1559 lines
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1559 lines
89 KiB
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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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<a href="#pri-methods">Private Member Functions</a> |
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<div class="headertitle"><div class="title">gridfire::FileDefinedEngineView Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
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<p>An engine view that uses a user-defined reaction network from a file.
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<p><code>#include <<a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>></code></p>
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Inheritance diagram for gridfire::FileDefinedEngineView:</div>
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<area href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations." alt="gridfire::DynamicEngine" shape="rect" coords="0,56,238,80"/>
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<area href="classgridfire_1_1_engine.html" title="Abstract base class for a reaction network engine." alt="gridfire::Engine" shape="rect" coords="0,0,238,24"/>
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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:a8f2f64bab0f516ed2a6fd529912e0acd" id="r_a8f2f64bab0f516ed2a6fd529912e0acd"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="#a8f2f64bab0f516ed2a6fd529912e0acd">FileDefinedEngineView</a> (<a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &baseEngine, const std::string &fileName, const <a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a> &parser)</td></tr>
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<tr class="memdesc:a8f2f64bab0f516ed2a6fd529912e0acd"><td class="mdescLeft"> </td><td class="mdescRight">Constructs a <a class="el" href="classgridfire_1_1_file_defined_engine_view.html" title="An engine view that uses a user-defined reaction network from a file.">FileDefinedEngineView</a>. <br /></td></tr>
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<tr class="separator:a8f2f64bab0f516ed2a6fd529912e0acd"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a4c8b273c5cb3d470567c5691b68493a3" id="r_a4c8b273c5cb3d470567c5691b68493a3"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="#a4c8b273c5cb3d470567c5691b68493a3">getBaseEngine</a> () const override</td></tr>
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<tr class="memdesc:a4c8b273c5cb3d470567c5691b68493a3"><td class="mdescLeft"> </td><td class="mdescRight">Gets the base engine. <br /></td></tr>
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<tr class="separator:a4c8b273c5cb3d470567c5691b68493a3"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a8bb583e039b49608272997ed2d3387fa" id="r_a8bb583e039b49608272997ed2d3387fa"><td class="memItemLeft" align="right" valign="top">const std::vector< fourdst::atomic::Species > & </td><td class="memItemRight" valign="bottom"><a class="el" href="#a8bb583e039b49608272997ed2d3387fa">getNetworkSpecies</a> () const override</td></tr>
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<tr class="memdesc:a8bb583e039b49608272997ed2d3387fa"><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:a8bb583e039b49608272997ed2d3387fa"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2c1d88b06568f9ea4c65e794d012ebfb" id="r_a2c1d88b06568f9ea4c65e794d012ebfb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>< double > </td><td class="memItemRight" valign="bottom"><a class="el" href="#a2c1d88b06568f9ea4c65e794d012ebfb">calculateRHSAndEnergy</a> (const std::vector< double > &Y_defined, const double T9, const double rho) const override</td></tr>
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<tr class="memdesc:a2c1d88b06568f9ea4c65e794d012ebfb"><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:a2c1d88b06568f9ea4c65e794d012ebfb"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a48b2451f96b8f5511ffc4071519c0810" id="r_a48b2451f96b8f5511ffc4071519c0810"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a48b2451f96b8f5511ffc4071519c0810">generateJacobianMatrix</a> (const std::vector< double > &Y_defined, const double T9, const double rho) override</td></tr>
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<tr class="memdesc:a48b2451f96b8f5511ffc4071519c0810"><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:a48b2451f96b8f5511ffc4071519c0810"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a0ef8804780d13bbfce0856237bb00470" id="r_a0ef8804780d13bbfce0856237bb00470"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="#a0ef8804780d13bbfce0856237bb00470">getJacobianMatrixEntry</a> (const int i_defined, const int j_defined) const override</td></tr>
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<tr class="memdesc:a0ef8804780d13bbfce0856237bb00470"><td class="mdescLeft"> </td><td class="mdescRight">Gets an entry from the Jacobian matrix for the active species. <br /></td></tr>
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<tr class="separator:a0ef8804780d13bbfce0856237bb00470"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a27a5163157cc15c4cb3b99a5d3564dbd" id="r_a27a5163157cc15c4cb3b99a5d3564dbd"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a27a5163157cc15c4cb3b99a5d3564dbd">generateStoichiometryMatrix</a> () override</td></tr>
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<tr class="memdesc:a27a5163157cc15c4cb3b99a5d3564dbd"><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:a27a5163157cc15c4cb3b99a5d3564dbd"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a9da9224f5c99a5068f3d8cbf066e4693" id="r_a9da9224f5c99a5068f3d8cbf066e4693"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="#a9da9224f5c99a5068f3d8cbf066e4693">getStoichiometryMatrixEntry</a> (const int speciesIndex_defined, const int reactionIndex_defined) const override</td></tr>
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<tr class="memdesc:a9da9224f5c99a5068f3d8cbf066e4693"><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:a9da9224f5c99a5068f3d8cbf066e4693"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ac371fb66fd0a76a04df204c9dd9a05ef" id="r_ac371fb66fd0a76a04df204c9dd9a05ef"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="#ac371fb66fd0a76a04df204c9dd9a05ef">calculateMolarReactionFlow</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &reaction, const std::vector< double > &Y_defined, const double T9, const double rho) const override</td></tr>
