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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_adaptive_engine_view.html
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@@ -145,34 +145,36 @@ Public Member Functions</h2></td></tr>
<tr class="memitem:ac83a8efe25c0e5b9bf7756ac3a500bb1" id="r_ac83a8efe25c0e5b9bf7756ac3a500bb1"><td class="memItemLeft" align="right" valign="top">const std::vector&lt; fourdst::atomic::Species &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ac83a8efe25c0e5b9bf7756ac3a500bb1">getNetworkSpecies</a> () const override</td></tr>
<tr class="memdesc:ac83a8efe25c0e5b9bf7756ac3a500bb1"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the list of active species in the network. <br /></td></tr>
<tr class="separator:ac83a8efe25c0e5b9bf7756ac3a500bb1"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af703ad17ea65ffff4b75bf8ccc00e5d5" id="r_af703ad17ea65ffff4b75bf8ccc00e5d5"><td class="memItemLeft" align="right" valign="top">std::expected&lt; <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#af703ad17ea65ffff4b75bf8ccc00e5d5">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y_culled, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:af703ad17ea65ffff4b75bf8ccc00e5d5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the right-hand side (dY/dt) and energy generation for the active species. <br /></td></tr>
<tr class="separator:af703ad17ea65ffff4b75bf8ccc00e5d5"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a03fc187d3d306b9058103b9522cbbaeb" id="r_a03fc187d3d306b9058103b9522cbbaeb"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a03fc187d3d306b9058103b9522cbbaeb">generateJacobianMatrix</a> (const std::vector&lt; double &gt; &amp;Y_dynamic, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:a03fc187d3d306b9058103b9522cbbaeb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generates the Jacobian matrix for the active species. <br /></td></tr>
<tr class="separator:a03fc187d3d306b9058103b9522cbbaeb"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a4710d218c8a0fd161e994ecd60b48e58" id="r_a4710d218c8a0fd161e994ecd60b48e58"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a4710d218c8a0fd161e994ecd60b48e58">getJacobianMatrixEntry</a> (const int i_culled, const int j_culled) const override</td></tr>
<tr class="memdesc:a4710d218c8a0fd161e994ecd60b48e58"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets an entry from the Jacobian matrix for the active species. <br /></td></tr>
<tr class="separator:a4710d218c8a0fd161e994ecd60b48e58"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac5545d546166de94514871d7ad7b8669" id="r_ac5545d546166de94514871d7ad7b8669"><td class="memItemLeft" align="right" valign="top">std::expected&lt; <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ac5545d546166de94514871d7ad7b8669">calculateRHSAndEnergy</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="memdesc:ac5545d546166de94514871d7ad7b8669"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the right-hand side (dY/dt) and energy generation for the active species. <br /></td></tr>
<tr class="separator:ac5545d546166de94514871d7ad7b8669"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5d1b50afd2fba6af75e976a4f9c9dcbc" id="r_a5d1b50afd2fba6af75e976a4f9c9dcbc"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1_energy_derivatives.html">EnergyDerivatives</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a5d1b50afd2fba6af75e976a4f9c9dcbc">calculateEpsDerivatives</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="separator:a5d1b50afd2fba6af75e976a4f9c9dcbc"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8da7664cf483cba7f979f855a74c3559" id="r_a8da7664cf483cba7f979f855a74c3559"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a8da7664cf483cba7f979f855a74c3559">generateJacobianMatrix</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="memdesc:a8da7664cf483cba7f979f855a74c3559"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generates the Jacobian matrix for the active species. <br /></td></tr>
<tr class="separator:a8da7664cf483cba7f979f855a74c3559"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:adf3b8a5734983509ca02b7a1a480119f" id="r_adf3b8a5734983509ca02b7a1a480119f"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#adf3b8a5734983509ca02b7a1a480119f">getJacobianMatrixEntry</a> (const fourdst::atomic::Species &amp;rowSpecies, const fourdst::atomic::Species &amp;colSpecies) const override</td></tr>
<tr class="memdesc:adf3b8a5734983509ca02b7a1a480119f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets an entry from the Jacobian matrix for the active species. <br /></td></tr>
<tr class="separator:adf3b8a5734983509ca02b7a1a480119f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a231193a61ba5a31e8eb92b0d4ce69111" id="r_a231193a61ba5a31e8eb92b0d4ce69111"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a231193a61ba5a31e8eb92b0d4ce69111">generateStoichiometryMatrix</a> () override</td></tr>
<tr class="memdesc:a231193a61ba5a31e8eb92b0d4ce69111"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generates the stoichiometry matrix for the active reactions and species. <br /></td></tr>
<tr class="separator:a231193a61ba5a31e8eb92b0d4ce69111"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a67b4ea8cad115394bb4a42cc39d696f9" id="r_a67b4ea8cad115394bb4a42cc39d696f9"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a67b4ea8cad115394bb4a42cc39d696f9">getStoichiometryMatrixEntry</a> (const int speciesIndex_culled, const int reactionIndex_culled) const override</td></tr>
<tr class="memdesc:a67b4ea8cad115394bb4a42cc39d696f9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets an entry from the stoichiometry matrix for the active species and reactions. <br /></td></tr>
<tr class="separator:a67b4ea8cad115394bb4a42cc39d696f9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a048d4b1d41ecb4125a558d1b9ed7cb31" id="r_a048d4b1d41ecb4125a558d1b9ed7cb31"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a048d4b1d41ecb4125a558d1b9ed7cb31">calculateMolarReactionFlow</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;reaction, const std::vector&lt; double &gt; &amp;Y_culled, double T9, double rho) const override</td></tr>
<tr class="memdesc:a048d4b1d41ecb4125a558d1b9ed7cb31"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the molar reaction flow for a given reaction in the active network. <br /></td></tr>
