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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_defined_engine_view.html
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@@ -134,34 +134,37 @@ Public Member Functions</h2></td></tr>
<tr class="memitem:a1a55f9748c45af6f13e16a6b6ceaa211" 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="#a1a55f9748c45af6f13e16a6b6ceaa211">getNetworkSpecies</a> () const override</td></tr>
<tr class="memdesc:a1a55f9748c45af6f13e16a6b6ceaa211"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a4b0d71367cb1d4c06bcd01251bbeb60d" 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="#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"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad25c722eaee1f28f8ed7b4d33a1f69ae" id="r_ad25c722eaee1f28f8ed7b4d33a1f69ae"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#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"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generates the Jacobian matrix for the active species. <br /></td></tr>
<tr class="separator:ad25c722eaee1f28f8ed7b4d33a1f69ae"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a273b175049f5ce7b9208e931ad139e1b" id="r_a273b175049f5ce7b9208e931ad139e1b"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a273b175049f5ce7b9208e931ad139e1b">getJacobianMatrixEntry</a> (const int i_defined, const int j_defined) const override</td></tr>
<tr class="memdesc:a273b175049f5ce7b9208e931ad139e1b"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af273b29d7700cdc34da6e2712fffc5c2" 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="#af273b29d7700cdc34da6e2712fffc5c2">calculateRHSAndEnergy</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="memdesc:af273b29d7700cdc34da6e2712fffc5c2"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
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<tr class="memdesc:a06aca977aafb4784fd167acb8c02dda2"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab80eadd713a40e9263e5231737e956d0" id="r_ab80eadd713a40e9263e5231737e956d0"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ab80eadd713a40e9263e5231737e956d0">generateJacobianMatrix</a> (const fourdst::composition::Composition &amp;comp, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:ab80eadd713a40e9263e5231737e956d0"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generates the Jacobian matrix for the active species. <br /></td></tr>
<tr class="separator:ab80eadd713a40e9263e5231737e956d0"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa49532266ff959ac66f501336f102ce8" id="r_aa49532266ff959ac66f501336f102ce8"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aa49532266ff959ac66f501336f102ce8">getJacobianMatrixEntry</a> (const fourdst::atomic::Species &amp;rowSpecies, const fourdst::atomic::Species &amp;colSpecies) const override</td></tr>
<tr class="memdesc:aa49532266ff959ac66f501336f102ce8"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad07221be49ae1b5133c5b987dafac3b6" id="r_ad07221be49ae1b5133c5b987dafac3b6"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad07221be49ae1b5133c5b987dafac3b6">generateStoichiometryMatrix</a> () override</td></tr>
<tr class="memdesc:ad07221be49ae1b5133c5b987dafac3b6"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:afa2820971397114d788730cc33feefe2" id="r_afa2820971397114d788730cc33feefe2"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#afa2820971397114d788730cc33feefe2">getStoichiometryMatrixEntry</a> (const int speciesIndex_defined, const int reactionIndex_defined) const override</td></tr>
<tr class="memdesc:afa2820971397114d788730cc33feefe2"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a142725470f96cba3edb48a29f1264032" id="r_a142725470f96cba3edb48a29f1264032"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#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"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae03b4f9afac03d4011a4d7cf0423535d" 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="#ae03b4f9afac03d4011a4d7cf0423535d">getNetworkReactions</a> () const override</td></tr>
<tr class="memdesc:ae03b4f9afac03d4011a4d7cf0423535d"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a9736edfb7c9148b60de30d50c0d3530d" id="r_a9736edfb7c9148b60de30d50c0d3530d"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac8daafabbc76f4b6811bede241a03d72" 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="#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"><td class="mdescLeft">&#160;</td><td class="mdescRight">Computes timescales for all active species in the network. <br /></td></tr>
<tr class="separator:ac8daafabbc76f4b6811bede241a03d72"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a3d58e36ed8a6a0d82bb65e91090f7491" 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="#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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af1843cfd2a95bfa46ab40d4c4de11ef9" id="r_af1843cfd2a95bfa46ab40d4c4de11ef9"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#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"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a74298377d0432ae3d577be0e9e6052b3" id="r_a74298377d0432ae3d577be0e9e6052b3"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#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"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5f9db5a9287aa03b2fa4d516e9a576b6" 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="#a5f9db5a9287aa03b2fa4d516e9a576b6">getNetworkReactions</a> () const override</td></tr>
