<ahref="engine__defined_8h.html">Go to the documentation of this file.</a><divclass="fragment"><divclass="line"><aid="l00001"name="l00001"></a><spanclass="lineno"> 1</span><spanclass="preprocessor">#pragma once</span></div>
<divclass="ttc"id="aclassgridfire_1_1_dynamic_engine_html"><divclass="ttname"><ahref="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><divclass="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><divclass="ttdef"><b>Definition</b><ahref="engine__abstract_8h_source.html#l00121">engine_abstract.h:121</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_engine_view_html"><divclass="ttname"><ahref="classgridfire_1_1_engine_view.html">gridfire::EngineView</a></div><divclass="ttdoc">Abstract base class for a "view" of a reaction network engine.</div><divclass="ttdef"><b>Definition</b><ahref="engine__view__abstract_8h_source.html#l00074">engine_view_abstract.h:74</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a0a9b07176cb93b54c677b6ce71fda500"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500">gridfire::FileDefinedEngineView::m_parser</a></div><divclass="ttdeci">const io::NetworkFileParser & m_parser</div><divclass="ttdoc">Active species in the defined engine.</div><divclass="ttdef"><b>Definition</b><ahref="#l00235">engine_defined.h:235</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a0ef8804780d13bbfce0856237bb00470"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a0ef8804780d13bbfce0856237bb00470">gridfire::FileDefinedEngineView::getJacobianMatrixEntry</a></div><divclass="ttdeci">double getJacobianMatrixEntry(const int i_defined, const int j_defined) const override</div><divclass="ttdoc">Gets an entry from the Jacobian matrix for the active species.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00056">engine_defined.cpp:56</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a1b343998b93955025a589b2b4541e33b"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a1b343998b93955025a589b2b4541e33b">gridfire::FileDefinedEngineView::m_fileName</a></div><divclass="ttdeci">std::string m_fileName</div><divclass="ttdoc">Parser for the network file.</div><divclass="ttdef"><b>Definition</b><ahref="#l00233">engine_defined.h:233</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a27a5163157cc15c4cb3b99a5d3564dbd"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a27a5163157cc15c4cb3b99a5d3564dbd">gridfire::FileDefinedEngineView::generateStoichiometryMatrix</a></div><divclass="ttdeci">void generateStoichiometryMatrix() override</div><divclass="ttdoc">Generates the stoichiometry matrix for the active reactions and species.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00068">engine_defined.cpp:68</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a299a0c61aa4f26029c770013c9feff5e"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a299a0c61aa4f26029c770013c9feff5e">gridfire::FileDefinedEngineView::m_activeSpecies</a></div><divclass="ttdeci">std::vector< fourdst::atomic::Species > m_activeSpecies</div><divclass="ttdoc">Active reactions in the defined engine.</div><divclass="ttdef"><b>Definition</b><ahref="#l00238">engine_defined.h:238</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a2c1d88b06568f9ea4c65e794d012ebfb"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a2c1d88b06568f9ea4c65e794d012ebfb">gridfire::FileDefinedEngineView::calculateRHSAndEnergy</a></div><divclass="ttdeci">StepDerivatives< double > calculateRHSAndEnergy(const std::vector< double >&Y_defined, const double T9, const double rho) const override</div><divclass="ttdoc">Calculates the right-hand side (dY/dt) and energy generation for the active species.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00029">engine_defined.cpp:29</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a3b5162b7be35405285ef9f825ec2663b"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a3b5162b7be35405285ef9f825ec2663b">gridfire::FileDefinedEngineView::buildFromFile</a></div><divclass="ttdeci">void buildFromFile(const std::string &fileName)</div><divclass="ttdoc">Builds the active species and reaction sets from a file.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00208">engine_defined.cpp:208</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a48b2451f96b8f5511ffc4071519c0810"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a48b2451f96b8f5511ffc4071519c0810">gridfire::FileDefinedEngineView::generateJacobianMatrix</a></div><divclass="ttdeci">void generateJacobianMatrix(const std::vector< double >&Y_defined, const double T9, const double rho) override</div><divclass="ttdoc">Generates the Jacobian matrix for the active species.