1838 lines
99 KiB
HTML
1838 lines
99 KiB
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<div id="projectname">GridFire<span id="projectnumber"> v0.7.1_rc2</span>
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<div id="projectbrief">General Purpose Nuclear Network</div>
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<a href="#pub-methods">Public Member Functions</a> |
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<div class="headertitle"><div class="title">gridfire::engine::DefinedEngineView Class Reference</div></div>
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<p><code>#include <engine_defined.h></code></p>
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Inheritance diagram for gridfire::engine::DefinedEngineView:</div>
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Collaboration diagram for gridfire::engine::DefinedEngineView:</div>
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<table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
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Public Member Functions</h2></td></tr>
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<tr class="memitem:ada2f326789dc8ae8305617c8d700ae05" id="r_ada2f326789dc8ae8305617c8d700ae05"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#ada2f326789dc8ae8305617c8d700ae05">DefinedEngineView</a> (const std::vector< std::string > &peNames, <a class="el" href="classgridfire_1_1engine_1_1GraphEngine.html">GraphEngine</a> &baseEngine)</td></tr>
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<tr class="separator:ada2f326789dc8ae8305617c8d700ae05"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ab6f82ef31b99bfe8a6c4e475bcdb96f8" id="r_ab6f82ef31b99bfe8a6c4e475bcdb96f8"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html">DynamicEngine</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#ab6f82ef31b99bfe8a6c4e475bcdb96f8">getBaseEngine</a> () const override</td></tr>
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<tr class="memdesc:ab6f82ef31b99bfe8a6c4e475bcdb96f8"><td class="mdescLeft"> </td><td class="mdescRight">Get the base engine associated with this defined engine view. <br /></td></tr>
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<tr class="separator:ab6f82ef31b99bfe8a6c4e475bcdb96f8"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a0af3e1ac0314a485171f1dda39929cb4" id="r_a0af3e1ac0314a485171f1dda39929cb4"><td class="memItemLeft" align="right" valign="top">const std::vector< fourdst::atomic::Species > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a0af3e1ac0314a485171f1dda39929cb4">getNetworkSpecies</a> () const override</td></tr>
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<tr class="memdesc:a0af3e1ac0314a485171f1dda39929cb4"><td class="mdescLeft"> </td><td class="mdescRight">Gets the list of active species in the network defined by the file. <br /></td></tr>
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<tr class="separator:a0af3e1ac0314a485171f1dda39929cb4"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a82cbef591ef1aafcb9a42e01bf38fc38" id="r_a82cbef591ef1aafcb9a42e01bf38fc38"><td class="memItemLeft" align="right" valign="top">std::expected< <a class="el" href="structgridfire_1_1engine_1_1StepDerivatives.html">StepDerivatives</a>< double >, <a class="el" href="namespacegridfire_1_1engine.html#a4d057e41b489bf20744dfa8d2958ad5a">engine::EngineStatus</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a82cbef591ef1aafcb9a42e01bf38fc38">calculateRHSAndEnergy</a> (const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override</td></tr>
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<tr class="memdesc:a82cbef591ef1aafcb9a42e01bf38fc38"><td class="mdescLeft"> </td><td class="mdescRight">Calculates the right-hand side (dY/dt) and energy generation for the active species. <br /></td></tr>
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<tr class="separator:a82cbef591ef1aafcb9a42e01bf38fc38"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2a866a7ba9572d36efab8efe72a063f5" id="r_a2a866a7ba9572d36efab8efe72a063f5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1engine_1_1EnergyDerivatives.html">EnergyDerivatives</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a2a866a7ba9572d36efab8efe72a063f5">calculateEpsDerivatives</a> (const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override</td></tr>
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<tr class="memdesc:a2a866a7ba9572d36efab8efe72a063f5"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the derivatives of the energy generation rate with respect to T and rho. <br /></td></tr>
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<tr class="separator:a2a866a7ba9572d36efab8efe72a063f5"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a4d90439d99da61107d95319b970760bc" id="r_a4d90439d99da61107d95319b970760bc"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1engine_1_1NetworkJacobian.html">NetworkJacobian</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a4d90439d99da61107d95319b970760bc">generateJacobianMatrix</a> (const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override</td></tr>
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<tr class="memdesc:a4d90439d99da61107d95319b970760bc"><td class="mdescLeft"> </td><td class="mdescRight">Generates the Jacobian matrix for the active species. <br /></td></tr>
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<tr class="separator:a4d90439d99da61107d95319b970760bc"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a4966f8cbc859ce2a8a465516d0c0abd0" id="r_a4966f8cbc859ce2a8a465516d0c0abd0"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1engine_1_1NetworkJacobian.html">NetworkJacobian</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a4966f8cbc859ce2a8a465516d0c0abd0">generateJacobianMatrix</a> (const fourdst::composition::CompositionAbstract &comp, double T9, double rho, const std::vector< fourdst::atomic::Species > &activeSpecies) const override</td></tr>
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<tr class="memdesc:a4966f8cbc859ce2a8a465516d0c0abd0"><td class="mdescLeft"> </td><td class="mdescRight">Generates the Jacobian matrix for the active species. <br /></td></tr>
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<tr class="separator:a4966f8cbc859ce2a8a465516d0c0abd0"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a1de5867a0e633de0d0d96ac4fbb141e5" id="r_a1de5867a0e633de0d0d96ac4fbb141e5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1engine_1_1NetworkJacobian.html">NetworkJacobian</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a1de5867a0e633de0d0d96ac4fbb141e5">generateJacobianMatrix</a> (const fourdst::composition::CompositionAbstract &comp, double T9, double rho, const <a class="el" href="namespacegridfire_1_1engine.html#af5175018d2d1e78a8826dd33ec6d675f">SparsityPattern</a> &sparsityPattern) const override</td></tr>
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<tr class="memdesc:a1de5867a0e633de0d0d96ac4fbb141e5"><td class="mdescLeft"> </td><td class="mdescRight">Generates the Jacobian matrix for a given sparsity pattern. <br /></td></tr>
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<tr class="separator:a1de5867a0e633de0d0d96ac4fbb141e5"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af4049e5570bd143d41cab1d4005b6824" id="r_af4049e5570bd143d41cab1d4005b6824"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#af4049e5570bd143d41cab1d4005b6824">generateStoichiometryMatrix</a> () override</td></tr>
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<tr class="memdesc:af4049e5570bd143d41cab1d4005b6824"><td class="mdescLeft"> </td><td class="mdescRight">Generates the stoichiometry matrix for the active reactions and species. <br /></td></tr>
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<tr class="separator:af4049e5570bd143d41cab1d4005b6824"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a600dd38a6011089527024f1625130935" id="r_a600dd38a6011089527024f1625130935"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a600dd38a6011089527024f1625130935">getStoichiometryMatrixEntry</a> (const fourdst::atomic::Species &species, const <a class="el" href="classgridfire_1_1reaction_1_1Reaction.html">reaction::Reaction</a> &reaction) const override</td></tr>
