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docs(docs): rebuilt docs with loads more detail for triggers and weak reactions

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Emily Boudreaux
2025-10-08 11:17:09 -04:00
parent 8a0b5b2c36
commit 274c566726
600 changed files with 39207 additions and 9125 deletions
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@@ -119,12 +119,12 @@ Inheritance diagram for PyScreening:</div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-methods" name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:a2b8756c197eb89e77cb6dd231c979315" id="r_a2b8756c197eb89e77cb6dd231c979315"><td class="memItemLeft" align="right" valign="top">std::vector&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a2b8756c197eb89e77cb6dd231c979315">calculateScreeningFactors</a> (const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a> &amp;reactions, const std::vector&lt; fourdst::atomic::Species &gt; &amp;species, const std::vector&lt; double &gt; &amp;Y, const double T9, const double rho) const override</td></tr>
<tr class="memdesc:a2b8756c197eb89e77cb6dd231c979315"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates screening factors for a set of reactions. <br /></td></tr>
<tr class="separator:a2b8756c197eb89e77cb6dd231c979315"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5539d59311c778cf7f0006acc8f84ade" id="r_a5539d59311c778cf7f0006acc8f84ade"><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a5539d59311c778cf7f0006acc8f84ade">calculateScreeningFactors</a> (const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a> &amp;reactions, const std::vector&lt; fourdst::atomic::Species &gt; &amp;species, const std::vector&lt; <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> &gt; &amp;Y, const <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> T9, const <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> rho) const override</td></tr>
<tr class="memdesc:a5539d59311c778cf7f0006acc8f84ade"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates screening factors using CppAD types for automatic differentiation. <br /></td></tr>
<tr class="separator:a5539d59311c778cf7f0006acc8f84ade"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa67b5f0528006d9c742033b8c5ab3a05" id="r_aa67b5f0528006d9c742033b8c5ab3a05"><td class="memItemLeft" align="right" valign="top">std::vector&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aa67b5f0528006d9c742033b8c5ab3a05">calculateScreeningFactors</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">gridfire::reaction::ReactionSet</a> &amp;reactions, const std::vector&lt; fourdst::atomic::Species &gt; &amp;species, const std::vector&lt; double &gt; &amp;Y, double T9, double rho) const override</td></tr>
<tr class="memdesc:aa67b5f0528006d9c742033b8c5ab3a05"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates screening factors for a set of reactions. <br /></td></tr>
<tr class="separator:aa67b5f0528006d9c742033b8c5ab3a05"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a68a126de903e1a87a1d7d1cfec8add0f" id="r_a68a126de903e1a87a1d7d1cfec8add0f"><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a68a126de903e1a87a1d7d1cfec8add0f">calculateScreeningFactors</a> (const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">gridfire::reaction::ReactionSet</a> &amp;reactions, const std::vector&lt; fourdst::atomic::Species &gt; &amp;species, const std::vector&lt; <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> &gt; &amp;Y, <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> T9, <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> rho) const override</td></tr>
<tr class="memdesc:a68a126de903e1a87a1d7d1cfec8add0f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculates screening factors using CppAD types for automatic differentiation. <br /></td></tr>
<tr class="separator:a68a126de903e1a87a1d7d1cfec8add0f"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="inherited" name="inherited"></a>
Additional Inherited Members</h2></td></tr>
@@ -138,8 +138,8 @@ Additional Inherited Members</h2></td></tr>
<tr class="separator:adef175acdbd911527f56a1f1592579a7 inherit pub_methods_classgridfire_1_1screening_1_1_screening_model"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<h2 class="groupheader">Member Function Documentation</h2>
<a id="a5539d59311c778cf7f0006acc8f84ade" name="a5539d59311c778cf7f0006acc8f84ade"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a5539d59311c778cf7f0006acc8f84ade">&#9670;&#160;</a></span>calculateScreeningFactors() <span class="overload">[1/2]</span></h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a68a126de903e1a87a1d7d1cfec8add0f">&#9670;&#160;</a></span>calculateScreeningFactors() <span class="overload">[1/2]</span></h2>
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@@ -150,7 +150,7 @@ Additional Inherited Members</h2></td></tr>
<tr>
<td class="memname">std::vector&lt; <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a> &gt; PyScreening::calculateScreeningFactors </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a> &amp;</td> <td class="paramname"><span class="paramname"><em>reactions</em></span>, </td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">gridfire::reaction::ReactionSet</a> &amp;</td> <td class="paramname"><span class="paramname"><em>reactions</em></span>, </td>
