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<dd> <dd>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl> Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>0.1</dd></dl> <dl class="section version"><dt>Version</dt><dd>0.1</dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000006">Bug:</a></b></dt><dd>No known bugs</dd></dl> <dl class="bug"><dt><b><a class="el" href="bug.html#_bug000007">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<p class="definition">Definition in file <a class="el" href="Particle_8cpp_source.html">Particle.cpp</a>.</p> <p class="definition">Definition in file <a class="el" href="Particle_8cpp_source.html">Particle.cpp</a>.</p>
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@ -102,24 +102,24 @@ $(document).ready(function(){initNavTree('Particle_8cpp_source.html',''); initRe
</div><!--header--> </div><!--header-->
<div class="contents"> <div class="contents">
<a href="Particle_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span> </div> <a href="Particle_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span> </div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="preprocessor">#include &quot;<a class="code" href="Particle_8hpp.html">Particle.hpp</a>&quot;</span></div> <div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#include &quot;<a class="code" href="Particle_8hpp.html">Particle.hpp</a>&quot;</span></div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span> </div> <div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> </div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"><a class="line" href="classParticle.html#a00e108823877a25513ccae7cac011b4c"> 16</a></span><a class="code hl_function" href="classParticle.html#a00e108823877a25513ccae7cac011b4c">Particle::Particle</a>(<span class="keywordtype">double</span> q, <span class="keywordtype">double</span> m,</div> <div class="line"><a id="l00015" name="l00015"></a><span class="lineno"><a class="line" href="classParticle.html#a7af9f8d1fef63dd7643b06629ac7bef4"> 15</a></span><a class="code hl_function" href="classParticle.html#a7af9f8d1fef63dd7643b06629ac7bef4">Particle::Particle</a>(<span class="keywordtype">double</span> q, <span class="keywordtype">double</span> m,</div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> arma::vec::fixed&lt;3&gt; r_vec,</div> <div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> arma::vec::fixed&lt;3&gt; r_vec,</div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span> arma::vec::fixed&lt;3&gt; v_vec)</div> <div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> arma::vec::fixed&lt;3&gt; v_vec)</div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span>{</div> <div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span>{</div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// Giving the particle its properties</span></div> <div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// Giving the particle its properties</span></div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span> this-&gt;q = <a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>;</div> <div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> this-&gt;q = <a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>;</div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> this-&gt;m = <a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>;</div> <div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span> this-&gt;m = <a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>;</div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> this-&gt;r_vec = <a class="code hl_variable" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a>;</div> <div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> this-&gt;r_vec = <a class="code hl_variable" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">r_vec</a>;</div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> this-&gt;v_vec = <a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a>;</div> <div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> this-&gt;v_vec = <a class="code hl_variable" href="classParticle.html#a879692772803d6ab65fa4993b54aea6e">v_vec</a>;</div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span>}</div> <div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</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_a00e108823877a25513ccae7cac011b4c"><div class="ttname"><a href="classParticle.html#a00e108823877a25513ccae7cac011b4c">Particle::Particle</a></div><div class="ttdeci">Particle(double q, double m, arma::vec::fixed&lt; 3 &gt; r_vec, arma::vec::fixed&lt; 3 &gt; v_vec)</div><div class="ttdoc">Initialize the particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8cpp_source.html#l00016">Particle.cpp:16</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#l00023">Particle.hpp:23</a></div></div>
<div class="ttc" id="aclassParticle_html_a4a5d22c7aeca66f67d083f270cba25df"><div class="ttname"><a href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">Particle::v_vec</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; v_vec</div><div class="ttdoc">velocity</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00024">Particle.hpp:24</a></div></div> <div class="ttc" id="aclassParticle_html_a7af9f8d1fef63dd7643b06629ac7bef4"><div class="ttname"><a href="classParticle.html#a7af9f8d1fef63dd7643b06629ac7bef4">Particle::Particle</a></div><div class="ttdeci">Particle(double q, double m, vec_3d r_vec, vec_3d v_vec)</div><div class="ttdoc">Initialize the particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8cpp_source.html#l00015">Particle.cpp:15</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#l00021">Particle.hpp:21</a></div></div> <div class="ttc" id="aclassParticle_html_a879692772803d6ab65fa4993b54aea6e"><div class="ttname"><a href="classParticle.html#a879692772803d6ab65fa4993b54aea6e">Particle::v_vec</a></div><div class="ttdeci">vec_3d 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_acf1a0f3c978b06d76df5bb4279594467"><div class="ttname"><a href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">Particle::r_vec</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; r_vec</div><div class="ttdoc">position</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00023">Particle.hpp:23</a></div></div> <div class="ttc" id="aclassParticle_html_aedcc7e1bc53b0e2b1a4a07c9a1b47563"><div class="ttname"><a href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle::m</a></div><div class="ttdeci">double m</div><div class="ttdoc">Mass.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00024">Particle.hpp:24</a></div></div>
<div class="ttc" id="aclassParticle_html_aedcc7e1bc53b0e2b1a4a07c9a1b47563"><div class="ttname"><a href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle::m</a></div><div class="ttdeci">double m</div><div class="ttdoc">Mass.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00022">Particle.hpp:22</a></div></div> <div class="ttc" id="aclassParticle_html_af9497cd8f2dcad0fad54f571ddb383e6"><div class="ttname"><a href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">Particle::r_vec</a></div><div class="ttdeci">vec_3d r_vec</div><div class="ttdoc">position</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00025">Particle.hpp:25</a></div></div>
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<p>A class that holds the properties of a particle. <p>A class that holds the properties of a particle.
<a href="#details">More...</a></p> <a href="#details">More...</a></p>
<div class="textblock"><code>#include &lt;armadillo&gt;</code><br /> <div class="textblock"><code>#include &lt;armadillo&gt;</code><br />
<code>#include &quot;<a class="el" href="typedefs_8hpp_source.html">typedefs.hpp</a>&quot;</code><br />
</div> </div>
<p><a href="Particle_8hpp_source.html">Go to the source code of this file.</a></p> <p><a href="Particle_8hpp_source.html">Go to the source code of this file.</a></p>
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@ -107,28 +107,30 @@ $(document).ready(function(){initNavTree('Particle_8hpp_source.html',''); initRe
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> </div> <div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> </div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include &lt;armadillo&gt;</span></div> <div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include &lt;armadillo&gt;</span></div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> </div> <div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> </div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"><a class="line" href="classParticle.html"> 19</a></span><span class="keyword">class </span><a class="code hl_class" href="classParticle.html">Particle</a> {</div> <div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="preprocessor">#include &quot;<a class="code" href="typedefs_8hpp.html">typedefs.hpp</a>&quot;</span></div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span><span class="keyword">private</span>:</div> <div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span> </div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"><a class="line" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1"> 21</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>; </div> <div class="line"><a id="l00021" name="l00021"></a><span class="lineno"><a class="line" href="classParticle.html"> 21</a></span><span class="keyword">class </span><a class="code hl_class" href="classParticle.html">Particle</a> {</div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"><a class="line" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563"> 22</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>; </div> <div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span><span class="keyword">private</span>:</div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"><a class="line" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467"> 23</a></span> arma::vec::fixed&lt;3&gt; <a class="code hl_variable" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a>; </div> <div class="line"><a id="l00023" name="l00023"></a><span class="lineno"><a class="line" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1"> 23</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>; </div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"><a class="line" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df"> 24</a></span> arma::vec::fixed&lt;3&gt; <a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a>; </div> <div class="line"><a id="l00024" name="l00024"></a><span class="lineno"><a class="line" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563"> 24</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>; </div>
<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"><a class="line" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6"> 25</a></span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_variable" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">r_vec</a>; </div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span><span class="keyword">public</span>:</div> <div class="line"><a id="l00026" name="l00026"></a><span class="lineno"><a class="line" href="classParticle.html#a879692772803d6ab65fa4993b54aea6e"> 26</a></span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_variable" href="classParticle.html#a879692772803d6ab65fa4993b54aea6e">v_vec</a>; </div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> <a class="code hl_class" href="classParticle.html">Particle</a>(<span class="keywordtype">double</span> <a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>, </div> <div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> </div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> arma::vec::fixed&lt;3&gt; <a class="code hl_variable" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a>, </div> <div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span><span class="keyword">public</span>:</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> arma::vec::fixed&lt;3&gt; <a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a>);</div> <div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> <a class="code hl_class" href="classParticle.html">Particle</a>(<span class="keywordtype">double</span> <a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>, <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_variable" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">r_vec</a>, <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_variable" href="classParticle.html#a879692772803d6ab65fa4993b54aea6e">v_vec</a>);</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> </div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"><a class="line" href="classParticle.html#aa797d319549dc2a0beb06cdbfd430232"> 38</a></span> <span class="keyword">friend</span> <span class="keyword">class </span><a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>;</div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span>};</div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> </div> <div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> </div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span><span class="preprocessor">#endif</span></div> <div class="line"><a id="l00043" name="l00043"></a><span class="lineno"><a class="line" href="classParticle.html#aa797d319549dc2a0beb06cdbfd430232"> 43</a></span> <span class="keyword">friend</span> <span class="keyword">class </span><a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>;</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#l00019">Particle.hpp:19</a></div></div> <div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span>};</div>
<div class="ttc" id="aclassParticle_html_a4a5d22c7aeca66f67d083f270cba25df"><div class="ttname"><a href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">Particle::v_vec</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; v_vec</div><div class="ttdoc">velocity</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00024">Particle.hpp:24</a></div></div> <div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> </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#l00021">Particle.hpp:21</a></div></div> <div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span><span class="preprocessor">#endif</span></div>
<div class="ttc" id="aclassParticle_html_acf1a0f3c978b06d76df5bb4279594467"><div class="ttname"><a href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">Particle::r_vec</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; r_vec</div><div class="ttdoc">position</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00023">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#l00021">Particle.hpp:21</a></div></div>
<div class="ttc" id="aclassParticle_html_aedcc7e1bc53b0e2b1a4a07c9a1b47563"><div class="ttname"><a href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle::m</a></div><div class="ttdeci">double m</div><div class="ttdoc">Mass.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00022">Particle.hpp:22</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#l00023">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#l00029">PenningTrap.hpp:29</a></div></div> <div class="ttc" id="aclassParticle_html_a879692772803d6ab65fa4993b54aea6e"><div class="ttname"><a href="classParticle.html#a879692772803d6ab65fa4993b54aea6e">Particle::v_vec</a></div><div class="ttdeci">vec_3d 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_aedcc7e1bc53b0e2b1a4a07c9a1b47563"><div class="ttname"><a href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle::m</a></div><div class="ttdeci">double m</div><div class="ttdoc">Mass.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00024">Particle.hpp:24</a></div></div>
<div class="ttc" id="aclassParticle_html_af9497cd8f2dcad0fad54f571ddb383e6"><div class="ttname"><a href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">Particle::r_vec</a></div><div class="ttdeci">vec_3d r_vec</div><div class="ttdoc">position</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00025">Particle.hpp:25</a></div></div>
<div class="ttc" id="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#l00030">PenningTrap.hpp:30</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_a9f33f4962c8fb62cc5ccd0e4e039a8df"><div class="ttname"><a href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; vec_3d</div><div class="ttdoc">Typedef for a fixed 3d arma vector.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00036">typedefs.hpp:36</a></div></div>
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<a href="#details">More...</a></p> <a href="#details">More...</a></p>
<div class="textblock"><code>#include &quot;<a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>&quot;</code><br /> <div class="textblock"><code>#include &quot;<a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>&quot;</code><br />
<code>#include &quot;<a class="el" href="constants_8hpp_source.html">constants.hpp</a>&quot;</code><br /> <code>#include &quot;<a class="el" href="constants_8hpp_source.html">constants.hpp</a>&quot;</code><br />
<code>#include &quot;<a class="el" href="typedefs_8hpp_source.html">typedefs.hpp</a>&quot;</code><br />
<code>#include &quot;<a class="el" href="utils_8hpp_source.html">utils.hpp</a>&quot;</code><br /> <code>#include &quot;<a class="el" href="utils_8hpp_source.html">utils.hpp</a>&quot;</code><br />
</div> </div>
<p><a href="PenningTrap_8cpp_source.html">Go to the source code of this file.</a></p> <p><a href="PenningTrap_8cpp_source.html">Go to the source code of this file.</a></p>
@ -115,10 +116,7 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp.html',''); initResiza
<dd> <dd>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl> Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>0.1</dd></dl> <dl class="section version"><dt>Version</dt><dd>0.1</dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000007">Bug:</a></b></dt><dd>No known bugs</dd></dl> <dl class="bug"><dt><b><a class="el" href="bug.html#_bug000008">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000001">Todo:</a></b></dt><dd><p class="startdd">Implement evolve_RK4 </p>
<p class="enddd">Implement evolve_forward_euler </p>
</dd></dl>
<p class="definition">Definition in file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p> <p class="definition">Definition in file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
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@ -102,205 +102,311 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp_source.html',''); ini
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<a href="PenningTrap_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span> </div> <a href="PenningTrap_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span> </div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div> <div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="preprocessor">#include &quot;<a class="code" href="constants_8hpp.html">constants.hpp</a>&quot;</span></div> <div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="preprocessor">#include &quot;<a class="code" href="constants_8hpp.html">constants.hpp</a>&quot;</span></div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#include &quot;<a class="code" href="utils_8hpp.html">utils.hpp</a>&quot;</span></div> <div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include &quot;<a class="code" href="typedefs_8hpp.html">typedefs.hpp</a>&quot;</span></div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span> </div> <div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="preprocessor">#include &quot;<a class="code" href="utils_8hpp.html">utils.hpp</a>&quot;</span></div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560"> 20</a></span><a class="code hl_function" href="classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560">PenningTrap::PenningTrap</a>(<span class="keywordtype">double</span> B_0, <span class="keywordtype">double</span> V_0, <span class="keywordtype">double</span> d)</div> <div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> </div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span>{</div> <div class="line"><a id="l00018" name="l00018"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ae670d7de621acdb343b01af098086f63"> 18</a></span><a class="code hl_function" href="classPenningTrap.html#ae670d7de621acdb343b01af098086f63">PenningTrap::PenningTrap</a>(<span class="keywordtype">double</span> B_0, std::function&lt;<span class="keywordtype">double</span>(<span class="keywordtype">double</span>)&gt; V_0,</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="l00019" name="l00019"></a><span class="lineno"> 19</span> <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</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="l00020" name="l00020"></a><span class="lineno"> 20</span>{</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="l00021" name="l00021"></a><span class="lineno"> 21</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> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#aaf105828121c4a33cc2b217453c20317">V_0</a> = <a class="code hl_variable" href="classPenningTrap.html#aaf105828121c4a33cc2b217453c20317">V_0</a>;</div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</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> 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>}</div> <div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span>}</div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> </div> <div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> </div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8"> 27</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="l00027" name="l00027"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a763700316b502d5900e587c1f61e6bf1"> 27</a></span><a class="code hl_function" href="classPenningTrap.html#ae670d7de621acdb343b01af098086f63">PenningTrap::PenningTrap</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i, <span class="keywordtype">double</span> B_0,</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> std::function&lt;<span class="keywordtype">double</span>(<span class="keywordtype">double</span>)&gt; 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> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(particle);</div> <div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</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>}</div> <div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span>{</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> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> r, v;</div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b"> 32</a></span>arma::vec <a class="code hl_function" href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">PenningTrap::external_E_field</a>(arma::vec r)</div> <div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; i; j++) {</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span>{</div> <div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> r = <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>().randn() * .1 * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> arma::vec::fixed&lt;3&gt; res;</div> <div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> v = <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>().randn() * .1 * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> <span class="keywordtype">double</span> f = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</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="l00035" name="l00035"></a><span class="lineno"> 35</span> this-&gt;<a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., r, v));</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> res(0) = r(0);</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> res(1) = r(1);</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> res(2) = -2. * r(2);</div> <div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> </div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> </div> <div class="line"><a id="l00039" name="l00039"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a67139e04ef69c0bcffde8f30f67cbf73"> 39</a></span><a class="code hl_function" href="classPenningTrap.html#ae670d7de621acdb343b01af098086f63">PenningTrap::PenningTrap</a>(std::vector&lt;Particle&gt; particles, <span class="keywordtype">double</span> B_0,</div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> <span class="keywordflow">return</span> f * res;</div> <div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> std::function&lt;<span class="keywordtype">double</span>(<span class="keywordtype">double</span>)&gt; V_0, <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span>}</div> <div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> : <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(B_0, V_0, d)</div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> </div> <div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span>{</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784"> 43</a></span>arma::vec <a class="code hl_function" href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">PenningTrap::external_B_field</a>(arma::vec r)</div> <div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> this-&gt;particles = <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span>{</div> <div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span>}</div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> arma::vec::fixed&lt;3&gt; res{0., 0., this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>};</div> <div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> </div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> </div> <div class="line"><a id="l00046" name="l00046"></a><span class="lineno"><a class="line" href="classPenningTrap.html#af98a720da60b0e1a62aefa5f5cb37c1e"> 46</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#af98a720da60b0e1a62aefa5f5cb37c1e">PenningTrap::v_func</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> j, <span class="keywordtype">double</span> dt)</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordflow">return</span> res;</div> <div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span>{</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span>}</div> <div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> <span class="keywordflow">switch</span> (i) {</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> </div> <div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> <span class="keywordflow">case</span> 0:</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182"> 50</a></span>arma::vec <a class="code hl_function" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">PenningTrap::force_on_particle</a>(<span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j)</div> <div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</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="l00051" name="l00051"></a><span class="lineno"> 51</span>{</div> <div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> <span class="keywordflow">case</span> 1:</div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> <span class="comment">// Calculate the difference between the particles&#39; position</span></div> <div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> <span class="keywordflow">return</span> .5 * dt * this-&gt;k_v[1][j];</div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> arma::vec::fixed&lt;3&gt; res =</div> <div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> <span class="keywordflow">case</span> 2:</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i).r_vec - this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(j).r_vec;</div> <div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> <span class="keywordflow">return</span> dt * this-&gt;k_v[2][j];</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> </div> <div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> <span class="keywordflow">case</span> 3:</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> <span class="comment">// Get the distance between the particles</span></div> <div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> <span class="keywordflow">return</span> (dt / 6.) * (this-&gt;k_v[0][j].eval() + this-&gt;k_v[1][j].eval() +</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> <span class="keywordtype">double</span> norm = arma::norm(res);</div> <div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> this-&gt;k_v[2][j].eval() + this-&gt;k_v[3][j].eval());</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> </div> <div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> <span class="keywordflow">default</span>:</div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> <span class="comment">// Multiply res with p_j&#39;s charge divided by the norm cubed</span></div> <div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> res *= this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(j).q / (norm * norm * norm);</div> <div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> abort();</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> <span class="keywordflow">return</span> res;</div> <div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span>}</div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span>}</div> <div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> </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"><a class="line" href="classPenningTrap.html#a43e74792ab4b3f9299f35cb64bdb2648"> 64</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#a43e74792ab4b3f9299f35cb64bdb2648">PenningTrap::r_func</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> j, <span class="keywordtype">double</span> dt)</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee"> 65</a></span>arma::vec <a class="code hl_function" href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">PenningTrap::total_force_external</a>(<span class="keywordtype">int</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>{</div> <div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> <span class="keywordflow">switch</span> (i) {</div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> <a class="code hl_class" href="classParticle.html">Particle</a> p = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i);</div> <div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> <span class="keywordflow">case</span> 0:</div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> </div> <div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</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="l00069" name="l00069"></a><span class="lineno"> 69</span> arma::vec::fixed&lt;3&gt; B = this-&gt;<a class="code hl_function" href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">external_B_field</a>(p.<a class="code hl_variable" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a>);</div> <div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> <span class="keywordflow">case</span> 1:</div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> </div> <div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> <span class="keywordflow">return</span> .5 * dt * this-&gt;k_r[1][j];</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> arma::vec::fixed&lt;3&gt; v_cross_B{p.<a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a>(1) * B(2) - p.<a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a>(2) * B(1),</div> <div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> <span class="keywordflow">case</span> 2:</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> p.<a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a>(2) * B(0) - p.<a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a>(0) * B(2),</div> <div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> <span class="keywordflow">return</span> dt * this-&gt;k_r[2][j];</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> p.<a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a>(0) * B(1) - p.<a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a>(1) * B(0)};</div> <div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> <span class="keywordflow">case</span> 3:</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> </div> <div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> <span class="keywordflow">return</span> (dt / 6.) * (this-&gt;k_r[0][j].eval() + this-&gt;k_r[1][j].eval() +</div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> arma::vec force = p.<a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a> * (this-&gt;<a class="code hl_function" href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">external_E_field</a>(p.<a class="code hl_variable" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a>) + v_cross_B);</div> <div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> this-&gt;k_r[2][j].eval() + this-&gt;k_r[3][j].eval());</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> <span class="keywordflow">default</span>:</div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> <span class="keywordflow">return</span> force;</div> <div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span>}</div> <div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> abort();</div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> </div> <div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> }</div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d"> 80</a></span>arma::vec <a class="code hl_function" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">PenningTrap::total_force_particles</a>(<span class="keywordtype">int</span> i)</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"> 82</span> <a class="code hl_class" href="classParticle.html">Particle</a> p = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i);</div> <div class="line"><a id="l00082" name="l00082"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8"> 82</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="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> arma::vec res(3);</div> <div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> this-&gt;particles.push_back(particle);</div>