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<tr class="memdesc:a600dd38a6011089527024f1625130935"><td class="mdescLeft"> </td><td class="mdescRight">Gets an entry from the stoichiometry matrix for the active species and reactions. <br /></td></tr>
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<tr class="separator:a600dd38a6011089527024f1625130935"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2f0ad1febc467bce87b5c6ad29b059fb" id="r_a2f0ad1febc467bce87b5c6ad29b059fb"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a2f0ad1febc467bce87b5c6ad29b059fb">calculateMolarReactionFlow</a> (const <a class="el" href="classgridfire_1_1reaction_1_1Reaction.html">reaction::Reaction</a> &reaction, const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override</td></tr>
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<tr class="memdesc:a2f0ad1febc467bce87b5c6ad29b059fb"><td class="mdescLeft"> </td><td class="mdescRight">Calculates the molar reaction flow for a given reaction in the active network. <br /></td></tr>
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<tr class="separator:a2f0ad1febc467bce87b5c6ad29b059fb"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a81732c1b2d08451849c1ddf833246892" id="r_a81732c1b2d08451849c1ddf833246892"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1reaction_1_1ReactionSet.html">reaction::ReactionSet</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a81732c1b2d08451849c1ddf833246892">getNetworkReactions</a> () const override</td></tr>
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<tr class="memdesc:a81732c1b2d08451849c1ddf833246892"><td class="mdescLeft"> </td><td class="mdescRight">Gets the set of active logical reactions in the network. <br /></td></tr>
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<tr class="separator:a81732c1b2d08451849c1ddf833246892"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ae89529e13f2b7fd2febcfa5af40d4666" id="r_ae89529e13f2b7fd2febcfa5af40d4666"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#ae89529e13f2b7fd2febcfa5af40d4666">setNetworkReactions</a> (const <a class="el" href="classgridfire_1_1reaction_1_1ReactionSet.html">reaction::ReactionSet</a> &reactions) override</td></tr>
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<tr class="memdesc:ae89529e13f2b7fd2febcfa5af40d4666"><td class="mdescLeft"> </td><td class="mdescRight">Sets the active reactions in the network. <br /></td></tr>
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<tr class="separator:ae89529e13f2b7fd2febcfa5af40d4666"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a1edda1a27247480660cf7a63410f5799" id="r_a1edda1a27247480660cf7a63410f5799"><td class="memItemLeft" align="right" valign="top">std::expected< std::unordered_map< fourdst::atomic::Species, double >, <a class="el" href="namespacegridfire_1_1engine.html#a4d057e41b489bf20744dfa8d2958ad5a">engine::EngineStatus</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a1edda1a27247480660cf7a63410f5799">getSpeciesTimescales</a> (const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override</td></tr>
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<tr class="memdesc:a1edda1a27247480660cf7a63410f5799"><td class="mdescLeft"> </td><td class="mdescRight">Computes timescales for all active species in the network. <br /></td></tr>
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<tr class="separator:a1edda1a27247480660cf7a63410f5799"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ab051d976dbecf325747d54efe7834d04" id="r_ab051d976dbecf325747d54efe7834d04"><td class="memItemLeft" align="right" valign="top">std::expected< std::unordered_map< fourdst::atomic::Species, double >, <a class="el" href="namespacegridfire_1_1engine.html#a4d057e41b489bf20744dfa8d2958ad5a">engine::EngineStatus</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#ab051d976dbecf325747d54efe7834d04">getSpeciesDestructionTimescales</a> (const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override</td></tr>
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<tr class="memdesc:ab051d976dbecf325747d54efe7834d04"><td class="mdescLeft"> </td><td class="mdescRight">Computes destruction timescales for all active species in the network. <br /></td></tr>
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<tr class="memitem:a1d99b55bf8e94bc2397715aa1f916733" id="r_a1d99b55bf8e94bc2397715aa1f916733"><td class="memItemLeft" align="right" valign="top">fourdst::composition::Composition </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a1d99b55bf8e94bc2397715aa1f916733">update</a> (const <a class="el" href="structgridfire_1_1NetIn.html">NetIn</a> &netIn) override</td></tr>
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<tr class="memdesc:a1d99b55bf8e94bc2397715aa1f916733"><td class="mdescLeft"> </td><td class="mdescRight">Updates the engine view if it is marked as stale. <br /></td></tr>
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<tr class="memitem:a6ef3052fce2d5e4fdaec6659df64c2bc" id="r_a6ef3052fce2d5e4fdaec6659df64c2bc"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a6ef3052fce2d5e4fdaec6659df64c2bc">isStale</a> (const <a class="el" href="structgridfire_1_1NetIn.html">NetIn</a> &netIn) override</td></tr>
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<tr class="memdesc:a6ef3052fce2d5e4fdaec6659df64c2bc"><td class="mdescLeft"> </td><td class="mdescRight">Checks if the engine view is stale. <br /></td></tr>
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<tr class="separator:a6ef3052fce2d5e4fdaec6659df64c2bc"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a68bd0e51d3e127e5f9fd74fdb8180fd9" id="r_a68bd0e51d3e127e5f9fd74fdb8180fd9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a68bd0e51d3e127e5f9fd74fdb8180fd9">setScreeningModel</a> (<a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> model) override</td></tr>
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<tr class="memdesc:a68bd0e51d3e127e5f9fd74fdb8180fd9"><td class="mdescLeft"> </td><td class="mdescRight">Sets the screening model for the base engine. <br /></td></tr>
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<tr class="separator:a68bd0e51d3e127e5f9fd74fdb8180fd9"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a413b111f6a643d7aecbae01dd0f82640" id="r_a413b111f6a643d7aecbae01dd0f82640"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a413b111f6a643d7aecbae01dd0f82640">getScreeningModel</a> () const override</td></tr>
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<tr class="memdesc:a413b111f6a643d7aecbae01dd0f82640"><td class="mdescLeft"> </td><td class="mdescRight">Gets the screening model from the base engine. <br /></td></tr>
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<tr class="separator:a413b111f6a643d7aecbae01dd0f82640"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:afb3c67ce20746b9acb2766920b8f397b" id="r_afb3c67ce20746b9acb2766920b8f397b"><td class="memItemLeft" align="right" valign="top">size_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#afb3c67ce20746b9acb2766920b8f397b">getSpeciesIndex</a> (const fourdst::atomic::Species &species) const override</td></tr>
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<tr class="memdesc:afb3c67ce20746b9acb2766920b8f397b"><td class="mdescLeft"> </td><td class="mdescRight">Maps a species from the full network to its index in the defined active network. <br /></td></tr>
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<tr class="separator:afb3c67ce20746b9acb2766920b8f397b"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa053696a7885b8e42562b2d22ee32d84" id="r_aa053696a7885b8e42562b2d22ee32d84"><td class="memItemLeft" align="right" valign="top">std::vector< double > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#aa053696a7885b8e42562b2d22ee32d84">mapNetInToMolarAbundanceVector</a> (const <a class="el" href="structgridfire_1_1NetIn.html">NetIn</a> &netIn) const override</td></tr>
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<tr class="memdesc:aa053696a7885b8e42562b2d22ee32d84"><td class="mdescLeft"> </td><td class="mdescRight">Map from a <a class="el" href="structgridfire_1_1NetIn.html">NetIn</a> object to a vector of molar abundances for the active species. <br /></td></tr>
