docs(docs): rebuilt docs with loads more detail for triggers and weak reactions
This commit is contained in:
@@ -117,9 +117,10 @@ Inheritance diagram for gridfire::screening::ScreeningModel:</div>
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<div class="center">
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<img src="classgridfire_1_1screening_1_1_screening_model.png" usemap="#gridfire::screening::ScreeningModel_map" alt=""/>
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<map id="gridfire::screening::ScreeningModel_map" name="gridfire::screening::ScreeningModel_map">
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<area href="class_py_screening.html" alt="PyScreening" shape="rect" coords="0,56,245,80"/>
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<area href="classgridfire_1_1screening_1_1_bare_screening_model.html" title="A screening model that applies no screening effect." alt="gridfire::screening::BareScreeningModel" shape="rect" coords="255,56,500,80"/>
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<area href="classgridfire_1_1screening_1_1_weak_screening_model.html" title="Implements the weak screening model based on the Debye-Hückel approximation." alt="gridfire::screening::WeakScreeningModel" shape="rect" coords="510,56,755,80"/>
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<area href="class_py_screening.html" alt="PyScreening" shape="rect" coords="0,56,282,80"/>
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<area href="classgridfire_1_1screening_1_1_bare_screening_model.html" title="A screening model that applies no screening effect." alt="gridfire::screening::BareScreeningModel" shape="rect" coords="292,56,574,80"/>
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<area href="classgridfire_1_1screening_1_1_intermediate_screening_model.html" alt="gridfire::screening::IntermediateScreeningModel" shape="rect" coords="584,56,866,80"/>
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<area href="classgridfire_1_1screening_1_1_weak_screening_model.html" title="Implements the weak screening model based on the Debye-Hückel approximation." alt="gridfire::screening::WeakScreeningModel" shape="rect" coords="876,56,1158,80"/>
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</map>
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</div></div>
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<table class="memberdecls">
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@@ -134,12 +135,12 @@ Public Member Functions</h2></td></tr>
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<tr class="memitem:adef175acdbd911527f56a1f1592579a7" id="r_adef175acdbd911527f56a1f1592579a7"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="#adef175acdbd911527f56a1f1592579a7">~ScreeningModel</a> ()=default</td></tr>
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<tr class="memdesc:adef175acdbd911527f56a1f1592579a7"><td class="mdescLeft"> </td><td class="mdescRight">Virtual destructor. <br /></td></tr>
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<tr class="separator:adef175acdbd911527f56a1f1592579a7"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aaec9184d80c86a2d8674e395dad81bde" id="r_aaec9184d80c86a2d8674e395dad81bde"><td class="memItemLeft" align="right" valign="top">virtual std::vector< double > </td><td class="memItemRight" valign="bottom"><a class="el" href="#aaec9184d80c86a2d8674e395dad81bde">calculateScreeningFactors</a> (const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &reactions, const std::vector< fourdst::atomic::Species > &species, const std::vector< double > &Y, const double T9, const double rho) const =0</td></tr>
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<tr class="memdesc:aaec9184d80c86a2d8674e395dad81bde"><td class="mdescLeft"> </td><td class="mdescRight">Calculates screening factors for a set of reactions. <br /></td></tr>
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<tr class="separator:aaec9184d80c86a2d8674e395dad81bde"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a6c381a823cb9c1680d3e9c846da4ae22" id="r_a6c381a823cb9c1680d3e9c846da4ae22"><td class="memItemLeft" align="right" valign="top">virtual std::vector< <a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="#a6c381a823cb9c1680d3e9c846da4ae22">calculateScreeningFactors</a> (const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &reactions, const std::vector< fourdst::atomic::Species > &species, const std::vector< <a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> > &Y, const <a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> T9, const <a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> rho) const =0</td></tr>
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<tr class="memdesc:a6c381a823cb9c1680d3e9c846da4ae22"><td class="mdescLeft"> </td><td class="mdescRight">Calculates screening factors using CppAD types for automatic differentiation. <br /></td></tr>
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<tr class="separator:a6c381a823cb9c1680d3e9c846da4ae22"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ab08c4490f9da18254a7c6f29be1f62ce" id="r_ab08c4490f9da18254a7c6f29be1f62ce"><td class="memItemLeft" align="right" valign="top">virtual std::vector< double > </td><td class="memItemRight" valign="bottom"><a class="el" href="#ab08c4490f9da18254a7c6f29be1f62ce">calculateScreeningFactors</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a> &reactions, const std::vector< fourdst::atomic::Species > &species, const std::vector< double > &Y, double T9, double rho) const =0</td></tr>
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<tr class="memdesc:ab08c4490f9da18254a7c6f29be1f62ce"><td class="mdescLeft"> </td><td class="mdescRight">Calculates screening factors for a set of reactions. <br /></td></tr>
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<tr class="separator:ab08c4490f9da18254a7c6f29be1f62ce"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a1da8242c7591ab32453d1e0109999d6c" id="r_a1da8242c7591ab32453d1e0109999d6c"><td class="memItemLeft" align="right" valign="top">virtual std::vector< <a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="#a1da8242c7591ab32453d1e0109999d6c">calculateScreeningFactors</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a> &reactions, const std::vector< fourdst::atomic::Species > &species, const std::vector< CppAD::AD< double > > &Y, <a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> T9, <a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> rho) const =0</td></tr>
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<tr class="memdesc:a1da8242c7591ab32453d1e0109999d6c"><td class="mdescLeft"> </td><td class="mdescRight">Calculates screening factors using CppAD types for automatic differentiation. <br /></td></tr>
