FYS3150/Project-3
3
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
d2824d7c1d
Project-3/docs/PenningTrap_8cpp_source.html
Cory d2824d7c1d
Update docs
2023-10-23 12:43:32 +02:00

471 lines
79 KiB
HTML
Raw Blame History

<!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" lang="en-US">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=11"/>
<meta name="generator" content="Doxygen 1.9.6"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>Penning Trap Simulation: src/PenningTrap.cpp 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="navtree.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="resize.js"></script>
<script type="text/javascript" src="navtreedata.js"></script>
<script type="text/javascript" src="navtree.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" />
<link href="doxygen-awesome.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 id="projectrow">
<td id="projectalign">
<div id="projectname">Penning Trap Simulation
</div>
<div id="projectbrief">Simulate particle behavior inside a Penning Trap</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.9.6 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
var searchBox = new SearchBox("searchBox", "search/",'.html');
/* @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:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
/* @license-end */
</script>
<div id="main-nav"></div>
</div><!-- top -->
<div id="side-nav" class="ui-resizable side-nav-resizable">
<div id="nav-tree">
<div id="nav-tree-contents">
<div id="nav-sync" class="sync"></div>
</div>
</div>
<div id="splitbar" style="-moz-user-select:none;"
class="ui-resizable-handle">
</div>
</div>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
$(document).ready(function(){initNavTree('PenningTrap_8cpp_source.html',''); initResizable(); });
/* @license-end */
</script>
<div id="doc-content">
<!-- 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">
<div id="MSearchResults">
<div class="SRPage">
<div id="SRIndex">
<div id="SRResults"></div>
<div class="SRStatus" id="Loading">Loading...</div>
<div class="SRStatus" id="Searching">Searching...</div>
<div class="SRStatus" id="NoMatches">No Matches</div>
</div>
</div>
</div>
</div>
<div class="header">
<div class="headertitle"><div class="title">PenningTrap.cpp</div></div>
</div><!--header-->
<div class="contents">
<a href="PenningTrap_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> </div>
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="preprocessor">#include &quot;<a class="code" href="typedefs_8hpp.html">typedefs.hpp</a>&quot;</span></div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include &lt;algorithm&gt;</span></div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="preprocessor">#include &lt;functional&gt;</span></div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="preprocessor">#include &lt;sys/types.h&gt;</span></div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span> </div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8"> 20</a></span><a class="code hl_function" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a>(<span class="keywordtype">double</span> B_0, <span class="keywordtype">double</span> V_0, <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span>{</div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> this-&gt;B_0 = <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>;</div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> this-&gt;V_0 = <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a>;</div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> this-&gt;d = <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span> this-&gt;t = <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>;</div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</a> = [](<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>) { <span class="keywordflow">return</span> 1.; };</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> </div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a830be1b8cbf59664e060b6edbeaa302f"> 29</a></span><a class="code hl_function" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a>(uint i, <span class="keywordtype">double</span> B_0, <span class="keywordtype">double</span> V_0, <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> : <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(B_0, V_0, d)</div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span>{</div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; i; j++) {</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> <a class="code hl_class" href="classParticle.html">Particle</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>().randn() * .1 * this-&gt;d),</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>().randn() * .1 * this-&gt;d)));</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> }</div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span>}</div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> </div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"><a class="line" href="classPenningTrap.html#addc96789dcfec07b75156e19fee82f4f"> 39</a></span><a class="code hl_function" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a>(std::vector&lt;Particle&gt; particles, <span class="keywordtype">double</span> B_0,</div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> <span class="keywordtype">double</span> V_0, <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> : <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(B_0, V_0, d)</div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span>{</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> this-&gt;particles = <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span>}</div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> </div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43"> 46</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">PenningTrap::set_pertubation</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V)</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span>{</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</a> = [f, omega_V](<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>) {</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> <span class="keywordflow">return</span> 1 + f * std::cos(omega_V * <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>);</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> };</div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span>}</div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> </div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"><a class="line" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea"> 53</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap::reinitialize</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V, <span class="keywordtype">double</span> t)</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span>{</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> this-&gt;t = <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>;</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> this-&gt;<a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">set_pertubation</a>(f, omega_V);</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); i++) {</div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec = <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>().randn() * .1 * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> }</div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span>}</div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> </div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2"> 63</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap::v_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt)</div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span>{</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> <span class="keywordflow">switch</span> (i) {</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> <span class="keywordflow">case</span> 0:</div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> <span class="keywordflow">return</span> .5 * dt * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>[0][j];</div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> <span class="keywordflow">case</span> 1:</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> <span class="keywordflow">return</span> .5 * dt * this-&gt;k_v[1][j];</div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> <span class="keywordflow">case</span> 2:</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> <span class="keywordflow">return</span> dt * this-&gt;k_v[2][j];</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> <span class="keywordflow">case</span> 3:</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((dt / 6.)</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> * (this-&gt;k_v[0][j] + 2. * this-&gt;k_v[1][j]</div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> + 2. * this-&gt;k_v[2][j] + this-&gt;k_v[3][j]));</div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> <span class="keywordflow">default</span>:</div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> abort();</div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> }</div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span>}</div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> </div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08"> 82</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">PenningTrap::r_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt)</div>
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span>{</div>
<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> <span class="keywordflow">switch</span> (i) {</div>
<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> <span class="keywordflow">case</span> 0:</div>
<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> <span class="keywordflow">return</span> .5 * dt * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>[0][j];</div>
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> <span class="keywordflow">case</span> 1:</div>
<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span> <span class="keywordflow">return</span> .5 * dt * this-&gt;k_r[1][j];</div>
<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> <span class="keywordflow">case</span> 2:</div>
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> <span class="keywordflow">return</span> dt * this-&gt;k_r[2][j];</div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> <span class="keywordflow">case</span> 3:</div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((dt / 6.)</div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> * (this-&gt;k_r[0][j] + 2. * this-&gt;k_r[1][j]</div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> + 2. * this-&gt;k_r[2][j] + this-&gt;k_r[3][j]));</div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> <span class="keywordflow">default</span>:</div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> abort();</div>
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> }</div>
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span>}</div>
<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> </div>
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8"> 101</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap::add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a> particle)</div>
<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span>{</div>
<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(particle);</div>
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span>}</div>
<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> </div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22"> 106</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">PenningTrap::external_E_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r)</div>
<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</span>{</div>
<div class="line"><a id="l00108" name="l00108"></a><span class="lineno"> 108</span> r(2) *= -2.;</div>
<div class="line"><a id="l00109" name="l00109"></a><span class="lineno"> 109</span> </div>
<div class="line"><a id="l00110" name="l00110"></a><span class="lineno"> 110</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</a>(this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>) / (this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>))</div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> * r);</div>
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span>}</div>
<div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span> </div>
<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655"> 114</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">PenningTrap::external_B_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r)</div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span>{</div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 0., this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>};</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span>}</div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> </div>
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598"> 119</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap::force_on_particle</a>(uint i, uint j)</div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span>{</div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> <span class="comment">// Calculate the difference between the particles&#39; position</span></div>
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec - this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].r_vec;</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">// Get the distance between the particles</span></div>