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<tr class="separator:aa053696a7885b8e42562b2d22ee32d84"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2bc32a84c9f5372587fca92f2da77595" id="r_a2bc32a84c9f5372587fca92f2da77595"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1engine_1_1PrimingReport.html">PrimingReport</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a2bc32a84c9f5372587fca92f2da77595">primeEngine</a> (const <a class="el" href="structgridfire_1_1NetIn.html">NetIn</a> &netIn) override</td></tr>
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<tr class="memdesc:a2bc32a84c9f5372587fca92f2da77595"><td class="mdescLeft"> </td><td class="mdescRight">Prime the engine view for calculations. This will delegate to the base engine. <br /></td></tr>
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<tr class="separator:a2bc32a84c9f5372587fca92f2da77595"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a25dc44af1a58561b665103b16abe9bbc" id="r_a25dc44af1a58561b665103b16abe9bbc"><td class="memItemLeft" align="right" valign="top">fourdst::composition::Composition </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a25dc44af1a58561b665103b16abe9bbc">collectComposition</a> (const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override</td></tr>
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<tr class="memdesc:a25dc44af1a58561b665103b16abe9bbc"><td class="mdescLeft"> </td><td class="mdescRight">Collects a Composition object from the base engine. <br /></td></tr>
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<tr class="separator:a25dc44af1a58561b665103b16abe9bbc"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a65af092785759559f4697c7e66bef2e3" id="r_a65af092785759559f4697c7e66bef2e3"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegridfire_1_1engine.html#a83c9d755597668bba3cf00cd0ea10ee3">SpeciesStatus</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a65af092785759559f4697c7e66bef2e3">getSpeciesStatus</a> (const fourdst::atomic::Species &species) const override</td></tr>
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<tr class="memdesc:a65af092785759559f4697c7e66bef2e3"><td class="mdescLeft"> </td><td class="mdescRight">Gets the status of a species in the active network. <br /></td></tr>
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<tr class="separator:a65af092785759559f4697c7e66bef2e3"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_methods_classgridfire_1_1engine_1_1DynamicEngine"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classgridfire_1_1engine_1_1DynamicEngine')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html">gridfire::engine::DynamicEngine</a></td></tr>
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<tr class="memitem:ac5a0def6b6af0bd93bf9057c25f048ff inherit pub_methods_classgridfire_1_1engine_1_1DynamicEngine" id="r_ac5a0def6b6af0bd93bf9057c25f048ff"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="namespacegridfire_1_1engine.html#a540b6420c7b6271717ec9b640140f6c0">BuildDepthType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#ac5a0def6b6af0bd93bf9057c25f048ff">getDepth</a> () const</td></tr>
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<tr class="memdesc:ac5a0def6b6af0bd93bf9057c25f048ff inherit pub_methods_classgridfire_1_1engine_1_1DynamicEngine"><td class="mdescLeft"> </td><td class="mdescRight">Get the depth of the network. <br /></td></tr>
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<tr class="separator:ac5a0def6b6af0bd93bf9057c25f048ff inherit pub_methods_classgridfire_1_1engine_1_1DynamicEngine"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2444b9ed3bc61920ce23c546444269e4 inherit pub_methods_classgridfire_1_1engine_1_1DynamicEngine" id="r_a2444b9ed3bc61920ce23c546444269e4"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a2444b9ed3bc61920ce23c546444269e4">rebuild</a> (const fourdst::composition::CompositionAbstract &comp, <a class="el" href="namespacegridfire_1_1engine.html#a540b6420c7b6271717ec9b640140f6c0">BuildDepthType</a> depth)</td></tr>
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<tr class="memdesc:a2444b9ed3bc61920ce23c546444269e4 inherit pub_methods_classgridfire_1_1engine_1_1DynamicEngine"><td class="mdescLeft"> </td><td class="mdescRight">Rebuild the network with a specified depth. <br /></td></tr>
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<tr class="separator:a2444b9ed3bc61920ce23c546444269e4 inherit pub_methods_classgridfire_1_1engine_1_1DynamicEngine"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_methods_classgridfire_1_1engine_1_1Engine"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classgridfire_1_1engine_1_1Engine')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classgridfire_1_1engine_1_1Engine.html">gridfire::engine::Engine</a></td></tr>
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<tr class="memitem:af0ea99416c28933d364a872fc6aff556 inherit pub_methods_classgridfire_1_1engine_1_1Engine" id="r_af0ea99416c28933d364a872fc6aff556"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1Engine.html#af0ea99416c28933d364a872fc6aff556">~Engine</a> ()=default</td></tr>
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<tr class="memdesc:af0ea99416c28933d364a872fc6aff556 inherit pub_methods_classgridfire_1_1engine_1_1Engine"><td class="mdescLeft"> </td><td class="mdescRight">Virtual destructor. <br /></td></tr>
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<tr class="separator:af0ea99416c28933d364a872fc6aff556 inherit pub_methods_classgridfire_1_1engine_1_1Engine"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_methods_classgridfire_1_1engine_1_1EngineView"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classgridfire_1_1engine_1_1EngineView')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classgridfire_1_1engine_1_1EngineView.html">gridfire::engine::EngineView< DynamicEngine ></a></td></tr>
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<tr class="memitem:a17d63e853d6efca31064e9147c80d497 inherit pub_methods_classgridfire_1_1engine_1_1EngineView" id="r_a17d63e853d6efca31064e9147c80d497"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1EngineView.html#a17d63e853d6efca31064e9147c80d497">~EngineView</a> ()=default</td></tr>
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<tr class="memdesc:a17d63e853d6efca31064e9147c80d497 inherit pub_methods_classgridfire_1_1engine_1_1EngineView"><td class="mdescLeft"> </td><td class="mdescRight">Virtual destructor. <br /></td></tr>
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<tr class="separator:a17d63e853d6efca31064e9147c80d497 inherit pub_methods_classgridfire_1_1engine_1_1EngineView"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pro-attribs" name="pro-attribs"></a>
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Protected Attributes</h2></td></tr>
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<tr class="memitem:a3156dfef68cd3636f8cf7a13b5388e75" id="r_a3156dfef68cd3636f8cf7a13b5388e75"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a3156dfef68cd3636f8cf7a13b5388e75">m_isStale</a> = true</td></tr>
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<tr class="separator:a3156dfef68cd3636f8cf7a13b5388e75"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a1e46935f049537e675fb132564d6eacd" id="r_a1e46935f049537e675fb132564d6eacd"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1engine_1_1GraphEngine.html">GraphEngine</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a1e46935f049537e675fb132564d6eacd">m_baseEngine</a></td></tr>
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<tr class="separator:a1e46935f049537e675fb132564d6eacd"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
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Private Member Functions</h2></td></tr>
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<tr class="memitem:a20b54c8b13616982eddb3ae3979b842d" id="r_a20b54c8b13616982eddb3ae3979b842d"><td class="memItemLeft" align="right" valign="top">std::vector< size_t > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a20b54c8b13616982eddb3ae3979b842d">constructSpeciesIndexMap</a> () const</td></tr>
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<tr class="memdesc:a20b54c8b13616982eddb3ae3979b842d"><td class="mdescLeft"> </td><td class="mdescRight">Constructs the species index map. <br /></td></tr>