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<tr class="separator:a1da8242c7591ab32453d1e0109999d6c"><td class="memSeparator" colspan="2"> </td></tr>
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</table>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<div class="textblock"><p>An abstract base class for plasma screening models. </p>
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@@ -192,8 +193,8 @@ Public Member Functions</h2></td></tr>
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</div>
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</div>
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<h2 class="groupheader">Member Function Documentation</h2>
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<a id="a6c381a823cb9c1680d3e9c846da4ae22" name="a6c381a823cb9c1680d3e9c846da4ae22"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a6c381a823cb9c1680d3e9c846da4ae22">◆ </a></span>calculateScreeningFactors() <span class="overload">[1/2]</span></h2>
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<a id="a1da8242c7591ab32453d1e0109999d6c" name="a1da8242c7591ab32453d1e0109999d6c"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a1da8242c7591ab32453d1e0109999d6c">◆ </a></span>calculateScreeningFactors() <span class="overload">[1/2]</span></h2>
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<div class="memitem">
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@@ -204,7 +205,7 @@ Public Member Functions</h2></td></tr>
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<tr>
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<td class="memname">virtual std::vector< <a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> > gridfire::screening::ScreeningModel::calculateScreeningFactors </td>
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<td>(</td>
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<td class="paramtype">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &</td> <td class="paramname"><span class="paramname"><em>reactions</em></span>, </td>
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<td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a> &</td> <td class="paramname"><span class="paramname"><em>reactions</em></span>, </td>
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</tr>
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<td class="paramkey"></td>
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@@ -214,22 +215,22 @@ Public Member Functions</h2></td></tr>
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<tr>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype">const std::vector< <a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> > &</td> <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
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<td class="paramtype">const std::vector< CppAD::AD< double > > &</td> <td class="paramname"><span class="paramname"><em>Y</em></span>, </td>
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</tr>
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<tr>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype">const <a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a></td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
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<td class="paramtype"><a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a></td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
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</tr>
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<tr>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype">const <a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a></td> <td class="paramname"><span class="paramname"><em>rho</em></span> ) const</td>
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<td class="paramtype"><a class="el" href="#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a></td> <td class="paramname"><span class="paramname"><em>rho</em></span> ) const</td>
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</tr>
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</table>
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</td>
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<td class="mlabels-right">
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<span class="mlabels"><span class="mlabel pure-virtual">pure virtual</span></span> </td>
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<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel pure-virtual">pure virtual</span></span> </td>
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</tr>
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</table>
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</div><div class="memdoc">
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@@ -240,7 +241,7 @@ Public Member Functions</h2></td></tr>
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<table class="params">
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<tr><td class="paramname">reactions</td><td>The set of logical reactions in the network. </td></tr>
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<tr><td class="paramname">species</td><td>A vector of all atomic species involved in the network. </td></tr>
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<tr><td class="paramname">Y</td><td>A vector of the molar abundances (mol/g) for each species, as AD types. </td></tr>
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<tr><td class="paramname">Y</td><td>The current composition, providing molar abundances (mol/g) for each species. </td></tr>
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<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K, as an AD type. </td></tr>
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<tr><td class="paramname">rho</td><td>The plasma density in g/cm^3, as an AD type. </td></tr>
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</table>
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@@ -249,12 +250,12 @@ Public Member Functions</h2></td></tr>
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<dl class="section return"><dt>Returns</dt><dd>A vector of screening factors (dimensionless), as AD types.</dd></dl>
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<p><b>Note</b> This method is essential for including the effects of screening in the Jacobian matrix of the reaction network. </p>
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<p>Implemented in <a class="el" href="classgridfire_1_1screening_1_1_bare_screening_model.html#ac5647d633cd5bbd7cb5136b7fa4cad99">gridfire::screening::BareScreeningModel</a>, <a class="el" href="classgridfire_1_1screening_1_1_weak_screening_model.html#ac6bc78769670a460af1ff88284cb8ad4">gridfire::screening::WeakScreeningModel</a>, and <a class="el" href="class_py_screening.html#a5539d59311c778cf7f0006acc8f84ade">PyScreening</a>.</p>
