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docs(docs): added doxygen html directory
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<div id="projectbrief">General Purpose Nuclear Network</div>
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<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="#pub-static-methods">Static Public Member Functions</a> &#124;
<a href="#pri-methods">Private Member Functions</a> &#124;
<a href="#pri-attribs">Private Attributes</a> &#124;
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<div class="headertitle"><div class="title">gridfire::GraphEngine Class Reference<span class="mlabels"><span class="mlabel final">final</span></span></div></div>
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<p>A reaction network engine that uses a graph-based representation.
<a href="#details">More...</a></p>
<p><code>#include &lt;<a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>&gt;</code></p>
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Inheritance diagram for gridfire::GraphEngine:</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="0,56,147,80"/>
<area href="classgridfire_1_1_engine.html" title="Abstract base class for a reaction network engine." alt="gridfire::Engine" shape="rect" coords="0,0,147,24"/>
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<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a9f74786ff930ab72664b31f29d05a30c" id="r_a9f74786ff930ab72664b31f29d05a30c"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a9f74786ff930ab72664b31f29d05a30c">GraphEngine</a> (const fourdst::composition::Composition &amp;composition)</td></tr>
<tr class="memdesc:a9f74786ff930ab72664b31f29d05a30c"><td class="mdescLeft">&#160;</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>
<tr class="separator:a9f74786ff930ab72664b31f29d05a30c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a9c285e3a38de6e73503a4e19666678e2" id="r_a9c285e3a38de6e73503a4e19666678e2"><td class="memItemLeft" align="right" valign="top">&#160;</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>
<tr class="memdesc:a9c285e3a38de6e73503a4e19666678e2"><td class="mdescLeft">&#160;</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>
<tr class="separator:a9c285e3a38de6e73503a4e19666678e2"><td class="memSeparator" colspan="2">&#160;</td></tr>
<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>&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a8b3baf29829c7ae0a61430ea70632bbf">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:a8b3baf29829c7ae0a61430ea70632bbf"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the right-hand side (dY/dt) and energy generation rate. <br /></td></tr>
<tr class="separator:a8b3baf29829c7ae0a61430ea70632bbf"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae347ff0316e532e0298ec8c913908105" id="r_ae347ff0316e532e0298ec8c913908105"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ae347ff0316e532e0298ec8c913908105">generateJacobianMatrix</a> (const std::vector&lt; double &gt; &amp;Y, const double T9, const double rho) override</td></tr>
<tr class="memdesc:ae347ff0316e532e0298ec8c913908105"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generates the Jacobian matrix for the current state. <br /></td></tr>
<tr class="separator:ae347ff0316e532e0298ec8c913908105"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aed726d36ee2b3796beff6067a1e4db38" id="r_aed726d36ee2b3796beff6067a1e4db38"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aed726d36ee2b3796beff6067a1e4db38">generateStoichiometryMatrix</a> () override</td></tr>
<tr class="memdesc:aed726d36ee2b3796beff6067a1e4db38"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generates the stoichiometry matrix for the network. <br /></td></tr>
<tr class="separator:aed726d36ee2b3796beff6067a1e4db38"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a9245642b741f215e52861d00e756fb3f" id="r_a9245642b741f215e52861d00e756fb3f"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a9245642b741f215e52861d00e756fb3f">calculateMolarReactionFlow</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;reaction, const std::vector&lt; double &gt; &amp;Y, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:a9245642b741f215e52861d00e756fb3f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the molar reaction flow for a given reaction. <br /></td></tr>
<tr class="separator:a9245642b741f215e52861d00e756fb3f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0ed390f3e598ebba4e245ac90bb78767" id="r_a0ed390f3e598ebba4e245ac90bb78767"><td class="memItemLeft" align="right" valign="top">const std::vector&lt; fourdst::atomic::Species &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0ed390f3e598ebba4e245ac90bb78767">getNetworkSpecies</a> () const override</td></tr>
<tr class="memdesc:a0ed390f3e598ebba4e245ac90bb78767"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the list of species in the network. <br /></td></tr>
<tr class="separator:a0ed390f3e598ebba4e245ac90bb78767"><td class="memSeparator" colspan="2">&#160;</td></tr>
<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> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad45650d10fc5dff1673ae3f806d067da">getNetworkReactions</a> () const override</td></tr>
<tr class="memdesc:ad45650d10fc5dff1673ae3f806d067da"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the set of logical reactions in the network. <br /></td></tr>
<tr class="separator:ad45650d10fc5dff1673ae3f806d067da"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a303e6093591cde91430f866a04a8be7c" id="r_a303e6093591cde91430f866a04a8be7c"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a303e6093591cde91430f866a04a8be7c">getJacobianMatrixEntry</a> (const int i, const int j) const override</td></tr>
<tr class="memdesc:a303e6093591cde91430f866a04a8be7c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets an entry from the previously generated Jacobian matrix. <br /></td></tr>
<tr class="separator:a303e6093591cde91430f866a04a8be7c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a6b5feaf788bade212b7c8df7ac8c8152" id="r_a6b5feaf788bade212b7c8df7ac8c8152"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a6b5feaf788bade212b7c8df7ac8c8152">getStoichiometryMatrixEntry</a> (const int speciesIndex, const int reactionIndex) const override</td></tr>