<tr class="separator:a048d4b1d41ecb4125a558d1b9ed7cb31"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a12cc2f352678fba9688363ba1876ab9c" id="r_a12cc2f352678fba9688363ba1876ab9c"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a12cc2f352678fba9688363ba1876ab9c">getNetworkReactions</a> () const override</td></tr>
<tr class="memdesc:a12cc2f352678fba9688363ba1876ab9c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the set of active logical reactions in the network. <br /></td></tr>
<tr class="separator:a12cc2f352678fba9688363ba1876ab9c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7b3a6b3ab0a52f0f84d2b142e74ea672" id="r_a7b3a6b3ab0a52f0f84d2b142e74ea672"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a7b3a6b3ab0a52f0f84d2b142e74ea672">setNetworkReactions</a> (const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;reactions) override</td></tr>
<tr class="separator:a7b3a6b3ab0a52f0f84d2b142e74ea672"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a4e856d6d4d2fc220952bbb7e6b2f85d9" id="r_a4e856d6d4d2fc220952bbb7e6b2f85d9"><td class="memItemLeft" align="right" valign="top">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a4e856d6d4d2fc220952bbb7e6b2f85d9">getSpeciesTimescales</a> (const std::vector&lt; double &gt; &amp;Y_culled, double T9, double rho) const override</td></tr>
<tr class="memdesc:a4e856d6d4d2fc220952bbb7e6b2f85d9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Computes timescales for all active species in the network. <br /></td></tr>
<tr class="separator:a4e856d6d4d2fc220952bbb7e6b2f85d9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a522e78bce9ff062939572248d57f8cea" id="r_a522e78bce9ff062939572248d57f8cea"><td class="memItemLeft" align="right" valign="top">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a522e78bce9ff062939572248d57f8cea">getSpeciesDestructionTimescales</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td></tr>
<tr class="separator:a522e78bce9ff062939572248d57f8cea"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:abe2ca6426e10cc6a10090eecf7098dbe" id="r_abe2ca6426e10cc6a10090eecf7098dbe"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#abe2ca6426e10cc6a10090eecf7098dbe">getStoichiometryMatrixEntry</a> (const fourdst::atomic::Species &amp;species, const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;reaction) const override</td></tr>
<tr class="memdesc:abe2ca6426e10cc6a10090eecf7098dbe"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets an entry from the stoichiometry matrix for the active species and reactions. <br /></td></tr>
<tr class="separator:abe2ca6426e10cc6a10090eecf7098dbe"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a3c1e27b45051c4ba481a2b87513982ed" id="r_a3c1e27b45051c4ba481a2b87513982ed"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a3c1e27b45051c4ba481a2b87513982ed">calculateMolarReactionFlow</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;reaction, const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="memdesc:a3c1e27b45051c4ba481a2b87513982ed"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the molar reaction flow for a given reaction in the active network. <br /></td></tr>
<tr class="separator:a3c1e27b45051c4ba481a2b87513982ed"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a3247c1e6a76de5622223ee7b5ca3452a" id="r_a3247c1e6a76de5622223ee7b5ca3452a"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a3247c1e6a76de5622223ee7b5ca3452a">getNetworkReactions</a> () const override</td></tr>
<tr class="memdesc:a3247c1e6a76de5622223ee7b5ca3452a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the set of active logical reactions in the network. <br /></td></tr>
<tr class="separator:a3247c1e6a76de5622223ee7b5ca3452a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:adedc8547568d643473bdfcc86040b488" id="r_adedc8547568d643473bdfcc86040b488"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#adedc8547568d643473bdfcc86040b488">setNetworkReactions</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a> &amp;reactions) override</td></tr>
<tr class="separator:adedc8547568d643473bdfcc86040b488"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a57a218c5a145f589531777c8615b7408" id="r_a57a218c5a145f589531777c8615b7408"><td class="memItemLeft" align="right" valign="top">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a57a218c5a145f589531777c8615b7408">getSpeciesTimescales</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="memdesc:a57a218c5a145f589531777c8615b7408"><td class="mdescLeft">&#160;</td><td class="mdescRight">Computes timescales for all active species in the network. <br /></td></tr>
<tr class="separator:a57a218c5a145f589531777c8615b7408"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa861db5f6fc4e85fb51f524e4e1367c6" id="r_aa861db5f6fc4e85fb51f524e4e1367c6"><td class="memItemLeft" align="right" valign="top">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aa861db5f6fc4e85fb51f524e4e1367c6">getSpeciesDestructionTimescales</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="separator:aa861db5f6fc4e85fb51f524e4e1367c6"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aee095b30a9dce5fcb5ae2fa1d2aa192c" id="r_aee095b30a9dce5fcb5ae2fa1d2aa192c"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aee095b30a9dce5fcb5ae2fa1d2aa192c">getBaseEngine</a> () const override</td></tr>
<tr class="memdesc:aee095b30a9dce5fcb5ae2fa1d2aa192c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the base engine. <br /></td></tr>
<tr class="separator:aee095b30a9dce5fcb5ae2fa1d2aa192c"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -182,9 +184,9 @@ Public Member Functions</h2></td></tr>
<tr class="memitem:a0ab1199f900a58f309c3c36532c9164f" id="r_a0ab1199f900a58f309c3c36532c9164f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0ab1199f900a58f309c3c36532c9164f">getScreeningModel</a> () const override</td></tr>
<tr class="memdesc:a0ab1199f900a58f309c3c36532c9164f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the screening model from the base engine. <br /></td></tr>
<tr class="separator:a0ab1199f900a58f309c3c36532c9164f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a9055feb245524a5a9549ace935f059ff" id="r_a9055feb245524a5a9549ace935f059ff"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a9055feb245524a5a9549ace935f059ff">getSpeciesIndex</a> (const fourdst::atomic::Species &amp;species) const override</td></tr>
