tboudreaux/GridFire
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

docs(docs): added extensive docs

Browse Source
This commit is contained in:
Emily Boudreaux
2025-07-01 15:06:22 -04:00
parent 5b4db3ea43
commit 131f61c9e7
134 changed files with 5101 additions and 2191 deletions
Download Patch File Download Diff File Expand all files Collapse all files

384
docs/html/classgridfire_1_1_file_defined_engine_view.html
View File

@@ -109,6 +109,9 @@ $(function(){initNavTree('classgridfire_1_1_file_defined_engine_view.html','');
</div><!--header-->
<div class="contents">
<p>An engine view that uses a user-defined reaction network from a file.
<a href="#details">More...</a></p>
<p><code>#include &lt;<a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>&gt;</code></p>
<div class="dynheader">
Inheritance diagram for gridfire::FileDefinedEngineView:</div>
@@ -125,44 +128,49 @@ Inheritance diagram for gridfire::FileDefinedEngineView:</div>
<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:a8f2f64bab0f516ed2a6fd529912e0acd" id="r_a8f2f64bab0f516ed2a6fd529912e0acd"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a8f2f64bab0f516ed2a6fd529912e0acd">FileDefinedEngineView</a> (<a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;baseEngine, const std::string &amp;fileName, const <a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a> &amp;parser)</td></tr>
<tr class="memdesc:a8f2f64bab0f516ed2a6fd529912e0acd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructs a <a class="el" href="classgridfire_1_1_file_defined_engine_view.html" title="An engine view that uses a user-defined reaction network from a file.">FileDefinedEngineView</a>. <br /></td></tr>
<tr class="separator:a8f2f64bab0f516ed2a6fd529912e0acd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a4c8b273c5cb3d470567c5691b68493a3" id="r_a4c8b273c5cb3d470567c5691b68493a3"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a4c8b273c5cb3d470567c5691b68493a3">getBaseEngine</a> () const override</td></tr>
<tr class="memdesc:a4c8b273c5cb3d470567c5691b68493a3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Access the underlying engine instance. <br /></td></tr>
<tr class="memdesc:a4c8b273c5cb3d470567c5691b68493a3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the base engine. <br /></td></tr>
<tr class="separator:a4c8b273c5cb3d470567c5691b68493a3"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8bb583e039b49608272997ed2d3387fa" id="r_a8bb583e039b49608272997ed2d3387fa"><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="#a8bb583e039b49608272997ed2d3387fa">getNetworkSpecies</a> () const override</td></tr>
<tr class="memdesc:a8bb583e039b49608272997ed2d3387fa"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the list of species in the network. <br /></td></tr>
<tr class="memdesc:a8bb583e039b49608272997ed2d3387fa"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the list of active species in the network defined by the file. <br /></td></tr>
<tr class="separator:a8bb583e039b49608272997ed2d3387fa"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a2c1d88b06568f9ea4c65e794d012ebfb" id="r_a2c1d88b06568f9ea4c65e794d012ebfb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a2c1d88b06568f9ea4c65e794d012ebfb">calculateRHSAndEnergy</a> (const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:a2c1d88b06568f9ea4c65e794d012ebfb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the right-hand side (dY/dt) and energy generation. <br /></td></tr>
<tr class="memdesc:a2c1d88b06568f9ea4c65e794d012ebfb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the right-hand side (dY/dt) and energy generation for the active species. <br /></td></tr>
<tr class="separator:a2c1d88b06568f9ea4c65e794d012ebfb"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a48b2451f96b8f5511ffc4071519c0810" id="r_a48b2451f96b8f5511ffc4071519c0810"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a48b2451f96b8f5511ffc4071519c0810">generateJacobianMatrix</a> (const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) override</td></tr>
<tr class="memdesc:a48b2451f96b8f5511ffc4071519c0810"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate the Jacobian matrix for the current state. <br /></td></tr>
<tr class="memdesc:a48b2451f96b8f5511ffc4071519c0810"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generates the Jacobian matrix for the active species. <br /></td></tr>
<tr class="separator:a48b2451f96b8f5511ffc4071519c0810"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0ef8804780d13bbfce0856237bb00470" id="r_a0ef8804780d13bbfce0856237bb00470"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0ef8804780d13bbfce0856237bb00470">getJacobianMatrixEntry</a> (const int i_defined, const int j_defined) const override</td></tr>
<tr class="memdesc:a0ef8804780d13bbfce0856237bb00470"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get an entry from the previously generated Jacobian matrix. <br /></td></tr>
<tr class="memdesc:a0ef8804780d13bbfce0856237bb00470"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets an entry from the Jacobian matrix for the active species. <br /></td></tr>
<tr class="separator:a0ef8804780d13bbfce0856237bb00470"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a27a5163157cc15c4cb3b99a5d3564dbd" id="r_a27a5163157cc15c4cb3b99a5d3564dbd"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a27a5163157cc15c4cb3b99a5d3564dbd">generateStoichiometryMatrix</a> () override</td></tr>
<tr class="memdesc:a27a5163157cc15c4cb3b99a5d3564dbd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate the stoichiometry matrix for the network. <br /></td></tr>
<tr class="memdesc:a27a5163157cc15c4cb3b99a5d3564dbd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generates the stoichiometry matrix for the active reactions and species. <br /></td></tr>
<tr class="separator:a27a5163157cc15c4cb3b99a5d3564dbd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a9da9224f5c99a5068f3d8cbf066e4693" id="r_a9da9224f5c99a5068f3d8cbf066e4693"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a9da9224f5c99a5068f3d8cbf066e4693">getStoichiometryMatrixEntry</a> (const int speciesIndex_defined, const int reactionIndex_defined) const override</td></tr>
<tr class="memdesc:a9da9224f5c99a5068f3d8cbf066e4693"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get an entry from the stoichiometry matrix. <br /></td></tr>
<tr class="memdesc:a9da9224f5c99a5068f3d8cbf066e4693"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets an entry from the stoichiometry matrix for the active species and reactions. <br /></td></tr>