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00045">engine_defined.cpp:45</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a4c8b273c5cb3d470567c5691b68493a3"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a4c8b273c5cb3d470567c5691b68493a3">gridfire::FileDefinedEngineView::getBaseEngine</a></div><divclass="ttdeci">const DynamicEngine & getBaseEngine() const override</div><divclass="ttdoc">Gets the base engine.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00021">engine_defined.cpp:21</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a51ba09ff01fdcac1125d42f276c9a0a7"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a51ba09ff01fdcac1125d42f276c9a0a7">gridfire::FileDefinedEngineView::constructSpeciesIndexMap</a></div><divclass="ttdeci">std::vector< size_t > constructSpeciesIndexMap() const</div><divclass="ttdoc">Constructs the species index map.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00147">engine_defined.cpp:147</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a5bbea17b69cc8f81bc251a04f4435a0c"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a5bbea17b69cc8f81bc251a04f4435a0c">gridfire::FileDefinedEngineView::getNetworkReactions</a></div><divclass="ttdeci">const reaction::LogicalReactionSet & getNetworkReactions() const override</div><divclass="ttdoc">Gets the set of active logical reactions in the network.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00102">engine_defined.cpp:102</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a6e421bc748933be31bed9ff53f12b595"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a6e421bc748933be31bed9ff53f12b595">gridfire::FileDefinedEngineView::m_isStale</a></div><divclass="ttdeci">bool m_isStale</div><divclass="ttdoc">A flag indicating whether the view is stale and needs to be updated.</div><divclass="ttdef"><b>Definition</b><ahref="#l00248">engine_defined.h:248</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a74217a1f8fd8e6daff969cb17885315c"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a74217a1f8fd8e6daff969cb17885315c">gridfire::FileDefinedEngineView::mapViewToFullReactionIndex</a></div><divclass="ttdeci">size_t mapViewToFullReactionIndex(size_t definedReactionIndex) const</div><divclass="ttdoc">Maps a culled reaction index to a full reaction index.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00294">engine_defined.cpp:294</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a7a80966c023ae722239491af58609362"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a7a80966c023ae722239491af58609362">gridfire::FileDefinedEngineView::m_config</a></div><divclass="ttdeci">Config & m_config</div><divclass="ttdoc">A reference to the singleton Config instance.</div><divclass="ttdef"><b>Definition</b><ahref="#l00226">engine_defined.h:226</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a8bb583e039b49608272997ed2d3387fa"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a8bb583e039b49608272997ed2d3387fa">gridfire::FileDefinedEngineView::getNetworkSpecies</a></div><divclass="ttdeci">const std::vector< fourdst::atomic::Species >& getNetworkSpecies() const override</div><divclass="ttdoc">Gets the list of active species in the network defined by the file.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00025">engine_defined.cpp:25</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a8f2f64bab0f516ed2a6fd529912e0acd"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a8f2f64bab0f516ed2a6fd529912e0acd">gridfire::FileDefinedEngineView::FileDefinedEngineView</a></div><divclass="ttdeci">FileDefinedEngineView(DynamicEngine &baseEngine, const std::string &fileName, const io::NetworkFileParser &parser)</div><divclass="ttdoc">Constructs a FileDefinedEngineView.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00008">engine_defined.cpp:8</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a92f14da849e99d07c1ff1347addb9263"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a92f14da849e99d07c1ff1347addb9263">gridfire::FileDefinedEngineView::setNetworkFile</a></div><divclass="ttdeci">void setNetworkFile(const std::string &fileName)</div><divclass="ttdoc">Sets a new network file to define the active reactions.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00133">engine_defined.cpp:133</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a97e5ee4651dbe6754678fe96e4702fee"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a97e5ee4651dbe6754678fe96e4702fee">gridfire::FileDefinedEngineView::mapFullToView</a></div><divclass="ttdeci">std::vector< double > mapFullToView(const std::vector< double >&full) const</div><divclass="ttdoc">Maps a vector of full abundances to a vector of culled abundances.