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451 lines
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<div class="headertitle"><div class="title">gridfire::engine::NetworkPrimingEngineView Class Reference<span class="mlabels"><span class="mlabel">final</span></span></div></div>
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<p>Provides a view of a <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> filtered to reactions involving a specified priming species.
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<a href="classgridfire_1_1engine_1_1NetworkPrimingEngineView.html#details">More...</a></p>
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<p><code>#include <engine_priming.h></code></p>
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Inheritance diagram for gridfire::engine::NetworkPrimingEngineView:</div>
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Collaboration diagram for gridfire::engine::NetworkPrimingEngineView:</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:ad4eec8af1ab1f918fd4e92fac47adaf4" id="r_ad4eec8af1ab1f918fd4e92fac47adaf4"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1NetworkPrimingEngineView.html#ad4eec8af1ab1f918fd4e92fac47adaf4">NetworkPrimingEngineView</a> (const std::string &primingSymbol, <a class="el" href="classgridfire_1_1engine_1_1GraphEngine.html">GraphEngine</a> &baseEngine)</td></tr>
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<tr class="memdesc:ad4eec8af1ab1f918fd4e92fac47adaf4"><td class="mdescLeft"> </td><td class="mdescRight">Constructs the view by looking up the priming species by symbol. <br /></td></tr>
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<tr class="separator:ad4eec8af1ab1f918fd4e92fac47adaf4"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a0d505b967dc3b50f6966a0110e53a6d7" id="r_a0d505b967dc3b50f6966a0110e53a6d7"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1NetworkPrimingEngineView.html#a0d505b967dc3b50f6966a0110e53a6d7">NetworkPrimingEngineView</a> (const fourdst::atomic::Species &primingSpecies, <a class="el" href="classgridfire_1_1engine_1_1GraphEngine.html">GraphEngine</a> &baseEngine)</td></tr>
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<tr class="memdesc:a0d505b967dc3b50f6966a0110e53a6d7"><td class="mdescLeft"> </td><td class="mdescRight">Constructs the view using an existing Species object. <br /></td></tr>
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<tr class="separator:a0d505b967dc3b50f6966a0110e53a6d7"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classgridfire_1_1engine_1_1DefinedEngineView')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html">gridfire::engine::DefinedEngineView</a></td></tr>
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<tr class="memitem:ada2f326789dc8ae8305617c8d700ae05 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ab6f82ef31b99bfe8a6c4e475bcdb96f8 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a0af3e1ac0314a485171f1dda39929cb4 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a82cbef591ef1aafcb9a42e01bf38fc38 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2a866a7ba9572d36efab8efe72a063f5 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a4d90439d99da61107d95319b970760bc inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a4966f8cbc859ce2a8a465516d0c0abd0 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a1de5867a0e633de0d0d96ac4fbb141e5 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af4049e5570bd143d41cab1d4005b6824 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a600dd38a6011089527024f1625130935 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2f0ad1febc467bce87b5c6ad29b059fb inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a81732c1b2d08451849c1ddf833246892 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ae89529e13f2b7fd2febcfa5af40d4666 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a1edda1a27247480660cf7a63410f5799 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ab051d976dbecf325747d54efe7834d04 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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="separator:ab051d976dbecf325747d54efe7834d04 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a1d99b55bf8e94bc2397715aa1f916733 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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="separator:a1d99b55bf8e94bc2397715aa1f916733 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a6ef3052fce2d5e4fdaec6659df64c2bc inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a68bd0e51d3e127e5f9fd74fdb8180fd9 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a413b111f6a643d7aecbae01dd0f82640 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:afb3c67ce20746b9acb2766920b8f397b inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa053696a7885b8e42562b2d22ee32d84 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2bc32a84c9f5372587fca92f2da77595 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a25dc44af1a58561b665103b16abe9bbc inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a65af092785759559f4697c7e66bef2e3 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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 inherit pub_methods_classgridfire_1_1engine_1_1DefinedEngineView"><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="pri-methods" name="pri-methods"></a>
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Private Member Functions</h2></td></tr>
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<tr class="memitem:acaf9433246a58f2365c5bd8907cbacbb" id="r_acaf9433246a58f2365c5bd8907cbacbb"><td class="memItemLeft" align="right" valign="top">std::vector< std::string > </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1NetworkPrimingEngineView.html#acaf9433246a58f2365c5bd8907cbacbb">constructPrimingReactionSet</a> (const fourdst::atomic::Species &primingSpecies, const <a class="el" href="classgridfire_1_1engine_1_1GraphEngine.html">GraphEngine</a> &baseEngine) const</td></tr>
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<tr class="memdesc:acaf9433246a58f2365c5bd8907cbacbb"><td class="mdescLeft"> </td><td class="mdescRight">Constructs the set of reaction names that involve the priming species. <br /></td></tr>