<tr class="separator:a9da9224f5c99a5068f3d8cbf066e4693"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac371fb66fd0a76a04df204c9dd9a05ef" id="r_ac371fb66fd0a76a04df204c9dd9a05ef"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ac371fb66fd0a76a04df204c9dd9a05ef">calculateMolarReactionFlow</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html">reaction::Reaction</a> &amp;reaction, const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:ac371fb66fd0a76a04df204c9dd9a05ef"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the molar reaction flow for a given reaction. <br /></td></tr>
<tr class="memdesc:ac371fb66fd0a76a04df204c9dd9a05ef"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates the molar reaction flow for a given reaction in the active network. <br /></td></tr>
<tr class="separator:ac371fb66fd0a76a04df204c9dd9a05ef"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5bbea17b69cc8f81bc251a04f4435a0c" id="r_a5bbea17b69cc8f81bc251a04f4435a0c"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a5bbea17b69cc8f81bc251a04f4435a0c">getNetworkReactions</a> () const override</td></tr>
<tr class="memdesc:a5bbea17b69cc8f81bc251a04f4435a0c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the set of logical reactions in the network. <br /></td></tr>
<tr class="memdesc:a5bbea17b69cc8f81bc251a04f4435a0c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the set of active logical reactions in the network. <br /></td></tr>
<tr class="separator:a5bbea17b69cc8f81bc251a04f4435a0c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ace3c6ea4841318c08695973ab3dcddc6" id="r_ace3c6ea4841318c08695973ab3dcddc6"><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="#ace3c6ea4841318c08695973ab3dcddc6">getSpeciesTimescales</a> (const std::vector&lt; double &gt; &amp;Y_defined, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:ace3c6ea4841318c08695973ab3dcddc6"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute timescales for all species in the network. <br /></td></tr>
<tr class="memdesc:ace3c6ea4841318c08695973ab3dcddc6"><td class="mdescLeft">&#160;</td><td class="mdescRight">Computes timescales for all active species in the network. <br /></td></tr>
<tr class="separator:ace3c6ea4841318c08695973ab3dcddc6"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ace3568eadaba69e7357b4386c5ca3eb0" id="r_ace3568eadaba69e7357b4386c5ca3eb0"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ace3568eadaba69e7357b4386c5ca3eb0">update</a> (const <a class="el" href="structgridfire_1_1_net_in.html">NetIn</a> &amp;netIn) override</td></tr>
<tr class="memdesc:ace3568eadaba69e7357b4386c5ca3eb0"><td class="mdescLeft">&#160;</td><td class="mdescRight">Updates the engine view if it is marked as stale. <br /></td></tr>
<tr class="separator:ace3568eadaba69e7357b4386c5ca3eb0"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a92f14da849e99d07c1ff1347addb9263" id="r_a92f14da849e99d07c1ff1347addb9263"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a92f14da849e99d07c1ff1347addb9263">setNetworkFile</a> (const std::string &amp;fileName)</td></tr>
<tr class="memdesc:a92f14da849e99d07c1ff1347addb9263"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets a new network file to define the active reactions. <br /></td></tr>
<tr class="separator:a92f14da849e99d07c1ff1347addb9263"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad96bbee6d3d37b50d9236a975ef704c0" id="r_ad96bbee6d3d37b50d9236a975ef704c0"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad96bbee6d3d37b50d9236a975ef704c0">setScreeningModel</a> (<a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a> model) override</td></tr>
<tr class="memdesc:ad96bbee6d3d37b50d9236a975ef704c0"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the screening model for the base engine. <br /></td></tr>
<tr class="separator:ad96bbee6d3d37b50d9236a975ef704c0"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:adbc50f397445f92b810d80cf329b8626" id="r_adbc50f397445f92b810d80cf329b8626"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegridfire_1_1screening.html#aa82aafbc4f8c28d0a75b60798e3a7d25">screening::ScreeningType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#adbc50f397445f92b810d80cf329b8626">getScreeningModel</a> () const override</td></tr>
<tr class="memdesc:adbc50f397445f92b810d80cf329b8626"><td class="mdescLeft">&#160;</td><td class="mdescRight">Gets the screening model from the base engine. <br /></td></tr>
<tr class="separator:adbc50f397445f92b810d80cf329b8626"><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>
@@ -183,6 +191,7 @@ Private Types</h2></td></tr>
<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:a3b5162b7be35405285ef9f825ec2663b" id="r_a3b5162b7be35405285ef9f825ec2663b"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a3b5162b7be35405285ef9f825ec2663b">buildFromFile</a> (const std::string &amp;fileName)</td></tr>
<tr class="memdesc:a3b5162b7be35405285ef9f825ec2663b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Builds the active species and reaction sets from a file. <br /></td></tr>
<tr class="separator:a3b5162b7be35405285ef9f825ec2663b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a51ba09ff01fdcac1125d42f276c9a0a7" id="r_a51ba09ff01fdcac1125d42f276c9a0a7"><td class="memItemLeft" align="right" valign="top">std::vector&lt; size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a51ba09ff01fdcac1125d42f276c9a0a7">constructSpeciesIndexMap</a> () const</td></tr>
<tr class="memdesc:a51ba09ff01fdcac1125d42f276c9a0a7"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructs the species index map. <br /></td></tr>
@@ -190,53 +199,62 @@ Private Member Functions</h2></td></tr>
<tr class="memitem:aebb3f3548f8781506f31580706810a4e" id="r_aebb3f3548f8781506f31580706810a4e"><td class="memItemLeft" align="right" valign="top">std::vector&lt; size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aebb3f3548f8781506f31580706810a4e">constructReactionIndexMap</a> () const</td></tr>
<tr class="memdesc:aebb3f3548f8781506f31580706810a4e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructs the reaction index map. <br /></td></tr>
<tr class="separator:aebb3f3548f8781506f31580706810a4e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac231044e37e0962f664f8465e1ccb022" id="r_ac231044e37e0962f664f8465e1ccb022"><td class="memItemLeft" align="right" valign="top">std::vector&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ac231044e37e0962f664f8465e1ccb022">mapViewToFull</a> (const std::vector&lt; double &gt; &amp;culled) const</td></tr>
<tr class="memdesc:ac231044e37e0962f664f8465e1ccb022"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps a vector of culled abundances to a vector of full abundances. <br /></td></tr>