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<tr class="memdesc:ac371fb66fd0a76a04df204c9dd9a05ef"><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:ac371fb66fd0a76a04df204c9dd9a05ef"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a5bbea17b69cc8f81bc251a04f4435a0c" id="r_a5bbea17b69cc8f81bc251a04f4435a0c"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="#a5bbea17b69cc8f81bc251a04f4435a0c">getNetworkReactions</a> () const override</td></tr>
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<tr class="memdesc:a5bbea17b69cc8f81bc251a04f4435a0c"><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:a5bbea17b69cc8f81bc251a04f4435a0c"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ace3c6ea4841318c08695973ab3dcddc6" id="r_ace3c6ea4841318c08695973ab3dcddc6"><td class="memItemLeft" align="right" valign="top">std::unordered_map< fourdst::atomic::Species, double > </td><td class="memItemRight" valign="bottom"><a class="el" href="#ace3c6ea4841318c08695973ab3dcddc6">getSpeciesTimescales</a> (const std::vector< double > &Y_defined, const double T9, const double rho) const override</td></tr>
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<tr class="memdesc:ace3c6ea4841318c08695973ab3dcddc6"><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:ace3c6ea4841318c08695973ab3dcddc6"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ace3568eadaba69e7357b4386c5ca3eb0" id="r_ace3568eadaba69e7357b4386c5ca3eb0"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#ace3568eadaba69e7357b4386c5ca3eb0">update</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &netIn) override</td></tr>
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<tr class="memdesc:ace3568eadaba69e7357b4386c5ca3eb0"><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:ace3568eadaba69e7357b4386c5ca3eb0"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a92f14da849e99d07c1ff1347addb9263" id="r_a92f14da849e99d07c1ff1347addb9263"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a92f14da849e99d07c1ff1347addb9263">setNetworkFile</a> (const std::string &fileName)</td></tr>
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<tr class="memdesc:a92f14da849e99d07c1ff1347addb9263"><td class="mdescLeft"> </td><td class="mdescRight">Sets a new network file to define the active reactions. <br /></td></tr>
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<tr class="separator:a92f14da849e99d07c1ff1347addb9263"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ad96bbee6d3d37b50d9236a975ef704c0" id="r_ad96bbee6d3d37b50d9236a975ef704c0"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#ad96bbee6d3d37b50d9236a975ef704c0">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:ad96bbee6d3d37b50d9236a975ef704c0"><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:ad96bbee6d3d37b50d9236a975ef704c0"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:adbc50f397445f92b810d80cf329b8626" id="r_adbc50f397445f92b810d80cf329b8626"><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="#adbc50f397445f92b810d80cf329b8626">getScreeningModel</a> () const override</td></tr>
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<tr class="memdesc:adbc50f397445f92b810d80cf329b8626"><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:adbc50f397445f92b810d80cf329b8626"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_methods_classgridfire_1_1_engine"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td></tr>
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<tr class="memitem:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine" id="r_a2e7970bed2100699f226f4141d5db037"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a> ()=default</td></tr>
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<tr class="memdesc:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft"> </td><td class="mdescRight">Virtual destructor. <br /></td></tr>
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<tr class="separator:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_methods_classgridfire_1_1_engine_view"><td colspan="2" onclick="javascript:dynsection.toggleInherit('pub_methods_classgridfire_1_1_engine_view')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine_view.html">gridfire::EngineView< DynamicEngine ></a></td></tr>
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<tr class="memitem:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view" id="r_a994660f2d553f3a123512dc5eb421e74"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine_view.html#a994660f2d553f3a123512dc5eb421e74">~EngineView</a> ()=default</td></tr>
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<tr class="memdesc:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view"><td class="mdescLeft"> </td><td class="mdescRight">Virtual destructor. <br /></td></tr>
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<tr class="separator:a994660f2d553f3a123512dc5eb421e74 inherit pub_methods_classgridfire_1_1_engine_view"><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-types" name="pri-types"></a>
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Private Types</h2></td></tr>
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<tr class="memitem:a63f8f85e75ecaab6fa39d48d7a846187" id="r_a63f8f85e75ecaab6fa39d48d7a846187"><td class="memItemLeft" align="right" valign="top">using </td><td class="memItemRight" valign="bottom"><a class="el" href="#a63f8f85e75ecaab6fa39d48d7a846187">Config</a> = fourdst::config::Config</td></tr>
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<tr class="separator:a63f8f85e75ecaab6fa39d48d7a846187"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:acbb1a9bcb775e6d50de512a333afed08" id="r_acbb1a9bcb775e6d50de512a333afed08"><td class="memItemLeft" align="right" valign="top">using </td><td class="memItemRight" valign="bottom"><a class="el" href="#acbb1a9bcb775e6d50de512a333afed08">LogManager</a> = fourdst::logging::LogManager</td></tr>
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<tr class="separator:acbb1a9bcb775e6d50de512a333afed08"><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:a3b5162b7be35405285ef9f825ec2663b" id="r_a3b5162b7be35405285ef9f825ec2663b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a3b5162b7be35405285ef9f825ec2663b">buildFromFile</a> (const std::string &fileName)</td></tr>