<tr class="memdesc:a5f9db5a9287aa03b2fa4d516e9a576b6"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a655e74357cce822c4508069a3bcac2c9" id="r_a655e74357cce822c4508069a3bcac2c9"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#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"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a18f46d92ea7e04068ad9e7af4ed605a8" 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="#a18f46d92ea7e04068ad9e7af4ed605a8">getSpeciesTimescales</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="memdesc:a18f46d92ea7e04068ad9e7af4ed605a8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Computes timescales for all active species in the network. <br /></td></tr>
<tr class="separator:a18f46d92ea7e04068ad9e7af4ed605a8"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7bcf169ba1e12e3356d4bcc27c3fc554" 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="#a7bcf169ba1e12e3356d4bcc27c3fc554">getSpeciesDestructionTimescales</a> (const fourdst::composition::Composition &amp;comp, double T9, double rho) const override</td></tr>
<tr class="separator:a7bcf169ba1e12e3356d4bcc27c3fc554"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae5762f395caea5381ec177507816b5ae" id="r_ae5762f395caea5381ec177507816b5ae"><td class="memItemLeft" align="right" valign="top">fourdst::composition::Composition&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#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"><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"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -173,9 +176,9 @@ Public Member Functions</h2></td></tr>
<tr class="memitem:a3c657b82a0117118a4bb0ce7f624ae0c" 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="#a3c657b82a0117118a4bb0ce7f624ae0c">getScreeningModel</a> () const override</td></tr>
<tr class="memdesc:a3c657b82a0117118a4bb0ce7f624ae0c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the screening model from the base engine. <br /></td></tr>
<tr class="separator:a3c657b82a0117118a4bb0ce7f624ae0c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:abfee22688617ffe91c69be93049c89b3" id="r_abfee22688617ffe91c69be93049c89b3"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#abfee22688617ffe91c69be93049c89b3">getSpeciesIndex</a> (const fourdst::atomic::Species &amp;species) const override</td></tr>
<tr class="memdesc:abfee22688617ffe91c69be93049c89b3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the index of a species in the network. <br /></td></tr>
<tr class="separator:abfee22688617ffe91c69be93049c89b3"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af3b355ffcda6a8f2841184cc56e3761a" id="r_af3b355ffcda6a8f2841184cc56e3761a"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#af3b355ffcda6a8f2841184cc56e3761a">getSpeciesIndex</a> (const fourdst::atomic::Species &amp;species) const override</td></tr>
<tr class="memdesc:af3b355ffcda6a8f2841184cc56e3761a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the index of a species in the network. <br /></td></tr>
<tr class="separator:af3b355ffcda6a8f2841184cc56e3761a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a72789c1c3379594b65b560da50192de2" 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="#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"><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:a72789c1c3379594b65b560da50192de2"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -183,8 +186,8 @@ Public Member Functions</h2></td></tr>
<tr class="memdesc:a13033abd3b44904f98b58c93e22da460"><td class="mdescLeft">&#160;</td><td class="mdescRight">Prime the engine with initial conditions. <br /></td></tr>
<tr class="separator:a13033abd3b44904f98b58c93e22da460"><td class="memSeparator" colspan="2">&#160;</td></tr>
<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>
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<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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@@ -240,9 +243,9 @@ Private Attributes</h2></td></tr>
<tr class="memitem:a64e9c79a36d529e1b296fe5786e57aae" id="r_a64e9c79a36d529e1b296fe5786e57aae"><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="#a64e9c79a36d529e1b296fe5786e57aae">m_activeSpecies</a></td></tr>
<tr class="memdesc:a64e9c79a36d529e1b296fe5786e57aae"><td class="mdescLeft">&#160;</td><td class="mdescRight">Active reactions in the defined engine. <br /></td></tr>
<tr class="separator:a64e9c79a36d529e1b296fe5786e57aae"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a373d4a83f30527a1bfaf1d74ad14c965" id="r_a373d4a83f30527a1bfaf1d74ad14c965"><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="#a373d4a83f30527a1bfaf1d74ad14c965">m_activeReactions</a></td></tr>
<tr class="memdesc:a373d4a83f30527a1bfaf1d74ad14c965"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps indices of active species to indices in the full network. <br /></td></tr>
<tr class="separator:a373d4a83f30527a1bfaf1d74ad14c965"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a824fe65ae22fa856051f2652764a0bb6" id="r_a824fe65ae22fa856051f2652764a0bb6"><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="#a824fe65ae22fa856051f2652764a0bb6">m_activeReactions</a></td></tr>
<tr class="memdesc:a824fe65ae22fa856051f2652764a0bb6"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps indices of active species to indices in the full network. <br /></td></tr>
<tr class="separator:a824fe65ae22fa856051f2652764a0bb6"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:acc4976262e208d1dd2185ebccbdd275e" id="r_acc4976262e208d1dd2185ebccbdd275e"><td class="memItemLeft" align="right" valign="top">std::vector&lt; size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#acc4976262e208d1dd2185ebccbdd275e">m_speciesIndexMap</a></td></tr>
<tr class="memdesc:acc4976262e208d1dd2185ebccbdd275e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps indices of active reactions to indices in the full network. <br /></td></tr>
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@@ -272,8 +275,56 @@ Private Attributes</h2></td></tr>
</div>
