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@ -109,147 +109,147 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp_source.html',''); ini
<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="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="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="l00019" name="l00019"></a><span class="lineno"> 19</span> </div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8"> 20</a></span><a class="code hl_function" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a>(<span class="keywordtype">double</span> B_0, <span class="keywordtype">double</span> V_0, <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</div> <div class="line"><a id="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="l00021" name="l00021"></a><span class="lineno"> 21</span>{</div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> this-&gt;B_0 = <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>;</div> <div class="line"><a id="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> this-&gt;V_0 = <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a>;</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> this-&gt;d = <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</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> this-&gt;t = <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>;</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> 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="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>}</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> </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"><a class="line" href="classPenningTrap.html#a830be1b8cbf59664e060b6edbeaa302f"> 29</a></span><a class="code hl_function" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a>(uint i, <span class="keywordtype">double</span> B_0, <span class="keywordtype">double</span> V_0, <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</div> <div class="line"><a id="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> : <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="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>{</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> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; i; 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> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(</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> <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="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> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>().randn() * .1 * this-&gt;d)));</div> <div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> abort();</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> }</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="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="l00038" name="l00038"></a><span class="lineno"> 38</span> </div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"><a class="line" href="classPenningTrap.html#addc96789dcfec07b75156e19fee82f4f"> 39</a></span><a class="code hl_function" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a>(std::vector&lt;Particle&gt; particles, <span class="keywordtype">double</span> B_0,</div> <div class="line"><a id="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> <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="l00040" name="l00040"></a><span class="lineno"> 40</span>{</div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> : <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(B_0, V_0, d)</div> <div class="line"><a id="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>{</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> this-&gt;particles = <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</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>}</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> </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"><a class="line" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43"> 46</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">PenningTrap::set_pertubation</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V)</div> <div class="line"><a id="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>{</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> 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="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> 1 + f * std::cos(omega_V * <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>);</div> <div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> <span class="keywordflow">return</span> <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> };</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>}</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> </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"><a class="line" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea"> 53</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap::reinitialize</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V, <span class="keywordtype">double</span> t)</div> <div class="line"><a id="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>{</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> this-&gt;t = <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</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> this-&gt;<a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">set_pertubation</a>(f, omega_V);</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="l00057" name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); i++) {</div> <div class="line"><a id="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> 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="l00059" name="l00059"></a><span class="lineno"> 59</span>{</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</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="l00061" name="l00061"></a><span class="lineno"> 61</span> </div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> </div> <div class="line"><a id="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"><a class="line" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2"> 63</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap::v_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt)</div> <div class="line"><a id="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="l00064" name="l00064"></a><span class="lineno"> 64</span>}</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> <span class="keywordflow">switch</span> (i) {</div> <div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> <span class="keywordflow">case</span> 0:</div> <div class="line"><a id="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> <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="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">case</span> 1:</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> <span class="keywordflow">return</span> .5 * dt * this-&gt;k_v[1][j];</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> <span class="keywordflow">case</span> 2:</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="keywordflow">return</span> dt * this-&gt;k_v[2][j];</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> <span class="keywordflow">case</span> 3:</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="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((dt / 6.)</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> * (this-&gt;k_v[0][j] + 2. * this-&gt;k_v[1][j]</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> + 2. * this-&gt;k_v[2][j] + this-&gt;k_v[3][j]));</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="keywordflow">default</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> std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</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> abort();</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> }</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="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="l00081" name="l00081"></a><span class="lineno"> 81</span> </div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08"> 82</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">PenningTrap::r_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt)</div> <div class="line"><a id="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="l00083" name="l00083"></a><span class="lineno"> 83</span>{</div>