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> <span class="keywordtype">double</span> norm = arma::norm(res, 2);</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="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].q / (norm * norm * norm)) * res);</div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span>}</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"><a class="line" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682"> 130</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap::total_force_external</a>(uint i)</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_class" href="classParticle.html">Particle</a> *p = &amp;this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i];</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="keywordflow">if</span> (arma::norm(p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>) &gt; this-&gt;d) {</div>
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 0., 0.};</div>
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span> }</div>
<div class="line"><a id="l00137" name="l00137"></a><span class="lineno"> 137</span> </div>
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(p-&gt;<a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a></div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> * (this-&gt;external_E_field(p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>)</div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> + arma::cross(p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a>, this-&gt;external_B_field(p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>))));</div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span>}</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"><a class="line" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c"> 143</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap::total_force_particles</a>(uint i)</div>
<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"> 144</span>{</div>
<div class="line"><a id="l00145" name="l00145"></a><span class="lineno"> 145</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res;</div>
<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"> 146</span> </div>
<div class="line"><a id="l00147" name="l00147"></a><span class="lineno"> 147</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); j++) {</div>
<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"> 148</span> <span class="keywordflow">if</span> (i != j)</div>
<div class="line"><a id="l00149" name="l00149"></a><span class="lineno"> 149</span> res += this-&gt;<a class="code hl_function" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">force_on_particle</a>(i, j);</div>
<div class="line"><a id="l00150" name="l00150"></a><span class="lineno"> 150</span> }</div>
<div class="line"><a id="l00151" name="l00151"></a><span class="lineno"> 151</span> </div>
<div class="line"><a id="l00152" name="l00152"></a><span class="lineno"> 152</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(res * (<a class="code hl_define" href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">K_E</a> * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].q));</div>
<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</span>}</div>
<div class="line"><a id="l00154" name="l00154"></a><span class="lineno"> 154</span> </div>
<div class="line"><a id="l00155" name="l00155"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3"> 155</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a>(uint i)</div>
<div class="line"><a id="l00156" name="l00156"></a><span class="lineno"> 156</span>{</div>
<div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</span> <span class="keywordflow">if</span> (arma::norm(this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec) &gt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>) {</div>
<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"> 158</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 0., 0.};</div>
<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span> }</div>
<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(this-&gt;<a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">total_force_external</a>(i) - this-&gt;<a class="code hl_function" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">total_force_particles</a>(i));</div>
<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span>}</div>
<div class="line"><a id="l00162" name="l00162"></a><span class="lineno"> 162</span> </div>
<div class="line"><a id="l00163" name="l00163"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e"> 163</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction)</div>
<div class="line"><a id="l00164" name="l00164"></a><span class="lineno"> 164</span>{</div>
<div class="line"><a id="l00165" name="l00165"></a><span class="lineno"> 165</span> </div>
<div class="line"><a id="l00166" name="l00166"></a><span class="lineno"> 166</span> std::vector&lt;Particle&gt; original_particles = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
<div class="line"><a id="l00167" name="l00167"></a><span class="lineno"> 167</span> std::vector&lt;Particle&gt; tmp_particles = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
<div class="line"><a id="l00168" name="l00168"></a><span class="lineno"> 168</span> </div>
<div class="line"><a id="l00169" name="l00169"></a><span class="lineno"> 169</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*force)(uint) = particle_interaction</div>
<div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> ? &amp;<a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div>
<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</span> : &amp;<a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap::total_force_external</a>;</div>
<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> </div>
<div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span> <span class="keywordtype">size_t</span> size = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div>
<div class="line"><a id="l00174" name="l00174"></a><span class="lineno"> 174</span> </div>
<div class="line"><a id="l00175" name="l00175"></a><span class="lineno"> 175</span> <span class="comment">// Allocating takes a long time, so reuse sim_arr if possible</span></div>
<div class="line"><a id="l00176" name="l00176"></a><span class="lineno"> 176</span> <span class="keywordflow">if</span> (this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>.size() != 4 || this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>.size() != 4</div>
<div class="line"><a id="l00177" name="l00177"></a><span class="lineno"> 177</span> || this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>[0].size() != size || this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>[0].size() != size) {</div>
<div class="line"><a id="l00178" name="l00178"></a><span class="lineno"> 178</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a> = <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(4, <a class="code hl_typedef" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a>(size));</div>
<div class="line"><a id="l00179" name="l00179"></a><span class="lineno"> 179</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a> = <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(4, <a class="code hl_typedef" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a>(size));</div>
<div class="line"><a id="l00180" name="l00180"></a><span class="lineno"> 180</span> }</div>
<div class="line"><a id="l00181" name="l00181"></a><span class="lineno"> 181</span> </div>
