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Develop #14

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coryab merged 124 commits from develop into main 2023-10-24 20:43:56 +00:00
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@ -917,7 +917,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.
INPUT = include src src/scripts README.md
INPUT = include src README.md
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

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docs/Particle_8cpp.html
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@ -113,7 +113,7 @@ $(document).ready(function(){initNavTree('Particle_8cpp.html',''); initResizable
<dd>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000007">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000008">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<p class="definition">Definition in file <a class="el" href="Particle_8cpp_source.html">Particle.cpp</a>.</p>
</div></div><!-- contents -->

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docs/PenningTrap_8cpp.html
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@ -104,12 +104,12 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp.html',''); initResiza
<p>The implementation of the <a class="el" href="classPenningTrap.html" title="A class that simulates a Penning trap.">PenningTrap</a> class.
<a href="#details">More...</a></p>
<div class="textblock"><code>#include &quot;<a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>&quot;</code><br />
<code>#include &quot;<a class="el" href="typedefs_8hpp_source.html">typedefs.hpp</a>&quot;</code><br />
<code>#include &lt;algorithm&gt;</code><br />
<div class="textblock"><code>#include &lt;algorithm&gt;</code><br />
<code>#include &lt;functional&gt;</code><br />
<code>#include &lt;sys/types.h&gt;</code><br />
<code>#include &lt;vector&gt;</code><br />
<code>#include &quot;<a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>&quot;</code><br />
<code>#include &quot;<a class="el" href="typedefs_8hpp_source.html">typedefs.hpp</a>&quot;</code><br />
</div>
<p><a href="PenningTrap_8cpp_source.html">Go to the source code of this file.</a></p>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
@ -118,7 +118,7 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp.html',''); initResiza
<dd>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000008">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000009">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<p class="definition">Definition in file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
</div></div><!-- contents -->

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docs/PenningTrap_8cpp_source.html
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@ -102,351 +102,367 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp_source.html',''); ini
</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#a3c0a44e4e0a94366ff609e81fe463fa2"> 20</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="l00021" name="l00021"></a><span class="lineno"> 21</span>{</div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> <span class="keywordflow">switch</span> (i) {</div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> <span class="keywordflow">case</span> 0:</div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</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="l00025" name="l00025"></a><span class="lineno"> 25</span> <span class="keywordflow">case</span> 1:</div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> <span class="keywordflow">return</span> .5 * dt * this-&gt;k_v[1][j];</div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> <span class="keywordflow">case</span> 2:</div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span> <span class="keywordflow">return</span> dt * this-&gt;k_v[2][j];</div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> <span class="keywordflow">case</span> 3:</div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</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="l00031" name="l00031"></a><span class="lineno"> 31</span> * (this-&gt;k_v[0][j] + 2. * this-&gt;k_v[1][j]</div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> + 2. * this-&gt;k_v[2][j] + this-&gt;k_v[3][j]));</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> <span class="keywordflow">default</span>:</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> abort();</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#a826b7fa8e709d481eb1dee7d0c2cdc08"> 39</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="l00040" name="l00040"></a><span class="lineno"> 40</span>{</div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> <span class="keywordflow">switch</span> (i) {</div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> <span class="keywordflow">case</span> 0:</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</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="l00044" name="l00044"></a><span class="lineno"> 44</span> <span class="keywordflow">case</span> 1:</div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> <span class="keywordflow">return</span> .5 * dt * this-&gt;k_r[1][j];</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> <span class="keywordflow">case</span> 2:</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordflow">return</span> dt * this-&gt;k_r[2][j];</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> <span class="keywordflow">case</span> 3:</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</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="l00050" name="l00050"></a><span class="lineno"> 50</span> * (this-&gt;k_r[0][j] + 2. * this-&gt;k_r[1][j]</div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> + 2. * this-&gt;k_r[2][j] + this-&gt;k_r[3][j]));</div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> <span class="keywordflow">default</span>:</div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> abort();</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> }</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span>}</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"><a class="line" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22"> 58</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="l00059" name="l00059"></a><span class="lineno"> 59</span>{</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> r(2) *= -2.;</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> <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="l00063" name="l00063"></a><span class="lineno"> 63</span> * r);</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> </div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655"> 66</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="l00067" name="l00067"></a><span class="lineno"> 67</span>{</div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</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="l00069" name="l00069"></a><span class="lineno"> 69</span>}</div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> </div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598"> 71</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="l00072" name="l00072"></a><span class="lineno"> 72</span>{</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> <span class="comment">// Calculate the difference between the particles&#39; position</span></div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</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="l00075" name="l00075"></a><span class="lineno"> 75</span> </div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> <span class="comment">// Get the distance between the particles</span></div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> <span class="keywordtype">double</span> norm = arma::norm(res, 2);</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> </div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</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="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#a2c01108b52c8e2a003cf9170da9e7682"> 82</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="l00083" name="l00083"></a><span class="lineno"> 83</span>{</div>
<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</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="l00085" name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</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="l00087" name="l00087"></a><span class="lineno"> 87</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="l00088" name="l00088"></a><span class="lineno"> 88</span> }</div>
<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> </div>
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</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="l00091" name="l00091"></a><span class="lineno"> 91</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="l00092" name="l00092"></a><span class="lineno"> 92</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="l00093" name="l00093"></a><span class="lineno"> 93</span>}</div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c"> 95</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="l00096" name="l00096"></a><span class="lineno"> 96</span>{</div>
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res;</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> <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="l00100" name="l00100"></a><span class="lineno"> 100</span> <span class="keywordflow">if</span> (i != j)</div>
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</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="l00102" name="l00102"></a><span class="lineno"> 102</span> }</div>
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#include &lt;algorithm&gt;</span></div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="preprocessor">#include &lt;functional&gt;</span></div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include &lt;sys/types.h&gt;</span></div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> </div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span><span class="preprocessor">#include &quot;<a class="code" href="typedefs_8hpp.html">typedefs.hpp</a>&quot;</span></div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> </div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2"> 21</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="l00022" name="l00022"></a><span class="lineno"> 22</span>{</div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> <span class="keywordflow">switch</span> (i) {</div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> <span class="keywordflow">case</span> 0:</div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</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="l00026" name="l00026"></a><span class="lineno"> 26</span> <span class="keywordflow">case</span> 1:</div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> <span class="keywordflow">return</span> .5 * dt * this-&gt;k_v[1][j];</div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span> <span class="keywordflow">case</span> 2:</div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> <span class="keywordflow">return</span> dt * this-&gt;k_v[2][j];</div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> <span class="keywordflow">case</span> 3:</div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</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="l00032" name="l00032"></a><span class="lineno"> 32</span> * (this-&gt;k_v[0][j] + 2. * this-&gt;k_v[1][j]</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> + 2. * this-&gt;k_v[2][j] + this-&gt;k_v[3][j]));</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> <span class="keywordflow">default</span>:</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> abort();</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"> 39</span> </div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08"> 40</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="l00041" name="l00041"></a><span class="lineno"> 41</span>{</div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> <span class="keywordflow">switch</span> (i) {</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> <span class="keywordflow">case</span> 0:</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</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="l00045" name="l00045"></a><span class="lineno"> 45</span> <span class="keywordflow">case</span> 1:</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> <span class="keywordflow">return</span> .5 * dt * this-&gt;k_r[1][j];</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordflow">case</span> 2:</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> <span class="keywordflow">return</span> dt * this-&gt;k_r[2][j];</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> <span class="keywordflow">case</span> 3:</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</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="l00051" name="l00051"></a><span class="lineno"> 51</span> * (this-&gt;k_r[0][j] + 2. * this-&gt;k_r[1][j]</div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> + 2. * this-&gt;k_r[2][j] + this-&gt;k_r[3][j]));</div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> <span class="keywordflow">default</span>:</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> abort();</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> }</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> </div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22"> 59</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="l00060" name="l00060"></a><span class="lineno"> 60</span>{</div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> r(2) *= -2.;</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"> 63</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(</div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> ((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>)) * r);</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span>}</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655"> 67</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="l00068" name="l00068"></a><span class="lineno"> 68</span>{</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</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="l00070" name="l00070"></a><span class="lineno"> 70</span>}</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> </div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598"> 72</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="l00073" name="l00073"></a><span class="lineno"> 73</span>{</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> <span class="comment">// Calculate the difference between the particles&#39; position</span></div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</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="l00076" name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> <span class="comment">// Get the distance between the particles</span></div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> <span class="keywordtype">double</span> norm = arma::norm(res, 2);</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> <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="l00081" name="l00081"></a><span class="lineno"> 81</span>}</div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> </div>
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682"> 83</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="l00084" name="l00084"></a><span class="lineno"> 84</span>{</div>
<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</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="l00086" name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</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="l00088" name="l00088"></a><span class="lineno"> 88</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="l00089" name="l00089"></a><span class="lineno"> 89</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="l00090" name="l00090"></a><span class="lineno"> 90</span>}</div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> </div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c"> 92</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="l00093" name="l00093"></a><span class="lineno"> 93</span>{</div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res;</div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> </div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</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="l00097" name="l00097"></a><span class="lineno"> 97</span> <span class="keywordflow">if</span> (i != j)</div>
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</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="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"> 101</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="l00102" name="l00102"></a><span class="lineno"> 102</span>}</div>
<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> </div>
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</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="l00105" name="l00105"></a><span class="lineno"> 105</span>}</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3"> 107</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="l00108" name="l00108"></a><span class="lineno"> 108</span>{</div>
<div class="line"><a id="l00109" name="l00109"></a><span class="lineno"> 109</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="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>{0., 0., 0.};</div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> }</div>
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</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="l00113" name="l00113"></a><span class="lineno"> 113</span>}</div>
<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8"> 115</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="l00116" name="l00116"></a><span class="lineno"> 116</span>{</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> this-&gt;B_0 = <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>;</div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> this-&gt;V_0 = <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a>;</div>
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> this-&gt;d = <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span> this-&gt;t = <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>;</div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</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="l00122" name="l00122"></a><span class="lineno"> 122</span>}</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"><a class="line" href="classPenningTrap.html#a830be1b8cbf59664e060b6edbeaa302f"> 124</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="l00125" name="l00125"></a><span class="lineno"> 125</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="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">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; i; j++) {</div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(</div>
<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</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="l00130" name="l00130"></a><span class="lineno"> 130</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="l00131" name="l00131"></a><span class="lineno"> 131</span> }</div>
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span>}</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"><a class="line" href="classPenningTrap.html#addc96789dcfec07b75156e19fee82f4f"> 134</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="l00135" name="l00135"></a><span class="lineno"> 135</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="l00136" name="l00136"></a><span class="lineno"> 136</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="l00137" name="l00137"></a><span class="lineno"> 137</span>{</div>
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> this-&gt;particles = <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span>}</div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> </div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43"> 141</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="l00104" name="l00104"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3"> 104</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="l00105" name="l00105"></a><span class="lineno"> 105</span>{</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</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="l00107" name="l00107"></a><span class="lineno"> 107</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="l00108" name="l00108"></a><span class="lineno"> 108</span> }</div>
<div class="line"><a id="l00109" name="l00109"></a><span class="lineno"> 109</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="l00110" name="l00110"></a><span class="lineno"> 110</span>}</div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> </div>
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018"> 112</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap::total_force_no_interaction</a>(uint i)</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"> 114</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="l00115" name="l00115"></a><span class="lineno"> 115</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="l00116" name="l00116"></a><span class="lineno"> 116</span> }</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</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));</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"> 119</span> </div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8"> 120</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="l00121" name="l00121"></a><span class="lineno"> 121</span>{</div>
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> this-&gt;B_0 = <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>;</div>
<div class="line"><a id="l00123" name="l00123"></a><span class="lineno"> 123</span> this-&gt;V_0 = <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a>;</div>
<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> this-&gt;d = <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</div>
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> this-&gt;t = <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>;</div>
<div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</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="l00127" name="l00127"></a><span class="lineno"> 127</span>}</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"><a class="line" href="classPenningTrap.html#a830be1b8cbf59664e060b6edbeaa302f"> 129</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="l00130" name="l00130"></a><span class="lineno"> 130</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="l00131" name="l00131"></a><span class="lineno"> 131</span>{</div>
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; i; j++) {</div>
