refactor(.gitignore): removed html/ from .gitignore
This commit is contained in:
@@ -129,7 +129,7 @@ Public Member Functions</h2></td></tr>
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<tr class="memitem:a9f74786ff930ab72664b31f29d05a30c" id="r_a9f74786ff930ab72664b31f29d05a30c"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="#a9f74786ff930ab72664b31f29d05a30c">GraphEngine</a> (const fourdst::composition::Composition &composition)</td></tr>
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<tr class="memdesc:a9f74786ff930ab72664b31f29d05a30c"><td class="mdescLeft"> </td><td class="mdescRight">Constructs a <a class="el" href="classgridfire_1_1_graph_engine.html" title="A reaction network engine that uses a graph-based representation.">GraphEngine</a> from a composition. <br /></td></tr>
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<tr class="separator:a9f74786ff930ab72664b31f29d05a30c"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a9c285e3a38de6e73503a4e19666678e2" id="r_a9c285e3a38de6e73503a4e19666678e2"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="#a9c285e3a38de6e73503a4e19666678e2">GraphEngine</a> (<a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">reaction::LogicalReactionSet</a> reactions)</td></tr>
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<tr class="memitem:a9c285e3a38de6e73503a4e19666678e2" id="r_a9c285e3a38de6e73503a4e19666678e2"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="#a9c285e3a38de6e73503a4e19666678e2">GraphEngine</a> (<a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> reactions)</td></tr>
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<tr class="memdesc:a9c285e3a38de6e73503a4e19666678e2"><td class="mdescLeft"> </td><td class="mdescRight">Constructs a <a class="el" href="classgridfire_1_1_graph_engine.html" title="A reaction network engine that uses a graph-based representation.">GraphEngine</a> from a set of reactions. <br /></td></tr>
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<tr class="separator:a9c285e3a38de6e73503a4e19666678e2"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a8b3baf29829c7ae0a61430ea70632bbf" id="r_a8b3baf29829c7ae0a61430ea70632bbf"><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="#a8b3baf29829c7ae0a61430ea70632bbf">calculateRHSAndEnergy</a> (const std::vector< double > &Y, const double T9, const double rho) const override</td></tr>
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@@ -147,7 +147,7 @@ Public Member Functions</h2></td></tr>
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<tr class="memitem:a0ed390f3e598ebba4e245ac90bb78767" id="r_a0ed390f3e598ebba4e245ac90bb78767"><td class="memItemLeft" align="right" valign="top">const std::vector< fourdst::atomic::Species > & </td><td class="memItemRight" valign="bottom"><a class="el" href="#a0ed390f3e598ebba4e245ac90bb78767">getNetworkSpecies</a> () const override</td></tr>
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<tr class="memdesc:a0ed390f3e598ebba4e245ac90bb78767"><td class="mdescLeft"> </td><td class="mdescRight">Gets the list of species in the network. <br /></td></tr>
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<tr class="separator:a0ed390f3e598ebba4e245ac90bb78767"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ad45650d10fc5dff1673ae3f806d067da" id="r_ad45650d10fc5dff1673ae3f806d067da"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">reaction::LogicalReactionSet</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="#ad45650d10fc5dff1673ae3f806d067da">getNetworkReactions</a> () const override</td></tr>
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<tr class="memitem:ad45650d10fc5dff1673ae3f806d067da" id="r_ad45650d10fc5dff1673ae3f806d067da"><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="#ad45650d10fc5dff1673ae3f806d067da">getNetworkReactions</a> () const override</td></tr>
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<tr class="memdesc:ad45650d10fc5dff1673ae3f806d067da"><td class="mdescLeft"> </td><td class="mdescRight">Gets the set of logical reactions in the network. <br /></td></tr>
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<tr class="separator:ad45650d10fc5dff1673ae3f806d067da"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a303e6093591cde91430f866a04a8be7c" id="r_a303e6093591cde91430f866a04a8be7c"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="#a303e6093591cde91430f866a04a8be7c">getJacobianMatrixEntry</a> (const int i, const int j) const override</td></tr>
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@@ -159,6 +159,8 @@ Public Member Functions</h2></td></tr>
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<tr class="memitem:a26215593544c3a52597194602e4e25dd" id="r_a26215593544c3a52597194602e4e25dd"><td class="memItemLeft" align="right" valign="top">std::unordered_map< fourdst::atomic::Species, double > </td><td class="memItemRight" valign="bottom"><a class="el" href="#a26215593544c3a52597194602e4e25dd">getSpeciesTimescales</a> (const std::vector< double > &Y, double T9, double rho) const override</td></tr>
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<tr class="memdesc:a26215593544c3a52597194602e4e25dd"><td class="mdescLeft"> </td><td class="mdescRight">Computes timescales for all species in the network. <br /></td></tr>
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<tr class="separator:a26215593544c3a52597194602e4e25dd"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a51b4cedf9b00de79fb6eef243631b04d" id="r_a51b4cedf9b00de79fb6eef243631b04d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a51b4cedf9b00de79fb6eef243631b04d">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="separator:a51b4cedf9b00de79fb6eef243631b04d"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa6202cee0c3c481eda77cc9a91bc126b" id="r_aa6202cee0c3c481eda77cc9a91bc126b"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="#aa6202cee0c3c481eda77cc9a91bc126b">involvesSpecies</a> (const fourdst::atomic::Species &species) const</td></tr>
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<tr class="memdesc:aa6202cee0c3c481eda77cc9a91bc126b"><td class="mdescLeft"> </td><td class="mdescRight">Checks if a given species is involved in the network. <br /></td></tr>
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<tr class="separator:aa6202cee0c3c481eda77cc9a91bc126b"><td class="memSeparator" colspan="2"> </td></tr>