<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> <span class="keywordflow">switch</span> (i) {</div> <div class="line"><a id="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> <span class="keywordflow">case</span> 0:</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">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="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">case</span> 1:</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> <span class="keywordflow">return</span> .5 * dt * this-&gt;k_r[1][j];</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="keywordflow">case</span> 2:</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> dt * this-&gt;k_r[2][j];</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> <span class="keywordflow">case</span> 3:</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> <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="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> * (this-&gt;k_r[0][j] + 2. * this-&gt;k_r[1][j]</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> + 2. * this-&gt;k_r[2][j] + this-&gt;k_r[3][j]));</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="keywordflow">default</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> std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</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> abort();</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="l00098" name="l00098"></a><span class="lineno"> 98</span> </div>
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span>}</div> <div class="line"><a id="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> </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"><a class="line" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8"> 101</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap::add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a> particle)</div> <div class="line"><a id="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="l00102" name="l00102"></a><span class="lineno"> 102</span> }</div>
<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(particle);</div> <div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> </div>
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</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="l00105" name="l00105"></a><span class="lineno"> 105</span>}</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22"> 106</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">PenningTrap::external_E_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r)</div> <div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</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> r(2) *= -2.;</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> </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>((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="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> * r);</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="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="l00113" name="l00113"></a><span class="lineno"> 113</span>}</div>
<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655"> 114</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">PenningTrap::external_B_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r)</div> <div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</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> <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="l00116" name="l00116"></a><span class="lineno"> 116</span>{</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</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> </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"><a class="line" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598"> 119</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap::force_on_particle</a>(uint i, uint j)</div> <div class="line"><a id="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>{</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> <span class="comment">// Calculate the difference between the particles&#39; position</span></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> <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="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="l00123" name="l00123"></a><span class="lineno"> 123</span> </div>
<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> <span class="comment">// Get the distance between the particles</span></div> <div class="line"><a id="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> <span class="keywordtype">double</span> norm = arma::norm(res, 2);</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="l00126" name="l00126"></a><span class="lineno"> 126</span>{</div>
<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].q / (norm * norm * norm)) * res);</div> <div class="line"><a id="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>}</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> </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"><a class="line" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682"> 130</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap::total_force_external</a>(uint i)</div> <div class="line"><a id="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="l00131" name="l00131"></a><span class="lineno"> 131</span> }</div>
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> <a class="code hl_class" href="classParticle.html">Particle</a> *p = &amp;this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i];</div> <div class="line"><a id="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="l00133" name="l00133"></a><span class="lineno"> 133</span> </div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> <span class="keywordflow">if</span> (arma::norm(p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>) &gt; this-&gt;d) {</div> <div class="line"><a id="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="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 0., 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> }</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="l00137" name="l00137"></a><span class="lineno"> 137</span>{</div>
