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docs(docs): rebuild with more usage examples

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Emily Boudreaux
2025-07-30 15:12:46 -04:00
parent 24870ffcbc
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@@ -510,19 +510,19 @@ $(function(){initNavTree('engine_2bindings_8cpp_source.html',''); initResizable(
<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_file_defined_engine_view_html_ae0c35d8963b6ed05aeb88089ce301718"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ae0c35d8963b6ed05aeb88089ce301718">gridfire::FileDefinedEngineView::getNetworkFile</a></div><div class="ttdeci">std::string getNetworkFile() const</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00266">engine_defined.h:266</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_aea834dc382ff1d663040db4532ea928f"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#aea834dc382ff1d663040db4532ea928f">gridfire::FileDefinedEngineView::getParser</a></div><div class="ttdeci">const io::NetworkFileParser &amp; getParser() const</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00267">engine_defined.h:267</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a015f8975701f028c29835d3a9794e00f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f">gridfire::GraphEngine::isPrecomputationEnabled</a></div><div class="ttdeci">bool isPrecomputationEnabled() const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00637">engine_graph.cpp:637</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a01fc9fd5d576b66d07360d05e821c755"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755">gridfire::GraphEngine::calculateReverseRateTwoBody</a></div><div class="ttdeci">double calculateReverseRateTwoBody(const reaction::Reaction &amp;reaction, const double T9, const double forwardRate, const double expFactor) const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00291">engine_graph.cpp:291</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a0b7b85f824e1021ae6e56b644db53b28"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28">gridfire::GraphEngine::calculateReverseRate</a></div><div class="ttdeci">double calculateReverseRate(const reaction::Reaction &amp;reaction, double T9) const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00262">engine_graph.cpp:262</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a409991d527ea4d4b05d1af907fe5d197"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197">gridfire::GraphEngine::setUseReverseReactions</a></div><div class="ttdeci">void setUseReverseReactions(bool useReverse)</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00413">engine_graph.cpp:413</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a6c5410878496abc349ba30b691cdf0f1"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1">gridfire::GraphEngine::setPrecomputation</a></div><div class="ttdeci">void setPrecomputation(bool precompute)</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00633">engine_graph.cpp:633</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a832e2fe066381811a3e0464806ff5e95"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95">gridfire::GraphEngine::exportToCSV</a></div><div class="ttdeci">void exportToCSV(const std::string &amp;filename) const</div><div class="ttdoc">Exports the network to a CSV file for analysis.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00810">engine_graph.cpp:810</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a8c29d8bbde407e913be5eb77efb2c0c9"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9">gridfire::GraphEngine::getNetReactionStoichiometry</a></div><div class="ttdeci">static std::unordered_map&lt; fourdst::atomic::Species, int &gt; getNetReactionStoichiometry(const reaction::Reaction &amp;reaction)</div><div class="ttdoc">Gets the net stoichiometry for a given reaction.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00749">engine_graph.cpp:749</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a015f8975701f028c29835d3a9794e00f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f">gridfire::GraphEngine::isPrecomputationEnabled</a></div><div class="ttdeci">bool isPrecomputationEnabled() const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00615">engine_graph.cpp:615</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a01fc9fd5d576b66d07360d05e821c755"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755">gridfire::GraphEngine::calculateReverseRateTwoBody</a></div><div class="ttdeci">double calculateReverseRateTwoBody(const reaction::Reaction &amp;reaction, const double T9, const double forwardRate, const double expFactor) const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00269">engine_graph.cpp:269</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a0b7b85f824e1021ae6e56b644db53b28"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28">gridfire::GraphEngine::calculateReverseRate</a></div><div class="ttdeci">double calculateReverseRate(const reaction::Reaction &amp;reaction, double T9) const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00242">engine_graph.cpp:242</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a409991d527ea4d4b05d1af907fe5d197"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197">gridfire::GraphEngine::setUseReverseReactions</a></div><div class="ttdeci">void setUseReverseReactions(bool useReverse)</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00391">engine_graph.cpp:391</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a6c5410878496abc349ba30b691cdf0f1"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1">gridfire::GraphEngine::setPrecomputation</a></div><div class="ttdeci">void setPrecomputation(bool precompute)</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00611">engine_graph.cpp:611</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a832e2fe066381811a3e0464806ff5e95"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95">gridfire::GraphEngine::exportToCSV</a></div><div class="ttdeci">void exportToCSV(const std::string &amp;filename) const</div><div class="ttdoc">Exports the network to a CSV file for analysis.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00788">engine_graph.cpp:788</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a8c29d8bbde407e913be5eb77efb2c0c9"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9">gridfire::GraphEngine::getNetReactionStoichiometry</a></div><div class="ttdeci">static std::unordered_map&lt; fourdst::atomic::Species, int &gt; getNetReactionStoichiometry(const reaction::Reaction &amp;reaction)</div><div class="ttdoc">Gets the net stoichiometry for a given reaction.