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docs(docs): rebuilt docs with loads more detail for triggers and weak reactions

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Emily Boudreaux
2025-10-08 11:17:09 -04:00
parent 8a0b5b2c36
commit 274c566726
600 changed files with 39207 additions and 9125 deletions
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docs/html/classgridfire_1_1_dynamic_engine-members.html
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@@ -105,28 +105,29 @@ $(function(){initNavTree('classgridfire_1_1_dynamic_engine.html',''); initResiza
<p>This is the complete list of members for <a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a>, including all inherited members.</p>
<table class="directory">
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">calculateMolarReactionFlow</a>(const reaction::Reaction &amp;reaction, const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb">calculateRHSAndEnergy</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a29bdd4231c29c3a4e524ad6ca66a127d">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7">generateJacobianMatrix</a>(const std::vector&lt; double &gt; &amp;Y_dynamic, double T9, double rho, const SparsityPattern &amp;sparsityPattern) const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</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="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">generateStoichiometryMatrix</a>()=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</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="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">getJacobianMatrixEntry</a>(int i, int j) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">getNetworkReactions</a>() const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">getNetworkSpecies</a>() const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">getScreeningModel</a>() const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a6ca0f315f75252ca505507a61556dda6">getSpeciesDestructionTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#ad3d56a8b9161b9cc7f4da51f6bf7e8c9">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a6772ac384b4c3d3e91712041e4aaa813">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">getStoichiometryMatrixEntry</a>(int speciesIndex, int reactionIndex) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a942e65ced17ca602482cc42e469d6398">isStale</a>(const NetIn &amp;netIn)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a55f1b7e5ebe2840e1d7c54665ca5411a">mapNetInToMolarAbundanceVector</a>(const NetIn &amp;netIn) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a21c34f59c080a853fafa38a25175124e">primeEngine</a>(const NetIn &amp;netIn)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">rebuild</a>(const fourdst::composition::Composition &amp;comp, BuildDepthType depth)</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</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="classgridfire_1_1_dynamic_engine.html#afb2ec904d88fc8aab516db4059d0e00f">setNetworkReactions</a>(const reaction::LogicalReactionSet &amp;reactions)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">setScreeningModel</a>(screening::ScreeningType model)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#aa799ff785e7e79bf35b11efd55f6282a">update</a>(const NetIn &amp;netIn)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure 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="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a264bd5a8891c8c5f0dff32867effe547">calculateEpsDerivatives</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a39cf5b738eea0a275bf8c0eb5789fab3">calculateMolarReactionFlow</a>(const reaction::Reaction &amp;reaction, const fourdst::composition::Composition &amp;comp, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#add48d3af9ebde17717e42e220e349740">calculateRHSAndEnergy</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a21d15531309456ee83f7675251e7a1bf">generateJacobianMatrix</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a11d602a708af4629f51873b17f7b8dbd">generateJacobianMatrix</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho, const SparsityPattern &amp;sparsityPattern) const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</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="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">generateStoichiometryMatrix</a>()=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</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="classgridfire_1_1_dynamic_engine.html#a88dbf350dc0ea3e2b64d825f489e0d60">getJacobianMatrixEntry</a>(const fourdst::atomic::Species &amp;rowSpecies, const fourdst::atomic::Species &amp;colSpecies) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#af496e04f7be9a0a51ac65dc95f901ffe">getNetworkReactions</a>() const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">getNetworkSpecies</a>() const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">getScreeningModel</a>() const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a25c040d3078f6ff2ef38f733eb68f1fa">getSpeciesDestructionTimescales</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a8f66fb76c9f983ee93bf8b95cdc85596">getSpeciesIndex</a>(const fourdst::atomic::Species &amp;species) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#ae7114f5ebc6667b5e5971c0450ed03d9">getSpeciesTimescales</a>(const fourdst::composition::Composition &amp;comp, double T9, double rho) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#ad19c8451b6f624e2938f771cc067d5c1">getStoichiometryMatrixEntry</a>(const fourdst::atomic::Species &amp;species, const reaction::Reaction &amp;reaction) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a942e65ced17ca602482cc42e469d6398">isStale</a>(const NetIn &amp;netIn)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a55f1b7e5ebe2840e1d7c54665ca5411a">mapNetInToMolarAbundanceVector</a>(const NetIn &amp;netIn) const =0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a21c34f59c080a853fafa38a25175124e">primeEngine</a>(const NetIn &amp;netIn)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">rebuild</a>(const fourdst::composition::Composition &amp;comp, BuildDepthType depth)</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</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="classgridfire_1_1_dynamic_engine.html#a49025489901e22a20cdf99b455ff2ff0">setNetworkReactions</a>(const reaction::ReactionSet &amp;reactions)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">setScreeningModel</a>(screening::ScreeningType model)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html#aa799ff785e7e79bf35b11efd55f6282a">update</a>(const NetIn &amp;netIn)=0</td><td class="entry"><a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr class="even"><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>
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