<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(</div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</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="l00135" name="l00135"></a><span class="lineno"> 135</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="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> </div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"><a class="line" href="classPenningTrap.html#addc96789dcfec07b75156e19fee82f4f"> 139</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="l00140" name="l00140"></a><span class="lineno"> 140</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="l00141" name="l00141"></a><span class="lineno"> 141</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="l00142" name="l00142"></a><span class="lineno"> 142</span>{</div>
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</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="l00144" name="l00144"></a><span class="lineno"> 144</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="l00145" name="l00145"></a><span class="lineno"> 145</span> };</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> </div>
<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"><a class="line" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea"> 148</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="l00149" name="l00149"></a><span class="lineno"> 149</span>{</div>
<div class="line"><a id="l00150" name="l00150"></a><span class="lineno"> 150</span> this-&gt;t = <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>;</div>
<div class="line"><a id="l00151" name="l00151"></a><span class="lineno"> 151</span> this-&gt;<a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">set_pertubation</a>(f, omega_V);</div>
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span> this-&gt;particles = <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</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> </div>
<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43"> 146</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="l00147" name="l00147"></a><span class="lineno"> 147</span>{</div>
<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"> 148</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="l00149" name="l00149"></a><span class="lineno"> 149</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="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> </div>
<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</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="l00154" name="l00154"></a><span class="lineno"> 154</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="l00155" name="l00155"></a><span class="lineno"> 155</span> }</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> </div>
<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8"> 158</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="l00159" name="l00159"></a><span class="lineno"> 159</span>{</div>
<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(particle);</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="l00153" name="l00153"></a><span class="lineno"><a class="line" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea"> 153</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="l00154" name="l00154"></a><span class="lineno"> 154</span>{</div>
<div class="line"><a id="l00155" name="l00155"></a><span class="lineno"> 155</span> this-&gt;t = <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>;</div>
<div class="line"><a id="l00156" name="l00156"></a><span class="lineno"> 156</span> this-&gt;<a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">set_pertubation</a>(f, omega_V);</div>
<div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</span> <a class="code hl_class" href="classParticle.html">Particle</a> *p;</div>
<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"> 158</span> </div>
<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</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="l00160" name="l00160"></a><span class="lineno"> 160</span> p = &amp;this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i];</div>
<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span> p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a> = <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="l00162" name="l00162"></a><span class="lineno"> 162</span> p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a> = <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="l00163" name="l00163"></a><span class="lineno"> 163</span> }</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="l00166" name="l00166"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8"> 166</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="l00167" name="l00167"></a><span class="lineno"> 167</span>{</div>
<div class="line"><a id="l00168" name="l00168"></a><span class="lineno"> 168</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(particle);</div>
<div class="line"><a id="l00169" name="l00169"></a><span class="lineno"> 169</span>}</div>
<div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> </div>
<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e"> 171</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="l00172" name="l00172"></a><span class="lineno"> 172</span>{</div>
<div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span> <a class="code hl_class" href="classParticle.html">Particle</a> *p;</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="l00175" name="l00175"></a><span class="lineno"> 175</span> <span class="comment">// Keep original particles</span></div>
<div class="line"><a id="l00176" name="l00176"></a><span class="lineno"> 176</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="l00177" name="l00177"></a><span class="lineno"> 177</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="l00178" name="l00178"></a><span class="lineno"> 178</span> </div>
<div class="line"><a id="l00179" name="l00179"></a><span class="lineno"> 179</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) =</div>
<div class="line"><a id="l00180" name="l00180"></a><span class="lineno"> 180</span> particle_interaction ? &amp;<a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div>
<div class="line"><a id="l00181" name="l00181"></a><span class="lineno"> 181</span> : &amp;<a class="code hl_function" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap::total_force_no_interaction</a>;</div>
<div class="line"><a id="l00182" name="l00182"></a><span class="lineno"> 182</span> </div>
<div class="line"><a id="l00183" name="l00183"></a><span class="lineno"> 183</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="l00184" name="l00184"></a><span class="lineno"> 184</span> </div>
<div class="line"><a id="l00185" name="l00185"></a><span class="lineno"> 185</span> <span class="comment">// Allocating takes a long time, so reuse sim_arr if possible</span></div>
<div class="line"><a id="l00186" name="l00186"></a><span class="lineno"> 186</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="l00187" name="l00187"></a><span class="lineno"> 187</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="l00188" name="l00188"></a><span class="lineno"> 188</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="l00189" name="l00189"></a><span class="lineno"> 189</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="l00190" name="l00190"></a><span class="lineno"> 190</span> }</div>
<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span> </div>
<div class="line"><a id="l00192" name="l00192"></a><span class="lineno"> 192</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="l00193" name="l00193"></a><span class="lineno"> 193</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 4; i++) {</div>
<div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> <span class="comment">// Inner loop is able to be parallelized</span></div>
<div class="line"><a id="l00195" name="l00195"></a><span class="lineno"> 195</span><span class="preprocessor">#pragma omp parallel for private(p)</span></div>
<div class="line"><a id="l00196" name="l00196"></a><span class="lineno"> 196</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; size; j++) {</div>
<div class="line"><a id="l00197" name="l00197"></a><span class="lineno"> 197</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="l00198" name="l00198"></a><span class="lineno"> 198</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="l00199" name="l00199"></a><span class="lineno"> 199</span> </div>
<div class="line"><a id="l00200" name="l00200"></a><span class="lineno"> 200</span> p = &amp;tmp_particles[j];</div>
<div class="line"><a id="l00201" name="l00201"></a><span class="lineno"> 201</span> </div>
<div class="line"><a id="l00202" name="l00202"></a><span class="lineno"> 202</span> p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a> = 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="l00203" name="l00203"></a><span class="lineno"> 203</span> p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a> = 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="l00204" name="l00204"></a><span class="lineno"> 204</span> }</div>
<div class="line"><a id="l00205" name="l00205"></a><span class="lineno"> 205</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a> = tmp_particles;</div>
<div class="line"><a id="l00206" name="l00206"></a><span class="lineno"> 206</span> }</div>
<div class="line"><a id="l00207" name="l00207"></a><span class="lineno"> 207</span> </div>
<div class="line"><a id="l00208" name="l00208"></a><span class="lineno"> 208</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> += dt;</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> </div>
<div class="line"><a id="l00211" name="l00211"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e"> 211</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="l00212" name="l00212"></a><span class="lineno"> 212</span>{</div>
<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</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="l00214" name="l00214"></a><span class="lineno"> 214</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> force_res[size];</div>
<div class="line"><a id="l00215" name="l00215"></a><span class="lineno"> 215</span> <a class="code hl_class" href="classParticle.html">Particle</a> *p;</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="l00217" name="l00217"></a><span class="lineno"> 217</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) =</div>
<div class="line"><a id="l00218" name="l00218"></a><span class="lineno"> 218</span> particle_interaction ? &amp;<a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div>
<div class="line"><a id="l00219" name="l00219"></a><span class="lineno"> 219</span> : &amp;<a class="code hl_function" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap::total_force_no_interaction</a>;</div>
<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span> </div>
<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"> 221</span> <span class="comment">// Calculating the force for each particle is independent and therefore</span></div>
<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> <span class="comment">// a good candidate for parallel execution</span></div>
<div class="line"><a id="l00223" name="l00223"></a><span class="lineno"> 223</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00224" name="l00224"></a><span class="lineno"> 224</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; size; i++) {</div>
<div class="line"><a id="l00225" name="l00225"></a><span class="lineno"> 225</span> force_res[i] = (this-&gt;*force)(i);</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="l00228" name="l00228"></a><span class="lineno"> 228</span> <span class="comment">// Updating the particles is also independent, so we can parallelize</span></div>
<div class="line"><a id="l00229" name="l00229"></a><span class="lineno"> 229</span> <span class="comment">// this as well</span></div>
<div class="line"><a id="l00230" name="l00230"></a><span class="lineno"> 230</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00231" name="l00231"></a><span class="lineno"> 231</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; size; i++) {</div>
<div class="line"><a id="l00232" name="l00232"></a><span class="lineno"> 232</span> p = &amp;this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i];</div>
<div class="line"><a id="l00233" name="l00233"></a><span class="lineno"> 233</span> p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a> += dt * p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a>;</div>
<div class="line"><a id="l00234" name="l00234"></a><span class="lineno"> 234</span> p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a> += dt * force_res[i] / p-&gt;<a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>;</div>
<div class="line"><a id="l00235" name="l00235"></a><span class="lineno"> 235</span> }</div>
<div class="line"><a id="l00236" name="l00236"></a><span class="lineno"> 236</span> </div>
<div class="line"><a id="l00237" name="l00237"></a><span class="lineno"> 237</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> += dt;</div>
<div class="line"><a id="l00238" name="l00238"></a><span class="lineno"> 238</span>}</div>
<div class="line"><a id="l00239" name="l00239"></a><span class="lineno"> 239</span> </div>
<div class="line"><a id="l00240" name="l00240"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a"> 240</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="l00241" name="l00241"></a><span class="lineno"> 241</span> <span class="keywordtype">bool</span> particle_interaction)</div>
<div class="line"><a id="l00242" name="l00242"></a><span class="lineno"> 242</span>{</div>
<div class="line"><a id="l00243" name="l00243"></a><span class="lineno"> 243</span> <a class="code hl_class" href="classParticle.html">Particle</a> *p;</div>
<div class="line"><a id="l00244" name="l00244"></a><span class="lineno"> 244</span> <span class="keywordtype">double</span> dt = time / (double)steps;</div>
<div class="line"><a id="l00245" name="l00245"></a><span class="lineno"> 245</span> </div>
<div class="line"><a id="l00246" name="l00246"></a><span class="lineno"> 246</span> uint size = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</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="l00248" name="l00248"></a><span class="lineno"> 248</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="l00249" name="l00249"></a><span class="lineno"> 249</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="l00250" name="l00250"></a><span class="lineno"> 250</span> </div>
<div class="line"><a id="l00251" name="l00251"></a><span class="lineno"> 251</span> void (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*func)(double, bool);</div>
<div class="line"><a id="l00252" name="l00252"></a><span class="lineno"> 252</span> <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;rk4&quot;</span>) {</div>
<div class="line"><a id="l00253" name="l00253"></a><span class="lineno"> 253</span> func = &amp;<a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a>;</div>
<div class="line"><a id="l00254" name="l00254"></a><span class="lineno"> 254</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="l00255" name="l00255"></a><span class="lineno"> 255</span> func = &amp;<a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>;</div>
<div class="line"><a id="l00256" name="l00256"></a><span class="lineno"> 256</span> } <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00257" name="l00257"></a><span class="lineno"> 257</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="l00258" name="l00258"></a><span class="lineno"> 258</span> abort();</div>
<div class="line"><a id="l00259" name="l00259"></a><span class="lineno"> 259</span> }</div>
<div class="line"><a id="l00260" name="l00260"></a><span class="lineno"> 260</span> </div>
<div class="line"><a id="l00261" name="l00261"></a><span class="lineno"> 261</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; steps; j++) {</div>
<div class="line"><a id="l00262" name="l00262"></a><span class="lineno"> 262</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; size; i++) {</div>
<div class="line"><a id="l00263" name="l00263"></a><span class="lineno"> 263</span> p = &amp;this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i];</div>
<div class="line"><a id="l00264" name="l00264"></a><span class="lineno"> 264</span> res.r_vecs[i][j] = p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>;</div>
<div class="line"><a id="l00265" name="l00265"></a><span class="lineno"> 265</span> res.v_vecs[i][j] = p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a>;</div>
<div class="line"><a id="l00266" name="l00266"></a><span class="lineno"> 266</span> }</div>
<div class="line"><a id="l00267" name="l00267"></a><span class="lineno"> 267</span> (this-&gt;*func)(dt, particle_interaction);</div>
<div class="line"><a id="l00268" name="l00268"></a><span class="lineno"> 268</span> }</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> <span class="keywordflow">return</span> res;</div>
<div class="line"><a id="l00271" name="l00271"></a><span class="lineno"> 271</span>}</div>
<div class="line"><a id="l00272" name="l00272"></a><span class="lineno"> 272</span> </div>
<div class="line"><a id="l00273" name="l00273"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b"> 273</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="l00274" name="l00274"></a><span class="lineno"> 274</span> uint steps, std::string method,</div>
<div class="line"><a id="l00275" name="l00275"></a><span class="lineno"> 275</span> <span class="keywordtype">bool</span> particle_interaction)</div>
<div class="line"><a id="l00276" name="l00276"></a><span class="lineno"> 276</span>{</div>
<div class="line"><a id="l00277" name="l00277"></a><span class="lineno"> 277</span> <span class="keywordflow">if</span> (path.back() != <span class="charliteral">&#39;/&#39;</span>) {</div>
<div class="line"><a id="l00278" name="l00278"></a><span class="lineno"> 278</span> path += <span class="charliteral">&#39;/&#39;</span>;</div>
<div class="line"><a id="l00279" name="l00279"></a><span class="lineno"> 279</span> }</div>
<div class="line"><a id="l00280" name="l00280"></a><span class="lineno"> 280</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="l00281" name="l00281"></a><span class="lineno"> 281</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="l00282" name="l00282"></a><span class="lineno"> 282</span> abort();</div>
<div class="line"><a id="l00283" name="l00283"></a><span class="lineno"> 283</span> }</div>
<div class="line"><a id="l00284" name="l00284"></a><span class="lineno"> 284</span> </div>
<div class="line"><a id="l00285" name="l00285"></a><span class="lineno"> 285</span> <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res =</div>
<div class="line"><a id="l00286" name="l00286"></a><span class="lineno"> 286</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="l00287" name="l00287"></a><span class="lineno"> 287</span> </div>
<div class="line"><a id="l00288" name="l00288"></a><span class="lineno"> 288</span> std::ofstream ofile;</div>
<div class="line"><a id="l00289" name="l00289"></a><span class="lineno"> 289</span> </div>
<div class="line"><a id="l00290" name="l00290"></a><span class="lineno"> 290</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="l00291" name="l00291"></a><span class="lineno"> 291</span> <span class="comment">// parallel.</span></div>
<div class="line"><a id="l00292" name="l00292"></a><span class="lineno"> 292</span><span class="preprocessor">#pragma omp parallel for private(ofile)</span></div>
<div class="line"><a id="l00293" name="l00293"></a><span class="lineno"> 293</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="l00294" name="l00294"></a><span class="lineno"> 294</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="l00295" name="l00295"></a><span class="lineno"> 295</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="l00296" name="l00296"></a><span class="lineno"> 296</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="l00297" name="l00297"></a><span class="lineno"> 297</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="l00298" name="l00298"></a><span class="lineno"> 298</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="l00299" name="l00299"></a><span class="lineno"> 299</span> }</div>
<div class="line"><a id="l00300" name="l00300"></a><span class="lineno"> 300</span> ofile.close();</div>
<div class="line"><a id="l00301" name="l00301"></a><span class="lineno"> 301</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="l00302" name="l00302"></a><span class="lineno"> 302</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="l00303" name="l00303"></a><span class="lineno"> 303</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="l00304" name="l00304"></a><span class="lineno"> 304</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="l00305" name="l00305"></a><span class="lineno"> 305</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="l00306" name="l00306"></a><span class="lineno"> 306</span> }</div>
<div class="line"><a id="l00307" name="l00307"></a><span class="lineno"> 307</span> ofile.close();</div>
<div class="line"><a id="l00308" name="l00308"></a><span class="lineno"> 308</span> }</div>
<div class="line"><a id="l00309" name="l00309"></a><span class="lineno"> 309</span>}</div>
<div class="line"><a id="l00310" name="l00310"></a><span class="lineno"> 310</span> </div>
<div class="line"><a id="l00311" name="l00311"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f"> 311</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="l00312" name="l00312"></a><span class="lineno"> 312</span> std::string method,</div>
<div class="line"><a id="l00313" name="l00313"></a><span class="lineno"> 313</span> <span class="keywordtype">bool</span> particle_interaction)</div>
<div class="line"><a id="l00314" name="l00314"></a><span class="lineno"> 314</span>{</div>
<div class="line"><a id="l00315" name="l00315"></a><span class="lineno"> 315</span> <span class="keywordtype">double</span> dt = time / (double)steps;</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="l00317" name="l00317"></a><span class="lineno"> 317</span> void (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*func)(double, bool);</div>
<div class="line"><a id="l00318" name="l00318"></a><span class="lineno"> 318</span> <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;rk4&quot;</span>) {</div>
<div class="line"><a id="l00319" name="l00319"></a><span class="lineno"> 319</span> func = &amp;<a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a>;</div>
<div class="line"><a id="l00320" name="l00320"></a><span class="lineno"> 320</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="l00321" name="l00321"></a><span class="lineno"> 321</span> func = &amp;<a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>;</div>
<div class="line"><a id="l00322" name="l00322"></a><span class="lineno"> 322</span> } <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00323" name="l00323"></a><span class="lineno"> 323</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="l00324" name="l00324"></a><span class="lineno"> 324</span> abort();</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="line"><a id="l00327" name="l00327"></a><span class="lineno"> 327</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; steps; j++) {</div>
<div class="line"><a id="l00328" name="l00328"></a><span class="lineno"> 328</span> (this-&gt;*func)(dt, particle_interaction);</div>