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<tr class="memdesc:a3b5162b7be35405285ef9f825ec2663b"><td class="mdescLeft"> </td><td class="mdescRight">Builds the active species and reaction sets from a file. <br /></td></tr>
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<tr class="separator:a3b5162b7be35405285ef9f825ec2663b"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a51ba09ff01fdcac1125d42f276c9a0a7" id="r_a51ba09ff01fdcac1125d42f276c9a0a7"><td class="memItemLeft" align="right" valign="top">std::vector< size_t > </td><td class="memItemRight" valign="bottom"><a class="el" href="#a51ba09ff01fdcac1125d42f276c9a0a7">constructSpeciesIndexMap</a> () const</td></tr>
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<tr class="memdesc:a51ba09ff01fdcac1125d42f276c9a0a7"><td class="mdescLeft"> </td><td class="mdescRight">Constructs the species index map. <br /></td></tr>
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<tr class="separator:a51ba09ff01fdcac1125d42f276c9a0a7"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aebb3f3548f8781506f31580706810a4e" id="r_aebb3f3548f8781506f31580706810a4e"><td class="memItemLeft" align="right" valign="top">std::vector< size_t > </td><td class="memItemRight" valign="bottom"><a class="el" href="#aebb3f3548f8781506f31580706810a4e">constructReactionIndexMap</a> () const</td></tr>
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<tr class="memdesc:aebb3f3548f8781506f31580706810a4e"><td class="mdescLeft"> </td><td class="mdescRight">Constructs the reaction index map. <br /></td></tr>
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<tr class="separator:aebb3f3548f8781506f31580706810a4e"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:adba3c11b11a04b2907c1635210d73dee" id="r_adba3c11b11a04b2907c1635210d73dee"><td class="memItemLeft" align="right" valign="top">std::vector< double > </td><td class="memItemRight" valign="bottom"><a class="el" href="#adba3c11b11a04b2907c1635210d73dee">mapViewToFull</a> (const std::vector< double > &defined) const</td></tr>
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<tr class="memdesc:adba3c11b11a04b2907c1635210d73dee"><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:adba3c11b11a04b2907c1635210d73dee"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a97e5ee4651dbe6754678fe96e4702fee" id="r_a97e5ee4651dbe6754678fe96e4702fee"><td class="memItemLeft" align="right" valign="top">std::vector< double > </td><td class="memItemRight" valign="bottom"><a class="el" href="#a97e5ee4651dbe6754678fe96e4702fee">mapFullToView</a> (const std::vector< double > &full) const</td></tr>
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<tr class="memdesc:a97e5ee4651dbe6754678fe96e4702fee"><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:a97e5ee4651dbe6754678fe96e4702fee"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa2373955ef5b0eabf7a57c7208e38bb1" id="r_aa2373955ef5b0eabf7a57c7208e38bb1"><td class="memItemLeft" align="right" valign="top">size_t </td><td class="memItemRight" valign="bottom"><a class="el" href="#aa2373955ef5b0eabf7a57c7208e38bb1">mapViewToFullSpeciesIndex</a> (size_t definedSpeciesIndex) const</td></tr>
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<tr class="memdesc:aa2373955ef5b0eabf7a57c7208e38bb1"><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:aa2373955ef5b0eabf7a57c7208e38bb1"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a74217a1f8fd8e6daff969cb17885315c" id="r_a74217a1f8fd8e6daff969cb17885315c"><td class="memItemLeft" align="right" valign="top">size_t </td><td class="memItemRight" valign="bottom"><a class="el" href="#a74217a1f8fd8e6daff969cb17885315c">mapViewToFullReactionIndex</a> (size_t definedReactionIndex) const</td></tr>
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<tr class="memdesc:a74217a1f8fd8e6daff969cb17885315c"><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:a74217a1f8fd8e6daff969cb17885315c"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ae3f99002ab2c56a5bcdec00839f8628f" id="r_ae3f99002ab2c56a5bcdec00839f8628f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#ae3f99002ab2c56a5bcdec00839f8628f">validateNetworkState</a> () const</td></tr>
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<tr class="memdesc:ae3f99002ab2c56a5bcdec00839f8628f"><td class="mdescLeft"> </td><td class="mdescRight">Validates that the <a class="el" href="classgridfire_1_1_file_defined_engine_view.html" title="An engine view that uses a user-defined reaction network from a file.">FileDefinedEngineView</a> is not stale. <br /></td></tr>
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<tr class="separator:ae3f99002ab2c56a5bcdec00839f8628f"><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:a7a80966c023ae722239491af58609362" id="r_a7a80966c023ae722239491af58609362"><td class="memItemLeft" align="right" valign="top"><a class="el" href="#a63f8f85e75ecaab6fa39d48d7a846187">Config</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="#a7a80966c023ae722239491af58609362">m_config</a> = Config::getInstance()</td></tr>
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<tr class="memdesc:a7a80966c023ae722239491af58609362"><td class="mdescLeft"> </td><td class="mdescRight">A reference to the singleton <a class="el" href="#a63f8f85e75ecaab6fa39d48d7a846187">Config</a> instance. <br /></td></tr>
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<tr class="separator:a7a80966c023ae722239491af58609362"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a9d93633ed4ab68de94b7274f879a0432" id="r_a9d93633ed4ab68de94b7274f879a0432"><td class="memItemLeft" align="right" valign="top">quill::Logger * </td><td class="memItemRight" valign="bottom"><a class="el" href="#a9d93633ed4ab68de94b7274f879a0432">m_logger</a> = LogManager::getInstance().getLogger("log")</td></tr>
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<tr class="memdesc:a9d93633ed4ab68de94b7274f879a0432"><td class="mdescLeft"> </td><td class="mdescRight">A pointer to the logger instance. <br /></td></tr>
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<tr class="memitem:ad8454c98fa9a4bb45dc81059bc51fc81" id="r_ad8454c98fa9a4bb45dc81059bc51fc81"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="#ad8454c98fa9a4bb45dc81059bc51fc81">m_baseEngine</a></td></tr>