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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:af5d4b8d6b11e83d57d6e08b12ce5882d" id="r_af5d4b8d6b11e83d57d6e08b12ce5882d"><td class="memItemLeft" align="right" valign="top">quill::Logger * </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1NetworkPrimingEngineView.html#af5d4b8d6b11e83d57d6e08b12ce5882d">m_logger</a> = LogManager::getInstance().getLogger("log")</td></tr>
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<tr class="memitem:ad78f293f31a7ff8120b85e26e5d6dcfd" id="r_ad78f293f31a7ff8120b85e26e5d6dcfd"><td class="memItemLeft" align="right" valign="top">fourdst::atomic::Species </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1engine_1_1NetworkPrimingEngineView.html#ad78f293f31a7ff8120b85e26e5d6dcfd">m_primingSpecies</a></td></tr>
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<tr class="memdesc:ad78f293f31a7ff8120b85e26e5d6dcfd"><td class="mdescLeft"> </td><td class="mdescRight">The priming species, if specified. <br /></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="inherited" name="inherited"></a>
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Additional Inherited Members</h2></td></tr>
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<tr class="inherit_header pro_attribs_classgridfire_1_1engine_1_1DefinedEngineView"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classgridfire_1_1engine_1_1DefinedEngineView')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classgridfire_1_1engine_1_1DefinedEngineView.html">gridfire::engine::DefinedEngineView</a></td></tr>
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<tr class="memitem:a3156dfef68cd3636f8cf7a13b5388e75 inherit pro_attribs_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pro_attribs_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a1e46935f049537e675fb132564d6eacd inherit pro_attribs_classgridfire_1_1engine_1_1DefinedEngineView" 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 inherit pro_attribs_classgridfire_1_1engine_1_1DefinedEngineView"><td class="memSeparator" colspan="2"> </td></tr>
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</table>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<div class="textblock"><p>Provides a view of a <a class="el" href="classgridfire_1_1engine_1_1DynamicEngine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> filtered to reactions involving a specified priming species. </p>
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<p>This view constructs a subset of the network reactions from the base engine that contain the given priming species and delegates all engine operations to the underlying engine.</p>
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<p>See implementation in <a class="el" href="engine__priming_8cpp.html">engine_priming.cpp</a> for details on reaction set construction.</p>
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<dl class="section note"><dt>Note</dt><dd>Throws std::runtime_error if no priming reactions are found for the species. </dd></dl>
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</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<a id="ad4eec8af1ab1f918fd4e92fac47adaf4" name="ad4eec8af1ab1f918fd4e92fac47adaf4"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ad4eec8af1ab1f918fd4e92fac47adaf4">◆ </a></span>NetworkPrimingEngineView() <span class="overload">[1/2]</span></h2>
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<td class="memname">gridfire::engine::NetworkPrimingEngineView::NetworkPrimingEngineView </td>
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<td>(</td>
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<td class="paramtype">const std::string & </td>
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<td class="paramname"><em>primingSymbol</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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</div><div class="memdoc">
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<p>Constructs the view by looking up the priming species by symbol. </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">primingSymbol</td><td>Symbol string of the species to prime. </td></tr>
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<tr><td class="paramname">baseEngine</td><td>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> to wrap. </td></tr>
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</table>
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</dd>
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</dl>
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<dl class="section pre"><dt>Precondition</dt><dd>primingSymbol must correspond to a valid species in atomic::species registry. </dd></dl>
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<dl class="section post"><dt>Postcondition</dt><dd>The view will contain only reactions that involve the priming species. </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::out_of_range</td><td>If primingSymbol is not found in the species registry. </td></tr>
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<tr><td class="paramname">std::runtime_error</td><td>If no reactions contain the priming species. </td></tr>
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<h2 class="memtitle"><span class="permalink"><a href="#a0d505b967dc3b50f6966a0110e53a6d7">◆ </a></span>NetworkPrimingEngineView() <span class="overload">[2/2]</span></h2>
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<td class="memname">gridfire::engine::NetworkPrimingEngineView::NetworkPrimingEngineView </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>primingSpecies</em>, </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><td></td>
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<p>Constructs the view using an existing Species object. </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">primingSpecies</td><td>The species object to prime. </td></tr>
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<tr><td class="paramname">baseEngine</td><td>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> to wrap. </td></tr>
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</table>
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</dd>
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</dl>
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<dl class="section pre"><dt>Precondition</dt><dd>primingSpecies must be valid and present in the network of baseEngine. </dd></dl>