<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> </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">for</span> (<span class="keywordtype">int</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="l00086" name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> <span class="keywordflow">if</span> (i == j) {</div> <div class="line"><a id="l00087" name="l00087"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9"> 87</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9">PenningTrap::external_E_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> r)</div>
<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span> <span class="keywordflow">continue</span>;</div> <div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span>{</div>
<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> }</div> <div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> r(2) *= -2.;</div>
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> </div> <div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> <span class="keywordtype">double</span> f = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#aaf105828121c4a33cc2b217453c20317">V_0</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="l00091" name="l00091"></a><span class="lineno"> 91</span> res += this-&gt;<a class="code hl_function" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">force_on_particle</a>(i, j);</div> <div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> </div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> }</div> <div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> <span class="keywordflow">return</span> f * r;</div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> </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> res *= <a class="code hl_define" href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">K_E</a> * (p.<a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a> / p.<a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>);</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> </div> <div class="line"><a id="l00095" name="l00095"></a><span class="lineno"><a class="line" href="classPenningTrap.html#acbf065c9c125682329ad82a8d166554c"> 95</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#acbf065c9c125682329ad82a8d166554c">PenningTrap::external_B_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> r)</div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> <span class="keywordflow">return</span> res;</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>}</div> <div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>{0., 0., this-&gt;B_0};</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"><a class="line" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be"> 99</a></span>arma::vec <a class="code hl_function" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">PenningTrap::total_force</a>(<span class="keywordtype">int</span> i)</div> <div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> </div>
<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span>{</div> <div class="line"><a id="l00100" name="l00100"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce"> 100</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce">PenningTrap::force_on_particle</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> j)</div>
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> <span class="keywordflow">return</span> this-&gt;<a class="code hl_function" href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">total_force_external</a>(i) - this-&gt;<a class="code hl_function" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">total_force_particles</a>(i);</div> <div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span>{</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> <a class="code hl_class" href="classParticle.html">Particle</a> p_j = this-&gt;particles[j];</div>
<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> </div> <div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> <span class="comment">// Calculate the difference between the particles&#39; position</span></div>
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9"> 104</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9">PenningTrap::evolve_RK4</a>(<span class="keywordtype">double</span> dt)</div> <div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> res = this-&gt;particles[i].<a class="code hl_variable" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">r_vec</a> - p_j.<a class="code hl_variable" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">r_vec</a>;</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"> 106</span> std::vector&lt;Particle&gt; tmp_particles = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div> <div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> <span class="comment">// Get the distance between the particles</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"> 107</span> <span class="keywordtype">double</span> norm = arma::norm(res, 2);</div>
<div class="line"><a id="l00108" name="l00108"></a><span class="lineno"> 108</span> arma::vec::fixed&lt;3&gt; *k_v = <span class="keyword">new</span> arma::vec::fixed&lt;3&gt;[this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size()*4];</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> arma::vec::fixed&lt;3&gt; *k_r = <span class="keyword">new</span> arma::vec::fixed&lt;3&gt;[this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size()*4];</div> <div class="line"><a id="l00109" name="l00109"></a><span class="lineno"> 109</span> <span class="comment">// Multiply res with p_j&#39;s charge divided by the norm cubed</span></div>
<div class="line"><a id="l00110" name="l00110"></a><span class="lineno"> 110</span> </div> <div class="line"><a id="l00110" name="l00110"></a><span class="lineno"> 110</span> </div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> <span class="keywordtype">int</span> size = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div> <div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>(res * p_j.<a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a> / (norm * norm * norm));</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>}</div>
<div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i=0; i&lt;size; i++) {</div> <div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span> </div>
<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span> k_v[i] = this-&gt;<a class="code hl_function" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">total_force</a>(i)/this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i).m;</div> <div class="line"><a id="l00114" name="l00114"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56"> 114</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">PenningTrap::total_force_external</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i)</div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> k_r[i] = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i).v_vec;</div> <div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span>{</div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> }</div> <div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> <a class="code hl_class" href="classParticle.html">Particle</a> p = this-&gt;particles[i];</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> </div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i=0; i&lt;size; i++) {</div> <div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> <span class="keywordflow">if</span> (arma::norm(p.<a class="code hl_variable" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">r_vec</a>) &gt; this-&gt;d) {</div>
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</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>.at(i);</div> <div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>{0., 0., 0.};</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> }</div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> p-&gt;<a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a> = tmp_particles.at(i).v_vec + (dt/2)*k_v[i];</div> <div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> </div>
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> p-&gt;<a class="code hl_variable" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a> = tmp_particles.at(i).r_vec + (dt/2)*k_r[i];</div> <div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> force =</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> p.<a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a> * (this-&gt;<a class="code hl_function" href="classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9">external_E_field</a>(p.<a class="code hl_variable" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">r_vec</a>) +</div>
<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> </div> <div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> arma::cross(p.<a class="code hl_variable" href="classParticle.html#a879692772803d6ab65fa4993b54aea6e">v_vec</a>, this-&gt;external_B_field(p.<a class="code hl_variable" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">r_vec</a>)));</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> </div>
<div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i=0; i&lt;size; i++) {</div> <div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</span> <span class="keywordflow">return</span> force;</div>
<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span> k_v[1*size + i] = this-&gt;<a class="code hl_function" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">total_force</a>(i)/this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i).m;</div> <div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span>}</div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> k_r[1*size + i] = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i).v_vec;</div> <div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> </div>
<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> }</div> <div class="line"><a id="l00129" name="l00129"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b"> 129</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b">PenningTrap::total_force_particles</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i)</div>
<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> </div> <div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span>{</div>
<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i=0; i&lt;size; i++) {</div> <div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> <a class="code hl_class" href="classParticle.html">Particle</a> p = this-&gt;particles[i];</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>.at(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> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> res;</div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> p-&gt;<a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a> = tmp_particles.at(i).v_vec + (dt/2)*k_v[1*size + i];</div> <div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> </div>
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> p-&gt;<a class="code hl_variable" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a> = tmp_particles.at(i).r_vec + (dt/2)*k_r[1*size + i];</div> <div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; this-&gt;particles.size(); j++) {</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> <span class="keywordflow">if</span> (i == j) {</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> <span class="keywordflow">continue</span>;</div>
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i=0; i&lt;size; i++) {</div> <div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> }</div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> k_v[2*size + i] = this-&gt;<a class="code hl_function" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">total_force</a>(i)/this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i).m;</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> k_r[2*size + i] = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i).v_vec;</div> <div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> res += this-&gt;<a class="code hl_function" href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce">force_on_particle</a>(i, j);</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"> 141</span> }</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"> 143</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i=0; i&lt;size; i++) {</div> <div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span> <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>(res * <a class="code hl_define" href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">K_E</a> * (p.<a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a> / p.<a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>));</div>
<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"> 144</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>.at(i);</div> <div class="line"><a id="l00144" name="l00144"></a><span class="lineno"> 144</span>}</div>
<div class="line"><a id="l00145" name="l00145"></a><span class="lineno"> 145</span> </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> p-&gt;<a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a> = tmp_particles.at(i).v_vec + dt*k_v[2*size + i];</div> <div class="line"><a id="l00146" name="l00146"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a1f668c4433421136ad51741741aa1bc8"> 146</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#a1f668c4433421136ad51741741aa1bc8">PenningTrap::total_force</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i)</div>
<div class="line"><a id="l00147" name="l00147"></a><span class="lineno"> 147</span> p-&gt;<a class="code hl_variable" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a> = tmp_particles.at(i).r_vec + dt*k_r[2*size + i];</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> }</div> <div class="line"><a id="l00148" name="l00148"></a><span class="lineno"> 148</span> <span class="keywordflow">return</span> this-&gt;<a class="code hl_function" href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">total_force_external</a>(i) - this-&gt;<a class="code hl_function" href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b">total_force_particles</a>(i);</div>
<div class="line"><a id="l00149" name="l00149"></a><span class="lineno"> 149</span> </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> </div>
<div class="line"><a id="l00151" name="l00151"></a><span class="lineno"> 151</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i=0; i&lt;size; i++) {</div> <div class="line"><a id="l00151" name="l00151"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e"> 151</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="l00152" name="l00152"></a><span class="lineno"> 152</span> k_v[3*size + i] = this-&gt;<a class="code hl_function" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">total_force</a>(i)/this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i).m;</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> k_r[3*size + i] = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i).v_vec;</div> <div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</span> </div>
<div class="line"><a id="l00154" name="l00154"></a><span class="lineno"> 154</span> }</div> <div class="line"><a id="l00154" name="l00154"></a><span class="lineno"> 154</span> std::vector&lt;Particle&gt; original_particles = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
<div class="line"><a id="l00155" name="l00155"></a><span class="lineno"> 155</span> </div> <div class="line"><a id="l00155" name="l00155"></a><span class="lineno"> 155</span> std::vector&lt;Particle&gt; tmp_particles = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
<div class="line"><a id="l00156" name="l00156"></a><span class="lineno"> 156</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i=0; i&lt;size; i++) {</div> <div class="line"><a id="l00156" name="l00156"></a><span class="lineno"> 156</span> </div>
<div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</span> <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>.at(i);</div> <div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*force)(<span class="keywordtype">unsigned</span> int);</div>
<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"> 158</span> </div> <div class="line"><a id="l00158" name="l00158"></a><span class="lineno"> 158</span> <span class="keywordflow">if</span> (particle_interaction) {</div>
<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span> p-&gt;<a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a> = tmp_particles.at(i).v_vec + dt*(k_v[i] + k_v[size + i] + k_v[2*size + i] + k_v[3*size + i])/6;</div> <div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span> force = &amp;<a class="code hl_function" href="classPenningTrap.html#a1f668c4433421136ad51741741aa1bc8">PenningTrap::total_force</a>;</div>
<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> p-&gt;<a class="code hl_variable" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a> = tmp_particles.at(i).r_vec + dt*(k_r[i] + k_r[size + i] + k_r[2*size + i] + k_r[3*size + i])/6;</div> <div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> }</div>
<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span> }</div> <div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span> <span class="keywordflow">else</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> force = &amp;<a class="code hl_function" href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">PenningTrap::total_force_external</a>;</div>
<div class="line"><a id="l00163" name="l00163"></a><span class="lineno"> 163</span> <span class="keyword">delete</span> [] k_v;</div> <div class="line"><a id="l00163" name="l00163"></a><span class="lineno"> 163</span> }</div>
<div class="line"><a id="l00164" name="l00164"></a><span class="lineno"> 164</span> <span class="keyword">delete</span> [] k_r;</div> <div class="line"><a id="l00164" name="l00164"></a><span class="lineno"> 164</span> </div>
<div class="line"><a id="l00165" name="l00165"></a><span class="lineno"> 165</span>}</div> <div class="line"><a id="l00165" name="l00165"></a><span class="lineno"> 165</span> <span class="keywordtype">size_t</span> size = this-&gt;particles.size();</div>
<div class="line"><a id="l00166" name="l00166"></a><span class="lineno"> 166</span> </div> <div class="line"><a id="l00166" name="l00166"></a><span class="lineno"> 166</span> </div>
<div class="line"><a id="l00167" name="l00167"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965"> 167</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965">PenningTrap::evolve_forward_euler</a>(<span class="keywordtype">double</span> dt)</div> <div class="line"><a id="l00167" name="l00167"></a><span class="lineno"> 167</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a> = <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(4, <a class="code hl_typedef" href="typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23">sim_cols</a>(size));</div>
<div class="line"><a id="l00168" name="l00168"></a><span class="lineno"> 168</span>{</div> <div class="line"><a id="l00168" name="l00168"></a><span class="lineno"> 168</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a> = <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(4, <a class="code hl_typedef" href="typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23">sim_cols</a>(size));</div>
<div class="line"><a id="l00169" name="l00169"></a><span class="lineno"> 169</span> std::vector&lt;Particle&gt; new_state = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div> <div class="line"><a id="l00169" name="l00169"></a><span class="lineno"> 169</span> </div>
<div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> </div> <div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 4; i++) {</div>
<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</span> <a class="code hl_class" href="classParticle.html">Particle</a> *p;</div> <div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> </div> <div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; this-&gt;particles.size(); j++) {</div>
<div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span><span class="preprocessor">#pragma omp parallel for private(p)</span></div> <div class="line"><a id="l00173" name="l00173"></a><span class="lineno"> 173</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>[i][j] = (this-&gt;*force)(j) / this-&gt;particles[j].m;</div>
<div class="line"><a id="l00174" name="l00174"></a><span class="lineno"> 174</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</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="l00174" name="l00174"></a><span class="lineno"> 174</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>[i][j] = this-&gt;particles[j].v_vec;</div>
<div class="line"><a id="l00175" name="l00175"></a><span class="lineno"> 175</span> p = &amp;new_state.at(i);</div> <div class="line"><a id="l00175" name="l00175"></a><span class="lineno"> 175</span> </div>
<div class="line"><a id="l00176" name="l00176"></a><span class="lineno"> 176</span> p-&gt;<a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a> += dt * this-&gt;<a class="code hl_function" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">total_force</a>(i) / new_state.at(i).m;</div> <div class="line"><a id="l00176" name="l00176"></a><span class="lineno"> 176</span> <a class="code hl_class" href="classParticle.html">Particle</a> *p = &amp;tmp_particles[j];</div>
<div class="line"><a id="l00177" name="l00177"></a><span class="lineno"> 177</span> p-&gt;<a class="code hl_variable" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a> += dt * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i).v_vec;</div> <div class="line"><a id="l00177" name="l00177"></a><span class="lineno"> 177</span> </div>
<div class="line"><a id="l00178" name="l00178"></a><span class="lineno"> 178</span> }</div> <div class="line"><a id="l00178" name="l00178"></a><span class="lineno"> 178</span> p-&gt;<a class="code hl_variable" href="classParticle.html#a879692772803d6ab65fa4993b54aea6e">v_vec</a> = original_particles[j].v_vec + this-&gt;<a class="code hl_function" href="classPenningTrap.html#af98a720da60b0e1a62aefa5f5cb37c1e">v_func</a>(i, j, dt);</div>
<div class="line"><a id="l00179" name="l00179"></a><span class="lineno"> 179</span> </div> <div class="line"><a id="l00179" name="l00179"></a><span class="lineno"> 179</span> p-&gt;<a class="code hl_variable" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">r_vec</a> = original_particles[j].r_vec + this-&gt;<a class="code hl_function" href="classPenningTrap.html#a43e74792ab4b3f9299f35cb64bdb2648">r_func</a>(i, j, dt);</div>
<div class="line"><a id="l00180" name="l00180"></a><span class="lineno"> 180</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a> = new_state;</div> <div class="line"><a id="l00180" name="l00180"></a><span class="lineno"> 180</span> }</div>
<div class="line"><a id="l00181" name="l00181"></a><span class="lineno"> 181</span>}</div> <div class="line"><a id="l00181" name="l00181"></a><span class="lineno"> 181</span> this-&gt;particles = tmp_particles;</div>
<div class="line"><a id="l00182" name="l00182"></a><span class="lineno"> 182</span> </div> <div class="line"><a id="l00182" name="l00182"></a><span class="lineno"> 182</span> }</div>
<div class="line"><a id="l00183" name="l00183"></a><span class="lineno"> 183</span>arma::vec PenningTrap::get_particle(<span class="keywordtype">int</span> i)</div> <div class="line"><a id="l00183" name="l00183"></a><span class="lineno"> 183</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> += dt;</div>
<div class="line"><a id="l00184" name="l00184"></a><span class="lineno"> 184</span>{</div> <div class="line"><a id="l00184" name="l00184"></a><span class="lineno"> 184</span>}</div>
<div class="line"><a id="l00185" name="l00185"></a><span class="lineno"> 185</span> <span class="keywordflow">return</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.at(i).r_vec;</div> <div class="line"><a id="l00185" name="l00185"></a><span class="lineno"> 185</span> </div>
<div class="line"><a id="l00186" name="l00186"></a><span class="lineno"> 186</span>}</div> <div class="line"><a id="l00186" name="l00186"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e"> 186</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction)</div>
<div class="line"><a id="l00187" name="l00187"></a><span class="lineno"> 187</span> </div> <div class="line"><a id="l00187" name="l00187"></a><span class="lineno"> 187</span>{</div>
<div class="line"><a id="l00188" name="l00188"></a><span class="lineno"> 188</span><span class="keywordtype">double</span> PenningTrap::get_d()</div> <div class="line"><a id="l00188" name="l00188"></a><span class="lineno"> 188</span> std::vector&lt;Particle&gt; new_state = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
<div class="line"><a id="l00189" name="l00189"></a><span class="lineno"> 189</span>{</div> <div class="line"><a id="l00189" name="l00189"></a><span class="lineno"> 189</span> </div>
<div class="line"><a id="l00190" name="l00190"></a><span class="lineno"> 190</span> <span class="keywordflow">return</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</div> <div class="line"><a id="l00190" name="l00190"></a><span class="lineno"> 190</span> <a class="code hl_class" href="classParticle.html">Particle</a> *p;</div>
<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span>}</div> <div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span> </div>
<div class="line"><a id="l00192" name="l00192"></a><span class="lineno"> 192</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*force)(<span class="keywordtype">unsigned</span> int);</div>
<div class="line"><a id="l00193" name="l00193"></a><span class="lineno"> 193</span> <span class="keywordflow">if</span> (particle_interaction) {</div>
<div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> force = &amp;<a class="code hl_function" href="classPenningTrap.html#a1f668c4433421136ad51741741aa1bc8">PenningTrap::total_force</a>;</div>
<div class="line"><a id="l00195" name="l00195"></a><span class="lineno"> 195</span> }</div>
<div class="line"><a id="l00196" name="l00196"></a><span class="lineno"> 196</span> <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00197" name="l00197"></a><span class="lineno"> 197</span> force = &amp;<a class="code hl_function" href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">PenningTrap::total_force_external</a>;</div>
<div class="line"><a id="l00198" name="l00198"></a><span class="lineno"> 198</span> }</div>
<div class="line"><a id="l00199" name="l00199"></a><span class="lineno"> 199</span> </div>
<div class="line"><a id="l00200" name="l00200"></a><span class="lineno"> 200</span><span class="preprocessor">#pragma omp parallel for private(p)</span></div>
<div class="line"><a id="l00201" name="l00201"></a><span class="lineno"> 201</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;particles.size(); i++) {</div>
<div class="line"><a id="l00202" name="l00202"></a><span class="lineno"> 202</span> p = &amp;new_state[i];</div>
<div class="line"><a id="l00203" name="l00203"></a><span class="lineno"> 203</span> p-&gt;<a class="code hl_variable" href="classParticle.html#a879692772803d6ab65fa4993b54aea6e">v_vec</a> += dt * (this-&gt;*force)(i) / p-&gt;<a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>;</div>
<div class="line"><a id="l00204" name="l00204"></a><span class="lineno"> 204</span> p-&gt;<a class="code hl_variable" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">r_vec</a> += dt * this-&gt;particles[i].v_vec;</div>
<div class="line"><a id="l00205" name="l00205"></a><span class="lineno"> 205</span> }</div>
<div class="line"><a id="l00206" name="l00206"></a><span class="lineno"> 206</span> </div>
<div class="line"><a id="l00207" name="l00207"></a><span class="lineno"> 207</span> this-&gt;particles = new_state;</div>
<div class="line"><a id="l00208" name="l00208"></a><span class="lineno"> 208</span> this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> += dt;</div>
<div class="line"><a id="l00209" name="l00209"></a><span class="lineno"> 209</span>}</div>
<div class="line"><a id="l00210" name="l00210"></a><span class="lineno"> 210</span> </div>
<div class="line"><a id="l00211" name="l00211"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a5331837e6dd7bce807a99edd2ba7e854"> 211</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a> <a class="code hl_function" href="classPenningTrap.html#a5331837e6dd7bce807a99edd2ba7e854">PenningTrap::simulate</a>(<span class="keywordtype">double</span> time, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> steps,</div>
<div class="line"><a id="l00212" name="l00212"></a><span class="lineno"> 212</span> std::string method, <span class="keywordtype">bool</span> particle_interaction)</div>
<div class="line"><a id="l00213" name="l00213"></a><span class="lineno"> 213</span>{</div>
<div class="line"><a id="l00214" name="l00214"></a><span class="lineno"> 214</span> <span class="keywordtype">double</span> dt = time / (double)steps;</div>
<div class="line"><a id="l00215" name="l00215"></a><span class="lineno"> 215</span> </div>
<div class="line"><a id="l00216" name="l00216"></a><span class="lineno"> 216</span> <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a> res(this-&gt;particles.size(), <a class="code hl_typedef" href="typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23">sim_cols</a>(steps));</div>
<div class="line"><a id="l00217" name="l00217"></a><span class="lineno"> 217</span> </div>