<tr class="memdesc:a9055feb245524a5a9549ace935f059ff"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the index of a species in the network. <br /></td></tr>
<tr class="separator:a9055feb245524a5a9549ace935f059ff"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:abb811382522c31f6456787edd4f59ace" id="r_abb811382522c31f6456787edd4f59ace"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#abb811382522c31f6456787edd4f59ace">getSpeciesIndex</a> (const fourdst::atomic::Species &amp;species) const override</td></tr>
<tr class="memdesc:abb811382522c31f6456787edd4f59ace"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the index of a species in the network. <br /></td></tr>
<tr class="separator:abb811382522c31f6456787edd4f59ace"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7d0237956bf3ec7230bc51d88e7f8019" id="r_a7d0237956bf3ec7230bc51d88e7f8019"><td class="memItemLeft" align="right" valign="top">std::vector&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a7d0237956bf3ec7230bc51d88e7f8019">mapNetInToMolarAbundanceVector</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) const override</td></tr>
<tr class="memdesc:a7d0237956bf3ec7230bc51d88e7f8019"><td class="mdescLeft">&#160;</td><td class="mdescRight">Map a <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> object to a vector of molar abundances. <br /></td></tr>
<tr class="separator:a7d0237956bf3ec7230bc51d88e7f8019"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -192,8 +194,8 @@ Public Member Functions</h2></td></tr>
<tr class="memdesc:a70005361262bc180d4417b608661e3c3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Prime the engine with initial conditions. <br /></td></tr>
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<tr class="inherit_header pub_methods_classgridfire_1_1_dynamic_engine"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_dynamic_engine')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></td></tr>
<tr class="memitem:a818d942efa843959393e4eed3263b7e7 inherit pub_methods_classgridfire_1_1_dynamic_engine" id="r_a818d942efa843959393e4eed3263b7e7"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><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 <a class="el" href="namespacegridfire.html#a898dfe22579e649935645cbd6f073178">SparsityPattern</a> &amp;sparsityPattern) const</td></tr>
<tr class="separator:a818d942efa843959393e4eed3263b7e7 inherit pub_methods_classgridfire_1_1_dynamic_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a11d602a708af4629f51873b17f7b8dbd inherit pub_methods_classgridfire_1_1_dynamic_engine" id="r_a11d602a708af4629f51873b17f7b8dbd"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a11d602a708af4629f51873b17f7b8dbd">generateJacobianMatrix</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho, const <a class="el" href="namespacegridfire.html#a898dfe22579e649935645cbd6f073178">SparsityPattern</a> &amp;sparsityPattern) const</td></tr>
<tr class="separator:a11d602a708af4629f51873b17f7b8dbd inherit pub_methods_classgridfire_1_1_dynamic_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a04317b66ef14d519264bc30ee69f5bf9 inherit pub_methods_classgridfire_1_1_dynamic_engine" id="r_a04317b66ef14d519264bc30ee69f5bf9"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="namespacegridfire.html#a3b1f70dc7ff5b501809330a97079e4f6">BuildDepthType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">getDepth</a> () const</td></tr>
<tr class="memdesc:a04317b66ef14d519264bc30ee69f5bf9 inherit pub_methods_classgridfire_1_1_dynamic_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the depth of the network. <br /></td></tr>
<tr class="separator:a04317b66ef14d519264bc30ee69f5bf9 inherit pub_methods_classgridfire_1_1_dynamic_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -215,8 +217,8 @@ Private Types</h2></td></tr>
<tr class="separator:afec39b2faa34ea65c5488dd8e11ba3c3"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5eaf7c3a4e28cd3a4f34979b88a80103" id="r_a5eaf7c3a4e28cd3a4f34979b88a80103"><td class="memItemLeft" align="right" valign="top">using&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a5eaf7c3a4e28cd3a4f34979b88a80103">LogManager</a> = fourdst::logging::LogManager</td></tr>
<tr class="separator:a5eaf7c3a4e28cd3a4f34979b88a80103"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a4ff60b5214ec0bdaf683feb6615573a5" id="r_a4ff60b5214ec0bdaf683feb6615573a5"><td class="memItemLeft" align="right" valign="top">typedef std::pair&lt; std::unordered_set&lt; const <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html">reaction::LogicalReaction</a> * &gt;, std::unordered_set&lt; fourdst::atomic::Species &gt; &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a4ff60b5214ec0bdaf683feb6615573a5">RescueSet</a></td></tr>
<tr class="separator:a4ff60b5214ec0bdaf683feb6615573a5"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac674338ddcbae4c33dd84b0441631806" id="r_ac674338ddcbae4c33dd84b0441631806"><td class="memItemLeft" align="right" valign="top">typedef std::pair&lt; std::unordered_set&lt; const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> * &gt;, std::unordered_set&lt; fourdst::atomic::Species &gt; &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ac674338ddcbae4c33dd84b0441631806">RescueSet</a></td></tr>
<tr class="separator:ac674338ddcbae4c33dd84b0441631806"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
Private Member Functions</h2></td></tr>
@@ -241,20 +243,20 @@ Private Member Functions</h2></td></tr>
<tr class="memitem:aedc0dedb51c81e03f253cc409a5d5c40" id="r_aedc0dedb51c81e03f253cc409a5d5c40"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aedc0dedb51c81e03f253cc409a5d5c40">validateState</a> () const</td></tr>
<tr class="memdesc:aedc0dedb51c81e03f253cc409a5d5c40"><td class="mdescLeft">&#160;</td><td class="mdescRight">Validates that the <a class="el" href="classgridfire_1_1_adaptive_engine_view.html" title="An engine view that dynamically adapts the reaction network based on runtime conditions.">AdaptiveEngineView</a> is not stale. <br /></td></tr>
<tr class="separator:aedc0dedb51c81e03f253cc409a5d5c40"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:abdbaf4b87629efe43ac1255dad424c0c" id="r_abdbaf4b87629efe43ac1255dad424c0c"><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html">ReactionFlow</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#abdbaf4b87629efe43ac1255dad424c0c">calculateAllReactionFlows</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn, std::vector&lt; double &gt; &amp;out_Y_Full) const</td></tr>