<tr class="memdesc:a6b5feaf788bade212b7c8df7ac8c8152"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets an entry from the stoichiometry matrix. <br /></td></tr>
<tr class="separator:a6b5feaf788bade212b7c8df7ac8c8152"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a26215593544c3a52597194602e4e25dd" id="r_a26215593544c3a52597194602e4e25dd"><td class="memItemLeft" align="right" valign="top">std::unordered_map&lt; fourdst::atomic::Species, double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a26215593544c3a52597194602e4e25dd">getSpeciesTimescales</a> (const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td></tr>
<tr class="memdesc:a26215593544c3a52597194602e4e25dd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Computes timescales for all species in the network. <br /></td></tr>
<tr class="separator:a26215593544c3a52597194602e4e25dd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa6202cee0c3c481eda77cc9a91bc126b" id="r_aa6202cee0c3c481eda77cc9a91bc126b"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aa6202cee0c3c481eda77cc9a91bc126b">involvesSpecies</a> (const fourdst::atomic::Species &amp;species) const</td></tr>
<tr class="memdesc:aa6202cee0c3c481eda77cc9a91bc126b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Checks if a given species is involved in the network. <br /></td></tr>
<tr class="separator:aa6202cee0c3c481eda77cc9a91bc126b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:adac8c7d62bae76e17fc060e86dadd929" id="r_adac8c7d62bae76e17fc060e86dadd929"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#adac8c7d62bae76e17fc060e86dadd929">exportToDot</a> (const std::string &amp;filename) const</td></tr>
<tr class="memdesc:adac8c7d62bae76e17fc060e86dadd929"><td class="mdescLeft">&#160;</td><td class="mdescRight">Exports the network to a DOT file for visualization. <br /></td></tr>
<tr class="separator:adac8c7d62bae76e17fc060e86dadd929"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a832e2fe066381811a3e0464806ff5e95" id="r_a832e2fe066381811a3e0464806ff5e95"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a832e2fe066381811a3e0464806ff5e95">exportToCSV</a> (const std::string &amp;filename) const</td></tr>
<tr class="memdesc:a832e2fe066381811a3e0464806ff5e95"><td class="mdescLeft">&#160;</td><td class="mdescRight">Exports the network to a CSV file for analysis. <br /></td></tr>
<tr class="separator:a832e2fe066381811a3e0464806ff5e95"><td class="memSeparator" colspan="2">&#160;</td></tr>
<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="-"/>&#160;Public Member Functions inherited from <a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td></tr>
<tr class="memitem:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine" id="r_a2e7970bed2100699f226f4141d5db037"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a> ()=default</td></tr>
<tr class="memdesc:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor. <br /></td></tr>
<tr class="separator:a2e7970bed2100699f226f4141d5db037 inherit pub_methods_classgridfire_1_1_engine"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-static-methods" name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr class="memitem:a8c29d8bbde407e913be5eb77efb2c0c9" id="r_a8c29d8bbde407e913be5eb77efb2c0c9"><td class="memItemLeft" align="right" valign="top">static std::unordered_map&lt; fourdst::atomic::Species, int &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a8c29d8bbde407e913be5eb77efb2c0c9">getNetReactionStoichiometry</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;reaction)</td></tr>
<tr class="memdesc:a8c29d8bbde407e913be5eb77efb2c0c9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the net stoichiometry for a given reaction. <br /></td></tr>
<tr class="separator:a8c29d8bbde407e913be5eb77efb2c0c9"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:acdce8d87e23a2cd1504bc9472e538c0f" id="r_acdce8d87e23a2cd1504bc9472e538c0f"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#acdce8d87e23a2cd1504bc9472e538c0f">syncInternalMaps</a> ()</td></tr>
<tr class="memdesc:acdce8d87e23a2cd1504bc9472e538c0f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Synchronizes the internal maps. <br /></td></tr>
<tr class="separator:acdce8d87e23a2cd1504bc9472e538c0f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aedf42d83bfcc28313b6b6454034d2efa" id="r_aedf42d83bfcc28313b6b6454034d2efa"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aedf42d83bfcc28313b6b6454034d2efa">collectNetworkSpecies</a> ()</td></tr>
<tr class="memdesc:aedf42d83bfcc28313b6b6454034d2efa"><td class="mdescLeft">&#160;</td><td class="mdescRight">Collects the unique species in the network. <br /></td></tr>
<tr class="separator:aedf42d83bfcc28313b6b6454034d2efa"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a26602e1b3c610780a47b5a6511d6d567" id="r_a26602e1b3c610780a47b5a6511d6d567"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a26602e1b3c610780a47b5a6511d6d567">populateReactionIDMap</a> ()</td></tr>
<tr class="memdesc:a26602e1b3c610780a47b5a6511d6d567"><td class="mdescLeft">&#160;</td><td class="mdescRight">Populates the reaction ID map. <br /></td></tr>
<tr class="separator:a26602e1b3c610780a47b5a6511d6d567"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a47202c43342b96480070874bffce1391" id="r_a47202c43342b96480070874bffce1391"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a47202c43342b96480070874bffce1391">populateSpeciesToIndexMap</a> ()</td></tr>
<tr class="memdesc:a47202c43342b96480070874bffce1391"><td class="mdescLeft">&#160;</td><td class="mdescRight">Populates the species-to-index map. <br /></td></tr>
<tr class="separator:a47202c43342b96480070874bffce1391"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5a5458ed01923124f2d7e1f04f32f138" id="r_a5a5458ed01923124f2d7e1f04f32f138"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a5a5458ed01923124f2d7e1f04f32f138">reserveJacobianMatrix</a> ()</td></tr>
<tr class="memdesc:a5a5458ed01923124f2d7e1f04f32f138"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reserves space for the Jacobian matrix. <br /></td></tr>
<tr class="separator:a5a5458ed01923124f2d7e1f04f32f138"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a95563f6bc86007d9ee053a0f1e15b889" id="r_a95563f6bc86007d9ee053a0f1e15b889"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a95563f6bc86007d9ee053a0f1e15b889">recordADTape</a> ()</td></tr>
