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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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@@ -140,34 +140,37 @@ Public Member Functions</h2></td></tr>
<tr class="memitem:a1a55f9748c45af6f13e16a6b6ceaa211 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a1a55f9748c45af6f13e16a6b6ceaa211"><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="classgridfire_1_1_defined_engine_view.html#a1a55f9748c45af6f13e16a6b6ceaa211">getNetworkSpecies</a> () const override</td></tr>
<tr class="memdesc:a1a55f9748c45af6f13e16a6b6ceaa211 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the list of active species in the network defined by the file. <br /></td></tr>
<tr class="separator:a1a55f9748c45af6f13e16a6b6ceaa211 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a4b0d71367cb1d4c06bcd01251bbeb60d inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a4b0d71367cb1d4c06bcd01251bbeb60d"><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="classgridfire_1_1_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:a4b0d71367cb1d4c06bcd01251bbeb60d inherit pub_methods_classgridfire_1_1_defined_engine_view"><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:a4b0d71367cb1d4c06bcd01251bbeb60d inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad25c722eaee1f28f8ed7b4d33a1f69ae inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_ad25c722eaee1f28f8ed7b4d33a1f69ae"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ad25c722eaee1f28f8ed7b4d33a1f69ae">generateJacobianMatrix</a> (const std::vector&lt; double &gt; &amp;Y_dynamic, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:ad25c722eaee1f28f8ed7b4d33a1f69ae inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generates the Jacobian matrix for the active species. <br /></td></tr>
<tr class="separator:ad25c722eaee1f28f8ed7b4d33a1f69ae inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a273b175049f5ce7b9208e931ad139e1b inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a273b175049f5ce7b9208e931ad139e1b"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a273b175049f5ce7b9208e931ad139e1b">getJacobianMatrixEntry</a> (const int i_defined, const int j_defined) const override</td></tr>
<tr class="memdesc:a273b175049f5ce7b9208e931ad139e1b inherit pub_methods_classgridfire_1_1_defined_engine_view"><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:a273b175049f5ce7b9208e931ad139e1b inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af273b29d7700cdc34da6e2712fffc5c2 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_af273b29d7700cdc34da6e2712fffc5c2"><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="classgridfire_1_1_defined_engine_view.html#af273b29d7700cdc34da6e2712fffc5c2">calculateRHSAndEnergy</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="memdesc:af273b29d7700cdc34da6e2712fffc5c2 inherit pub_methods_classgridfire_1_1_defined_engine_view"><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:af273b29d7700cdc34da6e2712fffc5c2 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a06aca977aafb4784fd167acb8c02dda2 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a06aca977aafb4784fd167acb8c02dda2"><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="classgridfire_1_1_defined_engine_view.html#a06aca977aafb4784fd167acb8c02dda2">calculateEpsDerivatives</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="memdesc:a06aca977aafb4784fd167acb8c02dda2 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the derivatives of the energy generation rate with respect to T and rho. <br /></td></tr>
<tr class="separator:a06aca977aafb4784fd167acb8c02dda2 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab80eadd713a40e9263e5231737e956d0 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_ab80eadd713a40e9263e5231737e956d0"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ab80eadd713a40e9263e5231737e956d0">generateJacobianMatrix</a> (const fourdst::composition::Composition &amp;comp, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:ab80eadd713a40e9263e5231737e956d0 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generates the Jacobian matrix for the active species. <br /></td></tr>
<tr class="separator:ab80eadd713a40e9263e5231737e956d0 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa49532266ff959ac66f501336f102ce8 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_aa49532266ff959ac66f501336f102ce8"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#aa49532266ff959ac66f501336f102ce8">getJacobianMatrixEntry</a> (const fourdst::atomic::Species &amp;rowSpecies, const fourdst::atomic::Species &amp;colSpecies) const override</td></tr>
<tr class="memdesc:aa49532266ff959ac66f501336f102ce8 inherit pub_methods_classgridfire_1_1_defined_engine_view"><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:aa49532266ff959ac66f501336f102ce8 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad07221be49ae1b5133c5b987dafac3b6 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_ad07221be49ae1b5133c5b987dafac3b6"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ad07221be49ae1b5133c5b987dafac3b6">generateStoichiometryMatrix</a> () override</td></tr>
