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   <div id="projectname">Aether
   &#160;<span id="projectnumber">0.0</span>
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   <div id="projectbrief">Ionosphere-Thermosphere model</div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<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>&#160;<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>&#160; </div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="preprocessor">#ifndef INCLUDE_AETHER_H_</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="preprocessor">#define INCLUDE_AETHER_H_</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160; </div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// The armadillo library is to allow the use of 3d cubes and other</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">// array types, with array math built in. This eliminates loops!</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="preprocessor">#include &lt;armadillo&gt;</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160; </div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">// Types</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">// Precision compile-time aliasing</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="preprocessor">#ifdef AETHER_USE_PRECISION_DOUBLE</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="keyword">using</span> precision_t = double;</div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="preprocessor">#else</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="keyword">using</span> precision_t = float;</div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160; </div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160; </div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="keyword">using</span> arma_vec = arma::Col&lt;precision_t&gt;;</div>
<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="keyword">using</span> arma_mat = arma::Mat&lt;precision_t&gt;;</div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="keyword">using</span> arma_cube = arma::Cube&lt;precision_t&gt;;</div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160; </div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160; </div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="preprocessor">#include &lt;nlohmann/json.hpp&gt;</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="keyword">using</span> json = nlohmann::json;</div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160; </div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160; </div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<span class="comment">// Aether includes</span></div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#include &quot;earth.h&quot;</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160; </div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="comment">// Contains all information about time in the code and wall time:</span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &quot;times.h&quot;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160; </div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="comment">// Contains a reporting system for the model include verbose level and timing:</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &quot;report.h&quot;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160; </div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &quot;inputs.h&quot;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160; </div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="comment">// Defines physical and conversion constants</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor">#include &quot;constants.h&quot;</span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160; </div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="comment">// Needs to be eliminated (but not right now!)</span></div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<span class="preprocessor">#include &quot;sizes.h&quot;</span></div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160; </div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;<span class="comment">// These are functions that convert time between different systems.</span></div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;<span class="preprocessor">#include &quot;time_conversion.h&quot;</span></div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160; </div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;<span class="comment">// Functions that assist in the reading of files.</span></div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;<span class="preprocessor">#include &quot;file_input.h&quot;</span></div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160; </div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;<span class="comment">// A class for keeping track of indices (1d vectors w/time)</span></div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;<span class="preprocessor">#include &quot;indices.h&quot;</span></div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160; </div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;<span class="comment">// Read indices (f107, omni) file types</span></div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;<span class="preprocessor">#include &quot;read_indices_files.h&quot;</span></div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160; </div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;<span class="comment">// A class for keeping track of all of the planetary characteristics</span></div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;<span class="preprocessor">#include &quot;planets.h&quot;</span></div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160; </div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;<span class="preprocessor">#include &quot;grid.h&quot;</span></div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160; </div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;<span class="comment">// Contains the neutral states and derived quantities</span></div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;<span class="preprocessor">#include &quot;neutrals.h&quot;</span></div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160; </div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;<span class="preprocessor">#include &quot;ions.h&quot;</span></div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160; </div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;<span class="preprocessor">#include &quot;bfield.h&quot;</span></div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160; </div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;<span class="comment">// Contains the electrodynamic states (potential and aurora)</span></div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;<span class="preprocessor">#include &quot;electrodynamics.h&quot;</span></div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160; </div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;<span class="preprocessor">#include &quot;aurora.h&quot;</span></div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160; </div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;<span class="comment">// Defines the Extreme Ultraviolet radiation above the atmosphere</span></div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;<span class="preprocessor">#include &quot;euv.h&quot;</span></div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160; </div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;<span class="preprocessor">#include &quot;calc_euv.h&quot;</span></div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;<span class="preprocessor">#include &quot;chemistry.h&quot;</span></div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;<span class="preprocessor">#include &quot;read_collision_file.h&quot;</span></div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;<span class="preprocessor">#include &quot;output.h&quot;</span></div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;<span class="preprocessor">#include &quot;advance.h&quot;</span></div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160; </div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;<span class="preprocessor">#include &quot;solvers.h&quot;</span></div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;<span class="preprocessor">#include &quot;tools.h&quot;</span></div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;<span class="preprocessor">#include &quot;transform.h&quot;</span></div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160; </div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;<span class="comment">// not done</span></div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;<span class="preprocessor">#include &quot;calc_grid_derived.h&quot;</span></div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160; </div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;<span class="preprocessor">#endif  // INCLUDE_AETHER_H_</span></div>
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