<tr class="memdesc:a95563f6bc86007d9ee053a0f1e15b889"><td class="mdescLeft">&#160;</td><td class="mdescRight">Records the AD tape for the right-hand side of the ODE. <br /></td></tr>
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<tr class="memitem:acf4cfccea20f5cb31c9886bf233a28be" id="r_acf4cfccea20f5cb31c9886bf233a28be"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#acf4cfccea20f5cb31c9886bf233a28be">validateConservation</a> () const</td></tr>
<tr class="memdesc:acf4cfccea20f5cb31c9886bf233a28be"><td class="mdescLeft">&#160;</td><td class="mdescRight">Validates mass and charge conservation across all reactions. <br /></td></tr>
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<tr class="memitem:aeeafeab40a5f4dbfae78bdc87e25e93f" id="r_aeeafeab40a5f4dbfae78bdc87e25e93f"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aeeafeab40a5f4dbfae78bdc87e25e93f">validateComposition</a> (const fourdst::composition::Composition &amp;composition, double culling, double T9)</td></tr>
<tr class="memdesc:aeeafeab40a5f4dbfae78bdc87e25e93f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Validates the composition against the current reaction set. <br /></td></tr>
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<tr class="memitem:a5e96b5a0b34c8932f0e14eabda57f1a4" id="r_a5e96b5a0b34c8932f0e14eabda57f1a4"><td class="memTemplParams" colspan="2">template&lt;IsArithmeticOrAD T&gt; </td></tr>
<tr class="memitem:a5e96b5a0b34c8932f0e14eabda57f1a4"><td class="memTemplItemLeft" align="right" valign="top">T&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="#a5e96b5a0b34c8932f0e14eabda57f1a4">calculateMolarReactionFlow</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;reaction, const std::vector&lt; T &gt; &amp;Y, const T T9, const T rho) const</td></tr>
<tr class="memdesc:a5e96b5a0b34c8932f0e14eabda57f1a4"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the molar reaction flow for a given reaction. <br /></td></tr>
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<tr class="memitem:af41df9ce979b6410e12642cb093916c9" id="r_af41df9ce979b6410e12642cb093916c9"><td class="memTemplParams" colspan="2">template&lt;IsArithmeticOrAD T&gt; </td></tr>
<tr class="memitem:af41df9ce979b6410e12642cb093916c9"><td class="memTemplItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; T &gt;&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="#af41df9ce979b6410e12642cb093916c9">calculateAllDerivatives</a> (const std::vector&lt; T &gt; &amp;Y_in, T T9, T rho) const</td></tr>
<tr class="memdesc:af41df9ce979b6410e12642cb093916c9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates all derivatives (dY/dt) and the energy generation rate. <br /></td></tr>
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<tr class="memdesc:aaf4d54e4b774ab8ec8eabec006579d31"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates all derivatives (dY/dt) and the energy generation rate (double precision). <br /></td></tr>
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<tr class="memitem:a71a3d1181b90c3becdc5d9a3da05b9c9" id="r_a71a3d1181b90c3becdc5d9a3da05b9c9"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; <a class="el" href="namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc">ADDouble</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a71a3d1181b90c3becdc5d9a3da05b9c9">calculateAllDerivatives</a> (const std::vector&lt; <a class="el" href="namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc">ADDouble</a> &gt; &amp;Y_in, const <a class="el" href="namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc">ADDouble</a> &amp;T9, const <a class="el" href="namespacegridfire.html#a1121d0b2d005195333412559fa29d3cc">ADDouble</a> &amp;rho) const</td></tr>
<tr class="memdesc:a71a3d1181b90c3becdc5d9a3da05b9c9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates all derivatives (dY/dt) and the energy generation rate (automatic differentiation). <br /></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
Private Attributes</h2></td></tr>
<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>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#acb7c4f5108b0efeae48ad15598e808c3">m_reactions</a></td></tr>
<tr class="memdesc:acb7c4f5108b0efeae48ad15598e808c3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Set of REACLIB reactions in the network. <br /></td></tr>
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<tr class="memitem:a5d6cc63b99b467c2a976d1fbaaa1dfa3" id="r_a5d6cc63b99b467c2a976d1fbaaa1dfa3"><td class="memItemLeft" align="right" valign="top">std::unordered_map&lt; std::string_view, <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> * &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a5d6cc63b99b467c2a976d1fbaaa1dfa3">m_reactionIDMap</a></td></tr>
<tr class="memdesc:a5d6cc63b99b467c2a976d1fbaaa1dfa3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a performance bottleneck. <br /></td></tr>
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<tr class="memitem:a92d26068ba139e47d335f5fe9e2814cc" id="r_a92d26068ba139e47d335f5fe9e2814cc"><td class="memItemLeft" align="right" valign="top">std::vector&lt; fourdst::atomic::Species &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a92d26068ba139e47d335f5fe9e2814cc">m_networkSpecies</a></td></tr>
<tr class="memdesc:a92d26068ba139e47d335f5fe9e2814cc"><td class="mdescLeft">&#160;</td><td class="mdescRight">Vector of unique species in the network. <br /></td></tr>
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<tr class="memitem:a30e09ed0bce6aa5fc89beaa316a7b827" id="r_a30e09ed0bce6aa5fc89beaa316a7b827"><td class="memItemLeft" align="right" valign="top">std::unordered_map&lt; std::string_view, fourdst::atomic::Species &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a30e09ed0bce6aa5fc89beaa316a7b827">m_networkSpeciesMap</a></td></tr>
<tr class="memdesc:a30e09ed0bce6aa5fc89beaa316a7b827"><td class="mdescLeft">&#160;</td><td class="mdescRight">Map from species name to Species object. <br /></td></tr>
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<tr class="memitem:ad8237c252145a75092202d00f5e1ddf7" id="r_ad8237c252145a75092202d00f5e1ddf7"><td class="memItemLeft" align="right" valign="top">std::unordered_map&lt; fourdst::atomic::Species, size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad8237c252145a75092202d00f5e1ddf7">m_speciesToIndexMap</a></td></tr>