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<tr class="memdesc:ad8454c98fa9a4bb45dc81059bc51fc81"><td class="mdescLeft"> </td><td class="mdescRight">The underlying engine to which this view delegates calculations. <br /></td></tr>
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<tr class="memitem:a1b343998b93955025a589b2b4541e33b" id="r_a1b343998b93955025a589b2b4541e33b"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="#a1b343998b93955025a589b2b4541e33b">m_fileName</a></td></tr>
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<tr class="memdesc:a1b343998b93955025a589b2b4541e33b"><td class="mdescLeft"> </td><td class="mdescRight">Parser for the network file. <br /></td></tr>
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<tr class="separator:a1b343998b93955025a589b2b4541e33b"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a0a9b07176cb93b54c677b6ce71fda500" id="r_a0a9b07176cb93b54c677b6ce71fda500"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="#a0a9b07176cb93b54c677b6ce71fda500">m_parser</a></td></tr>
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<tr class="memdesc:a0a9b07176cb93b54c677b6ce71fda500"><td class="mdescLeft"> </td><td class="mdescRight">Active species in the defined engine. <br /></td></tr>
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<tr class="separator:a0a9b07176cb93b54c677b6ce71fda500"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a299a0c61aa4f26029c770013c9feff5e" id="r_a299a0c61aa4f26029c770013c9feff5e"><td class="memItemLeft" align="right" valign="top">std::vector< fourdst::atomic::Species > </td><td class="memItemRight" valign="bottom"><a class="el" href="#a299a0c61aa4f26029c770013c9feff5e">m_activeSpecies</a></td></tr>
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<tr class="memdesc:a299a0c61aa4f26029c770013c9feff5e"><td class="mdescLeft"> </td><td class="mdescRight">Active reactions in the defined engine. <br /></td></tr>
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<tr class="separator:a299a0c61aa4f26029c770013c9feff5e"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ae012da2b1f6169cb13e6075a73353ab2" id="r_ae012da2b1f6169cb13e6075a73353ab2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="#ae012da2b1f6169cb13e6075a73353ab2">m_activeReactions</a></td></tr>
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<tr class="memdesc:ae012da2b1f6169cb13e6075a73353ab2"><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="separator:ae012da2b1f6169cb13e6075a73353ab2"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aebd4a1a584f2784f1df3d503645be03b" id="r_aebd4a1a584f2784f1df3d503645be03b"><td class="memItemLeft" align="right" valign="top">std::vector< size_t > </td><td class="memItemRight" valign="bottom"><a class="el" href="#aebd4a1a584f2784f1df3d503645be03b">m_speciesIndexMap</a></td></tr>
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<tr class="memdesc:aebd4a1a584f2784f1df3d503645be03b"><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:aebd4a1a584f2784f1df3d503645be03b"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af0a77a4749a15aae87bdecfccbd1736e" id="r_af0a77a4749a15aae87bdecfccbd1736e"><td class="memItemLeft" align="right" valign="top">std::vector< size_t > </td><td class="memItemRight" valign="bottom"><a class="el" href="#af0a77a4749a15aae87bdecfccbd1736e">m_reactionIndexMap</a></td></tr>
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<tr class="memitem:a6e421bc748933be31bed9ff53f12b595" id="r_a6e421bc748933be31bed9ff53f12b595"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="#a6e421bc748933be31bed9ff53f12b595">m_isStale</a> = true</td></tr>
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<tr class="memdesc:a6e421bc748933be31bed9ff53f12b595"><td class="mdescLeft"> </td><td class="mdescRight">A flag indicating whether the view is stale and needs to be updated. <br /></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>An engine view that uses a user-defined reaction network from a file. </p>
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<p>This class implements an <a class="el" href="classgridfire_1_1_engine_view.html" title="Abstract base class for a "view" of a reaction network engine.">EngineView</a> that restricts the reaction network to a specific set of reactions defined in an external file. It acts as a filter or a view on a larger, more comprehensive base engine. The file provides a list of reaction identifiers, and this view will only consider those reactions and the species involved in them.</p>
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<p>This is useful for focusing on a specific sub-network for analysis, debugging, or performance reasons, without modifying the underlying full network.</p>
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<p>The view maintains mappings between the indices of its active (defined) species and reactions and the corresponding indices in the full network of the base engine. All calculations are delegated to the base engine after mapping the inputs from the view's context to the full network context, and the results are mapped back.</p>
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<p><DynamicEngine> </p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00036">36</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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</div><h2 class="groupheader">Member Typedef Documentation</h2>
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<a id="a63f8f85e75ecaab6fa39d48d7a846187" name="a63f8f85e75ecaab6fa39d48d7a846187"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a63f8f85e75ecaab6fa39d48d7a846187">◆ </a></span>Config</h2>
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<td class="memname">using <a class="el" href="#a63f8f85e75ecaab6fa39d48d7a846187">gridfire::FileDefinedEngineView::Config</a> = fourdst::config::Config</td>
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<span class="mlabels"><span class="mlabel private">private</span></span> </td>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00223">223</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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</div>
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</div>
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<a id="acbb1a9bcb775e6d50de512a333afed08" name="acbb1a9bcb775e6d50de512a333afed08"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#acbb1a9bcb775e6d50de512a333afed08">◆ </a></span>LogManager</h2>