<div class="line"><a id="l00218" name="l00218"></a><span class="lineno"> 218</span> void (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*func)(double, bool);</div>
<div class="line"><a id="l00219" name="l00219"></a><span class="lineno"> 219</span> <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;rk4&quot;</span>) {</div>
<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span> func = &amp;<a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a>;</div>
<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"> 221</span> }</div>
<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</span> <span class="keywordflow">else</span> <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;euler&quot;</span>) {</div>
<div class="line"><a id="l00223" name="l00223"></a><span class="lineno"> 223</span> func = &amp;<a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>;</div>
<div class="line"><a id="l00224" name="l00224"></a><span class="lineno"> 224</span> }</div>
<div class="line"><a id="l00225" name="l00225"></a><span class="lineno"> 225</span> <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00226" name="l00226"></a><span class="lineno"> 226</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Not a valid method!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00227" name="l00227"></a><span class="lineno"> 227</span> abort();</div>
<div class="line"><a id="l00228" name="l00228"></a><span class="lineno"> 228</span> }</div>
<div class="line"><a id="l00229" name="l00229"></a><span class="lineno"> 229</span> </div>
<div class="line"><a id="l00230" name="l00230"></a><span class="lineno"> 230</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; steps; j++) {</div>
<div class="line"><a id="l00231" name="l00231"></a><span class="lineno"> 231</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;particles.size(); i++) {</div>
<div class="line"><a id="l00232" name="l00232"></a><span class="lineno"> 232</span> res[i][j] = this-&gt;particles[i].r_vec;</div>
<div class="line"><a id="l00233" name="l00233"></a><span class="lineno"> 233</span> }</div>
<div class="line"><a id="l00234" name="l00234"></a><span class="lineno"> 234</span> (this-&gt;*func)(dt, particle_interaction);</div>
<div class="line"><a id="l00235" name="l00235"></a><span class="lineno"> 235</span> }</div>
<div class="line"><a id="l00236" name="l00236"></a><span class="lineno"> 236</span> </div>
<div class="line"><a id="l00237" name="l00237"></a><span class="lineno"> 237</span> <span class="keywordflow">return</span> res;</div>
<div class="line"><a id="l00238" name="l00238"></a><span class="lineno"> 238</span>}</div>
<div class="line"><a id="l00239" name="l00239"></a><span class="lineno"> 239</span> </div>
<div class="line"><a id="l00240" name="l00240"></a><span class="lineno"><a class="line" href="classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57"> 240</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57">PenningTrap::write_simulation_to_dir</a>(std::string path, <span class="keywordtype">double</span> time,</div>
<div class="line"><a id="l00241" name="l00241"></a><span class="lineno"> 241</span> <span class="keywordtype">int</span> steps, std::string method,</div>
<div class="line"><a id="l00242" name="l00242"></a><span class="lineno"> 242</span> <span class="keywordtype">bool</span> particle_interaction)</div>
<div class="line"><a id="l00243" name="l00243"></a><span class="lineno"> 243</span>{</div>
<div class="line"><a id="l00244" name="l00244"></a><span class="lineno"> 244</span> <span class="keywordflow">if</span> (path.back() != <span class="charliteral">&#39;/&#39;</span>) {</div>
<div class="line"><a id="l00245" name="l00245"></a><span class="lineno"> 245</span> path += <span class="charliteral">&#39;/&#39;</span>;</div>
<div class="line"><a id="l00246" name="l00246"></a><span class="lineno"> 246</span> }</div>
<div class="line"><a id="l00247" name="l00247"></a><span class="lineno"> 247</span> <span class="keywordflow">if</span> (<a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path, 0777) != 0) {</div>
<div class="line"><a id="l00248" name="l00248"></a><span class="lineno"> 248</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Hello&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00249" name="l00249"></a><span class="lineno"> 249</span> <span class="keywordflow">return</span>;</div>
<div class="line"><a id="l00250" name="l00250"></a><span class="lineno"> 250</span> }</div>
<div class="line"><a id="l00251" name="l00251"></a><span class="lineno"> 251</span> </div>
<div class="line"><a id="l00252" name="l00252"></a><span class="lineno"> 252</span> <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a> res = this-&gt;<a class="code hl_function" href="classPenningTrap.html#a5331837e6dd7bce807a99edd2ba7e854">simulate</a>(time, steps, method, particle_interaction);</div>
<div class="line"><a id="l00253" name="l00253"></a><span class="lineno"> 253</span> </div>
<div class="line"><a id="l00254" name="l00254"></a><span class="lineno"> 254</span> std::ofstream ofile;</div>
<div class="line"><a id="l00255" name="l00255"></a><span class="lineno"> 255</span> </div>
<div class="line"><a id="l00256" name="l00256"></a><span class="lineno"> 256</span><span class="preprocessor">#pragma omp parallel for private(ofile)</span></div>
<div class="line"><a id="l00257" name="l00257"></a><span class="lineno"> 257</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;particles.size(); i++) {</div>
<div class="line"><a id="l00258" name="l00258"></a><span class="lineno"> 258</span> ofile.open(path + <span class="stringliteral">&quot;particle_&quot;</span> + std::to_string(i) + <span class="stringliteral">&quot;.txt&quot;</span>);</div>
<div class="line"><a id="l00259" name="l00259"></a><span class="lineno"> 259</span> <span class="keywordflow">for</span> (<a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> &amp;vec : res[i]) {</div>
<div class="line"><a id="l00260" name="l00260"></a><span class="lineno"> 260</span> ofile &lt;&lt; vec(0) &lt;&lt; <span class="stringliteral">&quot;,&quot;</span> &lt;&lt; vec(1) &lt;&lt; <span class="stringliteral">&quot;,&quot;</span> &lt;&lt; vec(2) &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a id="l00261" name="l00261"></a><span class="lineno"> 261</span> }</div>
<div class="line"><a id="l00262" name="l00262"></a><span class="lineno"> 262</span> ofile.close();</div>
<div class="line"><a id="l00263" name="l00263"></a><span class="lineno"> 263</span> }</div>
<div class="line"><a id="l00264" name="l00264"></a><span class="lineno"> 264</span>}</div>
<div class="line"><a id="l00265" name="l00265"></a><span class="lineno"> 265</span> </div>
<div class="line"><a id="l00266" name="l00266"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a0194be61c956a9259c747c23e4163c5b"> 266</a></span><span class="keywordtype">double</span> <a class="code hl_function" href="classPenningTrap.html#a0194be61c956a9259c747c23e4163c5b">PenningTrap::fraction_of_particles_left</a>(<span class="keywordtype">double</span> time, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> steps, std::string method, <span class="keywordtype">bool</span> particle_interaction)</div>
<div class="line"><a id="l00267" name="l00267"></a><span class="lineno"> 267</span>{</div>
<div class="line"><a id="l00268" name="l00268"></a><span class="lineno"> 268</span> <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a> res = this-&gt;<a class="code hl_function" href="classPenningTrap.html#a5331837e6dd7bce807a99edd2ba7e854">simulate</a>(time, steps, method, particle_interaction);</div>
<div class="line"><a id="l00269" name="l00269"></a><span class="lineno"> 269</span> </div>
<div class="line"><a id="l00270" name="l00270"></a><span class="lineno"> 270</span> <span class="keywordtype">int</span> particles_left = 0;</div>
<div class="line"><a id="l00271" name="l00271"></a><span class="lineno"> 271</span> </div>
<div class="line"><a id="l00272" name="l00272"></a><span class="lineno"> 272</span> <span class="keywordflow">for</span> (<a class="code hl_class" href="classParticle.html">Particle</a> p : this-&gt;particles) {</div>
<div class="line"><a id="l00273" name="l00273"></a><span class="lineno"> 273</span> <span class="keywordflow">if</span> (arma::norm(p.r_vec) &lt; this-&gt;d) {</div>
<div class="line"><a id="l00274" name="l00274"></a><span class="lineno"> 274</span> particles_left++;</div>
<div class="line"><a id="l00275" name="l00275"></a><span class="lineno"> 275</span> }</div>
<div class="line"><a id="l00276" name="l00276"></a><span class="lineno"> 276</span> }</div>
<div class="line"><a id="l00277" name="l00277"></a><span class="lineno"> 277</span> </div>
<div class="line"><a id="l00278" name="l00278"></a><span class="lineno"> 278</span> <span class="keywordflow">return</span> (<span class="keywordtype">double</span>) particles_left / (double) this-&gt;particles.size();</div>
<div class="line"><a id="l00279" name="l00279"></a><span class="lineno"> 279</span>}</div>
<div class="line"><a id="l00280" name="l00280"></a><span class="lineno"> 280</span> </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="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#l00019">Particle.hpp:19</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#l00021">Particle.hpp:21</a></div></div>
<div class="ttc" id="aclassParticle_html_a4a5d22c7aeca66f67d083f270cba25df"><div class="ttname"><a href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">Particle::v_vec</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; v_vec</div><div class="ttdoc">velocity</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00024">Particle.hpp:24</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#l00023">Particle.hpp:23</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#l00021">Particle.hpp:21</a></div></div> <div class="ttc" id="aclassParticle_html_a879692772803d6ab65fa4993b54aea6e"><div class="ttname"><a href="classParticle.html#a879692772803d6ab65fa4993b54aea6e">Particle::v_vec</a></div><div class="ttdeci">vec_3d 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_acf1a0f3c978b06d76df5bb4279594467"><div class="ttname"><a href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">Particle::r_vec</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; r_vec</div><div class="ttdoc">position</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00023">Particle.hpp:23</a></div></div> <div class="ttc" id="aclassParticle_html_aedcc7e1bc53b0e2b1a4a07c9a1b47563"><div class="ttname"><a href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle::m</a></div><div class="ttdeci">double m</div><div class="ttdoc">Mass.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00024">Particle.hpp:24</a></div></div>
<div class="ttc" id="aclassParticle_html_aedcc7e1bc53b0e2b1a4a07c9a1b47563"><div class="ttname"><a href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle::m</a></div><div class="ttdeci">double m</div><div class="ttdoc">Mass.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00022">Particle.hpp:22</a></div></div> <div class="ttc" id="aclassParticle_html_af9497cd8f2dcad0fad54f571ddb383e6"><div class="ttname"><a href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">Particle::r_vec</a></div><div class="ttdeci">vec_3d r_vec</div><div class="ttdoc">position</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00025">Particle.hpp:25</a></div></div>
<div class="ttc" id="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#l00034">PenningTrap.hpp:34</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#l00030">PenningTrap.hpp:30</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a045adb85e97a8e0c38fb36d2fd74eeee"><div class="ttname"><a href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">PenningTrap::total_force_external</a></div><div class="ttdeci">arma::vec total_force_external(int 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#l00065">PenningTrap.cpp:65</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#l00036">PenningTrap.hpp:36</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#l00031">PenningTrap.hpp:31</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a0194be61c956a9259c747c23e4163c5b"><div class="ttname"><a href="classPenningTrap.html#a0194be61c956a9259c747c23e4163c5b">PenningTrap::fraction_of_particles_left</a></div><div class="ttdeci">double fraction_of_particles_left(double time, unsigned int 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#l00266">PenningTrap.cpp:266</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a135db7d991d9b88b00fde4edee71f78d"><div class="ttname"><a href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">PenningTrap::total_force_particles</a></div><div class="ttdeci">arma::vec total_force_particles(int i)</div><div class="ttdoc">Calculate the total force on a particle from other particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00080">PenningTrap.cpp:80</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#l00032">PenningTrap.hpp:32</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a2a3e7f480ba52e9f24d4c50c3981a784"><div class="ttname"><a href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">PenningTrap::external_B_field</a></div><div class="ttdeci">arma::vec external_B_field(arma::vec r)</div><div class="ttdoc">Calculate B at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00043">PenningTrap.cpp:43</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a1d58feaa2c9e34cbf26b1c5ed75ca9d9"><div class="ttname"><a href="classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9">PenningTrap::external_E_field</a></div><div class="ttdeci">vec_3d external_E_field(vec_3d r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00087">PenningTrap.cpp:87</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a4790f41e4fbc6ede4991aa7bbda92182"><div class="ttname"><a href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">PenningTrap::force_on_particle</a></div><div class="ttdeci">arma::vec force_on_particle(int i, int j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00050">PenningTrap.cpp:50</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a1f668c4433421136ad51741741aa1bc8"><div class="ttname"><a href="classPenningTrap.html#a1f668c4433421136ad51741741aa1bc8">PenningTrap::total_force</a></div><div class="ttdeci">vec_3d total_force(unsigned int 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#l00146">PenningTrap.cpp:146</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a56544b6f4befb42984e9650cf2a40965"><div class="ttname"><a href="classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965">PenningTrap::evolve_forward_euler</a></div><div class="ttdeci">void evolve_forward_euler(double dt)</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#l00167">PenningTrap.cpp:167</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#l00039">PenningTrap.hpp:39</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#l00033">PenningTrap.hpp:33</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#l00151">PenningTrap.cpp:151</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#l00027">PenningTrap.cpp:27</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a43e74792ab4b3f9299f35cb64bdb2648"><div class="ttname"><a href="classPenningTrap.html#a43e74792ab4b3f9299f35cb64bdb2648">PenningTrap::r_func</a></div><div class="ttdeci">vec_3d r_func(unsigned int i, unsigned int 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#l00064">PenningTrap.cpp:64</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#l00032">PenningTrap.hpp:32</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a46a954a0946def199e30fb300ba1c47b"><div class="ttname"><a href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b">PenningTrap::total_force_particles</a></div><div class="ttdeci">vec_3d total_force_particles(unsigned int 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#l00129">PenningTrap.cpp:129</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a81add5063bd5f29d77f0b5c299c6c560"><div class="ttname"><a href="classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560">PenningTrap::PenningTrap</a></div><div class="ttdeci">PenningTrap(double B_0=T, double V_0=25.*V/1000., double d=500.)</div><div class="ttdoc">Set B_0, V_0 and d.</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_a5331837e6dd7bce807a99edd2ba7e854"><div class="ttname"><a href="classPenningTrap.html#a5331837e6dd7bce807a99edd2ba7e854">PenningTrap::simulate</a></div><div class="ttdeci">sim_arr simulate(double time, unsigned int 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#l00211">PenningTrap.cpp:211</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a83cc7a04dae009ed8e75453c38fdf8be"><div class="ttname"><a href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">PenningTrap::total_force</a></div><div class="ttdeci">arma::vec total_force(int i)</div><div class="ttdoc">calculate the total force on a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00099">PenningTrap.cpp:99</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#l00034">PenningTrap.hpp:34</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a978a2e2026a4b5308d5184712f81704b"><div class="ttname"><a href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">PenningTrap::external_E_field</a></div><div class="ttdeci">arma::vec external_E_field(arma::vec r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00032">PenningTrap.cpp:32</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#l00082">PenningTrap.cpp:82</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_ab891b839c40eeb38d8a2a636c70090a9"><div class="ttname"><a href="classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9">PenningTrap::evolve_RK4</a></div><div class="ttdeci">void evolve_RK4(double dt)</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#l00104">PenningTrap.cpp:104</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#l00035">PenningTrap.hpp:35</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a9ae34ad740a230e667e96bc6ee8730ce"><div class="ttname"><a href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce">PenningTrap::force_on_particle</a></div><div class="ttdeci">vec_3d force_on_particle(unsigned int i, unsigned int j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00100">PenningTrap.cpp:100</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_aaf105828121c4a33cc2b217453c20317"><div class="ttname"><a href="classPenningTrap.html#aaf105828121c4a33cc2b217453c20317">PenningTrap::V_0</a></div><div class="ttdeci">std::function&lt; double(double)&gt; V_0</div><div class="ttdoc">Applied potential.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00033">PenningTrap.hpp:33</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#l00186">PenningTrap.cpp:186</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_abbb832a85139b1a56ebde57d7b8f9a57"><div class="ttname"><a href="classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57">PenningTrap::write_simulation_to_dir</a></div><div class="ttdeci">void write_simulation_to_dir(std::string path, double time, unsigned int 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#l00240">PenningTrap.cpp:240</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_acbf065c9c125682329ad82a8d166554c"><div class="ttname"><a href="classPenningTrap.html#acbf065c9c125682329ad82a8d166554c">PenningTrap::external_B_field</a></div><div class="ttdeci">vec_3d external_B_field(vec_3d r)</div><div class="ttdoc">Calculate B at point r.</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_ae670d7de621acdb343b01af098086f63"><div class="ttname"><a href="classPenningTrap.html#ae670d7de621acdb343b01af098086f63">PenningTrap::PenningTrap</a></div><div class="ttdeci">PenningTrap(double B_0=T, std::function&lt; double(double)&gt; V_0=[](double t) { return 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#l00018">PenningTrap.cpp:18</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_ae72d203b0bfa1b9e72bea28cb2863c56"><div class="ttname"><a href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">PenningTrap::total_force_external</a></div><div class="ttdeci">vec_3d total_force_external(unsigned int 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#l00114">PenningTrap.cpp:114</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#l00037">PenningTrap.hpp:37</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_af98a720da60b0e1a62aefa5f5cb37c1e"><div class="ttname"><a href="classPenningTrap.html#af98a720da60b0e1a62aefa5f5cb37c1e">PenningTrap::v_func</a></div><div class="ttdeci">vec_3d v_func(unsigned int i, unsigned int 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#l00046">PenningTrap.cpp:46</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>
<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#l00015">constants.hpp:15</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#l00015">constants.hpp:15</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_a7c2dfa854274262c4e00e4ef0ab2ce23"><div class="ttname"><a href="typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23">sim_cols</a></div><div class="ttdeci">std::vector&lt; arma::vec::fixed&lt; 3 &gt; &gt; sim_cols</div><div class="ttdoc">Typedef for the column of the result vector from simulating particles.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00024">typedefs.hpp:24</a></div></div>
<div class="ttc" id="atypedefs_8hpp_html_a9f33f4962c8fb62cc5ccd0e4e039a8df"><div class="ttname"><a href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; vec_3d</div><div class="ttdoc">Typedef for a fixed 3d arma vector.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00036">typedefs.hpp:36</a></div></div>
<div class="ttc" id="atypedefs_8hpp_html_aec69d34220fff45de238b9e01f2686af"><div class="ttname"><a href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a></div><div class="ttdeci">std::vector&lt; sim_cols &gt; sim_arr</div><div class="ttdoc">Typedef for the result of the simulate method.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00032">typedefs.hpp:32</a></div></div>
<div class="ttc" id="autils_8hpp_html"><div class="ttname"><a href="utils_8hpp.html">utils.hpp</a></div><div class="ttdoc">Function prototypes and macros that are useful.</div></div> <div class="ttc" id="autils_8hpp_html"><div class="ttname"><a href="utils_8hpp.html">utils.hpp</a></div><div class="ttdoc">Function prototypes and macros that are useful.</div></div>
<div class="ttc" id="autils_8hpp_html_a6fdd7217b750aff5b6295ece7cbdeffa"><div class="ttname"><a href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a></div><div class="ttdeci">bool mkpath(std::string path, int mode=0777)</div><div class="ttdoc">Make path given.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00076">utils.cpp:76</a></div></div>
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@ -110,6 +110,7 @@ $(document).ready(function(){initNavTree('PenningTrap_8hpp.html',''); initResiza
<code>#include &lt;omp.h&gt;</code><br /> <code>#include &lt;omp.h&gt;</code><br />
<code>#include &quot;<a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>&quot;</code><br /> <code>#include &quot;<a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>&quot;</code><br />
<code>#include &quot;<a class="el" href="constants_8hpp_source.html">constants.hpp</a>&quot;</code><br /> <code>#include &quot;<a class="el" href="constants_8hpp_source.html">constants.hpp</a>&quot;</code><br />
<code>#include &quot;<a class="el" href="typedefs_8hpp_source.html">typedefs.hpp</a>&quot;</code><br />
</div> </div>
<p><a href="PenningTrap_8hpp_source.html">Go to the source code of this file.</a></p> <p><a href="PenningTrap_8hpp_source.html">Go to the source code of this file.</a></p>
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@ -110,63 +110,106 @@ $(document).ready(function(){initNavTree('PenningTrap_8hpp_source.html',''); ini
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> </div> <div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> </div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#include &quot;<a class="code" href="Particle_8hpp.html">Particle.hpp</a>&quot;</span></div> <div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#include &quot;<a class="code" href="Particle_8hpp.html">Particle.hpp</a>&quot;</span></div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span><span class="preprocessor">#include &quot;<a class="code" href="constants_8hpp.html">constants.hpp</a>&quot;</span></div> <div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span><span class="preprocessor">#include &quot;<a class="code" href="constants_8hpp.html">constants.hpp</a>&quot;</span></div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> </div> <div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span><span class="preprocessor">#include &quot;<a class="code" href="typedefs_8hpp.html">typedefs.hpp</a>&quot;</span></div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span><span class="preprocessor">#pragma omp declare reduction( + : arma::vec : omp_out += omp_in ) \</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><span class="preprocessor"> initializer( omp_priv = omp_orig )</span></div> <div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span><span class="preprocessor">#pragma omp declare reduction(+ : vec_3d : omp_out += omp_in) \</span></div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> </div> <div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span><span class="preprocessor"> initializer(omp_priv = omp_orig)</span></div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"><a class="line" href="classPenningTrap.html"> 29</a></span><span class="keyword">class </span><a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> {</div> <div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> </div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span><span class="keyword">private</span>:</div> <div class="line"><a id="l00030" name="l00030"></a><span class="lineno"><a class="line" href="classPenningTrap.html"> 30</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#a0cac3509aa96e71a26d3b2c902e27716"> 31</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="l00031" name="l00031"></a><span class="lineno"> 31</span><span class="keyword">private</span>:</div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89"> 32</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="l00032" name="l00032"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716"> 32</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="l00033" name="l00033"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2"> 33</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>; </div> <div class="line"><a id="l00033" name="l00033"></a><span class="lineno"><a class="line" href="classPenningTrap.html#aaf105828121c4a33cc2b217453c20317"> 33</a></span> std::function&lt;double(<span class="keywordtype">double</span>)&gt; <a class="code hl_variable" href="classPenningTrap.html#aaf105828121c4a33cc2b217453c20317">V_0</a>; </div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f"> 34</a></span> std::vector&lt;Particle&gt; <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>; </div> <div class="line"><a id="l00034" name="l00034"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2"> 34</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>; </div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> </div> <div class="line"><a id="l00035" name="l00035"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e"> 35</a></span> <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>; </div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span><span class="keyword">public</span>:</div> <div class="line"><a id="l00036" name="l00036"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f"> 36</a></span> std::vector&lt;Particle&gt; <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>; </div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</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="l00037" name="l00037"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4"> 37</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="l00040" name="l00040"></a><span class="lineno"> 40</span> </div> <div class="line"><a id="l00039" name="l00039"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640"> 39</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> <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="l00041" name="l00041"></a><span class="lineno"> 41</span> </div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> </div> <div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#af98a720da60b0e1a62aefa5f5cb37c1e">v_func</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> j, <span class="keywordtype">double</span> dt);</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> arma::vec <a class="code hl_function" href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">external_E_field</a>(arma::vec r);</div> <div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> </div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</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#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#a43e74792ab4b3f9299f35cb64bdb2648">r_func</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> j, <span class="keywordtype">double</span> dt);</div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> arma::vec <a class="code hl_function" href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">external_B_field</a>(arma::vec r);</div> <div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> </div> <div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span><span class="keyword">public</span>:</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> arma::vec <a class="code hl_function" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">force_on_particle</a>(<span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j);</div> <div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(</div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> </div> <div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> <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="l00065" name="l00065"></a><span class="lineno"> 65</span> arma::vec <a class="code hl_function" href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">total_force_external</a>(<span class="keywordtype">int</span> i);</div> <div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> std::function&lt;<span class="keywordtype">double</span>(<span class="keywordtype">double</span>)&gt; <a class="code hl_variable" href="classPenningTrap.html#aaf105828121c4a33cc2b217453c20317">V_0</a> =</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> </div> <div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> [](<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>) { <span class="keywordflow">return</span> 25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a> / 1000.; },</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> arma::vec <a class="code hl_function" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">total_force_particles</a>(<span class="keywordtype">int</span> i);</div> <div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</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="l00070" name="l00070"></a><span class="lineno"> 70</span> </div> <div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> arma::vec <a class="code hl_function" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">total_force</a>(<span class="keywordtype">int</span> i);</div> <div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> </div> <div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> 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>,</div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9">evolve_RK4</a>(<span class="keywordtype">double</span> dt);</div> <div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> std::function&lt;<span class="keywordtype">double</span>(<span class="keywordtype">double</span>)&gt; <a class="code hl_variable" href="classPenningTrap.html#aaf105828121c4a33cc2b217453c20317">V_0</a> =</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> </div> <div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> [](<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>) { <span class="keywordflow">return</span> 25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a> / 1000.; },</div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965">evolve_forward_euler</a>(<span class="keywordtype">double</span> dt);</div> <div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</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="l00082" name="l00082"></a><span class="lineno"> 82</span> </div> <div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> arma::vec get_particle(<span class="keywordtype">int</span> i);</div> <div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(</div>