<div class="line"><a id="l00182" name="l00182"></a><span class="lineno"> 182</span> <span class="comment">// Each k_{i+1} is dependent on k_i, so outer loop is not parallelizable</span></div>
<div class="line"><a id="l00183" name="l00183"></a><span class="lineno"> 183</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 4; i++) {</div>
<div class="line"><a id="l00184" name="l00184"></a><span class="lineno"> 184</span> <span class="comment">// Inner loop is able to be parallelized</span></div>
<div class="line"><a id="l00185" name="l00185"></a><span class="lineno"> 185</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00186" name="l00186"></a><span class="lineno"> 186</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; size; j++) {</div>
<div class="line"><a id="l00187" name="l00187"></a><span class="lineno"> 187</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>[i][j] = (this-&gt;*force)(j) / this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].m;</div>
<div class="line"><a id="l00188" name="l00188"></a><span class="lineno"> 188</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>[i][j] = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].v_vec;</div>
<div class="line"><a id="l00189" name="l00189"></a><span class="lineno"> 189</span> </div>
<div class="line"><a id="l00190" name="l00190"></a><span class="lineno"> 190</span> tmp_particles[j].v_vec =</div>
<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span> original_particles[j].v_vec + this-&gt;<a class="code hl_function" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">v_func</a>(i, j, dt);</div>
<div class="line"><a id="l00192" name="l00192"></a><span class="lineno"> 192</span> tmp_particles[j].r_vec =</div>
<div class="line"><a id="l00193" name="l00193"></a><span class="lineno"> 193</span> original_particles[j].r_vec + this-&gt;<a class="code hl_function" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">r_func</a>(i, j, dt);</div>
<div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> }</div>
<div class="line"><a id="l00195" name="l00195"></a><span class="lineno"> 195</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a> = tmp_particles;</div>
<div class="line"><a id="l00196" name="l00196"></a><span class="lineno"> 196</span> }</div>
<div class="line"><a id="l00197" name="l00197"></a><span class="lineno"> 197</span> </div>
<div class="line"><a id="l00198" name="l00198"></a><span class="lineno"> 198</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> += dt;</div>
<div class="line"><a id="l00199" name="l00199"></a><span class="lineno"> 199</span>}</div>
<div class="line"><a id="l00200" name="l00200"></a><span class="lineno"> 200</span> </div>
<div class="line"><a id="l00201" name="l00201"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e"> 201</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction)</div>
<div class="line"><a id="l00202" name="l00202"></a><span class="lineno"> 202</span>{</div>
<div class="line"><a id="l00203" name="l00203"></a><span class="lineno"> 203</span> <span class="keywordtype">size_t</span> size = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div>
<div class="line"><a id="l00204" name="l00204"></a><span class="lineno"> 204</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> force_res[size];</div>
<div class="line"><a id="l00205" name="l00205"></a><span class="lineno"> 205</span> </div>
<div class="line"><a id="l00206" name="l00206"></a><span class="lineno"> 206</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*force)(uint) = particle_interaction</div>
<div class="line"><a id="l00207" name="l00207"></a><span class="lineno"> 207</span> ? &amp;<a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div>
<div class="line"><a id="l00208" name="l00208"></a><span class="lineno"> 208</span> : &amp;<a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap::total_force_external</a>;</div>
<div class="line"><a id="l00209" name="l00209"></a><span class="lineno"> 209</span> </div>
<div class="line"><a id="l00210" name="l00210"></a><span class="lineno"> 210</span> <span class="comment">// Calculating the force for each particle is independent and therefore</span></div>
<div class="line"><a id="l00211" name="l00211"></a><span class="lineno"> 211</span> <span class="comment">// a good candidate for parallel execution</span></div>
<div class="line"><a id="l00212" name="l00212"></a><span class="lineno"> 212</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; size; i++) {</div>
<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span> force_res[i] = (this-&gt;*force)(i);</div>
<div class="line"><a id="l00215" name="l00215"></a><span class="lineno"> 215</span> }</div>
<div class="line"><a id="l00216" name="l00216"></a><span class="lineno"> 216</span> </div>
<div class="line"><a id="l00217" name="l00217"></a><span class="lineno"> 217</span> <span class="comment">// Updating the particles is also independent, so we can parallelize</span></div>
<div class="line"><a id="l00218" name="l00218"></a><span class="lineno"> 218</span> <span class="comment">// this as well</span></div>
<div class="line"><a id="l00219" name="l00219"></a><span class="lineno"> 219</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; size; i++) {</div>
<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"> 221</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec += dt * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].v_vec;</div>
<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].v_vec += dt * force_res[i] / this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].m;</div>
<div class="line"><a id="l00223" name="l00223"></a><span class="lineno"> 223</span> }</div>
<div class="line"><a id="l00224" name="l00224"></a><span class="lineno"> 224</span> </div>
<div class="line"><a id="l00225" name="l00225"></a><span class="lineno"> 225</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> += dt;</div>
<div class="line"><a id="l00226" name="l00226"></a><span class="lineno"> 226</span>}</div>
<div class="line"><a id="l00227" name="l00227"></a><span class="lineno"> 227</span> </div>
<div class="line"><a id="l00228" name="l00228"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a"> 228</a></span><a class="code hl_struct" href="structsimulation.html">simulation_t</a> <a class="code hl_function" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap::simulate</a>(<span class="keywordtype">double</span> time, uint steps, std::string method,</div>
<div class="line"><a id="l00229" name="l00229"></a><span class="lineno"> 229</span> <span class="keywordtype">bool</span> particle_interaction)</div>
<div class="line"><a id="l00230" name="l00230"></a><span class="lineno"> 230</span>{</div>
<div class="line"><a id="l00231" name="l00231"></a><span class="lineno"> 231</span> <span class="keywordtype">double</span> dt = time / (double)steps;</div>
<div class="line"><a id="l00232" name="l00232"></a><span class="lineno"> 232</span> </div>
