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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// Copyright 2020, the Aether Development Team (see doc/dev_team.md for members)</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// Full license can be found in License.md</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span>  </div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#ifndef INCLUDE_CHEMISTRY_H_</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#define INCLUDE_CHEMISTRY_H_</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span>  </div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor">#include <string></span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span>  </div>
<div class="line"><a name="l00010"></a><span class="lineno"><a class="line" href="classChemistry.html"> 10</a></span> <span class="keyword">class </span><a class="code" href="classChemistry.html">Chemistry</a> {</div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span>  </div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  <span class="keyword">public</span>:</div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span>  </div>
<div class="line"><a name="l00014"></a><span class="lineno"><a class="line" href="structChemistry_1_1reaction__type.html"> 14</a></span>  <span class="keyword">struct </span><a class="code" href="structChemistry_1_1reaction__type.html">reaction_type</a> {</div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  <span class="comment">// Reactions:</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  <span class="comment">// loss1 + loss2 + loss3 -> source1 + source2 + source3</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  std::vector<std::string> sources_names;</div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  std::vector<std::string> losses_names;</div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  </div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  std::vector<int> sources_ids;</div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  std::vector<bool> sources_IsNeutral;</div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  </div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  std::vector<int> losses_ids;</div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  std::vector<bool> losses_IsNeutral;</div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  </div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  <span class="keywordtype">int</span> nSources;</div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  <span class="keywordtype">int</span> nLosses;</div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  </div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  precision_t energy;</div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  precision_t rate;</div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  precision_t branching_ratio;</div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  };</div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  </div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  std::vector<reaction_type> reactions;</div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  int64_t nReactions;</div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  </div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <a class="code" href="classChemistry.html">Chemistry</a>(<a class="code" href="classNeutrals.html">Neutrals</a> neutrals,</div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <a class="code" href="classIons.html">Ions</a> ions,</div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <a class="code" href="classInputs.html">Inputs</a> args,</div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  </div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordtype">void</span> calc_chemistry(<a class="code" href="classNeutrals.html">Neutrals</a> &neutrals,</div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <a class="code" href="classIons.html">Ions</a> &ions,</div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <a class="code" href="classTimes.html">Times</a> time,</div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <a class="code" href="classGrid.html">Grid</a> grid,</div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  </div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keywordtype">void</span> calc_chemical_sources(<a class="code" href="classNeutrals.html">Neutrals</a> &neutrals,</div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <a class="code" href="classIons.html">Ions</a> &ions,</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  </div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keyword">private</span>:</div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  </div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="keyword">struct </span>sources_and_losses_type {</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  </div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  precision_t neutral_sources[nSpecies];</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  precision_t neutral_losses[nSpecies];</div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  precision_t ion_sources[nIons];</div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  precision_t ion_losses[nIons];</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  </div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  precision_t heat_neutrals;</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  precision_t heat_ions;</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  precision_t heat_electrons;</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  };</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  </div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  sources_and_losses_type sources_and_losses;</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  </div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keywordtype">int</span> read_chemistry_file(<a class="code" href="classNeutrals.html">Neutrals</a> neutrals,</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <a class="code" href="classIons.html">Ions</a> ions,</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <a class="code" href="classInputs.html">Inputs</a> args,</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  </div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  reaction_type interpret_reaction_line(<a class="code" href="classNeutrals.html">Neutrals</a> neutrals,</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <a class="code" href="classIons.html">Ions</a> ions,</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  std::vector<std::string> line,</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  </div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordtype">void</span> find_species_id(std::string name,</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <a class="code" href="classNeutrals.html">Neutrals</a> neutrals,</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <a class="code" href="classIons.html">Ions</a> ions,</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordtype">int</span> &id_,</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordtype">bool</span> &IsNeutral,</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  </div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordtype">void</span> display_reaction(reaction_type reaction);</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> };</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  </div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> <span class="preprocessor">#endif // INCLUDE_CHEMISTRY_H_</span></div>
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<div class="ttc" id="aclassChemistry_html"><div class="ttname"><a href="classChemistry.html">Chemistry</a></div><div class="ttdef"><b>Definition:</b> chemistry.h:10</div></div>
<div class="ttc" id="astructChemistry_1_1reaction__type_html"><div class="ttname"><a href="structChemistry_1_1reaction__type.html">Chemistry::reaction_type</a></div><div class="ttdef"><b>Definition:</b> chemistry.h:14</div></div>
<div class="ttc" id="aclassInputs_html"><div class="ttname"><a href="classInputs.html">Inputs</a></div><div class="ttdef"><b>Definition:</b> inputs.h:10</div></div>
<div class="ttc" id="aclassReport_html"><div class="ttname"><a href="classReport.html">Report</a></div><div class="ttdef"><b>Definition:</b> report.h:28</div></div>
<div class="ttc" id="aclassIons_html"><div class="ttname"><a href="classIons.html">Ions</a></div><div class="ttdef"><b>Definition:</b> ions.h:10</div></div>
<div class="ttc" id="aclassTimes_html"><div class="ttname"><a href="classTimes.html">Times</a></div><div class="ttdef"><b>Definition:</b> times.h:21</div></div>
<div class="ttc" id="aclassGrid_html"><div class="ttname"><a href="classGrid.html">Grid</a></div><div class="ttdef"><b>Definition:</b> arm_vars.h:11</div></div>
<div class="ttc" id="aclassNeutrals_html"><div class="ttname"><a href="classNeutrals.html">Neutrals</a></div><div class="ttdef"><b>Definition:</b> neutrals.h:26</div></div>
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