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docs(docs): rebuilt docs

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Emily Boudreaux
2025-11-24 09:08:28 -05:00
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@@ -105,32 +105,31 @@ $(function(){initNavTree('class_py_dynamic_engine.html',''); initResizable(true)
<p>This is the complete list of members for <a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a>, including all inherited members.</p>
<table class="directory">
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a09eb8874b0c687aacc84a7bc7a5e2330">calculateEpsDerivatives</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a1b7f2e7c92b4702efcabe7c2a1faa153">calculateMolarReactionFlow</a>(const gridfire::reaction::Reaction &amp;reaction, const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a6bd76ef1df93d361bf5791270390c914">calculateRHSAndEnergy</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a6c5397f57fb9e115495188a1d2296147">collectComposition</a>(fourdst::composition::Composition &amp;comp) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2a63d0132254983a2143f31e863a5c18">generateJacobianMatrix</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#aae45b9260d0ec645213541c96b48a468">generateJacobianMatrix</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho, const std::vector&lt; fourdst::atomic::Species &gt; &amp;activeSpecies) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a36f2dbd2278608fe8a4ef7f08d7e4963">generateJacobianMatrix</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho, const gridfire::SparsityPattern &amp;sparsityPattern) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2066649ca11a869c054079ea12d8d0e9">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#adba68716d832b6100e08d32fbc36f13c">getDepth</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a63bbe8f6d3849e99dd41b6d9613ff1f0">getJacobianMatrixEntry</a>(const fourdst::atomic::Species &amp;rowSpecies, const fourdst::atomic::Species &amp;colSpecies) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a1d5143640666631501cf229bc491516e">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#afc745e7ab5da5d8b3cf916044515cd7d">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ab4cfdca5e15957c5cef75ffa6dedeee5">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a16c27e5af29ddf187e5ab82a6e6db57b">getSpeciesDestructionTimescales</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a95d10a7b240d543a1bc6c67ddf2dc8e0">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a598eb1575937d165b4b383959cf8c417">getSpeciesTimescales</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a3dd5cf419f25e76e144af35df15a2067">getStoichiometryMatrixEntry</a>(const fourdst::atomic::Species &amp;species, const gridfire::reaction::Reaction &amp;reaction) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a55bf19ed7534a312a36faf74753f7b14">isStale</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a09eb8874b0c687aacc84a7bc7a5e2330">calculateEpsDerivatives</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a8facba88b6df6e016ce53a0ff3cff125">calculateMolarReactionFlow</a>(const gridfire::reaction::Reaction &amp;reaction, const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a339e7238d290665ae9823c701e0ba32e">calculateRHSAndEnergy</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a6c5397f57fb9e115495188a1d2296147">collectComposition</a>(fourdst::composition::Composition &amp;comp) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2a63d0132254983a2143f31e863a5c18">generateJacobianMatrix</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2c0a465848ed6da8d3aaef5f6824375d">generateJacobianMatrix</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho, const std::vector&lt; fourdst::atomic::Species &gt; &amp;activeSpecies) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a36f2dbd2278608fe8a4ef7f08d7e4963">generateJacobianMatrix</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho, const gridfire::SparsityPattern &amp;sparsityPattern) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2066649ca11a869c054079ea12d8d0e9">generateStoichiometryMatrix</a>() override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#adba68716d832b6100e08d32fbc36f13c">getDepth</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a63bbe8f6d3849e99dd41b6d9613ff1f0">getJacobianMatrixEntry</a>(const fourdst::atomic::Species &amp;rowSpecies, const fourdst::atomic::Species &amp;colSpecies) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a1d5143640666631501cf229bc491516e">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#afc745e7ab5da5d8b3cf916044515cd7d">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ab4cfdca5e15957c5cef75ffa6dedeee5">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a16c27e5af29ddf187e5ab82a6e6db57b">getSpeciesDestructionTimescales</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a95d10a7b240d543a1bc6c67ddf2dc8e0">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a8bbf2956e0a3d01065c14e74cdc71626">getSpeciesTimescales</a>(const fourdst::composition::CompositionAbstract &amp;comp, double T9, double rho) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a3dd5cf419f25e76e144af35df15a2067">getStoichiometryMatrixEntry</a>(const fourdst::atomic::Species &amp;species, const gridfire::reaction::Reaction &amp;reaction) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a55bf19ed7534a312a36faf74753f7b14">isStale</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a2246382b1c98ba69cdb419bba63a6d03">m_species_cache</a></td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a61bb4b430fe740cfb2c24e5cc673e4ac">mapNetInToMolarAbundanceVector</a>(const gridfire::NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ac22a10412be6649bf379e6d61113c878">primeEngine</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a3d30a9116825ab2c5c209bc2712126bc">rebuild</a>(const fourdst::composition::Composition &amp;comp, gridfire::BuildDepthType depth) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#af469cba3be850d53f659ec173f0eb4e4">setNetworkReactions</a>(const gridfire::reaction::ReactionSet &amp;reactions) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#afa3abfd612033336a656f092721c14ac">setScreeningModel</a>(gridfire::screening::ScreeningType model) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#af8e6a8cd44f278535d7bcc9a896d6da8">update</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a61bb4b430fe740cfb2c24e5cc673e4ac">mapNetInToMolarAbundanceVector</a>(const gridfire::NetIn &amp;netIn) const override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#ac22a10412be6649bf379e6d61113c878">primeEngine</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#a8e39a86c2ba1ac7f1669362554f07fcf">rebuild</a>(const fourdst::composition::CompositionAbstract &amp;comp, gridfire::BuildDepthType depth) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#af469cba3be850d53f659ec173f0eb4e4">setNetworkReactions</a>(const gridfire::reaction::ReactionSet &amp;reactions) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#afa3abfd612033336a656f092721c14ac">setScreeningModel</a>(gridfire::screening::ScreeningType model) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="class_py_dynamic_engine.html#af8e6a8cd44f278535d7bcc9a896d6da8">update</a>(const gridfire::NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="class_py_dynamic_engine.html">PyDynamicEngine</a></td><td class="entry"></td></tr>
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