<div class="line"><a id="l00233" name="l00233"></a><span class="lineno"> 233</span> uint size = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div>
<div class="line"><a id="l00234" name="l00234"></a><span class="lineno"> 234</span> </div>
<div class="line"><a id="l00235" name="l00235"></a><span class="lineno"> 235</span> <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res{<a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(size, <a class="code hl_typedef" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a>(steps)),</div>
<div class="line"><a id="l00236" name="l00236"></a><span class="lineno"> 236</span> <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(size, <a class="code hl_typedef" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a>(steps))};</div>
<div class="line"><a id="l00237" name="l00237"></a><span class="lineno"> 237</span> </div>
<div class="line"><a id="l00238" name="l00238"></a><span class="lineno"> 238</span> void (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*func)(double, bool);</div>
<div class="line"><a id="l00239" name="l00239"></a><span class="lineno"> 239</span> <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;rk4&quot;</span>) {</div>
<div class="line"><a id="l00240" name="l00240"></a><span class="lineno"> 240</span> func = &amp;<a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a>;</div>
<div class="line"><a id="l00241" name="l00241"></a><span class="lineno"> 241</span> } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;euler&quot;</span>) {</div>
<div class="line"><a id="l00242" name="l00242"></a><span class="lineno"> 242</span> func = &amp;<a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>;</div>
<div class="line"><a id="l00243" name="l00243"></a><span class="lineno"> 243</span> } <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00244" name="l00244"></a><span class="lineno"> 244</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Not a valid method!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00245" name="l00245"></a><span class="lineno"> 245</span> abort();</div>
<div class="line"><a id="l00246" name="l00246"></a><span class="lineno"> 246</span> }</div>
<div class="line"><a id="l00247" name="l00247"></a><span class="lineno"> 247</span> </div>
<div class="line"><a id="l00248" name="l00248"></a><span class="lineno"> 248</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; steps; j++) {</div>
<div class="line"><a id="l00249" name="l00249"></a><span class="lineno"> 249</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; size; i++) {</div>
<div class="line"><a id="l00250" name="l00250"></a><span class="lineno"> 250</span> res.r_vecs[i][j] = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec;</div>
<div class="line"><a id="l00251" name="l00251"></a><span class="lineno"> 251</span> res.v_vecs[i][j] = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].v_vec;</div>
<div class="line"><a id="l00252" name="l00252"></a><span class="lineno"> 252</span> }</div>
<div class="line"><a id="l00253" name="l00253"></a><span class="lineno"> 253</span> (this-&gt;*func)(dt, particle_interaction);</div>
<div class="line"><a id="l00254" name="l00254"></a><span class="lineno"> 254</span> }</div>
<div class="line"><a id="l00255" name="l00255"></a><span class="lineno"> 255</span> </div>
<div class="line"><a id="l00256" name="l00256"></a><span class="lineno"> 256</span> <span class="keywordflow">return</span> res;</div>
<div class="line"><a id="l00257" name="l00257"></a><span class="lineno"> 257</span>}</div>
<div class="line"><a id="l00258" name="l00258"></a><span class="lineno"> 258</span> </div>
<div class="line"><a id="l00259" name="l00259"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b"> 259</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap::write_simulation_to_dir</a>(std::string path, <span class="keywordtype">double</span> time,</div>
<div class="line"><a id="l00260" name="l00260"></a><span class="lineno"> 260</span> uint steps, std::string method,</div>
<div class="line"><a id="l00261" name="l00261"></a><span class="lineno"> 261</span> <span class="keywordtype">bool</span> particle_interaction)</div>
<div class="line"><a id="l00262" name="l00262"></a><span class="lineno"> 262</span>{</div>
<div class="line"><a id="l00263" name="l00263"></a><span class="lineno"> 263</span> <span class="keywordflow">if</span> (path.back() != <span class="charliteral">&#39;/&#39;</span>) {</div>
<div class="line"><a id="l00264" name="l00264"></a><span class="lineno"> 264</span> path += <span class="charliteral">&#39;/&#39;</span>;</div>
<div class="line"><a id="l00265" name="l00265"></a><span class="lineno"> 265</span> }</div>
<div class="line"><a id="l00266" name="l00266"></a><span class="lineno"> 266</span> <span class="keywordflow">if</span> (<a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path, 0777) != 0) {</div>
<div class="line"><a id="l00267" name="l00267"></a><span class="lineno"> 267</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Failed to make path&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00268" name="l00268"></a><span class="lineno"> 268</span> abort();</div>
<div class="line"><a id="l00269" name="l00269"></a><span class="lineno"> 269</span> }</div>
<div class="line"><a id="l00270" name="l00270"></a><span class="lineno"> 270</span> </div>
<div class="line"><a id="l00271" name="l00271"></a><span class="lineno"> 271</span> <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res =</div>
<div class="line"><a id="l00272" name="l00272"></a><span class="lineno"> 272</span> this-&gt;<a class="code hl_function" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">simulate</a>(time, steps, method, particle_interaction);</div>
<div class="line"><a id="l00273" name="l00273"></a><span class="lineno"> 273</span> </div>
<div class="line"><a id="l00274" name="l00274"></a><span class="lineno"> 274</span> std::ofstream ofile;</div>
<div class="line"><a id="l00275" name="l00275"></a><span class="lineno"> 275</span> </div>
<div class="line"><a id="l00276" name="l00276"></a><span class="lineno"> 276</span> <span class="comment">// Writing each particle to its own file is independent and can be run in</span></div>
<div class="line"><a id="l00277" name="l00277"></a><span class="lineno"> 277</span> <span class="comment">// parallel.</span></div>
<div class="line"><a id="l00278" name="l00278"></a><span class="lineno"> 278</span><span class="preprocessor">#pragma omp parallel for private(ofile)</span></div>
<div class="line"><a id="l00279" name="l00279"></a><span class="lineno"> 279</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); i++) {</div>
<div class="line"><a id="l00280" name="l00280"></a><span class="lineno"> 280</span> ofile.open(path + <span class="stringliteral">&quot;particle_&quot;</span> + std::to_string(i) + <span class="stringliteral">&quot;_r.txt&quot;</span>);</div>
<div class="line"><a id="l00281" name="l00281"></a><span class="lineno"> 281</span> <span class="keywordflow">for</span> (<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> &amp;vec : res.r_vecs[i]) {</div>