<tr class="memdesc:ad8237c252145a75092202d00f5e1ddf7"><td class="mdescLeft">&#160;</td><td class="mdescRight">Map from species to their index in the stoichiometry matrix. <br /></td></tr>
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<tr class="memitem:ad1cb5fd32efc37668e2d9ecf0c72ad24" id="r_ad1cb5fd32efc37668e2d9ecf0c72ad24"><td class="memItemLeft" align="right" valign="top">boost::numeric::ublas::compressed_matrix&lt; int &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad1cb5fd32efc37668e2d9ecf0c72ad24">m_stoichiometryMatrix</a></td></tr>
<tr class="memdesc:ad1cb5fd32efc37668e2d9ecf0c72ad24"><td class="mdescLeft">&#160;</td><td class="mdescRight">Stoichiometry matrix (species x reactions). <br /></td></tr>
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<tr class="memitem:a2f1718c89d4aaad028102724d18fa910" id="r_a2f1718c89d4aaad028102724d18fa910"><td class="memItemLeft" align="right" valign="top">boost::numeric::ublas::compressed_matrix&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a2f1718c89d4aaad028102724d18fa910">m_jacobianMatrix</a></td></tr>
<tr class="memdesc:a2f1718c89d4aaad028102724d18fa910"><td class="mdescLeft">&#160;</td><td class="mdescRight">Jacobian matrix (species x species). <br /></td></tr>
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<tr class="memitem:a2e22b111f6d00ecc9e3804a71f1ce876" id="r_a2e22b111f6d00ecc9e3804a71f1ce876"><td class="memItemLeft" align="right" valign="top">CppAD::ADFun&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a2e22b111f6d00ecc9e3804a71f1ce876">m_rhsADFun</a></td></tr>
<tr class="memdesc:a2e22b111f6d00ecc9e3804a71f1ce876"><td class="mdescLeft">&#160;</td><td class="mdescRight">CppAD function for the right-hand side of the ODE. <br /></td></tr>
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<tr class="memitem:a3b17102b143435ddfdc015d7a50c4b18" id="r_a3b17102b143435ddfdc015d7a50c4b18"><td class="memItemLeft" align="right" valign="top">Config &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a3b17102b143435ddfdc015d7a50c4b18">m_config</a> = Config::getInstance()</td></tr>
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<tr class="memitem:a0837bab6dcd111d9075c9343b90d64f1" id="r_a0837bab6dcd111d9075c9343b90d64f1"><td class="memItemLeft" align="right" valign="top">Constants &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0837bab6dcd111d9075c9343b90d64f1">m_constants</a> = Constants::getInstance()</td></tr>
<tr class="memdesc:a0837bab6dcd111d9075c9343b90d64f1"><td class="mdescLeft">&#160;</td><td class="mdescRight">Access to physical constants. <br /></td></tr>
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<tr class="memitem:a483979fc154adc88d029b3b672066d53" id="r_a483979fc154adc88d029b3b672066d53"><td class="memItemLeft" align="right" valign="top">quill::Logger *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a483979fc154adc88d029b3b672066d53">m_logger</a> = LogManager::getInstance().getLogger(&quot;log&quot;)</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>A reaction network engine that uses a graph-based representation. </p>
<p>The <a class="el" href="classgridfire_1_1_graph_engine.html" title="A reaction network engine that uses a graph-based representation.">GraphEngine</a> class implements the <a class="el" href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> interface using a graph-based representation of the reaction network. It uses sparse matrices for efficient storage and computation of the stoichiometry and Jacobian matrices. Automatic differentiation (AD) is used to calculate the Jacobian matrix.</p>
<p>The engine supports:</p><ul>
<li>Calculation of the right-hand side (dY/dt) and energy generation rate.</li>
<li>Generation and access to the Jacobian matrix.</li>
<li>Generation and access to the stoichiometry matrix.</li>
<li>Calculation of molar reaction flows.</li>
<li>Access to the set of logical reactions in the network.</li>
<li>Computation of timescales for each species.</li>
<li>Exporting the network to DOT and CSV formats for visualization and analysis.</li>
</ul>
<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>
<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>
</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a9f74786ff930ab72664b31f29d05a30c">&#9670;&#160;</a></span>GraphEngine() <span class="overload">[1/2]</span></h2>
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<td class="memname">gridfire::GraphEngine::GraphEngine </td>
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<td class="paramtype">const fourdst::composition::Composition &amp;</td> <td class="paramname"><span class="paramname"><em>composition</em></span></td><td>)</td>
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<p>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. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">composition</td><td>The composition of the material.</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>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="namespacegridfire.html#aa77f83539d9ae90e3bf541309bd9c83a">build_reaclib_nuclear_network</a> </dd></dl>
<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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<td class="memname">gridfire::GraphEngine::GraphEngine </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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<p>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. </p>
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<tr><td class="paramname">reactions</td><td>The set of reactions to use in the network.</td></tr>
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<p>This constructor uses the given set of reactions to construct the reaction network. </p>
<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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<h2 class="groupheader">Member Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a71a3d1181b90c3becdc5d9a3da05b9c9">&#9670;&#160;</a></span>calculateAllDerivatives() <span class="overload">[1/3]</span></h2>
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<p>Calculates all derivatives (dY/dt) and the energy generation rate (automatic differentiation). </p>