<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> </div> <div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> 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="l00085" name="l00085"></a><span class="lineno"> 85</span> <span class="keywordtype">double</span> get_d();</div> <div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> std::function&lt;<span class="keywordtype">double</span>(<span class="keywordtype">double</span>)&gt; <a class="code hl_variable" href="classPenningTrap.html#aaf105828121c4a33cc2b217453c20317">V_0</a> =</div>
<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span>};</div> <div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> [](<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>) { <span class="keywordflow">return</span> 25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a> / 1000.; },</div>
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> </div> <div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</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="l00088" name="l00088"></a><span class="lineno"> 88</span><span class="preprocessor">#endif</span></div> <div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</span> </div>
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</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="l00113" name="l00113"></a><span class="lineno"> 113</span> </div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9">external_E_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> r);</div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> </div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#acbf065c9c125682329ad82a8d166554c">external_B_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> r);</div>
<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> </div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce">force_on_particle</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> j);</div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span> </div>
<div class="line"><a id="l00151" name="l00151"></a><span class="lineno"> 151</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">total_force_external</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i);</div>
<div class="line"><a id="l00152" name="l00152"></a><span class="lineno"> 152</span> </div>
<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b">total_force_particles</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i);</div>
<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> </div>
<div class="line"><a id="l00167" name="l00167"></a><span class="lineno"> 167</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="code hl_function" href="classPenningTrap.html#a1f668c4433421136ad51741741aa1bc8">total_force</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i);</div>
<div class="line"><a id="l00168" name="l00168"></a><span class="lineno"> 168</span> </div>
<div class="line"><a id="l00174" name="l00174"></a><span class="lineno"> 174</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="l00175" name="l00175"></a><span class="lineno"> 175</span> </div>
<div class="line"><a id="l00181" name="l00181"></a><span class="lineno"> 181</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="l00182" name="l00182"></a><span class="lineno"> 182</span> </div>
<div class="line"><a id="l00191" name="l00191"></a><span class="lineno"> 191</span> <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a> <a class="code hl_function" href="classPenningTrap.html#a5331837e6dd7bce807a99edd2ba7e854">simulate</a>(<span class="keywordtype">double</span> time, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> steps,</div>
<div class="line"><a id="l00192" name="l00192"></a><span class="lineno"> 192</span> std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
<div class="line"><a id="l00193" name="l00193"></a><span class="lineno"> 193</span> <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00194" name="l00194"></a><span class="lineno"> 194</span> </div>
<div class="line"><a id="l00203" name="l00203"></a><span class="lineno"> 203</span> <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57">write_simulation_to_dir</a>(std::string path, <span class="keywordtype">double</span> time,</div>
<div class="line"><a id="l00204" name="l00204"></a><span class="lineno"> 204</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> steps, std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
<div class="line"><a id="l00205" name="l00205"></a><span class="lineno"> 205</span> <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00206" name="l00206"></a><span class="lineno"> 206</span> </div>
<div class="line"><a id="l00217" name="l00217"></a><span class="lineno"> 217</span> <span class="keywordtype">double</span> <a class="code hl_function" href="classPenningTrap.html#a0194be61c956a9259c747c23e4163c5b">fraction_of_particles_left</a>(<span class="keywordtype">double</span> time, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> steps,</div>
<div class="line"><a id="l00218" name="l00218"></a><span class="lineno"> 218</span> std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
<div class="line"><a id="l00219" name="l00219"></a><span class="lineno"> 219</span> <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
<div class="line"><a id="l00220" name="l00220"></a><span class="lineno"> 220</span>};</div>
<div class="line"><a id="l00221" name="l00221"></a><span class="lineno"> 221</span> </div>
<div class="line"><a id="l00222" name="l00222"></a><span class="lineno"> 222</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#l00019">Particle.hpp:19</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#l00021">Particle.hpp:21</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#l00029">PenningTrap.hpp:29</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#l00030">PenningTrap.hpp:30</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#l00034">PenningTrap.hpp:34</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#l00036">PenningTrap.hpp:36</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a045adb85e97a8e0c38fb36d2fd74eeee"><div class="ttname"><a href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">PenningTrap::total_force_external</a></div><div class="ttdeci">arma::vec total_force_external(int 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#l00065">PenningTrap.cpp:65</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a0194be61c956a9259c747c23e4163c5b"><div class="ttname"><a href="classPenningTrap.html#a0194be61c956a9259c747c23e4163c5b">PenningTrap::fraction_of_particles_left</a></div><div class="ttdeci">double fraction_of_particles_left(double time, unsigned int 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#l00266">PenningTrap.cpp:266</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#l00031">PenningTrap.hpp:31</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#l00032">PenningTrap.hpp:32</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a135db7d991d9b88b00fde4edee71f78d"><div class="ttname"><a href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">PenningTrap::total_force_particles</a></div><div class="ttdeci">arma::vec total_force_particles(int i)</div><div class="ttdoc">Calculate the total force on a particle from other particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00080">PenningTrap.cpp:80</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a1d58feaa2c9e34cbf26b1c5ed75ca9d9"><div class="ttname"><a href="classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9">PenningTrap::external_E_field</a></div><div class="ttdeci">vec_3d external_E_field(vec_3d r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00087">PenningTrap.cpp:87</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a2a3e7f480ba52e9f24d4c50c3981a784"><div class="ttname"><a href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">PenningTrap::external_B_field</a></div><div class="ttdeci">arma::vec external_B_field(arma::vec r)</div><div class="ttdoc">Calculate B at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00043">PenningTrap.cpp:43</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a1f668c4433421136ad51741741aa1bc8"><div class="ttname"><a href="classPenningTrap.html#a1f668c4433421136ad51741741aa1bc8">PenningTrap::total_force</a></div><div class="ttdeci">vec_3d total_force(unsigned int 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#l00146">PenningTrap.cpp:146</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a4790f41e4fbc6ede4991aa7bbda92182"><div class="ttname"><a href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">PenningTrap::force_on_particle</a></div><div class="ttdeci">arma::vec force_on_particle(int i, int j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00050">PenningTrap.cpp:50</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#l00039">PenningTrap.hpp:39</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a56544b6f4befb42984e9650cf2a40965"><div class="ttname"><a href="classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965">PenningTrap::evolve_forward_euler</a></div><div class="ttdeci">void evolve_forward_euler(double dt)</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#l00167">PenningTrap.cpp:167</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#l00151">PenningTrap.cpp:151</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#l00033">PenningTrap.hpp:33</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a43e74792ab4b3f9299f35cb64bdb2648"><div class="ttname"><a href="classPenningTrap.html#a43e74792ab4b3f9299f35cb64bdb2648">PenningTrap::r_func</a></div><div class="ttdeci">vec_3d r_func(unsigned int i, unsigned int 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#l00064">PenningTrap.cpp:64</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#l00027">PenningTrap.cpp:27</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a46a954a0946def199e30fb300ba1c47b"><div class="ttname"><a href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b">PenningTrap::total_force_particles</a></div><div class="ttdeci">vec_3d total_force_particles(unsigned int 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#l00129">PenningTrap.cpp:129</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#l00032">PenningTrap.hpp:32</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a5331837e6dd7bce807a99edd2ba7e854"><div class="ttname"><a href="classPenningTrap.html#a5331837e6dd7bce807a99edd2ba7e854">PenningTrap::simulate</a></div><div class="ttdeci">sim_arr simulate(double time, unsigned int 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#l00211">PenningTrap.cpp:211</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a83cc7a04dae009ed8e75453c38fdf8be"><div class="ttname"><a href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">PenningTrap::total_force</a></div><div class="ttdeci">arma::vec total_force(int i)</div><div class="ttdoc">calculate the total force on a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00099">PenningTrap.cpp:99</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#l00034">PenningTrap.hpp:34</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a978a2e2026a4b5308d5184712f81704b"><div class="ttname"><a href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">PenningTrap::external_E_field</a></div><div class="ttdeci">arma::vec external_E_field(arma::vec r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00032">PenningTrap.cpp:32</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#l00082">PenningTrap.cpp:82</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_ab891b839c40eeb38d8a2a636c70090a9"><div class="ttname"><a href="classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9">PenningTrap::evolve_RK4</a></div><div class="ttdeci">void evolve_RK4(double dt)</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#l00104">PenningTrap.cpp:104</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#l00035">PenningTrap.hpp:35</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a9ae34ad740a230e667e96bc6ee8730ce"><div class="ttname"><a href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce">PenningTrap::force_on_particle</a></div><div class="ttdeci">vec_3d force_on_particle(unsigned int i, unsigned int j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00100">PenningTrap.cpp:100</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_aaf105828121c4a33cc2b217453c20317"><div class="ttname"><a href="classPenningTrap.html#aaf105828121c4a33cc2b217453c20317">PenningTrap::V_0</a></div><div class="ttdeci">std::function&lt; double(double)&gt; V_0</div><div class="ttdoc">Applied potential.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00033">PenningTrap.hpp:33</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#l00186">PenningTrap.cpp:186</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_abbb832a85139b1a56ebde57d7b8f9a57"><div class="ttname"><a href="classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57">PenningTrap::write_simulation_to_dir</a></div><div class="ttdeci">void write_simulation_to_dir(std::string path, double time, unsigned int 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#l00240">PenningTrap.cpp:240</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_acbf065c9c125682329ad82a8d166554c"><div class="ttname"><a href="classPenningTrap.html#acbf065c9c125682329ad82a8d166554c">PenningTrap::external_B_field</a></div><div class="ttdeci">vec_3d external_B_field(vec_3d r)</div><div class="ttdoc">Calculate B at point r.</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_ae72d203b0bfa1b9e72bea28cb2863c56"><div class="ttname"><a href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">PenningTrap::total_force_external</a></div><div class="ttdeci">vec_3d total_force_external(unsigned int 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#l00114">PenningTrap.cpp:114</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#l00037">PenningTrap.hpp:37</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_af98a720da60b0e1a62aefa5f5cb37c1e"><div class="ttname"><a href="classPenningTrap.html#af98a720da60b0e1a62aefa5f5cb37c1e">PenningTrap::v_func</a></div><div class="ttdeci">vec_3d v_func(unsigned int i, unsigned int 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#l00046">PenningTrap.cpp:46</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>
<div class="ttc" id="aconstants_8hpp_html_a0acb682b8260ab1c60b918599864e2e5"><div class="ttname"><a href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a></div><div class="ttdeci">#define T</div><div class="ttdoc">1 Tesla. unit:</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00017">constants.hpp:17</a></div></div> <div class="ttc" id="aconstants_8hpp_html_a0acb682b8260ab1c60b918599864e2e5"><div class="ttname"><a href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a></div><div class="ttdeci">#define T</div><div class="ttdoc">1 Tesla. unit:</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00017">constants.hpp:17</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#l00019">constants.hpp:19</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#l00019">constants.hpp:19</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_a9f33f4962c8fb62cc5ccd0e4e039a8df"><div class="ttname"><a href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; vec_3d</div><div class="ttdoc">Typedef for a fixed 3d arma vector.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00036">typedefs.hpp:36</a></div></div>
<div class="ttc" id="atypedefs_8hpp_html_aec69d34220fff45de238b9e01f2686af"><div class="ttname"><a href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a></div><div class="ttdeci">std::vector&lt; sim_cols &gt; sim_arr</div><div class="ttdoc">Typedef for the result of the simulate method.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00032">typedefs.hpp:32</a></div></div>
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<div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="keyword">import</span> matplotlib.pyplot <span class="keyword">as</span> plt</div> <div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="keyword">import</span> matplotlib.pyplot <span class="keyword">as</span> plt</div>
<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span><span class="keyword">import</span> numpy <span class="keyword">as</span> np</div> <div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span><span class="keyword">import</span> numpy <span class="keyword">as</span> np</div>
<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="keyword">from</span> mpl_toolkits.mplot3d <span class="keyword">import</span> Axes3D</div> <div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="keyword">from</span> matplotlib <span class="keyword">import</span> animation</div>
<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span><span class="keyword">from</span> matplotlib <span class="keyword">import</span> animation</div> <div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span><span class="keyword">from</span> mpl_toolkits.mplot3d <span class="keyword">import</span> Axes3D</div>
<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span> </div> <div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span> </div>
<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="keyword">def </span>get_data(files):</div> <div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span> </div>
<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span> res = []</div> <div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span><span class="keyword">def </span>get_data(files):</div>
<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span> <span class="keywordflow">for</span> file <span class="keywordflow">in</span> files:</div> <div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span> res = []</div>
<div class="line"><a id="l00009" name="l00009"></a><span class="lineno"> 9</span> arr = [[], [], []]</div> <div class="line"><a id="l00009" name="l00009"></a><span class="lineno"> 9</span> <span class="keywordflow">for</span> file <span class="keywordflow">in</span> files:</div>
<div class="line"><a id="l00010" name="l00010"></a><span class="lineno"> 10</span> <span class="keyword">with</span> open(file, encoding=<span class="stringliteral">&quot;utf8&quot;</span>) <span class="keyword">as</span> f:</div> <div class="line"><a id="l00010" name="l00010"></a><span class="lineno"> 10</span> arr = [[], [], []]</div>
<div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span> lines = f.readlines()</div> <div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span> <span class="keyword">with</span> open(file, encoding=<span class="stringliteral">&quot;utf8&quot;</span>) <span class="keyword">as</span> f:</div>
<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span> </div> <div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span> lines = f.readlines()</div>
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span> <span class="keywordflow">for</span> line <span class="keywordflow">in</span> lines:</div> <div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span> </div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> xi,yi,zi = map(float, line.strip().split(<span class="stringliteral">&quot;,&quot;</span>))</div> <div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> <span class="keywordflow">for</span> line <span class="keywordflow">in</span> lines:</div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span> arr[0].append(xi)</div> <div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span> xi, yi, zi = map(float, line.strip().split(<span class="stringliteral">&quot;,&quot;</span>))</div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> arr[1].append(yi)</div> <div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> arr[0].append(xi)</div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> arr[2].append(zi)</div> <div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> arr[1].append(yi)</div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span> res.append(arr)</div> <div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span> arr[2].append(zi)</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> res.append(arr)</div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> <span class="keywordflow">return</span> np.array(res)</div> <div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> </div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span> </div> <div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span> <span class="keywordflow">return</span> np.array(res)</div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span><span class="keyword">def </span>update(num, lines, arr):</div> <div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> </div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> <span class="keywordflow">for</span> line, a <span class="keywordflow">in</span> zip(lines, arr):</div> <div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> </div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> line.set_data(a[:2, num])</div> <div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span><span class="keyword">def </span>update(num, lines, arr):</div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span> line.set_3d_properties(a[2, num])</div> <div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span> <span class="keywordflow">for</span> line, a <span class="keywordflow">in</span> zip(lines, arr):</div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> </div> <div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> line.set_data(a[:2, num - 1 : num])</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> line.set_3d_properties(a[2, num])</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> </div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span><span class="keyword">def </span>animate():</div> <div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> </div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> plt.style.use(<span class="stringliteral">&quot;dark_background&quot;</span>)</div> <div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span><span class="keyword">def </span>animate():</div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span> fig = plt.figure()</div> <div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span> plt.style.use(<span class="stringliteral">&quot;dark_background&quot;</span>)</div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> ax = fig.add_subplot(projection=<span class="stringliteral">&quot;3d&quot;</span>)</div> <div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> fig = plt.figure()</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> </div> <div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> ax = fig.add_subplot(projection=<span class="stringliteral">&quot;3d&quot;</span>)</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> </div> <div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> arr = get_data([f<span class="stringliteral">&quot;output/p{i}_RK4.txt&quot;</span> <span class="keywordflow">for</span> i <span class="keywordflow">in</span> range(100)])</div> <div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> arr = get_data([f<span class="stringliteral">&quot;output/simulate_100_particles/particle_{i}.txt&quot;</span> <span class="keywordflow">for</span> i <span class="keywordflow">in</span> range(100)])</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> arr = arr[:,:,::10]</div> <div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> arr = arr[:, :, ::10]</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"> 39</span> N = len(arr[0][0])</div> <div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> N = len(arr[0][0])</div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> </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> lines = [ax.plot(*a[:,1], <span class="stringliteral">&quot;o&quot;</span>)[0] <span class="keywordflow">for</span> a <span class="keywordflow">in</span> arr]</div> <div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> lines = [ax.plot(*a[:, 1], <span class="stringliteral">&quot;o&quot;</span>)[0] <span class="keywordflow">for</span> a <span class="keywordflow">in</span> arr]</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> </div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> ax.set_xlim3d([-500.0, 500.0])</div> <div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> ax.set_title(<span class="stringliteral">&quot;100 particles inside a Penning trap&quot;</span>)</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> ax.set_xlabel(<span class="stringliteral">&#39;X&#39;</span>)</div> <div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> plt.figtext(</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> 0.5,</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> ax.set_ylim3d([-500.0, 500.0])</div> <div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> 0.01,</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> ax.set_ylabel(<span class="stringliteral">&#39;Y&#39;</span>)</div> <div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="stringliteral">&quot;100 randomly generated particles &quot;</span></div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> </div> <div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> <span class="stringliteral">&quot;evolving over a time of 50 microseconds.&quot;</span>,</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> ax.set_zlim3d([-500.0, 500.0])</div> <div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> fontsize=12,</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> ax.set_zlabel(<span class="stringliteral">&#39;Z&#39;</span>) </div> <div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> horizontalalignment=<span class="stringliteral">&quot;center&quot;</span>,</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> )</div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> ani = animation.FuncAnimation(fig, update, N, fargs=(lines, arr), </div> <div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> </div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> interval=1,</div> <div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> ax.set_xlim3d([-500.0, 500.0])</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> blit=<span class="keyword">False</span>)</div> <div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> ax.set_xlabel(<span class="stringliteral">&quot;X (micrometers)&quot;</span>)</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> </div> <div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> </div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> </div> <div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> ax.set_ylim3d([-500.0, 500.0])</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> ani.save(<span class="stringliteral">&quot;100_particles.gif&quot;</span>, writer=animation.FFMpegFileWriter(fps=30))</div> <div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> ax.set_ylabel(<span class="stringliteral">&quot;Y (micrometers)&quot;</span>)</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> plt.show()</div> <div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> </div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> </div> <div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> ax.set_zlim3d([-500.0, 500.0])</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> ax.set_zlabel(<span class="stringliteral">&quot;Z (micrometers)&quot;</span>)</div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span><span class="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</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> animate()</div> <div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> ani = animation.FuncAnimation(</div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> </div> <div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> fig, update, N, fargs=(lines, arr), interval=1, blit=<span class="keyword">False</span></div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> </div> <div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> )</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> <span class="comment"># ani.save(&quot;../images/100_particles.gif&quot;, writer=animation.FFMpegFileWriter(fps=50))</span></div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> plt.show()</div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> </div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span><span class="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> animate()</div>
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14
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@ -105,21 +105,23 @@ $(document).ready(function(){initNavTree('bug.html',''); initResizable(); });
<dt>File <a class="el" href="constants_8hpp.html">constants.hpp</a> </dt> <dt>File <a class="el" href="constants_8hpp.html">constants.hpp</a> </dt>
<dd><a class="anchor" id="_bug000001"></a>No known bugs </dd> <dd><a class="anchor" id="_bug000001"></a>No known bugs </dd>
<dt>File <a class="el" href="main_8cpp.html">main.cpp</a> </dt> <dt>File <a class="el" href="main_8cpp.html">main.cpp</a> </dt>
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<dd><a class="anchor" id="_bug000002"></a>No known bugs </dd> <dd><a class="anchor" id="_bug000002"></a>No known bugs </dd>
<dt>File <a class="el" href="PenningTrap_8cpp.html">PenningTrap.cpp</a> </dt> <dt>File <a class="el" href="PenningTrap_8cpp.html">PenningTrap.cpp</a> </dt>
<dd><a class="anchor" id="_bug000007"></a>No known bugs </dd> <dd><a class="anchor" id="_bug000008"></a>No known bugs </dd>
<dt>File <a class="el" href="PenningTrap_8hpp.html">PenningTrap.hpp</a> </dt> <dt>File <a class="el" href="PenningTrap_8hpp.html">PenningTrap.hpp</a> </dt>
<dd><a class="anchor" id="_bug000003"></a>No known bugs </dd> <dd><a class="anchor" id="_bug000003"></a>No known bugs </dd>
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<dd><a class="anchor" id="_bug000008"></a>No known bugs </dd>
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<dd><a class="anchor" id="_bug000009"></a>No known bugs </dd> <dd><a class="anchor" id="_bug000009"></a>No known bugs </dd>
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<p>This is the complete list of members for <a class="el" href="classParticle.html">Particle</a>, including all inherited members.</p> <p>This is the complete list of members for <a class="el" href="classParticle.html">Particle</a>, including all inherited members.</p>
<table class="directory"> <table class="directory">
<tr class="even"><td class="entry"><a class="el" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a></td><td class="entry"><a class="el" href="classParticle.html">Particle</a></td><td class="entry"><span class="mlabel">private</span></td></tr> <tr class="even"><td class="entry"><a class="el" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a></td><td class="entry"><a class="el" href="classParticle.html">Particle</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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<tr class="memdesc:a00e108823877a25513ccae7cac011b4c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Initialize the particle. <br /></td></tr> <tr class="memdesc:a7af9f8d1fef63dd7643b06629ac7bef4"><td class="mdescLeft">&#160;</td><td class="mdescRight">Initialize the particle. <br /></td></tr>