<tr class="memdesc:ad07221be49ae1b5133c5b987dafac3b6 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generates the stoichiometry matrix for the active reactions and species. <br /></td></tr>
<tr class="separator:ad07221be49ae1b5133c5b987dafac3b6 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:afa2820971397114d788730cc33feefe2 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_afa2820971397114d788730cc33feefe2"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#afa2820971397114d788730cc33feefe2">getStoichiometryMatrixEntry</a> (const int speciesIndex_defined, const int reactionIndex_defined) const override</td></tr>
<tr class="memdesc:afa2820971397114d788730cc33feefe2 inherit pub_methods_classgridfire_1_1_defined_engine_view"><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:afa2820971397114d788730cc33feefe2 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a142725470f96cba3edb48a29f1264032 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a142725470f96cba3edb48a29f1264032"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032">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_defined, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:a142725470f96cba3edb48a29f1264032 inherit pub_methods_classgridfire_1_1_defined_engine_view"><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:a142725470f96cba3edb48a29f1264032 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae03b4f9afac03d4011a4d7cf0423535d inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_ae03b4f9afac03d4011a4d7cf0423535d"><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="classgridfire_1_1_defined_engine_view.html#ae03b4f9afac03d4011a4d7cf0423535d">getNetworkReactions</a> () const override</td></tr>
<tr class="memdesc:ae03b4f9afac03d4011a4d7cf0423535d inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the set of active logical reactions in the network. <br /></td></tr>
<tr class="separator:ae03b4f9afac03d4011a4d7cf0423535d inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a9736edfb7c9148b60de30d50c0d3530d inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a9736edfb7c9148b60de30d50c0d3530d"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a9736edfb7c9148b60de30d50c0d3530d">setNetworkReactions</a> (const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;reactions) override</td></tr>
<tr class="separator:a9736edfb7c9148b60de30d50c0d3530d inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac8daafabbc76f4b6811bede241a03d72 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_ac8daafabbc76f4b6811bede241a03d72"><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="classgridfire_1_1_defined_engine_view.html#ac8daafabbc76f4b6811bede241a03d72">getSpeciesTimescales</a> (const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:ac8daafabbc76f4b6811bede241a03d72 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Computes timescales for all active species in the network. <br /></td></tr>
<tr class="separator:ac8daafabbc76f4b6811bede241a03d72 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a3d58e36ed8a6a0d82bb65e91090f7491 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a3d58e36ed8a6a0d82bb65e91090f7491"><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="classgridfire_1_1_defined_engine_view.html#a3d58e36ed8a6a0d82bb65e91090f7491">getSpeciesDestructionTimescales</a> (const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td></tr>
<tr class="separator:a3d58e36ed8a6a0d82bb65e91090f7491 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af1843cfd2a95bfa46ab40d4c4de11ef9 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_af1843cfd2a95bfa46ab40d4c4de11ef9"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#af1843cfd2a95bfa46ab40d4c4de11ef9">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:af1843cfd2a95bfa46ab40d4c4de11ef9 inherit pub_methods_classgridfire_1_1_defined_engine_view"><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:af1843cfd2a95bfa46ab40d4c4de11ef9 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a74298377d0432ae3d577be0e9e6052b3 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a74298377d0432ae3d577be0e9e6052b3"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a74298377d0432ae3d577be0e9e6052b3">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:a74298377d0432ae3d577be0e9e6052b3 inherit pub_methods_classgridfire_1_1_defined_engine_view"><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:a74298377d0432ae3d577be0e9e6052b3 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5f9db5a9287aa03b2fa4d516e9a576b6 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a5f9db5a9287aa03b2fa4d516e9a576b6"><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="classgridfire_1_1_defined_engine_view.html#a5f9db5a9287aa03b2fa4d516e9a576b6">getNetworkReactions</a> () const override</td></tr>
<tr class="memdesc:a5f9db5a9287aa03b2fa4d516e9a576b6 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the set of active logical reactions in the network. <br /></td></tr>
