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Emily Boudreaux
2025-07-31 10:54:31 -04:00
parent 2aaeb6440e
commit 63265a2dc3
271 changed files with 5003 additions and 5941 deletions
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docs/html/classgridfire_1_1_defined_engine_view.html
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@@ -109,7 +109,7 @@ $(function(){initNavTree('classgridfire_1_1_defined_engine_view.html',''); initR
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<p><code>#include &lt;<a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>&gt;</code></p>
<p><code>#include &lt;engine_defined.h&gt;</code></p>
<div class="dynheader">
Inheritance diagram for gridfire::DefinedEngineView:</div>
<div class="dyncontent">
@@ -244,10 +244,7 @@ Private Attributes</h2></td></tr>
<tr class="memitem:affda6d60651c53ee02532806104671bd" id="r_affda6d60651c53ee02532806104671bd"><td class="memItemLeft" align="right" valign="top">std::vector&lt; size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#affda6d60651c53ee02532806104671bd">m_reactionIndexMap</a></td></tr>
<tr class="separator:affda6d60651c53ee02532806104671bd"><td class="memSeparator" colspan="2">&#160;</td></tr>
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<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">Constructor &amp; Destructor Documentation</h2>
<h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
<a id="a9b319b4a1bd5a08381ebb183daf72c92" name="a9b319b4a1bd5a08381ebb183daf72c92"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a9b319b4a1bd5a08381ebb183daf72c92">&#9670;&#160;</a></span>DefinedEngineView()</h2>
@@ -267,8 +264,6 @@ Private Attributes</h2></td></tr>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00017">17</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="groupheader">Member Function Documentation</h2>
@@ -329,8 +324,6 @@ Private Attributes</h2></td></tr>
<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#l00091">91</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb">gridfire::Engine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00030">30</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00321">321</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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</dd>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00245">245</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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</dd>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00216">216</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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@@ -539,8 +524,6 @@ Private Attributes</h2></td></tr>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a29bdd4231c29c3a4e524ad6ca66a127d">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00051">51</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<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#l00074">74</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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@@ -607,12 +588,10 @@ Private Attributes</h2></td></tr>
<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#l00130">engine_abstract.h:130</a></div></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> engine_abstract.h:130</div></div>
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<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#l00022">22</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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@@ -661,8 +640,6 @@ Private Attributes</h2></td></tr>
<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#l00062">62</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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@@ -699,8 +676,6 @@ Private Attributes</h2></td></tr>
<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#l00108">108</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<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#l00026">26</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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@@ -763,8 +736,6 @@ Private Attributes</h2></td></tr>
<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#l00184">184</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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@@ -801,8 +772,6 @@ Private Attributes</h2></td></tr>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6ca0f315f75252ca505507a61556dda6">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00146">146</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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@@ -830,8 +799,6 @@ Private Attributes</h2></td></tr>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad3d56a8b9161b9cc7f4da51f6bf7e8c9">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00188">188</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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@@ -885,8 +852,6 @@ Private Attributes</h2></td></tr>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6772ac384b4c3d3e91712041e4aaa813">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00122">122</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<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#l00080">80</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a942e65ced17ca602482cc42e469d6398">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00175">175</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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</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#l00286">286</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a55f1b7e5ebe2840e1d7c54665ca5411a">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00201">201</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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</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 defined vector. </dd></dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00277">277</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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</dd>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00304">304</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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</dd>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00295">295</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a21c34f59c080a853fafa38a25175124e">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00212">212</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afb2ec904d88fc8aab516db4059d0e00f">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00114">114</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<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#l00180">180</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aa799ff785e7e79bf35b11efd55f6282a">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00171">171</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00313">313</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
@@ -1337,8 +1278,6 @@ Private Attributes</h2></td></tr>
<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#l00184">184</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<p>Active reactions in the defined engine. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00182">182</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00178">178</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00177">177</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<p>Active species in the defined engine. </p>
<p>Logger instance for trace and debug information. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00180">180</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00189">189</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<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#l00187">187</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<hr/>The documentation for this class was generated from the following files:<ul>
<li>src/include/gridfire/engine/views/<a class="el" href="engine__defined_8h_source.html">engine_defined.h</a></li>
<li>src/lib/engine/views/<a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a></li>
<li>src/include/gridfire/engine/views/<a class="el" href="engine__defined_8h.html">engine_defined.h</a></li>
<li>src/lib/engine/views/<a class="el" href="engine__defined_8cpp.html">engine_defined.cpp</a></li>
</ul>
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