<div class="line"><a id="l00329" name="l00329"></a><span class="lineno"> 329</span> }</div>
<div class="line"><a id="l00330" name="l00330"></a><span class="lineno"> 330</span> </div>
<div class="line"><a id="l00331" name="l00331"></a><span class="lineno"> 331</span> <span class="keywordtype">int</span> particles_left = 0;</div>
<div class="line"><a id="l00332" name="l00332"></a><span class="lineno"> 332</span> </div>
<div class="line"><a id="l00333" name="l00333"></a><span class="lineno"> 333</span> <span class="comment">// A reduction is perfect here</span></div>
<div class="line"><a id="l00334" name="l00334"></a><span class="lineno"> 334</span><span class="preprocessor">#pragma omp parallel for reduction(+ : particles_left)</span></div>
<div class="line"><a id="l00335" name="l00335"></a><span class="lineno"> 335</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="l00336" name="l00336"></a><span class="lineno"> 336</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="l00337" name="l00337"></a><span class="lineno"> 337</span> particles_left++;</div>
<div class="line"><a id="l00338" name="l00338"></a><span class="lineno"> 338</span> }</div>
<div class="line"><a id="l00339" name="l00339"></a><span class="lineno"> 339</span> }</div>
<div class="line"><a id="l00340" name="l00340"></a><span class="lineno"> 340</span> </div>
<div class="line"><a id="l00341" name="l00341"></a><span class="lineno"> 341</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="l00342" name="l00342"></a><span class="lineno"> 342</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="aclassParticle_html_aedcc7e1bc53b0e2b1a4a07c9a1b47563"><div class="ttname"><a href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle::m</a></div><div class="ttdeci">double m</div><div class="ttdoc">Mass.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00028">Particle.hpp:28</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#l00042">PenningTrap.hpp:42</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#l00037">PenningTrap.hpp:37</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#l00082">PenningTrap.cpp:82</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#l00083">PenningTrap.cpp:83</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="ttdoc">A 2D vector containing all where is the index of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00052">PenningTrap.hpp:52</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#l00095">PenningTrap.cpp:95</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#l00066">PenningTrap.cpp:66</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#l00020">PenningTrap.cpp:20</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#l00058">PenningTrap.cpp:58</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#l00115">PenningTrap.cpp:115</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#l00092">PenningTrap.cpp:92</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#l00067">PenningTrap.cpp:67</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#l00171">PenningTrap.cpp:171</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#l00021">PenningTrap.cpp:21</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#l00059">PenningTrap.cpp:59</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#l00120">PenningTrap.cpp:120</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a6069f82d8dbc7cadaebd228dbcd95018"><div class="ttname"><a href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap::total_force_no_interaction</a></div><div class="ttdeci">vec3 total_force_no_interaction(uint i)</div><div class="ttdoc">calculate the total force on a particle p_i without interaction</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00112">PenningTrap.cpp:112</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#l00040">PenningTrap.hpp:40</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#l00158">PenningTrap.cpp:158</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#l00166">PenningTrap.cpp:166</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#l00038">PenningTrap.hpp:38</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#l00071">PenningTrap.cpp:71</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#l00039">PenningTrap.cpp:39</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#l00240">PenningTrap.cpp:240</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#l00072">PenningTrap.cpp:72</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#l00040">PenningTrap.cpp:40</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#l00041">PenningTrap.hpp:41</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#l00107">PenningTrap.cpp:107</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#l00141">PenningTrap.cpp:141</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#l00148">PenningTrap.cpp:148</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_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#l00104">PenningTrap.cpp:104</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#l00146">PenningTrap.cpp:146</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#l00153">PenningTrap.cpp:153</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#l00211">PenningTrap.cpp:211</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#l00311">PenningTrap.cpp:311</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#l00273">PenningTrap.cpp:273</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#l00039">PenningTrap.hpp:39</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="ttdoc">A 2D vector containing all where is the index of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00047">PenningTrap.hpp:47</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>

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<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> </div>
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">total_force</a>(uint 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="keyword">public</span>:</div>
<div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a> = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> = (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>) / 1000., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> = 500.,</div>
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"> 144</span> </div>
<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(uint i, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a> = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> = (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>) / 1000.,</div>
<div class="line"><a id="l00154" name="l00154"></a><span class="lineno"> 154</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> = 500., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
<div class="line"><a id="l00155" name="l00155"></a><span class="lineno"> 155</span> </div>
<div class="line"><a id="l00164" name="l00164"></a><span class="lineno"> 164</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(std::vector&lt;Particle&gt; <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a> = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>,</div>
<div class="line"><a id="l00165" name="l00165"></a><span class="lineno"> 165</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> = (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>) / 1000., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> = 500., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
<div class="line"><a id="l00166" name="l00166"></a><span class="lineno"> 166</span> </div>
<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">set_pertubation</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V);</div>
<div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span> </div>
<div class="line"><a id="l00180" name="l00180"></a><span class="lineno"> 180</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">total_force_no_interaction</a>(uint i);</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><span class="keyword">public</span>:</div>
<div class="line"><a id="l00150" name="l00150"></a><span class="lineno"> 150</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a> = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> = (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>) / 1000., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> = 500.,</div>
<div class="line"><a id="l00151" name="l00151"></a><span class="lineno"> 151</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
<div class="line"><a id="l00152" name="l00152"></a><span class="lineno"> 152</span> </div>
<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(uint i, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a> = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> = (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>) / 1000.,</div>
<div class="line"><a id="l00162" name="l00162"></a><span class="lineno"> 162</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> = 500., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
<div class="line"><a id="l00163" name="l00163"></a><span class="lineno"> 163</span> </div>
<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(std::vector&lt;Particle&gt; <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a> = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>,</div>
<div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> = (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>) / 1000., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> = 500., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
<div class="line"><a id="l00174" name="l00174"></a><span class="lineno"> 174</span> </div>
<div class="line"><a id="l00180" name="l00180"></a><span class="lineno"> 180</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">set_pertubation</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V);</div>
<div class="line"><a id="l00181" name="l00181"></a><span class="lineno"> 181</span> </div>
<div class="line"><a id="l00186" name="l00186"></a><span class="lineno"> 186</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a> particle);</div>
<div class="line"><a id="l00187" name="l00187"></a><span class="lineno"> 187</span> </div>
<div class="line"><a id="l00193" name="l00193"></a><span class="lineno"> 193</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">evolve_RK4</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> </div>
<div class="line"><a id="l00200" name="l00200"></a><span class="lineno"> 200</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">evolve_forward_euler</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00201" name="l00201"></a><span class="lineno"> 201</span> </div>
<div class="line"><a id="l00212" name="l00212"></a><span class="lineno"> 212</span> <a class="code hl_struct" href="structsimulation.html">simulation_t</a> <a class="code hl_function" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">simulate</a>(<span class="keywordtype">double</span> time, uint steps, std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</span> <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span> </div>
<div class="line"><a id="l00223" name="l00223"></a><span class="lineno"> 223</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(std::string path, <span class="keywordtype">double</span> time, uint steps,</div>
<div class="line"><a id="l00224" name="l00224"></a><span class="lineno"> 224</span> std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
<div class="line"><a id="l00225" name="l00225"></a><span class="lineno"> 225</span> <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00226" name="l00226"></a><span class="lineno"> 226</span> </div>
<div class="line"><a id="l00237" name="l00237"></a><span class="lineno"> 237</span> <span class="keywordtype">double</span> <a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(<span class="keywordtype">double</span> time, uint steps,</div>
<div class="line"><a id="l00238" name="l00238"></a><span class="lineno"> 238</span> std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
<div class="line"><a id="l00239" name="l00239"></a><span class="lineno"> 239</span> <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00240" name="l00240"></a><span class="lineno"> 240</span> </div>
<div class="line"><a id="l00241" name="l00241"></a><span class="lineno"> 241</span>};</div>
<div class="line"><a id="l00242" name="l00242"></a><span class="lineno"> 242</span> </div>
<div class="line"><a id="l00243" name="l00243"></a><span class="lineno"> 243</span><span class="preprocessor">#endif</span></div>
<div class="line"><a id="l00188" name="l00188"></a><span class="lineno"> 188</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
<div class="line"><a id="l00189" name="l00189"></a><span class="lineno"> 189</span> </div>
<div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a> particle);</div>
<div class="line"><a id="l00195" name="l00195"></a><span class="lineno"> 195</span> </div>
<div class="line"><a id="l00201" name="l00201"></a><span class="lineno"> 201</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">evolve_RK4</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00202" name="l00202"></a><span class="lineno"> 202</span> </div>
<div class="line"><a id="l00208" name="l00208"></a><span class="lineno"> 208</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">evolve_forward_euler</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00209" name="l00209"></a><span class="lineno"> 209</span> </div>
<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span> <a class="code hl_struct" href="structsimulation.html">simulation_t</a> <a class="code hl_function" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">simulate</a>(<span class="keywordtype">double</span> time, uint steps, std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"> 221</span> <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> </div>
<div class="line"><a id="l00231" name="l00231"></a><span class="lineno"> 231</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(std::string path, <span class="keywordtype">double</span> time, uint steps,</div>
<div class="line"><a id="l00232" name="l00232"></a><span class="lineno"> 232</span> std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
<div class="line"><a id="l00233" name="l00233"></a><span class="lineno"> 233</span> <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00234" name="l00234"></a><span class="lineno"> 234</span> </div>
<div class="line"><a id="l00245" name="l00245"></a><span class="lineno"> 245</span> <span class="keywordtype">double</span> <a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(<span class="keywordtype">double</span> time, uint steps,</div>
<div class="line"><a id="l00246" name="l00246"></a><span class="lineno"> 246</span> std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
<div class="line"><a id="l00247" name="l00247"></a><span class="lineno"> 247</span> <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00248" name="l00248"></a><span class="lineno"> 248</span> </div>
<div class="line"><a id="l00249" name="l00249"></a><span class="lineno"> 249</span>};</div>
<div class="line"><a id="l00250" name="l00250"></a><span class="lineno"> 250</span> </div>
<div class="line"><a id="l00251" name="l00251"></a><span class="lineno"> 251</span><span class="preprocessor">#endif</span></div>
<div class="ttc" id="aParticle_8hpp_html"><div class="ttname"><a href="Particle_8hpp.html">Particle.hpp</a></div><div class="ttdoc">A class that holds the properties of a particle.</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="aclassPenningTrapTest_html"><div class="ttname"><a href="classPenningTrapTest.html">PenningTrapTest</a></div><div class="ttdoc">Test class for the Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="test__suite_8cpp_source.html#l00023">test_suite.cpp:24</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#l00042">PenningTrap.hpp:42</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#l00037">PenningTrap.hpp:37</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#l00082">PenningTrap.cpp:82</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#l00083">PenningTrap.cpp:83</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="ttdoc">A 2D vector containing all where is the index of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00052">PenningTrap.hpp:52</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#l00095">PenningTrap.cpp:95</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#l00066">PenningTrap.cpp:66</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#l00020">PenningTrap.cpp:20</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#l00058">PenningTrap.cpp:58</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#l00092">PenningTrap.cpp:92</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#l00067">PenningTrap.cpp:67</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#l00171">PenningTrap.cpp:171</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#l00021">PenningTrap.cpp:21</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#l00059">PenningTrap.cpp:59</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a6069f82d8dbc7cadaebd228dbcd95018"><div class="ttname"><a href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap::total_force_no_interaction</a></div><div class="ttdeci">vec3 total_force_no_interaction(uint i)</div><div class="ttdoc">calculate the total force on a particle p_i without interaction</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00112">PenningTrap.cpp:112</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#l00040">PenningTrap.hpp:40</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#l00158">PenningTrap.cpp:158</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#l00166">PenningTrap.cpp:166</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#l00038">PenningTrap.hpp:38</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#l00071">PenningTrap.cpp:71</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#l00039">PenningTrap.cpp:39</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#l00240">PenningTrap.cpp:240</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#l00072">PenningTrap.cpp:72</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#l00040">PenningTrap.cpp:40</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#l00041">PenningTrap.hpp:41</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#l00107">PenningTrap.cpp:107</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#l00141">PenningTrap.cpp:141</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#l00148">PenningTrap.cpp:148</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_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#l00104">PenningTrap.cpp:104</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#l00146">PenningTrap.cpp:146</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#l00153">PenningTrap.cpp:153</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#l00211">PenningTrap.cpp:211</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#l00311">PenningTrap.cpp:311</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#l00273">PenningTrap.cpp:273</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#l00039">PenningTrap.hpp:39</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="ttdoc">A 2D vector containing all where is the index of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00047">PenningTrap.hpp:47</a></div></div>
<div class="ttc" id="aconstants_8hpp_html"><div class="ttname"><a href="constants_8hpp.html">constants.hpp</a></div><div class="ttdoc">Library of constants.</div></div>

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<dt>File <a class="el" href="constants_8hpp.html">constants.hpp</a> </dt>
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<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">total_force</a>(uint i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">total_force_particles</a>(uint i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(std::string path, double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">total_force_no_interaction</a>(uint i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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@ -175,6 +175,9 @@ Private Member Functions</h2></td></tr>
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Private Attributes</h2></td></tr>
@ -264,7 +267,7 @@ Friends</h2></td></tr>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00115">115</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00120">120</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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@ -324,7 +327,7 @@ Friends</h2></td></tr>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00124">124</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00129">129</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00134">134</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00139">139</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00158">158</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00166">166</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00201">201</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00211">211</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00163">163</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00171">171</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00066">66</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00067">67</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00058">58</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00059">59</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00071">71</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00072">72</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00297">297</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00311">311</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00039">39</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00040">40</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00148">148</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00153">153</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00141">141</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00146">146</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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@ -861,7 +864,7 @@ Friends</h2></td></tr>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00228">228</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00240">240</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00107">107</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00104">104</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<dl class="section return"><dt>Returns</dt><dd>vec3 </dd></dl>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00082">82</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00083">83</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a6069f82d8dbc7cadaebd228dbcd95018">&#9670;&#160;</a></span>total_force_no_interaction()</h2>
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<td class="memname"><a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> PenningTrap::total_force_no_interaction </td>
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<p>Sweep of the frequencies from 1.1 to 1.7 using a small time step.