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<tr><td class="paramname">Y_in</td><td>Vector of current abundances for all species. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
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<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&lt;ADDouble&gt;</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 automatic differentiation. </p>
<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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<td class="memname"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt; gridfire::GraphEngine::calculateAllDerivatives </td>
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<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_in</em></span>, </td>
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<p>Calculates all derivatives (dY/dt) and the energy generation rate (double precision). </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">Y_in</td><td>Vector of current abundances for all species. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
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</dd>
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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&lt;double&gt;</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>
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<h2 class="memtitle"><span class="permalink"><a href="#af41df9ce979b6410e12642cb093916c9">&#9670;&#160;</a></span>calculateAllDerivatives() <span class="overload">[3/3]</span></h2>
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<td class="memname"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; T &gt; gridfire::GraphEngine::calculateAllDerivatives </td>
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<p>Calculates all derivatives (dY/dt) and the energy generation rate. </p>
<dl class="tparams"><dt>Template Parameters</dt><dd>
<table class="tparams">
<tr><td class="paramname">T</td><td>The numeric type to use for the calculation. </td></tr>
</table>
</dd>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">Y_in</td><td>Vector of current abundances for all species. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
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</dd>
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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&lt;T&gt;</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>
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<h2 class="memtitle"><span class="permalink"><a href="#a9245642b741f215e52861d00e756fb3f">&#9670;&#160;</a></span>calculateMolarReactionFlow() <span class="overload">[1/2]</span></h2>
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<td class="memname">double gridfire::GraphEngine::calculateMolarReactionFlow </td>
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<td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;</td> <td class="paramname"><span class="paramname"><em>reaction</em></span>, </td>
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<p>Calculates the molar reaction flow for a given reaction. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">reaction</td><td>The reaction for which to calculate the flow. </td></tr>
<tr><td class="paramname">Y</td><td>Vector of current abundances. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
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</dd>
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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>
<p>This method computes the net rate at which the given reaction proceeds under the current state. </p>
<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>
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<h2 class="memtitle"><span class="permalink"><a href="#a5e96b5a0b34c8932f0e14eabda57f1a4">&#9670;&#160;</a></span>calculateMolarReactionFlow() <span class="overload">[2/2]</span></h2>
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<td class="memname">T gridfire::GraphEngine::calculateMolarReactionFlow </td>
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<td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;</td> <td class="paramname"><span class="paramname"><em>reaction</em></span>, </td>
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<p>Calculates the molar reaction flow for a given reaction. </p>
<dl class="tparams"><dt>Template Parameters</dt><dd>
<table class="tparams">
<tr><td class="paramname">T</td><td>The numeric type to use for the calculation. </td></tr>
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<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">reaction</td><td>The reaction for which to calculate the flow. </td></tr>
<tr><td class="paramname">Y</td><td>Vector of current abundances. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
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</dd>
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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>
<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>
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<h2 class="memtitle"><span class="permalink"><a href="#a8b3baf29829c7ae0a61430ea70632bbf">&#9670;&#160;</a></span>calculateRHSAndEnergy()</h2>
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<td class="memname"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt; gridfire::GraphEngine::calculateRHSAndEnergy </td>
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<p>Calculates the right-hand side (dY/dt) and energy generation rate. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">Y</td><td>Vector of current abundances for all species. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
</table>
</dd>
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<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives&lt;double&gt;</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>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives</a> </dd></dl>
<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>
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<h2 class="memtitle"><span class="permalink"><a href="#aedf42d83bfcc28313b6b6454034d2efa">&#9670;&#160;</a></span>collectNetworkSpecies()</h2>