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<h2 class="groupheader">Member Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a142725470f96cba3edb48a29f1264032">&#9670;&#160;</a></span>calculateMolarReactionFlow()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a06aca977aafb4784fd167acb8c02dda2">&#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::DefinedEngineView::calculateEpsDerivatives </td>
<td>(</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">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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<p>Calculate the derivatives of the energy generation rate with respect to T and rho. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<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>
</table>
</dd>
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<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_energy_derivatives.html">EnergyDerivatives</a> containing dEps/dT and dEps/dRho.</dd></dl>
<p>This method computes the partial derivatives of the specific nuclear energy generation rate with respect to temperature and density for the current state. </p>
<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="#a74298377d0432ae3d577be0e9e6052b3">&#9670;&#160;</a></span>calculateMolarReactionFlow()</h2>
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<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_defined</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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@@ -313,7 +364,7 @@ Private Attributes</h2></td></tr>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">reaction</td><td>The reaction for which to calculate the flow. </td></tr>
<tr><td class="paramname">Y_defined</td><td>Vector of current abundances for the active species. </td></tr>
<tr><td class="paramname">comp</td><td>A Composition object containing the current composition of the system </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>
</table>
@@ -327,12 +378,12 @@ Private Attributes</h2></td></tr>
</dd>
</dl>
<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="#a4b0d71367cb1d4c06bcd01251bbeb60d">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#af273b29d7700cdc34da6e2712fffc5c2">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
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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::DefinedEngineView::calculateRHSAndEnergy </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_defined</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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@@ -366,7 +417,7 @@ 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_defined</td><td>A vector of abundances for the active species. </td></tr>
<tr><td class="paramname">comp</td><td>A Composition object containing 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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@@ -380,7 +431,7 @@ Private Attributes</h2></td></tr>
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<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="#ad25c722eaee1f28f8ed7b4d33a1f69ae">&#9670;&#160;</a></span>generateJacobianMatrix()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#ab80eadd713a40e9263e5231737e956d0">&#9670;&#160;</a></span>generateJacobianMatrix()</h2>
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<td class="memname">void gridfire::DefinedEngineView::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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<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>A Composition object containing 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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@@ -527,7 +578,7 @@ Private Attributes</h2></td></tr>
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<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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<dl class="section return"><dt>Returns</dt><dd>Const reference to the underlying engine.</dd></dl>
<p>This method must be implemented by derived classes to provide access to the base engine. The returned reference should remain valid for the lifetime of the <a class="el" href="classgridfire_1_1_engine_view.html" title="Abstract base class for a &quot;view&quot; of a reaction network engine.">EngineView</a>.</p>
<p>Example: </p><div class="fragment"><div class="line"><span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>&amp; engine = myView.getBaseEngine();</div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><div class="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><div class="ttdef"><b>Definition</b> engine_abstract.h:130</div></div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><div class="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><div class="ttdef"><b>Definition</b> engine_abstract.h:142</div></div>
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<p>Implements <a class="el" href="classgridfire_1_1_engine_view.html#ad294227f8b5cf6d970c349eabf5447a6">gridfire::EngineView&lt; DynamicEngine &gt;</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a273b175049f5ce7b9208e931ad139e1b">&#9670;&#160;</a></span>getJacobianMatrixEntry()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#aa49532266ff959ac66f501336f102ce8">&#9670;&#160;</a></span>getJacobianMatrixEntry()</h2>
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<td class="memname">double gridfire::DefinedEngineView::getJacobianMatrixEntry </td>
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<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>i_defined</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_defined</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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<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_defined</td><td>The row index (species index) in the defined matrix. </td></tr>