<a href="#details">More...</a></p>
<div class="textblock"><code>#include &lt;cmath&gt;</code><br />
<code>#include &lt;complex&gt;</code><br />
<code>#include &lt;fstream&gt;</code><br />
<code>#include &lt;omp.h&gt;</code><br />
<code>#include &lt;string&gt;</code><br />
<code>#include &lt;vector&gt;</code><br />
<code>#include &quot;<a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>&quot;</code><br />
<code>#include &quot;<a class="el" href="constants_8hpp_source.html">constants.hpp</a>&quot;</code><br />
<code>#include &quot;<a class="el" href="utils_8hpp_source.html">utils.hpp</a>&quot;</code><br />
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Functions</h2></td></tr>
<tr class="memitem:a33d9b1c76c3c80902f89a58b1a6d96ea"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a> ()</td></tr>
<tr class="memdesc:a33d9b1c76c3c80902f89a58b1a6d96ea"><td class="mdescLeft">&#160;</td><td class="mdescRight">Simulate 100 particles over 500 \( \mu s \) using a time dependent potential. <br /></td></tr>
<tr class="separator:a33d9b1c76c3c80902f89a58b1a6d96ea"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac1816f70ec612edc27848ef7f0875fdb"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a> ()</td></tr>
<tr class="memdesc:ac1816f70ec612edc27848ef7f0875fdb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Simulate 100 particles over 500 \( \mu s \) using a time dependent potential. <br /></td></tr>
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<tr class="memitem:ae66f6b31b5ad750f1fe042a706a4e3d4"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="frequency__narrow__sweeps__long_8cpp.html#ae66f6b31b5ad750f1fe042a706a4e3d4">main</a> ()</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Sweep of the frequencies from 1.1 to 1.7 using a small time step. </p>
<dl class="section author"><dt>Author</dt><dd>Cory Alexander Balaton (coryab) </dd>
<dd>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000006">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<p class="definition">Definition in file <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html">frequency_narrow_sweeps_long.cpp</a>.</p>
</div><h2 class="groupheader">Macro Definition Documentation</h2>
<a id="a0240ac851181b84ac374872dc5434ee4" name="a0240ac851181b84ac374872dc5434ee4"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a0240ac851181b84ac374872dc5434ee4">&#9670;&#160;</a></span>N</h2>
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<td class="memname">#define N&#160;&#160;&#160;40000</td>
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<p class="definition">Definition at line <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html#l00025">25</a> of file <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html">frequency_narrow_sweeps_long.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a7b24a37e8ce9d243351bfc9b24945e63">&#9670;&#160;</a></span>PARTICLES</h2>
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<td class="memname">#define PARTICLES&#160;&#160;&#160;100</td>
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<p class="definition">Definition at line <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html#l00024">24</a> of file <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html">frequency_narrow_sweeps_long.cpp</a>.</p>
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<h2 class="groupheader">Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#ae66f6b31b5ad750f1fe042a706a4e3d4">&#9670;&#160;</a></span>main()</h2>
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<td class="memname">int main </td>
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<p class="definition">Definition at line <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html#l00139">139</a> of file <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html">frequency_narrow_sweeps_long.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a33d9b1c76c3c80902f89a58b1a6d96ea">&#9670;&#160;</a></span>potential_resonance_narrow_sweep()</h2>
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<td class="memname">void potential_resonance_narrow_sweep </td>
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<p>Simulate 100 particles over 500 \( \mu s \) using a time dependent potential. </p>
<p>The simulation sweeps over different frequencies in [1., 1.7] MHz. </p>
<p class="definition">Definition at line <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html#l00034">34</a> of file <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html">frequency_narrow_sweeps_long.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ac1816f70ec612edc27848ef7f0875fdb">&#9670;&#160;</a></span>potential_resonance_narrow_sweep_interaction()</h2>
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<td class="memname">void potential_resonance_narrow_sweep_interaction </td>
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<p>Simulate 100 particles over 500 \( \mu s \) using a time dependent potential. </p>
<p>The simulation sweeps over different frequencies in [1., 1.7] MHz. </p>
<p class="definition">Definition at line <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html#l00091">91</a> of file <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html">frequency_narrow_sweeps_long.cpp</a>.</p>
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<a href="frequency__narrow__sweeps__long_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 &lt;cmath&gt;</span></div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="preprocessor">#include &lt;complex&gt;</span></div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include &lt;fstream&gt;</span></div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="preprocessor">#include &lt;omp.h&gt;</span></div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="preprocessor">#include &lt;string&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"> 20</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span><span class="preprocessor">#include &quot;<a class="code" href="constants_8hpp.html">constants.hpp</a>&quot;</span></div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span><span class="preprocessor">#include &quot;<a class="code" href="utils_8hpp.html">utils.hpp</a>&quot;</span></div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> </div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span><span class="preprocessor">#define PARTICLES 100</span></div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span><span class="preprocessor">#define N 40000</span></div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> </div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"><a class="line" href="frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea"> 34</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>()</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span>{</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> <span class="keywordtype">double</span> time = 500.;</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> <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> </div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> <span class="keywordtype">double</span> freq_start = 1.1;</div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> <span class="keywordtype">double</span> freq_end = 1.7;</div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> <span class="keywordtype">double</span> freq_increment = .0005;</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> <span class="keywordtype">size_t</span> freq_iterations =</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> (size_t)((freq_end - freq_start) / freq_increment) + 1;</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"> 46</span> <span class="keywordtype">double</span> res[4][freq_iterations];</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> std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</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> std::ofstream ofile;</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"> 53</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> <span class="comment">// Insert frequencies</span></div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> res[0][i] = freq_start + freq_increment * i;</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> </div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span><span class="preprocessor">#pragma omp parallel</span></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> <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> <span class="comment">// the sweep.</span></div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)PARTICLES);</div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> <span class="comment">// Reset particles and give new time dependent potential.</span></div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> res[i + 1][j] =</div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> }</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> }</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> }</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> </div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> <span class="comment">// Write results to file</span></div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> ofile.open(path + <span class="stringliteral">&quot;narrow_sweep_fine.txt&quot;</span>);</div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</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> ofile.close();</div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span>}</div>
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"><a class="line" href="frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb"> 91</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>()</div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span>{</div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> <span class="keywordtype">double</span> time = 500.;</div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> </div>
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> <span class="keywordtype">double</span> freq_start = 1.1;</div>
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> <span class="keywordtype">double</span> freq_end = 1.7;</div>
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> <span class="keywordtype">double</span> freq_increment = .0005;</div>
<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> <span class="keywordtype">size_t</span> freq_iterations =</div>
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> (size_t)((freq_end - freq_start) / freq_increment) + 1;</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> <span class="keywordtype">double</span> res[4][freq_iterations];</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> std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</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> std::ofstream ofile;</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="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span> res[0][i] = freq_start + freq_increment * i;</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"> 114</span> </div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span><span class="preprocessor">#pragma omp parallel</span></div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> {</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> <span class="comment">// the sweep.</span></div>
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)PARTICLES);</div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
<div class="line"><a id="l00123" name="l00123"></a><span class="lineno"> 123</span> <span class="comment">// Reset particles and give new time dependent potential.</span></div>
<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> res[i + 1][j] = trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N);</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> }</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"> 130</span> <span class="comment">// Write results to file</span></div>
<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> ofile.open(path + <span class="stringliteral">&quot;narrow_sweep_interactions_fine.txt&quot;</span>);</div>
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span> ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> }</div>
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span> ofile.close();</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> </div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span><span class="keywordtype">int</span> main()</div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span>{</div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span> <span class="keywordtype">double</span> start, end;</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"> 143</span> start = omp_get_wtime();</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_function" href="frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>();</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> <a class="code hl_function" href="frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>();</div>
<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"> 148</span> </div>
<div class="line"><a id="l00149" name="l00149"></a><span class="lineno"> 149</span> end = omp_get_wtime();</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> std::cout &lt;&lt; <span class="stringliteral">&quot;Time: &quot;</span> &lt;&lt; end - start &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00152" name="l00152"></a><span class="lineno"> 152</span> </div>
<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</span> <span class="keywordflow">return</span> 0;</div>
<div class="line"><a id="l00154" name="l00154"></a><span class="lineno"> 154</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="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_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#l00153">PenningTrap.cpp:153</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#l00311">PenningTrap.cpp:311</a></div></div>
<div class="ttc" id="aconstants_8hpp_html"><div class="ttname"><a href="constants_8hpp.html">constants.hpp</a></div><div class="ttdoc">Library of constants.</div></div>
<div class="ttc" id="afrequency__narrow__sweeps__long_8cpp_html_a33d9b1c76c3c80902f89a58b1a6d96ea"><div class="ttname"><a href="frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a></div><div class="ttdeci">void potential_resonance_narrow_sweep()</div><div class="ttdoc">Simulate 100 particles over 500 using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="frequency__narrow__sweeps__long_8cpp_source.html#l00034">frequency_narrow_sweeps_long.cpp:34</a></div></div>
<div class="ttc" id="afrequency__narrow__sweeps__long_8cpp_html_ac1816f70ec612edc27848ef7f0875fdb"><div class="ttname"><a href="frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a></div><div class="ttdeci">void potential_resonance_narrow_sweep_interaction()</div><div class="ttdoc">Simulate 100 particles over 500 using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="frequency__narrow__sweeps__long_8cpp_source.html#l00091">frequency_narrow_sweeps_long.cpp:91</a></div></div>
<div class="ttc" id="autils_8hpp_html"><div class="ttname"><a href="utils_8hpp.html">utils.hpp</a></div><div class="ttdoc">Function prototypes and macros that are useful.</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>
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@ -176,6 +176,7 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
<li>test_total_force_particles()&#160;:&#160;<a class="el" href="classPenningTrapTest.html#a68449d508e66205bc8b27fa5f60db508">PenningTrapTest</a></li>
<li>total_force()&#160;:&#160;<a class="el" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap</a></li>
<li>total_force_external()&#160;:&#160;<a class="el" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap</a></li>
<li>total_force_no_interaction()&#160;:&#160;<a class="el" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap</a></li>
<li>total_force_particles()&#160;:&#160;<a class="el" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap</a></li>
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@ -119,6 +119,7 @@ $(document).ready(function(){initNavTree('functions_func.html',''); initResizabl
<li>test_total_force_particles()&#160;:&#160;<a class="el" href="classPenningTrapTest.html#a68449d508e66205bc8b27fa5f60db508">PenningTrapTest</a></li>
<li>total_force()&#160;:&#160;<a class="el" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap</a></li>
<li>total_force_external()&#160;:&#160;<a class="el" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap</a></li>
<li>total_force_no_interaction()&#160;:&#160;<a class="el" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap</a></li>
<li>total_force_particles()&#160;:&#160;<a class="el" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap</a></li>
<li>v_func()&#160;:&#160;<a class="el" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap</a></li>
<li>write_simulation_to_dir()&#160;:&#160;<a class="el" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap</a></li>

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<h3><a id="index_p" name="index_p"></a>- p -</h3><ul>
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<li>p2&#160;:&#160;<a class="el" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">main.cpp</a></li>
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@ -126,6 +126,16 @@ Operating systems</h2>
</li>
</ul>
<h2><a class="anchor" id="autotoc_md3"></a>
Tools</h2>
<ul>
<li>Profiling<ul>
<li><a href="https://ftp.gnu.org/old-gnu/Manuals/gprof-2.9.1/html_mono/gprof.html">gprof</a></li>
<li><a href="https://www.scalasca.org/">scalasca</a></li>
<li><a href="https://www.vi-hps.org/projects/score-p">score-p</a></li>
</ul>
</li>
</ul>
<h2><a class="anchor" id="autotoc_md4"></a>
Libraries</h2>
<ul>
<li>Python<ul>
@ -139,30 +149,65 @@ Libraries</h2>
</ul>
</li>
</ul>
<h1><a class="anchor" id="autotoc_md4"></a>
<h1><a class="anchor" id="autotoc_md5"></a>
Compiling</h1>
<p>Compiling is as easy as running this command while being inside the src directory:</p>
<div class="fragment"><div class="line">make</div>
</div><!-- fragment --><h1><a class="anchor" id="autotoc_md5"></a>
</div><!-- fragment --><h1><a class="anchor" id="autotoc_md6"></a>
Running programs</h1>
<h2><a class="anchor" id="autotoc_md6"></a>
<h2><a class="anchor" id="autotoc_md7"></a>
C++ binaries</h2>
<p>To run <b>main</b> or <b>test_suite</b>, just run this command while being inside src:</p>
<div class="fragment"><div class="line">./&lt;program-name&gt;</div>
</div><!-- fragment --><h2><a class="anchor" id="autotoc_md7"></a>
</div><!-- fragment --><h2><a class="anchor" id="autotoc_md8"></a>
Python scripts</h2>
<h3><a class="anchor" id="autotoc_md8"></a>
<h3><a class="anchor" id="autotoc_md9"></a>
Install libraries</h3>
<p>Before running the scripts, make sure that all libraries are installed. Using pip, you can install all requirements like this:</p>
<div class="fragment"><div class="line">pip install -r requirements.txt</div>
</div><!-- fragment --><p>This recursively install all the packages that are listed in <b>requirements.txt</b>.</p>
<h3><a class="anchor" id="autotoc_md9"></a>
<h3><a class="anchor" id="autotoc_md10"></a>
Running scripts</h3>
<p>For the Python scripts, run them from the src directory like this:</p>
<div class="fragment"><div class="line">python scripts/&lt;script-name&gt;</div>
</div><!-- fragment --><p>If you have any problems running the scripts, you might have to run this instead:</p>
<div class="fragment"><div class="line">python3 scripts/&lt;script-name&gt;</div>
</div><!-- fragment --><h1><a class="anchor" id="autotoc_md10"></a>
</div><!-- fragment --><h2><a class="anchor" id="autotoc_md11"></a>
Batch system</h2>
<p>For the <b>frequency_narrow_sweeps_long</b> program, the is a script called <b>job.script</b> that comes along with it. This is to be able to run it on a batch system using Slurm if you have access to one. This is the recommended way to use this program as it takes approximately 90 minutes to complete when using 16 cores.</p>
<p>If you happen to have such a system available to you, then you should clone this repo on that system, then compile it by running:</p>
<div class="fragment"><div class="line">make frequency_narrow_sweeps_long</div>
</div><!-- fragment --><p>You might have to load the Armadillo library before compiling.</p>
<p>After compiling, you can schedule it by running:</p>
<div class="fragment"><div class="line">sbatch job.script</div>
</div><!-- fragment --><h1><a class="anchor" id="autotoc_md12"></a>
Performance</h1>
<p>This section aims to give an idea to the time it takes for the program to run so that you know a bit what to expect if you decide to run it for yourself.</p>
<h2><a class="anchor" id="autotoc_md13"></a>
CPU</h2>
<p>The times mentioned here are times achieved on a computer with these specifications:</p>
<ul>
<li>CPU model<ul>
<li>Intel i7-9850H</li>
</ul>
</li>
<li>Threads<ul>
<li>12</li>
</ul>
</li>
<li>Clock speed<ul>
<li>4.6GHz</li>
</ul>
</li>
</ul>
<h2><a class="anchor" id="autotoc_md14"></a>
Times</h2>
<p>All times mentioned use the <b>evolve_RK4</b> method.</p>
