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docs(docs): rebuilt docs

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Emily Boudreaux
2025-11-24 09:08:28 -05:00
parent 9fab4fbfae
commit 22c0329de0
2410 changed files with 309008 additions and 146081 deletions
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docs/html/engine_8h.html
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@@ -118,7 +118,7 @@ Include dependency graph for engine.h:</div>
</div><div class="textblock"><div class="dynheader">
This graph shows which files directly or indirectly include this file:</div>
<div class="dyncontent">
<div class="center"><iframe scrolling="no" frameborder="0" src="engine_8h__dep__incl.svg" width="435" height="230"><p><b>This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead.</b></p></iframe></div>
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</div>
</div><a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Core header for the GridFire reaction network engine module. </p>
@@ -163,8 +163,7 @@ GraphEngine Example</h2>
<div class="line">fourdst::composition::Composition composition;</div>
<div class="line"> </div>
<div class="line"><span class="comment">// Create a GraphEngine</span></div>
<div class="line"><a class="code hl_class" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a> engine(composition);</div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></div><div class="ttdoc">A reaction network engine that uses a graph-based representation.</div><div class="ttdef"><b>Definition</b> engine_graph.h:99</div></div>
<div class="line">gridfire::GraphEngine engine(composition);</div>
<div class="ttc" id="aengine__graph_8h_html"><div class="ttname"><a href="engine__graph_8h.html">engine_graph.h</a></div></div>
</div><!-- fragment --><h2><a class="anchor" id="AdaptiveEngineViewExample"></a>
AdaptiveEngineView Example</h2>
@@ -177,11 +176,10 @@ AdaptiveEngineView Example</h2>
<div class="line">fourdst::composition::Composition composition;</div>
<div class="line"> </div>
<div class="line"><span class="comment">// Create a GraphEngine</span></div>
<div class="line"><a class="code hl_class" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a> baseEngine(composition);</div>
<div class="line">gridfire::GraphEngine baseEngine(composition);</div>
<div class="line"> </div>
<div class="line"><span class="comment">// Create an AdaptiveEngineView</span></div>
<div class="line"><a class="code hl_class" href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a> engine(baseEngine);</div>
<div class="ttc" id="aclassgridfire_1_1_adaptive_engine_view_html"><div class="ttname"><a href="classgridfire_1_1_adaptive_engine_view.html">gridfire::AdaptiveEngineView</a></div><div class="ttdoc">An engine view that dynamically adapts the reaction network based on runtime conditions.</div><div class="ttdef"><b>Definition</b> engine_adaptive.h:49</div></div>
<div class="line">gridfire::AdaptiveEngineView engine(baseEngine);</div>
<div class="ttc" id="aengine__adaptive_8h_html"><div class="ttname"><a href="engine__adaptive_8h.html">engine_adaptive.h</a></div></div>
</div><!-- fragment --><h2><a class="anchor" id="DefinedEngineViewExample"></a>
DefinedEngineView Example</h2>
@@ -194,12 +192,11 @@ DefinedEngineView Example</h2>
<div class="line">fourdst::composition::Composition composition;</div>
<div class="line"> </div>
<div class="line"><span class="comment">// Create a GraphEngine</span></div>
<div class="line"><a class="code hl_class" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a> baseEngine(composition);</div>
<div class="line">gridfire::GraphEngine baseEngine(composition);</div>
<div class="line"> </div>
<div class="line"><span class="comment">// Create a DefinedEngineView</span></div>
<div class="line">std::vector&lt;std::string&gt; peNames = {<span class="stringliteral">&quot;p(p,e+)d&quot;</span>, <span class="stringliteral">&quot;he4(a,g)be8&quot;</span>};</div>
<div class="line"><a class="code hl_class" href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a> engine(peNames, baseEngine);</div>
<div class="ttc" id="aclassgridfire_1_1_defined_engine_view_html"><div class="ttname"><a href="classgridfire_1_1_defined_engine_view.html">gridfire::DefinedEngineView</a></div><div class="ttdef"><b>Definition</b> engine_defined.h:17</div></div>
<div class="line">gridfire::DefinedEngineView engine(peNames, baseEngine);</div>
<div class="ttc" id="aengine__defined_8h_html"><div class="ttname"><a href="engine__defined_8h.html">engine_defined.h</a></div></div>
</div><!-- fragment --><h2><a class="anchor" id="MultiscalePartitioningEngineViewExample"></a>
MultiscalePartitioningEngineView Example</h2>
@@ -212,11 +209,10 @@ MultiscalePartitioningEngineView Example</h2>
<div class="line">fourdst::composition::Composition composition;</div>
<div class="line"> </div>
<div class="line"><span class="comment">// Create a GraphEngine</span></div>
<div class="line"><a class="code hl_class" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a> baseEngine(composition);</div>
<div class="line">gridfire::GraphEngine baseEngine(composition);</div>
<div class="line"> </div>
<div class="line"><span class="comment">// Create a MultiscalePartitioningEngineView</span></div>
<div class="line"><a class="code hl_class" href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a> engine(baseEngine);</div>
<div class="ttc" id="aclassgridfire_1_1_multiscale_partitioning_engine_view_html"><div class="ttname"><a href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></div><div class="ttdoc">An engine view that partitions the reaction network into multiple groups based on timescales.</div><div class="ttdef"><b>Definition</b> engine_multiscale.h:180</div></div>
<div class="line">gridfire::MultiscalePartitioningEngineView engine(baseEngine);</div>
<div class="ttc" id="aengine__multiscale_8h_html"><div class="ttname"><a href="engine__multiscale_8h.html">engine_multiscale.h</a></div></div>
</div><!-- fragment --><h2><a class="anchor" id="NetworkPrimingEngineViewExample"></a>
NetworkPrimingEngineView Example</h2>
@@ -229,12 +225,11 @@ NetworkPrimingEngineView Example</h2>
<div class="line">fourdst::composition::Composition composition;</div>
<div class="line"> </div>
<div class="line"><span class="comment">// Create a GraphEngine</span></div>
<div class="line"><a class="code hl_class" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a> baseEngine(composition);</div>
<div class="line">gridfire::GraphEngine baseEngine(composition);</div>
<div class="line"> </div>
<div class="line"><span class="comment">// Create a NetworkPrimingEngineView</span></div>
<div class="line">std::string primingSymbol = <span class="stringliteral">&quot;p&quot;</span>;</div>
<div class="line"><a class="code hl_class" href="classgridfire_1_1_network_priming_engine_view.html">gridfire::NetworkPrimingEngineView</a> engine(primingSymbol, baseEngine);</div>
<div class="ttc" id="aclassgridfire_1_1_network_priming_engine_view_html"><div class="ttname"><a href="classgridfire_1_1_network_priming_engine_view.html">gridfire::NetworkPrimingEngineView</a></div><div class="ttdoc">Provides a view of a DynamicEngine filtered to reactions involving a specified priming species.</div><div class="ttdef"><b>Definition</b> engine_priming.h:26</div></div>
<div class="line">gridfire::NetworkPrimingEngineView engine(primingSymbol, baseEngine);</div>
<div class="ttc" id="aengine__priming_8h_html"><div class="ttname"><a href="engine__priming_8h.html">engine_priming.h</a></div></div>
</div><!-- fragment --> </div></div><!-- contents -->
</div><!-- doc-content -->