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<tr class="separator:a20b54c8b13616982eddb3ae3979b842d"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a8464c50142f34583201c4abc7fbcba36" id="r_a8464c50142f34583201c4abc7fbcba36"><td class="memItemLeft" align="right" valign="top">std::vector< size_t > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a8464c50142f34583201c4abc7fbcba36">constructReactionIndexMap</a> () const</td></tr>
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<tr class="memdesc:a8464c50142f34583201c4abc7fbcba36"><td class="mdescLeft"> </td><td class="mdescRight">Constructs the reaction index map. <br /></td></tr>
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<tr class="separator:a8464c50142f34583201c4abc7fbcba36"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa352f3ba0e689d3f81711c17f4f67dfc" id="r_aa352f3ba0e689d3f81711c17f4f67dfc"><td class="memItemLeft" align="right" valign="top">std::vector< double > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#aa352f3ba0e689d3f81711c17f4f67dfc">mapViewToFull</a> (const std::vector< double > &defined) const</td></tr>
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<tr class="memdesc:aa352f3ba0e689d3f81711c17f4f67dfc"><td class="mdescLeft"> </td><td class="mdescRight">Maps a vector of culled abundances to a vector of full abundances. <br /></td></tr>
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<tr class="separator:aa352f3ba0e689d3f81711c17f4f67dfc"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a391bc4b5d946ea606cf7661955191d12" id="r_a391bc4b5d946ea606cf7661955191d12"><td class="memItemLeft" align="right" valign="top">std::vector< double > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a391bc4b5d946ea606cf7661955191d12">mapFullToView</a> (const std::vector< double > &full) const</td></tr>
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<tr class="memdesc:a391bc4b5d946ea606cf7661955191d12"><td class="mdescLeft"> </td><td class="mdescRight">Maps a vector of full abundances to a vector of culled abundances. <br /></td></tr>
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<tr class="separator:a391bc4b5d946ea606cf7661955191d12"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ad6986fa5cda1d9ed9d4f54f444f402e8" id="r_ad6986fa5cda1d9ed9d4f54f444f402e8"><td class="memItemLeft" align="right" valign="top">size_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#ad6986fa5cda1d9ed9d4f54f444f402e8">mapViewToFullSpeciesIndex</a> (size_t definedSpeciesIndex) const</td></tr>
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<tr class="memdesc:ad6986fa5cda1d9ed9d4f54f444f402e8"><td class="mdescLeft"> </td><td class="mdescRight">Maps a culled species index to a full species index. <br /></td></tr>
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<tr class="separator:ad6986fa5cda1d9ed9d4f54f444f402e8"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:afa9aeb6d11645e4b9cecf56fb63b51ef" id="r_afa9aeb6d11645e4b9cecf56fb63b51ef"><td class="memItemLeft" align="right" valign="top">size_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#afa9aeb6d11645e4b9cecf56fb63b51ef">mapViewToFullReactionIndex</a> (size_t definedReactionIndex) const</td></tr>
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<tr class="memdesc:afa9aeb6d11645e4b9cecf56fb63b51ef"><td class="mdescLeft"> </td><td class="mdescRight">Maps a culled reaction index to a full reaction index. <br /></td></tr>
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<tr class="separator:afa9aeb6d11645e4b9cecf56fb63b51ef"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a91ea88e43c17f99ff0d95a8f54b09cbf" id="r_a91ea88e43c17f99ff0d95a8f54b09cbf"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a91ea88e43c17f99ff0d95a8f54b09cbf">validateNetworkState</a> () const</td></tr>
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<tr class="separator:a91ea88e43c17f99ff0d95a8f54b09cbf"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a38191e2b3b219d348eba0109dce271c3" id="r_a38191e2b3b219d348eba0109dce271c3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a38191e2b3b219d348eba0109dce271c3">collect</a> (const std::vector< std::string > &peNames)</td></tr>
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<tr class="separator:a38191e2b3b219d348eba0109dce271c3"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
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Private Attributes</h2></td></tr>
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<tr class="memitem:a3ba348cf85f0098071d23b0a3cea7078" id="r_a3ba348cf85f0098071d23b0a3cea7078"><td class="memItemLeft" align="right" valign="top">quill::Logger * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a3ba348cf85f0098071d23b0a3cea7078">m_logger</a> = fourdst::logging::LogManager::getInstance().getLogger("log")</td></tr>
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<tr class="memdesc:a3ba348cf85f0098071d23b0a3cea7078"><td class="mdescLeft"> </td><td class="mdescRight">Active species in the defined engine. <br /></td></tr>
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<tr class="separator:a3ba348cf85f0098071d23b0a3cea7078"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aad986ed7c9602ba042999cf0a30ed70c" id="r_aad986ed7c9602ba042999cf0a30ed70c"><td class="memItemLeft" align="right" valign="top">std::set< fourdst::atomic::Species > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#aad986ed7c9602ba042999cf0a30ed70c">m_activeSpecies</a></td></tr>
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<tr class="memdesc:aad986ed7c9602ba042999cf0a30ed70c"><td class="mdescLeft"> </td><td class="mdescRight">Cache for the active species vector to avoid dangling references. <br /></td></tr>
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<tr class="separator:aad986ed7c9602ba042999cf0a30ed70c"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:add093054fe3ba60f99b04f7f3bda4ba3" id="r_add093054fe3ba60f99b04f7f3bda4ba3"><td class="memItemLeft" align="right" valign="top">std::optional< std::vector< fourdst::atomic::Species > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#add093054fe3ba60f99b04f7f3bda4ba3">m_activeSpeciesVectorCache</a> = std::nullopt</td></tr>
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<tr class="memdesc:add093054fe3ba60f99b04f7f3bda4ba3"><td class="mdescLeft"> </td><td class="mdescRight">Active reactions in the defined engine. <br /></td></tr>
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<tr class="separator:add093054fe3ba60f99b04f7f3bda4ba3"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ae8ac4dc44a6c9f3588d6dd02b39a4cc9" id="r_ae8ac4dc44a6c9f3588d6dd02b39a4cc9"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1reaction_1_1ReactionSet.html">reaction::ReactionSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#ae8ac4dc44a6c9f3588d6dd02b39a4cc9">m_activeReactions</a></td></tr>
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<tr class="memdesc:ae8ac4dc44a6c9f3588d6dd02b39a4cc9"><td class="mdescLeft"> </td><td class="mdescRight">Maps indices of active species to indices in the full network. <br /></td></tr>
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<tr class="memitem:a26af4be40216ee3ea5b7fff49fe7a00c" id="r_a26af4be40216ee3ea5b7fff49fe7a00c"><td class="memItemLeft" align="right" valign="top">std::vector< size_t > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a26af4be40216ee3ea5b7fff49fe7a00c">m_speciesIndexMap</a></td></tr>
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<tr class="memdesc:a26af4be40216ee3ea5b7fff49fe7a00c"><td class="mdescLeft"> </td><td class="mdescRight">Maps indices of active reactions to indices in the full network. <br /></td></tr>
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<tr class="separator:a26af4be40216ee3ea5b7fff49fe7a00c"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa9a26262300b0982b847a72425dc373a" id="r_aa9a26262300b0982b847a72425dc373a"><td class="memItemLeft" align="right" valign="top">std::vector< size_t > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#aa9a26262300b0982b847a72425dc373a">m_reactionIndexMap</a></td></tr>
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<tr class="separator:aa9a26262300b0982b847a72425dc373a"><td class="memSeparator" colspan="2"> </td></tr>
