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refactor(.gitignore): removed html/ from .gitignore

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Emily Boudreaux
2025-07-01 11:40:51 -04:00
parent 0c16e81e98
commit 7df6f60912
197 changed files with 6248 additions and 4744 deletions
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@@ -132,7 +132,7 @@ $(function(){initNavTree('reaclib_8cpp_source.html',''); initResizable(true); })
</div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> </div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacegridfire_1_1reaclib.html">gridfire::reaclib</a> {</div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"><a class="line" href="namespacegridfire_1_1reaclib.html#a5dba5efc372d2a9e9e846dfd6563f3c0"> 29</a></span> <span class="keyword">static</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">reaction::LogicalReactionSet</a>* <a class="code hl_variable" href="namespacegridfire_1_1reaclib.html#a5dba5efc372d2a9e9e846dfd6563f3c0">s_all_reaclib_reactions_ptr</a> = <span class="keyword">nullptr</span>;</div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"><a class="line" href="namespacegridfire_1_1reaclib.html#a5dba5efc372d2a9e9e846dfd6563f3c0"> 29</a></span> <span class="keyword">static</span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a>* <a class="code hl_variable" href="namespacegridfire_1_1reaclib.html#a5dba5efc372d2a9e9e846dfd6563f3c0">s_all_reaclib_reactions_ptr</a> = <span class="keyword">nullptr</span>;</div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> </div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span><span class="preprocessor"> #pragma pack(push, 1)</span></div>
<div class="foldopen" id="foldopen00032" data-start="{" data-end="};">
@@ -235,40 +235,43 @@ $(function(){initNavTree('reaclib_8cpp_source.html',''); initResizable(true); })
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> }</div>
<div class="line"><a id="l00123" name="l00123"></a><span class="lineno"> 123</span> </div>
<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> <span class="comment">// The ReactionSet takes the vector of all individual reactions.</span></div>
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_reaction_set.html">reaction::ReactionSet</a> reaction_set(std::move(reaction_list));</div>
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#ad838ce3fb6cc02c3fd90b924a0dd91b1">reaction::ReactionSet</a> reaction_set(std::move(reaction_list));</div>
<div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</span> </div>
<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span> <span class="comment">// The LogicalReactionSet groups reactions by their peName, which is what we want.</span></div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> <a class="code hl_variable" href="namespacegridfire_1_1reaclib.html#a5dba5efc372d2a9e9e846dfd6563f3c0">s_all_reaclib_reactions_ptr</a> = <span class="keyword">new</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">reaction::LogicalReactionSet</a>(reaction_set);</div>
<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> </div>
<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> <a class="code hl_variable" href="namespacegridfire_1_1reaclib.html#af6ff0dfe7ffe34c73ba9acbab5ef8a66">s_initialized</a> = <span class="keyword">true</span>;</div>
<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> }</div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> <a class="code hl_variable" href="namespacegridfire_1_1reaclib.html#a5dba5efc372d2a9e9e846dfd6563f3c0">s_all_reaclib_reactions_ptr</a> = <span class="keyword">new</span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a>(</div>
<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> <a class="code hl_function" href="namespacegridfire_1_1reaction.html#abfcfafc0cda0c3ed56930a12e7ead67f">reaction::packReactionSetToLogicalReactionSet</a>(reaction_set)</div>
<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> );</div>
<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> </div>
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> <a class="code hl_variable" href="namespacegridfire_1_1reaclib.html#af6ff0dfe7ffe34c73ba9acbab5ef8a66">s_initialized</a> = <span class="keyword">true</span>;</div>
<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span> }</div>
</div>
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> </div>