<p>Running a simulation with 100 particles without particle interactions over 40000 steps takes around 1.8 seconds. With particle interactions, it takes around 4.8 seconds.</p>
<p><b>potential_resonance_wide_sweep</b> takes around 56 seconds to complete.</p>
<p><b>potential_resonance_narrow_sweep</b> takes around 172 seconds to complete.</p>
<p><b>potential_resonance_narrow_sweep_interaction</b> takes around 936 seconds to complete.</p>
<h1><a class="anchor" id="autotoc_md15"></a>
Credits</h1>
<p>The Doxygen theme used here is <a href="https://github.com/jothepro/doxygen-awesome-css">doxygen-awesome-css</a>. </p>
</div></div><!-- PageDoc -->

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@ -173,7 +173,7 @@ Variables</h2></td></tr>
<dd>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000006">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000007">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<p class="definition">Definition in file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
</div><h2 class="groupheader">Macro Definition Documentation</h2>
@ -254,7 +254,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00309">309</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00314">314</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
</div>
</div>
@ -276,7 +276,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<p>Simulate 100 particles over 500 \( \mu s \) using a time dependent potential. </p>
<p>The simulation sweeps over different frequencies in [1., 1.7] MHz. </p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00206">206</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00209">209</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
</div>
</div>
@ -298,7 +298,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<p>Simulate 100 particles over 500 \( \mu s \) using a time dependent potential. </p>
<p>The simulation sweeps over different frequencies in [1., 1.7] MHz. </p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00262">262</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00266">266</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
</div>
</div>
@ -320,7 +320,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<p>Simulate 100 particles over 500 \( \mu s \) using a time dependent potential. </p>
<p>The simulation sweeps over different frequencies in [0.2, 2.5] MHz. </p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00149">149</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00152">152</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
</div>
</div>
@ -341,7 +341,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<p>Simulate 100 particles over 50 \( \mu s \). </p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00132">132</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00134">134</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
</div>
</div>
@ -362,7 +362,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<p>Simulate a single particle over the period of 50 \( \mu s \). </p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00054">54</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00055">55</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
</div>
</div>
@ -383,7 +383,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<p>Simulate a single particle over 50 \( \mu s \) using different amount of steps and different methods. </p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00087">87</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00088">88</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
</div>
</div>
@ -404,7 +404,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<p>Simulate 2 particles over the period of 50 \( \mu s \) with and without particle interactions. </p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00069">69</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00070">70</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
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@ -128,317 +128,367 @@ $(document).ready(function(){initNavTree('main_8cpp_source.html',''); initResiza
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> <span class="keywordtype">double</span> w_n = (w_0 - std::sqrt(w_0 * w_0 - 2. * w_z2)) / 2.;</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> <span class="keywordtype">double</span> A_p = (25. + w_n * 20.) / (w_n - w_p);</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> <span class="keywordtype">double</span> A_n = -(25. + w_p * 20.) / (w_n - w_p);</div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> std::complex&lt;double&gt; f =</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> A_p * std::exp(std::complex&lt;double&gt;(0., -w_p * t))</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> + A_n * std::exp(std::complex&lt;double&gt;(0., -w_n * t));</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res{std::real(f), std::imag(f), 20. * std::cos(std::sqrt(w_z2) * t)};</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> <span class="keywordflow">return</span> res;</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="l00054" name="l00054"></a><span class="lineno"><a class="line" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6"> 54</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a>()</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span>{</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> <span class="comment">// Initialize trap with particle 1</span></div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>});</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> </div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></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> <span class="comment">// Simulate and write results to file</span></div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> trap.<a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(<span class="stringliteral">&quot;output/simulate_single_particle&quot;</span>, time, N,</div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</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> </div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"><a class="line" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1"> 69</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a>()</div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span>{</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> <span class="comment">// Initialize traps with particles</span></div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap_no_interaction(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>, <a class="code hl_variable" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">p2</a>});</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap_with_interaction(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>, <a class="code hl_variable" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">p2</a>});</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> </div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> <span class="comment">// Simulate and write results to files</span></div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> trap_no_interaction.<a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(</div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> <span class="stringliteral">&quot;output/simulate_2_particles/no_interaction&quot;</span>, time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> trap_with_interaction.write_simulation_to_dir(</div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> <span class="stringliteral">&quot;output/simulate_2_particles/with_interaction&quot;</span>, time, N);</div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span>}</div>
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"><a class="line" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2"> 87</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a>()</div>
<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span>{</div>
<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> </div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> std::ofstream ofile;</div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> </div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> <span class="comment">// Calculate relative error for RK4</span></div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> std::string path = <span class="stringliteral">&quot;output/relative_error/RK4/&quot;</span>;</div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; 4; i++) {</div>
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> <span class="keywordtype">int</span> steps = 4000 * std::pow(2, i);</div>
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> <span class="keywordtype">double</span> dt = time / (double)steps;</div>
<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> ofile.open(path + std::to_string(steps) + <span class="stringliteral">&quot;_steps.txt&quot;</span>);</div>
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>});</div>
<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res = trap.simulate(time, steps, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; steps; i++) {</div>
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> ofile &lt;&lt; arma::norm(res.r_vecs[0][i]</div>
<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> - <a class="code hl_function" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a>(dt * i))</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</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> ofile.close();</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> </div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> <span class="comment">// Calculate relative error for forward Euler</span></div>
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span> path = <span class="stringliteral">&quot;output/relative_error/euler/&quot;</span>;</div>
<div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; 4; i++) {</div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> <span class="keywordtype">int</span> steps = 4000 * std::pow(2, i);</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> <span class="keywordtype">double</span> dt = time / (double)steps;</div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> ofile.open(path + std::to_string(steps) + <span class="stringliteral">&quot;_steps.txt&quot;</span>);</div>
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>});</div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span> <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res = trap.simulate(time, steps, <span class="stringliteral">&quot;euler&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; steps; i++) {</div>
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> ofile &lt;&lt; arma::norm(res.r_vecs[0][i]</div>
<div class="line"><a id="l00123" name="l00123"></a><span class="lineno"> 123</span> - <a class="code hl_function" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a>(dt * i))</div>
<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> }</div>
<div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</span> ofile.close();</div>
<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span> }</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="l00132" name="l00132"></a><span class="lineno"><a class="line" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513"> 132</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a>()</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> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((<span class="keywordtype">unsigned</span>)100);</div>
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> </div>
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span> <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> std::cout &lt;&lt; A_p &lt;&lt; <span class="stringliteral">&quot;,&quot;</span> &lt;&lt; A_n &lt;&lt; std::endl;</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> std::complex&lt;double&gt; f =</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> A_p * std::exp(std::complex&lt;double&gt;(0., -w_p * t))</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> + A_n * std::exp(std::complex&lt;double&gt;(0., -w_n * t));</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res{std::real(f), std::imag(f), 20. * std::cos(std::sqrt(w_z2) * t)};</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> <span class="keywordflow">return</span> res;</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="l00055" name="l00055"></a><span class="lineno"><a class="line" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6"> 55</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a>()</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span>{</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> <span class="comment">// Initialize trap with particle 1</span></div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>});</div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> </div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</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> <span class="comment">// Simulate and write results to file</span></div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> trap.<a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(<span class="stringliteral">&quot;output/simulate_single_particle&quot;</span>, time, N,</div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span>}</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"><a class="line" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1"> 70</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a>()</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span>{</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> <span class="comment">// Initialize traps with particles</span></div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap_no_interaction(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>, <a class="code hl_variable" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">p2</a>});</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap_with_interaction(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>, <a class="code hl_variable" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">p2</a>});</div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> </div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> </div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> <span class="comment">// Simulate and write results to files</span></div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> trap_no_interaction.<a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(</div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> <span class="stringliteral">&quot;output/simulate_2_particles/no_interaction&quot;</span>, time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> trap_with_interaction.write_simulation_to_dir(</div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> <span class="stringliteral">&quot;output/simulate_2_particles/with_interaction&quot;</span>, time, N);</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> </div>
<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"><a class="line" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2"> 88</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a>()</div>
<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span>{</div>
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> </div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> std::ofstream ofile;</div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> <span class="comment">// Calculate relative error for RK4</span></div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> std::string path = <span class="stringliteral">&quot;output/relative_error/RK4/&quot;</span>;</div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span><span class="preprocessor">#pragma omp parallel for private(ofile)</span></div>
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; 4; i++) {</div>
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> <span class="keywordtype">int</span> steps = 4000 * std::pow(2, i);</div>
<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> std::cout &lt;&lt; steps &lt;&lt; std::endl;</div>
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> <span class="keywordtype">double</span> dt = time / (double)steps;</div>
<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> ofile.open(path + std::to_string(steps) + <span class="stringliteral">&quot;_steps.txt&quot;</span>);</div>
<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>});</div>
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res = trap.simulate(time, steps, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; steps; i++) {</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> ofile &lt;&lt; arma::norm(res.r_vecs[0][i]</div>
<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</span> - <a class="code hl_function" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a>(dt * i))</div>
<div class="line"><a id="l00108" name="l00108"></a><span class="lineno"> 108</span> &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</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> ofile.close();</div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> }</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> <span class="comment">// Calculate relative error for forward Euler</span></div>
<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span> path = <span class="stringliteral">&quot;output/relative_error/euler/&quot;</span>;</div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span><span class="preprocessor">#pragma omp parallel for private(ofile)</span></div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; 4; i++) {</div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> <span class="keywordtype">int</span> steps = 4000 * std::pow(2, i);</div>
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> <span class="keywordtype">double</span> dt = time / (double)steps;</div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span> ofile.open(path + std::to_string(steps) + <span class="stringliteral">&quot;_steps.txt&quot;</span>);</div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>});</div>
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res = trap.simulate(time, steps, <span class="stringliteral">&quot;euler&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00123" name="l00123"></a><span class="lineno"> 123</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; steps; i++) {</div>
<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> ofile &lt;&lt; arma::norm(res.r_vecs[0][i]</div>
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> - <a class="code hl_function" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a>(dt * i))</div>
<div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</span> &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span> }</div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> ofile.close();</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"> 130</span>}</div>
<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> </div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"><a class="line" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513"> 134</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a>()</div>
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span>{</div>
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((<span class="keywordtype">unsigned</span>)100);</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> trap.<a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(<span class="stringliteral">&quot;output/simulate_100_particles&quot;</span>, time, N,</div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span>}</div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span> </div>
<div class="line"><a id="l00149" name="l00149"></a><span class="lineno"><a class="line" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1"> 149</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a>()</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> <span class="keywordtype">double</span> time = 500.;</div>
<div class="line"><a id="l00152" name="l00152"></a><span class="lineno"> 152</span> </div>
<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</span> <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</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"> 155</span> <span class="keywordtype">double</span> freq_start = .2;</div>
<div class="line"><a id="l00156" name="l00156"></a><span class="lineno"> 156</span> <span class="keywordtype">double</span> freq_end = 2.5;</div>
<div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</span> <span class="keywordtype">double</span> freq_increment = .02;</div>
<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"> 158</span> <span class="keywordtype">size_t</span> freq_iterations =</div>
<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span> (size_t)((freq_end - freq_start) / freq_increment) + 1;</div>
<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> </div>
<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span> <span class="keywordtype">double</span> res[4][freq_iterations];</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"> 163</span> std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