<tr><td class="paramname">j_defined</td><td>The column index (species index) in the defined matrix. </td></tr>
<tr><td class="paramname">rowSpecies</td><td>The species corresponding to the row index. </td></tr>
<tr><td class="paramname">colSpecies</td><td>The species corresponding to the column index. </td></tr>
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</dd>
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<dl class="section return"><dt>Returns</dt><dd>The value of the Jacobian matrix at (i_defined, j_defined).</dd></dl>
<dl class="section return"><dt>Returns</dt><dd>The value of the Jacobian matrix at (row species index, col species index).</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
@@ -643,12 +694,12 @@ Private Attributes</h2></td></tr>
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<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="#ae03b4f9afac03d4011a4d7cf0423535d">&#9670;&#160;</a></span>getNetworkReactions()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a5f9db5a9287aa03b2fa4d516e9a576b6">&#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::DefinedEngineView::getNetworkReactions </td>
<td class="memname">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a> &amp; gridfire::DefinedEngineView::getNetworkReactions </td>
<td>(</td>
<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
<td> const</td>
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<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
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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>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
@@ -679,7 +730,7 @@ Private Attributes</h2></td></tr>
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<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="#a3d58e36ed8a6a0d82bb65e91090f7491">&#9670;&#160;</a></span>getSpeciesDestructionTimescales()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a7bcf169ba1e12e3356d4bcc27c3fc554">&#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::DefinedEngineView::getSpeciesDestructionTimescales </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_defined</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>
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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>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="#abfee22688617ffe91c69be93049c89b3">&#9670;&#160;</a></span>getSpeciesIndex()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#af3b355ffcda6a8f2841184cc56e3761a">&#9670;&#160;</a></span>getSpeciesIndex()</h2>
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<td class="memname">int gridfire::DefinedEngineView::getSpeciesIndex </td>
<td class="memname">size_t gridfire::DefinedEngineView::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>
<td> const</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="#ac8daafabbc76f4b6811bede241a03d72">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a18f46d92ea7e04068ad9e7af4ed605a8">&#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::DefinedEngineView::getSpeciesTimescales </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_defined</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>
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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>Computes timescales for all active species in the network. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">Y_defined</td><td>Vector of current abundances for the active species. </td></tr>
<tr><td class="paramname">comp</td><td>A Composition object containing the current composition of the system </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="#afa2820971397114d788730cc33feefe2">&#9670;&#160;</a></span>getStoichiometryMatrixEntry()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#af1843cfd2a95bfa46ab40d4c4de11ef9">&#9670;&#160;</a></span>getStoichiometryMatrixEntry()</h2>
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<td class="memname">int gridfire::DefinedEngineView::getStoichiometryMatrixEntry </td>
<td>(</td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>speciesIndex_defined</em></span>, </td>
<td class="paramtype">const fourdst::atomic::Species &amp;</td> <td class="paramname"><span class="paramname"><em>species</em></span>, </td>
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<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>reactionIndex_defined</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>
<table class="params">
<tr><td class="paramname">speciesIndex_defined</td><td>The index of the species in the defined species list. </td></tr>
<tr><td class="paramname">reactionIndex_defined</td><td>The index of the reaction in the defined 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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<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="#a9736edfb7c9148b60de30d50c0d3530d">&#9670;&#160;</a></span>setNetworkReactions()</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a655e74357cce822c4508069a3bcac2c9">&#9670;&#160;</a></span>setNetworkReactions()</h2>
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<td class="memname">void gridfire::DefinedEngineView::setNetworkReactions </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>reactions</em></span></td><td>)</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>reactions</em></span></td><td>)</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="groupheader">Member Data Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a373d4a83f30527a1bfaf1d74ad14c965">&#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::DefinedEngineView::m_activeReactions</td>
<td class="memname"><a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a> gridfire::DefinedEngineView::m_activeReactions</td>
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