<div class="line"><a id="l00282" name="l00282"></a><span class="lineno"> 282</span> ofile &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(0), 10, 8) &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
<div class="line"><a id="l00283" name="l00283"></a><span class="lineno"> 283</span> &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(1), 10, 8) &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
<div class="line"><a id="l00284" name="l00284"></a><span class="lineno"> 284</span> &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(2), 10, 8) &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
<div class="line"><a id="l00285" name="l00285"></a><span class="lineno"> 285</span> }</div>
<div class="line"><a id="l00286" name="l00286"></a><span class="lineno"> 286</span> ofile.close();</div>
<div class="line"><a id="l00287" name="l00287"></a><span class="lineno"> 287</span> ofile.open(path + <span class="stringliteral">&quot;particle_&quot;</span> + std::to_string(i) + <span class="stringliteral">&quot;_v.txt&quot;</span>);</div>
<div class="line"><a id="l00288" name="l00288"></a><span class="lineno"> 288</span> <span class="keywordflow">for</span> (<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> &amp;vec : res.v_vecs[i]) {</div>
<div class="line"><a id="l00289" name="l00289"></a><span class="lineno"> 289</span> ofile &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(0), 10, 8) &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
<div class="line"><a id="l00290" name="l00290"></a><span class="lineno"> 290</span> &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(1), 10, 8) &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
<div class="line"><a id="l00291" name="l00291"></a><span class="lineno"> 291</span> &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(2), 10, 8) &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
<div class="line"><a id="l00292" name="l00292"></a><span class="lineno"> 292</span> }</div>
<div class="line"><a id="l00293" name="l00293"></a><span class="lineno"> 293</span> ofile.close();</div>
<div class="line"><a id="l00294" name="l00294"></a><span class="lineno"> 294</span> }</div>
<div class="line"><a id="l00295" name="l00295"></a><span class="lineno"> 295</span>}</div>
<div class="line"><a id="l00296" name="l00296"></a><span class="lineno"> 296</span> </div>
<div class="line"><a id="l00297" name="l00297"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f"> 297</a></span><span class="keywordtype">double</span> <a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap::fraction_of_particles_left</a>(<span class="keywordtype">double</span> time, uint steps,</div>
<div class="line"><a id="l00298" name="l00298"></a><span class="lineno"> 298</span> std::string method,</div>
<div class="line"><a id="l00299" name="l00299"></a><span class="lineno"> 299</span> <span class="keywordtype">bool</span> particle_interaction)</div>
<div class="line"><a id="l00300" name="l00300"></a><span class="lineno"> 300</span>{</div>
<div class="line"><a id="l00301" name="l00301"></a><span class="lineno"> 301</span> <span class="keywordtype">double</span> dt = time / (double)steps;</div>
<div class="line"><a id="l00302" name="l00302"></a><span class="lineno"> 302</span> </div>
<div class="line"><a id="l00303" name="l00303"></a><span class="lineno"> 303</span> void (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*func)(double, bool);</div>
<div class="line"><a id="l00304" name="l00304"></a><span class="lineno"> 304</span> <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;rk4&quot;</span>) {</div>
<div class="line"><a id="l00305" name="l00305"></a><span class="lineno"> 305</span> func = &amp;<a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a>;</div>
<div class="line"><a id="l00306" name="l00306"></a><span class="lineno"> 306</span> } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;euler&quot;</span>) {</div>
<div class="line"><a id="l00307" name="l00307"></a><span class="lineno"> 307</span> func = &amp;<a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>;</div>
<div class="line"><a id="l00308" name="l00308"></a><span class="lineno"> 308</span> } <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00309" name="l00309"></a><span class="lineno"> 309</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Not a valid method!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00310" name="l00310"></a><span class="lineno"> 310</span> abort();</div>
<div class="line"><a id="l00311" name="l00311"></a><span class="lineno"> 311</span> }</div>
<div class="line"><a id="l00312" name="l00312"></a><span class="lineno"> 312</span> </div>
<div class="line"><a id="l00313" name="l00313"></a><span class="lineno"> 313</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; steps; j++) {</div>
<div class="line"><a id="l00314" name="l00314"></a><span class="lineno"> 314</span> (this-&gt;*func)(dt, particle_interaction);</div>
<div class="line"><a id="l00315" name="l00315"></a><span class="lineno"> 315</span> }</div>
<div class="line"><a id="l00316" name="l00316"></a><span class="lineno"> 316</span> </div>
<div class="line"><a id="l00317" name="l00317"></a><span class="lineno"> 317</span> <span class="keywordtype">int</span> particles_left = 0;</div>
<div class="line"><a id="l00318" name="l00318"></a><span class="lineno"> 318</span> </div>
<div class="line"><a id="l00319" name="l00319"></a><span class="lineno"> 319</span> <span class="comment">// A reduction is perfect here</span></div>
<div class="line"><a id="l00320" name="l00320"></a><span class="lineno"> 320</span><span class="preprocessor">#pragma omp parallel for reduction(+ : particles_left)</span></div>
<div class="line"><a id="l00321" name="l00321"></a><span class="lineno"> 321</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); i++) {</div>
<div class="line"><a id="l00322" name="l00322"></a><span class="lineno"> 322</span> <span class="keywordflow">if</span> (arma::norm(this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec) &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>) {</div>
<div class="line"><a id="l00323" name="l00323"></a><span class="lineno"> 323</span> particles_left++;</div>
<div class="line"><a id="l00324" name="l00324"></a><span class="lineno"> 324</span> }</div>
<div class="line"><a id="l00325" name="l00325"></a><span class="lineno"> 325</span> }</div>
<div class="line"><a id="l00326" name="l00326"></a><span class="lineno"> 326</span> </div>
<div class="line"><a id="l00327" name="l00327"></a><span class="lineno"> 327</span> <span class="keywordflow">return</span> (<span class="keywordtype">double</span>)particles_left / (double)this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div>
<div class="line"><a id="l00328" name="l00328"></a><span class="lineno"> 328</span>}</div>
<div class="ttc" id="aPenningTrap_8hpp_html"><div class="ttname"><a href="PenningTrap_8hpp.html">PenningTrap.hpp</a></div><div class="ttdoc">A class for simulating a Penning trap.</div></div>
