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refactor(.gitignore): removed html/ from .gitignore

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This commit is contained in:
Emily Boudreaux
2025-07-01 11:40:51 -04:00
parent 0c16e81e98
commit 7df6f60912
197 changed files with 6248 additions and 4744 deletions
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docs/html/classgridfire_1_1_graph_engine-members.html
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@@ -120,30 +120,35 @@ $(function(){initNavTree('classgridfire_1_1_graph_engine.html',''); initResizabl
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9">getNetReactionStoichiometry</a>(const reaction::Reaction &amp;reaction)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ad45650d10fc5dff1673ae3f806d067da">getNetworkReactions</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</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_graph_engine.html#a0ed390f3e598ebba4e245ac90bb78767">getNetworkSpecies</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</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_graph_engine.html#a26215593544c3a52597194602e4e25dd">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</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_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152">getStoichiometryMatrixEntry</a>(const int speciesIndex, const int reactionIndex) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</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_graph_engine.html#a9f74786ff930ab72664b31f29d05a30c">GraphEngine</a>(const fourdst::composition::Composition &amp;composition)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a9c285e3a38de6e73503a4e19666678e2">GraphEngine</a>(reaction::LogicalReactionSet reactions)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b">involvesSpecies</a>(const fourdst::atomic::Species &amp;species) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a3b17102b143435ddfdc015d7a50c4b18">m_config</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a0837bab6dcd111d9075c9343b90d64f1">m_constants</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">m_reactionIDMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567">populateReactionIDMap</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391">populateSpeciesToIndexMap</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889">recordADTape</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a5a5458ed01923124f2d7e1f04f32f138">reserveJacobianMatrix</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a697f2004e0d02c59e83c7890742d7c9a">getScreeningModel</a>() const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</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_graph_engine.html#a26215593544c3a52597194602e4e25dd">getSpeciesTimescales</a>(const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</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_graph_engine.html#a6b5feaf788bade212b7c8df7ac8c8152">getStoichiometryMatrixEntry</a>(const int speciesIndex, const int reactionIndex) const override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</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_graph_engine.html#a9f74786ff930ab72664b31f29d05a30c">GraphEngine</a>(const fourdst::composition::Composition &amp;composition)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a9c285e3a38de6e73503a4e19666678e2">GraphEngine</a>(reaction::LogicalReactionSet reactions)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">explicit</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b">involvesSpecies</a>(const fourdst::atomic::Species &amp;species) const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a3b17102b143435ddfdc015d7a50c4b18">m_config</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a0837bab6dcd111d9075c9343b90d64f1">m_constants</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a483979fc154adc88d029b3b672066d53">m_logger</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a5d6cc63b99b467c2a976d1fbaaa1dfa3">m_reactionIDMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#af17cf3762abac3efcab9a8e87c961210">m_screeningModel</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a52edc3e88f1e8fc497e1e63972d63c80">m_screeningType</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a></td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a26602e1b3c610780a47b5a6511d6d567">populateReactionIDMap</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a47202c43342b96480070874bffce1391">populateSpeciesToIndexMap</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a95563f6bc86007d9ee053a0f1e15b889">recordADTape</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a5a5458ed01923124f2d7e1f04f32f138">reserveJacobianMatrix</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a8110e687844f921438bb517e1d8ce62f">setScreeningModel</a>(screening::ScreeningType) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</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_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">syncInternalMaps</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aeeafeab40a5f4dbfae78bdc87e25e93f">validateComposition</a>(const fourdst::composition::Composition &amp;composition, double culling, double T9)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be">validateConservation</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</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>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a51b4cedf9b00de79fb6eef243631b04d">update</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</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_graph_engine.html#aeeafeab40a5f4dbfae78bdc87e25e93f">validateComposition</a>(const fourdst::composition::Composition &amp;composition, double culling, double T9)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be">validateConservation</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</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>
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