<tr class="separator:ac231044e37e0962f664f8465e1ccb022"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:adba3c11b11a04b2907c1635210d73dee" id="r_adba3c11b11a04b2907c1635210d73dee"><td class="memItemLeft" align="right" valign="top">std::vector&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#adba3c11b11a04b2907c1635210d73dee">mapViewToFull</a> (const std::vector&lt; double &gt; &amp;defined) const</td></tr>
<tr class="memdesc:adba3c11b11a04b2907c1635210d73dee"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps a vector of culled abundances to a vector of full abundances. <br /></td></tr>
<tr class="separator:adba3c11b11a04b2907c1635210d73dee"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a97e5ee4651dbe6754678fe96e4702fee" id="r_a97e5ee4651dbe6754678fe96e4702fee"><td class="memItemLeft" align="right" valign="top">std::vector&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a97e5ee4651dbe6754678fe96e4702fee">mapFullToView</a> (const std::vector&lt; double &gt; &amp;full) const</td></tr>
<tr class="memdesc:a97e5ee4651dbe6754678fe96e4702fee"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps a vector of full abundances to a vector of culled abundances. <br /></td></tr>
<tr class="separator:a97e5ee4651dbe6754678fe96e4702fee"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf" id="r_a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf">mapViewToFullSpeciesIndex</a> (size_t culledSpeciesIndex) const</td></tr>
<tr class="memdesc:a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps a culled species index to a full species index. <br /></td></tr>
<tr class="separator:a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae7d6f0ff9076d59d1245c047bbd1bdb9" id="r_ae7d6f0ff9076d59d1245c047bbd1bdb9"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ae7d6f0ff9076d59d1245c047bbd1bdb9">mapViewToFullReactionIndex</a> (size_t culledReactionIndex) const</td></tr>
<tr class="memdesc:ae7d6f0ff9076d59d1245c047bbd1bdb9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps a culled reaction index to a full reaction index. <br /></td></tr>
<tr class="separator:ae7d6f0ff9076d59d1245c047bbd1bdb9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa2373955ef5b0eabf7a57c7208e38bb1" id="r_aa2373955ef5b0eabf7a57c7208e38bb1"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aa2373955ef5b0eabf7a57c7208e38bb1">mapViewToFullSpeciesIndex</a> (size_t definedSpeciesIndex) const</td></tr>
<tr class="memdesc:aa2373955ef5b0eabf7a57c7208e38bb1"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps a culled species index to a full species index. <br /></td></tr>
<tr class="separator:aa2373955ef5b0eabf7a57c7208e38bb1"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a74217a1f8fd8e6daff969cb17885315c" id="r_a74217a1f8fd8e6daff969cb17885315c"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a74217a1f8fd8e6daff969cb17885315c">mapViewToFullReactionIndex</a> (size_t definedReactionIndex) const</td></tr>
<tr class="memdesc:a74217a1f8fd8e6daff969cb17885315c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps a culled reaction index to a full reaction index. <br /></td></tr>
<tr class="separator:a74217a1f8fd8e6daff969cb17885315c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae3f99002ab2c56a5bcdec00839f8628f" id="r_ae3f99002ab2c56a5bcdec00839f8628f"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ae3f99002ab2c56a5bcdec00839f8628f">validateNetworkState</a> () const</td></tr>
<tr class="memdesc:ae3f99002ab2c56a5bcdec00839f8628f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Validates that the <a class="el" href="classgridfire_1_1_file_defined_engine_view.html" title="An engine view that uses a user-defined reaction network from a file.">FileDefinedEngineView</a> is not stale. <br /></td></tr>
<tr class="separator:ae3f99002ab2c56a5bcdec00839f8628f"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<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:a7a80966c023ae722239491af58609362" id="r_a7a80966c023ae722239491af58609362"><td class="memItemLeft" align="right" valign="top"><a class="el" href="#a63f8f85e75ecaab6fa39d48d7a846187">Config</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a7a80966c023ae722239491af58609362">m_config</a> = Config::getInstance()</td></tr>
<tr class="memdesc:a7a80966c023ae722239491af58609362"><td class="mdescLeft">&#160;</td><td class="mdescRight">A reference to the singleton <a class="el" href="#a63f8f85e75ecaab6fa39d48d7a846187">Config</a> instance. <br /></td></tr>
<tr class="separator:a7a80966c023ae722239491af58609362"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a9d93633ed4ab68de94b7274f879a0432" id="r_a9d93633ed4ab68de94b7274f879a0432"><td class="memItemLeft" align="right" valign="top">quill::Logger *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a9d93633ed4ab68de94b7274f879a0432">m_logger</a> = LogManager::getInstance().getLogger(&quot;log&quot;)</td></tr>
<tr class="memdesc:a9d93633ed4ab68de94b7274f879a0432"><td class="mdescLeft">&#160;</td><td class="mdescRight">A pointer to the logger instance. <br /></td></tr>
<tr class="separator:a9d93633ed4ab68de94b7274f879a0432"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad8454c98fa9a4bb45dc81059bc51fc81" id="r_ad8454c98fa9a4bb45dc81059bc51fc81"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ad8454c98fa9a4bb45dc81059bc51fc81">m_baseEngine</a></td></tr>
<tr class="memdesc:ad8454c98fa9a4bb45dc81059bc51fc81"><td class="mdescLeft">&#160;</td><td class="mdescRight">The underlying engine to which this view delegates calculations. <br /></td></tr>
<tr class="separator:ad8454c98fa9a4bb45dc81059bc51fc81"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1b343998b93955025a589b2b4541e33b" id="r_a1b343998b93955025a589b2b4541e33b"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a1b343998b93955025a589b2b4541e33b">m_fileName</a></td></tr>
<tr class="memdesc:a1b343998b93955025a589b2b4541e33b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Name of the file defining the reaction set considered by the engine view. <br /></td></tr>
<tr class="memdesc:a1b343998b93955025a589b2b4541e33b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Parser for the network file. <br /></td></tr>
<tr class="separator:a1b343998b93955025a589b2b4541e33b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0a9b07176cb93b54c677b6ce71fda500" id="r_a0a9b07176cb93b54c677b6ce71fda500"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classgridfire_1_1io_1_1_network_file_parser.html">io::NetworkFileParser</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a0a9b07176cb93b54c677b6ce71fda500">m_parser</a></td></tr>
<tr class="memdesc:a0a9b07176cb93b54c677b6ce71fda500"><td class="mdescLeft">&#160;</td><td class="mdescRight">Parser for the network file. <br /></td></tr>
<tr class="memdesc:a0a9b07176cb93b54c677b6ce71fda500"><td class="mdescLeft">&#160;</td><td class="mdescRight">Active species in the defined engine. <br /></td></tr>