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<p>Implemented in <a class="el" href="classgridfire_1_1screening_1_1_bare_screening_model.html#a0ac3685a90c1e65a84e03cfb2fed29e5">gridfire::screening::BareScreeningModel</a>, <a class="el" href="classgridfire_1_1screening_1_1_intermediate_screening_model.html#a765e369256282f0f25e66e13c33dcbd9">gridfire::screening::IntermediateScreeningModel</a>, <a class="el" href="classgridfire_1_1screening_1_1_weak_screening_model.html#a8b0590814e7058b4ff3f0cd6f4124773">gridfire::screening::WeakScreeningModel</a>, and <a class="el" href="class_py_screening.html#a68a126de903e1a87a1d7d1cfec8add0f">PyScreening</a>.</p>
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<a id="aaec9184d80c86a2d8674e395dad81bde" name="aaec9184d80c86a2d8674e395dad81bde"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#aaec9184d80c86a2d8674e395dad81bde">◆ </a></span>calculateScreeningFactors() <span class="overload">[2/2]</span></h2>
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<a id="ab08c4490f9da18254a7c6f29be1f62ce" name="ab08c4490f9da18254a7c6f29be1f62ce"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ab08c4490f9da18254a7c6f29be1f62ce">◆ </a></span>calculateScreeningFactors() <span class="overload">[2/2]</span></h2>
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<div class="memitem">
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<div class="memproto">
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@@ -265,7 +266,7 @@ Public Member Functions</h2></td></tr>
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<tr>
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<td class="memname">virtual std::vector< double > gridfire::screening::ScreeningModel::calculateScreeningFactors </td>
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<td>(</td>
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<td class="paramtype">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a> &</td> <td class="paramname"><span class="paramname"><em>reactions</em></span>, </td>
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<td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a> &</td> <td class="paramname"><span class="paramname"><em>reactions</em></span>, </td>
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</tr>
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<td class="paramkey"></td>
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@@ -280,17 +281,17 @@ Public Member Functions</h2></td></tr>
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<tr>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
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<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
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</tr>
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<tr>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>rho</em></span> ) const</td>
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<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>rho</em></span> ) const</td>
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</tr>
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</table>
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</td>
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<td class="mlabels-right">
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<span class="mlabels"><span class="mlabel pure-virtual">pure virtual</span></span> </td>
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<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel pure-virtual">pure virtual</span></span> </td>
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</tr>
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</table>
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</div><div class="memdoc">
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@@ -301,7 +302,7 @@ Public Member Functions</h2></td></tr>
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<table class="params">
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<tr><td class="paramname">reactions</td><td>The set of logical reactions in the network. </td></tr>
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<tr><td class="paramname">species</td><td>A vector of all atomic species involved in the network. </td></tr>
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<tr><td class="paramname">Y</td><td>A vector of the molar abundances (mol/g) for each species. </td></tr>
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<tr><td class="paramname">Y</td><td>The current composition, providing molar abundances (mol/g) for each species. </td></tr>
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<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K. </td></tr>
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<tr><td class="paramname">rho</td><td>The plasma density in g/cm^3. </td></tr>
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</table>
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@@ -325,7 +326,7 @@ Public Member Functions</h2></td></tr>
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<div class="line"> <span class="comment">// ... use screening_factors[i] ...</span></div>
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<div class="line">}</div>
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</div><!-- fragment -->
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<p>Implemented in <a class="el" href="classgridfire_1_1screening_1_1_bare_screening_model.html#ac35ad34c5da7e1b5087552aa5c83fe60">gridfire::screening::BareScreeningModel</a>, <a class="el" href="classgridfire_1_1screening_1_1_weak_screening_model.html#afbaeaefe6b3ab3ecf81889ddc1cff76c">gridfire::screening::WeakScreeningModel</a>, and <a class="el" href="class_py_screening.html#a2b8756c197eb89e77cb6dd231c979315">PyScreening</a>.</p>
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<p>Implemented in <a class="el" href="classgridfire_1_1screening_1_1_bare_screening_model.html#ad252ce1de82401bab24747aabf0c8a3a">gridfire::screening::BareScreeningModel</a>, <a class="el" href="classgridfire_1_1screening_1_1_intermediate_screening_model.html#a86a218ce82306ed582296cbeb3de0250">gridfire::screening::IntermediateScreeningModel</a>, <a class="el" href="classgridfire_1_1screening_1_1_weak_screening_model.html#a6a215d082b0d05126fb2b19fd1983446">gridfire::screening::WeakScreeningModel</a>, and <a class="el" href="class_py_screening.html#aa67b5f0528006d9c742033b8c5ab3a05">PyScreening</a>.</p>
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</div>
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