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(p-&gt;<a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a></div> <div class="line"><a id="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> * (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="l00139" name="l00139"></a><span class="lineno"> 139</span>}</div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> + arma::cross(p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a>, this-&gt;external_B_field(p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>))));</div> <div class="line"><a id="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="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="l00142" name="l00142"></a><span class="lineno"> 142</span> </div> <div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span>{</div>
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c"> 143</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap::total_force_particles</a>(uint i)</div> <div class="line"><a id="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>{</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> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res;</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="l00146" name="l00146"></a><span class="lineno"> 146</span>}</div>
<div class="line"><a id="l00147" name="l00147"></a><span class="lineno"> 147</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); j++) {</div> <div class="line"><a id="l00147" name="l00147"></a><span class="lineno"> 147</span> </div>
<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"> 148</span> <span class="keywordflow">if</span> (i != j)</div> <div class="line"><a id="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> res += this-&gt;<a class="code hl_function" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">force_on_particle</a>(i, j);</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> }</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> </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="l00152" name="l00152"></a><span class="lineno"> 152</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(res * (<a class="code hl_define" href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">K_E</a> * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].q));</div> <div class="line"><a id="l00152" name="l00152"></a><span class="lineno"> 152</span> </div>
<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</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> </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"><a class="line" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3"> 155</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a>(uint i)</div> <div class="line"><a id="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="l00156" name="l00156"></a><span class="lineno"> 156</span>}</div>
<div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</span> <span class="keywordflow">if</span> (arma::norm(this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec) &gt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>) {</div> <div class="line"><a id="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="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 0., 0.};</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="l00159" name="l00159"></a><span class="lineno"> 159</span>{</div>
<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(this-&gt;<a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">total_force_external</a>(i) - this-&gt;<a class="code hl_function" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">total_force_particles</a>(i));</div> <div class="line"><a id="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="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="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="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>
@ -424,31 +424,31 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp_source.html',''); ini
<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_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_a566dcc1de4bdc01251776948798ea8e1"><div class="ttname"><a href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">Particle::q</a></div><div class="ttdeci">double q</div><div class="ttdoc">Charge.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00027">Particle.hpp:27</a></div></div>
<div class="ttc" id="aclassPenningTrap_html"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00031">PenningTrap.hpp:32</a></div></div> <div class="ttc" id="aclassPenningTrap_html"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00031">PenningTrap.hpp:32</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a0112525d9e79a472e761f8ef402a339f"><div class="ttname"><a href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">PenningTrap::particles</a></div><div class="ttdeci">std::vector&lt; Particle &gt; particles</div><div class="ttdoc">The particles in the Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00039">PenningTrap.hpp:39</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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#l00034">PenningTrap.hpp:34</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#l00130">PenningTrap.cpp:130</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_a2f168622587709b9e3c49077f0b9a640"><div class="ttname"><a href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">PenningTrap::k_r</a></div><div class="ttdeci">sim_arr k_r</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00042">PenningTrap.hpp:42</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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#l00143">PenningTrap.cpp:143</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#l00114">PenningTrap.cpp:114</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_a36946152fd951b1f7c346c51ff900d8e"><div class="ttname"><a href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a></div><div class="ttdeci">void evolve_RK4(double dt, bool particle_interaction=true)</div><div class="ttdoc">Go forward one timestep using the RK4 method.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00163">PenningTrap.cpp:163</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a3c0a44e4e0a94366ff609e81fe463fa2"><div class="ttname"><a href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap::v_func</a></div><div class="ttdeci">vec3 v_func(uint i, uint j, double dt)</div><div class="ttdoc">Helper for evolve_RK4 when calculating values.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00063">PenningTrap.cpp:63</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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#l00106">PenningTrap.cpp:106</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#l00020">PenningTrap.cpp:20</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_a66dfe89c68716b9502927b97f59c27d2"><div class="ttname"><a href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">PenningTrap::d</a></div><div class="ttdeci">double d</div><div class="ttdoc">Characteristic dimension.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00037">PenningTrap.hpp:37</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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#l00101">PenningTrap.cpp:101</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_a715329844d75ec4c04f8391421fb4e89"><div class="ttname"><a href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">PenningTrap::V_0</a></div><div class="ttdeci">double V_0</div><div class="ttdoc">Applied potential.