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@@ -168,6 +170,10 @@ Public Member Functions</h2></td></tr>
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<tr class="memitem:a832e2fe066381811a3e0464806ff5e95" id="r_a832e2fe066381811a3e0464806ff5e95"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a832e2fe066381811a3e0464806ff5e95">exportToCSV</a> (const std::string &filename) const</td></tr>
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<tr class="memdesc:a832e2fe066381811a3e0464806ff5e95"><td class="mdescLeft"> </td><td class="mdescRight">Exports the network to a CSV file for analysis. <br /></td></tr>
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<tr class="separator:a832e2fe066381811a3e0464806ff5e95"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a8110e687844f921438bb517e1d8ce62f" id="r_a8110e687844f921438bb517e1d8ce62f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="#a8110e687844f921438bb517e1d8ce62f">setScreeningModel</a> (<a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a>) override</td></tr>
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<tr class="separator:a8110e687844f921438bb517e1d8ce62f"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a697f2004e0d02c59e83c7890742d7c9a" id="r_a697f2004e0d02c59e83c7890742d7c9a"><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="#a697f2004e0d02c59e83c7890742d7c9a">getScreeningModel</a> () const override</td></tr>
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<tr class="separator:a697f2004e0d02c59e83c7890742d7c9a"><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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@@ -222,7 +228,7 @@ Private Member Functions</h2></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:acb7c4f5108b0efeae48ad15598e808c3" id="r_acb7c4f5108b0efeae48ad15598e808c3"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">reaction::LogicalReactionSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a></td></tr>
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<tr class="memitem:acb7c4f5108b0efeae48ad15598e808c3" id="r_acb7c4f5108b0efeae48ad15598e808c3"><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="#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a></td></tr>
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<tr class="memdesc:acb7c4f5108b0efeae48ad15598e808c3"><td class="mdescLeft"> </td><td class="mdescRight">Set of REACLIB reactions in the network. <br /></td></tr>
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<tr class="separator:acb7c4f5108b0efeae48ad15598e808c3"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a5d6cc63b99b467c2a976d1fbaaa1dfa3" id="r_a5d6cc63b99b467c2a976d1fbaaa1dfa3"><td class="memItemLeft" align="right" valign="top">std::unordered_map< std::string_view, <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> * > </td><td class="memItemRight" valign="bottom"><a class="el" href="#a5d6cc63b99b467c2a976d1fbaaa1dfa3">m_reactionIDMap</a></td></tr>
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@@ -246,6 +252,11 @@ Private Attributes</h2></td></tr>
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<tr class="memitem:a2e22b111f6d00ecc9e3804a71f1ce876" id="r_a2e22b111f6d00ecc9e3804a71f1ce876"><td class="memItemLeft" align="right" valign="top">CppAD::ADFun< double > </td><td class="memItemRight" valign="bottom"><a class="el" href="#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a></td></tr>
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<tr class="memdesc:a2e22b111f6d00ecc9e3804a71f1ce876"><td class="mdescLeft"> </td><td class="mdescRight">CppAD function for the right-hand side of the ODE. <br /></td></tr>
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<tr class="separator:a2e22b111f6d00ecc9e3804a71f1ce876"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a52edc3e88f1e8fc497e1e63972d63c80" id="r_a52edc3e88f1e8fc497e1e63972d63c80"><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="#a52edc3e88f1e8fc497e1e63972d63c80">m_screeningType</a> = <a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25ad80b95b1abb9c8659fa4cc9d3d29bb71">screening::ScreeningType::BARE</a></td></tr>
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<tr class="memdesc:a52edc3e88f1e8fc497e1e63972d63c80"><td class="mdescLeft"> </td><td class="mdescRight">Screening type for the reaction network. Default to no screening. <br /></td></tr>
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<tr class="separator:a52edc3e88f1e8fc497e1e63972d63c80"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af17cf3762abac3efcab9a8e87c961210" id="r_af17cf3762abac3efcab9a8e87c961210"><td class="memItemLeft" align="right" valign="top">std::unique_ptr< <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html">screening::ScreeningModel</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="#af17cf3762abac3efcab9a8e87c961210">m_screeningModel</a> = <a class="el" href="namespacegridfire_1_1screening.html#a6ca8556d27ac373e176f5b23437c416e">screening::selectScreeningModel</a>(<a class="el" href="#a52edc3e88f1e8fc497e1e63972d63c80">m_screeningType</a>)</td></tr>
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<tr class="separator:af17cf3762abac3efcab9a8e87c961210"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a3b17102b143435ddfdc015d7a50c4b18" id="r_a3b17102b143435ddfdc015d7a50c4b18"><td class="memItemLeft" align="right" valign="top">Config & </td><td class="memItemRight" valign="bottom"><a class="el" href="#a3b17102b143435ddfdc015d7a50c4b18">m_config</a> = Config::getInstance()</td></tr>
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<tr class="separator:a3b17102b143435ddfdc015d7a50c4b18"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a0837bab6dcd111d9075c9343b90d64f1" id="r_a0837bab6dcd111d9075c9343b90d64f1"><td class="memItemLeft" align="right" valign="top">Constants & </td><td class="memItemRight" valign="bottom"><a class="el" href="#a0837bab6dcd111d9075c9343b90d64f1">m_constants</a> = Constants::getInstance()</td></tr>
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@@ -268,7 +279,7 @@ Private Attributes</h2></td></tr>