<tr class="memdesc:abdbaf4b87629efe43ac1255dad424c0c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the molar reaction flow rate for all reactions in the full network. <br /></td></tr>
<tr class="separator:abdbaf4b87629efe43ac1255dad424c0c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab5397d217039f096acededd4d2779780" id="r_ab5397d217039f096acededd4d2779780"><td class="memItemLeft" align="right" valign="top">std::pair&lt; std::vector&lt; <a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html">ReactionFlow</a> &gt;, fourdst::composition::Composition &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ab5397d217039f096acededd4d2779780">calculateAllReactionFlows</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) const</td></tr>
<tr class="memdesc:ab5397d217039f096acededd4d2779780"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the molar reaction flow rate for all reactions in the full network. <br /></td></tr>
<tr class="separator:ab5397d217039f096acededd4d2779780"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0ed21f7e7c1034fc87b40d4116c4221b" id="r_a0ed21f7e7c1034fc87b40d4116c4221b"><td class="memItemLeft" align="right" valign="top">std::unordered_set&lt; fourdst::atomic::Species &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0ed21f7e7c1034fc87b40d4116c4221b">findReachableSpecies</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) const</td></tr>
<tr class="memdesc:a0ed21f7e7c1034fc87b40d4116c4221b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Finds all species that are reachable from the initial fuel through the reaction network. <br /></td></tr>
<tr class="separator:a0ed21f7e7c1034fc87b40d4116c4221b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a42417e96fe9fd623458af109401daf08" id="r_a42417e96fe9fd623458af109401daf08"><td class="memItemLeft" align="right" valign="top">std::vector&lt; const <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html">reaction::LogicalReaction</a> * &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a42417e96fe9fd623458af109401daf08">cullReactionsByFlow</a> (const std::vector&lt; <a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html">ReactionFlow</a> &gt; &amp;allFlows, const std::unordered_set&lt; fourdst::atomic::Species &gt; &amp;reachableSpecies, const std::vector&lt; double &gt; &amp;Y_full, double maxFlow) const</td></tr>
<tr class="memdesc:a42417e96fe9fd623458af109401daf08"><td class="mdescLeft">&#160;</td><td class="mdescRight">Culls reactions from the network based on their flow rates. <br /></td></tr>
<tr class="separator:a42417e96fe9fd623458af109401daf08"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a823c665ba89452aa2b3d5422fa5d313f" id="r_a823c665ba89452aa2b3d5422fa5d313f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="#a4ff60b5214ec0bdaf683feb6615573a5">RescueSet</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a823c665ba89452aa2b3d5422fa5d313f">rescueEdgeSpeciesDestructionChannel</a> (const std::vector&lt; double &gt; &amp;Y_full, const double T9, const double rho, const std::vector&lt; fourdst::atomic::Species &gt; &amp;activeSpecies, const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;activeReactions) const</td></tr>
<tr class="separator:a823c665ba89452aa2b3d5422fa5d313f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa79fb382c98461b02a2c30668491e6c5" id="r_aa79fb382c98461b02a2c30668491e6c5"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aa79fb382c98461b02a2c30668491e6c5">finalizeActiveSet</a> (const std::vector&lt; const <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html">reaction::LogicalReaction</a> * &gt; &amp;finalReactions)</td></tr>
<tr class="memdesc:aa79fb382c98461b02a2c30668491e6c5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Finalizes the set of active species and reactions. <br /></td></tr>
<tr class="separator:aa79fb382c98461b02a2c30668491e6c5"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a95fbfb7f2bdbf80195f1ea0aff8d62fb" id="r_a95fbfb7f2bdbf80195f1ea0aff8d62fb"><td class="memItemLeft" align="right" valign="top">std::vector&lt; const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> * &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a95fbfb7f2bdbf80195f1ea0aff8d62fb">cullReactionsByFlow</a> (const std::vector&lt; <a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html">ReactionFlow</a> &gt; &amp;allFlows, const std::unordered_set&lt; fourdst::atomic::Species &gt; &amp;reachableSpecies, const fourdst::composition::Composition &amp;comp, double maxFlow) const</td></tr>
<tr class="memdesc:a95fbfb7f2bdbf80195f1ea0aff8d62fb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Culls reactions from the network based on their flow rates. <br /></td></tr>
<tr class="separator:a95fbfb7f2bdbf80195f1ea0aff8d62fb"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0439f464865b4c01bad0f6be6055c3fc" id="r_a0439f464865b4c01bad0f6be6055c3fc"><td class="memItemLeft" align="right" valign="top"><a class="el" href="#ac674338ddcbae4c33dd84b0441631806">RescueSet</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0439f464865b4c01bad0f6be6055c3fc">rescueEdgeSpeciesDestructionChannel</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho, const std::vector&lt; fourdst::atomic::Species &gt; &amp;activeSpecies, const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a> &amp;activeReactions) const</td></tr>
<tr class="separator:a0439f464865b4c01bad0f6be6055c3fc"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7b8b3a786b973e4383e721358e61b7ed" id="r_a7b8b3a786b973e4383e721358e61b7ed"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a7b8b3a786b973e4383e721358e61b7ed">finalizeActiveSet</a> (const std::vector&lt; const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> * &gt; &amp;finalReactions)</td></tr>
<tr class="memdesc:a7b8b3a786b973e4383e721358e61b7ed"><td class="mdescLeft">&#160;</td><td class="mdescRight">Finalizes the set of active species and reactions. <br /></td></tr>
<tr class="separator:a7b8b3a786b973e4383e721358e61b7ed"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
Private Attributes</h2></td></tr>
@@ -270,9 +272,9 @@ Private Attributes</h2></td></tr>
<tr class="memitem:af4bc9fc6e4afcd6a53c49ca6e2a95940" id="r_af4bc9fc6e4afcd6a53c49ca6e2a95940"><td class="memItemLeft" align="right" valign="top">std::vector&lt; fourdst::atomic::Species &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#af4bc9fc6e4afcd6a53c49ca6e2a95940">m_activeSpecies</a></td></tr>