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<dl class="section post"><dt>Postcondition</dt><dd>The view will contain only reactions that involve the priming species. </dd></dl>
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||
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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 no reactions contain the priming species. </td></tr>
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<h2 class="groupheader">Member Function Documentation</h2>
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||
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<a id="acaf9433246a58f2365c5bd8907cbacbb" name="acaf9433246a58f2365c5bd8907cbacbb"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#acaf9433246a58f2365c5bd8907cbacbb">◆ </a></span>constructPrimingReactionSet()</h2>
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<td class="memname">std::vector< std::string > gridfire::engine::NetworkPrimingEngineView::constructPrimingReactionSet </td>
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<td>(</td>
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||
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<td class="paramtype">const fourdst::atomic::Species & </td>
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<td class="paramname"><em>primingSpecies</em>, </td>
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<td class="paramtype">const <a class="el" href="classgridfire_1_1engine_1_1GraphEngine.html">GraphEngine</a> & </td>
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<span class="mlabels"><span class="mlabel">private</span></span> </td>
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</tr>
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</table>
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</div><div class="memdoc">
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<p>Constructs the set of reaction names that involve the priming species. </p>
|
||
|
|
<dl class="params"><dt>Parameters</dt><dd>
|
||
|
|
<table class="params">
|
||
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<tr><td class="paramname">primingSpecies</td><td>Species for which to collect priming reactions. </td></tr>
|
||
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<tr><td class="paramname">baseEngine</td><td>Base engine containing the full network of reactions. </td></tr>
|
||
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</table>
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||
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|
||
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</dl>
|
||
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<dl class="section pre"><dt>Precondition</dt><dd>baseEngine.getNetworkReactions() returns a valid iterable set of reactions. </dd></dl>
|
||
|
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<dl class="section post"><dt>Postcondition</dt><dd>Returns a vector of unique reaction name strings containing the priming species. </dd></dl>
|
||
|
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<dl class="section return"><dt>Returns</dt><dd>Vector of reaction name strings containing the priming species. </dd></dl>
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||
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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 no reactions involve the priming species. </td></tr>
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||
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<h2 class="groupheader">Member Data Documentation</h2>
|
||
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<a id="af5d4b8d6b11e83d57d6e08b12ce5882d" name="af5d4b8d6b11e83d57d6e08b12ce5882d"></a>
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||
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<h2 class="memtitle"><span class="permalink"><a href="#af5d4b8d6b11e83d57d6e08b12ce5882d">◆ </a></span>m_logger</h2>
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<div class="memitem">
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<td class="memname">quill::Logger* gridfire::engine::NetworkPrimingEngineView::m_logger = LogManager::getInstance().getLogger("log")</td>
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<a id="ad78f293f31a7ff8120b85e26e5d6dcfd" name="ad78f293f31a7ff8120b85e26e5d6dcfd"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ad78f293f31a7ff8120b85e26e5d6dcfd">◆ </a></span>m_primingSpecies</h2>
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<td class="memname">fourdst::atomic::Species gridfire::engine::NetworkPrimingEngineView::m_primingSpecies</td>
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||
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|
||
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|
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</td>
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||
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<span class="mlabels"><span class="mlabel">private</span></span> </td>
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||
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||
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<p>The priming species, if specified. </p>
|
||
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|
||
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</div>
|
||
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</div>
|
||
|
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<hr/>The documentation for this class was generated from the following files:<ul>
|
||
|
|
<li>src/include/gridfire/engine/views/<a class="el" href="engine__priming_8h.html">engine_priming.h</a></li>
|
||
|
|
<li>src/lib/engine/views/<a class="el" href="engine__priming_8cpp.html">engine_priming.cpp</a></li>
|
||
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</ul>
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||
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</div><!-- contents -->
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||
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<li class="navelem"><a class="el" href="namespacegridfire.html">gridfire</a></li><li class="navelem"><a class="el" href="namespacegridfire_1_1engine.html">engine</a></li><li class="navelem"><a class="el" href="classgridfire_1_1engine_1_1NetworkPrimingEngineView.html">NetworkPrimingEngineView</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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