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</ul>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="engine__abstract_8h.html" title="Abstract interfaces for reaction network engines in GridFire.">engine_abstract.h</a> </dd></dl>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00086">86</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00089">89</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<a id="a9f74786ff930ab72664b31f29d05a30c" name="a9f74786ff930ab72664b31f29d05a30c"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a9f74786ff930ab72664b31f29d05a30c">◆ </a></span>GraphEngine() <span class="overload">[1/2]</span></h2>
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@@ -303,7 +314,7 @@ Private Attributes</h2></td></tr>
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<p>This constructor builds the reaction network from the given composition using the <code>build_reaclib_nuclear_network</code> function.</p>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="namespacegridfire.html#aa77f83539d9ae90e3bf541309bd9c83a">build_reaclib_nuclear_network</a> </dd></dl>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00025">25</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00026">26</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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</div>
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</div>
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@@ -319,7 +330,7 @@ Private Attributes</h2></td></tr>
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<tr>
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<td class="memname">gridfire::GraphEngine::GraphEngine </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">reaction::LogicalReactionSet</a></td> <td class="paramname"><span class="paramname"><em>reactions</em></span></td><td>)</td>
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<td class="paramtype"><a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a></td> <td class="paramname"><span class="paramname"><em>reactions</em></span></td><td>)</td>
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<td></td>
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</tr>
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</table>
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@@ -339,7 +350,7 @@ Private Attributes</h2></td></tr>
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</dl>
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<p>This constructor uses the given set of reactions to construct the reaction network. </p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00032">32</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00033">33</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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</div>
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</div>
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@@ -371,7 +382,7 @@ Private Attributes</h2></td></tr>
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</table>
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</td>
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<td class="mlabels-right">
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<span class="mlabels"><span class="mlabel private">private</span></span> </td>
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<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel private">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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@@ -388,7 +399,7 @@ Private Attributes</h2></td></tr>
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<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives<ADDouble></a> containing dY/dt and energy generation rate.</dd></dl>
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<p>This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state using automatic differentiation. </p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00257">257</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00258">258</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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</div>
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</div>
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@@ -419,7 +430,7 @@ Private Attributes</h2></td></tr>
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</table>
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</td>
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<td class="mlabels-right">
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<span class="mlabels"><span class="mlabel private">private</span></span> </td>
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<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel private">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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@@ -436,7 +447,7 @@ Private Attributes</h2></td></tr>
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<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives<double></a> containing dY/dt and energy generation rate.</dd></dl>
|
||||
<p>This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state using double precision arithmetic. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00249">249</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00250">250</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -469,7 +480,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
</table>
|
||||
</td>
|
||||
<td class="mlabels-right">
|
||||
<span class="mlabels"><span class="mlabel private">private</span></span> </td>
|
||||
<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel private">private</span></span> </td>
|
||||
</tr>
|
||||
</table>
|
||||
</div><div class="memdoc">
|
||||
@@ -492,7 +503,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives<T></a> containing dY/dt and energy generation rate.</dd></dl>
|
||||
<p>This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00475">475</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00487">487</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -528,7 +539,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
</table>
|
||||
</td>
|
||||
<td class="mlabels-right">
|
||||
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
|
||||
<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
|
||||
</tr>
|
||||
</table>
|
||||
</div><div class="memdoc">
|
||||
@@ -548,7 +559,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine</a>.</p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00265">265</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00275">275</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -610,7 +621,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