<tr class="memdesc:af4bc9fc6e4afcd6a53c49ca6e2a95940"><td class="mdescLeft">&#160;</td><td class="mdescRight">The set of species that are currently active in the network. <br /></td></tr>
<tr class="separator:af4bc9fc6e4afcd6a53c49ca6e2a95940"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a19fc7e02e216b797aa643fa35e429800" id="r_a19fc7e02e216b797aa643fa35e429800"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a19fc7e02e216b797aa643fa35e429800">m_activeReactions</a></td></tr>
<tr class="memdesc:a19fc7e02e216b797aa643fa35e429800"><td class="mdescLeft">&#160;</td><td class="mdescRight">The set of reactions that are currently active in the network. <br /></td></tr>
<tr class="separator:a19fc7e02e216b797aa643fa35e429800"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab5ab06941bf6d97007d0a76658bf2aa6" id="r_ab5ab06941bf6d97007d0a76658bf2aa6"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ab5ab06941bf6d97007d0a76658bf2aa6">m_activeReactions</a></td></tr>
<tr class="memdesc:ab5ab06941bf6d97007d0a76658bf2aa6"><td class="mdescLeft">&#160;</td><td class="mdescRight">The set of reactions that are currently active in the network. <br /></td></tr>
<tr class="separator:ab5ab06941bf6d97007d0a76658bf2aa6"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5f66204a0ff5b27eed243afddecb0093" id="r_a5f66204a0ff5b27eed243afddecb0093"><td class="memItemLeft" align="right" valign="top">std::vector&lt; size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a5f66204a0ff5b27eed243afddecb0093">m_speciesIndexMap</a></td></tr>
<tr class="memdesc:a5f66204a0ff5b27eed243afddecb0093"><td class="mdescLeft">&#160;</td><td class="mdescRight">A map from the indices of the active species to the indices of the corresponding species in the full network. <br /></td></tr>
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@@ -345,8 +347,8 @@ Private Attributes</h2></td></tr>
</div>
</div>
<a id="a4ff60b5214ec0bdaf683feb6615573a5" name="a4ff60b5214ec0bdaf683feb6615573a5"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a4ff60b5214ec0bdaf683feb6615573a5">&#9670;&#160;</a></span>RescueSet</h2>
<a id="ac674338ddcbae4c33dd84b0441631806" name="ac674338ddcbae4c33dd84b0441631806"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ac674338ddcbae4c33dd84b0441631806">&#9670;&#160;</a></span>RescueSet</h2>
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@@ -355,7 +357,7 @@ Private Attributes</h2></td></tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">typedef std::pair&lt;std::unordered_set&lt;const <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html">reaction::LogicalReaction</a>*&gt;, std::unordered_set&lt;fourdst::atomic::Species&gt; &gt; <a class="el" href="#a4ff60b5214ec0bdaf683feb6615573a5">gridfire::AdaptiveEngineView::RescueSet</a></td>
<td class="memname">typedef std::pair&lt;std::unordered_set&lt;const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a>*&gt;, std::unordered_set&lt;fourdst::atomic::Species&gt; &gt; <a class="el" href="#ac674338ddcbae4c33dd84b0441631806">gridfire::AdaptiveEngineView::RescueSet</a></td>
</tr>
</table>
</td>
@@ -403,8 +405,8 @@ Private Attributes</h2></td></tr>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a id="abdbaf4b87629efe43ac1255dad424c0c" name="abdbaf4b87629efe43ac1255dad424c0c"></a>
<h2 class="memtitle"><span class="permalink"><a href="#abdbaf4b87629efe43ac1255dad424c0c">&#9670;&#160;</a></span>calculateAllReactionFlows()</h2>
<a id="ab5397d217039f096acededd4d2779780" name="ab5397d217039f096acededd4d2779780"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ab5397d217039f096acededd4d2779780">&#9670;&#160;</a></span>calculateAllReactionFlows()</h2>
<div class="memitem">
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@@ -413,14 +415,10 @@ Private Attributes</h2></td></tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::vector&lt; <a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html">AdaptiveEngineView::ReactionFlow</a> &gt; gridfire::AdaptiveEngineView::calculateAllReactionFlows </td>
<td class="memname">std::pair&lt; std::vector&lt; <a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html">AdaptiveEngineView::ReactionFlow</a> &gt;, fourdst::composition::Composition &gt; gridfire::AdaptiveEngineView::calculateAllReactionFlows </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td> <td class="paramname"><span class="paramname"><em>netIn</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>out_Y_Full</em></span>&#160;) const</td>
<td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;</td> <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
@@ -435,13 +433,11 @@ Private Attributes</h2></td></tr>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">netIn</td><td>The current network input, containing temperature, density, and composition. </td></tr>
<tr><td class="paramname">out_Y_Full</td><td>A vector that will be populated with the molar abundances of all species in the full network. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>A vector of <a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html" title="A struct to hold a reaction and its flow rate.">ReactionFlow</a> structs, each containing a pointer to a reaction and its calculated flow rate.</dd></dl>
<dl class="section return"><dt>Returns</dt><dd>A pair with the first element a vector of <a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html" title="A struct to hold a reaction and its flow rate.">ReactionFlow</a> structs, each containing a pointer to a reaction and its calculated flow rate and the second being a composition object where species which were not present in netIn but are present in the definition of the base engine are registered but have 0 mass fraction.</dd></dl>
<dl class="section user"><dt>Algorithm:</dt><dd><ol type="1">
<li>Clears and reserves space in <code>out_Y_Full</code>.</li>
<li>Iterates through all species in the base engine's network.</li>
<li>For each species, it retrieves the molar abundance from <code>netIn.composition</code>. If the species is not found, its abundance is set to 0.0.</li>
<li>Converts the temperature from Kelvin to T9.</li>
@@ -453,8 +449,53 @@ Private Attributes</h2></td></tr>
</div>
</div>
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<h2 class="memtitle"><span class="permalink"><a href="#a048d4b1d41ecb4125a558d1b9ed7cb31">&#9670;&#160;</a></span>calculateMolarReactionFlow()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a5d1b50afd2fba6af75e976a4f9c9dcbc">&#9670;&#160;</a></span>calculateEpsDerivatives()</h2>
