-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathions_8h_source.html
More file actions
184 lines (182 loc) · 16.4 KB
/
ions_8h_source.html
File metadata and controls
184 lines (182 loc) · 16.4 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.17"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>Aether: include/ions.h Source File</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
extensions: ["tex2jax.js"],
jax: ["input/TeX","output/HTML-CSS"],
});
</script>
<script type="text/javascript" async="async" src="https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Aether
 <span id="projectnumber">0.0</span>
</div>
<div id="projectbrief">Ionosphere-Thermosphere model</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.17 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&dn=gpl-2.0.txt GPL-v2 */
var searchBox = new SearchBox("searchBox", "search",false,'Search');
/* @license-end */
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&dn=gpl-2.0.txt GPL-v2 */
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
/* @license-end */</script>
<div id="main-nav"></div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="dir_d44c64559bbebec7f509842c48db8b23.html">include</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="headertitle">
<div class="title">ions.h</div> </div>
</div><!--header-->
<div class="contents">
<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_IONS_H_</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#define INCLUDE_IONS_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 <string></span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor">#include <vector></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="classIons.html"> 10</a></span> <span class="keyword">class </span><a class="code" href="classIons.html">Ions</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"> 14</span>  <span class="comment">// This struct contains all of the information needed for a single</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  <span class="comment">// species of ion. We will then have a vector of these species.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  </div>
<div class="line"><a name="l00017"></a><span class="lineno"><a class="line" href="structIons_1_1species__chars.html"> 17</a></span>  <span class="keyword">struct </span><a class="code" href="structIons_1_1species__chars.html">species_chars</a> {</div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  std::string cName;</div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  precision_t mass;</div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  <span class="keywordtype">int</span> charge;</div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  </div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  <span class="keywordtype">int</span> DoAdvect;</div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  </div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  std::vector<precision_t> nu_ion_neutral_coef;</div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  std::vector<bool> nu_is_resonant;</div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  std::vector<precision_t> nu_ion_ion;</div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  std::vector<precision_t> nu_ion_electron;</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>  std::vector<precision_t> nu_in_res_temp_min;</div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  std::vector<precision_t> nu_in_res_coef1;</div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  std::vector<precision_t> nu_in_res_coef2;</div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  std::vector<precision_t> nu_in_res_tn_frac;</div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  std::vector<precision_t> nu_in_res_ti_frac;</div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  std::vector<arma_cube> nu_ion_neutral_vcgc;</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>  <span class="comment">// Sources and Losses:</span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  </div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  arma_cube density_scgc;</div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  std::vector<arma_cube> par_velocity_vcgc;</div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  std::vector<arma_cube> perp_velocity_vcgc;</div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  </div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  arma_cube temperature_scgc;</div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  </div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="comment">// Sources and Losses:</span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  </div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  arma_cube ionization_scgc;</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  </div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  arma_cube sources_scgc;</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  arma_cube losses_scgc;</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>  </div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="comment">// bulk quantities (states):</span></div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  arma_cube density_scgc;</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  std::vector<arma_cube> velocity_vcgc;</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  arma_cube ion_temperature_scgc;</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  arma_cube electron_temperature_scgc;</div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  </div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="comment">// This is the vector that will contain all of the different species:</span></div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  std::vector<species_chars> species;</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  </div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="comment">// Electrodynamics:</span></div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  arma_cube potential_scgc;</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  std::vector<arma_cube> efield_vcgc;</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  std::vector<arma_cube> exb_vcgc;</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  arma_mat eflux;</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  arma_mat avee;</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  </div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="comment">// ------------------------------</span></div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="comment">// Functions:</span></div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  </div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <a class="code" href="classIons.html">Ions</a>(<a class="code" href="classGrid.html">Grid</a> grid, <a class="code" href="classInputs.html">Inputs</a> input, <a class="code" href="classReport.html">Report</a> report);</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <a class="code" href="structIons_1_1species__chars.html">species_chars</a> create_species(<a class="code" href="classGrid.html">Grid</a> grid);</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordtype">int</span> read_planet_file(<a class="code" href="classInputs.html">Inputs</a> input, <a class="code" href="classReport.html">Report</a> report);</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keywordtype">void</span> fill_electrons(<a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keywordtype">int</span> get_species_id(std::string name, <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordtype">void</span> calc_efield(<a class="code" href="classGrid.html">Grid</a> grid, <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordtype">void</span> calc_exb_drift(<a class="code" href="classGrid.html">Grid</a> grid, <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordtype">void</span> calc_ion_drift(<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="classGrid.html">Grid</a> grid,</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  precision_t dt,</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="keywordtype">void</span> calc_ion_neutral_coll_freq(<a class="code" href="classNeutrals.html">Neutrals</a> neutrals, <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  std::vector<arma_cube> calc_ion_electron_pressure_gradient(int64_t iIon,</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <a class="code" href="classGrid.html">Grid</a> grid,</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordtype">void</span> calc_ion_temperature(<a class="code" href="classNeutrals.html">Neutrals</a> neutrals, <a class="code" href="classGrid.html">Grid</a> grid, <a class="code" href="classReport.html">Report</a> &report);</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> };</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> <span class="preprocessor">#endif // INCLUDE_IONS_H_</span></div>
</div><!-- fragment --></div><!-- contents -->
<div class="ttc" id="astructIons_1_1species__chars_html"><div class="ttname"><a href="structIons_1_1species__chars.html">Ions::species_chars</a></div><div class="ttdef"><b>Definition:</b> ions.h:17</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="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>
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by  <a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.17
</small></address>
</body>
</html>