<tr class="separator:a0a9b07176cb93b54c677b6ce71fda500"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a299a0c61aa4f26029c770013c9feff5e" id="r_a299a0c61aa4f26029c770013c9feff5e"><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="#a299a0c61aa4f26029c770013c9feff5e">m_activeSpecies</a></td></tr>
<tr class="memdesc:a299a0c61aa4f26029c770013c9feff5e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Active species in the defined engine. <br /></td></tr>
<tr class="memdesc:a299a0c61aa4f26029c770013c9feff5e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Active reactions in the defined engine. <br /></td></tr>
<tr class="separator:a299a0c61aa4f26029c770013c9feff5e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae012da2b1f6169cb13e6075a73353ab2" id="r_ae012da2b1f6169cb13e6075a73353ab2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ae012da2b1f6169cb13e6075a73353ab2">m_activeReactions</a></td></tr>
<tr class="memdesc:ae012da2b1f6169cb13e6075a73353ab2"><td class="mdescLeft">&#160;</td><td class="mdescRight">Active reactions in the defined engine. <br /></td></tr>
<tr class="memdesc:ae012da2b1f6169cb13e6075a73353ab2"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps indices of active species to indices in the full network. <br /></td></tr>
<tr class="separator:ae012da2b1f6169cb13e6075a73353ab2"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aebd4a1a584f2784f1df3d503645be03b" id="r_aebd4a1a584f2784f1df3d503645be03b"><td class="memItemLeft" align="right" valign="top">std::vector&lt; size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aebd4a1a584f2784f1df3d503645be03b">m_speciesIndexMap</a></td></tr>
<tr class="memdesc:aebd4a1a584f2784f1df3d503645be03b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps indices of active species to indices in the full network. <br /></td></tr>
<tr class="memdesc:aebd4a1a584f2784f1df3d503645be03b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps indices of active reactions to indices in the full network. <br /></td></tr>
<tr class="separator:aebd4a1a584f2784f1df3d503645be03b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af0a77a4749a15aae87bdecfccbd1736e" id="r_af0a77a4749a15aae87bdecfccbd1736e"><td class="memItemLeft" align="right" valign="top">std::vector&lt; size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#af0a77a4749a15aae87bdecfccbd1736e">m_reactionIndexMap</a></td></tr>
<tr class="memdesc:af0a77a4749a15aae87bdecfccbd1736e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Maps indices of active reactions to indices in the full network. <br /></td></tr>
<tr class="separator:af0a77a4749a15aae87bdecfccbd1736e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a6e421bc748933be31bed9ff53f12b595" id="r_a6e421bc748933be31bed9ff53f12b595"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a6e421bc748933be31bed9ff53f12b595">m_isStale</a> = true</td></tr>
<tr class="memdesc:a6e421bc748933be31bed9ff53f12b595"><td class="mdescLeft">&#160;</td><td class="mdescRight">A flag indicating whether the view is stale and needs to be updated. <br /></td></tr>
<tr class="separator:a6e421bc748933be31bed9ff53f12b595"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00016">16</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<div class="textblock"><p>An engine view that uses a user-defined reaction network from a file. </p>
<p>This class implements an <a class="el" href="classgridfire_1_1_engine_view.html" title="Abstract base class for a &quot;view&quot; of a reaction network engine.">EngineView</a> that restricts the reaction network to a specific set of reactions defined in an external file. It acts as a filter or a view on a larger, more comprehensive base engine. The file provides a list of reaction identifiers, and this view will only consider those reactions and the species involved in them.</p>
<p>This is useful for focusing on a specific sub-network for analysis, debugging, or performance reasons, without modifying the underlying full network.</p>
<p>The view maintains mappings between the indices of its active (defined) species and reactions and the corresponding indices in the full network of the base engine. All calculations are delegated to the base engine after mapping the inputs from the view's context to the full network context, and the results are mapped back.</p>
<p>&lt;DynamicEngine&gt; </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00036">36</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
<a id="a63f8f85e75ecaab6fa39d48d7a846187" name="a63f8f85e75ecaab6fa39d48d7a846187"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a63f8f85e75ecaab6fa39d48d7a846187">&#9670;&#160;</a></span>Config</h2>
@@ -258,7 +276,7 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00071">71</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00223">223</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
@@ -282,7 +300,7 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00072">72</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00224">224</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
@@ -319,6 +337,29 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Constructs a <a class="el" href="classgridfire_1_1_file_defined_engine_view.html" title="An engine view that uses a user-defined reaction network from a file.">FileDefinedEngineView</a>. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">baseEngine</td><td>The underlying <a class="el" href="classgridfire_1_1_dynamic_engine.html" title="Abstract class for engines supporting Jacobian and stoichiometry operations.">DynamicEngine</a> to which this view delegates calculations. </td></tr>
<tr><td class="paramname">fileName</td><td>The path to the file that defines the reaction network for this view. </td></tr>
<tr><td class="paramname">parser</td><td>A reference to a parser object capable of parsing the network file.</td></tr>
</table>
</dd>
</dl>
<dl class="section user"><dt>Usage Example:</dt><dd><div class="fragment"><div class="line">MyParser parser;</div>
<div class="line"><a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a> baseEngine(...);</div>
<div class="line"><a class="code hl_function" href="#a8f2f64bab0f516ed2a6fd529912e0acd">FileDefinedEngineView</a> view(baseEngine, <span class="stringliteral">&quot;my_network.net&quot;</span>, parser);</div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><div class="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00121">engine_abstract.h:121</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_a8f2f64bab0f516ed2a6fd529912e0acd"><div class="ttname"><a href="#a8f2f64bab0f516ed2a6fd529912e0acd">gridfire::FileDefinedEngineView::FileDefinedEngineView</a></div><div class="ttdeci">FileDefinedEngineView(DynamicEngine &amp;baseEngine, const std::string &amp;fileName, const io::NetworkFileParser &amp;parser)</div><div class="ttdoc">Constructs a FileDefinedEngineView.</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8cpp_source.html#l00008">engine_defined.cpp:8</a></div></div>