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<td class="memname"><a class="el" href="structgridfire_1_1_energy_derivatives.html">EnergyDerivatives</a> gridfire::AdaptiveEngineView::calculateEpsDerivatives </td>
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<td class="paramtype">const fourdst::composition::Composition &amp;</td> <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
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<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
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<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
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<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">comp</td><td>The current composition of the system. </td></tr>
<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>The density in g/cm^3. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>A struct containing the derivatives of the energy generation rate with respect to temperature and density. </dd></dl>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a264bd5a8891c8c5f0dff32867effe547">gridfire::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a3c1e27b45051c4ba481a2b87513982ed">&#9670;&#160;</a></span>calculateMolarReactionFlow()</h2>
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@@ -470,7 +511,7 @@ Private Attributes</h2></td></tr>
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<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_culled</em></span>, </td>
<td class="paramtype">const fourdst::composition::Composition &amp;</td> <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">reaction</td><td>The reaction for which to calculate the flow. </td></tr>
<tr><td class="paramname">Y_culled</td><td>Vector of current abundances for the active species. </td></tr>
<tr><td class="paramname">comp</td><td>Composition object containing current abundances. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
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@@ -510,12 +551,12 @@ Private Attributes</h2></td></tr>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine</a>.</p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a39cf5b738eea0a275bf8c0eb5789fab3">gridfire::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#af703ad17ea65ffff4b75bf8ccc00e5d5">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#ac5545d546166de94514871d7ad7b8669">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
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@@ -526,17 +567,17 @@ Private Attributes</h2></td></tr>
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<td class="memname">std::expected&lt; <a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::AdaptiveEngineView::calculateRHSAndEnergy </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_culled</em></span>, </td>
<td class="paramtype">const fourdst::composition::Composition &amp;</td> <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
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<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
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<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
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@@ -549,7 +590,7 @@ Private Attributes</h2></td></tr>
<p>Calculates the right-hand side (dY/dt) and energy generation for the active species. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">Y_culled</td><td>A vector of abundances for the active species. </td></tr>
<tr><td class="paramname">comp</td><td>The current composition of the system. </td></tr>
<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>The density in g/cm^3. </td></tr>
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@@ -565,7 +606,7 @@ Private Attributes</h2></td></tr>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
<p>Implements <a class="el" href="classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb">gridfire::Engine</a>.</p>
<p>Implements <a class="el" href="classgridfire_1_1_engine.html#add48d3af9ebde17717e42e220e349740">gridfire::Engine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a42417e96fe9fd623458af109401daf08">&#9670;&#160;</a></span>cullReactionsByFlow()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a95fbfb7f2bdbf80195f1ea0aff8d62fb">&#9670;&#160;</a></span>cullReactionsByFlow()</h2>
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<td class="memname">std::vector&lt; const <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html">reaction::LogicalReaction</a> * &gt; gridfire::AdaptiveEngineView::cullReactionsByFlow </td>
<td class="memname">std::vector&lt; const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> * &gt; gridfire::AdaptiveEngineView::cullReactionsByFlow </td>
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<td class="paramtype">const std::vector&lt; <a class="el" href="structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html">ReactionFlow</a> &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>allFlows</em></span>, </td>
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<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_full</em></span>, </td>
<td class="paramtype">const fourdst::composition::Composition &amp;</td> <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
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<tr><td class="paramname">allFlows</td><td>A vector of all reactions and their flow rates. </td></tr>
<tr><td class="paramname">reachableSpecies</td><td>A set of all species reachable from the initial fuel. </td></tr>
<tr><td class="paramname">Y_full</td><td>A vector of molar abundances for all species in the full network. </td></tr>
<tr><td class="paramname">comp</td><td>The current composition of the system. </td></tr>
<tr><td class="paramname">maxFlow</td><td>The maximum reaction flow rate in the network. </td></tr>
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<h2 class="memtitle"><span class="permalink"><a href="#aa79fb382c98461b02a2c30668491e6c5">&#9670;&#160;</a></span>finalizeActiveSet()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a7b8b3a786b973e4383e721358e61b7ed">&#9670;&#160;</a></span>finalizeActiveSet()</h2>
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<td class="memname">void gridfire::AdaptiveEngineView::finalizeActiveSet </td>