<div class="ttc" id="aclassParticle_html"><div class="ttname"><a href="classParticle.html">Particle</a></div><div class="ttdoc">A class that holds attributes of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00022">Particle.hpp:23</a></div></div>
<div class="ttc" id="aclassParticle_html_a1c59101411db43624828b766f87ad460"><div class="ttname"><a href="classParticle.html#a1c59101411db43624828b766f87ad460">Particle::r_vec</a></div><div class="ttdeci">vec3 r_vec</div><div class="ttdoc">position</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00025">Particle.hpp:25</a></div></div>
<div class="ttc" id="aclassParticle_html_a3a10400add8dd22b8031330c2aafb6fe"><div class="ttname"><a href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">Particle::v_vec</a></div><div class="ttdeci">vec3 v_vec</div><div class="ttdoc">velocity</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00026">Particle.hpp:26</a></div></div>
<div class="ttc" id="aclassParticle_html_a566dcc1de4bdc01251776948798ea8e1"><div class="ttname"><a href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">Particle::q</a></div><div class="ttdeci">double q</div><div class="ttdoc">Charge.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00027">Particle.hpp:27</a></div></div>
<div class="ttc" id="aclassPenningTrap_html"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00031">PenningTrap.hpp:32</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a0112525d9e79a472e761f8ef402a339f"><div class="ttname"><a href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">PenningTrap::particles</a></div><div class="ttdeci">std::vector&lt; Particle &gt; particles</div><div class="ttdoc">The particles in the Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00039">PenningTrap.hpp:39</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a0cac3509aa96e71a26d3b2c902e27716"><div class="ttname"><a href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">PenningTrap::B_0</a></div><div class="ttdeci">double B_0</div><div class="ttdoc">Magnetic field strength.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00034">PenningTrap.hpp:34</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a2c01108b52c8e2a003cf9170da9e7682"><div class="ttname"><a href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap::total_force_external</a></div><div class="ttdeci">vec3 total_force_external(uint i)</div><div class="ttdoc">Calculate the total external force on a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00130">PenningTrap.cpp:130</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a2f168622587709b9e3c49077f0b9a640"><div class="ttname"><a href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">PenningTrap::k_r</a></div><div class="ttdeci">sim_arr k_r</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00042">PenningTrap.hpp:42</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a2fe1cefbae18fa5808155ee0d2df713c"><div class="ttname"><a href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap::total_force_particles</a></div><div class="ttdeci">vec3 total_force_particles(uint i)</div><div class="ttdoc">Calculate the total force on a particle p_i from other particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00143">PenningTrap.cpp:143</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a361f2c4862c90b5e8e2a2f50c6a95655"><div class="ttname"><a href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">PenningTrap::external_B_field</a></div><div class="ttdeci">vec3 external_B_field(vec3 r)</div><div class="ttdoc">Calculate B at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00114">PenningTrap.cpp:114</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a36946152fd951b1f7c346c51ff900d8e"><div class="ttname"><a href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a></div><div class="ttdeci">void evolve_RK4(double dt, bool particle_interaction=true)</div><div class="ttdoc">Go forward one timestep using the RK4 method.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00163">PenningTrap.cpp:163</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a3c0a44e4e0a94366ff609e81fe463fa2"><div class="ttname"><a href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap::v_func</a></div><div class="ttdeci">vec3 v_func(uint i, uint j, double dt)</div><div class="ttdoc">Helper for evolve_RK4 when calculating values.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00063">PenningTrap.cpp:63</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a5846c8f75cdc543fd9cf0b2185a3ef22"><div class="ttname"><a href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">PenningTrap::external_E_field</a></div><div class="ttdeci">vec3 external_E_field(vec3 r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00106">PenningTrap.cpp:106</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a5b6c6d4636f3a6e279ccde59d4a345e8"><div class="ttname"><a href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a></div><div class="ttdeci">PenningTrap(double B_0=T, double V_0=(25. *V)/1000., double d=500., double t=0.)</div><div class="ttdoc">Constructor for the PenningTrap class.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00020">PenningTrap.cpp:20</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a66dfe89c68716b9502927b97f59c27d2"><div class="ttname"><a href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">PenningTrap::d</a></div><div class="ttdeci">double d</div><div class="ttdoc">Characteristic dimension.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00037">PenningTrap.hpp:37</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a6e9776ff5b149f01080800716455d7c8"><div class="ttname"><a href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap::add_particle</a></div><div class="ttdeci">void add_particle(Particle particle)</div><div class="ttdoc">Add a particle to the system.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00101">PenningTrap.cpp:101</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a715329844d75ec4c04f8391421fb4e89"><div class="ttname"><a href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">PenningTrap::V_0</a></div><div class="ttdeci">double V_0</div><div class="ttdoc">Applied potential.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00035">PenningTrap.hpp:35</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a7a1d9f0528a12308de25bc30718da20a"><div class="ttname"><a href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap::simulate</a></div><div class="ttdeci">simulation_t simulate(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate the particle system inside the Penning trap over a certain amount of time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00228">PenningTrap.cpp:228</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a7f210bb2768a5d79ced4b0df0df97598"><div class="ttname"><a href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap::force_on_particle</a></div><div class="ttdeci">vec3 force_on_particle(uint i, uint j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00119">PenningTrap.cpp:119</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a826b7fa8e709d481eb1dee7d0c2cdc08"><div class="ttname"><a href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">PenningTrap::r_func</a></div><div class="ttdeci">vec3 r_func(uint i, uint j, double dt)</div><div class="ttdoc">Helper for evolve_RK4 when calculating values.