<dl class="section return"><dt>Returns</dt><dd>Molar flow rate for the reaction (e.g., mol/g/s).</dd></dl>
|
||||
<p>This method computes the net rate at which the given reaction proceeds under the current state. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00536">536</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00555">555</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -641,7 +652,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
</table>
|
||||
</td>
|
||||
<td class="mlabels-right">
|
||||
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
|
||||
<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
|
||||
</tr>
|
||||
</table>
|
||||
</div><div class="memdoc">
|
||||
@@ -661,7 +672,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>Implements <a class="el" href="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">gridfire::Engine</a>.</p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00037">37</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00038">38</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -691,7 +702,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
<p>Collects the unique species in the network. </p>
|
||||
<p>This method collects the unique species in the network from the reactants and products of all reactions. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00056">56</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00057">57</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -726,7 +737,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
</dl>
|
||||
<p>Example usage: </p><div class="fragment"><div class="line">engine.exportToCSV(<span class="stringliteral">"network.csv"</span>);</div>
|
||||
</div><!-- fragment -->
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00372">372</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00382">382</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -761,7 +772,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
</dl>
|
||||
<p>Example usage: </p><div class="fragment"><div class="line">engine.exportToDot(<span class="stringliteral">"network.dot"</span>);</div>
|
||||
</div><!-- fragment -->
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00324">324</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00334">334</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -811,7 +822,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f">gridfire::DynamicEngine</a>.</p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00274">274</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00284">284</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -843,7 +854,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">gridfire::DynamicEngine</a>.</p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00208">208</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00209">209</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -888,7 +899,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">gridfire::DynamicEngine</a>.</p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00307">307</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00317">317</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -924,7 +935,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
</dl>
|
||||
<dl class="section return"><dt>Returns</dt><dd>Map of species to their stoichiometric coefficients. </dd></dl>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00311">311</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00321">321</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -938,7 +949,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
<td class="mlabels-left">
|
||||
<table class="memname">
|
||||
<tr>
|
||||
<td class="memname">const <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">reaction::LogicalReactionSet</a> & gridfire::GraphEngine::getNetworkReactions </td>
|
||||
<td class="memname">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> & gridfire::GraphEngine::getNetworkReactions </td>
|
||||
<td>(</td>
|
||||
<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
|
||||
<td> const</td>
|
||||
@@ -956,7 +967,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">gridfire::DynamicEngine</a>.</p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00118">118</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00119">119</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -988,7 +999,36 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>Implements <a class="el" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">gridfire::Engine</a>.</p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00112">112</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00113">113</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<a id="a697f2004e0d02c59e83c7890742d7c9a" name="a697f2004e0d02c59e83c7890742d7c9a"></a>
|
||||
<h2 class="memtitle"><span class="permalink"><a href="#a697f2004e0d02c59e83c7890742d7c9a">◆ </a></span>getScreeningModel()</h2>
|
||||
|
||||
<div class="memitem">
|
||||
<div class="memproto">
|
||||
<table class="mlabels">
|
||||
<tr>
|
||||
<td class="mlabels-left">
|
||||
<table class="memname">
|
||||
<tr>
|
||||
<td class="memname"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> gridfire::GraphEngine::getScreeningModel </td>
|
||||
<td>(</td>
|
||||
<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
|
||||
<td> const</td>
|
||||
</tr>
|
||||
</table>
|
||||
</td>
|
||||
<td class="mlabels-right">
|
||||
<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
|
||||
</tr>
|
||||
</table>
|
||||
</div><div class="memdoc">
|
||||
|
||||
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">gridfire::DynamicEngine</a>.</p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00271">271</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -1038,7 +1078,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15">gridfire::DynamicEngine</a>.</p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00426">426</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00436">436</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -1083,7 +1123,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">gridfire::DynamicEngine</a>.</p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00317">317</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00327">327</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -1119,7 +1159,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