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<td class="memname">using <a class="el" href="#acbb1a9bcb775e6d50de512a333afed08">gridfire::FileDefinedEngineView::LogManager</a> = fourdst::logging::LogManager</td>
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<span class="mlabels"><span class="mlabel private">private</span></span> </td>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00224">224</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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</div>
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</div>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<a id="a8f2f64bab0f516ed2a6fd529912e0acd" name="a8f2f64bab0f516ed2a6fd529912e0acd"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a8f2f64bab0f516ed2a6fd529912e0acd">◆ </a></span>FileDefinedEngineView()</h2>
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<td class="memname">gridfire::FileDefinedEngineView::FileDefinedEngineView </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &</td> <td class="paramname"><span class="paramname"><em>baseEngine</em></span>, </td>
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<td></td>
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<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>fileName</em></span>, </td>
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<td class="paramtype">const <a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a> &</td> <td class="paramname"><span class="paramname"><em>parser</em></span> )</td>
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<span class="mlabels"><span class="mlabel explicit">explicit</span></span> </td>
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<p>Constructs a <a class="el" href="classgridfire_1_1_file_defined_engine_view.html" title="An engine view that uses a user-defined reaction network from a file.">FileDefinedEngineView</a>. </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">baseEngine</td><td>The underlying <a class="el" href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> to which this view delegates calculations. </td></tr>
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<tr><td class="paramname">fileName</td><td>The path to the file that defines the reaction network for this view. </td></tr>
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<tr><td class="paramname">parser</td><td>A reference to a parser object capable of parsing the network file.</td></tr>
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<dl class="section user"><dt>Usage Example:</dt><dd><div class="fragment"><div class="line">MyParser parser;</div>
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<div class="line"><a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> baseEngine(...);</div>
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<div class="line"><a class="code hl_function" href="#a8f2f64bab0f516ed2a6fd529912e0acd">FileDefinedEngineView</a> view(baseEngine, <span class="stringliteral">"my_network.net"</span>, parser);</div>
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<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><div class="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00121">engine_abstract.h:121</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a8f2f64bab0f516ed2a6fd529912e0acd"><div class="ttname"><a href="#a8f2f64bab0f516ed2a6fd529912e0acd">gridfire::FileDefinedEngineView::FileDefinedEngineView</a></div><div class="ttdeci">FileDefinedEngineView(DynamicEngine &baseEngine, const std::string &fileName, const io::NetworkFileParser &parser)</div><div class="ttdoc">Constructs a FileDefinedEngineView.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00008">engine_defined.cpp:8</a></div></div>
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</div><!-- fragment --></dd></dl>
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<dl class="section post"><dt>Postcondition</dt><dd>The view is initialized with the reactions and species from the specified file. </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 a reaction from the file is not found in the base engine. </td></tr>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00008">8</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a3b5162b7be35405285ef9f825ec2663b">◆ </a></span>buildFromFile()</h2>
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<td class="memname">void gridfire::FileDefinedEngineView::buildFromFile </td>
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<td>(</td>
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<td class="paramtype">const std::string &</td> <td class="paramname"><span class="paramname"><em>fileName</em></span></td><td>)</td>
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<span class="mlabels"><span class="mlabel private">private</span></span> </td>
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<p>Builds the active species and reaction sets from a file. </p>
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<p>This method uses the provided parser to read reaction names from the given file. It then finds these reactions in the base engine's full network and populates the <code>m_activeReactions</code> and <code>m_activeSpecies</code> members. Finally, it constructs the index maps for the active sets.</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">fileName</td><td>The path to the network definition file.</td></tr>
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<dl class="section post"><dt>Postcondition</dt><dd><ul>
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<li><code>m_activeReactions</code> and <code>m_activeSpecies</code> are populated.</li>
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<li><code>m_speciesIndexMap</code> and <code>m_reactionIndexMap</code> are constructed.</li>
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<li><code>m_isStale</code> is set to false.</li>
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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 a reaction from the file is not found in the base engine. </td></tr>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00208">208</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ac371fb66fd0a76a04df204c9dd9a05ef">◆ </a></span>calculateMolarReactionFlow()</h2>