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00035">PenningTrap.hpp:35</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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_a7a1d9f0528a12308de25bc30718da20a"><div class="ttname"><a href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap::simulate</a></div><div class="ttdeci">simulation_t simulate(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate the particle system inside the Penning trap over a certain amount of time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00228">PenningTrap.cpp:228</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a7f210bb2768a5d79ced4b0df0df97598"><div class="ttname"><a href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap::force_on_particle</a></div><div class="ttdeci">vec3 force_on_particle(uint i, uint j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00119">PenningTrap.cpp:119</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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#l00082">PenningTrap.cpp:82</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_a8ca4e21291f60fde619c14099d8c4e8e"><div class="ttname"><a href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">PenningTrap::t</a></div><div class="ttdeci">double t</div><div class="ttdoc">Current time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00038">PenningTrap.hpp:38</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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#l00155">PenningTrap.cpp:155</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#l00046">PenningTrap.cpp:46</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#l00053">PenningTrap.cpp:53</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_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_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_ad8bc4df7ab3eed53b16cfdff38e7760b"><div class="ttname"><a href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap::write_simulation_to_dir</a></div><div class="ttdeci">void write_simulation_to_dir(std::string path, double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and write the displacement of all particles to files.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00259">PenningTrap.cpp:259</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_ae915f6ad0eef1fb46530e836b6e071e5"><div class="ttname"><a href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">PenningTrap::perturbation</a></div><div class="ttdeci">std::function&lt; double(double)&gt; perturbation</div><div class="ttdoc">Time-dependent perturbation.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00036">PenningTrap.hpp:36</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00040">PenningTrap.hpp:40</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> <div class="ttc" id="aconstants_8hpp_html_a4e451456ad7e9276ed0afa42826e7ccb"><div class="ttname"><a href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">K_E</a></div><div class="ttdeci">#define K_E</div><div class="ttdoc">Coulomb constant. unit: .</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00017">constants.hpp:17</a></div></div>
<div class="ttc" id="astructsimulation_html"><div class="ttname"><a href="structsimulation.html">simulation</a></div><div class="ttdoc">Typedef for PenningTrap::simulation return value.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00040">typedefs.hpp:40</a></div></div> <div class="ttc" id="astructsimulation_html"><div class="ttname"><a href="structsimulation.html">simulation</a></div><div class="ttdoc">Typedef for PenningTrap::simulation return value.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00040">typedefs.hpp:40</a></div></div>
<div class="ttc" id="atypedefs_8hpp_html"><div class="ttname"><a href="typedefs_8hpp.html">typedefs.hpp</a></div><div class="ttdoc">Useful typedefs for cleaner code.</div></div> <div class="ttc" id="atypedefs_8hpp_html"><div class="ttname"><a href="typedefs_8hpp.html">typedefs.hpp</a></div><div class="ttdoc">Useful typedefs for cleaner code.</div></div>

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<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span> </div> <div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span> </div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"><a class="line" href="classPenningTrap.html"> 31</a></span><span class="keyword">class </span><a class="code hl_class" href="classPenningTrap.html">PenningTrap</a></div> <div class="line"><a id="l00031" name="l00031"></a><span class="lineno"><a class="line" href="classPenningTrap.html"> 31</a></span><span class="keyword">class </span><a class="code hl_class" href="classPenningTrap.html">PenningTrap</a></div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span>{</div> <div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span>{</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span><span class="keyword">private</span>:</div> <div class="line"><a id="l00035" name="l00035"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae"> 35</a></span> <span class="keyword">friend</span> <span class="keyword">class </span><a class="code hl_class" href="classPenningTrapTest.html">PenningTrapTest</a>;</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716"> 34</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>; </div> <div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span><span class="keyword">private</span>:</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89"> 35</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a>; </div> <div class="line"><a id="l00037" name="l00037"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716"> 37</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>; </div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5"> 36</a></span> std::function&lt;double(<span class="keywordtype">double</span>)&gt; <a class="code hl_variable" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</a>; </div> <div class="line"><a id="l00038" name="l00038"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89"> 38</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a>; </div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2"> 37</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>; </div> <div class="line"><a id="l00039" name="l00039"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5"> 39</a></span> std::function&lt;double(<span class="keywordtype">double</span>)&gt; <a class="code hl_variable" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</a>; </div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e"> 38</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>; </div> <div class="line"><a id="l00040" name="l00040"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2"> 40</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>; </div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f"> 39</a></span> std::vector&lt;Particle&gt; <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>; </div> <div class="line"><a id="l00041" name="l00041"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e"> 41</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>; </div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4"> 40</a></span> <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a> <a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>; </div> <div class="line"><a id="l00042" name="l00042"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f"> 