docs(docs): asdded and cleaned up docs

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2025-07-24 11:10:45 -04:00
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@@ -116,10 +116,15 @@ Inheritance diagram for gridfire::Engine:</div>
<div class="center">
<img src="classgridfire_1_1_engine.png" usemap="#gridfire::Engine_map" alt=""/>
<map id="gridfire::Engine_map" name="gridfire::Engine_map">
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<table class="memberdecls">
@@ -131,9 +136,9 @@ Public Member Functions</h2></td></tr>
<tr class="memitem:a020e1b493d6964cafdad08fde697ceb3" id="r_a020e1b493d6964cafdad08fde697ceb3"><td class="memItemLeft" align="right" valign="top">virtual const std::vector&lt; fourdst::atomic::Species &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a020e1b493d6964cafdad08fde697ceb3">getNetworkSpecies</a> () const =0</td></tr>
<tr class="memdesc:a020e1b493d6964cafdad08fde697ceb3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the list of species in the network. <br /></td></tr>
<tr class="separator:a020e1b493d6964cafdad08fde697ceb3"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac8b56124b6b49cd1802addb74a9a47c2" id="r_ac8b56124b6b49cd1802addb74a9a47c2"><td class="memItemLeft" align="right" valign="top">virtual <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="#ac8b56124b6b49cd1802addb74a9a47c2">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td></tr>
<tr class="memdesc:ac8b56124b6b49cd1802addb74a9a47c2"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the right-hand side (dY/dt) and energy generation. <br /></td></tr>
<tr class="separator:ac8b56124b6b49cd1802addb74a9a47c2"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a89f714d19b84a93a004a7afbb487a6cb" id="r_a89f714d19b84a93a004a7afbb487a6cb"><td class="memItemLeft" align="right" valign="top">virtual std::expected&lt; <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a89f714d19b84a93a004a7afbb487a6cb">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td></tr>
<tr class="memdesc:a89f714d19b84a93a004a7afbb487a6cb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the right-hand side (dY/dt) and energy generation. <br /></td></tr>
<tr class="separator:a89f714d19b84a93a004a7afbb487a6cb"><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>Abstract base class for a reaction network engine. </p>
@@ -142,9 +147,9 @@ Public Member Functions</h2></td></tr>
<p>Example: </p><div class="fragment"><div class="line"><span class="keyword">class </span>MyEngine : <span class="keyword">public</span> <a class="code hl_class" href="classgridfire_1_1_engine.html">gridfire::Engine</a> {</div>
<div class="line"> <span class="comment">// Implement required methods...</span></div>
<div class="line">};</div>
<div class="ttc" id="aclassgridfire_1_1_engine_html"><div class="ttname"><a href="classgridfire_1_1_engine.html">gridfire::Engine</a></div><div class="ttdoc">Abstract base class for a reaction network engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00075">engine_abstract.h:75</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_engine_html"><div class="ttname"><a href="classgridfire_1_1_engine.html">gridfire::Engine</a></div><div class="ttdoc">Abstract base class for a reaction network engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00084">engine_abstract.h:84</a></div></div>
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<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00075">75</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__abstract_8h_source.html#l00084">84</a> of file <a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a>.</p>
</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
<a id="a2e7970bed2100699f226f4141d5db037" name="a2e7970bed2100699f226f4141d5db037"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a2e7970bed2100699f226f4141d5db037">&#9670;&#160;</a></span>~Engine()</h2>
@@ -174,8 +179,8 @@ Public Member Functions</h2></td></tr>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a id="ac8b56124b6b49cd1802addb74a9a47c2" name="ac8b56124b6b49cd1802addb74a9a47c2"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ac8b56124b6b49cd1802addb74a9a47c2">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
<a id="a89f714d19b84a93a004a7afbb487a6cb" name="a89f714d19b84a93a004a7afbb487a6cb"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a89f714d19b84a93a004a7afbb487a6cb">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
<div class="memitem">
<div class="memproto">
@@ -184,7 +189,7 @@ Public Member Functions</h2></td></tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">virtual <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt; gridfire::Engine::calculateRHSAndEnergy </td>
<td class="memname">virtual std::expected&lt; <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::Engine::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>
@@ -218,7 +223,7 @@ Public Member Functions</h2></td></tr>
<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>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7b276b7210be588263395bdb0497fc6d">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a2c1d88b06568f9ea4c65e794d012ebfb">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a8b3baf29829c7ae0a61430ea70632bbf">gridfire::GraphEngine</a>.</p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#af703ad17ea65ffff4b75bf8ccc00e5d5">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#aaed3743a52246b0f7bf03995e1c12081">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a716d7357e944e8394d8b8e0b5e7625eb">gridfire::MultiscalePartitioningEngineView</a>, <a class="el" href="class_py_dynamic_engine.html#a5b7f0cfe327c634ec125303256de8b9a">PyDynamicEngine</a>, and <a class="el" href="class_py_engine.html#a2f92602ecf210414b46838fc0a9ae26d">PyEngine</a>.</p>
</div>
</div>
@@ -248,12 +253,12 @@ Public Member Functions</h2></td></tr>
<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>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac83a8efe25c0e5b9bf7756ac3a500bb1">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a8bb583e039b49608272997ed2d3387fa">gridfire::FileDefinedEngineView</a>, and <a class="el" href="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767">gridfire::GraphEngine</a>.</p>
<p>Implemented in <a class="el" href="classgridfire_1_1_adaptive_engine_view.html#ac83a8efe25c0e5b9bf7756ac3a500bb1">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a1a55f9748c45af6f13e16a6b6ceaa211">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a696f74f5135bbd62169b6577f92fee80">gridfire::MultiscalePartitioningEngineView</a>, <a class="el" href="class_py_dynamic_engine.html#afc745e7ab5da5d8b3cf916044515cd7d">PyDynamicEngine</a>, and <a class="el" href="class_py_engine.html#a2d240423899e039c2ca688e96f8af1f2">PyEngine</a>.</p>
</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>src/network/include/gridfire/engine/<a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a></li>
<li>src/include/gridfire/engine/<a class="el" href="engine__abstract_8h_source.html">engine_abstract.h</a></li>
</ul>
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</div><!-- doc-content -->