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<div id="projectname">fourdst::libcomposition<span id="projectnumber"> v2.0.1</span>
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<div id="projectbrief">Robust atomic species information library</div>
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<a href="utils_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="preprocessor">#include "<a class="code" href="composition_8h.html">fourdst/composition/composition.h</a>"</span></div>
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<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span><span class="preprocessor">#include "<a class="code" href="exceptions__composition_8h.html">fourdst/composition/exceptions/exceptions_composition.h</a>"</span></div>
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<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="preprocessor">#include "<a class="code" href="atomic_species_8h.html">fourdst/atomic/atomicSpecies.h</a>"</span></div>
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<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span><span class="preprocessor">#include "<a class="code" href="species_8h.html">fourdst/atomic/species.h</a>"</span></div>
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<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span><span class="preprocessor">#include "<a class="code" href="utils_8h.html">fourdst/composition/utils.h</a>"</span></div>
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<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="preprocessor">#include "fourdst/logging/logging.h"</span></div>
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<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span> </div>
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<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span><span class="preprocessor">#include <numeric></span></div>
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<div class="line"><a id="l00009" name="l00009"></a><span class="lineno"> 9</span><span class="preprocessor">#include <ranges></span></div>
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<div class="line"><a id="l00010" name="l00010"></a><span class="lineno"> 10</span><span class="preprocessor">#include <vector></span></div>
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<div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span><span class="preprocessor">#include <set></span></div>
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<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span><span class="preprocessor">#include <string></span></div>
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<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span> </div>
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<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="preprocessor">#include "quill/LogMacros.h"</span></div>
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<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span> </div>
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<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="keyword">namespace </span>{</div>
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<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> std::optional<fourdst::atomic::Species> getSpecies(<span class="keyword">const</span> std::string& symbol) {</div>
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<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span> <span class="keywordflow">if</span> (!<a class="code hl_variable" href="namespacefourdst_1_1atomic.html#a3f619cc8f8b2cd718a4082c6adb0de90">fourdst::atomic::species</a>.contains(symbol)) {</div>
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<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span> <span class="keywordflow">return</span> std::nullopt;</div>
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<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> }</div>
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<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span> <span class="keywordflow">return</span> <a class="code hl_variable" href="namespacefourdst_1_1atomic.html#a3f619cc8f8b2cd718a4082c6adb0de90">fourdst::atomic::species</a>.at(symbol);</div>
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<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> }</div>
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<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> </div>
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<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> quill::Logger* getLogger() {</div>
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<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span> <span class="keyword">static</span> quill::Logger* logger = fourdst::logging::LogManager::getInstance().getLogger(<span class="stringliteral">"log"</span>);</div>
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<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> <span class="keywordflow">return</span> logger;</div>
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<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> }</div>
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<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span> </div>
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<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> <span class="keywordtype">void</span> throw_unknown_symbol(<span class="keyword">const</span> std::string& symbol) {</div>
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<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> LOG_ERROR(getLogger(), <span class="stringliteral">"Symbol {} is not a valid species symbol (not in the species database)"</span>, symbol);</div>
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<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span> <span class="keywordflow">throw</span> <a class="code hl_class" href="classfourdst_1_1composition_1_1exceptions_1_1_unknown_symbol_error.html">fourdst::composition::exceptions::UnknownSymbolError</a>(<span class="stringliteral">"Symbol "</span> + symbol + <span class="stringliteral">" is not a valid species symbol (not in the species database)"</span>);</div>
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<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> }</div>
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<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span>}</div>
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<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> </div>