</div><!-- fragment --></dd></dl>
<dl class="section post"><dt>Postcondition</dt><dd>The view is initialized with the reactions and species from the specified file. </dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If a reaction from the file is not found in the base engine. </td></tr>
</table>
</dd>
</dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00008">8</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
@@ -347,6 +388,27 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Builds the active species and reaction sets from a file. </p>
<p>This method uses the provided parser to read reaction names from the given file. It then finds these reactions in the base engine's full network and populates the <code>m_activeReactions</code> and <code>m_activeSpecies</code> members. Finally, it constructs the index maps for the active sets.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">fileName</td><td>The path to the network definition file.</td></tr>
</table>
</dd>
</dl>
<dl class="section post"><dt>Postcondition</dt><dd><ul>
<li><code>m_activeReactions</code> and <code>m_activeSpecies</code> are populated.</li>
<li><code>m_speciesIndexMap</code> and <code>m_reactionIndexMap</code> are constructed.</li>
<li><code>m_isStale</code> is set to false.</li>
</ul>
</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If a reaction from the file is not found in the base engine. </td></tr>
</table>
</dd>
</dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00208">208</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
@@ -368,7 +430,7 @@ Private Attributes</h2></td></tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_defined</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
@@ -388,18 +450,23 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Calculate the molar reaction flow for a given reaction. </p>
<p>Calculates the molar reaction flow for a given reaction in the active network. </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">Y_defined</td><td>Vector of current abundances for the active 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>
</dl>
<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>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If the view is stale or if the reaction is not in the active set. </td></tr>
</table>
</dd>
</dl>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine</a>.</p>
@@ -419,7 +486,7 @@ Private Attributes</h2></td></tr>
<tr>
<td class="memname"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt; gridfire::FileDefinedEngineView::calculateRHSAndEnergy </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_defined</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
@@ -439,17 +506,22 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Calculate the right-hand side (dY/dt) and energy generation. </p>
<p>Calculates the right-hand side (dY/dt) and energy generation for the active species. </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>
<tr><td class="paramname">Y_defined</td><td>A vector of abundances for the active species. </td></tr>
<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>The density in g/cm^3. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>A <a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives</a> struct containing the derivatives of the active species and the nuclear energy generation rate.</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If the view is stale (i.e., <code><a class="el" href="#ace3568eadaba69e7357b4386c5ca3eb0" title="Updates the engine view if it is marked as stale.">update()</a></code> has not been called after <code><a class="el" href="#a92f14da849e99d07c1ff1347addb9263" title="Sets a new network file to define the active reactions.">setNetworkFile()</a></code>). </td></tr>
</table>
</dd>
</dl>
<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 function must be implemented by derived classes to compute the time derivatives of all species and the specific nuclear energy generation rate for the current state. </p>
<p>Implements <a class="el" href="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">gridfire::Engine</a>.</p>
@@ -481,9 +553,14 @@ Private Attributes</h2></td></tr>
</div><div class="memdoc">
<p>Constructs the reaction index map. </p>
<dl class="section return"><dt>Returns</dt><dd>A vector mapping culled reaction indices to full reaction indices.</dd></dl>
<dl class="section return"><dt>Returns</dt><dd>A vector mapping defined reaction indices to full reaction indices.</dd></dl>
<p>This method creates a map from the indices of the active reactions to the indices of the corresponding reactions in the full network.</p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If an active reaction is not found in the base engine's reaction list. </td></tr>
</table>
</dd>
</dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00176">176</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
@@ -513,9 +590,14 @@ Private Attributes</h2></td></tr>
</div><div class="memdoc">
<p>Constructs the species index map. </p>
<dl class="section return"><dt>Returns</dt><dd>A vector mapping culled species indices to full species indices.</dd></dl>
<dl class="section return"><dt>Returns</dt><dd>A vector mapping defined species indices to full species indices.</dd></dl>
<p>This method creates a map from the indices of the active species to the indices of the corresponding species in the full network.</p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7d61e73f5158f1574cda3edc90c51f7e" title="Updates the active species and reactions based on the current conditions.">AdaptiveEngineView::update()</a> </dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If an active species is not found in the base engine's species list. </td></tr>
</table>
</dd>
</dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00147">147</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
@@ -533,7 +615,7 @@ Private Attributes</h2></td></tr>
<tr>
<td class="memname">void gridfire::FileDefinedEngineView::generateJacobianMatrix </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_defined</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
@@ -553,16 +635,21 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Generate the Jacobian matrix for the current state. </p>
<p>Generates the Jacobian matrix for the active species. </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>