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@@ -165,17 +165,17 @@ Additional Inherited Members</h2></td></tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a></td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
<td class="paramtype"><a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a></td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a></td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
<td class="paramtype"><a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a107ff2897f040d6f27f69d56a0bdd28d">ADDouble</a></td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span> </td>
<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span> </td>
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@@ -186,7 +186,7 @@ Additional Inherited Members</h2></td></tr>
<table class="params">
<tr><td class="paramname">reactions</td><td>The set of logical reactions in the network. </td></tr>
<tr><td class="paramname">species</td><td>A vector of all atomic species involved in the network. </td></tr>
<tr><td class="paramname">Y</td><td>A vector of the molar abundances (mol/g) for each species, as AD types. </td></tr>
<tr><td class="paramname">Y</td><td>The current composition, providing molar abundances (mol/g) for each species. </td></tr>
<tr><td class="paramname">T9</td><td>The temperature in units of 10^9 K, as an AD type. </td></tr>
<tr><td class="paramname">rho</td><td>The plasma density in g/cm^3, as an AD type. </td></tr>
</table>
@@ -195,12 +195,12 @@ Additional Inherited Members</h2></td></tr>
<dl class="section return"><dt>Returns</dt><dd>A vector of screening factors (dimensionless), as AD types.</dd></dl>
<p><b>Note</b> This method is essential for including the effects of screening in the Jacobian matrix of the reaction network. </p>
<p>Implements <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a6c381a823cb9c1680d3e9c846da4ae22">gridfire::screening::ScreeningModel</a>.</p>
<p>Implements <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#a1da8242c7591ab32453d1e0109999d6c">gridfire::screening::ScreeningModel</a>.</p>
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<a id="a2b8756c197eb89e77cb6dd231c979315" name="a2b8756c197eb89e77cb6dd231c979315"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a2b8756c197eb89e77cb6dd231c979315">&#9670;&#160;</a></span>calculateScreeningFactors() <span class="overload">[2/2]</span></h2>
<a id="aa67b5f0528006d9c742033b8c5ab3a05" name="aa67b5f0528006d9c742033b8c5ab3a05"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aa67b5f0528006d9c742033b8c5ab3a05">&#9670;&#160;</a></span>calculateScreeningFactors() <span class="overload">[2/2]</span></h2>
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@@ -211,7 +211,7 @@ Additional Inherited Members</h2></td></tr>
<tr>
<td class="memname">std::vector&lt; double &gt; PyScreening::calculateScreeningFactors </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a> &amp;</td> <td class="paramname"><span class="paramname"><em>reactions</em></span>, </td>
<td class="paramtype">const <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html">gridfire::reaction::ReactionSet</a> &amp;</td> <td class="paramname"><span class="paramname"><em>reactions</em></span>, </td>
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@@ -226,17 +226,17 @@ Additional Inherited Members</h2></td></tr>
<tr>
<td class="paramkey"></td>
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<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>rho</em></span>&#160;) const</td>
</tr>
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<span class="mlabels"><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span> </td>
<span class="mlabels"><span class="mlabel nodiscard">nodiscard</span><span class="mlabel override">override</span><span class="mlabel private">private</span><span class="mlabel virtual">virtual</span></span> </td>
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</div><div class="memdoc">
@@ -247,7 +247,7 @@ Additional Inherited Members</h2></td></tr>
<table class="params">
<tr><td class="paramname">reactions</td><td>The set of logical reactions in the network. </td></tr>
<tr><td class="paramname">species</td><td>A vector of all atomic species involved in the network. </td></tr>
<tr><td class="paramname">Y</td><td>A vector of the molar abundances (mol/g) for each species. </td></tr>
<tr><td class="paramname">Y</td><td>The current composition, providing molar abundances (mol/g) for each 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 plasma density in g/cm^3. </td></tr>
</table>
@@ -271,7 +271,7 @@ Additional Inherited Members</h2></td></tr>
<div class="line"> <span class="comment">// ... use screening_factors[i] ...</span></div>
<div class="line">}</div>
</div><!-- fragment -->
<p>Implements <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#aaec9184d80c86a2d8674e395dad81bde">gridfire::screening::ScreeningModel</a>.</p>
<p>Implements <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#ab08c4490f9da18254a7c6f29be1f62ce">gridfire::screening::ScreeningModel</a>.</p>
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