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<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacefourdst_1_1composition.html">fourdst::composition</a> {</div>
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<div class="foldopen" id="foldopen00036" data-start="{" data-end="}">
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<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"><a class="line" href="namespacefourdst_1_1composition.html#a2cb98194b465f646973ceba38d0e7d95"> 36</a></span> <a class="code hl_class" href="classfourdst_1_1composition_1_1_composition.html">Composition</a> <a class="code hl_function" href="namespacefourdst_1_1composition.html#aa90b1ef07d607c0c829bedccf381cf54">buildCompositionFromMassFractions</a>(</div>
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<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> <span class="keyword">const</span> std::set<atomic::Species> &species,</div>
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<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> <span class="keyword">const</span> std::vector<double> &massFractions</div>
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<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> ) {</div>
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<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> <span class="keyword">const</span> <span class="keywordtype">double</span> sum = std::accumulate(</div>
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<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> massFractions.begin(),</div>
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<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> massFractions.end(),</div>
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<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> 0.0</div>
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<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> );</div>
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<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> </div>
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<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> <span class="keywordflow">if</span> (std::abs(sum - 1.0) > 1e-10) {</div>
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<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordflow">throw</span> <a class="code hl_class" href="classfourdst_1_1composition_1_1exceptions_1_1_invalid_composition_error.html">exceptions::InvalidCompositionError</a>(</div>
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<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> <span class="stringliteral">"Mass fractions must sum to 1.0, got "</span> + std::to_string(sum)</div>
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<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> );</div>
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<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> }</div>
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<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> </div>
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<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> <span class="keywordflow">if</span> (species.size() != massFractions.size()) {</div>
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<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> <span class="keywordflow">throw</span> <a class="code hl_class" href="classfourdst_1_1composition_1_1exceptions_1_1_invalid_composition_error.html">exceptions::InvalidCompositionError</a>(</div>
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<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> <span class="stringliteral">"The number of species and mass fractions must be equal. Got "</span> +</div>
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<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> std::to_string(species.size()) + <span class="stringliteral">" species and "</span> +</div>
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<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> std::to_string(massFractions.size()) + <span class="stringliteral">" mass fractions."</span></div>
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<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> );</div>
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<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> }</div>
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<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> </div>
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<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> <a class="code hl_class" href="classfourdst_1_1composition_1_1_composition.html">Composition</a> <a class="code hl_namespace" href="namespacefourdst_1_1composition.html">composition</a>;</div>
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<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> </div>
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<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& [sp, xi] : std::views::zip(species, massFractions)) {</div>
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<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> <a class="code hl_namespace" href="namespacefourdst_1_1composition.html">composition</a>.registerSpecies(sp);</div>
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<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> <a class="code hl_namespace" href="namespacefourdst_1_1composition.html">composition</a>.setMolarAbundance(sp, xi/sp.mass());</div>
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<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> }</div>
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<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> </div>
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<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> <span class="keywordflow">return</span> <a class="code hl_namespace" href="namespacefourdst_1_1composition.html">composition</a>;</div>
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<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> }</div>
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</div>
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<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> </div>
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<div class="foldopen" id="foldopen00070" data-start="{" data-end="}">