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<td class="memname">void gridfire::GraphEngine::collectNetworkSpecies </td>
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<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>
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<h2 class="memtitle"><span class="permalink"><a href="#a832e2fe066381811a3e0464806ff5e95">&#9670;&#160;</a></span>exportToCSV()</h2>
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<td class="memname">void gridfire::GraphEngine::exportToCSV </td>
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<p>Exports the network to a CSV file for analysis. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">filename</td><td>The name of the CSV file to create.</td></tr>
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</dd>
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<p>This method generates a CSV file containing information about the reactions in the network, including the reactants, products, Q-value, and reaction rate coefficients.</p>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If the file cannot be opened for writing.</td></tr>
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<p>Example usage: </p><div class="fragment"><div class="line">engine.exportToCSV(<span class="stringliteral">&quot;network.csv&quot;</span>);</div>
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<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>
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<h2 class="memtitle"><span class="permalink"><a href="#adac8c7d62bae76e17fc060e86dadd929">&#9670;&#160;</a></span>exportToDot()</h2>
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<td class="memname">void gridfire::GraphEngine::exportToDot </td>
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<p>Exports the network to a DOT file for visualization. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">filename</td><td>The name of the DOT file to create.</td></tr>
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</dd>
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<p>This method generates a DOT file that can be used to visualize the reaction network as a graph. The DOT file can be converted to a graphical image using Graphviz.</p>
<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">std::runtime_error</td><td>If the file cannot be opened for writing.</td></tr>
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<p>Example usage: </p><div class="fragment"><div class="line">engine.exportToDot(<span class="stringliteral">&quot;network.dot&quot;</span>);</div>
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<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>
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<h2 class="memtitle"><span class="permalink"><a href="#ae347ff0316e532e0298ec8c913908105">&#9670;&#160;</a></span>generateJacobianMatrix()</h2>
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<td class="memname">void gridfire::GraphEngine::generateJacobianMatrix </td>
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<p>Generates the Jacobian matrix for the current state. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">Y</td><td>Vector of current abundances. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3.</td></tr>
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<p>This method computes and stores the Jacobian matrix (∂(dY/dt)_i/∂Y_j) for the current state using automatic differentiation. The matrix can then be accessed via <code><a class="el" href="#a303e6093591cde91430f866a04a8be7c" title="Gets an entry from the previously generated Jacobian matrix.">getJacobianMatrixEntry()</a></code>.</p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="#a303e6093591cde91430f866a04a8be7c" title="Gets an entry from the previously generated Jacobian matrix.">getJacobianMatrixEntry()</a> </dd></dl>
<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>
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<h2 class="memtitle"><span class="permalink"><a href="#aed726d36ee2b3796beff6067a1e4db38">&#9670;&#160;</a></span>generateStoichiometryMatrix()</h2>
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<td class="memname">void gridfire::GraphEngine::generateStoichiometryMatrix </td>
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<p>Generates the stoichiometry matrix for the network. </p>
<p>This method computes and stores the stoichiometry matrix, which encodes the net change of each species in each reaction. </p>
<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>
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<h2 class="memtitle"><span class="permalink"><a href="#a303e6093591cde91430f866a04a8be7c">&#9670;&#160;</a></span>getJacobianMatrixEntry()</h2>
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<td class="memname">double gridfire::GraphEngine::getJacobianMatrixEntry </td>
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<p>Gets an entry from the previously generated Jacobian matrix. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">i</td><td>Row index (species index). </td></tr>
<tr><td class="paramname">j</td><td>Column index (species index). </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>Value of the Jacobian matrix at (i, j).</dd></dl>
<p>The Jacobian must have been generated by <code><a class="el" href="#ae347ff0316e532e0298ec8c913908105" title="Generates the Jacobian matrix for the current state.">generateJacobianMatrix()</a></code> before calling this.</p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="#ae347ff0316e532e0298ec8c913908105" title="Generates the Jacobian matrix for the current state.">generateJacobianMatrix()</a> </dd></dl>
<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>
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<h2 class="memtitle"><span class="permalink"><a href="#a8c29d8bbde407e913be5eb77efb2c0c9">&#9670;&#160;</a></span>getNetReactionStoichiometry()</h2>
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<td class="memname">std::unordered_map&lt; fourdst::atomic::Species, int &gt; gridfire::GraphEngine::getNetReactionStoichiometry </td>
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<p>Gets the net stoichiometry for a given reaction. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">reaction</td><td>The reaction for which to get the stoichiometry. </td></tr>