<div class="line"><a id="l00164" name="l00164"></a><span class="lineno"> 164</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> </div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> <span class="comment">// trap.write_simulation_to_dir(&quot;output/simulate_100_particles&quot;, time, N,</span></div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span> <span class="comment">//&quot;rk4&quot;, false);</span></div>
<div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span> trap.<a class="code hl_function" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">simulate</a>(time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">true</span>);</div>
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span>}</div>
<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"> 144</span> </div>
<div class="line"><a id="l00152" name="l00152"></a><span class="lineno"><a class="line" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1"> 152</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a>()</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> <span class="keywordtype">double</span> time = 500.;</div>
<div class="line"><a id="l00155" name="l00155"></a><span class="lineno"> 155</span> </div>
<div class="line"><a id="l00156" name="l00156"></a><span class="lineno"> 156</span> <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
<div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</span> </div>
<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"> 158</span> <span class="keywordtype">double</span> freq_start = .2;</div>
<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span> <span class="keywordtype">double</span> freq_end = 2.5;</div>
<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> <span class="keywordtype">double</span> freq_increment = .02;</div>
<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span> <span class="keywordtype">size_t</span> freq_iterations =</div>
<div class="line"><a id="l00162" name="l00162"></a><span class="lineno"> 162</span> (size_t)((freq_end - freq_start) / freq_increment) + 1;</div>
<div class="line"><a id="l00163" name="l00163"></a><span class="lineno"> 163</span> </div>
<div class="line"><a id="l00164" name="l00164"></a><span class="lineno"> 164</span> <span class="keywordtype">double</span> res[4][freq_iterations];</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::ofstream ofile;</div>
<div class="line"><a id="l00167" name="l00167"></a><span class="lineno"> 167</span> </div>
<div class="line"><a id="l00168" name="l00168"></a><span class="lineno"> 168</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00169" name="l00169"></a><span class="lineno"> 169</span> <span class="comment">// Insert frequencies</span></div>
<div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</span> res[0][i] = freq_start + freq_increment * i;</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> </div>
<div class="line"><a id="l00174" name="l00174"></a><span class="lineno"> 174</span><span class="preprocessor">#pragma omp parallel</span></div>
<div class="line"><a id="l00175" name="l00175"></a><span class="lineno"> 175</span> {</div>
<div class="line"><a id="l00176" name="l00176"></a><span class="lineno"> 176</span> <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
<div class="line"><a id="l00177" name="l00177"></a><span class="lineno"> 177</span> <span class="comment">// the sweep.</span></div>
<div class="line"><a id="l00178" name="l00178"></a><span class="lineno"> 178</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)100);</div>
<div class="line"><a id="l00179" name="l00179"></a><span class="lineno"> 179</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
<div class="line"><a id="l00180" name="l00180"></a><span class="lineno"> 180</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
<div class="line"><a id="l00181" name="l00181"></a><span class="lineno"> 181</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
<div class="line"><a id="l00182" name="l00182"></a><span class="lineno"> 182</span> <span class="comment">// Reset particles and give new time dependent potential.</span></div>
<div class="line"><a id="l00183" name="l00183"></a><span class="lineno"> 183</span> trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
<div class="line"><a id="l00184" name="l00184"></a><span class="lineno"> 184</span> res[i + 1][j] =</div>
<div class="line"><a id="l00185" name="l00185"></a><span class="lineno"> 185</span> trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00186" name="l00186"></a><span class="lineno"> 186</span> }</div>
<div class="line"><a id="l00187" name="l00187"></a><span class="lineno"> 187</span> }</div>
<div class="line"><a id="l00188" name="l00188"></a><span class="lineno"> 188</span> }</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> <span class="comment">// Write results to file</span></div>
<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span> ofile.open(path + <span class="stringliteral">&quot;wide_sweep.txt&quot;</span>);</div>
<div class="line"><a id="l00192" name="l00192"></a><span class="lineno"> 192</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00193" name="l00193"></a><span class="lineno"> 193</span> ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
<div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
<div class="line"><a id="l00195" name="l00195"></a><span class="lineno"> 195</span> }</div>
<div class="line"><a id="l00196" name="l00196"></a><span class="lineno"> 196</span> ofile.close();</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> </div>
<div class="line"><a id="l00206" name="l00206"></a><span class="lineno"><a class="line" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea"> 206</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>()</div>
<div class="line"><a id="l00207" name="l00207"></a><span class="lineno"> 207</span>{</div>
<div class="line"><a id="l00208" name="l00208"></a><span class="lineno"> 208</span> <span class="keywordtype">double</span> time = 500.;</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="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
<div class="line"><a id="l00211" name="l00211"></a><span class="lineno"> 211</span> </div>
<div class="line"><a id="l00212" name="l00212"></a><span class="lineno"> 212</span> <span class="keywordtype">double</span> freq_start = 1.;</div>
<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</span> <span class="keywordtype">double</span> freq_end = 1.7;</div>
<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span> <span class="keywordtype">double</span> freq_increment = .002;</div>
<div class="line"><a id="l00215" name="l00215"></a><span class="lineno"> 215</span> <span class="keywordtype">size_t</span> freq_iterations = (size_t)((freq_end - freq_start) / freq_increment);</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="keywordtype">double</span> res[4][freq_iterations];</div>
<div class="line"><a id="l00218" name="l00218"></a><span class="lineno"> 218</span> </div>
<div class="line"><a id="l00219" name="l00219"></a><span class="lineno"> 219</span> std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"> 221</span> </div>
<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> std::ofstream ofile;</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><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00225" name="l00225"></a><span class="lineno"> 225</span> <span class="comment">// Insert frequencies</span></div>
<div class="line"><a id="l00226" name="l00226"></a><span class="lineno"> 226</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00227" name="l00227"></a><span class="lineno"> 227</span> res[0][i] = freq_start + freq_increment * i;</div>
<div class="line"><a id="l00228" name="l00228"></a><span class="lineno"> 228</span> }</div>
<div class="line"><a id="l00229" name="l00229"></a><span class="lineno"> 229</span> </div>
<div class="line"><a id="l00230" name="l00230"></a><span class="lineno"> 230</span><span class="preprocessor">#pragma omp parallel</span></div>
<div class="line"><a id="l00231" name="l00231"></a><span class="lineno"> 231</span> {</div>
<div class="line"><a id="l00232" name="l00232"></a><span class="lineno"> 232</span> <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
<div class="line"><a id="l00233" name="l00233"></a><span class="lineno"> 233</span> <span class="comment">// the sweep.</span></div>
<div class="line"><a id="l00234" name="l00234"></a><span class="lineno"> 234</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)100);</div>
<div class="line"><a id="l00235" name="l00235"></a><span class="lineno"> 235</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
<div class="line"><a id="l00236" name="l00236"></a><span class="lineno"> 236</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
<div class="line"><a id="l00237" name="l00237"></a><span class="lineno"> 237</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
<div class="line"><a id="l00238" name="l00238"></a><span class="lineno"> 238</span> <span class="comment">// Reset particles and give new time dependent potential.</span></div>
<div class="line"><a id="l00239" name="l00239"></a><span class="lineno"> 239</span> trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
<div class="line"><a id="l00240" name="l00240"></a><span class="lineno"> 240</span> res[i + 1][j] =</div>
<div class="line"><a id="l00241" name="l00241"></a><span class="lineno"> 241</span> trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00242" name="l00242"></a><span class="lineno"> 242</span> }</div>
<div class="line"><a id="l00243" name="l00243"></a><span class="lineno"> 243</span> }</div>
<div class="line"><a id="l00244" name="l00244"></a><span class="lineno"> 244</span> }</div>
<div class="line"><a id="l00245" name="l00245"></a><span class="lineno"> 245</span> </div>
<div class="line"><a id="l00246" name="l00246"></a><span class="lineno"> 246</span> <span class="comment">// Write results to file</span></div>
<div class="line"><a id="l00247" name="l00247"></a><span class="lineno"> 247</span> ofile.open(path + <span class="stringliteral">&quot;narrow_sweep.txt&quot;</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> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00249" name="l00249"></a><span class="lineno"> 249</span> ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
<div class="line"><a id="l00250" name="l00250"></a><span class="lineno"> 250</span> &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
<div class="line"><a id="l00251" name="l00251"></a><span class="lineno"> 251</span> }</div>
<div class="line"><a id="l00252" name="l00252"></a><span class="lineno"> 252</span> ofile.close();</div>
<div class="line"><a id="l00253" name="l00253"></a><span class="lineno"> 253</span>}</div>
<div class="line"><a id="l00254" name="l00254"></a><span class="lineno"> 254</span> </div>
<div class="line"><a id="l00262" name="l00262"></a><span class="lineno"><a class="line" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb"> 262</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>()</div>
<div class="line"><a id="l00263" name="l00263"></a><span class="lineno"> 263</span>{</div>
<div class="line"><a id="l00264" name="l00264"></a><span class="lineno"> 264</span> <span class="keywordtype">double</span> time = 500.;</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="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
<div class="line"><a id="l00267" name="l00267"></a><span class="lineno"> 267</span> </div>
<div class="line"><a id="l00268" name="l00268"></a><span class="lineno"> 268</span> <span class="keywordtype">double</span> freq_start = 1.;</div>
<div class="line"><a id="l00269" name="l00269"></a><span class="lineno"> 269</span> <span class="keywordtype">double</span> freq_end = 1.7;</div>
<div class="line"><a id="l00270" name="l00270"></a><span class="lineno"> 270</span> <span class="keywordtype">double</span> freq_increment = .002;</div>
<div class="line"><a id="l00271" name="l00271"></a><span class="lineno"> 271</span> <span class="keywordtype">size_t</span> freq_iterations = (size_t)((freq_end - freq_start) / freq_increment);</div>
<div class="line"><a id="l00272" name="l00272"></a><span class="lineno"> 272</span> </div>
<div class="line"><a id="l00273" name="l00273"></a><span class="lineno"> 273</span> <span class="keywordtype">double</span> res[4][freq_iterations];</div>
<div class="line"><a id="l00274" name="l00274"></a><span class="lineno"> 274</span> </div>
<div class="line"><a id="l00275" name="l00275"></a><span class="lineno"> 275</span> std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
<div class="line"><a id="l00276" name="l00276"></a><span class="lineno"> 276</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
<div class="line"><a id="l00166" name="l00166"></a><span class="lineno"> 166</span> std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
<div class="line"><a id="l00167" name="l00167"></a><span class="lineno"> 167</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</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> std::ofstream ofile;</div>
<div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> </div>
<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> <span class="comment">// Insert frequencies</span></div>
<div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00174" name="l00174"></a><span class="lineno"> 174</span> res[0][i] = freq_start + freq_increment * i;</div>
<div class="line"><a id="l00175" name="l00175"></a><span class="lineno"> 175</span> }</div>
<div class="line"><a id="l00176" name="l00176"></a><span class="lineno"> 176</span> </div>
<div class="line"><a id="l00177" name="l00177"></a><span class="lineno"> 177</span><span class="preprocessor">#pragma omp parallel</span></div>
<div class="line"><a id="l00178" name="l00178"></a><span class="lineno"> 178</span> {</div>
<div class="line"><a id="l00179" name="l00179"></a><span class="lineno"> 179</span> <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
<div class="line"><a id="l00180" name="l00180"></a><span class="lineno"> 180</span> <span class="comment">// the sweep.</span></div>
<div class="line"><a id="l00181" name="l00181"></a><span class="lineno"> 181</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)100);</div>
<div class="line"><a id="l00182" name="l00182"></a><span class="lineno"> 182</span><span class="preprocessor">#pragma omp for collapse(2)</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; 3; i++) {</div>
<div class="line"><a id="l00184" name="l00184"></a><span class="lineno"> 184</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
<div class="line"><a id="l00185" name="l00185"></a><span class="lineno"> 185</span> <span class="comment">// Reset particles and give new time dependent potential.</span></div>
<div class="line"><a id="l00186" name="l00186"></a><span class="lineno"> 186</span> trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
<div class="line"><a id="l00187" name="l00187"></a><span class="lineno"> 187</span> res[i + 1][j] =</div>
<div class="line"><a id="l00188" name="l00188"></a><span class="lineno"> 188</span> trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</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> }</div>
<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span> }</div>
<div class="line"><a id="l00192" name="l00192"></a><span class="lineno"> 192</span> </div>
<div class="line"><a id="l00193" name="l00193"></a><span class="lineno"> 193</span> <span class="comment">// Write results to file</span></div>
<div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> ofile.open(path + <span class="stringliteral">&quot;wide_sweep.txt&quot;</span>);</div>
<div class="line"><a id="l00195" name="l00195"></a><span class="lineno"> 195</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00196" name="l00196"></a><span class="lineno"> 196</span> ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
<div class="line"><a id="l00197" name="l00197"></a><span class="lineno"> 197</span> &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
<div class="line"><a id="l00198" name="l00198"></a><span class="lineno"> 198</span> }</div>
<div class="line"><a id="l00199" name="l00199"></a><span class="lineno"> 199</span> ofile.close();</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"> 201</span> </div>
<div class="line"><a id="l00209" name="l00209"></a><span class="lineno"><a class="line" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea"> 209</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>()</div>
<div class="line"><a id="l00210" name="l00210"></a><span class="lineno"> 210</span>{</div>
<div class="line"><a id="l00211" name="l00211"></a><span class="lineno"> 211</span> <span class="keywordtype">double</span> time = 500.;</div>
<div class="line"><a id="l00212" name="l00212"></a><span class="lineno"> 212</span> </div>
<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</span> <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span> </div>
<div class="line"><a id="l00215" name="l00215"></a><span class="lineno"> 215</span> <span class="keywordtype">double</span> freq_start = 1.1;</div>
<div class="line"><a id="l00216" name="l00216"></a><span class="lineno"> 216</span> <span class="keywordtype">double</span> freq_end = 1.7;</div>
<div class="line"><a id="l00217" name="l00217"></a><span class="lineno"> 217</span> <span class="keywordtype">double</span> freq_increment = .002;</div>
<div class="line"><a id="l00218" name="l00218"></a><span class="lineno"> 218</span> <span class="keywordtype">size_t</span> freq_iterations =</div>
<div class="line"><a id="l00219" name="l00219"></a><span class="lineno"> 219</span> (size_t)((freq_end - freq_start) / freq_increment) + 1;</div>
<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span> </div>
<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"> 221</span> <span class="keywordtype">double</span> res[4][freq_iterations];</div>
<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> </div>
<div class="line"><a id="l00223" name="l00223"></a><span class="lineno"> 223</span> std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
<div class="line"><a id="l00224" name="l00224"></a><span class="lineno"> 224</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
<div class="line"><a id="l00225" name="l00225"></a><span class="lineno"> 225</span> </div>
<div class="line"><a id="l00226" name="l00226"></a><span class="lineno"> 226</span> std::ofstream ofile;</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"> 228</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00229" name="l00229"></a><span class="lineno"> 229</span> <span class="comment">// Insert frequencies</span></div>
<div class="line"><a id="l00230" name="l00230"></a><span class="lineno"> 230</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00231" name="l00231"></a><span class="lineno"> 231</span> res[0][i] = freq_start + freq_increment * i;</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> </div>
<div class="line"><a id="l00234" name="l00234"></a><span class="lineno"> 234</span><span class="preprocessor">#pragma omp parallel</span></div>
<div class="line"><a id="l00235" name="l00235"></a><span class="lineno"> 235</span> {</div>
<div class="line"><a id="l00236" name="l00236"></a><span class="lineno"> 236</span> <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
<div class="line"><a id="l00237" name="l00237"></a><span class="lineno"> 237</span> <span class="comment">// the sweep.</span></div>
<div class="line"><a id="l00238" name="l00238"></a><span class="lineno"> 238</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)100);</div>
<div class="line"><a id="l00239" name="l00239"></a><span class="lineno"> 239</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
<div class="line"><a id="l00240" name="l00240"></a><span class="lineno"> 240</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
<div class="line"><a id="l00241" name="l00241"></a><span class="lineno"> 241</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
<div class="line"><a id="l00242" name="l00242"></a><span class="lineno"> 242</span> <span class="comment">// Reset particles and give new time dependent potential.</span></div>
<div class="line"><a id="l00243" name="l00243"></a><span class="lineno"> 243</span> trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
<div class="line"><a id="l00244" name="l00244"></a><span class="lineno"> 244</span> res[i + 1][j] =</div>
<div class="line"><a id="l00245" name="l00245"></a><span class="lineno"> 245</span> trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</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> }</div>
<div class="line"><a id="l00249" name="l00249"></a><span class="lineno"> 249</span> </div>
<div class="line"><a id="l00250" name="l00250"></a><span class="lineno"> 250</span> <span class="comment">// Write results to file</span></div>
<div class="line"><a id="l00251" name="l00251"></a><span class="lineno"> 251</span> ofile.open(path + <span class="stringliteral">&quot;narrow_sweep.txt&quot;</span>);</div>
<div class="line"><a id="l00252" name="l00252"></a><span class="lineno"> 252</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00253" name="l00253"></a><span class="lineno"> 253</span> ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