42</a></span> std::vector&lt;Particle&gt; <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>; </div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640"> 42</a></span> <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a> <a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>; </div> <div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> </div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> </div> <div class="line"><a id="l00047" name="l00047"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4"> 47</a></span> <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a> <a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>;</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">v_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt);</div> <div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> </div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> </div> <div class="line"><a id="l00052" name="l00052"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640"> 52</a></span> <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a> <a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>;</div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">r_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt);</div> <div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> </div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> </div> <div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">v_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt);</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> <a class="code hl_function" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">external_E_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r);</div> <div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> </div> <div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">r_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt);</div>
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">external_B_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r);</div> <div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> </div>
<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> </div> <div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">external_E_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r);</div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">force_on_particle</a>(uint i, uint j);</div> <div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> </div> <div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">external_B_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r);</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">total_force_external</a>(uint i);</div> <div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</span> </div> <div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">force_on_particle</a>(uint i, uint j);</div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">total_force_particles</a>(uint i);</div> <div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> </div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">total_force_external</a>(uint i);</div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> </div> <div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> </div>
<div class="line"><a id="l00123" name="l00123"></a><span class="lineno"> 123</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="l00124" name="l00124"></a><span class="lineno"> 124</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">total_force_particles</a>(uint i);</div>
<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> </div> <div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> </div>
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span><span class="keyword">public</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> <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="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="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</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="l00135" name="l00135"></a><span class="lineno"> 135</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="l00144" name="l00144"></a><span class="lineno"> 144</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="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="l00145" name="l00145"></a><span class="lineno"> 145</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="l00144" name="l00144"></a><span class="lineno"> 144</span> </div>
<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"> 146</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="l00155" name="l00155"></a><span class="lineno"> 155</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="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="l00156" name="l00156"></a><span class="lineno"> 156</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="l00155" name="l00155"></a><span class="lineno"> 155</span> </div>
<div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</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="l00163" name="l00163"></a><span class="lineno"> 163</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="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="l00164" name="l00164"></a><span class="lineno"> 164</span> </div> <div class="line"><a id="l00166" name="l00166"></a><span class="lineno"> 166</span> </div>
<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</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="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="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="l00177" name="l00177"></a><span class="lineno"> 177</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="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="l00178" name="l00178"></a><span class="lineno"> 178</span> </div> <div class="line"><a id="l00181" name="l00181"></a><span class="lineno"> 181</span> </div>
<div class="line"><a id="l00184" name="l00184"></a><span class="lineno"> 184</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="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="l00185" name="l00185"></a><span class="lineno"> 185</span> </div> <div class="line"><a id="l00187" name="l00187"></a><span class="lineno"> 187</span> </div>
<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</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="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="l00192" name="l00192"></a><span class="lineno"> 192</span> </div> <div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> </div>
<div class="line"><a id="l00203" name="l00203"></a><span class="lineno"> 203</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="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="l00204" name="l00204"></a><span class="lineno"> 204</span> <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="l00205" name="l00205"></a><span class="lineno"> 205</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="l00214" name="l00214"></a><span class="lineno"> 214</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="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="l00215" name="l00215"></a><span class="lineno"> 215</span> std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div> <div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span> </div>