<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span> </div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> <span class="comment">// --- Public Interface Implementation ---</span></div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> </div>
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> </div>
<div class="foldopen" id="foldopen00136" data-start="{" data-end="}">
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"><a class="line" href="namespacegridfire_1_1reaclib.html#a91c7971c9d0a2971b9a6fa4d841c761d"> 136</a></span> <span class="keyword">const</span> <a class="code hl_class" href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">reaction::LogicalReactionSet</a>&amp; <a class="code hl_function" href="namespacegridfire_1_1reaclib.html#a91c7971c9d0a2971b9a6fa4d841c761d">get_all_reactions</a>() {</div>
<div class="line"><a id="l00137" name="l00137"></a><span class="lineno"> 137</span> <span class="comment">// This ensures that the initialization happens only on the first call.</span></div>
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> <span class="keywordflow">if</span> (!<a class="code hl_variable" href="namespacegridfire_1_1reaclib.html#af6ff0dfe7ffe34c73ba9acbab5ef8a66">s_initialized</a>) {</div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> <a class="code hl_function" href="namespacegridfire_1_1reaclib.html#a02ff11b88be94392151873e06a30b276">initializeAllReaclibReactions</a>();</div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> }</div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span> <span class="keywordflow">if</span> (<a class="code hl_variable" href="namespacegridfire_1_1reaclib.html#a5dba5efc372d2a9e9e846dfd6563f3c0">s_all_reaclib_reactions_ptr</a> == <span class="keyword">nullptr</span>) {</div>
<div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">&quot;Reaclib reactions have not been initialized.&quot;</span>);</div>
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span> }</div>
<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"> 144</span> <span class="keywordflow">return</span> *<a class="code hl_variable" href="namespacegridfire_1_1reaclib.html#a5dba5efc372d2a9e9e846dfd6563f3c0">s_all_reaclib_reactions_ptr</a>;</div>
<div class="line"><a id="l00145" name="l00145"></a><span class="lineno"> 145</span> }</div>
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span> <span class="comment">// --- Public Interface Implementation ---</span></div>
<div class="line"><a id="l00137" name="l00137"></a><span class="lineno"> 137</span> </div>
<div class="foldopen" id="foldopen00138" data-start="{" data-end="}">
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"><a class="line" href="namespacegridfire_1_1reaclib.html#a91c7971c9d0a2971b9a6fa4d841c761d"> 138</a></span> <span class="keyword">const</span> <a class="code hl_typedef" href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">reaction::LogicalReactionSet</a>&amp; <a class="code hl_function" href="namespacegridfire_1_1reaclib.html#a91c7971c9d0a2971b9a6fa4d841c761d">get_all_reactions</a>() {</div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> <span class="comment">// This ensures that the initialization happens only on the first call.</span></div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> <span class="keywordflow">if</span> (!<a class="code hl_variable" href="namespacegridfire_1_1reaclib.html#af6ff0dfe7ffe34c73ba9acbab5ef8a66">s_initialized</a>) {</div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span> <a class="code hl_function" href="namespacegridfire_1_1reaclib.html#a02ff11b88be94392151873e06a30b276">initializeAllReaclibReactions</a>();</div>
<div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span> }</div>
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span> <span class="keywordflow">if</span> (<a class="code hl_variable" href="namespacegridfire_1_1reaclib.html#a5dba5efc372d2a9e9e846dfd6563f3c0">s_all_reaclib_reactions_ptr</a> == <span class="keyword">nullptr</span>) {</div>
<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"> 144</span> <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">&quot;Reaclib reactions have not been initialized.&quot;</span>);</div>
<div class="line"><a id="l00145" name="l00145"></a><span class="lineno"> 145</span> }</div>
<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"> 146</span> <span class="keywordflow">return</span> *<a class="code hl_variable" href="namespacegridfire_1_1reaclib.html#a5dba5efc372d2a9e9e846dfd6563f3c0">s_all_reaclib_reactions_ptr</a>;</div>