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00082">PenningTrap.cpp:82</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a8ca4e21291f60fde619c14099d8c4e8e"><div class="ttname"><a href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">PenningTrap::t</a></div><div class="ttdeci">double t</div><div class="ttdoc">Current time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00038">PenningTrap.hpp:38</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a9a301b0540078c36697880ef204afdf3"><div class="ttname"><a href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div><div class="ttdeci">vec3 total_force(uint i)</div><div class="ttdoc">calculate the total force on a particle p_i.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00155">PenningTrap.cpp:155</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a9d1d8e90ca839b928aee1ad0cd4aff43"><div class="ttname"><a href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">PenningTrap::set_pertubation</a></div><div class="ttdeci">void set_pertubation(double f, double omega_V)</div><div class="ttdoc">Time dependent perturbation to V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00046">PenningTrap.cpp:46</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_aaee129f177657455348d0c8ae1441dea"><div class="ttname"><a href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap::reinitialize</a></div><div class="ttdeci">void reinitialize(double f, double omega_V, double t=0.)</div><div class="ttdoc">Give all particles new positions and velocities, and change t and V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00053">PenningTrap.cpp:53</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_ab9ea97a406534bbe621a95215144875e"><div class="ttname"><a href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a></div><div class="ttdeci">void evolve_forward_euler(double dt, bool particle_interaction=true)</div><div class="ttdoc">Go forward one timestep using the forward Euler method.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00201">PenningTrap.cpp:201</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_ac529aa26c288f34eae184a67e6bac41f"><div class="ttname"><a href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap::fraction_of_particles_left</a></div><div class="ttdeci">double fraction_of_particles_left(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and calculate what fraction of particles are still left inside the Penning trap after the si...</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00297">PenningTrap.cpp:297</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_ad8bc4df7ab3eed53b16cfdff38e7760b"><div class="ttname"><a href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap::write_simulation_to_dir</a></div><div class="ttdeci">void write_simulation_to_dir(std::string path, double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and write the displacement of all particles to files.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00259">PenningTrap.cpp:259</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_ae915f6ad0eef1fb46530e836b6e071e5"><div class="ttname"><a href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">PenningTrap::perturbation</a></div><div class="ttdeci">std::function&lt; double(double)&gt; perturbation</div><div class="ttdoc">Time-dependent perturbation.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00036">PenningTrap.hpp:36</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_ae9b5afdaa5cd366e94bd294452a1eed4"><div class="ttname"><a href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">PenningTrap::k_v</a></div><div class="ttdeci">sim_arr k_v</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00040">PenningTrap.hpp:40</a></div></div>
<div class="ttc" id="aconstants_8hpp_html_a4e451456ad7e9276ed0afa42826e7ccb"><div class="ttname"><a href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">K_E</a></div><div class="ttdeci">#define K_E</div><div class="ttdoc">Coulomb constant. unit: .</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00017">constants.hpp:17</a></div></div>
<div class="ttc" id="astructsimulation_html"><div class="ttname"><a href="structsimulation.html">simulation</a></div><div class="ttdoc">Typedef for PenningTrap::simulation return value.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00040">typedefs.hpp:40</a></div></div>
<div class="ttc" id="atypedefs_8hpp_html"><div class="ttname"><a href="typedefs_8hpp.html">typedefs.hpp</a></div><div class="ttdoc">Useful typedefs for cleaner code.</div></div>
<div class="ttc" id="atypedefs_8hpp_html_a3bdfb73a02f88ae32b6128ef747c4aea"><div class="ttname"><a href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; vec3</div><div class="ttdoc">Typedef for a fixed 3d arma vector.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00023">typedefs.hpp:23</a></div></div>
<div class="ttc" id="atypedefs_8hpp_html_a46482a2697556c00556c9d73f461784f"><div class="ttname"><a href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a></div><div class="ttdeci">std::vector&lt; vec3 &gt; sim_cols</div><div class="ttdoc">Typedef for the column of the result vector from simulating particles.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00028">typedefs.hpp:28</a></div></div>
<div class="ttc" id="atypedefs_8hpp_html_aec69d34220fff45de238b9e01f2686af"><div class="ttname"><a href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a></div><div class="ttdeci">std::vector&lt; sim_cols &gt; sim_arr</div><div class="ttdoc">Typedef for the result of the simulate method.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00036">typedefs.hpp:36</a></div></div>
<div class="ttc" id="autils_8hpp_html_a6fdd7217b750aff5b6295ece7cbdeffa"><div class="ttname"><a href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a></div><div class="ttdeci">bool mkpath(std::string path, int mode=0777)</div><div class="ttdoc">Make path given.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00072">utils.cpp:72</a></div></div>
<div class="ttc" id="autils_8hpp_html_adfb618b2fdff47ef30a4a2b62c04f384"><div class="ttname"><a href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a></div><div class="ttdeci">std::string scientific_format(double d, int width=20, int prec=10)</div><div class="ttdoc">Turns a double into a string written in scientific format.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00015">utils.cpp:15</a></div></div>
</div><!-- fragment --></div><!-- contents -->
</div><!-- doc-content -->
<!-- start footer part -->
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
<ul>
<li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="PenningTrap_8cpp.html">PenningTrap.cpp</a></li>
<li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.6 </li>
</ul>
</div>
</body>
</html>
Reference in New Issue View Git Blame Copy Permalink