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<td class="paramtype">const std::vector&lt; const <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html">reaction::LogicalReaction</a> * &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>finalReactions</em></span></td><td>)</td>
<td class="paramtype">const std::vector&lt; const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> * &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>finalReactions</em></span></td><td>)</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a03fc187d3d306b9058103b9522cbbaeb">&#9670;&#160;</a></span>generateJacobianMatrix()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a8da7664cf483cba7f979f855a74c3559">&#9670;&#160;</a></span>generateJacobianMatrix()</h2>
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<td class="memname">void gridfire::AdaptiveEngineView::generateJacobianMatrix </td>
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<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_dynamic</em></span>, </td>
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<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
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<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
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<p>Generates the Jacobian matrix for the active species. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">Y_dynamic</td><td>A vector of abundances for the active species. </td></tr>
<tr><td class="paramname">comp</td><td>The current composition of the system. </td></tr>
<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>The density in g/cm^3.</td></tr>
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@@ -822,7 +863,7 @@ Private Attributes</h2></td></tr>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a29bdd4231c29c3a4e524ad6ca66a127d">gridfire::DynamicEngine</a>.</p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a21d15531309456ee83f7675251e7a1bf">gridfire::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a4710d218c8a0fd161e994ecd60b48e58">&#9670;&#160;</a></span>getJacobianMatrixEntry()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#adf3b8a5734983509ca02b7a1a480119f">&#9670;&#160;</a></span>getJacobianMatrixEntry()</h2>
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<td class="memname">double gridfire::AdaptiveEngineView::getJacobianMatrixEntry </td>
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<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>i_culled</em></span>, </td>
<td class="paramtype">const fourdst::atomic::Species &amp;</td> <td class="paramname"><span class="paramname"><em>rowSpecies</em></span>, </td>
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<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>j_culled</em></span>&#160;) const</td>
<td class="paramtype">const fourdst::atomic::Species &amp;</td> <td class="paramname"><span class="paramname"><em>colSpecies</em></span>&#160;) const</td>
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@@ -923,8 +964,8 @@ Private Attributes</h2></td></tr>
<p>Gets an entry from the Jacobian matrix for the active species. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">i_culled</td><td>The row index (species index) in the culled matrix. </td></tr>
<tr><td class="paramname">j_culled</td><td>The column index (species index) in the culled matrix. </td></tr>
<tr><td class="paramname">rowSpecies</td><td>The species corresponding to the row index in the culled species list. </td></tr>
<tr><td class="paramname">colSpecies</td><td>The species corresponding to the column index in the culled species list </td></tr>
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@@ -939,12 +980,12 @@ Private Attributes</h2></td></tr>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">gridfire::DynamicEngine</a>.</p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a88dbf350dc0ea3e2b64d825f489e0d60">gridfire::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a12cc2f352678fba9688363ba1876ab9c">&#9670;&#160;</a></span>getNetworkReactions()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a3247c1e6a76de5622223ee7b5ca3452a">&#9670;&#160;</a></span>getNetworkReactions()</h2>
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<td class="memname">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp; gridfire::AdaptiveEngineView::getNetworkReactions </td>
<td class="memname">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a> &amp; gridfire::AdaptiveEngineView::getNetworkReactions </td>
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@@ -967,9 +1008,9 @@ Private Attributes</h2></td></tr>
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<p>Gets the set of active logical reactions in the network. </p>
<dl class="section return"><dt>Returns</dt><dd>Reference to the <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31" title="A set of logical reactions.">LogicalReactionSet</a> containing all active reactions. </dd></dl>
<dl class="section return"><dt>Returns</dt><dd>Reference to the LogicalReactionSet containing all active reactions. </dd></dl>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">gridfire::DynamicEngine</a>.</p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#af496e04f7be9a0a51ac65dc95f901ffe">gridfire::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a522e78bce9ff062939572248d57f8cea">&#9670;&#160;</a></span>getSpeciesDestructionTimescales()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#aa861db5f6fc4e85fb51f524e4e1367c6">&#9670;&#160;</a></span>getSpeciesDestructionTimescales()</h2>
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<td class="memname">std::expected&lt; std::unordered_map&lt; fourdst::atomic::Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::AdaptiveEngineView::getSpeciesDestructionTimescales </td>
<td class="memname">std::expected&lt; std::unordered_map&lt; Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::AdaptiveEngineView::getSpeciesDestructionTimescales </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
<td class="paramtype">const fourdst::composition::Composition &amp;</td> <td class="paramname"><span class="paramname"><em>comp</em></span>, </td>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6ca0f315f75252ca505507a61556dda6">gridfire::DynamicEngine</a>.</p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a25c040d3078f6ff2ef38f733eb68f1fa">gridfire::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a9055feb245524a5a9549ace935f059ff">&#9670;&#160;</a></span>getSpeciesIndex()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#abb811382522c31f6456787edd4f59ace">&#9670;&#160;</a></span>getSpeciesIndex()</h2>