<tr><td class="paramname">Y_defined</td><td>A vector of abundances for the active species. </td></tr>
<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
<tr><td class="paramname">rho</td><td>The density in g/cm^3.</td></tr>
</table>
</dd>
</dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
</table>
</dd>
</dl>
<p>This method must compute and store the Jacobian matrix (∂(dY/dt)_i/∂Y_j) for the current state. The matrix can then be accessed via <a class="el" href="#a0ef8804780d13bbfce0856237bb00470" title="Get an entry from the previously generated Jacobian matrix.">getJacobianMatrixEntry()</a>. </p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a0a2fb3435ee3271ab9c806f225c61a7f">gridfire::DynamicEngine</a>.</p>
@@ -593,8 +680,13 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Generate the stoichiometry matrix for the network. </p>
<p>This method must compute and store the stoichiometry matrix, which encodes the net change of each species in each reaction. </p>
<p>Generates the stoichiometry matrix for the active reactions and species. </p>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
</table>
</dd>
</dl>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">gridfire::DynamicEngine</a>.</p>
@@ -625,12 +717,9 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Access the underlying engine instance. </p>
<dl class="section return"><dt>Returns</dt><dd>Const reference to the underlying engine.</dd></dl>
<p>This method must be implemented by derived classes to provide access to the base engine. The returned reference should remain valid for the lifetime of the <a class="el" href="classgridfire_1_1_engine_view.html" title="Abstract base class for a &quot;view&quot; of a reaction network engine.">EngineView</a>.</p>
<p>Example: </p><div class="fragment"><div class="line"><span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1_dynamic_engine.html">DynamicEngine</a>&amp; engine = myView.getBaseEngine();</div>
<div class="ttc" id="aclassgridfire_1_1_dynamic_engine_html"><div class="ttname"><a href="classgridfire_1_1_dynamic_engine.html">gridfire::DynamicEngine</a></div><div class="ttdoc">Abstract class for engines supporting Jacobian and stoichiometry operations.</div><div class="ttdef"><b>Definition</b> <a href="engine__abstract_8h_source.html#l00121">engine_abstract.h:121</a></div></div>
</div><!-- fragment -->
<p>Gets the base engine. </p>
<dl class="section return"><dt>Returns</dt><dd>A const reference to the base engine. </dd></dl>
<p>Implements <a class="el" href="classgridfire_1_1_engine_view.html#ad294227f8b5cf6d970c349eabf5447a6">gridfire::EngineView&lt; DynamicEngine &gt;</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00021">21</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
@@ -649,12 +738,12 @@ Private Attributes</h2></td></tr>
<tr>
<td class="memname">double gridfire::FileDefinedEngineView::getJacobianMatrixEntry </td>
<td>(</td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>i</em></span>, </td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>i_defined</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>j</em></span>&#160;) const</td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>j_defined</em></span>&#160;) const</td>
</tr>
</table>
</td>
@@ -664,16 +753,22 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Get an entry from the previously generated Jacobian matrix. </p>
<p>Gets an entry from the Jacobian matrix for the active species. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<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>
<tr><td class="paramname">i_defined</td><td>The row index (species index) in the defined matrix. </td></tr>
<tr><td class="paramname">j_defined</td><td>The column index (species index) in the defined matrix. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>The value of the Jacobian matrix at (i_defined, j_defined).</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
<tr><td class="paramname">std::out_of_range</td><td>If an index is out of bounds. </td></tr>
</table>
</dd>
</dl>
<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 <a class="el" href="#a48b2451f96b8f5511ffc4071519c0810" title="Generate the Jacobian matrix for the current state.">generateJacobianMatrix()</a> before calling this. </p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">gridfire::DynamicEngine</a>.</p>
@@ -704,8 +799,14 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Get 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>Gets the set of active logical reactions in the network. </p>
<dl class="section return"><dt>Returns</dt><dd>Reference to the LogicalReactionSet containing all active reactions.</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
</table>
</dd>
</dl>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad2a82099edbb374bbb2c9509ccdb1037">gridfire::DynamicEngine</a>.</p>
@@ -736,8 +837,8 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Get 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>Gets the list of active species in the network defined by the file. </p>
<dl class="section return"><dt>Returns</dt><dd>A const reference to the vector of active species. </dd></dl>
<p>Implements <a class="el" href="classgridfire_1_1_engine.html#a020e1b493d6964cafdad08fde697ceb3">gridfire::Engine</a>.</p>
@@ -768,6 +869,9 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Gets the screening model from the base engine. </p>
<dl class="section return"><dt>Returns</dt><dd>The current screening model type. </dd></dl>
<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__defined_8cpp_source.html#l00143">143</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
@@ -786,7 +890,7 @@ Private Attributes</h2></td></tr>
<tr>
<td class="memname">std::unordered_map&lt; Species, double &gt; gridfire::FileDefinedEngineView::getSpeciesTimescales </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>Y_defined</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
@@ -806,17 +910,22 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Compute timescales for all species in the network. </p>
<p>Computes timescales for all active species in the network. </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">Y_defined</td><td>Vector of current abundances for the active 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>
</dl>
<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, diagnostics, and reaction network culling. </p>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
</table>
</dd>
</dl>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a5d8ba98b230d2849035ee2507728fa15">gridfire::DynamicEngine</a>.</p>
@@ -836,12 +945,12 @@ Private Attributes</h2></td></tr>