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<tr class="memdesc:aedcc7e1bc53b0e2b1a4a07c9a1b47563"><td class="mdescLeft">&#160;</td><td class="mdescRight">Mass. <br /></td></tr> <tr class="memdesc:aedcc7e1bc53b0e2b1a4a07c9a1b47563"><td class="mdescLeft">&#160;</td><td class="mdescRight">Mass. <br /></td></tr>
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<tr class="memitem:acf1a0f3c978b06d76df5bb4279594467"><td class="memItemLeft" align="right" valign="top">arma::vec::fixed&lt; 3 &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a></td></tr> <tr class="memitem:af9497cd8f2dcad0fad54f571ddb383e6"><td class="memItemLeft" align="right" valign="top"><a class="el" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">r_vec</a></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>
<div class="textblock"><p>A class that holds attributes of a particle. </p> <div class="textblock"><p>A class that holds attributes of a particle. </p>
<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00019">19</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p> <p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00021">21</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2> </div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
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<p>Initialize the particle. </p> <p>Initialize the particle. </p>
<p>Initialize the particle with a charge, mass, position and velocity. </p> <p>Initialize the particle with a charge, mass, position and velocity.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">q</td><td>The charge of the particle </td></tr>
<tr><td class="paramname">m</td><td>The mass of the particle </td></tr>
<tr><td class="paramname">r_vec</td><td>The initial position of the particle </td></tr>
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<p class="definition">Definition at line <a class="el" href="Particle_8cpp_source.html#l00016">16</a> of file <a class="el" href="Particle_8cpp_source.html">Particle.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="Particle_8cpp_source.html#l00015">15</a> of file <a class="el" href="Particle_8cpp_source.html">Particle.cpp</a>.</p>
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<p>Make private attributes available for <a class="el" href="classPenningTrap.html" title="A class that simulates a Penning trap.">PenningTrap</a>. </p> <p>Make private attributes available for <a class="el" href="classPenningTrap.html" title="A class that simulates a Penning trap.">PenningTrap</a>. </p>
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<p>Mass. </p> <p>Mass. </p>
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<p>Charge. </p> <p>Charge. </p>
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<p>position </p> <p>position </p>
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<p>velocity </p> <p>velocity </p>
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<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr> <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965">evolve_forward_euler</a>(double dt)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr> <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">evolve_forward_euler</a>(double dt, bool particle_interaction=true)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9">evolve_RK4</a>(double dt)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr> <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">evolve_RK4</a>(double dt, bool particle_interaction=true)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">external_B_field</a>(arma::vec r)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr> <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#acbf065c9c125682329ad82a8d166554c">external_B_field</a>(vec_3d r)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">external_E_field</a>(arma::vec r)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr> <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9">external_E_field</a>(vec_3d r)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">force_on_particle</a>(int i, int j)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr> <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce">force_on_particle</a>(unsigned int i, unsigned int j)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_d</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"></td></tr> <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a0194be61c956a9259c747c23e4163c5b">fraction_of_particles_left</a>(double time, unsigned int steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr bgcolor="#f0f0f0" class="odd"><td class="entry"><b>get_particle</b>(int i) (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"></td></tr> <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr> <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560">PenningTrap</a>(double B_0=T, double V_0=25.*V/1000., double d=500.)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr> <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">total_force</a>(int i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr> <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#ae670d7de621acdb343b01af098086f63">PenningTrap</a>(double B_0=T, std::function&lt; double(double)&gt; V_0=[](double t) { return 25. *V/1000.;}, double d=500., double t=0.)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">total_force_external</a>(int i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr> <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a763700316b502d5900e587c1f61e6bf1">PenningTrap</a>(unsigned int i, double B_0=T, std::function&lt; double(double)&gt; V_0=[](double t) { return 25. *V/1000.;}, double d=500., double t=0.)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">total_force_particles</a>(int i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr> <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a67139e04ef69c0bcffde8f30f67cbf73">PenningTrap</a>(std::vector&lt; Particle &gt; particles, double B_0=T, std::function&lt; double(double)&gt; V_0=[](double t) { return 25. *V/1000.;}, double d=500., double t=0.)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr> <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a43e74792ab4b3f9299f35cb64bdb2648">r_func</a>(unsigned int i, unsigned int j, double dt)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a5331837e6dd7bce807a99edd2ba7e854">simulate</a>(double time, unsigned int steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a1f668c4433421136ad51741741aa1bc8">total_force</a>(unsigned int i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">total_force_external</a>(unsigned int i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b">total_force_particles</a>(unsigned int i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#aaf105828121c4a33cc2b217453c20317">V_0</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#af98a720da60b0e1a62aefa5f5cb37c1e">v_func</a>(unsigned int i, unsigned int j, double dt)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57">write_simulation_to_dir</a>(std::string path, double time, unsigned int steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
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34
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docs/functions_func.html
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docs/functions_vars.html
View File

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<div id="projectbrief">Simulate particle behavior inside a Penning Trap</div>
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<p>The main program for this project. <p>The main program for this project.
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<div class="textblock"><code>#include &lt;fstream&gt;</code><br /> <div class="textblock"><code>#include &lt;cmath&gt;</code><br />
<code>#include &lt;fstream&gt;</code><br />
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Variables</h2></td></tr>
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<a class="el" href="classParticle.html">Particle</a>&#160;</td><td class="memItemRight" valign="bottom"><b>p1</b> (CHARGE, MASS, <a class="el" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>{20., 0., 20.}, <a class="el" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>{0., 25., 0.})</td></tr>
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<a class="el" href="classParticle.html">Particle</a>&#160;</td><td class="memItemRight" valign="bottom"><b>p2</b> (CHARGE, MASS, <a class="el" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>{25., 25., 0.}, <a class="el" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>{0., 40., 5.})</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>
<div class="textblock"><p>The main program for this project. </p> <div class="textblock"><p>The main program for this project. </p>
@ -138,7 +160,7 @@ Functions</h2></td></tr>
<dd> <dd>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl> Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>0.1</dd></dl> <dl class="section version"><dt>Version</dt><dd>0.1</dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000005">Bug:</a></b></dt><dd>No known bugs </dd></dl> <dl class="bug"><dt><b><a class="el" href="bug.html#_bug000006">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<p class="definition">Definition in file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p> <p class="definition">Definition in file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
</div><h2 class="groupheader">Macro Definition Documentation</h2> </div><h2 class="groupheader">Macro Definition Documentation</h2>
@ -154,7 +176,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
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<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00021">21</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00025">25</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00022">22</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00026">26</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00020">20</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00024">24</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00019">19</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00023">23</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
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@ -222,7 +244,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
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<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00077">77</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00124">124</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00024">24</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00077">77</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a330668384dc073980ba11116309bacc5">&#9670;&#160;</a></span>simulate_100_particles_with_time_potential()</h2>
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<td class="memname">void simulate_100_particles_with_time_potential </td>
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<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00091">91</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a8fdbe2d5a872e50ef5ec1263243589d6">&#9670;&#160;</a></span>simulate_single_particle()</h2>
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<td class="memname">void simulate_single_particle </td>
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<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00031">31</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ac67e0d59227856c4d42e7d01c75e0ad2">&#9670;&#160;</a></span>simulate_single_particle_with_different_steps()</h2>
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<td class="memname">void simulate_single_particle_with_different_steps </td>
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<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00055">55</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a783789519f97c6430081171cacb0ffb1">&#9670;&#160;</a></span>simulate_two_particles()</h2>
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<td class="memname">void simulate_two_particles </td>
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<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00042">42</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
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@ -102,87 +102,149 @@ $(document).ready(function(){initNavTree('main_8cpp_source.html',''); initResiza
</div><!--header--> </div><!--header-->
<div class="contents"> <div class="contents">
<a href="main_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span> </div> <a href="main_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span> </div>
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#include &lt;fstream&gt;</span></div> <div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#include &lt;cmath&gt;</span></div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="preprocessor">#include &lt;omp.h&gt;</span></div> <div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="preprocessor">#include &lt;fstream&gt;</span></div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include &lt;sys/stat.h&gt;</span></div> <div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include &lt;omp.h&gt;</span></div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> </div> <div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="preprocessor">#include &lt;string&gt;</span></div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div> <div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="preprocessor">#include &lt;sys/stat.h&gt;</span></div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</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><span class="preprocessor">#define PARTICLES 100</span></div> <div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span> </div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span><span class="preprocessor">#define N 10000</span></div> <div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span><span class="preprocessor">#define CHARGE 1.</span></div> <div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span><span class="preprocessor">#include &quot;<a class="code" href="utils_8hpp.html">utils.hpp</a>&quot;</span></div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span><span class="preprocessor">#define MASS 40. </span><span class="comment">// unit: amu</span></div> <div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> </div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> </div> <div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span><span class="preprocessor">#define PARTICLES 100</span></div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span><span class="keywordtype">void</span> simulate_100_particles()</div> <div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span><span class="preprocessor">#define N 10000</span></div>
<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><span class="preprocessor">#define CHARGE 1.</span></div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap;</div> <div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span><span class="preprocessor">#define MASS 40. </span><span class="comment">// unit: amu</span></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> </div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// Add particles inside trap</span></div> <div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span><a class="code hl_class" href="classParticle.html">Particle</a> p1(CHARGE, MASS, <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>{20., 0., 20.}, <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>{0., 25., 0.});</div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; PARTICLES; i++) {</div> <div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span><a class="code hl_class" href="classParticle.html">Particle</a> p2(CHARGE, MASS, <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>{25., 25., 0.}, <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>{0., 40., 5.});</div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> arma::vec r = arma::vec(3).randn() * 0.1 *</div> <div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> </div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span> trap.get_d(); <span class="comment">// random initial position</span></div> <div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span><span class="keywordtype">void</span> simulate_single_particle()</div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> arma::vec v = arma::vec(3).randn() * 0.1 *</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> trap.get_d(); <span class="comment">// random initial velocity</span></div> <div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> <a class="code hl_define" href="utils_8hpp.html#aecc1f7a8a2493b9e021e5bff76a00a5b">DEBUG</a>(<span class="stringliteral">&quot;Inside single particle sim&quot;</span>);</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> trap.<a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a>(CHARGE, MASS, r, v));</div> <div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{p1});</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> }</div> <div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> </div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> </div> <div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</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> <span class="keywordtype">double</span> dt = time / (double)N;</div> <div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> <a class="code hl_define" href="utils_8hpp.html#aecc1f7a8a2493b9e021e5bff76a00a5b">DEBUG</a>(<span class="stringliteral">&quot;Write to dir&quot;</span>);</div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> </div> <div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> trap.write_simulation_to_dir(<span class="stringliteral">&quot;output/simulate_single_particle&quot;</span>, time, N);</div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> <span class="keyword">auto</span> res = <span class="keyword">new</span> arma::vec::fixed&lt;3&gt;[PARTICLES][N];</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> </div> <div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> </div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> <span class="keywordtype">int</span> counter = 0;</div> <div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span><span class="keywordtype">void</span> simulate_two_particles()</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> </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> <span class="comment">// Get the path of all particles</span></div> <div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap_no_interaction(std::vector&lt;Particle&gt;{p1, p2});</div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> j = 0; j &lt; N; j++) {</div> <div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap_with_interaction(std::vector&lt;Particle&gt;{p1, p2});</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span><span class="preprocessor">#pragma omp parallel for</span></div> <div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> </div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; PARTICLES; i++) {</div> <div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> res[i][j] = trap.get_particle(i);</div> <div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> </div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> }</div> <div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> trap_no_interaction.<a class="code hl_function" href="classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57">write_simulation_to_dir</a>(</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> trap.<a class="code hl_function" href="classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9">evolve_RK4</a>(dt);</div> <div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> <span class="stringliteral">&quot;output/simulate_2_particles/no_interaction&quot;</span>, time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> }</div> <div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> trap_with_interaction.write_simulation_to_dir(</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="stringliteral">&quot;output/simulate_2_particles/with_interaction&quot;</span>, time, N);</div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> std::cout &lt;&lt; counter &lt;&lt; std::endl;</div> <div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span>}</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> </div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> arma::vec::fixed&lt;3&gt; *cur_row;</div> <div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span><span class="keywordtype">void</span> simulate_single_particle_with_different_steps()</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> arma::vec::fixed&lt;3&gt; cur_elem;</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> mkdir(<span class="stringliteral">&quot;output&quot;</span>, 0777);</div> <div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> <span class="keywordtype">double</span> time = 50; <span class="comment">// microseconds</span></div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> mkdir(<span class="stringliteral">&quot;output/simulate_100_particles&quot;</span>, 0777);</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> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; 4; i++) {</div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> std::ofstream ofile;</div> <div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> <span class="keywordtype">int</span> steps = 4000 * (i + 1);</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> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{p1});</div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span><span class="comment">// Write particle paths to file</span></div> <div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> trap.<a class="code hl_function" href="classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57">write_simulation_to_dir</a>(<span class="stringliteral">&quot;output/N_steps/RK4/&quot;</span> +</div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span><span class="preprocessor">#pragma omp parallel for private(cur_row, cur_elem, ofile)</span></div> <div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> std::to_string(steps) + <span class="stringliteral">&quot;_steps&quot;</span>,</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; PARTICLES; i++) {</div> <div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> time, steps, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> cur_row = res[i];</div> <div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> }</div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> ofile.open(<span class="stringliteral">&quot;output/simulate_100_particles/p&quot;</span> + std::to_string(i) + <span class="stringliteral">&quot;.txt&quot;</span>);</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">for</span> (<span class="keywordtype">int</span> j = 0; j &lt; N; j++) {</div> <div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; 4; i++) {</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> cur_elem = cur_row[j];</div> <div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> <span class="keywordtype">int</span> steps = 4000 * (i + 1);</div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> ofile &lt;&lt; cur_elem(0) &lt;&lt; <span class="stringliteral">&quot;,&quot;</span> &lt;&lt; cur_elem(1) &lt;&lt; <span class="stringliteral">&quot;,&quot;</span> &lt;&lt; cur_elem(2)</div> <div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{p1});</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div> <div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> trap.<a class="code hl_function" href="classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57">write_simulation_to_dir</a>(<span class="stringliteral">&quot;output/N_steps/euler/&quot;</span> +</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> }</div> <div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> std::to_string(steps) + <span class="stringliteral">&quot;_steps&quot;</span>,</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> ofile.close();</div> <div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> time, steps, <span class="stringliteral">&quot;euler&quot;</span>, <span class="keyword">false</span>);</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> }</div> <div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> }</div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span>}</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> </div> <div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span><span class="keywordtype">int</span> main()</div> <div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span><span class="keywordtype">void</span> simulate_100_particles()</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span>{</div> <div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span>{</div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> <span class="keywordtype">double</span> start = omp_get_wtime();</div> <div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((<span class="keywordtype">unsigned</span>)100, <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>,</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> [](<span class="keywordtype">double</span> t) {</div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> simulate_100_particles();</div> <div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> <span class="keywordflow">return</span> 25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a> / 1000. *</div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> </div> <div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> (1. + .4 * std::cos(1.5 * t));</div>
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> <span class="keywordtype">double</span> end = omp_get_wtime();</div> <div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> },</div>
<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> </div> <div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> 500., 0);</div>
<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Time: &quot;</span> &lt;&lt; end - start &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div> <div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> </div> <div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> <span class="keywordtype">double</span> time = 500.; <span class="comment">// microseconds</span></div>
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> <span class="keywordflow">return</span> 0;</div> <div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> </div>
<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span>}</div> <div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span> trap.<a class="code hl_function" href="classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57">write_simulation_to_dir</a>(<span class="stringliteral">&quot;output/simulate_100_particles&quot;</span>, time, N*5);</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> </div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span><span class="keywordtype">void</span> simulate_100_particles_with_time_potential()</div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span>{</div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> <span class="keywordtype">double</span> freq_start = .2;</div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> <span class="keywordtype">double</span> freq_end = 2.5;</div>
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> <span class="keywordtype">double</span> freq_increment = .02;</div>
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> <span class="keywordtype">size_t</span> freq_iterations = (size_t) ((freq_end - freq_start) / freq_increment);</div>
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> </div>
<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</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> std::ofstream ofile;</div>
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> </div>
<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> <span class="keywordflow">for</span> (<span class="keywordtype">double</span> f : amplitudes) {</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> ofile.open(path + <span class="stringliteral">&quot;f_&quot;</span> + std::to_string(f) + <span class="stringliteral">&quot;.txt&quot;</span>);</div>
<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</span><span class="preprocessor"> #pragma omp parallel for ordered schedule(static, 1)</span></div>
<div class="line"><a id="l00108" name="l00108"></a><span class="lineno"> 108</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i=0; i &lt; freq_iterations; i++) {</div>
<div class="line"><a id="l00109" name="l00109"></a><span class="lineno"> 109</span> <span class="keywordtype">double</span> freq = freq_start + i*freq_increment;</div>
<div class="line"><a id="l00110" name="l00110"></a><span class="lineno"> 110</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((<span class="keywordtype">unsigned</span>)100, <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>,</div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> [f, freq](<span class="keywordtype">double</span> t) {</div>
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span> <span class="keywordflow">return</span> (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a> / 1000.) *</div>
<div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span> (1. + f * std::cos(freq * t));</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> 500., 0.);</div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> <span class="keywordtype">double</span> res = trap.<a class="code hl_function" href="classPenningTrap.html#a0194be61c956a9259c747c23e4163c5b">fraction_of_particles_left</a>(500., 40000, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">true</span>);</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span><span class="preprocessor"> #pragma omp ordered</span></div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> ofile &lt;&lt; freq &lt;&lt; <span class="stringliteral">&quot;,&quot;</span> &lt;&lt; res &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> }</div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span> ofile.close();</div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> }</div>
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span>}</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="keywordtype">int</span> main()</div>
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span>{</div>
<div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</span> </div>
<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span> simulate_single_particle();</div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> </div>
<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> simulate_two_particles();</div>
<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> </div>
<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> simulate_single_particle_with_different_steps();</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> <span class="keywordtype">double</span> start = omp_get_wtime();</div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> </div>