<div class="line"><a id="l00254" name="l00254"></a><span class="lineno"> 254</span> &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</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> ofile.close();</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="l00266" name="l00266"></a><span class="lineno"><a class="line" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb"> 266</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>()</div>
<div class="line"><a id="l00267" name="l00267"></a><span class="lineno"> 267</span>{</div>
<div class="line"><a id="l00268" name="l00268"></a><span class="lineno"> 268</span> <span class="keywordtype">double</span> time = 500.;</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> <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
<div class="line"><a id="l00271" name="l00271"></a><span class="lineno"> 271</span> </div>
<div class="line"><a id="l00272" name="l00272"></a><span class="lineno"> 272</span> <span class="keywordtype">double</span> freq_start = 1.1;</div>
<div class="line"><a id="l00273" name="l00273"></a><span class="lineno"> 273</span> <span class="keywordtype">double</span> freq_end = 1.7;</div>
<div class="line"><a id="l00274" name="l00274"></a><span class="lineno"> 274</span> <span class="keywordtype">double</span> freq_increment = .002;</div>
<div class="line"><a id="l00275" name="l00275"></a><span class="lineno"> 275</span> <span class="keywordtype">size_t</span> freq_iterations =</div>
<div class="line"><a id="l00276" name="l00276"></a><span class="lineno"> 276</span> (size_t)((freq_end - freq_start) / freq_increment) + 1;</div>
<div class="line"><a id="l00277" name="l00277"></a><span class="lineno"> 277</span> </div>
<div class="line"><a id="l00278" name="l00278"></a><span class="lineno"> 278</span> std::ofstream ofile;</div>
<div class="line"><a id="l00278" name="l00278"></a><span class="lineno"> 278</span> <span class="keywordtype">double</span> res[4][freq_iterations];</div>
<div class="line"><a id="l00279" name="l00279"></a><span class="lineno"> 279</span> </div>
<div class="line"><a id="l00280" name="l00280"></a><span class="lineno"> 280</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00281" name="l00281"></a><span class="lineno"> 281</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00282" name="l00282"></a><span class="lineno"> 282</span> res[0][i] = freq_start + freq_increment * i;</div>
<div class="line"><a id="l00283" name="l00283"></a><span class="lineno"> 283</span> }</div>
<div class="line"><a id="l00280" name="l00280"></a><span class="lineno"> 280</span> std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
<div class="line"><a id="l00281" name="l00281"></a><span class="lineno"> 281</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
<div class="line"><a id="l00282" name="l00282"></a><span class="lineno"> 282</span> </div>
<div class="line"><a id="l00283" name="l00283"></a><span class="lineno"> 283</span> std::ofstream ofile;</div>
<div class="line"><a id="l00284" name="l00284"></a><span class="lineno"> 284</span> </div>
<div class="line"><a id="l00285" name="l00285"></a><span class="lineno"> 285</span><span class="preprocessor">#pragma omp parallel</span></div>
<div class="line"><a id="l00286" name="l00286"></a><span class="lineno"> 286</span> {</div>
<div class="line"><a id="l00287" name="l00287"></a><span class="lineno"> 287</span> <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
<div class="line"><a id="l00288" name="l00288"></a><span class="lineno"> 288</span> <span class="comment">// the sweep.</span></div>
<div class="line"><a id="l00289" name="l00289"></a><span class="lineno"> 289</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)100);</div>
<div class="line"><a id="l00290" name="l00290"></a><span class="lineno"> 290</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
<div class="line"><a id="l00291" name="l00291"></a><span class="lineno"> 291</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
<div class="line"><a id="l00292" name="l00292"></a><span class="lineno"> 292</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
<div class="line"><a id="l00293" name="l00293"></a><span class="lineno"> 293</span> <span class="comment">// Reset particles and give new time dependent potential.</span></div>
<div class="line"><a id="l00294" name="l00294"></a><span class="lineno"> 294</span> trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
<div class="line"><a id="l00295" name="l00295"></a><span class="lineno"> 295</span> res[i + 1][j] = trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N);</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"> 297</span> }</div>
<div class="line"><a id="l00298" name="l00298"></a><span class="lineno"> 298</span> }</div>
<div class="line"><a id="l00299" name="l00299"></a><span class="lineno"> 299</span> </div>
<div class="line"><a id="l00300" name="l00300"></a><span class="lineno"> 300</span> <span class="comment">// Write results to file</span></div>
<div class="line"><a id="l00301" name="l00301"></a><span class="lineno"> 301</span> ofile.open(path + <span class="stringliteral">&quot;narrow_sweep_interactions.txt&quot;</span>);</div>
<div class="line"><a id="l00302" name="l00302"></a><span class="lineno"> 302</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00303" name="l00303"></a><span class="lineno"> 303</span> ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
<div class="line"><a id="l00304" name="l00304"></a><span class="lineno"> 304</span> &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
<div class="line"><a id="l00305" name="l00305"></a><span class="lineno"> 305</span> }</div>
<div class="line"><a id="l00306" name="l00306"></a><span class="lineno"> 306</span> ofile.close();</div>
<div class="line"><a id="l00307" name="l00307"></a><span class="lineno"> 307</span>}</div>
<div class="line"><a id="l00308" name="l00308"></a><span class="lineno"> 308</span> </div>
<div class="line"><a id="l00309" name="l00309"></a><span class="lineno"> 309</span><span class="keywordtype">int</span> main()</div>
<div class="line"><a id="l00310" name="l00310"></a><span class="lineno"> 310</span>{</div>
<div class="line"><a id="l00311" name="l00311"></a><span class="lineno"> 311</span> <span class="keywordtype">double</span> start, end, t1, t2;</div>
<div class="line"><a id="l00312" name="l00312"></a><span class="lineno"> 312</span> start = omp_get_wtime();</div>
<div class="line"><a id="l00285" name="l00285"></a><span class="lineno"> 285</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00286" name="l00286"></a><span class="lineno"> 286</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00287" name="l00287"></a><span class="lineno"> 287</span> res[0][i] = freq_start + freq_increment * i;</div>
<div class="line"><a id="l00288" name="l00288"></a><span class="lineno"> 288</span> }</div>
<div class="line"><a id="l00289" name="l00289"></a><span class="lineno"> 289</span> </div>
<div class="line"><a id="l00290" name="l00290"></a><span class="lineno"> 290</span><span class="preprocessor">#pragma omp parallel</span></div>
<div class="line"><a id="l00291" name="l00291"></a><span class="lineno"> 291</span> {</div>
<div class="line"><a id="l00292" name="l00292"></a><span class="lineno"> 292</span> <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
<div class="line"><a id="l00293" name="l00293"></a><span class="lineno"> 293</span> <span class="comment">// the sweep.</span></div>
<div class="line"><a id="l00294" name="l00294"></a><span class="lineno"> 294</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)100);</div>
<div class="line"><a id="l00295" name="l00295"></a><span class="lineno"> 295</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
<div class="line"><a id="l00296" name="l00296"></a><span class="lineno"> 296</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
<div class="line"><a id="l00297" name="l00297"></a><span class="lineno"> 297</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
<div class="line"><a id="l00298" name="l00298"></a><span class="lineno"> 298</span> <span class="comment">// Reset particles and give new time dependent potential.</span></div>
<div class="line"><a id="l00299" name="l00299"></a><span class="lineno"> 299</span> trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
<div class="line"><a id="l00300" name="l00300"></a><span class="lineno"> 300</span> res[i + 1][j] = trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N);</div>
<div class="line"><a id="l00301" name="l00301"></a><span class="lineno"> 301</span> }</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> }</div>
<div class="line"><a id="l00304" name="l00304"></a><span class="lineno"> 304</span> </div>
<div class="line"><a id="l00305" name="l00305"></a><span class="lineno"> 305</span> <span class="comment">// Write results to file</span></div>
<div class="line"><a id="l00306" name="l00306"></a><span class="lineno"> 306</span> ofile.open(path + <span class="stringliteral">&quot;narrow_sweep_interactions.txt&quot;</span>);</div>
<div class="line"><a id="l00307" name="l00307"></a><span class="lineno"> 307</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00308" name="l00308"></a><span class="lineno"> 308</span> ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
<div class="line"><a id="l00309" name="l00309"></a><span class="lineno"> 309</span> &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
<div class="line"><a id="l00310" name="l00310"></a><span class="lineno"> 310</span> }</div>
<div class="line"><a id="l00311" name="l00311"></a><span class="lineno"> 311</span> ofile.close();</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> </div>
<div class="line"><a id="l00314" name="l00314"></a><span class="lineno"> 314</span> <a class="code hl_function" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a>();</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> <a class="code hl_function" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a>();</div>
<div class="line"><a id="l00317" name="l00317"></a><span class="lineno"> 317</span> </div>
<div class="line"><a id="l00318" name="l00318"></a><span class="lineno"> 318</span> <a class="code hl_function" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a>();</div>
<div class="line"><a id="l00319" name="l00319"></a><span class="lineno"> 319</span> </div>
<div class="line"><a id="l00320" name="l00320"></a><span class="lineno"> 320</span> t2 = omp_get_wtime();</div>
<div class="line"><a id="l00321" name="l00321"></a><span class="lineno"> 321</span> </div>
<div class="line"><a id="l00322" name="l00322"></a><span class="lineno"> 322</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Time single and double : &quot;</span> &lt;&lt; (t2 - start)</div>
<div class="line"><a id="l00323" name="l00323"></a><span class="lineno"> 323</span> &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</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> t1 = omp_get_wtime();</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> <a class="code hl_function" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a>();</div>
<div class="line"><a id="l00328" name="l00328"></a><span class="lineno"> 328</span> </div>
<div class="line"><a id="l00329" name="l00329"></a><span class="lineno"> 329</span> t2 = omp_get_wtime();</div>
<div class="line"><a id="l00330" name="l00330"></a><span class="lineno"> 330</span> </div>
<div class="line"><a id="l00331" name="l00331"></a><span class="lineno"> 331</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Time 100 particles : &quot;</span> &lt;&lt; (t2 - t1)</div>
<div class="line"><a id="l00332" name="l00332"></a><span class="lineno"> 332</span> &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00333" name="l00333"></a><span class="lineno"> 333</span> </div>
<div class="line"><a id="l00334" name="l00334"></a><span class="lineno"> 334</span> t1 = omp_get_wtime();</div>
<div class="line"><a id="l00335" name="l00335"></a><span class="lineno"> 335</span> </div>
<div class="line"><a id="l00336" name="l00336"></a><span class="lineno"> 336</span> <a class="code hl_function" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a>();</div>
<div class="line"><a id="l00337" name="l00337"></a><span class="lineno"> 337</span> </div>
<div class="line"><a id="l00338" name="l00338"></a><span class="lineno"> 338</span> t2 = omp_get_wtime();</div>
<div class="line"><a id="l00339" name="l00339"></a><span class="lineno"> 339</span> </div>
<div class="line"><a id="l00340" name="l00340"></a><span class="lineno"> 340</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Time wide sweep : &quot;</span> &lt;&lt; (t2 - t1)</div>
<div class="line"><a id="l00341" name="l00341"></a><span class="lineno"> 341</span> &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00342" name="l00342"></a><span class="lineno"> 342</span> </div>
<div class="line"><a id="l00343" name="l00343"></a><span class="lineno"> 343</span> t1 = omp_get_wtime();</div>
<div class="line"><a id="l00344" name="l00344"></a><span class="lineno"> 344</span> </div>
<div class="line"><a id="l00345" name="l00345"></a><span class="lineno"> 345</span> <a class="code hl_function" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>();</div>
<div class="line"><a id="l00346" name="l00346"></a><span class="lineno"> 346</span> </div>
<div class="line"><a id="l00347" name="l00347"></a><span class="lineno"> 347</span> t2 = omp_get_wtime();</div>
<div class="line"><a id="l00348" name="l00348"></a><span class="lineno"> 348</span> </div>
<div class="line"><a id="l00349" name="l00349"></a><span class="lineno"> 349</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Time narrow sweep no interaction : &quot;</span> &lt;&lt; (t2 - t1)</div>
<div class="line"><a id="l00350" name="l00350"></a><span class="lineno"> 350</span> &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00351" name="l00351"></a><span class="lineno"> 351</span> </div>
<div class="line"><a id="l00352" name="l00352"></a><span class="lineno"> 352</span> t1 = omp_get_wtime();</div>
<div class="line"><a id="l00314" name="l00314"></a><span class="lineno"> 314</span><span class="keywordtype">int</span> main()</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> <span class="keywordtype">int</span> option = 1;</div>
<div class="line"><a id="l00317" name="l00317"></a><span class="lineno"> 317</span> <span class="keywordtype">bool</span> chosen = <span class="keyword">false</span>;</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> system(<span class="stringliteral">&quot;clear&quot;</span>);</div>
<div class="line"><a id="l00320" name="l00320"></a><span class="lineno"> 320</span> std::cout &lt;&lt; <span class="stringliteral">&quot;(1) All (default)\n&quot;</span></div>
<div class="line"><a id="l00321" name="l00321"></a><span class="lineno"> 321</span> &lt;&lt; <span class="stringliteral">&quot;(2) Simulate single particle\n&quot;</span></div>
<div class="line"><a id="l00322" name="l00322"></a><span class="lineno"> 322</span> &lt;&lt; <span class="stringliteral">&quot;(3) simulate 2 particles\n&quot;</span></div>
<div class="line"><a id="l00323" name="l00323"></a><span class="lineno"> 323</span> &lt;&lt; <span class="stringliteral">&quot;(4) Simulate single particle with different time steps\n&quot;</span></div>
<div class="line"><a id="l00324" name="l00324"></a><span class="lineno"> 324</span> &lt;&lt; <span class="stringliteral">&quot;(5) Simulate 100 particles\n&quot;</span></div>
<div class="line"><a id="l00325" name="l00325"></a><span class="lineno"> 325</span> &lt;&lt; <span class="stringliteral">&quot;(6) Potential resonance wide sweep\n&quot;</span></div>
<div class="line"><a id="l00326" name="l00326"></a><span class="lineno"> 326</span> &lt;&lt; <span class="stringliteral">&quot;(7) Potential resonance narrow sweep without particle &quot;</span></div>
<div class="line"><a id="l00327" name="l00327"></a><span class="lineno"> 327</span> <span class="stringliteral">&quot;interactions\n&quot;</span></div>
<div class="line"><a id="l00328" name="l00328"></a><span class="lineno"> 328</span> &lt;&lt; <span class="stringliteral">&quot;(8) Potential resonance narrow sweep with particle &quot;</span></div>
<div class="line"><a id="l00329" name="l00329"></a><span class="lineno"> 329</span> <span class="stringliteral">&quot;interaction\n&quot;</span></div>
<div class="line"><a id="l00330" name="l00330"></a><span class="lineno"> 330</span> &lt;&lt; <span class="stringliteral">&quot;Select what to run: &quot;</span>;</div>
<div class="line"><a id="l00331" name="l00331"></a><span class="lineno"> 331</span> std::cin &gt;&gt; std::noskipws;</div>
<div class="line"><a id="l00332" name="l00332"></a><span class="lineno"> 332</span> <span class="keywordflow">do</span> {</div>
<div class="line"><a id="l00333" name="l00333"></a><span class="lineno"> 333</span> <span class="keywordflow">if</span> (!(std::cin &gt;&gt; option) || option &lt; 1 || option &gt; 8) {</div>
<div class="line"><a id="l00334" name="l00334"></a><span class="lineno"> 334</span> std::cin.clear();</div>
<div class="line"><a id="l00335" name="l00335"></a><span class="lineno"> 335</span> std::cin.ignore(std::numeric_limits&lt;std::streamsize&gt;::max(), <span class="charliteral">&#39;\n&#39;</span>);</div>
<div class="line"><a id="l00336" name="l00336"></a><span class="lineno"> 336</span> system(<span class="stringliteral">&quot;clear&quot;</span>);</div>
<div class="line"><a id="l00337" name="l00337"></a><span class="lineno"> 337</span> std::cout</div>
<div class="line"><a id="l00338" name="l00338"></a><span class="lineno"> 338</span> &lt;&lt; <span class="stringliteral">&quot;(1) All (default)\n&quot;</span></div>
<div class="line"><a id="l00339" name="l00339"></a><span class="lineno"> 339</span> &lt;&lt; <span class="stringliteral">&quot;(2) Simulate single particle\n&quot;</span></div>
<div class="line"><a id="l00340" name="l00340"></a><span class="lineno"> 340</span> &lt;&lt; <span class="stringliteral">&quot;(3) simulate 2 particles\n&quot;</span></div>
<div class="line"><a id="l00341" name="l00341"></a><span class="lineno"> 341</span> &lt;&lt; <span class="stringliteral">&quot;(4) Simulate single particle with different time steps\n&quot;</span></div>
<div class="line"><a id="l00342" name="l00342"></a><span class="lineno"> 342</span> &lt;&lt; <span class="stringliteral">&quot;(5) Simulate 100 particles\n&quot;</span></div>
<div class="line"><a id="l00343" name="l00343"></a><span class="lineno"> 343</span> &lt;&lt; <span class="stringliteral">&quot;(6) Potential resonance wide sweep\n&quot;</span></div>
<div class="line"><a id="l00344" name="l00344"></a><span class="lineno"> 344</span> &lt;&lt; <span class="stringliteral">&quot;(7) Potential resonance narrow sweep without particle &quot;</span></div>
<div class="line"><a id="l00345" name="l00345"></a><span class="lineno"> 345</span> <span class="stringliteral">&quot;interactions\n&quot;</span></div>
<div class="line"><a id="l00346" name="l00346"></a><span class="lineno"> 346</span> &lt;&lt; <span class="stringliteral">&quot;(8) Potential resonance narrow sweep with particle &quot;</span></div>
<div class="line"><a id="l00347" name="l00347"></a><span class="lineno"> 347</span> <span class="stringliteral">&quot;interaction\n&quot;</span></div>
<div class="line"><a id="l00348" name="l00348"></a><span class="lineno"> 348</span> &lt;&lt; <span class="stringliteral">&quot;Not a valid option, please enter a valid number: &quot;</span>;</div>
<div class="line"><a id="l00349" name="l00349"></a><span class="lineno"> 349</span> } <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00350" name="l00350"></a><span class="lineno"> 350</span> chosen = <span class="keyword">true</span>;</div>
<div class="line"><a id="l00351" name="l00351"></a><span class="lineno"> 351</span> }</div>
<div class="line"><a id="l00352" name="l00352"></a><span class="lineno"> 352</span> } <span class="keywordflow">while</span> (!chosen);</div>
<div class="line"><a id="l00353" name="l00353"></a><span class="lineno"> 353</span> </div>
<div class="line"><a id="l00354" name="l00354"></a><span class="lineno"> 354</span> <a class="code hl_function" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>();</div>
<div class="line"><a id="l00354" name="l00354"></a><span class="lineno"> 354</span> <span class="keywordtype">double</span> start, end;</div>
<div class="line"><a id="l00355" name="l00355"></a><span class="lineno"> 355</span> </div>
<div class="line"><a id="l00356" name="l00356"></a><span class="lineno"> 356</span> t2 = omp_get_wtime();</div>
<div class="line"><a id="l00356" name="l00356"></a><span class="lineno"> 356</span> system(<span class="stringliteral">&quot;clear&quot;</span>);</div>
<div class="line"><a id="l00357" name="l00357"></a><span class="lineno"> 357</span> </div>
<div class="line"><a id="l00358" name="l00358"></a><span class="lineno"> 358</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Time narrow sweep with interaction: &quot;</span> &lt;&lt; (t2 - t1)</div>
<div class="line"><a id="l00359" name="l00359"></a><span class="lineno"> 359</span> &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00360" name="l00360"></a><span class="lineno"> 360</span> </div>