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00276">engine_defined.cpp:276</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a9d93633ed4ab68de94b7274f879a0432"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a9d93633ed4ab68de94b7274f879a0432">gridfire::FileDefinedEngineView::m_logger</a></div><divclass="ttdeci">quill::Logger * m_logger</div><divclass="ttdoc">A pointer to the logger instance.</div><divclass="ttdef"><b>Definition</b><ahref="#l00228">engine_defined.h:228</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_a9da9224f5c99a5068f3d8cbf066e4693"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#a9da9224f5c99a5068f3d8cbf066e4693">gridfire::FileDefinedEngineView::getStoichiometryMatrixEntry</a></div><divclass="ttdeci">int getStoichiometryMatrixEntry(const int speciesIndex_defined, const int reactionIndex_defined) const override</div><divclass="ttdoc">Gets an entry from the stoichiometry matrix for the active species and reactions.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00074">engine_defined.cpp:74</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_aa2373955ef5b0eabf7a57c7208e38bb1"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#aa2373955ef5b0eabf7a57c7208e38bb1">gridfire::FileDefinedEngineView::mapViewToFullSpeciesIndex</a></div><divclass="ttdeci">size_t mapViewToFullSpeciesIndex(size_t definedSpeciesIndex) const</div><divclass="ttdoc">Maps a culled species index to a full species index.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00285">engine_defined.cpp:285</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_ac371fb66fd0a76a04df204c9dd9a05ef"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#ac371fb66fd0a76a04df204c9dd9a05ef">gridfire::FileDefinedEngineView::calculateMolarReactionFlow</a></div><divclass="ttdeci">double calculateMolarReactionFlow(const reaction::Reaction &reaction, const std::vector< double >&Y_defined, const double T9, const double rho) const override</div><divclass="ttdoc">Calculates the molar reaction flow for a given reaction in the active network.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00085">engine_defined.cpp:85</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_ace3568eadaba69e7357b4386c5ca3eb0"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#ace3568eadaba69e7357b4386c5ca3eb0">gridfire::FileDefinedEngineView::update</a></div><divclass="ttdeci">void update(const NetIn &netIn) override</div><divclass="ttdoc">Updates the engine view if it is marked as stale.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00127">engine_defined.cpp:127</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_ace3c6ea4841318c08695973ab3dcddc6"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#ace3c6ea4841318c08695973ab3dcddc6">gridfire::FileDefinedEngineView::getSpeciesTimescales</a></div><divclass="ttdeci">std::unordered_map< fourdst::atomic::Species, double > getSpeciesTimescales(const std::vector< double >&Y_defined, const double T9, const double rho) const override</div><divclass="ttdoc">Computes timescales for all active species in the network.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00108">engine_defined.cpp:108</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_ad8454c98fa9a4bb45dc81059bc51fc81"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81">gridfire::FileDefinedEngineView::m_baseEngine</a></div><divclass="ttdeci">DynamicEngine & m_baseEngine</div><divclass="ttdoc">The underlying engine to which this view delegates calculations.</div><divclass="ttdef"><b>Definition</b><ahref="#l00231">engine_defined.h:231</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_ad96bbee6d3d37b50d9236a975ef704c0"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#ad96bbee6d3d37b50d9236a975ef704c0">gridfire::FileDefinedEngineView::setScreeningModel</a></div><divclass="ttdeci">void setScreeningModel(screening::ScreeningType model) override</div><divclass="ttdoc">Sets the screening model for the base engine.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00139">engine_defined.cpp:139</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_adba3c11b11a04b2907c1635210d73dee"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#adba3c11b11a04b2907c1635210d73dee">gridfire::FileDefinedEngineView::mapViewToFull</a></div><divclass="ttdeci">std::vector< double > mapViewToFull(const std::vector< double >&defined) const</div><divclass="ttdoc">Maps a vector of culled abundances to a vector of full abundances.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00267">engine_defined.cpp:267</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_adbc50f397445f92b810d80cf329b8626"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#adbc50f397445f92b810d80cf329b8626">gridfire::FileDefinedEngineView::getScreeningModel</a></div><divclass="ttdeci">screening::ScreeningType getScreeningModel() const override</div><divclass="ttdoc">Gets the screening model from the base engine.