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> <span class="comment">//simulate_100_particles();</span></div>
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span> </div>
<div class="line"><a id="l00137" name="l00137"></a><span class="lineno"> 137</span> simulate_100_particles_with_time_potential();</div>
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> </div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> <span class="keywordtype">double</span> end = omp_get_wtime();</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> std::cout &lt;&lt; <span class="stringliteral">&quot;Time: &quot;</span> &lt;&lt; end - start &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span> </div>
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span> <span class="keywordflow">return</span> 0;</div>
<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"> 144</span>}</div>
<div class="ttc" id="aPenningTrap_8hpp_html"><div class="ttname"><a href="PenningTrap_8hpp.html">PenningTrap.hpp</a></div><div class="ttdoc">A class for simulating a Penning trap.</div></div> <div class="ttc" id="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#l00019">Particle.hpp:19</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#l00021">Particle.hpp:21</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#l00029">PenningTrap.hpp:29</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#l00030">PenningTrap.hpp:30</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#l00027">PenningTrap.cpp:27</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a0194be61c956a9259c747c23e4163c5b"><div class="ttname"><a href="classPenningTrap.html#a0194be61c956a9259c747c23e4163c5b">PenningTrap::fraction_of_particles_left</a></div><div class="ttdeci">double fraction_of_particles_left(double time, unsigned int 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#l00266">PenningTrap.cpp:266</a></div></div>
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<div id="projectname">Penning Trap Simulation
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<div id="projectbrief">Simulate particle behavior inside a Penning Trap</div>
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<div class="headertitle"><div class="title">plot_particles_left.py</div></div>
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<div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="keyword">import</span> matplotlib.pyplot <span class="keyword">as</span> plt</div>
<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span> </div>
<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="keyword">def </span>main():</div>
<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span> files = [</div>
<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span> <span class="stringliteral">&quot;output/time_dependent_potential/f_0.100000.txt&quot;</span>,</div>
<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span> <span class="stringliteral">&quot;output/time_dependent_potential/f_0.400000.txt&quot;</span>,</div>
<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span> <span class="stringliteral">&quot;output/time_dependent_potential/f_0.700000.txt&quot;</span>,</div>
<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span> ]</div>
<div class="line"><a id="l00009" name="l00009"></a><span class="lineno"> 9</span> vals = [</div>
<div class="line"><a id="l00010" name="l00010"></a><span class="lineno"> 10</span> .1,</div>
<div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span> .4,</div>
<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span> .7</div>
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span> ]</div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> <span class="keywordflow">for</span> i <span class="keywordflow">in</span> range(3):</div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span> <span class="keyword">with</span> open(files[i]) <span class="keyword">as</span> f:</div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> lines = f.readlines()</div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> x = []</div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span> y = []</div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span> <span class="keywordflow">for</span> line <span class="keywordflow">in</span> lines:</div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> a,b = line.strip().split(<span class="stringliteral">&quot;,&quot;</span>)</div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span> x.append(float(a))</div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> y.append(float(b))</div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> plt.plot(x,y,label=f<span class="stringliteral">&quot;amplitude: {vals[i]}&quot;</span>)</div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> </div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span> plt.xlabel(<span class="stringliteral">r&quot;$\omega_V$&quot;</span>)</div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> plt.ylabel(<span class="stringliteral">r&quot;Fraction of particles left&quot;</span>)</div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> plt.title(<span class="stringliteral">r&quot;The fraction of particles left in the Penning trap &quot;</span></div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span> <span class="stringliteral">&quot;after 500 microseconds for different amplitudes and frequencies&quot;</span>)</div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> plt.legend()</div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> plt.show()</div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span> </div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span><span class="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> main()</div>
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<li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><b>plot_particles_left.py</b></li>
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<dd> <dd>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl> Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>0.1</dd></dl> <dl class="section version"><dt>Version</dt><dd>0.1</dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000008">Bug:</a></b></dt><dd>No known bugs </dd></dl> <dl class="bug"><dt><b><a class="el" href="bug.html#_bug000009">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<p class="definition">Definition in file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p> <p class="definition">Definition in file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
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<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> std::stringstream msg;</div> <div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> std::stringstream msg;</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; tests.size(); i++) {</div> <div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; tests.size(); i++) {</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> v = tests.at(i).first;</div> <div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> v = tests.at(i).first;</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> result = trap.<a class="code hl_function" href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">external_E_field</a>(v);</div> <div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> result = trap.<a class="code hl_function" href="classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9">external_E_field</a>(v);</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> </div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> msg.str(<span class="stringliteral">&quot;&quot;</span>);</div> <div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> msg.str(<span class="stringliteral">&quot;&quot;</span>);</div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> msg &lt;&lt; <span class="stringliteral">&quot;Testing the external E field at (&quot;</span> &lt;&lt; std::setprecision(2)</div> <div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> msg &lt;&lt; <span class="stringliteral">&quot;Testing the external E field at (&quot;</span> &lt;&lt; std::setprecision(2)</div>
@ -154,7 +154,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> <span class="comment">// on position.</span></div> <div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> <span class="comment">// on position.</span></div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap;</div> <div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap;</div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> arma::vec expected{0., 0., <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>};</div> <div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> arma::vec expected{0., 0., <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>};</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">external_B_field</a>(arma::vec{0., 0., 0.});</div> <div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#acbf065c9c125682329ad82a8d166554c">external_B_field</a>(arma::vec{0., 0., 0.});</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div> <div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> <span class="stringliteral">&quot;Testing the external B field at (0,0,0)&quot;</span>);</div> <div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> <span class="stringliteral">&quot;Testing the external B field at (0,0,0)&quot;</span>);</div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> }</div> <div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> }</div>
@ -171,14 +171,14 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
<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> </div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> <span class="comment">// Test p0 and p1</span></div> <div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> <span class="comment">// Test p0 and p1</span></div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> arma::vec expected{-1., 0., 0.};</div> <div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> arma::vec expected{-1., 0., 0.};</div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">force_on_particle</a>(0, 1);</div> <div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce">force_on_particle</a>(0, 1);</div>
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div> <div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div>
<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> <span class="stringliteral">&quot;Testing the force on a particle at (0,0,0) from a &quot;</span></div> <div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> <span class="stringliteral">&quot;Testing the force on a particle at (0,0,0) from a &quot;</span></div>
<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> <span class="stringliteral">&quot;particle at (1,0,0).&quot;</span>);</div> <div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> <span class="stringliteral">&quot;particle at (1,0,0).&quot;</span>);</div>
<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> </div> <div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> <span class="comment">// Test p0 and p2</span></div> <div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> <span class="comment">// Test p0 and p2</span></div>
<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span> expected = arma::vec{0, -.024, -.032};</div> <div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span> expected = arma::vec{0, -.024, -.032};</div>
<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> result = trap.<a class="code hl_function" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">force_on_particle</a>(0, 2);</div> <div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> result = trap.<a class="code hl_function" href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce">force_on_particle</a>(0, 2);</div>
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div> <div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> <span class="stringliteral">&quot;Testing the force on a particle at (0,0,0) from a &quot;</span></div> <div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> <span class="stringliteral">&quot;Testing the force on a particle at (0,0,0) from a &quot;</span></div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> <span class="stringliteral">&quot;particle at (0,3,4).&quot;</span>);</div> <div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> <span class="stringliteral">&quot;particle at (0,3,4).&quot;</span>);</div>
@ -191,7 +191,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> <a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{1., 2., 3.}, arma::vec{3., 4., 5.}));</div> <div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> <a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{1., 2., 3.}, arma::vec{3., 4., 5.}));</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> </div>
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> arma::vec expected{395.58954878, -270.15871624, -57.89115348};</div> <div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> arma::vec expected{395.58954878, -270.15871624, -57.89115348};</div>
<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">total_force_external</a>(0);</div> <div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">total_force_external</a>(0);</div>
<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div> <div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div>
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> <span class="stringliteral">&quot;Testing the total external force on a particle at &quot;</span></div> <div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> <span class="stringliteral">&quot;Testing the total external force on a particle at &quot;</span></div>
<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> <span class="stringliteral">&quot;(1,2,3) with velocity (3,4,5)&quot;</span>);</div> <div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> <span class="stringliteral">&quot;(1,2,3) with velocity (3,4,5)&quot;</span>);</div>
@ -204,7 +204,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span> <a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{0., 0., 0.}, arma::vec{0., 0., 0.}));</div> <div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span> <a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{0., 0., 0.}, arma::vec{0., 0., 0.}));</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"> 114</span> arma::vec expected{0., 0., 0.};</div> <div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span> arma::vec expected{0., 0., 0.};</div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">total_force_particles</a>(0);</div> <div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b">total_force_particles</a>(0);</div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div> <div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> <span class="stringliteral">&quot;Testing the total force of all particles on particle 0 &quot;</span></div> <div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> <span class="stringliteral">&quot;Testing the total force of all particles on particle 0 &quot;</span></div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> <span class="stringliteral">&quot;with only a single particle&quot;</span>);</div> <div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> <span class="stringliteral">&quot;with only a single particle&quot;</span>);</div>
@ -217,7 +217,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> <a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{0., 0., 1.}, arma::vec{0., 0., 0.}));</div> <div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> <a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{0., 0., 1.}, arma::vec{0., 0., 0.}));</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> expected = arma::vec(3, arma::fill::value(-3473.383325));</div> <div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span> expected = arma::vec(3, arma::fill::value(-3473.383325));</div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> result = trap.<a class="code hl_function" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">total_force_particles</a>(0);</div> <div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> result = trap.<a class="code hl_function" href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b">total_force_particles</a>(0);</div>
<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div> <div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div>
<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> <span class="stringliteral">&quot;Testing the total force of all particles on particle 0 &quot;</span></div> <div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> <span class="stringliteral">&quot;Testing the total force of all particles on particle 0 &quot;</span></div>
<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> <span class="stringliteral">&quot;with 3 other particles.&quot;</span>);</div> <div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> <span class="stringliteral">&quot;with 3 other particles.&quot;</span>);</div>
@ -234,18 +234,18 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
<div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span> <span class="keywordflow">return</span> 0;</div> <div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span> <span class="keywordflow">return</span> 0;</div>
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span>}</div> <div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span>}</div>
<div class="ttc" id="aPenningTrap_8hpp_html"><div class="ttname"><a href="PenningTrap_8hpp.html">PenningTrap.hpp</a></div><div class="ttdoc">A class for simulating a Penning trap.</div></div> <div class="ttc" id="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#l00019">Particle.hpp:19</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#l00021">Particle.hpp:21</a></div></div>
<div class="ttc" id="aclassPenningTrapTest_html"><div class="ttname"><a href="classPenningTrapTest.html">PenningTrapTest</a></div><div class="ttdef"><b>Definition:</b> <a href="test__suite_8cpp_source.html#l00020">test_suite.cpp:20</a></div></div> <div class="ttc" id="aclassPenningTrapTest_html"><div class="ttname"><a href="classPenningTrapTest.html">PenningTrapTest</a></div><div class="ttdef"><b>Definition:</b> <a href="test__suite_8cpp_source.html#l00020">test_suite.cpp:20</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#l00029">PenningTrap.hpp:29</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#l00030">PenningTrap.hpp:30</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a045adb85e97a8e0c38fb36d2fd74eeee"><div class="ttname"><a href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">PenningTrap::total_force_external</a></div><div class="ttdeci">arma::vec total_force_external(int 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#l00065">PenningTrap.cpp:65</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a1d58feaa2c9e34cbf26b1c5ed75ca9d9"><div class="ttname"><a href="classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9">PenningTrap::external_E_field</a></div><div class="ttdeci">vec_3d external_E_field(vec_3d r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00087">PenningTrap.cpp:87</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a135db7d991d9b88b00fde4edee71f78d"><div class="ttname"><a href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">PenningTrap::total_force_particles</a></div><div class="ttdeci">arma::vec total_force_particles(int i)</div><div class="ttdoc">Calculate the total force on a particle from other particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00080">PenningTrap.cpp:80</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a46a954a0946def199e30fb300ba1c47b"><div class="ttname"><a href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b">PenningTrap::total_force_particles</a></div><div class="ttdeci">vec_3d total_force_particles(unsigned int 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#l00129">PenningTrap.cpp:129</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a2a3e7f480ba52e9f24d4c50c3981a784"><div class="ttname"><a href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">PenningTrap::external_B_field</a></div><div class="ttdeci">arma::vec external_B_field(arma::vec r)</div><div class="ttdoc">Calculate B at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00043">PenningTrap.cpp:43</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#l00082">PenningTrap.cpp:82</a></div></div>
<div class="ttc" id="aclassPenningTrap_html_a4790f41e4fbc6ede4991aa7bbda92182"><div class="ttname"><a href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">PenningTrap::force_on_particle</a></div><div class="ttdeci">arma::vec force_on_particle(int i, int j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00050">PenningTrap.cpp:50</a></div></div> <div class="ttc" id="aclassPenningTrap_html_a9ae34ad740a230e667e96bc6ee8730ce"><div class="ttname"><a href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce">PenningTrap::force_on_particle</a></div><div class="ttdeci">vec_3d force_on_particle(unsigned int i, unsigned int j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00100">PenningTrap.cpp:100</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#l00027">PenningTrap.cpp:27</a></div></div> <div class="ttc" id="aclassPenningTrap_html_acbf065c9c125682329ad82a8d166554c"><div class="ttname"><a href="classPenningTrap.html#acbf065c9c125682329ad82a8d166554c">PenningTrap::external_B_field</a></div><div class="ttdeci">vec_3d external_B_field(vec_3d r)</div><div class="ttdoc">Calculate B at point r.</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_a978a2e2026a4b5308d5184712f81704b"><div class="ttname"><a href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">PenningTrap::external_E_field</a></div><div class="ttdeci">arma::vec external_E_field(arma::vec r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00032">PenningTrap.cpp:32</a></div></div> <div class="ttc" id="aclassPenningTrap_html_ae72d203b0bfa1b9e72bea28cb2863c56"><div class="ttname"><a href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">PenningTrap::total_force_external</a></div><div class="ttdeci">vec_3d total_force_external(unsigned int 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#l00114">PenningTrap.cpp:114</a></div></div>
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<a href="#typedef-members">Typedefs</a> </div>
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<p>Useful typedefs for cleaner code.
<a href="#details">More...</a></p>
<div class="textblock"><code>#include &lt;vector&gt;</code><br />
<code>#include &lt;armadillo&gt;</code><br />
</div>
<p><a href="typedefs_8hpp_source.html">Go to the source code of this file.</a></p>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="typedef-members" name="typedef-members"></a>
Typedefs</h2></td></tr>
<tr class="memitem:a7c2dfa854274262c4e00e4ef0ab2ce23"><td class="memItemLeft" align="right" valign="top">typedef std::vector&lt; arma::vec::fixed&lt; 3 &gt; &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23">sim_cols</a></td></tr>
<tr class="memdesc:a7c2dfa854274262c4e00e4ef0ab2ce23"><td class="mdescLeft">&#160;</td><td class="mdescRight">Typedef for the column of the result vector from simulating particles. <br /></td></tr>
<tr class="separator:a7c2dfa854274262c4e00e4ef0ab2ce23"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8502989b1b361725834fc185bd575f66"><td class="memItemLeft" align="right" valign="top">typedef std::vector&lt; arma::vec::fixed&lt; 3 &gt; &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="typedefs_8hpp.html#a8502989b1b361725834fc185bd575f66">sim_rows</a></td></tr>
<tr class="memdesc:a8502989b1b361725834fc185bd575f66"><td class="mdescLeft">&#160;</td><td class="mdescRight">Typedef for the row of the result vector from simulating particles. <br /></td></tr>
<tr class="separator:a8502989b1b361725834fc185bd575f66"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aec69d34220fff45de238b9e01f2686af"><td class="memItemLeft" align="right" valign="top">typedef std::vector&lt; <a class="el" href="typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23">sim_cols</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a></td></tr>
<tr class="memdesc:aec69d34220fff45de238b9e01f2686af"><td class="mdescLeft">&#160;</td><td class="mdescRight">Typedef for the result of the simulate method. <br /></td></tr>
<tr class="separator:aec69d34220fff45de238b9e01f2686af"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a9f33f4962c8fb62cc5ccd0e4e039a8df"><td class="memItemLeft" align="right" valign="top">typedef arma::vec::fixed&lt; 3 &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a></td></tr>
<tr class="memdesc:a9f33f4962c8fb62cc5ccd0e4e039a8df"><td class="mdescLeft">&#160;</td><td class="mdescRight">Typedef for a fixed 3d arma vector. <br /></td></tr>
<tr class="separator:a9f33f4962c8fb62cc5ccd0e4e039a8df"><td class="memSeparator" colspan="2">&#160;</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Useful typedefs for cleaner code. </p>
<dl class="section author"><dt>Author</dt><dd>Cory Alexander Balaton (coryab) </dd>
<dd>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
<p>These typedefs make the code more readable and easy to follow along.</p>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000004">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<p class="definition">Definition in file <a class="el" href="typedefs_8hpp_source.html">typedefs.hpp</a>.</p>
</div><h2 class="groupheader">Typedef Documentation</h2>
<a id="aec69d34220fff45de238b9e01f2686af" name="aec69d34220fff45de238b9e01f2686af"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aec69d34220fff45de238b9e01f2686af">&#9670;&#160;</a></span>sim_arr</h2>
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<td class="memname">typedef std::vector&lt;<a class="el" href="typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23">sim_cols</a>&gt; <a class="el" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a></td>
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<p>Typedef for the result of the simulate method. </p>
<p class="definition">Definition at line <a class="el" href="typedefs_8hpp_source.html#l00032">32</a> of file <a class="el" href="typedefs_8hpp_source.html">typedefs.hpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a7c2dfa854274262c4e00e4ef0ab2ce23">&#9670;&#160;</a></span>sim_cols</h2>
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<td class="memname">typedef std::vector&lt;arma::vec::fixed&lt;3&gt; &gt; <a class="el" href="typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23">sim_cols</a></td>
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<p>Typedef for the column of the result vector from simulating particles. </p>
<p class="definition">Definition at line <a class="el" href="typedefs_8hpp_source.html#l00024">24</a> of file <a class="el" href="typedefs_8hpp_source.html">typedefs.hpp</a>.</p>
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<td class="memname">typedef std::vector&lt;arma::vec::fixed&lt;3&gt; &gt; <a class="el" href="typedefs_8hpp.html#a8502989b1b361725834fc185bd575f66">sim_rows</a></td>
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<p>Typedef for the row of the result vector from simulating particles. </p>
<p class="definition">Definition at line <a class="el" href="typedefs_8hpp_source.html#l00028">28</a> of file <a class="el" href="typedefs_8hpp_source.html">typedefs.hpp</a>.</p>
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<td class="memname">typedef arma::vec::fixed&lt;3&gt; <a class="el" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a></td>
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<p>Typedef for a fixed 3d arma vector. </p>
<p class="definition">Definition at line <a class="el" href="typedefs_8hpp_source.html#l00036">36</a> of file <a class="el" href="typedefs_8hpp_source.html">typedefs.hpp</a>.</p>
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<a href="typedefs_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span> </div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#ifndef __TYPEDEFS__</span></div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span><span class="preprocessor">#define __TYPEDEFS__</span></div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> </div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span><span class="preprocessor">#include &lt;armadillo&gt;</span></div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> </div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"><a class="line" href="typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23"> 24</a></span><span class="keyword">typedef</span> std::vector&lt;arma::vec::fixed&lt;3&gt;&gt; <a class="code hl_typedef" href="typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23">sim_cols</a>;</div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span> </div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"><a class="line" href="typedefs_8hpp.html#a8502989b1b361725834fc185bd575f66"> 28</a></span><span class="keyword">typedef</span> std::vector&lt;arma::vec::fixed&lt;3&gt;&gt; <a class="code hl_typedef" href="typedefs_8hpp.html#a8502989b1b361725834fc185bd575f66">sim_rows</a>;</div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> </div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"><a class="line" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af"> 32</a></span><span class="keyword">typedef</span> std::vector&lt;sim_cols&gt; <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>;</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> </div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"><a class="line" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df"> 36</a></span><span class="keyword">typedef</span> arma::vec::fixed&lt;3&gt; <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>;</div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> </div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span><span class="preprocessor">#endif</span></div>
<div class="ttc" id="atypedefs_8hpp_html_a7c2dfa854274262c4e00e4ef0ab2ce23"><div class="ttname"><a href="typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23">sim_cols</a></div><div class="ttdeci">std::vector&lt; arma::vec::fixed&lt; 3 &gt; &gt; sim_cols</div><div class="ttdoc">Typedef for the column of the result vector from simulating particles.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00024">typedefs.hpp:24</a></div></div>
<div class="ttc" id="atypedefs_8hpp_html_a8502989b1b361725834fc185bd575f66"><div class="ttname"><a href="typedefs_8hpp.html#a8502989b1b361725834fc185bd575f66">sim_rows</a></div><div class="ttdeci">std::vector&lt; arma::vec::fixed&lt; 3 &gt; &gt; sim_rows</div><div class="ttdoc">Typedef for the row of the result vector from simulating particles.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00028">typedefs.hpp:28</a></div></div>
<div class="ttc" id="atypedefs_8hpp_html_a9f33f4962c8fb62cc5ccd0e4e039a8df"><div class="ttname"><a href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; vec_3d</div><div class="ttdoc">Typedef for a fixed 3d arma vector.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00036">typedefs.hpp:36</a></div></div>
<div class="ttc" id="atypedefs_8hpp_html_aec69d34220fff45de238b9e01f2686af"><div class="ttname"><a href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a></div><div class="ttdeci">std::vector&lt; sim_cols &gt; sim_arr</div><div class="ttdoc">Typedef for the result of the simulate method.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00032">typedefs.hpp:32</a></div></div>
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@ -106,7 +106,8 @@ $(document).ready(function(){initNavTree('utils_8cpp.html',''); initResizable();
<p>Implementation of the utils. <p>Implementation of the utils.