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<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"><a class="line" href="namespacefourdst_1_1composition.html#a39d4f84dfa85ddda3b9feb5dda1afc1e"> 70</a></span> <a class="code hl_class" href="classfourdst_1_1composition_1_1_composition.html">Composition</a> <a class="code hl_function" href="namespacefourdst_1_1composition.html#aa90b1ef07d607c0c829bedccf381cf54">buildCompositionFromMassFractions</a>(<span class="keyword">const</span> std::vector<atomic::Species> &species, <span class="keyword">const</span> std::vector<double> &massFractions) {</div>
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<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> <span class="keywordflow">return</span> <a class="code hl_function" href="namespacefourdst_1_1composition.html#aa90b1ef07d607c0c829bedccf381cf54">buildCompositionFromMassFractions</a>(std::set<atomic::Species>(species.begin(), species.end()), massFractions);</div>
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<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> }</div>
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</div>
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<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> </div>
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<div class="foldopen" id="foldopen00074" data-start="{" data-end="}">
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<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"><a class="line" href="namespacefourdst_1_1composition.html#aa90b1ef07d607c0c829bedccf381cf54"> 74</a></span> <a class="code hl_class" href="classfourdst_1_1composition_1_1_composition.html">Composition</a> <a class="code hl_function" href="namespacefourdst_1_1composition.html#aa90b1ef07d607c0c829bedccf381cf54">buildCompositionFromMassFractions</a>(<span class="keyword">const</span> std::vector<std::string> &symbols, <span class="keyword">const</span> std::vector<double> &massFractions) {</div>
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<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> std::set<atomic::Species> species;</div>
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<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> <span class="keywordflow">for</span> (<span class="keyword">const</span> <span class="keyword">auto</span>& symbol : symbols) {</div>
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<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> <span class="keyword">auto</span> result = getSpecies(symbol);</div>
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<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> <span class="keywordflow">if</span> (!result) {</div>
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<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> throw_unknown_symbol(symbol);</div>
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<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> }</div>
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<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> species.insert(result.value());</div>
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<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> }</div>
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<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> <span class="keywordflow">return</span> <a class="code hl_function" href="namespacefourdst_1_1composition.html#aa90b1ef07d607c0c829bedccf381cf54">buildCompositionFromMassFractions</a>(species, massFractions);</div>
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<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> }</div>
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</div>
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<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span>}</div>
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<div class="ttc" id="aatomic_species_8h_html"><div class="ttname"><a href="atomic_species_8h.html">atomicSpecies.h</a></div></div>
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<div class="ttc" id="aclassfourdst_1_1composition_1_1_composition_html"><div class="ttname"><a href="classfourdst_1_1composition_1_1_composition.html">fourdst::composition::Composition</a></div><div class="ttdoc">Manages a collection of chemical species and their abundances.</div><div class="ttdef"><b>Definition</b> <a href="composition_8h_source.html#l00097">composition.h:97</a></div></div>
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<div class="ttc" id="aclassfourdst_1_1composition_1_1exceptions_1_1_invalid_composition_error_html"><div class="ttname"><a href="classfourdst_1_1composition_1_1exceptions_1_1_invalid_composition_error.html">fourdst::composition::exceptions::InvalidCompositionError</a></div><div class="ttdoc">Exception thrown when a composition is in an invalid or inconsistent state.</div><div class="ttdef"><b>Definition</b> <a href="exceptions__composition_8h_source.html#l00041">exceptions_composition.h:41</a></div></div>
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<div class="ttc" id="aclassfourdst_1_1composition_1_1exceptions_1_1_unknown_symbol_error_html"><div class="ttname"><a href="classfourdst_1_1composition_1_1exceptions_1_1_unknown_symbol_error.html">fourdst::composition::exceptions::UnknownSymbolError</a></div><div class="ttdoc">Exception thrown when an unknown symbol is encountered.</div><div class="ttdef"><b>Definition</b> <a href="exceptions__composition_8h_source.html#l00077">exceptions_composition.h:77</a></div></div>
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<div class="ttc" id="anamespacefourdst_1_1atomic_html_a3f619cc8f8b2cd718a4082c6adb0de90"><div class="ttname"><a href="namespacefourdst_1_1atomic.html#a3f619cc8f8b2cd718a4082c6adb0de90">fourdst::atomic::species</a></div><div class="ttdeci">static const std::unordered_map< std::string, const Species & > species</div><div class="ttdoc">Map of species names to their corresponding Species objects.</div><div class="ttdef"><b>Definition</b> <a href="species_8h_source.html#l03579">species.h:3579</a></div></div>
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<div class="ttc" id="anamespacefourdst_1_1composition_html_aa90b1ef07d607c0c829bedccf381cf54"><div class="ttname"><a href="namespacefourdst_1_1composition.html#aa90b1ef07d607c0c829bedccf381cf54">fourdst::composition::buildCompositionFromMassFractions</a></div><div class="ttdeci">Composition buildCompositionFromMassFractions(const std::vector< std::string > &symbols, const std::vector< double > &massFractions)</div><div class="ttdoc">Build a Composition object from symbols and their corresponding mass fractions.</div><div class="ttdef"><b>Definition</b> <a href="#l00074">utils.cpp:74</a></div></div>
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