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<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>
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<h2 class="memtitle"><span class="permalink"><a href="#ad45650d10fc5dff1673ae3f806d067da">&#9670;&#160;</a></span>getNetworkReactions()</h2>
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<td class="memname">const <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">reaction::LogicalReactionSet</a> &amp; gridfire::GraphEngine::getNetworkReactions </td>
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<p>Gets the set of logical reactions in the network. </p>
<dl class="section return"><dt>Returns</dt><dd>Reference to the LogicalReactionSet containing all reactions. </dd></dl>
<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>
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<h2 class="memtitle"><span class="permalink"><a href="#a0ed390f3e598ebba4e245ac90bb78767">&#9670;&#160;</a></span>getNetworkSpecies()</h2>
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<td class="memname">const std::vector&lt; fourdst::atomic::Species &gt; &amp; gridfire::GraphEngine::getNetworkSpecies </td>
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<p>Gets the list of species in the network. </p>
<dl class="section return"><dt>Returns</dt><dd>Vector of Species objects representing all network species. </dd></dl>
<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>
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<h2 class="memtitle"><span class="permalink"><a href="#a26215593544c3a52597194602e4e25dd">&#9670;&#160;</a></span>getSpeciesTimescales()</h2>
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<td class="memname">std::unordered_map&lt; fourdst::atomic::Species, double &gt; gridfire::GraphEngine::getSpeciesTimescales </td>
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<p>Computes timescales for all species in the network. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">Y</td><td>Vector of current abundances. </td></tr>
<tr><td class="paramname">T9</td><td>Temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>Density in g/cm^3. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>Map from Species to their characteristic timescales (s).</dd></dl>
<p>This method estimates the timescale for abundance change of each species, which can be used for timestep control or diagnostics. </p>
<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>
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<h2 class="memtitle"><span class="permalink"><a href="#a6b5feaf788bade212b7c8df7ac8c8152">&#9670;&#160;</a></span>getStoichiometryMatrixEntry()</h2>
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<td class="memname">int gridfire::GraphEngine::getStoichiometryMatrixEntry </td>
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<p>Gets an entry from the stoichiometry matrix. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">speciesIndex</td><td>Index of the species. </td></tr>
<tr><td class="paramname">reactionIndex</td><td>Index of the reaction. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>Stoichiometric coefficient for the species in the reaction.</dd></dl>
<p>The stoichiometry matrix must have been generated by <code><a class="el" href="#aed726d36ee2b3796beff6067a1e4db38" title="Generates the stoichiometry matrix for the network.">generateStoichiometryMatrix()</a></code>.</p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="#aed726d36ee2b3796beff6067a1e4db38" title="Generates the stoichiometry matrix for the network.">generateStoichiometryMatrix()</a> </dd></dl>
<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>
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<h2 class="memtitle"><span class="permalink"><a href="#aa6202cee0c3c481eda77cc9a91bc126b">&#9670;&#160;</a></span>involvesSpecies()</h2>
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<td class="memname">bool gridfire::GraphEngine::involvesSpecies </td>
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<p>Checks if a given species is involved in the network. </p>
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<tr><td class="paramname">species</td><td>The species to check. </td></tr>
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<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>
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<h2 class="memtitle"><span class="permalink"><a href="#a26602e1b3c610780a47b5a6511d6d567">&#9670;&#160;</a></span>populateReactionIDMap()</h2>
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<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>
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<h2 class="memtitle"><span class="permalink"><a href="#a47202c43342b96480070874bffce1391">&#9670;&#160;</a></span>populateSpeciesToIndexMap()</h2>
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<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>
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<h2 class="memtitle"><span class="permalink"><a href="#a95563f6bc86007d9ee053a0f1e15b889">&#9670;&#160;</a></span>recordADTape()</h2>
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<p>Records the AD tape for the right-hand side of the ODE. </p>
<p>This method records the AD tape for the right-hand side of the ODE, which is used to calculate the Jacobian matrix using automatic differentiation.</p>
<dl class="exception"><dt>Exceptions</dt><dd>
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<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>
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<h2 class="memtitle"><span class="permalink"><a href="#a5a5458ed01923124f2d7e1f04f32f138">&#9670;&#160;</a></span>reserveJacobianMatrix()</h2>
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<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>
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<h2 class="memtitle"><span class="permalink"><a href="#acdce8d87e23a2cd1504bc9472e538c0f">&#9670;&#160;</a></span>syncInternalMaps()</h2>
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<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>