<a href="#details">More...</a></p> <a href="#details">More...</a></p>
<div class="textblock"><code>#include &quot;<a class="el" href="utils_8hpp_source.html">utils.hpp</a>&quot;</code><br /> <div class="textblock"><code>#include &lt;sys/stat.h&gt;</code><br />
<code>#include &quot;<a class="el" href="utils_8hpp_source.html">utils.hpp</a>&quot;</code><br />
</div> </div>
<p><a href="utils_8cpp_source.html">Go to the source code of this file.</a></p> <p><a href="utils_8cpp_source.html">Go to the source code of this file.</a></p>
<table class="memberdecls"> <table class="memberdecls">
@ -124,6 +125,9 @@ Functions</h2></td></tr>
<tr class="memitem:a5d2e1e032fd19614f2fbb58149a7b02a"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="utils_8cpp.html#a5d2e1e032fd19614f2fbb58149a7b02a">arma_vector_close_to</a> (arma::vec &amp;a, arma::vec &amp;b, double tol)</td></tr> <tr class="memitem:a5d2e1e032fd19614f2fbb58149a7b02a"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="utils_8cpp.html#a5d2e1e032fd19614f2fbb58149a7b02a">arma_vector_close_to</a> (arma::vec &amp;a, arma::vec &amp;b, double tol)</td></tr>
<tr class="memdesc:a5d2e1e032fd19614f2fbb58149a7b02a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Test if two armadillo vectors are close to each other. <br /></td></tr> <tr class="memdesc:a5d2e1e032fd19614f2fbb58149a7b02a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Test if two armadillo vectors are close to each other. <br /></td></tr>
<tr class="separator:a5d2e1e032fd19614f2fbb58149a7b02a"><td class="memSeparator" colspan="2">&#160;</td></tr> <tr class="separator:a5d2e1e032fd19614f2fbb58149a7b02a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:acf13f4e492199cb7231bfa646dbd08de"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="utils_8cpp.html#acf13f4e492199cb7231bfa646dbd08de">mkpath</a> (std::string path, int mode)</td></tr>
<tr class="memdesc:acf13f4e492199cb7231bfa646dbd08de"><td class="mdescLeft">&#160;</td><td class="mdescRight">Make path given. <br /></td></tr>
<tr class="separator:acf13f4e492199cb7231bfa646dbd08de"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table> </table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Implementation of the utils. </p> <div class="textblock"><p>Implementation of the utils. </p>
@ -131,7 +135,7 @@ Functions</h2></td></tr>
<dd> <dd>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl> Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl> <dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000009">Bug:</a></b></dt><dd>No known bugs </dd></dl> <dl class="bug"><dt><b><a class="el" href="bug.html#_bug000010">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<p class="definition">Definition in file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p> <p class="definition">Definition in file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
</div><h2 class="groupheader">Function Documentation</h2> </div><h2 class="groupheader">Function Documentation</h2>
@ -177,9 +181,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</table> </table>
</dd> </dd>
</dl> </dl>
<dl class="section return"><dt>Returns</dt><dd>Boolean </dd></dl> <dl class="section return"><dt>Returns</dt><dd>bool </dd></dl>
<p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00059">59</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00062">62</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
</div> </div>
</div> </div>
@ -247,7 +251,48 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</dd> </dd>
</dl> </dl>
<p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00040">40</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00043">43</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
</div>
</div>
<a id="acf13f4e492199cb7231bfa646dbd08de" name="acf13f4e492199cb7231bfa646dbd08de"></a>
<h2 class="memtitle"><span class="permalink"><a href="#acf13f4e492199cb7231bfa646dbd08de">&#9670;&#160;</a></span>mkpath()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool mkpath </td>
<td>(</td>
<td class="paramtype">std::string&#160;</td>
<td class="paramname"><em>path</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int&#160;</td>
<td class="paramname"><em>mode</em> = <code>0777</code>&#160;</td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
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<p>Make path given. </p>
<p>This tries to be the equivalent to "mkdir -p" and creates a new directory whenever it needs to.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">path</td><td>The path to be created </td></tr>
<tr><td class="paramname">mode</td><td>The mode/permissions for all the new directories</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>bool </dd></dl>
<p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00076">76</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
</div> </div>
</div> </div>
@ -284,6 +329,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</div><div class="memdoc"> </div><div class="memdoc">
<p>Turns a vector of doubles into a string written in scientific format. </p> <p>Turns a vector of doubles into a string written in scientific format. </p>
<p>The code is stolen from <a href="https://github.com/anderkve/FYS3150">https://github.com/anderkve/FYS3150</a>.</p>
<dl class="params"><dt>Parameters</dt><dd> <dl class="params"><dt>Parameters</dt><dd>
<table class="params"> <table class="params">
<tr><td class="paramname">v</td><td>The vector to stringify </td></tr> <tr><td class="paramname">v</td><td>The vector to stringify </td></tr>
@ -292,9 +338,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</table> </table>
</dd> </dd>
</dl> </dl>
<dl class="section return"><dt>Returns</dt><dd>String </dd></dl> <dl class="section return"><dt>Returns</dt><dd>std::string </dd></dl>
<p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00021">21</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00024">24</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
</div> </div>
</div> </div>
@ -331,7 +377,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</div><div class="memdoc"> </div><div class="memdoc">
<p>Turns a double into a string written in scientific format. </p> <p>Turns a double into a string written in scientific format. </p>
<p>Code stolen from <a href="https://github.com/anderkve/FYS3150">https://github.com/anderkve/FYS3150</a> Header: <a href="https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/include/utils.hpp">https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/include/utils.hpp</a> Source: <a href="https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/src/utils.cpp">https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/src/utils.cpp</a> </p> <p>The code is stolen from <a href="https://github.com/anderkve/FYS3150">https://github.com/anderkve/FYS3150</a>.</p>
<dl class="params"><dt>Parameters</dt><dd> <dl class="params"><dt>Parameters</dt><dd>
<table class="params"> <table class="params">
<tr><td class="paramname">d</td><td>The number to stringify </td></tr> <tr><td class="paramname">d</td><td>The number to stringify </td></tr>
@ -340,9 +386,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</table> </table>
</dd> </dd>
</dl> </dl>
<dl class="section return"><dt>Returns</dt><dd>String </dd></dl> <dl class="section return"><dt>Returns</dt><dd>std::string </dd></dl>
<p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00014">14</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00017">17</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
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<a href="utils_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span> </div> <a href="utils_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span> </div>
<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span><span class="preprocessor">#include &quot;<a class="code" href="utils_8hpp.html">utils.hpp</a>&quot;</span></div> <div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#include &lt;sys/stat.h&gt;</span></div>
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span> </div> <div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> </div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"><a class="line" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384"> 14</a></span>std::string <a class="code hl_function" href="utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746">scientific_format</a>(<span class="keywordtype">double</span> d, <span class="keywordtype">int</span> width, <span class="keywordtype">int</span> prec)</div> <div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="preprocessor">#include &quot;<a class="code" href="utils_8hpp.html">utils.hpp</a>&quot;</span></div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span>{</div> <div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> </div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> std::stringstream ss;</div> <div class="line"><a id="l00017" name="l00017"></a><span class="lineno"><a class="line" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384"> 17</a></span>std::string <a class="code hl_function" href="utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746">scientific_format</a>(<span class="keywordtype">double</span> d, <span class="keywordtype">int</span> width, <span class="keywordtype">int</span> prec)</div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> ss &lt;&lt; std::setw(width) &lt;&lt; std::setprecision(prec) &lt;&lt; std::scientific &lt;&lt; d;</div> <div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span>{</div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span> <span class="keywordflow">return</span> ss.str();</div> <div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span> std::stringstream ss;</div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span>}</div> <div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> ss &lt;&lt; std::setw(width) &lt;&lt; std::setprecision(prec) &lt;&lt; std::scientific &lt;&lt; d;</div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> </div> <div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span> <span class="keywordflow">return</span> ss.str();</div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"><a class="line" href="utils_8hpp.html#ad54b96a1074f9df4dc892a41d115b72d"> 21</a></span>std::string <a class="code hl_function" href="utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746">scientific_format</a>(<span class="keyword">const</span> std::vector&lt;double&gt; &amp;v, <span class="keywordtype">int</span> width, <span class="keywordtype">int</span> prec)</div> <div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span>}</div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span>{</div> <div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> </div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> std::stringstream ss;</div> <div class="line"><a id="l00024" name="l00024"></a><span class="lineno"><a class="line" href="utils_8hpp.html#ad54b96a1074f9df4dc892a41d115b72d"> 24</a></span>std::string <a class="code hl_function" href="utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746">scientific_format</a>(<span class="keyword">const</span> std::vector&lt;double&gt; &amp;v, <span class="keywordtype">int</span> width, <span class="keywordtype">int</span> prec)</div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span> <span class="keywordflow">for</span> (<span class="keywordtype">double</span> elem : v) {</div> <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> ss &lt;&lt; <a class="code hl_function" href="utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746">scientific_format</a>(elem, width, prec);</div> <div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> std::stringstream ss;</div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span> }</div> <div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> <span class="keywordflow">for</span> (<span class="keywordtype">double</span> elem : v) {</div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> <span class="keywordflow">return</span> ss.str();</div> <div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span> ss &lt;&lt; <a class="code hl_function" href="utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746">scientific_format</a>(elem, width, prec);</div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span>}</div> <div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> }</div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> </div> <div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> <span class="keywordflow">return</span> ss.str();</div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span><span class="keyword">static</span> <span class="keywordtype">void</span> print_message(std::string msg)</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>{</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> <span class="keywordflow">if</span> (msg.size() &gt; 0) {</div> <div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span><span class="keyword">static</span> <span class="keywordtype">void</span> print_message(std::string msg)</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> std::cout &lt;&lt; <span class="stringliteral">&quot;message: &quot;</span> &lt;&lt; msg &lt;&lt; <span class="stringliteral">&quot;\n\n&quot;</span>;</div> <div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span>{</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> }</div> <div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> <span class="keywordflow">if</span> (msg.size() &gt; 0) {</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> <span class="keywordflow">else</span> {</div> <div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> std::cout &lt;&lt; <span class="stringliteral">&quot;message: &quot;</span> &lt;&lt; msg &lt;&lt; <span class="stringliteral">&quot;\n\n&quot;</span>;</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> std::cout &lt;&lt; <span class="stringliteral">&quot;\n&quot;</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> <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> </div> <div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> std::cout &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"><a class="line" href="utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38"> 40</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="utils_8cpp.html#aff5e07c3c1d321709b0cc38e999f427b">m_assert</a>(<span class="keywordtype">bool</span> expr, std::string expr_str, std::string f, std::string file,</div> <div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> }</div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> <span class="keywordtype">int</span> line, std::string msg)</div> <div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span>}</div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span>{</div> <div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> </div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> std::string new_assert(f.size() + (expr ? 4 : 6), <span class="charliteral">&#39;-&#39;</span>);</div> <div class="line"><a id="l00043" name="l00043"></a><span class="lineno"><a class="line" href="utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38"> 43</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="utils_8cpp.html#aff5e07c3c1d321709b0cc38e999f427b">m_assert</a>(<span class="keywordtype">bool</span> expr, std::string expr_str, std::string f, std::string file,</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> std::cout &lt;&lt; <span class="stringliteral">&quot;\x1B[36m&quot;</span> &lt;&lt; new_assert &lt;&lt; <span class="stringliteral">&quot;\033[0m\n&quot;</span>;</div> <div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> <span class="keywordtype">int</span> line, std::string msg)</div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> std::cout &lt;&lt; f &lt;&lt; <span class="stringliteral">&quot;: &quot;</span>;</div> <div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span>{</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> <span class="keywordflow">if</span> (expr) {</div> <div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> std::string new_assert(f.size() + (expr ? 4 : 6), <span class="charliteral">&#39;-&#39;</span>);</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> std::cout &lt;&lt; <span class="stringliteral">&quot;\x1B[32mOK\033[0m\n&quot;</span>;</div> <div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> std::cout &lt;&lt; <span class="stringliteral">&quot;\x1B[36m&quot;</span> &lt;&lt; new_assert &lt;&lt; <span class="stringliteral">&quot;\033[0m\n&quot;</span>;</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> print_message(msg);</div> <div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> std::cout &lt;&lt; f &lt;&lt; <span class="stringliteral">&quot;: &quot;</span>;</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> }</div> <div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> <span class="keywordflow">if</span> (expr) {</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> <span class="keywordflow">else</span> {</div> <div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> std::cout &lt;&lt; <span class="stringliteral">&quot;\x1B[32mOK\033[0m\n&quot;</span>;</div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> std::cout &lt;&lt; <span class="stringliteral">&quot;\x1B[31mFAIL\033[0m\n&quot;</span>;</div> <div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> print_message(msg);</div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> print_message(msg);</div> <div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> }</div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> std::cout &lt;&lt; file &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; line &lt;&lt; <span class="stringliteral">&quot;: Assertion \&quot;&quot;</span> &lt;&lt; expr_str</div> <div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> &lt;&lt; <span class="stringliteral">&quot;\&quot; Failed\n\n&quot;</span>;</div> <div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> std::cout &lt;&lt; <span class="stringliteral">&quot;\x1B[31mFAIL\033[0m\n&quot;</span>;</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> abort();</div> <div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> print_message(msg);</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> }</div> <div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> std::cout &lt;&lt; file &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; line &lt;&lt; <span class="stringliteral">&quot;: Assertion \&quot;&quot;</span> &lt;&lt; expr_str</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> &lt;&lt; <span class="stringliteral">&quot;\&quot; Failed\n\n&quot;</span>;</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> </div> <div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> abort();</div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"><a class="line" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772"> 59</a></span><span class="keywordtype">bool</span> <a class="code hl_function" href="utils_8cpp.html#a5d2e1e032fd19614f2fbb58149a7b02a">arma_vector_close_to</a>(arma::vec &amp;a, arma::vec &amp;b, <span class="keywordtype">double</span> tol)</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>}</div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> <span class="keywordflow">if</span> (a.n_elem != b.n_elem) {</div> <div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> </div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div> <div class="line"><a id="l00062" name="l00062"></a><span class="lineno"><a class="line" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772"> 62</a></span><span class="keywordtype">bool</span> <a class="code hl_function" href="utils_8cpp.html#a5d2e1e032fd19614f2fbb58149a7b02a">arma_vector_close_to</a>(arma::vec &amp;a, arma::vec &amp;b, <span class="keywordtype">double</span> tol)</div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> }</div> <div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span>{</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> <span class="keywordflow">if</span> (a.n_elem != b.n_elem) {</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; a.n_elem; i++) {</div> <div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> <span class="keywordflow">if</span> (std::abs(a(i) - b(i)) &gt;= tol) {</div> <div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> }</div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</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> }</div> <div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; a.n_elem; i++) {</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> }</div> <div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> <span class="keywordflow">if</span> (std::abs(a(i) - b(i)) &gt;= tol) {</div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div> <div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span>}</div> <div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> }</div>
<div class="ttc" id="autils_8cpp_html_a5d2e1e032fd19614f2fbb58149a7b02a"><div class="ttname"><a href="utils_8cpp.html#a5d2e1e032fd19614f2fbb58149a7b02a">arma_vector_close_to</a></div><div class="ttdeci">bool arma_vector_close_to(arma::vec &amp;a, arma::vec &amp;b, double tol)</div><div class="ttdoc">Test if two armadillo vectors are close to each other.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00059">utils.cpp:59</a></div></div> <div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> }</div>
<div class="ttc" id="autils_8cpp_html_acd2a9c7a7d5a7fe9163be8c4cc110746"><div class="ttname"><a href="utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746">scientific_format</a></div><div class="ttdeci">std::string scientific_format(double d, int width, int prec)</div><div class="ttdoc">Turns a double into a string written in scientific format.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00014">utils.cpp:14</a></div></div> <div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="ttc" id="autils_8cpp_html_aff5e07c3c1d321709b0cc38e999f427b"><div class="ttname"><a href="utils_8cpp.html#aff5e07c3c1d321709b0cc38e999f427b">m_assert</a></div><div class="ttdeci">void m_assert(bool expr, std::string expr_str, std::string f, std::string file, int line, std::string msg)</div><div class="ttdoc">Test an expression, confirm that test is ok, or abort execution.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00040">utils.cpp:40</a></div></div> <div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span>}</div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> </div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"><a class="line" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa"> 76</a></span><span class="keywordtype">bool</span> <a class="code hl_function" href="utils_8cpp.html#acf13f4e492199cb7231bfa646dbd08de">mkpath</a>(std::string path, <span class="keywordtype">int</span> mode)</div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span>{</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> std::string cur_dir;</div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> std::string::size_type pos = -1;</div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> <span class="keyword">struct </span>stat buf;</div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> </div>
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<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> <span class="keywordflow">if</span> (mkdir(cur_dir.c_str(), mode) != 0 &amp;&amp; stat(cur_dir.c_str(), &amp;buf) != 0) {</div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> <span class="keywordflow">return</span> -1;</div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> }</div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> }</div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> <span class="keywordflow">else</span> {</div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> <span class="keywordflow">break</span>;</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> }</div>
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> <span class="keywordflow">return</span> 0;</div>
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span>}</div>
<div class="ttc" id="autils_8cpp_html_a5d2e1e032fd19614f2fbb58149a7b02a"><div class="ttname"><a href="utils_8cpp.html#a5d2e1e032fd19614f2fbb58149a7b02a">arma_vector_close_to</a></div><div class="ttdeci">bool arma_vector_close_to(arma::vec &amp;a, arma::vec &amp;b, double tol)</div><div class="ttdoc">Test if two armadillo vectors are close to each other.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00062">utils.cpp:62</a></div></div>
<div class="ttc" id="autils_8cpp_html_acd2a9c7a7d5a7fe9163be8c4cc110746"><div class="ttname"><a href="utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746">scientific_format</a></div><div class="ttdeci">std::string scientific_format(double d, int width, int prec)</div><div class="ttdoc">Turns a double into a string written in scientific format.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00017">utils.cpp:17</a></div></div>
<div class="ttc" id="autils_8cpp_html_acf13f4e492199cb7231bfa646dbd08de"><div class="ttname"><a href="utils_8cpp.html#acf13f4e492199cb7231bfa646dbd08de">mkpath</a></div><div class="ttdeci">bool mkpath(std::string path, int mode)</div><div class="ttdoc">Make path given.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00076">utils.cpp:76</a></div></div>
<div class="ttc" id="autils_8cpp_html_aff5e07c3c1d321709b0cc38e999f427b"><div class="ttname"><a href="utils_8cpp.html#aff5e07c3c1d321709b0cc38e999f427b">m_assert</a></div><div class="ttdeci">void m_assert(bool expr, std::string expr_str, std::string f, std::string file, int line, std::string msg)</div><div class="ttdoc">Test an expression, confirm that test is ok, or abort execution.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00043">utils.cpp:43</a></div></div>
<div class="ttc" id="autils_8hpp_html"><div class="ttname"><a href="utils_8hpp.html">utils.hpp</a></div><div class="ttdoc">Function prototypes and macros that are useful.</div></div> <div class="ttc" id="autils_8hpp_html"><div class="ttname"><a href="utils_8hpp.html">utils.hpp</a></div><div class="ttdoc">Function prototypes and macros that are useful.</div></div>
</div><!-- fragment --></div><!-- contents --> </div><!-- fragment --></div><!-- contents -->
</div><!-- doc-content --> </div><!-- doc-content -->

73
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@ -124,6 +124,7 @@ Macros</h2></td></tr>
<tr class="memdesc:a73d4f21ad937dbc50a0c0538c78fd4f9"><td class="mdescLeft">&#160;</td><td class="mdescRight">A prettier assertion function. <br /></td></tr> <tr class="memdesc:a73d4f21ad937dbc50a0c0538c78fd4f9"><td class="mdescLeft">&#160;</td><td class="mdescRight">A prettier assertion function. <br /></td></tr>