<div class="line"><a id="l00216" name="l00216"></a><span class="lineno"> 216</span> <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</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="l00217" name="l00217"></a><span class="lineno"> 217</span> </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="l00228" name="l00228"></a><span class="lineno"> 228</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="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="l00229" name="l00229"></a><span class="lineno"> 229</span> std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div> <div class="line"><a id="l00226" name="l00226"></a><span class="lineno"> 226</span> </div>
<div class="line"><a id="l00230" name="l00230"></a><span class="lineno"> 230</span> <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</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="l00231" name="l00231"></a><span class="lineno"> 231</span> </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="l00232" name="l00232"></a><span class="lineno"> 232</span> <span class="keyword">friend</span> <span class="keyword">class </span><a class="code hl_class" href="classPenningTrapTest.html">PenningTrapTest</a>;</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="l00233" name="l00233"></a><span class="lineno"> 233</span>};</div> <div class="line"><a id="l00240" name="l00240"></a><span class="lineno"> 240</span> </div>
<div class="line"><a id="l00234" name="l00234"></a><span class="lineno"> 234</span> </div> <div class="line"><a id="l00241" name="l00241"></a><span class="lineno"> 241</span>};</div>
<div class="line"><a id="l00235" name="l00235"></a><span class="lineno"> 235</span><span class="preprocessor">#endif</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="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="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="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="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"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00031">PenningTrap.hpp:32</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a0112525d9e79a472e761f8ef402a339f"><div class="ttname"><a href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">PenningTrap::particles</a></div><div class="ttdeci">std::vector&lt; Particle &gt; particles</div><div class="ttdoc">The particles in the Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00039">PenningTrap.hpp:39</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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#l00034">PenningTrap.hpp:34</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#l00130">PenningTrap.cpp:130</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_a2f168622587709b9e3c49077f0b9a640"><div class="ttname"><a href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">PenningTrap::k_r</a></div><div class="ttdeci">sim_arr k_r</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00042">PenningTrap.hpp:42</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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#l00143">PenningTrap.cpp:143</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#l00114">PenningTrap.cpp:114</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_a36946152fd951b1f7c346c51ff900d8e"><div class="ttname"><a href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a></div><div class="ttdeci">void evolve_RK4(double dt, bool particle_interaction=true)</div><div class="ttdoc">Go forward one timestep using the RK4 method.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00163">PenningTrap.cpp:163</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a3c0a44e4e0a94366ff609e81fe463fa2"><div class="ttname"><a href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap::v_func</a></div><div class="ttdeci">vec3 v_func(uint i, uint j, double dt)</div><div class="ttdoc">Helper for evolve_RK4 when calculating values.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00063">PenningTrap.cpp:63</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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#l00106">PenningTrap.cpp:106</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_a66dfe89c68716b9502927b97f59c27d2"><div class="ttname"><a href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">PenningTrap::d</a></div><div class="ttdeci">double d</div><div class="ttdoc">Characteristic dimension.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00037">PenningTrap.hpp:37</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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#l00101">PenningTrap.cpp:101</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_a715329844d75ec4c04f8391421fb4e89"><div class="ttname"><a href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">PenningTrap::V_0</a></div><div class="ttdeci">double V_0</div><div class="ttdoc">Applied potential.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00035">PenningTrap.hpp:35</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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_a7a1d9f0528a12308de25bc30718da20a"><div class="ttname"><a href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap::simulate</a></div><div class="ttdeci">simulation_t simulate(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate the particle system inside the Penning trap over a certain amount of time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00228">PenningTrap.cpp:228</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a7f210bb2768a5d79ced4b0df0df97598"><div class="ttname"><a href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap::force_on_particle</a></div><div class="ttdeci">vec3 force_on_particle(uint i, uint j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00119">PenningTrap.cpp:119</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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#l00082">PenningTrap.cpp:82</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_a8ca4e21291f60fde619c14099d8c4e8e"><div class="ttname"><a href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">PenningTrap::t</a></div><div class="ttdeci">double t</div><div class="ttdoc">Current time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00038">PenningTrap.hpp:38</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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#l00155">PenningTrap.cpp:155</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#l00046">PenningTrap.cpp:46</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#l00053">PenningTrap.cpp:53</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_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_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_ad8bc4df7ab3eed53b16cfdff38e7760b"><div class="ttname"><a href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap::write_simulation_to_dir</a></div><div class="ttdeci">void write_simulation_to_dir(std::string path, double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and write the displacement of all particles to files.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00259">PenningTrap.cpp:259</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_ae915f6ad0eef1fb46530e836b6e071e5"><div class="ttname"><a href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">PenningTrap::perturbation</a></div><div class="ttdeci">std::function&lt; double(double)&gt; perturbation</div><div class="ttdoc">Time-dependent perturbation.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00036">PenningTrap.hpp:36</a></div></div> <div class="ttc" id="aclassPenningTrap_html_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="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00040">PenningTrap.hpp:40</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> <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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<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="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>