<tr>
<td class="memname">int gridfire::FileDefinedEngineView::getStoichiometryMatrixEntry </td>
<td>(</td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>speciesIndex</em></span>, </td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>speciesIndex_defined</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>reactionIndex</em></span>&#160;) const</td>
<td class="paramtype">const int</td> <td class="paramname"><span class="paramname"><em>reactionIndex_defined</em></span>&#160;) const</td>
</tr>
</table>
</td>
@@ -851,16 +960,22 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Get an entry from the stoichiometry matrix. </p>
<p>Gets an entry from the stoichiometry matrix for the active species and reactions. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<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>
<tr><td class="paramname">speciesIndex_defined</td><td>The index of the species in the defined species list. </td></tr>
<tr><td class="paramname">reactionIndex_defined</td><td>The index of the reaction in the defined reaction list. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>The stoichiometric coefficient for the given species and reaction.</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If the view is stale. </td></tr>
<tr><td class="paramname">std::out_of_range</td><td>If an index is out of bounds. </td></tr>
</table>
</dd>
</dl>
<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 <a class="el" href="#a27a5163157cc15c4cb3b99a5d3564dbd" title="Generate the stoichiometry matrix for the network.">generateStoichiometryMatrix()</a>. </p>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">gridfire::DynamicEngine</a>.</p>
@@ -904,8 +1019,8 @@ Private Attributes</h2></td></tr>
</div>
</div>
<a id="ac231044e37e0962f664f8465e1ccb022" name="ac231044e37e0962f664f8465e1ccb022"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ac231044e37e0962f664f8465e1ccb022">&#9670;&#160;</a></span>mapViewToFull()</h2>
<a id="adba3c11b11a04b2907c1635210d73dee" name="adba3c11b11a04b2907c1635210d73dee"></a>
<h2 class="memtitle"><span class="permalink"><a href="#adba3c11b11a04b2907c1635210d73dee">&#9670;&#160;</a></span>mapViewToFull()</h2>
<div class="memitem">
<div class="memproto">
@@ -916,7 +1031,7 @@ Private Attributes</h2></td></tr>
<tr>
<td class="memname">std::vector&lt; double &gt; gridfire::FileDefinedEngineView::mapViewToFull </td>
<td>(</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>culled</em></span></td><td>)</td>
<td class="paramtype">const std::vector&lt; double &gt; &amp;</td> <td class="paramname"><span class="paramname"><em>defined</em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
@@ -930,18 +1045,18 @@ Private Attributes</h2></td></tr>
<p>Maps a vector of culled abundances to a vector of full abundances. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">culled</td><td>A vector of abundances for the active species. </td></tr>
<tr><td class="paramname">defined</td><td>A vector of abundances for the active species. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>A vector of abundances for the full network, with the abundances of the active species copied from the culled vector. </dd></dl>
<dl class="section return"><dt>Returns</dt><dd>A vector of abundances for the full network, with the abundances of the active species copied from the defined vector. </dd></dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00267">267</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
</div>
<a id="ae7d6f0ff9076d59d1245c047bbd1bdb9" name="ae7d6f0ff9076d59d1245c047bbd1bdb9"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ae7d6f0ff9076d59d1245c047bbd1bdb9">&#9670;&#160;</a></span>mapViewToFullReactionIndex()</h2>
<a id="a74217a1f8fd8e6daff969cb17885315c" name="a74217a1f8fd8e6daff969cb17885315c"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a74217a1f8fd8e6daff969cb17885315c">&#9670;&#160;</a></span>mapViewToFullReactionIndex()</h2>
<div class="memitem">
<div class="memproto">
@@ -952,7 +1067,7 @@ Private Attributes</h2></td></tr>
<tr>
<td class="memname">size_t gridfire::FileDefinedEngineView::mapViewToFullReactionIndex </td>
<td>(</td>
<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>culledReactionIndex</em></span></td><td>)</td>
<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>definedReactionIndex</em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
@@ -966,14 +1081,14 @@ Private Attributes</h2></td></tr>
<p>Maps a culled reaction index to a full reaction index. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">culledReactionIndex</td><td>The index of the reaction in the culled reaction list. </td></tr>
<tr><td class="paramname">definedReactionIndex</td><td>The index of the reaction in the defined reaction list. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>The index of the corresponding reaction in the full network.</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::out_of_range</td><td>If the culled index is out of bounds for the reaction index map. </td></tr>
<tr><td class="paramname">std::out_of_range</td><td>If the defined index is out of bounds for the reaction index map. </td></tr>
</table>
</dd>
</dl>
@@ -982,8 +1097,8 @@ Private Attributes</h2></td></tr>
</div>
</div>
<a id="a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf" name="a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf">&#9670;&#160;</a></span>mapViewToFullSpeciesIndex()</h2>
<a id="aa2373955ef5b0eabf7a57c7208e38bb1" name="aa2373955ef5b0eabf7a57c7208e38bb1"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aa2373955ef5b0eabf7a57c7208e38bb1">&#9670;&#160;</a></span>mapViewToFullSpeciesIndex()</h2>
<div class="memitem">
<div class="memproto">
@@ -994,7 +1109,7 @@ Private Attributes</h2></td></tr>
<tr>
<td class="memname">size_t gridfire::FileDefinedEngineView::mapViewToFullSpeciesIndex </td>
<td>(</td>
<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>culledSpeciesIndex</em></span></td><td>)</td>
<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>definedSpeciesIndex</em></span></td><td>)</td>
<td> const</td>
</tr>
</table>
@@ -1008,14 +1123,14 @@ Private Attributes</h2></td></tr>
<p>Maps a culled species index to a full species index. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">culledSpeciesIndex</td><td>The index of the species in the culled species list. </td></tr>
<tr><td class="paramname">definedSpeciesIndex</td><td>The index of the species in the defined species list. </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>The index of the corresponding species in the full network.</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::out_of_range</td><td>If the culled index is out of bounds for the species index map. </td></tr>