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</table>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<a id="ada2f326789dc8ae8305617c8d700ae05" name="ada2f326789dc8ae8305617c8d700ae05"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ada2f326789dc8ae8305617c8d700ae05">◆ </a></span>DefinedEngineView()</h2>
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<td class="memname">gridfire::engine::DefinedEngineView::DefinedEngineView </td>
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<td>(</td>
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<td class="paramtype">const std::vector< std::string > & </td>
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<td class="paramname"><em>peNames</em>, </td>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype"><a class="el" href="classgridfire_1_1engine_1_1GraphEngine.html">GraphEngine</a> & </td>
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<td class="paramname"><em>baseEngine</em> </td>
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<td>)</td>
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<h2 class="groupheader">Member Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a2a866a7ba9572d36efab8efe72a063f5">◆ </a></span>calculateEpsDerivatives()</h2>
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<td class="memname"><a class="el" href="structgridfire_1_1engine_1_1EnergyDerivatives.html">EnergyDerivatives</a> gridfire::engine::DefinedEngineView::calculateEpsDerivatives </td>
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<td>(</td>
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<td class="paramtype">const fourdst::composition::CompositionAbstract & </td>
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<p>Calculate the derivatives of the energy generation rate with respect to T and rho. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<table class="params">
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<tr><td class="paramname">comp</td><td>Composition object containing current abundances. </td></tr>
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<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
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<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
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</dd>
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<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1engine_1_1EnergyDerivatives.html" title="Structure holding derivatives of energy generation rate with respect to T and rho.">EnergyDerivatives</a> containing dEps/dT and dEps/dRho.</dd></dl>
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<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>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#ada6a1295a92c2aede841672ecae0cede">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a2f0ad1febc467bce87b5c6ad29b059fb">◆ </a></span>calculateMolarReactionFlow()</h2>
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<td class="memname">double gridfire::engine::DefinedEngineView::calculateMolarReactionFlow </td>
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<td>(</td>
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<td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1Reaction.html">reaction::Reaction</a> & </td>
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<td></td><td> const</td>
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<p>Calculates the molar reaction flow for a given reaction in the active network. </p>
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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>
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<tr><td class="paramname">comp</td><td>A Composition object containing the current composition of the system </td></tr>
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<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
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<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>Molar flow rate for the reaction (e.g., mol/g/s).</dd></dl>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<table class="exception">
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<tr><td class="paramname">std::runtime_error</td><td>If the view is stale or if the reaction is not in the active set. </td></tr>
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</dd>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#aa57fa5e58b98a03fba31bcddda8001d4">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a82cbef591ef1aafcb9a42e01bf38fc38">◆ </a></span>calculateRHSAndEnergy()</h2>
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<td class="memname">std::expected< <a class="el" href="structgridfire_1_1engine_1_1StepDerivatives.html">StepDerivatives</a>< double >, <a class="el" href="namespacegridfire_1_1engine.html#a4d057e41b489bf20744dfa8d2958ad5a">EngineStatus</a> > gridfire::engine::DefinedEngineView::calculateRHSAndEnergy </td>
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<td>(</td>
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<p>Calculates the right-hand side (dY/dt) and energy generation for the active species. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">comp</td><td>A Composition object containing the current composition of the system </td></tr>
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<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
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<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 <a class="el" href="structgridfire_1_1engine_1_1StepDerivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives</a> struct containing the derivatives of the active species and the nuclear energy generation rate.</dd></dl>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">std::runtime_error</td><td>If the view is stale (i.e., <code><a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html#a1d99b55bf8e94bc2397715aa1f916733" title="Updates the engine view if it is marked as stale.">update()</a></code> has not been called after <code>setNetworkFile()</code>). </td></tr>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1Engine.html#a764fc091c72c12c8529105d7c96badb2">gridfire::engine::Engine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a38191e2b3b219d348eba0109dce271c3">◆ </a></span>collect()</h2>
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<td class="memname">void gridfire::engine::DefinedEngineView::collect </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a25dc44af1a58561b665103b16abe9bbc">◆ </a></span>collectComposition()</h2>
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<td class="memname">fourdst::composition::Composition gridfire::engine::DefinedEngineView::collectComposition </td>
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<p>Collects a Composition object from the base engine. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">comp</td><td>The full Composition object. </td></tr>
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<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
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<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 composition object representing the state of the engine stack and the current view. </dd></dl>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a41877719ae5e8de53c1692c7cf9bfbfc">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a8464c50142f34583201c4abc7fbcba36">◆ </a></span>constructReactionIndexMap()</h2>
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<p>Constructs the reaction index map. </p>
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<dl class="section return"><dt>Returns</dt><dd>A vector mapping defined reaction indices to full reaction indices.</dd></dl>
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<p>This method creates a map from the indices of the active reactions to the indices of the corresponding reactions in the full network.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a20b54c8b13616982eddb3ae3979b842d">◆ </a></span>constructSpeciesIndexMap()</h2>
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<p>Constructs the species index map. </p>
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<dl class="section return"><dt>Returns</dt><dd>A vector mapping defined species indices to full species indices.</dd></dl>