<div class="line"><a id="l00147" name="l00147"></a><span class="lineno"> 147</span> }</div>
</div>
<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"> 146</span>} <span class="comment">// namespace gridfire::reaclib</span></div>
<div class="ttc" id="aclassgridfire_1_1reaction_1_1_logical_reaction_set_html"><div class="ttname"><a href="classgridfire_1_1reaction_1_1_logical_reaction_set.html">gridfire::reaction::LogicalReactionSet</a></div><div class="ttdoc">A collection of LogicalReaction objects.</div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00554">reaction.h:554</a></div></div>
<div class="ttc" id="aclassgridfire_1_1reaction_1_1_reaction_set_html"><div class="ttname"><a href="classgridfire_1_1reaction_1_1_reaction_set.html">gridfire::reaction::ReactionSet</a></div><div class="ttdoc">A collection of Reaction objects.</div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00307">reaction.h:307</a></div></div>
<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"> 148</span>} <span class="comment">// namespace gridfire::reaclib</span></div>
<div class="ttc" id="anamespacegridfire_1_1reaclib_html"><div class="ttname"><a href="namespacegridfire_1_1reaclib.html">gridfire::reaclib</a></div><div class="ttdef"><b>Definition</b> <a href="reaclib_8h_source.html#l00005">reaclib.h:5</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1reaclib_html_a02ff11b88be94392151873e06a30b276"><div class="ttname"><a href="namespacegridfire_1_1reaclib.html#a02ff11b88be94392151873e06a30b276">gridfire::reaclib::initializeAllReaclibReactions</a></div><div class="ttdeci">static void initializeAllReaclibReactions()</div><div class="ttdef"><b>Definition</b> <a href="#l00079">reaclib.cpp:79</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1reaclib_html_a5dba5efc372d2a9e9e846dfd6563f3c0"><div class="ttname"><a href="namespacegridfire_1_1reaclib.html#a5dba5efc372d2a9e9e846dfd6563f3c0">gridfire::reaclib::s_all_reaclib_reactions_ptr</a></div><div class="ttdeci">static reaction::LogicalReactionSet * s_all_reaclib_reactions_ptr</div><div class="ttdef"><b>Definition</b> <a href="#l00029">reaclib.cpp:29</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1reaclib_html_a6bb94d5adc7bb9db5a67f770f7453e63"><div class="ttname"><a href="namespacegridfire_1_1reaclib.html#a6bb94d5adc7bb9db5a67f770f7453e63">gridfire::reaclib::operator&lt;&lt;</a></div><div class="ttdeci">std::ostream &amp; operator&lt;&lt;(std::ostream &amp;os, const ReactionRecord &amp;r)</div><div class="ttdef"><b>Definition</b> <a href="#l00044">reaclib.cpp:44</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1reaclib_html_a91c7971c9d0a2971b9a6fa4d841c761d"><div class="ttname"><a href="namespacegridfire_1_1reaclib.html#a91c7971c9d0a2971b9a6fa4d841c761d">gridfire::reaclib::get_all_reactions</a></div><div class="ttdeci">const reaction::LogicalReactionSet &amp; get_all_reactions()</div><div class="ttdoc">Provides global access to the fully initialized REACLIB reaction set.</div><div class="ttdef"><b>Definition</b> <a href="#l00136">reaclib.cpp:136</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1reaclib_html_a91c7971c9d0a2971b9a6fa4d841c761d"><div class="ttname"><a href="namespacegridfire_1_1reaclib.html#a91c7971c9d0a2971b9a6fa4d841c761d">gridfire::reaclib::get_all_reactions</a></div><div class="ttdeci">const reaction::LogicalReactionSet &amp; get_all_reactions()</div><div class="ttdoc">Provides global access to the fully initialized REACLIB reaction set.</div><div class="ttdef"><b>Definition</b> <a href="#l00138">reaclib.cpp:138</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1reaclib_html_af6ff0dfe7ffe34c73ba9acbab5ef8a66"><div class="ttname"><a href="namespacegridfire_1_1reaclib.html#af6ff0dfe7ffe34c73ba9acbab5ef8a66">gridfire::reaclib::s_initialized</a></div><div class="ttdeci">static bool s_initialized</div><div class="ttdef"><b>Definition</b> <a href="reaclib_8h_source.html#l00007">reaclib.h:7</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1reaclib_html_afc0deac6cbef076e8884e66fd3ab66e0"><div class="ttname"><a href="namespacegridfire_1_1reaclib.html#afc0deac6cbef076e8884e66fd3ab66e0">gridfire::reaclib::parseSpeciesString</a></div><div class="ttdeci">static std::vector&lt; fourdst::atomic::Species &gt; parseSpeciesString(const std::string_view str)</div><div class="ttdef"><b>Definition</b> <a href="#l00058">reaclib.cpp:58</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1reaction_html_aa86f08712565f278adacc7cd2361eb31"><div class="ttname"><a href="namespacegridfire_1_1reaction.html#aa86f08712565f278adacc7cd2361eb31">gridfire::reaction::LogicalReactionSet</a></div><div class="ttdeci">TemplatedReactionSet&lt; LogicalReaction &gt; LogicalReactionSet</div><div class="ttdoc">A set of logical reactions.