</dl>
|
||||
<dl class="section return"><dt>Returns</dt><dd>True if the species is involved in the network, false otherwise. </dd></dl>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00124">124</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00125">125</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -1149,7 +1189,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
<p>Populates the reaction ID map. </p>
|
||||
<p>This method populates the reaction ID map, which maps reaction IDs to REACLIBReaction objects. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00085">85</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00086">86</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -1179,7 +1219,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
<p>Populates the species-to-index map. </p>
|
||||
<p>This method populates the species-to-index map, which maps species to their index in the stoichiometry matrix. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00094">94</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00095">95</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -1215,7 +1255,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
</dd>
|
||||
</dl>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00442">442</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00456">456</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
@@ -1245,7 +1285,36 @@ template<IsArithmeticOrAD T> </div>
|
||||
<p>Reserves space for the Jacobian matrix. </p>
|
||||
<p>This method reserves space for the Jacobian matrix, which is used to store the partial derivatives of the right-hand side of the ODE with respect to the species abundances. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00101">101</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00102">102</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<a id="a8110e687844f921438bb517e1d8ce62f" name="a8110e687844f921438bb517e1d8ce62f"></a>
|
||||
<h2 class="memtitle"><span class="permalink"><a href="#a8110e687844f921438bb517e1d8ce62f">◆ </a></span>setScreeningModel()</h2>
|
||||
|
||||
<div class="memitem">
|
||||
<div class="memproto">
|
||||
<table class="mlabels">
|
||||
<tr>
|
||||
<td class="mlabels-left">
|
||||
<table class="memname">
|
||||
<tr>
|
||||
<td class="memname">void gridfire::GraphEngine::setScreeningModel </td>
|
||||
<td>(</td>
|
||||
<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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<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
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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__graph_8cpp_source.html#l00266">266</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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||||
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||||
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||||
@@ -1275,7 +1344,36 @@ template<IsArithmeticOrAD T> </div>
|
||||
<p>Synchronizes the internal maps. </p>
|
||||
<p>This method synchronizes the internal maps used by the engine, including the species map, reaction ID map, and species-to-index map. It also generates the stoichiometry matrix and records the AD tape. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00046">46</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00047">47</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
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||||
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||||
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||||
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|
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<h2 class="memtitle"><span class="permalink"><a href="#a51b4cedf9b00de79fb6eef243631b04d">◆ </a></span>update()</h2>
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||||
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|
||||
<td class="memname">void gridfire::GraphEngine::update </td>
|
||||
<td>(</td>
|
||||
<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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||||
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||||
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|
||||
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|
||||
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel virtual">virtual</span></span> </td>
|
||||
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||||
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|
||||
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|
||||
|
||||
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#acd500e1cd788df1dc105d28a20dc5f4f">gridfire::DynamicEngine</a>.</p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00452">452</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
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|
||||
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|
||||
@@ -1322,7 +1420,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
</dl>
|
||||
<p>This method validates the composition against the current reaction set. If the composition is not compatible with the reaction set, the reaction set is rebuilt from the composition. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00187">187</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00188">188</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
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|
||||
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|
||||
@@ -1353,7 +1451,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
<dl class="section return"><dt>Returns</dt><dd>True if all reactions conserve mass and charge, false otherwise.</dd></dl>
|
||||
<p>This method checks that all reactions in the network conserve mass and charge. If any reaction does not conserve mass or charge, an error message is logged and false is returned. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00132">132</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00133">133</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
|
||||
|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00310">310</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00322">322</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
||||
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||||