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<p>This method creates a map from the indices of the active species to the indices of the corresponding species in the full network.</p>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">std::runtime_error</td><td>If an active species is not found in the base engine's species list. </td></tr>
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<h2 class="memtitle"><span class="permalink"><a href="#a4d90439d99da61107d95319b970760bc">◆ </a></span>generateJacobianMatrix() <span class="overload">[1/3]</span></h2>
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<td class="memname"><a class="el" href="classgridfire_1_1engine_1_1NetworkJacobian.html">NetworkJacobian</a> gridfire::engine::DefinedEngineView::generateJacobianMatrix </td>
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<td>(</td>
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<td class="paramtype">const fourdst::composition::CompositionAbstract & </td>
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<p>Generates the Jacobian matrix for the active species. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">comp</td><td>A Composition object containing the current composition of the system </td></tr>
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<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
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<tr><td class="paramname">rho</td><td>The density in g/cm^3.</td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a53276f09346b531f8676db355e1219eb">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a1de5867a0e633de0d0d96ac4fbb141e5">◆ </a></span>generateJacobianMatrix() <span class="overload">[2/3]</span></h2>
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<td class="memname"><a class="el" href="classgridfire_1_1engine_1_1NetworkJacobian.html">NetworkJacobian</a> gridfire::engine::DefinedEngineView::generateJacobianMatrix </td>
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<td>(</td>
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<td class="paramtype">const fourdst::composition::CompositionAbstract & </td>
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<td class="paramtype">const <a class="el" href="namespacegridfire_1_1engine.html#af5175018d2d1e78a8826dd33ec6d675f">SparsityPattern</a> & </td>
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<p>Generates the Jacobian matrix for a given sparsity pattern. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">comp</td><td>A Composition object containing the current composition of the system </td></tr>
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<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
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<tr><td class="paramname">rho</td><td>The density in g/cm^3. </td></tr>
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<tr><td class="paramname">sparsityPattern</td><td>The sparsity pattern to use for the Jacobian matrix.</td></tr>
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<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a51d55a21be28e372021b2b8e5ecdc551">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a4966f8cbc859ce2a8a465516d0c0abd0">◆ </a></span>generateJacobianMatrix() <span class="overload">[3/3]</span></h2>
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<td class="memname"><a class="el" href="classgridfire_1_1engine_1_1NetworkJacobian.html">NetworkJacobian</a> gridfire::engine::DefinedEngineView::generateJacobianMatrix </td>
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<td>(</td>
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<td class="paramtype">const fourdst::composition::CompositionAbstract & </td>
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<p>Generates the Jacobian matrix for the active species. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">comp</td><td>A Composition object containing the current composition of the system </td></tr>
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<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
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<tr><td class="paramname">rho</td><td>The density in g/cm^3. </td></tr>
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<tr><td class="paramname">activeSpecies</td><td>The vector of active species to include in the Jacobian.</td></tr>
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<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a15d53dac8b622a3b7d0f928a3995dbde">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#af4049e5570bd143d41cab1d4005b6824">◆ </a></span>generateStoichiometryMatrix()</h2>
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<td class="memname">void gridfire::engine::DefinedEngineView::generateStoichiometryMatrix </td>
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<p>Generates the stoichiometry matrix for the active reactions and species. </p>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a5e2c45a3e415b53e41def8f743f93464">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ab6f82ef31b99bfe8a6c4e475bcdb96f8">◆ </a></span>getBaseEngine()</h2>
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<td class="memname">const <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html">DynamicEngine</a> & gridfire::engine::DefinedEngineView::getBaseEngine </td>
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<p>Get the base engine associated with this defined engine view. </p>
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<dl class="section return"><dt>Returns</dt><dd>A const reference to the base <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a>. </dd></dl>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1EngineView.html#a7884ea8e5618e295e64150f3ecf2c6b5">gridfire::engine::EngineView< DynamicEngine ></a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a81732c1b2d08451849c1ddf833246892">◆ </a></span>getNetworkReactions()</h2>
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<td class="memname">const <a class="el" href="classgridfire_1_1reaction_1_1ReactionSet.html">reaction::ReactionSet</a> & gridfire::engine::DefinedEngineView::getNetworkReactions </td>
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<p>Gets the set of active logical reactions in the network. </p>
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<dl class="section return"><dt>Returns</dt><dd>Reference to the LogicalReactionSet containing all active reactions.</dd></dl>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a26b59a4c7622bf820c0eeec6a7522aa8">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a0af3e1ac0314a485171f1dda39929cb4">◆ </a></span>getNetworkSpecies()</h2>
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<td class="memname">const std::vector< Species > & gridfire::engine::DefinedEngineView::getNetworkSpecies </td>
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<p>Gets the list of active species in the network defined by the file. </p>
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<dl class="section return"><dt>Returns</dt><dd>A const reference to the vector of active species. </dd></dl>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1Engine.html#a3263c3fde2509d5d8ec4da3b6e946c48">gridfire::engine::Engine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a413b111f6a643d7aecbae01dd0f82640">◆ </a></span>getScreeningModel()</h2>
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<td class="memname"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> gridfire::engine::DefinedEngineView::getScreeningModel </td>
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<p>Gets the screening model from the base engine. </p>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a24103027a38e02d4342161164554d332">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ab051d976dbecf325747d54efe7834d04">◆ </a></span>getSpeciesDestructionTimescales()</h2>
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<td class="memname">std::expected< std::unordered_map< Species, double >, <a class="el" href="namespacegridfire_1_1engine.html#a4d057e41b489bf20744dfa8d2958ad5a">EngineStatus</a> > gridfire::engine::DefinedEngineView::getSpeciesDestructionTimescales </td>