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<td class="memname">int gridfire::AdaptiveEngineView::getSpeciesIndex </td>
<td class="memname">size_t gridfire::AdaptiveEngineView::getSpeciesIndex </td>
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<td class="paramtype">const fourdst::atomic::Species &amp;</td> <td class="paramname"><span class="paramname"><em>species</em></span></td><td>)</td>
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<p>This method allows querying the index of a specific species in the engine's internal representation. It is useful for accessing species data efficiently. </p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad3d56a8b9161b9cc7f4da51f6bf7e8c9">gridfire::DynamicEngine</a>.</p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a8f66fb76c9f983ee93bf8b95cdc85596">gridfire::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a4e856d6d4d2fc220952bbb7e6b2f85d9">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a57a218c5a145f589531777c8615b7408">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
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<td class="memname">std::expected&lt; std::unordered_map&lt; Species, double &gt;, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html">expectations::StaleEngineError</a> &gt; gridfire::AdaptiveEngineView::getSpeciesTimescales </td>
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<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_culled</em></span>, </td>
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<p>Computes timescales for all active species in the network. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">Y_culled</td><td>Vector of current abundances for the active species. </td></tr>
<tr><td class="paramname">comp</td><td>Composition object containing current abundances. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6772ac384b4c3d3e91712041e4aaa813">gridfire::DynamicEngine</a>.</p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ae7114f5ebc6667b5e5971c0450ed03d9">gridfire::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a67b4ea8cad115394bb4a42cc39d696f9">&#9670;&#160;</a></span>getStoichiometryMatrixEntry()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#abe2ca6426e10cc6a10090eecf7098dbe">&#9670;&#160;</a></span>getStoichiometryMatrixEntry()</h2>
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<td class="memname">int gridfire::AdaptiveEngineView::getStoichiometryMatrixEntry </td>
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<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>speciesIndex_culled</em></span>, </td>
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<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>reactionIndex_culled</em></span>&#160;) const</td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;</td> <td class="paramname"><span class="paramname"><em>reaction</em></span>&#160;) const</td>
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<p>Gets an entry from the stoichiometry matrix for the active species and reactions. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">speciesIndex_culled</td><td>The index of the species in the culled species list. </td></tr>
<tr><td class="paramname">reactionIndex_culled</td><td>The index of the reaction in the culled reaction list. </td></tr>
<tr><td class="paramname">species</td><td>The species for which to get the stoichiometric coefficient. </td></tr>
<tr><td class="paramname">reaction</td><td>The reaction for which to get the stoichiometric coefficient. </td></tr>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a2a7ecf985a326b4bea43e00cf9ee43dd" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">gridfire::DynamicEngine</a>.</p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad19c8451b6f624e2938f771cc067d5c1">gridfire::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a823c665ba89452aa2b3d5422fa5d313f">&#9670;&#160;</a></span>rescueEdgeSpeciesDestructionChannel()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a0439f464865b4c01bad0f6be6055c3fc">&#9670;&#160;</a></span>rescueEdgeSpeciesDestructionChannel()</h2>
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<td class="memname"><a class="el" href="#a4ff60b5214ec0bdaf683feb6615573a5">AdaptiveEngineView::RescueSet</a> gridfire::AdaptiveEngineView::rescueEdgeSpeciesDestructionChannel </td>
<td class="memname"><a class="el" href="#ac674338ddcbae4c33dd84b0441631806">AdaptiveEngineView::RescueSet</a> gridfire::AdaptiveEngineView::rescueEdgeSpeciesDestructionChannel </td>
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<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_full</em></span>, </td>
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<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
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<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>, </td>
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<td class="paramtype">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;</td> <td class="paramname"><span class="paramname"><em>activeReactions</em></span>&#160;) const</td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a> &amp;</td> <td class="paramname"><span class="paramname"><em>activeReactions</em></span>&#160;) const</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a7b3a6b3ab0a52f0f84d2b142e74ea672">&#9670;&#160;</a></span>setNetworkReactions()</h2>
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<td class="memname">void gridfire::AdaptiveEngineView::setNetworkReactions </td>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afb2ec904d88fc8aab516db4059d0e00f">gridfire::DynamicEngine</a>.</p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a49025489901e22a20cdf99b455ff2ff0">gridfire::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a19fc7e02e216b797aa643fa35e429800">&#9670;&#160;</a></span>m_activeReactions</h2>
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<td class="memname"><a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> gridfire::AdaptiveEngineView::m_activeReactions</td>
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