<tr class="separator:a5f9db5a9287aa03b2fa4d516e9a576b6 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a655e74357cce822c4508069a3bcac2c9 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a655e74357cce822c4508069a3bcac2c9"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a655e74357cce822c4508069a3bcac2c9">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:a655e74357cce822c4508069a3bcac2c9 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a18f46d92ea7e04068ad9e7af4ed605a8 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a18f46d92ea7e04068ad9e7af4ed605a8"><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="classgridfire_1_1_defined_engine_view.html#a18f46d92ea7e04068ad9e7af4ed605a8">getSpeciesTimescales</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="memdesc:a18f46d92ea7e04068ad9e7af4ed605a8 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Computes timescales for all active species in the network. <br /></td></tr>
<tr class="separator:a18f46d92ea7e04068ad9e7af4ed605a8 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7bcf169ba1e12e3356d4bcc27c3fc554 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a7bcf169ba1e12e3356d4bcc27c3fc554"><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="classgridfire_1_1_defined_engine_view.html#a7bcf169ba1e12e3356d4bcc27c3fc554">getSpeciesDestructionTimescales</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="separator:a7bcf169ba1e12e3356d4bcc27c3fc554 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae5762f395caea5381ec177507816b5ae inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_ae5762f395caea5381ec177507816b5ae"><td class="memItemLeft" align="right" valign="top">fourdst::composition::Composition&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#ae5762f395caea5381ec177507816b5ae">update</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) override</td></tr>
<tr class="memdesc:ae5762f395caea5381ec177507816b5ae inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Updates the engine view if it is marked as stale. <br /></td></tr>
<tr class="separator:ae5762f395caea5381ec177507816b5ae inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -179,9 +182,9 @@ Public Member Functions</h2></td></tr>
<tr class="memitem:a3c657b82a0117118a4bb0ce7f624ae0c inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a3c657b82a0117118a4bb0ce7f624ae0c"><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="classgridfire_1_1_defined_engine_view.html#a3c657b82a0117118a4bb0ce7f624ae0c">getScreeningModel</a> () const override</td></tr>
<tr class="memdesc:a3c657b82a0117118a4bb0ce7f624ae0c inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the screening model from the base engine. <br /></td></tr>
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<tr class="memitem:abfee22688617ffe91c69be93049c89b3 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_abfee22688617ffe91c69be93049c89b3"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#abfee22688617ffe91c69be93049c89b3">getSpeciesIndex</a> (const fourdst::atomic::Species &amp;species) const override</td></tr>
<tr class="memdesc:abfee22688617ffe91c69be93049c89b3 inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the index of a species in the network. <br /></td></tr>
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<tr class="memitem:af3b355ffcda6a8f2841184cc56e3761a inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_af3b355ffcda6a8f2841184cc56e3761a"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#af3b355ffcda6a8f2841184cc56e3761a">getSpeciesIndex</a> (const fourdst::atomic::Species &amp;species) const override</td></tr>
<tr class="memdesc:af3b355ffcda6a8f2841184cc56e3761a inherit pub_methods_classgridfire_1_1_defined_engine_view"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the index of a species in the network. <br /></td></tr>
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<tr class="memitem:a72789c1c3379594b65b560da50192de2 inherit pub_methods_classgridfire_1_1_defined_engine_view" id="r_a72789c1c3379594b65b560da50192de2"><td class="memItemLeft" align="right" valign="top">std::vector&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_defined_engine_view.html#a72789c1c3379594b65b560da50192de2">mapNetInToMolarAbundanceVector</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) const override</td></tr>
<tr class="memdesc:a72789c1c3379594b65b560da50192de2 inherit pub_methods_classgridfire_1_1_defined_engine_view"><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>
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@@ -189,8 +192,8 @@ Public Member Functions</h2></td></tr>
<tr class="memdesc:a13033abd3b44904f98b58c93e22da460 inherit pub_methods_classgridfire_1_1_defined_engine_view"><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>
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<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>
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@@ -334,7 +337,7 @@ Additional Inherited Members</h2></td></tr>
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@@ -359,7 +362,7 @@ Additional Inherited Members</h2></td></tr>
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