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<td class="memname">double gridfire::FileDefinedEngineView::calculateMolarReactionFlow </td>
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<td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &</td> <td class="paramname"><span class="paramname"><em>reaction</em></span>, </td>
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<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
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<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>rho</em></span> ) 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">Y_defined</td><td>Vector of current abundances for the active species. </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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<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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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00085">85</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a2c1d88b06568f9ea4c65e794d012ebfb">◆ </a></span>calculateRHSAndEnergy()</h2>
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<td class="memname"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>< double > gridfire::FileDefinedEngineView::calculateRHSAndEnergy </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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<tr><td class="paramname">Y_defined</td><td>A vector of abundances for the active species. </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_1_step_derivatives.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="#ace3568eadaba69e7357b4386c5ca3eb0" title="Updates the engine view if it is marked as stale.">update()</a></code> has not been called after <code><a class="el" href="#a92f14da849e99d07c1ff1347addb9263" title="Sets a new network file to define the active reactions.">setNetworkFile()</a></code>). </td></tr>
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<p>Implements <a class="el" href="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">gridfire::Engine</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00029">29</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aebb3f3548f8781506f31580706810a4e">◆ </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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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">std::runtime_error</td><td>If an active reaction is not found in the base engine's reaction list. </td></tr>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00176">176</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a51ba09ff01fdcac1125d42f276c9a0a7">◆ </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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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00147">147</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a48b2451f96b8f5511ffc4071519c0810">◆ </a></span>generateJacobianMatrix()</h2>
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<p>Generates the Jacobian matrix for the active species. </p>
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<tr><td class="paramname">Y_defined</td><td>A vector of abundances for the active species. </td></tr>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f">gridfire::DynamicEngine</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00045">45</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a27a5163157cc15c4cb3b99a5d3564dbd">◆ </a></span>generateStoichiometryMatrix()</h2>
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<p>Generates the stoichiometry matrix for the active reactions and species. </p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">gridfire::DynamicEngine</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00068">68</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<td class="memname">const <a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> & gridfire::FileDefinedEngineView::getBaseEngine </td>
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<p>Gets the base engine. </p>
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<dl class="section return"><dt>Returns</dt><dd>A const reference to the base engine. </dd></dl>
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<p>Implements <a class="el" href="classgridfire_1_1_engine_view.html#ad294227f8b5cf6d970c349eabf5447a6">gridfire::EngineView< DynamicEngine ></a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00021">21</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a0ef8804780d13bbfce0856237bb00470">◆ </a></span>getJacobianMatrixEntry()</h2>
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<td class="memname">double gridfire::FileDefinedEngineView::getJacobianMatrixEntry </td>
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<p>Gets an entry from 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">i_defined</td><td>The row index (species index) in the defined matrix. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>The value of the Jacobian matrix at (i_defined, j_defined).</dd></dl>
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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_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">gridfire::DynamicEngine</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00056">56</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a5bbea17b69cc8f81bc251a04f4435a0c">◆ </a></span>getNetworkReactions()</h2>
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<td class="memname">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> & gridfire::FileDefinedEngineView::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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<dl class="exception"><dt>Exceptions</dt><dd>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">gridfire::DynamicEngine</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00102">102</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a8bb583e039b49608272997ed2d3387fa">◆ </a></span>getNetworkSpecies()</h2>
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<td class="memname">const std::vector< Species > & gridfire::FileDefinedEngineView::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_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">gridfire::Engine</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00025">25</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#adbc50f397445f92b810d80cf329b8626">◆ </a></span>getScreeningModel()</h2>