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<h2 class="memtitle"><span class="permalink"><a href="#aeeafeab40a5f4dbfae78bdc87e25e93f">&#9670;&#160;</a></span>validateComposition()</h2>
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<p>Validates the composition against the current reaction set. </p>
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<tr><td class="paramname">composition</td><td>The composition to validate. </td></tr>
<tr><td class="paramname">culling</td><td>The culling threshold to use. </td></tr>
<tr><td class="paramname">T9</td><td>The temperature to use.</td></tr>
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<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>
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<h2 class="memtitle"><span class="permalink"><a href="#acf4cfccea20f5cb31c9886bf233a28be">&#9670;&#160;</a></span>validateConservation()</h2>
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<p>Validates mass and charge conservation across all reactions. </p>
<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>
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<h2 class="groupheader">Member Data Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a3b17102b143435ddfdc015d7a50c4b18">&#9670;&#160;</a></span>m_config</h2>
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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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<h2 class="memtitle"><span class="permalink"><a href="#a0837bab6dcd111d9075c9343b90d64f1">&#9670;&#160;</a></span>m_constants</h2>
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<td class="memname">Constants&amp; gridfire::GraphEngine::m_constants = Constants::getInstance()</td>
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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>
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<h2 class="memtitle"><span class="permalink"><a href="#a2f1718c89d4aaad028102724d18fa910">&#9670;&#160;</a></span>m_jacobianMatrix</h2>
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<td class="memname">boost::numeric::ublas::compressed_matrix&lt;double&gt; gridfire::GraphEngine::m_jacobianMatrix</td>
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<p>Jacobian matrix (species x species). </p>
<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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<h2 class="memtitle"><span class="permalink"><a href="#a483979fc154adc88d029b3b672066d53">&#9670;&#160;</a></span>m_logger</h2>
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<td class="memname">quill::Logger* gridfire::GraphEngine::m_logger = LogManager::getInstance().getLogger(&quot;log&quot;)</td>
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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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<h2 class="memtitle"><span class="permalink"><a href="#a92d26068ba139e47d335f5fe9e2814cc">&#9670;&#160;</a></span>m_networkSpecies</h2>
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<td class="memname">std::vector&lt;fourdst::atomic::Species&gt; gridfire::GraphEngine::m_networkSpecies</td>
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<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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<h2 class="memtitle"><span class="permalink"><a href="#a30e09ed0bce6aa5fc89beaa316a7b827">&#9670;&#160;</a></span>m_networkSpeciesMap</h2>
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<td class="memname">std::unordered_map&lt;std::string_view, fourdst::atomic::Species&gt; gridfire::GraphEngine::m_networkSpeciesMap</td>
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<p>Map from species name to Species object. </p>
<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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<h2 class="memtitle"><span class="permalink"><a href="#a5d6cc63b99b467c2a976d1fbaaa1dfa3">&#9670;&#160;</a></span>m_reactionIDMap</h2>
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<td class="memname">std::unordered_map&lt;std::string_view, <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a>*&gt; gridfire::GraphEngine::m_reactionIDMap</td>
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<p>Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a performance bottleneck. </p>
<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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<td class="memname"><a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">reaction::LogicalReactionSet</a> gridfire::GraphEngine::m_reactions</td>
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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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<td class="memname">CppAD::ADFun&lt;double&gt; gridfire::GraphEngine::m_rhsADFun</td>
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<p>CppAD function for the right-hand side of the ODE. </p>
<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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<h2 class="memtitle"><span class="permalink"><a href="#ad8237c252145a75092202d00f5e1ddf7">&#9670;&#160;</a></span>m_speciesToIndexMap</h2>
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<td class="memname">std::unordered_map&lt;fourdst::atomic::Species, size_t&gt; gridfire::GraphEngine::m_speciesToIndexMap</td>
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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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<h2 class="memtitle"><span class="permalink"><a href="#ad1cb5fd32efc37668e2d9ecf0c72ad24">&#9670;&#160;</a></span>m_stoichiometryMatrix</h2>
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<td class="memname">boost::numeric::ublas::compressed_matrix&lt;int&gt; gridfire::GraphEngine::m_stoichiometryMatrix</td>
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<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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<hr/>The documentation for this class was generated from the following files:<ul>
<li>src/network/include/gridfire/engine/<a class="el" href="engine__graph_8h_source.html">engine_graph.h</a></li>
<li>src/network/lib/engine/<a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a></li>
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