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00143">engine_defined.cpp:143</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_ae012da2b1f6169cb13e6075a73353ab2"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#ae012da2b1f6169cb13e6075a73353ab2">gridfire::FileDefinedEngineView::m_activeReactions</a></div><divclass="ttdeci">reaction::LogicalReactionSet m_activeReactions</div><divclass="ttdoc">Maps indices of active species to indices in the full network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00240">engine_defined.h:240</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_ae3f99002ab2c56a5bcdec00839f8628f"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#ae3f99002ab2c56a5bcdec00839f8628f">gridfire::FileDefinedEngineView::validateNetworkState</a></div><divclass="ttdeci">void validateNetworkState() const</div><divclass="ttdoc">Validates that the FileDefinedEngineView is not stale.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00303">engine_defined.cpp:303</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_aebb3f3548f8781506f31580706810a4e"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#aebb3f3548f8781506f31580706810a4e">gridfire::FileDefinedEngineView::constructReactionIndexMap</a></div><divclass="ttdeci">std::vector< size_t > constructReactionIndexMap() const</div><divclass="ttdoc">Constructs the reaction index map.</div><divclass="ttdef"><b>Definition</b><ahref="engine__defined_8cpp_source.html#l00176">engine_defined.cpp:176</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1_file_defined_engine_view_html_aebd4a1a584f2784f1df3d503645be03b"><divclass="ttname"><ahref="classgridfire_1_1_file_defined_engine_view.html#aebd4a1a584f2784f1df3d503645be03b">gridfire::FileDefinedEngineView::m_speciesIndexMap</a></div><divclass="ttdeci">std::vector< size_t > m_speciesIndexMap</div><divclass="ttdoc">Maps indices of active reactions to indices in the full network.</div><divclass="ttdef"><b>Definition</b><ahref="#l00243">engine_defined.h:243</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1io_1_1_network_file_parser_html"><divclass="ttname"><ahref="classgridfire_1_1io_1_1_network_file_parser.html">gridfire::io::NetworkFileParser</a></div><divclass="ttdoc">An abstract base class for network file parsers.</div><divclass="ttdef"><b>Definition</b><ahref="network__file_8h_source.html#l00038">network_file.h:38</a></div></div>
<divclass="ttc"id="aclassgridfire_1_1reaction_1_1_reaction_html"><divclass="ttname"><ahref="classgridfire_1_1reaction_1_1_reaction.html">gridfire::reaction::Reaction</a></div><divclass="ttdoc">Represents a single nuclear reaction from a specific data source.</div><divclass="ttdef"><b>Definition</b><ahref="reaction_8h_source.html#l00072">reaction.h:72</a></div></div>
<divclass="ttc"id="aengine__abstract_8h_html"><divclass="ttname"><ahref="engine__abstract_8h.html">engine_abstract.h</a></div><divclass="ttdoc">Abstract interfaces for reaction network engines in GridFire.</div></div>
<divclass="ttc"id="aengine__view__abstract_8h_html"><divclass="ttname"><ahref="engine__view__abstract_8h.html">engine_view_abstract.h</a></div><divclass="ttdoc">Abstract interfaces for engine "views" in GridFire.</div></div>
<divclass="ttc"id="anamespacegridfire_1_1reaction_html_aa86f08712565f278adacc7cd2361eb31"><divclass="ttname"><ahref="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a></div><divclass="ttdeci">TemplatedReactionSet< LogicalReaction > LogicalReactionSet</div><divclass="ttdoc">A set of logical reactions.</div><divclass="ttdef"><b>Definition</b><ahref="reaction_8h_source.html#l00557">reaction.h:557</a></div></div>
<divclass="ttc"id="anamespacegridfire_1_1screening_html_aa82aafbc4f8c28d0a75b60798e3a7d25"><divclass="ttname"><ahref="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">gridfire::screening::ScreeningType</a></div><divclass="ttdeci">ScreeningType</div><divclass="ttdoc">Enumerates the available plasma screening models.</div><divclass="ttdef"><b>Definition</b><ahref="screening__types_8h_source.html#l00015">screening_types.h:15</a></div></div>
<divclass="ttc"id="astructgridfire_1_1_step_derivatives_html"><divclass="ttname"><ahref="structgridfire_1_1_step_derivatives.html">gridfire::StepDerivatives</a></div><divclass="ttdoc">Structure holding derivatives and energy generation for a network step.</div><divclass="ttdef"><b>Definition</b><ahref="engine__abstract_8h_source.html#l00053">engine_abstract.h:53</a></div></div>
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