<tr><td class="paramname">std::out_of_range</td><td>If the defined index is out of bounds for the species index map. </td></tr>
</table>
</dd>
</dl>
@@ -1039,6 +1154,18 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Sets a new network file to define the active reactions. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">fileName</td><td>The path to the new network definition file.</td></tr>
</table>
</dd>
</dl>
<dl class="section user"><dt>Usage Example:</dt><dd><div class="fragment"><div class="line">view.setNetworkFile(<span class="stringliteral">&quot;another_network.net&quot;</span>);</div>
<div class="line">view.update(netIn); <span class="comment">// Must be called before using the view again</span></div>
</div><!-- fragment --></dd></dl>
<dl class="section post"><dt>Postcondition</dt><dd>The view is marked as stale. <code><a class="el" href="#ace3568eadaba69e7357b4386c5ca3eb0" title="Updates the engine view if it is marked as stale.">update()</a></code> must be called before further use. </dd></dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00133">133</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
@@ -1066,6 +1193,14 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Sets the screening model for the base engine. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">model</td><td>The screening model to set. </td></tr>
</table>
</dd>
</dl>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00139">139</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
@@ -1095,6 +1230,16 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Updates the engine view if it is marked as stale. </p>
<p>This method checks if the view is stale (e.g., after <code>setNetworkFile</code> was called). If it is, it rebuilds the active network from the currently set file. The <code>netIn</code> parameter is not used by this implementation but is required by the interface.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">netIn</td><td>The current network input (unused).</td></tr>
</table>
</dd>
</dl>
<dl class="section post"><dt>Postcondition</dt><dd>If the view was stale, it is rebuilt and is no longer stale. </dd></dl>
<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__defined_8cpp_source.html#l00127">127</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
@@ -1124,6 +1269,14 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Validates that the <a class="el" href="classgridfire_1_1_file_defined_engine_view.html" title="An engine view that uses a user-defined reaction network from a file.">FileDefinedEngineView</a> is not stale. </p>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">std::runtime_error</td><td>If the view is stale (i.e., <code><a class="el" href="#ace3568eadaba69e7357b4386c5ca3eb0" title="Updates the engine view if it is marked as stale.">update()</a></code> has not been called after the view was made stale). </td></tr>
</table>
</dd>
</dl>
<p class="definition">Definition at line <a class="el" href="engine__defined_8cpp_source.html#l00303">303</a> of file <a class="el" href="engine__defined_8cpp_source.html">engine_defined.cpp</a>.</p>
</div>
@@ -1149,9 +1302,9 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Active reactions in the defined engine. </p>
<p>Maps indices of active species to indices in the full network. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00081">81</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00240">240</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
@@ -1175,9 +1328,9 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Active species in the defined engine. </p>
<p>Active reactions in the defined engine. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00080">80</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00238">238</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
@@ -1201,7 +1354,10 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00076">76</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<p>The underlying engine to which this view delegates calculations. </p>
<p>Name of the file defining the reaction set considered by the engine view. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00231">231</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
@@ -1225,7 +1381,9 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00073">73</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<p>A reference to the singleton <a class="el" href="#a63f8f85e75ecaab6fa39d48d7a846187">Config</a> instance. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00226">226</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
@@ -1249,9 +1407,9 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Name of the file defining the reaction set considered by the engine view. </p>
<p>Parser for the network file. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00077">77</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00233">233</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
@@ -1275,7 +1433,9 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00086">86</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<p>A flag indicating whether the view is stale and needs to be updated. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00248">248</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
@@ -1299,7 +1459,9 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00074">74</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<p>A pointer to the logger instance. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00228">228</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
@@ -1323,9 +1485,9 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Parser for the network file. </p>
<p>Active species in the defined engine. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00078">78</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00235">235</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
@@ -1349,9 +1511,7 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Maps indices of active reactions to indices in the full network. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00084">84</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00245">245</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>
@@ -1375,9 +1535,9 @@ Private Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p>Maps indices of active species to indices in the full network. </p>
<p>Maps indices of active reactions to indices in the full network. </p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00083">83</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__defined_8h_source.html#l00243">243</a> of file <a class="el" href="engine__defined_8h_source.html">engine_defined.h</a>.</p>
</div>
</div>