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<tr bgcolor="#f0f0f0" class="odd"><td class="entry"><b>PenningTrapTest</b> (defined in <a class="el" href="classPenningTrap.html">PenningTrap</a>)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">friend</span></td></tr> <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae">PenningTrapTest</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
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@ -197,13 +197,16 @@ Private Attributes</h2></td></tr>
<tr class="memdesc:a0112525d9e79a472e761f8ef402a339f"><td class="mdescLeft">&#160;</td><td class="mdescRight">The particles in the Penning trap. <br /></td></tr> <tr class="memdesc:a0112525d9e79a472e761f8ef402a339f"><td class="mdescLeft">&#160;</td><td class="mdescRight">The particles in the Penning trap. <br /></td></tr>
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<tr class="memdesc:ae9b5afdaa5cd366e94bd294452a1eed4"><td class="mdescLeft">&#160;</td><td class="mdescRight">A 2D vector containing all \(k_{v,i,j}\) where \(j\) is the index of a particle. <br /></td></tr>
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<tr class="memdesc:a2f168622587709b9e3c49077f0b9a640"><td class="mdescLeft">&#160;</td><td class="mdescRight">A 2D vector containing all \(k_{r,i,j}\) where \(j\) is the index of a particle. <br /></td></tr>
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Friends</h2></td></tr> Friends</h2></td></tr>
<tr class="memitem:a869f032f37d0569ed16f224b4c4356ae"><td class="memItemLeft" align="right" valign="top">class&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae">PenningTrapTest</a></td></tr> <tr class="memitem:a869f032f37d0569ed16f224b4c4356ae"><td class="memItemLeft" align="right" valign="top">class&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae">PenningTrapTest</a></td></tr>
<tr class="memdesc:a869f032f37d0569ed16f224b4c4356ae"><td class="mdescLeft">&#160;</td><td class="mdescRight">Make <a class="el" href="classPenningTrapTest.html" title="Test class for the Penning trap.">PenningTrapTest</a> a friend of <a class="el" href="classPenningTrap.html" title="A class that simulates a Penning trap.">PenningTrap</a>. <br /></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
@ -261,7 +264,7 @@ Friends</h2></td></tr>
</dd> </dd>
</dl> </dl>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00020">20</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#l00115">115</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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@ -321,7 +324,7 @@ Friends</h2></td></tr>
</dd> </dd>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00029">29</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#l00124">124</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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@ -381,7 +384,7 @@ Friends</h2></td></tr>
</dd> </dd>
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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#l00134">134</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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@ -410,7 +413,7 @@ Friends</h2></td></tr>
</dd> </dd>
</dl> </dl>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00101">101</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#l00158">158</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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@ -525,7 +528,7 @@ Friends</h2></td></tr>
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<dl class="section return"><dt>Returns</dt><dd>vec3 </dd></dl> <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#l00114">114</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#l00066">66</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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@ -562,7 +565,7 @@ Friends</h2></td></tr>
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<dl class="section return"><dt>Returns</dt><dd>vec3 </dd></dl> <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#l00106">106</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#l00058">58</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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@ -611,7 +614,7 @@ Friends</h2></td></tr>
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<dl class="section return"><dt>Returns</dt><dd>vec3 </dd></dl> <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#l00119">119</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#l00071">71</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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@ -721,7 +724,7 @@ Friends</h2></td></tr>
</dl> </dl>
<dl class="section return"><dt>Returns</dt><dd>vec3 </dd></dl> <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#l00039">39</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
</div> </div>
</div> </div>
@ -766,7 +769,7 @@ Friends</h2></td></tr>
</dd> </dd>
</dl> </dl>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00053">53</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#l00148">148</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
</div> </div>
</div> </div>
@ -804,7 +807,7 @@ Friends</h2></td></tr>
</dd> </dd>
</dl> </dl>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8cpp_source.html#l00046">46</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#l00141">141</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
</div> </div>
</div> </div>
@ -895,7 +898,7 @@ Friends</h2></td></tr>
</dl> </dl>
<dl class="section return"><dt>Returns</dt><dd>vec3 </dd></dl> <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#l00155">155</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#l00107">107</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
</div> </div>
</div> </div>
@ -933,7 +936,7 @@ Friends</h2></td></tr>
</dl> </dl>
<dl class="section return"><dt>Returns</dt><dd>vec3 </dd></dl> <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#l00130">130</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#l00082">82</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
</div> </div>
</div> </div>
@ -970,7 +973,7 @@ Friends</h2></td></tr>
</dl> </dl>
<dl class="section return"><dt>Returns</dt><dd>vec3 </dd></dl> <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#l00143">143</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#l00095">95</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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@ -1026,7 +1029,7 @@ Friends</h2></td></tr>
</dl> </dl>
<dl class="section return"><dt>Returns</dt><dd>vec3 </dd></dl> <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#l00063">63</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#l00020">20</a> of file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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@ -1111,7 +1114,9 @@ Friends</h2></td></tr>