</div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00557">reaction.h:557</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1reaction_html_abfcfafc0cda0c3ed56930a12e7ead67f"><div class="ttname"><a href="namespacegridfire_1_1reaction.html#abfcfafc0cda0c3ed56930a12e7ead67f">gridfire::reaction::packReactionSetToLogicalReactionSet</a></div><div class="ttdeci">LogicalReactionSet packReactionSetToLogicalReactionSet(const ReactionSet &amp;reactionSet)</div><div class="ttdef"><b>Definition</b> <a href="reaction_8cpp_source.html#l00201">reaction.cpp:201</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1reaction_html_ad838ce3fb6cc02c3fd90b924a0dd91b1"><div class="ttname"><a href="namespacegridfire_1_1reaction.html#ad838ce3fb6cc02c3fd90b924a0dd91b1">gridfire::reaction::ReactionSet</a></div><div class="ttdeci">TemplatedReactionSet&lt; Reaction &gt; ReactionSet</div><div class="ttdoc">A set of reactions, typically from a single source like REACLIB.</div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00556">reaction.h:556</a></div></div>
<div class="ttc" id="anamespacegridfire_html_a8b245f261cd8d1711ae8d593b054cf98"><div class="ttname"><a href="namespacegridfire.html#a8b245f261cd8d1711ae8d593b054cf98">gridfire::trim_whitespace</a></div><div class="ttdeci">std::string trim_whitespace(const std::string &amp;str)</div><div class="ttdef"><b>Definition</b> <a href="network_8cpp_source.html#l00091">network.cpp:91</a></div></div>
<div class="ttc" id="anetwork_8h_html"><div class="ttname"><a href="network_8h.html">network.h</a></div></div>
<div class="ttc" id="areaclib_8cpp_html_a2c6902cf3e699a1a65e871efa878a6ab"><div class="ttname"><a href="reaclib_8cpp.html#a2c6902cf3e699a1a65e871efa878a6ab">trim_whitespace</a></div><div class="ttdeci">std::string trim_whitespace(const std::string &amp;str)</div><div class="ttdef"><b>Definition</b> <a href="#l00013">reaclib.cpp:13</a></div></div>
@@ -285,7 +288,7 @@ $(function(){initNavTree('reaclib_8cpp_source.html',''); initResizable(true); })
<div class="ttc" id="astructgridfire_1_1reaclib_1_1_reaction_record_html_aa1fd4f510d7c00d2e4197e9b9caf29fd"><div class="ttname"><a href="structgridfire_1_1reaclib_1_1_reaction_record.html#aa1fd4f510d7c00d2e4197e9b9caf29fd">gridfire::reaclib::ReactionRecord::reverse</a></div><div class="ttdeci">bool reverse</div><div class="ttdef"><b>Definition</b> <a href="#l00036">reaclib.cpp:36</a></div></div>
<div class="ttc" id="astructgridfire_1_1reaclib_1_1_reaction_record_html_aeeb8a1e078a27420e398663825cce644"><div class="ttname"><a href="structgridfire_1_1reaclib_1_1_reaction_record.html#aeeb8a1e078a27420e398663825cce644">gridfire::reaclib::ReactionRecord::qValue</a></div><div class="ttdeci">double qValue</div><div class="ttdef"><b>Definition</b> <a href="#l00034">reaclib.cpp:34</a></div></div>
<div class="ttc" id="astructgridfire_1_1reaclib_1_1_reaction_record_html_af1b1d3b0308d965ef0697b247fcf9082"><div class="ttname"><a href="structgridfire_1_1reaclib_1_1_reaction_record.html#af1b1d3b0308d965ef0697b247fcf9082">gridfire::reaclib::ReactionRecord::products_str</a></div><div class="ttdeci">char products_str[128]</div><div class="ttdef"><b>Definition</b> <a href="#l00040">reaclib.cpp:40</a></div></div>
<div class="ttc" id="astructgridfire_1_1reaction_1_1_rate_coefficient_set_html"><div class="ttname"><a href="structgridfire_1_1reaction_1_1_rate_coefficient_set.html">gridfire::reaction::RateCoefficientSet</a></div><div class="ttdoc">Holds the seven coefficients for the REACLIB rate equation.</div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00032">reaction.h:32</a></div></div>
<div class="ttc" id="astructgridfire_1_1reaction_1_1_rate_coefficient_set_html"><div class="ttname"><a href="structgridfire_1_1reaction_1_1_rate_coefficient_set.html">gridfire::reaction::RateCoefficientSet</a></div><div class="ttdoc">Holds the seven coefficients for the REACLIB rate equation.</div><div class="ttdef"><b>Definition</b> <a href="reaction_8h_source.html#l00033">reaction.h:33</a></div></div>
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