&#160;</td>
<td class="paramname"><em>E_full</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>relTol</em></span>, </td>
<td class="paramtype">double&#160;</td>
<td class="paramname"><em>relTol</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>absTol</em></span>, </td>
<td class="paramtype">double&#160;</td>
<td class="paramname"><em>absTol</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>top_n</em></span><span class="paramdefsep"> = </span><span class="paramdefval">10</span>, </td>
<td class="paramtype">size_t&#160;</td>
<td class="paramname"><em>top_n</em> = <code>10</code>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool</td> <td class="paramname"><span class="paramname"><em>json</em></span><span class="paramdefsep"> = </span><span class="paramdefval">false</span>&#160;)</td>
<td class="paramtype">bool&#160;</td>
<td class="paramname"><em>json</em> = <code>false</code>&#160;</td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
@@ -272,7 +298,7 @@ Functions</h2></td></tr>
<p>Report the species that are limiting the accuracy of the integration. This is useful for identifying species that may be limiting the timestepping due to their high relative errors compared to the specified tolerances. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">engine</td><td>Constant reference to the <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> instance. </td></tr>
<tr><td class="paramname">engine</td><td>Constant reference to the <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> instance. </td></tr>
<tr><td class="paramname">Y_full</td><td>Vector of the current species molar abundances sorted in the same order as the dynamic engine species list. </td></tr>
<tr><td class="paramname">E_full</td><td>Vector of the current species molar abundance errors sorted in the same order as the dynamic engine species list. </td></tr>
<tr><td class="paramname">relTol</td><td>Relative tolerance for the integration. </td></tr>
@@ -295,12 +321,19 @@ Functions</h2></td></tr>
<tr>
<td class="memname">void gridfire::engine::diagnostics::save_jacobian_to_file </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1engine_1_1_network_jacobian.html">NetworkJacobian</a> &amp;</td> <td class="paramname"><span class="paramname"><em>jacobian</em></span>, </td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1engine_1_1NetworkJacobian.html">NetworkJacobian</a> &amp;&#160;</td>
<td class="paramname"><em>jacobian</em>, </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>&#160;)</td>
<td class="paramtype">const std::string &amp;&#160;</td>
<td class="paramname"><em>filename</em>&#160;</td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
@@ -308,7 +341,7 @@ Functions</h2></td></tr>
<p>Save the Jacobian matrix to a file for external analysis. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">jacobian</td><td>Constant reference to the <a class="el" href="classgridfire_1_1engine_1_1_network_jacobian.html" title="A wrapper class for handling the network Jacobian matrix.">NetworkJacobian</a> instance to be saved. </td></tr>
<tr><td class="paramname">jacobian</td><td>Constant reference to the <a class="el" href="classgridfire_1_1engine_1_1NetworkJacobian.html" title="A wrapper class for handling the network Jacobian matrix.">NetworkJacobian</a> instance to be saved. </td></tr>
<tr><td class="paramname">filename</td><td>The name of the file where the Jacobian will be saved. </td></tr>
</table>
</dd>
@@ -322,7 +355,7 @@ Functions</h2></td></tr>
<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="namespacegridfire_1_1engine.html">engine</a></li><li class="navelem"><a class="el" href="namespacegridfire_1_1engine_1_1diagnostics.html">diagnostics</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>
<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> 1.9.8 </li>
</ul>
</div>
</body>