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<td>(</td>
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<p>Computes destruction timescales for all active species in the network. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<table class="params">
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<tr><td class="paramname">comp</td><td>A Composition object containing the current composition of the system </td></tr>
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<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
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<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
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</dd>
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<dl class="section return"><dt>Returns</dt><dd>Map from Species to their destruction timescales (s).</dd></dl>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<table class="exception">
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<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#aefc5d0f7842b27a108ba1e4ca346e9a0">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#afb3c67ce20746b9acb2766920b8f397b">◆ </a></span>getSpeciesIndex()</h2>
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<td class="memname">size_t gridfire::engine::DefinedEngineView::getSpeciesIndex </td>
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<td>(</td>
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<td class="paramtype">const fourdst::atomic::Species & </td>
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<td class="paramname"><em>species</em></td><td>)</td>
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<p>Maps a species from the full network to its index in the defined active network. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">species</td><td>The species to map. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>The index of the species in the active network.</dd></dl>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<table class="exception">
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<tr><td class="paramname">std::runtime_error</td><td>If the species is not in the active set. </td></tr>
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</dd>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#ac0f40017603e8e6887b75dc7360d7c5e">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a65af092785759559f4697c7e66bef2e3">◆ </a></span>getSpeciesStatus()</h2>
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<td class="memname"><a class="el" href="namespacegridfire_1_1engine.html#a83c9d755597668bba3cf00cd0ea10ee3">SpeciesStatus</a> gridfire::engine::DefinedEngineView::getSpeciesStatus </td>
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<td>(</td>
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<td class="paramtype">const fourdst::atomic::Species & </td>
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<p>Gets the status of a species in the active network. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<table class="params">
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<tr><td class="paramname">species</td><td>The species for which to get the status. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>The SpeciesStatus indicating if the species is active, inactive, or not present. </dd></dl>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a8aebefad50c1aa34207e118e92d7ccf0">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a1edda1a27247480660cf7a63410f5799">◆ </a></span>getSpeciesTimescales()</h2>
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<td class="memname">std::expected< std::unordered_map< Species, double >, <a class="el" href="namespacegridfire_1_1engine.html#a4d057e41b489bf20744dfa8d2958ad5a">EngineStatus</a> > gridfire::engine::DefinedEngineView::getSpeciesTimescales </td>
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<td>(</td>
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<td class="paramtype">const fourdst::composition::CompositionAbstract & </td>
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<td></td><td> const</td>
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<p>Computes timescales for all active species in the network. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">comp</td><td>A Composition object containing the current composition of the system </td></tr>
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<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
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<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>Map from Species to their characteristic timescales (s).</dd></dl>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
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</dd>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#aef6ed91d922c0b1733fd7835e99d0efe">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a600dd38a6011089527024f1625130935">◆ </a></span>getStoichiometryMatrixEntry()</h2>
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<td class="memname">int gridfire::engine::DefinedEngineView::getStoichiometryMatrixEntry </td>
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<td class="paramtype">const fourdst::atomic::Species & </td>
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<td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1Reaction.html">reaction::Reaction</a> & </td>
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<td class="paramname"><em>reaction</em> </td>
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<td>)</td>
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<td></td><td> const</td>
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<span class="mlabels"><span class="mlabel">override</span><span class="mlabel">virtual</span></span> </td>
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<p>Gets an entry from the stoichiometry matrix for the active species and reactions. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">species</td><td>The species for which to get the stoichiometric coefficient. </td></tr>
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<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 return"><dt>Returns</dt><dd>The stoichiometric coefficient for the given species and reaction.</dd></dl>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
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<tr><td class="paramname">std::out_of_range</td><td>If an index is out of bounds. </td></tr>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a5ce6ff370e3f0964c6b2688fb3f4bb7e">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a6ef3052fce2d5e4fdaec6659df64c2bc">◆ </a></span>isStale()</h2>
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<td>(</td>
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<td class="paramtype">const <a class="el" href="structgridfire_1_1NetIn.html">NetIn</a> & </td>
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<td class="paramname"><em>netIn</em></td><td>)</td>
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<p>Checks if the engine view is stale. </p>
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<tr><td class="paramname">netIn</td><td>The current network input (unused). </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>True if the view is stale and needs to be updated; false otherwise. </dd></dl>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a79423b9f67b4cac702547b4f1d8bd14c">gridfire::engine::DynamicEngine</a>.</p>
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<a id="a391bc4b5d946ea606cf7661955191d12" name="a391bc4b5d946ea606cf7661955191d12"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a391bc4b5d946ea606cf7661955191d12">◆ </a></span>mapFullToView()</h2>
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<td>(</td>
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<td class="paramtype">const std::vector< double > & </td>
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<td class="paramname"><em>full</em></td><td>)</td>
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<td> const</td>