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|
||||
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|
||||
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|
||||
|
||||
<p>Access to physical constants. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00311">311</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00323">323</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
||||
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||||
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|
||||
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|
||||
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|
||||
|
||||
<p>Jacobian matrix (species x species). </p>
|
||||
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||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00306">306</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00315">315</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
||||
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||||
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||||
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||||
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||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00312">312</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00324">324</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
||||
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||||
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|
||||
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|
||||
@@ -1480,7 +1578,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>Vector of unique species in the network. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00301">301</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00310">310</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
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||||
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||||
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||||
@@ -1506,7 +1604,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
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||||
<p>Map from species name to Species object. </p>
|
||||
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||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00302">302</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00311">311</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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||||
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|
||||
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|
||||
@@ -1532,7 +1630,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a performance bottleneck. </p>
|
||||
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||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00299">299</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00308">308</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<td class="memname"><a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">reaction::LogicalReactionSet</a> gridfire::GraphEngine::m_reactions</td>
|
||||
<td class="memname"><a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> gridfire::GraphEngine::m_reactions</td>
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||||
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|
||||
|
||||
<p>Set of REACLIB reactions in the network. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00298">298</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00307">307</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -1584,7 +1682,57 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>CppAD function for the right-hand side of the ODE. </p>
|
||||
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00308">308</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00317">317</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<a id="af17cf3762abac3efcab9a8e87c961210" name="af17cf3762abac3efcab9a8e87c961210"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#af17cf3762abac3efcab9a8e87c961210">◆ </a></span>m_screeningModel</h2>
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<td class="memname">std::unique_ptr<<a class="el" href="classgridfire_1_1screening_1_1_screening_model.html">screening::ScreeningModel</a>> gridfire::GraphEngine::m_screeningModel = <a class="el" href="namespacegridfire_1_1screening.html#a6ca8556d27ac373e176f5b23437c416e">screening::selectScreeningModel</a>(<a class="el" href="#a52edc3e88f1e8fc497e1e63972d63c80">m_screeningType</a>)</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__graph_8h_source.html#l00320">320</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a52edc3e88f1e8fc497e1e63972d63c80">◆ </a></span>m_screeningType</h2>
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<td class="memname"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> gridfire::GraphEngine::m_screeningType = <a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25ad80b95b1abb9c8659fa4cc9d3d29bb71">screening::ScreeningType::BARE</a></td>
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<p>Screening type for the reaction network. Default to no screening. </p>
|
||||
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00319">319</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
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|
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|
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@@ -1610,7 +1758,7 @@ template<IsArithmeticOrAD T> </div>
|
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|
||||
<p>Map from species to their index in the stoichiometry matrix. </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00303">303</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00312">312</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
|
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|
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|
||||
@@ -1636,7 +1784,7 @@ template<IsArithmeticOrAD T> </div>
|
||||
|
||||
<p>Stoichiometry matrix (species x reactions). </p>
|
||||
|
||||
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00305">305</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00314">314</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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</div>
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Reference in New Issue
Block a user