<div class="line"><a id="l00361" name="l00361"></a><span class="lineno"> 361</span> end = omp_get_wtime();</div>
<div class="line"><a id="l00362" name="l00362"></a><span class="lineno"> 362</span> </div>
<div class="line"><a id="l00363" name="l00363"></a><span class="lineno"> 363</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Time : &quot;</span> &lt;&lt; (end - start)</div>
<div class="line"><a id="l00364" name="l00364"></a><span class="lineno"> 364</span> &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00365" name="l00365"></a><span class="lineno"> 365</span> </div>
<div class="line"><a id="l00366" name="l00366"></a><span class="lineno"> 366</span> <span class="keywordflow">return</span> 0;</div>
<div class="line"><a id="l00367" name="l00367"></a><span class="lineno"> 367</span>}</div>
<div class="line"><a id="l00358" name="l00358"></a><span class="lineno"> 358</span> start = omp_get_wtime();</div>
<div class="line"><a id="l00359" name="l00359"></a><span class="lineno"> 359</span> <span class="keywordflow">switch</span> (option) {</div>
<div class="line"><a id="l00360" name="l00360"></a><span class="lineno"> 360</span> <span class="keywordflow">case</span> 1:</div>
<div class="line"><a id="l00361" name="l00361"></a><span class="lineno"> 361</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_single_particle\n&quot;</span>;</div>
<div class="line"><a id="l00362" name="l00362"></a><span class="lineno"> 362</span> <a class="code hl_function" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a>();</div>
<div class="line"><a id="l00363" name="l00363"></a><span class="lineno"> 363</span> </div>
<div class="line"><a id="l00364" name="l00364"></a><span class="lineno"> 364</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_two_particles\n&quot;</span>;</div>
<div class="line"><a id="l00365" name="l00365"></a><span class="lineno"> 365</span> <a class="code hl_function" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a>();</div>
<div class="line"><a id="l00366" name="l00366"></a><span class="lineno"> 366</span> </div>
<div class="line"><a id="l00367" name="l00367"></a><span class="lineno"> 367</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_single_particle_with_different_steps\n&quot;</span>;</div>
<div class="line"><a id="l00368" name="l00368"></a><span class="lineno"> 368</span> <a class="code hl_function" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a>();</div>
<div class="line"><a id="l00369" name="l00369"></a><span class="lineno"> 369</span> </div>
<div class="line"><a id="l00370" name="l00370"></a><span class="lineno"> 370</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_100_particles\n&quot;</span>;</div>
<div class="line"><a id="l00371" name="l00371"></a><span class="lineno"> 371</span> <a class="code hl_function" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a>();</div>
<div class="line"><a id="l00372" name="l00372"></a><span class="lineno"> 372</span> </div>
<div class="line"><a id="l00373" name="l00373"></a><span class="lineno"> 373</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running potential_resonance_wide_sweep\n&quot;</span>;</div>
<div class="line"><a id="l00374" name="l00374"></a><span class="lineno"> 374</span> <a class="code hl_function" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a>();</div>
<div class="line"><a id="l00375" name="l00375"></a><span class="lineno"> 375</span> </div>
<div class="line"><a id="l00376" name="l00376"></a><span class="lineno"> 376</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running potential_resonance_narrow_sweep\n&quot;</span>;</div>
<div class="line"><a id="l00377" name="l00377"></a><span class="lineno"> 377</span> <a class="code hl_function" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>();</div>
<div class="line"><a id="l00378" name="l00378"></a><span class="lineno"> 378</span> </div>
<div class="line"><a id="l00379" name="l00379"></a><span class="lineno"> 379</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running potential_resonance_narrow_sweep_interaction\n&quot;</span>;</div>
<div class="line"><a id="l00380" name="l00380"></a><span class="lineno"> 380</span> <a class="code hl_function" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>();</div>
<div class="line"><a id="l00381" name="l00381"></a><span class="lineno"> 381</span> <span class="keywordflow">break</span>;</div>
<div class="line"><a id="l00382" name="l00382"></a><span class="lineno"> 382</span> <span class="keywordflow">case</span> 2:</div>
<div class="line"><a id="l00383" name="l00383"></a><span class="lineno"> 383</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_single_particle\n&quot;</span>;</div>
<div class="line"><a id="l00384" name="l00384"></a><span class="lineno"> 384</span> <a class="code hl_function" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a>();</div>
<div class="line"><a id="l00385" name="l00385"></a><span class="lineno"> 385</span> <span class="keywordflow">break</span>;</div>
<div class="line"><a id="l00386" name="l00386"></a><span class="lineno"> 386</span> <span class="keywordflow">case</span> 3:</div>
<div class="line"><a id="l00387" name="l00387"></a><span class="lineno"> 387</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_two_particles\n&quot;</span>;</div>
<div class="line"><a id="l00388" name="l00388"></a><span class="lineno"> 388</span> <a class="code hl_function" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a>();</div>
<div class="line"><a id="l00389" name="l00389"></a><span class="lineno"> 389</span> <span class="keywordflow">break</span>;</div>
<div class="line"><a id="l00390" name="l00390"></a><span class="lineno"> 390</span> <span class="keywordflow">case</span> 4:</div>
<div class="line"><a id="l00391" name="l00391"></a><span class="lineno"> 391</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_single_particle_with_different_steps\n&quot;</span>;</div>
<div class="line"><a id="l00392" name="l00392"></a><span class="lineno"> 392</span> <a class="code hl_function" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a>();</div>
<div class="line"><a id="l00393" name="l00393"></a><span class="lineno"> 393</span> <span class="keywordflow">break</span>;</div>
<div class="line"><a id="l00394" name="l00394"></a><span class="lineno"> 394</span> <span class="keywordflow">case</span> 5:</div>
<div class="line"><a id="l00395" name="l00395"></a><span class="lineno"> 395</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_100_particles\n&quot;</span>;</div>
<div class="line"><a id="l00396" name="l00396"></a><span class="lineno"> 396</span> <a class="code hl_function" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a>();</div>
<div class="line"><a id="l00397" name="l00397"></a><span class="lineno"> 397</span> <span class="keywordflow">break</span>;</div>
<div class="line"><a id="l00398" name="l00398"></a><span class="lineno"> 398</span> <span class="keywordflow">case</span> 6:</div>
<div class="line"><a id="l00399" name="l00399"></a><span class="lineno"> 399</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running potential_resonance_wide_sweep\n&quot;</span>;</div>
<div class="line"><a id="l00400" name="l00400"></a><span class="lineno"> 400</span> <a class="code hl_function" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a>();</div>
<div class="line"><a id="l00401" name="l00401"></a><span class="lineno"> 401</span> <span class="keywordflow">break</span>;</div>
<div class="line"><a id="l00402" name="l00402"></a><span class="lineno"> 402</span> <span class="keywordflow">case</span> 7:</div>
<div class="line"><a id="l00403" name="l00403"></a><span class="lineno"> 403</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running potential_resonance_narrow_sweep\n&quot;</span>;</div>
<div class="line"><a id="l00404" name="l00404"></a><span class="lineno"> 404</span> <a class="code hl_function" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>();</div>
<div class="line"><a id="l00405" name="l00405"></a><span class="lineno"> 405</span> <span class="keywordflow">break</span>;</div>
<div class="line"><a id="l00406" name="l00406"></a><span class="lineno"> 406</span> <span class="keywordflow">case</span> 8:</div>
<div class="line"><a id="l00407" name="l00407"></a><span class="lineno"> 407</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Running potential_resonance_narrow_sweep_interaction\n&quot;</span>;</div>
<div class="line"><a id="l00408" name="l00408"></a><span class="lineno"> 408</span> <a class="code hl_function" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>();</div>
<div class="line"><a id="l00409" name="l00409"></a><span class="lineno"> 409</span> <span class="keywordflow">break</span>;</div>
<div class="line"><a id="l00410" name="l00410"></a><span class="lineno"> 410</span> }</div>
<div class="line"><a id="l00411" name="l00411"></a><span class="lineno"> 411</span> end = omp_get_wtime();</div>
<div class="line"><a id="l00412" name="l00412"></a><span class="lineno"> 412</span> </div>
<div class="line"><a id="l00413" name="l00413"></a><span class="lineno"> 413</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Time: &quot;</span> &lt;&lt; end - start &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00414" name="l00414"></a><span class="lineno"> 414</span> </div>
<div class="line"><a id="l00415" name="l00415"></a><span class="lineno"> 415</span> <span class="keywordflow">return</span> 0;</div>
<div class="line"><a id="l00416" name="l00416"></a><span class="lineno"> 416</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="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_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#l00148">PenningTrap.cpp:148</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_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#l00240">PenningTrap.cpp:240</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#l00153">PenningTrap.cpp:153</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#l00311">PenningTrap.cpp:311</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#l00273">PenningTrap.cpp:273</a></div></div>
<div class="ttc" id="aconstants_8hpp_html"><div class="ttname"><a href="constants_8hpp.html">constants.hpp</a></div><div class="ttdoc">Library of constants.</div></div>
<div class="ttc" id="aconstants_8hpp_html_a0acb682b8260ab1c60b918599864e2e5"><div class="ttname"><a href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a></div><div class="ttdeci">#define T</div><div class="ttdoc">1 Tesla. unit:</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00021">constants.hpp:21</a></div></div>
<div class="ttc" id="aconstants_8hpp_html_a2ff491cc7958ffd5e749c518a4a60ec8"><div class="ttname"><a href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">CA_MASS</a></div><div class="ttdeci">#define CA_MASS</div><div class="ttdoc">Mass of a single calcium ion. unit: amu.</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00029">constants.hpp:29</a></div></div>
<div class="ttc" id="aconstants_8hpp_html_af40a326b23c68a27cebe60f16634a2cb"><div class="ttname"><a href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a></div><div class="ttdeci">#define V</div><div class="ttdoc">1 Volt. unit:</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00025">constants.hpp:25</a></div></div>
<div class="ttc" id="amain_8cpp_html_a213713d6ecc02a32b588ffd179dc7513"><div class="ttname"><a href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a></div><div class="ttdeci">void simulate_100_particles()</div><div class="ttdoc">Simulate 100 particles over 50 .</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00132">main.cpp:132</a></div></div>
<div class="ttc" id="amain_8cpp_html_a213713d6ecc02a32b588ffd179dc7513"><div class="ttname"><a href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a></div><div class="ttdeci">void simulate_100_particles()</div><div class="ttdoc">Simulate 100 particles over 50 .</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00134">main.cpp:134</a></div></div>
<div class="ttc" id="amain_8cpp_html_a2efa69bb9d93049429ce4637075f1d30"><div class="ttname"><a href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a></div><div class="ttdeci">Particle p1(vec3{20., 0., 20.}, vec3{0., 25., 0.})</div><div class="ttdoc">Particle 1.</div></div>
<div class="ttc" id="amain_8cpp_html_a33d9b1c76c3c80902f89a58b1a6d96ea"><div class="ttname"><a href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a></div><div class="ttdeci">void potential_resonance_narrow_sweep()</div><div class="ttdoc">Simulate 100 particles over 500 using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00206">main.cpp:206</a></div></div>
<div class="ttc" id="amain_8cpp_html_a6b38b477c18e2f4268779751a88edab1"><div class="ttname"><a href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a></div><div class="ttdeci">void potential_resonance_wide_sweep()</div><div class="ttdoc">Simulate 100 particles over 500 using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00149">main.cpp:149</a></div></div>
<div class="ttc" id="amain_8cpp_html_a783789519f97c6430081171cacb0ffb1"><div class="ttname"><a href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a></div><div class="ttdeci">void simulate_two_particles()</div><div class="ttdoc">Simulate 2 particles over the period of 50 with and without particle interactions.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00069">main.cpp:69</a></div></div>
<div class="ttc" id="amain_8cpp_html_a33d9b1c76c3c80902f89a58b1a6d96ea"><div class="ttname"><a href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a></div><div class="ttdeci">void potential_resonance_narrow_sweep()</div><div class="ttdoc">Simulate 100 particles over 500 using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00209">main.cpp:209</a></div></div>
<div class="ttc" id="amain_8cpp_html_a6b38b477c18e2f4268779751a88edab1"><div class="ttname"><a href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a></div><div class="ttdeci">void potential_resonance_wide_sweep()</div><div class="ttdoc">Simulate 100 particles over 500 using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00152">main.cpp:152</a></div></div>
<div class="ttc" id="amain_8cpp_html_a783789519f97c6430081171cacb0ffb1"><div class="ttname"><a href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a></div><div class="ttdeci">void simulate_two_particles()</div><div class="ttdoc">Simulate 2 particles over the period of 50 with and without particle interactions.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00070">main.cpp:70</a></div></div>
<div class="ttc" id="amain_8cpp_html_a8d92fb2ad085065fbd14718647551657"><div class="ttname"><a href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a></div><div class="ttdeci">vec3 analytical_solution_particle_1(double t)</div><div class="ttdoc">The analytical solution for particle p1.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00037">main.cpp:37</a></div></div>
<div class="ttc" id="amain_8cpp_html_a8fdbe2d5a872e50ef5ec1263243589d6"><div class="ttname"><a href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a></div><div class="ttdeci">void simulate_single_particle()</div><div class="ttdoc">Simulate a single particle over the period of 50 .</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00054">main.cpp:54</a></div></div>
<div class="ttc" id="amain_8cpp_html_ac1816f70ec612edc27848ef7f0875fdb"><div class="ttname"><a href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a></div><div class="ttdeci">void potential_resonance_narrow_sweep_interaction()</div><div class="ttdoc">Simulate 100 particles over 500 using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00262">main.cpp:262</a></div></div>
<div class="ttc" id="amain_8cpp_html_ac67e0d59227856c4d42e7d01c75e0ad2"><div class="ttname"><a href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a></div><div class="ttdeci">void simulate_single_particle_with_different_steps()</div><div class="ttdoc">Simulate a single particle over 50 using different amount of steps and different methods.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00087">main.cpp:87</a></div></div>
<div class="ttc" id="amain_8cpp_html_a8fdbe2d5a872e50ef5ec1263243589d6"><div class="ttname"><a href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a></div><div class="ttdeci">void simulate_single_particle()</div><div class="ttdoc">Simulate a single particle over the period of 50 .</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00055">main.cpp:55</a></div></div>
<div class="ttc" id="amain_8cpp_html_ac1816f70ec612edc27848ef7f0875fdb"><div class="ttname"><a href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a></div><div class="ttdeci">void potential_resonance_narrow_sweep_interaction()</div><div class="ttdoc">Simulate 100 particles over 500 using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00266">main.cpp:266</a></div></div>
<div class="ttc" id="amain_8cpp_html_ac67e0d59227856c4d42e7d01c75e0ad2"><div class="ttname"><a href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a></div><div class="ttdeci">void simulate_single_particle_with_different_steps()</div><div class="ttdoc">Simulate a single particle over 50 using different amount of steps and different methods.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00088">main.cpp:88</a></div></div>
<div class="ttc" id="amain_8cpp_html_ac70b61df65f4336f57ea9b4c35250df7"><div class="ttname"><a href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">p2</a></div><div class="ttdeci">Particle p2(vec3{25., 25., 0.}, vec3{0., 40., 5.})</div><div class="ttdoc">Particle 2.</div></div>
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<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>

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@ -133,7 +133,7 @@ Functions</h2></td></tr>
<dd>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000009">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000010">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<p class="definition">Definition in file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
</div><h2 class="groupheader">Function Documentation</h2>

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@ -239,12 +239,12 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
<div class="ttc" id="aclassPenningTrapTest_html_ad668d7d875bdc1909a42426bf9dead9e"><div class="ttname"><a href="classPenningTrapTest.html#ad668d7d875bdc1909a42426bf9dead9e">PenningTrapTest::test_external_B_field</a></div><div class="ttdeci">void test_external_B_field()</div><div class="ttdoc">Test that the external B field gives correct values.</div><div class="ttdef"><b>Definition:</b> <a href="test__suite_8cpp_source.html#l00066">test_suite.cpp:66</a></div></div>
<div class="ttc" id="aclassPenningTrapTest_html_ae6d0c8e0d80338fb7c7edefc97331046"><div class="ttname"><a href="classPenningTrapTest.html#ae6d0c8e0d80338fb7c7edefc97331046">PenningTrapTest::test_total_force_external</a></div><div class="ttdeci">void test_total_force_external()</div><div class="ttdoc">Test that the total external force returns expected results.</div><div class="ttdef"><b>Definition:</b> <a href="test__suite_8cpp_source.html#l00107">test_suite.cpp:107</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_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#l00082">PenningTrap.cpp:82</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#l00095">PenningTrap.cpp:95</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#l00066">PenningTrap.cpp:66</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#l00058">PenningTrap.cpp:58</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#l00158">PenningTrap.cpp:158</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#l00071">PenningTrap.cpp:71</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#l00083">PenningTrap.cpp:83</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#l00092">PenningTrap.cpp:92</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#l00067">PenningTrap.cpp:67</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#l00059">PenningTrap.cpp:59</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#l00166">PenningTrap.cpp:166</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#l00072">PenningTrap.cpp:72</a></div></div>
<div class="ttc" id="aconstants_8hpp_html"><div class="ttname"><a href="constants_8hpp.html">constants.hpp</a></div><div class="ttdoc">Library of constants.</div></div>
<div class="ttc" id="aconstants_8hpp_html_a0acb682b8260ab1c60b918599864e2e5"><div class="ttname"><a href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a></div><div class="ttdeci">#define T</div><div class="ttdoc">1 Tesla. unit:</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00021">constants.hpp:21</a></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>

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@ -134,7 +134,7 @@ Functions</h2></td></tr>
<dd>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000010">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000011">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<p class="definition">Definition in file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
</div><h2 class="groupheader">Function Documentation</h2>