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00727">engine_graph.cpp:727</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_aa6202cee0c3c481eda77cc9a91bc126b"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b">gridfire::GraphEngine::involvesSpecies</a></div><div class="ttdeci">bool involvesSpecies(const fourdst::atomic::Species &amp;species) const</div><div class="ttdoc">Checks if a given species is involved in the network.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00179">engine_graph.cpp:179</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ad049a295e2bb0f3e97b76d5742875119"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119">gridfire::GraphEngine::generateJacobianMatrix</a></div><div class="ttdeci">void generateJacobianMatrix(const std::vector&lt; double &gt; &amp;Y_dynamic, const double T9, const double rho) const override</div><div class="ttdoc">Generates the Jacobian matrix for the current state.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00654">engine_graph.cpp:654</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_adac8c7d62bae76e17fc060e86dadd929"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929">gridfire::GraphEngine::exportToDot</a></div><div class="ttdeci">void exportToDot(const std::string &amp;filename) const</div><div class="ttdoc">Exports the network to a DOT file for visualization.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00762">engine_graph.cpp:762</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_add98ece49ec5c538bddf3cc77004fe44"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#add98ece49ec5c538bddf3cc77004fe44">gridfire::GraphEngine::getPartitionFunction</a></div><div class="ttdeci">const partition::PartitionFunction &amp; getPartitionFunction() const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00641">engine_graph.cpp:641</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ae7a210d9ab13ad5fb0c612f027acabd0"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ae7a210d9ab13ad5fb0c612f027acabd0">gridfire::GraphEngine::isUsingReverseReactions</a></div><div class="ttdeci">bool isUsingReverseReactions() const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00409">engine_graph.cpp:409</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_af28950c5af3a92eb03a1a64ed0f913e7"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#af28950c5af3a92eb03a1a64ed0f913e7">gridfire::GraphEngine::calculateReverseRateTwoBodyDerivative</a></div><div class="ttdeci">double calculateReverseRateTwoBodyDerivative(const reaction::Reaction &amp;reaction, const double T9, const double reverseRate) const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00368">engine_graph.cpp:368</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ad049a295e2bb0f3e97b76d5742875119"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119">gridfire::GraphEngine::generateJacobianMatrix</a></div><div class="ttdeci">void generateJacobianMatrix(const std::vector&lt; double &gt; &amp;Y_dynamic, const double T9, const double rho) const override</div><div class="ttdoc">Generates the Jacobian matrix for the current state.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00632">engine_graph.cpp:632</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_adac8c7d62bae76e17fc060e86dadd929"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929">gridfire::GraphEngine::exportToDot</a></div><div class="ttdeci">void exportToDot(const std::string &amp;filename) const</div><div class="ttdoc">Exports the network to a DOT file for visualization.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00740">engine_graph.cpp:740</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_add98ece49ec5c538bddf3cc77004fe44"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#add98ece49ec5c538bddf3cc77004fe44">gridfire::GraphEngine::getPartitionFunction</a></div><div class="ttdeci">const partition::PartitionFunction &amp; getPartitionFunction() const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00619">engine_graph.cpp:619</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ae7a210d9ab13ad5fb0c612f027acabd0"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ae7a210d9ab13ad5fb0c612f027acabd0">gridfire::GraphEngine::isUsingReverseReactions</a></div><div class="ttdeci">bool isUsingReverseReactions() const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00387">engine_graph.cpp:387</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_af28950c5af3a92eb03a1a64ed0f913e7"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#af28950c5af3a92eb03a1a64ed0f913e7">gridfire::GraphEngine::calculateReverseRateTwoBodyDerivative</a></div><div class="ttdeci">double calculateReverseRateTwoBodyDerivative(const reaction::Reaction &amp;reaction, const double T9, const double reverseRate) const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00346">engine_graph.cpp:346</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a1e04e8cb8c84b1bd033ac599accf0888"><div class="ttname"><a href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a1e04e8cb8c84b1bd033ac599accf0888">gridfire::MultiscalePartitioningEngineView::getDynamicSpecies</a></div><div class="ttdeci">const std::vector&lt; fourdst::atomic::Species &gt; &amp; getDynamicSpecies() const</div><div class="ttdoc">Gets the dynamic species in the network.</div><div class="ttdef"><b>Definition</b> <a href="engine__multiscale_8cpp_source.html#l00789">engine_multiscale.cpp:789</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a22bd1f0e821ed415611d75bac67063d1"><div class="ttname"><a href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a22bd1f0e821ed415611d75bac67063d1">gridfire::MultiscalePartitioningEngineView::getBaseEngine</a></div><div class="ttdeci">const DynamicEngine &amp; getBaseEngine() const override</div><div class="ttdoc">Gets the base engine.</div><div class="ttdef"><b>Definition</b> <a href="engine__multiscale_8cpp_source.html#l00412">engine_multiscale.cpp:412</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a3c82e4e082d1c82b1b090ac9847c7c5e"><div class="ttname"><a href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a3c82e4e082d1c82b1b090ac9847c7c5e">gridfire::MultiscalePartitioningEngineView::getFastSpecies</a></div><div class="ttdeci">std::vector&lt; fourdst::atomic::Species &gt; getFastSpecies() const</div><div class="ttdoc">Gets the fast species in the network.</div><div class="ttdef"><b>Definition</b> <a href="engine__multiscale_8cpp_source.html#l00776">engine_multiscale.cpp:776</a></div></div>