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<td class="memname"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> gridfire::FileDefinedEngineView::getScreeningModel </td>
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<p>Gets the screening model from the base engine. </p>
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<dl class="section return"><dt>Returns</dt><dd>The current screening model type. </dd></dl>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">gridfire::DynamicEngine</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00143">143</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ace3c6ea4841318c08695973ab3dcddc6">◆ </a></span>getSpeciesTimescales()</h2>
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<td class="memname">std::unordered_map< Species, double > gridfire::FileDefinedEngineView::getSpeciesTimescales </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">Y_defined</td><td>Vector of current abundances for the active species. </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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<dl class="section return"><dt>Returns</dt><dd>Map from Species to their characteristic timescales (s).</dd></dl>
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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_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15">gridfire::DynamicEngine</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00108">108</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a9da9224f5c99a5068f3d8cbf066e4693">◆ </a></span>getStoichiometryMatrixEntry()</h2>
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<p>Gets an entry from the stoichiometry matrix for the active species and reactions. </p>
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<tr><td class="paramname">speciesIndex_defined</td><td>The index of the species in the defined species list. </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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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">gridfire::DynamicEngine</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00074">74</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a97e5ee4651dbe6754678fe96e4702fee">◆ </a></span>mapFullToView()</h2>
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<p>Maps a vector of full abundances to a vector of culled abundances. </p>
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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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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00276">276</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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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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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00267">267</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<td>(</td>
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<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>definedReactionIndex</em></span></td><td>)</td>
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<span class="mlabels"><span class="mlabel private">private</span></span> </td>
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<p>Maps a culled reaction index to a full reaction index. </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">definedReactionIndex</td><td>The index of the reaction in the defined reaction list. </td></tr>
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</dd>
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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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<table class="exception">
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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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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00294">294</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aa2373955ef5b0eabf7a57c7208e38bb1">◆ </a></span>mapViewToFullSpeciesIndex()</h2>
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<td class="memname">size_t gridfire::FileDefinedEngineView::mapViewToFullSpeciesIndex </td>
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<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>definedSpeciesIndex</em></span></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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<tr><td class="paramname">definedSpeciesIndex</td><td>The index of the species in the defined species list. </td></tr>
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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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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00285">285</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a92f14da849e99d07c1ff1347addb9263">◆ </a></span>setNetworkFile()</h2>
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<td class="memname">void gridfire::FileDefinedEngineView::setNetworkFile </td>
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<p>Sets a new network file to define the active reactions. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">fileName</td><td>The path to the new network definition file.</td></tr>
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<dl class="section user"><dt>Usage Example:</dt><dd><div class="fragment"><div class="line">view.setNetworkFile(<span class="stringliteral">"another_network.net"</span>);</div>
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<div class="line">view.update(netIn); <span class="comment">// Must be called before using the view again</span></div>
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<dl class="section post"><dt>Postcondition</dt><dd>The view is marked as stale. <code><a class="el" href="#ace3568eadaba69e7357b4386c5ca3eb0" title="Updates the engine view if it is marked as stale.">update()</a></code> must be called before further use. </dd></dl>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00133">133</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ad96bbee6d3d37b50d9236a975ef704c0">◆ </a></span>setScreeningModel()</h2>