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<p>Maps a vector of full abundances to a vector of culled abundances. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">full</td><td>A vector of abundances for the full network. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>A vector of abundances for the active species, with the abundances of the active species copied from the full vector. </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#aa053696a7885b8e42562b2d22ee32d84">◆ </a></span>mapNetInToMolarAbundanceVector()</h2>
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<td>(</td>
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<td class="paramtype">const <a class="el" href="structgridfire_1_1NetIn.html">NetIn</a> & </td>
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<p>Map from a <a class="el" href="structgridfire_1_1NetIn.html">NetIn</a> object to a vector of molar abundances for the active species. </p>
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<dl class="section return"><dt>Returns</dt><dd>A vector of molar abundances for the active species. </dd></dl>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#aa9d55b81c1963113aad86aa60c19676f">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aa352f3ba0e689d3f81711c17f4f67dfc">◆ </a></span>mapViewToFull()</h2>
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<p>Maps a vector of culled abundances to a vector of full abundances. </p>
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<dl class="section return"><dt>Returns</dt><dd>A vector of abundances for the full network, with the abundances of the active species copied from the defined vector. </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#afa9aeb6d11645e4b9cecf56fb63b51ef">◆ </a></span>mapViewToFullReactionIndex()</h2>
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<p>Maps a culled reaction index to a full reaction index. </p>
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<dl class="section return"><dt>Returns</dt><dd>The index of the corresponding reaction in the full network.</dd></dl>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">std::out_of_range</td><td>If the defined index is out of bounds for the reaction index map. </td></tr>
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<h2 class="memtitle"><span class="permalink"><a href="#ad6986fa5cda1d9ed9d4f54f444f402e8">◆ </a></span>mapViewToFullSpeciesIndex()</h2>
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<td class="memname">size_t gridfire::engine::DefinedEngineView::mapViewToFullSpeciesIndex </td>
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<td>(</td>
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<td class="paramtype">size_t </td>
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<td class="paramname"><em>definedSpeciesIndex</em></td><td>)</td>
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<p>Maps a culled species index to a full species index. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<dl class="section return"><dt>Returns</dt><dd>The index of the corresponding species in the full network.</dd></dl>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">std::out_of_range</td><td>If the defined index is out of bounds for the species index map. </td></tr>
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<h2 class="memtitle"><span class="permalink"><a href="#a2bc32a84c9f5372587fca92f2da77595">◆ </a></span>primeEngine()</h2>
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<td class="memname"><a class="el" href="structgridfire_1_1engine_1_1PrimingReport.html">PrimingReport</a> gridfire::engine::DefinedEngineView::primeEngine </td>
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<td class="paramtype">const <a class="el" href="structgridfire_1_1NetIn.html">NetIn</a> & </td>
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<p>Prime the engine view for calculations. This will delegate to the base engine. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<dl class="section return"><dt>Returns</dt><dd>The <a class="el" href="structgridfire_1_1engine_1_1PrimingReport.html" title="Captures the result of a network priming operation.">PrimingReport</a> from the base engine. </dd></dl>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a70e270bb50910c0055a75575c1ef1e95">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ae89529e13f2b7fd2febcfa5af40d4666">◆ </a></span>setNetworkReactions()</h2>
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<td class="memname">void gridfire::engine::DefinedEngineView::setNetworkReactions </td>
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<p>Sets the active reactions in the network. </p>
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<dl class="section post"><dt>Postcondition</dt><dd>The view is marked as stale and will need to be updated. </dd></dl>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#ab321170954bffc53b1bedaf54f6976be">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a68bd0e51d3e127e5f9fd74fdb8180fd9">◆ </a></span>setScreeningModel()</h2>
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<p>Sets the screening model for the base engine. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a50e76977d0dc3cc23d52b51842d35003">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a1d99b55bf8e94bc2397715aa1f916733">◆ </a></span>update()</h2>
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<td>(</td>
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<td class="paramtype">const <a class="el" href="structgridfire_1_1NetIn.html">NetIn</a> & </td>
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<p>Updates the engine view if it is marked as stale. </p>
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<p>This method checks if the view is stale (e.g., after <code>setNetworkFile</code> was called). If it is, it rebuilds the active network from the currently set file. The <code>netIn</code> parameter is not used by this implementation but is required by the interface.</p>
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<dl class="params"><dt>Parameters</dt><dd>
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<dl class="section post"><dt>Postcondition</dt><dd>If the view was stale, it is rebuilt and is no longer stale. </dd></dl>
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<p>Implements <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html#a8dd85442ec54f20d91743c72364e36ff">gridfire::engine::DynamicEngine</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a91ea88e43c17f99ff0d95a8f54b09cbf">◆ </a></span>validateNetworkState()</h2>
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<h2 class="groupheader">Member Data Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#ae8ac4dc44a6c9f3588d6dd02b39a4cc9">◆ </a></span>m_activeReactions</h2>
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<td class="memname"><a class="el" href="classgridfire_1_1reaction_1_1ReactionSet.html">reaction::ReactionSet</a> gridfire::engine::DefinedEngineView::m_activeReactions</td>
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<p>Maps indices of active species to indices in the full network. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#aad986ed7c9602ba042999cf0a30ed70c">◆ </a></span>m_activeSpecies</h2>
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<p>Cache for the active species vector to avoid dangling references. </p>
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<p>Active reactions in the defined engine. </p>
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<p>Active species in the defined engine. </p>
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<span class="mlabels"><span class="mlabel">private</span></span> </td>
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<p>Maps indices of active reactions to indices in the full network. </p>
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<hr/>The documentation for this class was generated from the following files:<ul>
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<li>src/include/gridfire/engine/views/<a class="el" href="engine__defined_8h.html">engine_defined.h</a></li>
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<li>src/lib/engine/views/<a class="el" href="engine__defined_8cpp.html">engine_defined.cpp</a></li>
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<li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.8 </li>
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