</table> </table>
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<p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00232">232</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p> <p>Make <a class="el" href="classPenningTrapTest.html" title="Test class for the Penning trap.">PenningTrapTest</a> a friend of <a class="el" href="classPenningTrap.html" title="A class that simulates a Penning trap.">PenningTrap</a>. </p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00035">35</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p>
</div> </div>
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@ -1138,7 +1143,7 @@ Friends</h2></td></tr>
<p>Magnetic field strength. </p> <p>Magnetic field strength. </p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00034">34</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p> <p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00037">37</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p>
</div> </div>
</div> </div>
@ -1164,7 +1169,7 @@ Friends</h2></td></tr>
<p>Characteristic dimension. </p> <p>Characteristic dimension. </p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00037">37</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p> <p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00040">40</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p>
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@ -1187,9 +1192,10 @@ Friends</h2></td></tr>
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<p>A 2D vector containing all \(k_{i,j}\) where \(j\) is the index of a particle </p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00042">42</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p> <p>A 2D vector containing all \(k_{r,i,j}\) where \(j\) is the index of a particle. </p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00052">52</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p>
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@ -1212,9 +1218,10 @@ Friends</h2></td></tr>
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<p>A 2D vector containing all \(k_{i,j}\) where \(j\) is the index of a particle </p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00040">40</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p> <p>A 2D vector containing all \(k_{v,i,j}\) where \(j\) is the index of a particle. </p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00047">47</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p>
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@ -1240,7 +1247,7 @@ Friends</h2></td></tr>
<p>The particles in the Penning trap. </p> <p>The particles in the Penning trap. </p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00039">39</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p> <p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00042">42</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p>
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@ -1266,7 +1273,7 @@ Friends</h2></td></tr>
<p>Time-dependent perturbation. </p> <p>Time-dependent perturbation. </p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00036">36</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p> <p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00039">39</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p>
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@ -1292,7 +1299,7 @@ Friends</h2></td></tr>
<p>Current time. </p> <p>Current time. </p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00038">38</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p> <p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00041">41</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p>
</div> </div>
</div> </div>
@ -1318,7 +1325,7 @@ Friends</h2></td></tr>
<p>Applied potential. </p> <p>Applied potential. </p>
<p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00035">35</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p> <p class="definition">Definition at line <a class="el" href="PenningTrap_8hpp_source.html#l00038">38</a> of file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p>
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1
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<li>particles&#160;:&#160;<a class="el" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">PenningTrap</a></li> <li>particles&#160;:&#160;<a class="el" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">PenningTrap</a></li>
<li>PenningTrap&#160;:&#160;<a class="el" href="classParticle.html#aa797d319549dc2a0beb06cdbfd430232">Particle</a>, <a class="el" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap</a></li> <li>PenningTrap&#160;:&#160;<a class="el" href="classParticle.html#aa797d319549dc2a0beb06cdbfd430232">Particle</a>, <a class="el" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap</a></li>
<li>PenningTrapTest&#160;:&#160;<a class="el" href="classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae">PenningTrap</a></li>
<li>perturbation&#160;:&#160;<a class="el" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">PenningTrap</a></li> <li>perturbation&#160;:&#160;<a class="el" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">PenningTrap</a></li>
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1
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@ -100,6 +100,7 @@ $(document).ready(function(){initNavTree('functions_rela.html',''); initResizabl
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&#160;<ul> &#160;<ul>
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<li>PenningTrapTest&#160;:&#160;<a class="el" href="classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae">PenningTrap</a></li>
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2
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@ -423,7 +423,7 @@ $(document).ready(function(){initNavTree('main_8cpp_source.html',''); initResiza
<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="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"><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"><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#l00053">PenningTrap.cpp:53</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_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_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>
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17
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<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_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="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"><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#l00130">PenningTrap.cpp:130</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#l00143">PenningTrap.cpp:143</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#l00114">PenningTrap.cpp:114</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#l00106">PenningTrap.cpp:106</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#l00101">PenningTrap.cpp:101</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#l00119">PenningTrap.cpp:119</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="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"><div class="ttname"><a href="constants_8hpp.html">constants.hpp</a></div><div class="ttdoc">Library of constants.</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> <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>