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<td class="memname">void gridfire::FileDefinedEngineView::setScreeningModel </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a></td> <td class="paramname"><span class="paramname"><em>model</em></span></td><td>)</td>
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<p>Sets the screening model for the base engine. </p>
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<tr><td class="paramname">model</td><td>The screening model to set. </td></tr>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">gridfire::DynamicEngine</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00139">139</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ace3568eadaba69e7357b4386c5ca3eb0">◆ </a></span>update()</h2>
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<td class="memname">void gridfire::FileDefinedEngineView::update </td>
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<td>(</td>
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<td class="paramtype">const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &</td> <td class="paramname"><span class="paramname"><em>netIn</em></span></td><td>)</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_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f">gridfire::DynamicEngine</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00127">127</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ae3f99002ab2c56a5bcdec00839f8628f">◆ </a></span>validateNetworkState()</h2>
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<td class="memname">void gridfire::FileDefinedEngineView::validateNetworkState </td>
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<p>Validates that the <a class="el" href="classgridfire_1_1_file_defined_engine_view.html" title="An engine view that uses a user-defined reaction network from a file.">FileDefinedEngineView</a> is not stale. </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 (i.e., <code><a class="el" href="#ace3568eadaba69e7357b4386c5ca3eb0" title="Updates the engine view if it is marked as stale.">update()</a></code> has not been called after the view was made stale). </td></tr>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00303">303</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<a id="ae012da2b1f6169cb13e6075a73353ab2" name="ae012da2b1f6169cb13e6075a73353ab2"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ae012da2b1f6169cb13e6075a73353ab2">◆ </a></span>m_activeReactions</h2>
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<td class="memname"><a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> gridfire::FileDefinedEngineView::m_activeReactions</td>
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<p>Maps indices of active species to indices in the full network. </p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00240">240</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a299a0c61aa4f26029c770013c9feff5e">◆ </a></span>m_activeSpecies</h2>
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<p>Active reactions in the defined engine. </p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00238">238</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ad8454c98fa9a4bb45dc81059bc51fc81">◆ </a></span>m_baseEngine</h2>
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<p>The underlying engine to which this view delegates calculations. </p>
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<p>Name of the file defining the reaction set considered by the engine view. </p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00231">231</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<p>A reference to the singleton <a class="el" href="#a63f8f85e75ecaab6fa39d48d7a846187">Config</a> instance. </p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00226">226</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<p>Parser for the network file. </p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00233">233</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<p>A flag indicating whether the view is stale and needs to be updated. </p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00248">248</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a9d93633ed4ab68de94b7274f879a0432">◆ </a></span>m_logger</h2>
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<td class="memname">quill::Logger* gridfire::FileDefinedEngineView::m_logger = LogManager::getInstance().getLogger("log")</td>
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<p>A pointer to the logger instance. </p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00228">228</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a0a9b07176cb93b54c677b6ce71fda500">◆ </a></span>m_parser</h2>
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<td class="memname">const <a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a>& gridfire::FileDefinedEngineView::m_parser</td>
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<p>Active species in the defined engine. </p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00235">235</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#af0a77a4749a15aae87bdecfccbd1736e">◆ </a></span>m_reactionIndexMap</h2>
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<td class="memname">std::vector<size_t> gridfire::FileDefinedEngineView::m_reactionIndexMap</td>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00245">245</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aebd4a1a584f2784f1df3d503645be03b">◆ </a></span>m_speciesIndexMap</h2>
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<td class="memname">std::vector<size_t> gridfire::FileDefinedEngineView::m_speciesIndexMap</td>
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<p>Maps indices of active reactions to indices in the full network. </p>
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<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00243">243</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
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<hr/>The documentation for this class was generated from the following files:<ul>
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<li>src/network/include/gridfire/engine/views/<a class="el" href="engine__defined_8h_source.html">engine_defined.h</a></li>
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<li>src/network/lib/engine/views/<a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a></li>
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