<tr class="separator:a73d4f21ad937dbc50a0c0538c78fd4f9"><td class="memSeparator" colspan="2">&#160;</td></tr> <tr class="separator:a73d4f21ad937dbc50a0c0538c78fd4f9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a60dca3177fb9cb5256609adc7af55168"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168">__METHOD_NAME__</a>&#160;&#160;&#160;methodName(__PRETTY_FUNCTION__)</td></tr> <tr class="memitem:a60dca3177fb9cb5256609adc7af55168"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168">__METHOD_NAME__</a>&#160;&#160;&#160;methodName(__PRETTY_FUNCTION__)</td></tr>
<tr class="memdesc:a60dca3177fb9cb5256609adc7af55168"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the name of the current method/function. <br /></td></tr>
<tr class="separator:a60dca3177fb9cb5256609adc7af55168"><td class="memSeparator" colspan="2">&#160;</td></tr> <tr class="separator:a60dca3177fb9cb5256609adc7af55168"><td class="memSeparator" colspan="2">&#160;</td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a> <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
@ -140,6 +141,9 @@ Functions</h2></td></tr>
<tr class="memitem:a0c95c4791692b06f8811905a76dbd772"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a> (arma::vec &amp;a, arma::vec &amp;b, double tol=1e-8)</td></tr> <tr class="memitem:a0c95c4791692b06f8811905a76dbd772"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a> (arma::vec &amp;a, arma::vec &amp;b, double tol=1e-8)</td></tr>
<tr class="memdesc:a0c95c4791692b06f8811905a76dbd772"><td class="mdescLeft">&#160;</td><td class="mdescRight">Test if two armadillo vectors are close to each other. <br /></td></tr> <tr class="memdesc:a0c95c4791692b06f8811905a76dbd772"><td class="mdescLeft">&#160;</td><td class="mdescRight">Test if two armadillo vectors are close to each other. <br /></td></tr>
<tr class="separator:a0c95c4791692b06f8811905a76dbd772"><td class="memSeparator" colspan="2">&#160;</td></tr> <tr class="separator:a0c95c4791692b06f8811905a76dbd772"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a6fdd7217b750aff5b6295ece7cbdeffa"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a> (std::string path, int mode=0777)</td></tr>
<tr class="memdesc:a6fdd7217b750aff5b6295ece7cbdeffa"><td class="mdescLeft">&#160;</td><td class="mdescRight">Make path given. <br /></td></tr>
<tr class="separator:a6fdd7217b750aff5b6295ece7cbdeffa"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table> </table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Function prototypes and macros that are useful. </p> <div class="textblock"><p>Function prototypes and macros that are useful. </p>
@ -148,7 +152,7 @@ Functions</h2></td></tr>
Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl> Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl> <dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
<p>These utility function are mainly for convenience and aren't directly related to the project.</p> <p>These utility function are mainly for convenience and aren't directly related to the project.</p>
<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000004">Bug:</a></b></dt><dd>No known bugs </dd></dl> <dl class="bug"><dt><b><a class="el" href="bug.html#_bug000005">Bug:</a></b></dt><dd>No known bugs </dd></dl>
<p class="definition">Definition in file <a class="el" href="utils_8hpp_source.html">utils.hpp</a>.</p> <p class="definition">Definition in file <a class="el" href="utils_8hpp_source.html">utils.hpp</a>.</p>
</div><h2 class="groupheader">Macro Definition Documentation</h2> </div><h2 class="groupheader">Macro Definition Documentation</h2>
@ -164,7 +168,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</table> </table>
</div><div class="memdoc"> </div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="utils_8hpp_source.html#l00048">48</a> of file <a class="el" href="utils_8hpp_source.html">utils.hpp</a>.</p> <p>Get the name of the current method/function. </p>
<p class="definition">Definition at line <a class="el" href="utils_8hpp_source.html#l00051">51</a> of file <a class="el" href="utils_8hpp_source.html">utils.hpp</a>.</p>
</div> </div>
</div> </div>
@ -193,9 +199,10 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</tr> </tr>
</table> </table>
</div><div class="memdoc"> </div><div class="memdoc">
<b>Value:</b><div class="fragment"><div class="line"> <a class="code hl_function" href="utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38">m_assert</a>(expr, #expr, __METHOD_NAME__, __FILE__, \</div> <b>Value:</b><div class="fragment"><div class="line"> <a class="code hl_function" href="utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38">m_assert</a>(expr, #expr, <a class="code hl_define" href="utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168">__METHOD_NAME__</a>, __FILE__, \</div>
<div class="line"> __LINE__, msg)</div> <div class="line"> __LINE__, msg)</div>
<div class="ttc" id="autils_8hpp_html_a2cc3a2cdb635bac3c8b02e89d4d6af38"><div class="ttname"><a href="utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38">m_assert</a></div><div class="ttdeci">void m_assert(bool expr, std::string expr_str, std::string func, std::string file, int line, std::string msg)</div><div class="ttdoc">Test an expression, confirm that test is ok, or abort execution.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00040">utils.cpp:40</a></div></div> <div class="ttc" id="autils_8hpp_html_a2cc3a2cdb635bac3c8b02e89d4d6af38"><div class="ttname"><a href="utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38">m_assert</a></div><div class="ttdeci">void m_assert(bool expr, std::string expr_str, std::string func, std::string file, int line, std::string msg)</div><div class="ttdoc">Test an expression, confirm that test is ok, or abort execution.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00043">utils.cpp:43</a></div></div>
<div class="ttc" id="autils_8hpp_html_a60dca3177fb9cb5256609adc7af55168"><div class="ttname"><a href="utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168">__METHOD_NAME__</a></div><div class="ttdeci">#define __METHOD_NAME__</div><div class="ttdoc">Get the name of the current method/function.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8hpp_source.html#l00051">utils.hpp:51</a></div></div>
</div><!-- fragment --> </div><!-- fragment -->
<p>A prettier assertion function. </p> <p>A prettier assertion function. </p>
<p>This macro calls the m_assert function which is a more informative assertion function than the regular assert function from cassert. </p> <p>This macro calls the m_assert function which is a more informative assertion function than the regular assert function from cassert. </p>
@ -270,9 +277,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</table> </table>
</dd> </dd>
</dl> </dl>
<dl class="section return"><dt>Returns</dt><dd>Boolean </dd></dl> <dl class="section return"><dt>Returns</dt><dd>bool </dd></dl>
<p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00059">59</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00062">62</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
</div> </div>
</div> </div>
@ -340,7 +347,48 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</dd> </dd>
</dl> </dl>
<p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00040">40</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00043">43</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
</div>
</div>
<a id="a6fdd7217b750aff5b6295ece7cbdeffa" name="a6fdd7217b750aff5b6295ece7cbdeffa"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a6fdd7217b750aff5b6295ece7cbdeffa">&#9670;&#160;</a></span>mkpath()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool mkpath </td>
<td>(</td>
<td class="paramtype">std::string&#160;</td>
<td class="paramname"><em>path</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int&#160;</td>
<td class="paramname"><em>mode</em> = <code>0777</code>&#160;</td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Make path given. </p>
<p>This tries to be the equivalent to "mkdir -p" and creates a new directory whenever it needs to.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">path</td><td>The path to be created </td></tr>
<tr><td class="paramname">mode</td><td>The mode/permissions for all the new directories</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>bool </dd></dl>
<p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00076">76</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
</div> </div>
</div> </div>
@ -377,6 +425,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</div><div class="memdoc"> </div><div class="memdoc">
<p>Turns a vector of doubles into a string written in scientific format. </p> <p>Turns a vector of doubles into a string written in scientific format. </p>
<p>The code is stolen from <a href="https://github.com/anderkve/FYS3150">https://github.com/anderkve/FYS3150</a>.</p>
<dl class="params"><dt>Parameters</dt><dd> <dl class="params"><dt>Parameters</dt><dd>
<table class="params"> <table class="params">
<tr><td class="paramname">v</td><td>The vector to stringify </td></tr> <tr><td class="paramname">v</td><td>The vector to stringify </td></tr>
@ -385,9 +434,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</table> </table>
</dd> </dd>
</dl> </dl>
<dl class="section return"><dt>Returns</dt><dd>String </dd></dl> <dl class="section return"><dt>Returns</dt><dd>std::string </dd></dl>
<p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00021">21</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00024">24</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
</div> </div>
</div> </div>
@ -424,7 +473,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</div><div class="memdoc"> </div><div class="memdoc">
<p>Turns a double into a string written in scientific format. </p> <p>Turns a double into a string written in scientific format. </p>
<p>Code stolen from <a href="https://github.com/anderkve/FYS3150">https://github.com/anderkve/FYS3150</a> Header: <a href="https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/include/utils.hpp">https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/include/utils.hpp</a> Source: <a href="https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/src/utils.cpp">https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/src/utils.cpp</a> </p> <p>The code is stolen from <a href="https://github.com/anderkve/FYS3150">https://github.com/anderkve/FYS3150</a>.</p>
<dl class="params"><dt>Parameters</dt><dd> <dl class="params"><dt>Parameters</dt><dd>
<table class="params"> <table class="params">
<tr><td class="paramname">d</td><td>The number to stringify </td></tr> <tr><td class="paramname">d</td><td>The number to stringify </td></tr>
@ -433,9 +482,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
</table> </table>
</dd> </dd>
</dl> </dl>
<dl class="section return"><dt>Returns</dt><dd>String </dd></dl> <dl class="section return"><dt>Returns</dt><dd>std::string </dd></dl>
<p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00014">14</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="utils_8cpp_source.html#l00017">17</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
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<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"><a class="line" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9"> 45</a></span><span class="preprocessor">#define ASSERT(expr, msg) m_assert(expr, #expr, __METHOD_NAME__, __FILE__, \</span></div> <div class="line"><a id="l00045" name="l00045"></a><span class="lineno"><a class="line" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9"> 45</a></span><span class="preprocessor">#define ASSERT(expr, msg) m_assert(expr, #expr, __METHOD_NAME__, __FILE__, \</span></div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span><span class="preprocessor"> __LINE__, msg)</span></div> <div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span><span class="preprocessor"> __LINE__, msg)</span></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> </div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span><span class="preprocessor">#define __METHOD_NAME__ methodName(__PRETTY_FUNCTION__)</span></div> <div class="line"><a id="l00051" name="l00051"></a><span class="lineno"><a class="line" href="utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168"> 51</a></span><span class="preprocessor">#define __METHOD_NAME__ methodName(__PRETTY_FUNCTION__)</span></div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> </div> <div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> </div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> </div> <div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> </div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span>std::string <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(<span class="keywordtype">double</span> d, <span class="keywordtype">int</span> width=20, <span class="keywordtype">int</span> prec=10);</div> <div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span>std::string <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(<span class="keywordtype">double</span> d, <span class="keywordtype">int</span> width=20, <span class="keywordtype">int</span> prec=10);</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> </div> <div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span>std::string <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(<span class="keyword">const</span> std::vector&lt;double&gt;&amp; v, </div> <div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> <span class="keywordtype">int</span> width=20, </div> <div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span>std::string <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(<span class="keyword">const</span> std::vector&lt;double&gt;&amp; v, </div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> <span class="keywordtype">int</span> prec=10);</div> <div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> <span class="keywordtype">int</span> width=20, </div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> </div> <div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> <span class="keywordtype">int</span> prec=10);</div>
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span><span class="keywordtype">void</span> <a class="code hl_function" href="utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38">m_assert</a>(<span class="keywordtype">bool</span> expr, </div> <div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> </div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> std::string expr_str, </div> <div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> </div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> std::string func, </div> <div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span><span class="keywordtype">void</span> <a class="code hl_function" href="utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38">m_assert</a>(<span class="keywordtype">bool</span> expr, </div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> std::string file, </div> <div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> std::string expr_str, </div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> <span class="keywordtype">int</span> line,</div> <div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> std::string func, </div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> std::string msg);</div> <div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> std::string file, </div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> </div> <div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> <span class="keywordtype">int</span> line,</div>
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> </div> <div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> std::string msg);</div>
<div class="line"><a id="l00109" name="l00109"></a><span class="lineno"> 109</span><span class="keywordtype">bool</span> <a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(arma::vec &amp;a, arma::vec &amp;b, <span class="keywordtype">double</span> tol=1e-8);</div> <div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> </div>
<div class="line"><a id="l00110" name="l00110"></a><span class="lineno"> 110</span> </div> <div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> </div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> </div> <div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span><span class="keywordtype">bool</span> <a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(arma::vec &amp;a, arma::vec &amp;b, <span class="keywordtype">double</span> tol=1e-8);</div>
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span><span class="keyword">static</span> <span class="keyword">inline</span> std::string methodName(<span class="keyword">const</span> std::string&amp; prettyFunction)</div> <div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span>{</div> <div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> </div>
<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span> <span class="keywordtype">size_t</span> colons = prettyFunction.find(<span class="stringliteral">&quot;::&quot;</span>);</div> <div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</span><span class="keyword">static</span> <span class="keyword">inline</span> std::string methodName(<span class="keyword">const</span> std::string&amp; pretty_function)</div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> <span class="keywordtype">size_t</span> begin = prettyFunction.substr(0,colons).rfind(<span class="stringliteral">&quot; &quot;</span>) + 1;</div> <div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span>{</div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> <span class="keywordtype">size_t</span> end = prettyFunction.rfind(<span class="stringliteral">&quot;(&quot;</span>) - begin;</div> <div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> <span class="keywordtype">size_t</span> colons = pretty_function.find(<span class="stringliteral">&quot;::&quot;</span>);</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> </div> <div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> <span class="keywordtype">size_t</span> begin = pretty_function.substr(0,colons).rfind(<span class="stringliteral">&quot; &quot;</span>) + 1;</div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> <span class="keywordflow">return</span> prettyFunction.substr(begin,end) + <span class="stringliteral">&quot;()&quot;</span>;</div> <div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> <span class="keywordtype">size_t</span> end = pretty_function.rfind(<span class="stringliteral">&quot;(&quot;</span>) - begin;</div>
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span>}</div> <div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> </div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span> </div> <div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> <span class="keywordflow">return</span> pretty_function.substr(begin,end) + <span class="stringliteral">&quot;()&quot;</span>;</div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span><span class="preprocessor">#endif</span></div> <div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span>}</div>
<div class="ttc" id="autils_8hpp_html_a0c95c4791692b06f8811905a76dbd772"><div class="ttname"><a href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a></div><div class="ttdeci">bool arma_vector_close_to(arma::vec &amp;a, arma::vec &amp;b, double tol=1e-8)</div><div class="ttdoc">Test if two armadillo vectors are close to each other.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00059">utils.cpp:59</a></div></div> <div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> </div>
<div class="ttc" id="autils_8hpp_html_a2cc3a2cdb635bac3c8b02e89d4d6af38"><div class="ttname"><a href="utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38">m_assert</a></div><div class="ttdeci">void m_assert(bool expr, std::string expr_str, std::string func, std::string file, int line, std::string msg)</div><div class="ttdoc">Test an expression, confirm that test is ok, or abort execution.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00040">utils.cpp:40</a></div></div> <div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> </div>
<div class="ttc" id="autils_8hpp_html_adfb618b2fdff47ef30a4a2b62c04f384"><div class="ttname"><a href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a></div><div class="ttdeci">std::string scientific_format(double d, int width=20, int prec=10)</div><div class="ttdoc">Turns a double into a string written in scientific format.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00014">utils.cpp:14</a></div></div> <div class="line"><a id="l00146" name="l00146"></a><span class="lineno"> 146</span><span class="keywordtype">bool</span> <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(std::string path, <span class="keywordtype">int</span> mode = 0777);</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="preprocessor">#endif</span></div>
<div class="ttc" id="autils_8hpp_html_a0c95c4791692b06f8811905a76dbd772"><div class="ttname"><a href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a></div><div class="ttdeci">bool arma_vector_close_to(arma::vec &amp;a, arma::vec &amp;b, double tol=1e-8)</div><div class="ttdoc">Test if two armadillo vectors are close to each other.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00062">utils.cpp:62</a></div></div>
<div class="ttc" id="autils_8hpp_html_a2cc3a2cdb635bac3c8b02e89d4d6af38"><div class="ttname"><a href="utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38">m_assert</a></div><div class="ttdeci">void m_assert(bool expr, std::string expr_str, std::string func, std::string file, int line, std::string msg)</div><div class="ttdoc">Test an expression, confirm that test is ok, or abort execution.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00043">utils.cpp:43</a></div></div>
<div class="ttc" id="autils_8hpp_html_a6fdd7217b750aff5b6295ece7cbdeffa"><div class="ttname"><a href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a></div><div class="ttdeci">bool mkpath(std::string path, int mode=0777)</div><div class="ttdoc">Make path given.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00076">utils.cpp:76</a></div></div>
<div class="ttc" id="autils_8hpp_html_adfb618b2fdff47ef30a4a2b62c04f384"><div class="ttname"><a href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a></div><div class="ttdeci">std::string scientific_format(double d, int width=20, int prec=10)</div><div class="ttdoc">Turns a double into a string written in scientific format.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00017">utils.cpp:17</a></div></div>
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41
man_pages/man3/Particle.3
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@ -1,4 +1,4 @@
.TH "Particle" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- .TH "Particle" 3 "Sat Oct 14 2023" "Penning Trap Simulation" \" -*- nroff -*-
.ad l .ad l
.nh .nh
.SH NAME .SH NAME
@ -13,7 +13,7 @@ Particle \- A class that holds attributes of a particle\&.
.in +1c .in +1c
.ti -1c .ti -1c
.RI "\fBParticle\fP (double \fBq\fP, double \fBm\fP, arma::vec::fixed< 3 > \fBr_vec\fP, arma::vec::fixed< 3 > \fBv_vec\fP)" .RI "\fBParticle\fP (double \fBq\fP, double \fBm\fP, \fBvec_3d\fP \fBr_vec\fP, \fBvec_3d\fP \fBv_vec\fP)"
.br .br
.RI "Initialize the particle\&. " .RI "Initialize the particle\&. "
.in -1c .in -1c
@ -29,11 +29,11 @@ Particle \- A class that holds attributes of a particle\&.
.br .br
.RI "Mass\&. " .RI "Mass\&. "
.ti -1c .ti -1c
.RI "arma::vec::fixed< 3 > \fBr_vec\fP" .RI "\fBvec_3d\fP \fBr_vec\fP"
.br .br
.RI "position " .RI "position "
.ti -1c .ti -1c
.RI "arma::vec::fixed< 3 > \fBv_vec\fP" .RI "\fBvec_3d\fP \fBv_vec\fP"
.br .br
.RI "velocity " .RI "velocity "
.in -1c .in -1c
@ -49,15 +49,28 @@ Particle \- A class that holds attributes of a particle\&.
.PP .PP
A class that holds attributes of a particle\&. A class that holds attributes of a particle\&.
.PP .PP
Definition at line \fB19\fP of file \fBParticle\&.hpp\fP\&. Definition at line \fB21\fP of file \fBParticle\&.hpp\fP\&.
.SH "Constructor & Destructor Documentation" .SH "Constructor & Destructor Documentation"
.PP .PP
.SS "Particle::Particle (double q, double m, arma::vec::fixed< 3 > r_vec, arma::vec::fixed< 3 > v_vec)" .SS "Particle::Particle (double q, double m, \fBvec_3d\fP r_vec, \fBvec_3d\fP v_vec)"
.PP .PP
Initialize the particle\&. Initialize the particle with a charge, mass, position and velocity\&. Initialize the particle\&. Initialize the particle with a charge, mass, position and velocity\&.
.PP .PP
Definition at line \fB16\fP of file \fBParticle\&.cpp\fP\&. \fBParameters\fP
.RS 4
\fIq\fP The charge of the particle
.br
\fIm\fP The mass of the particle
.br
\fIr_vec\fP The initial position of the particle
.br
\fIv_vec\fP The initial velocity of the particle
.RE
.PP
.PP
Definition at line \fB15\fP of file \fBParticle\&.cpp\fP\&.
.SH "Friends And Related Function Documentation" .SH "Friends And Related Function Documentation"
.PP .PP
.SS "friend class \fBPenningTrap\fP\fC [friend]\fP" .SS "friend class \fBPenningTrap\fP\fC [friend]\fP"
@ -65,7 +78,7 @@ Definition at line \fB16\fP of file \fBParticle\&.cpp\fP\&.
.PP .PP
Make private attributes available for \fBPenningTrap\fP\&. Make private attributes available for \fBPenningTrap\fP\&.
.PP .PP
Definition at line \fB38\fP of file \fBParticle\&.hpp\fP\&. Definition at line \fB43\fP of file \fBParticle\&.hpp\fP\&.
.SH "Member Data Documentation" .SH "Member Data Documentation"
.PP .PP
.SS "double Particle::m\fC [private]\fP" .SS "double Particle::m\fC [private]\fP"
@ -73,25 +86,25 @@ Definition at line \fB38\fP of file \fBParticle\&.hpp\fP\&.
.PP .PP
Mass\&. Mass\&.
.PP .PP
Definition at line \fB22\fP of file \fBParticle\&.hpp\fP\&. Definition at line \fB24\fP of file \fBParticle\&.hpp\fP\&.
.SS "double Particle::q\fC [private]\fP" .SS "double Particle::q\fC [private]\fP"
.PP .PP
Charge\&. Charge\&.
.PP .PP
Definition at line \fB21\fP of file \fBParticle\&.hpp\fP\&. Definition at line \fB23\fP of file \fBParticle\&.hpp\fP\&.
.SS "arma::vec::fixed<3> Particle::r_vec\fC [private]\fP" .SS "\fBvec_3d\fP Particle::r_vec\fC [private]\fP"
.PP .PP
position position
.PP .PP
Definition at line \fB23\fP of file \fBParticle\&.hpp\fP\&. Definition at line \fB25\fP of file \fBParticle\&.hpp\fP\&.
.SS "arma::vec::fixed<3> Particle::v_vec\fC [private]\fP" .SS "\fBvec_3d\fP Particle::v_vec\fC [private]\fP"
.PP .PP
velocity velocity
.PP .PP
Definition at line \fB24\fP of file \fBParticle\&.hpp\fP\&. Definition at line \fB26\fP of file \fBParticle\&.hpp\fP\&.
.SH "Author" .SH "Author"
.PP .PP

2
man_pages/man3/Particle.cpp.3
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@ -1,4 +1,4 @@
.TH "src/Particle.cpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- .TH "src/Particle.cpp" 3 "Sat Oct 14 2023" "Penning Trap Simulation" \" -*- nroff -*-
.ad l .ad l
.nh .nh
.SH NAME .SH NAME

4
man_pages/man3/Particle.hpp.3
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@ -1,4 +1,4 @@
.TH "include/Particle.hpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- .TH "include/Particle.hpp" 3 "Sat Oct 14 2023" "Penning Trap Simulation" \" -*- nroff -*-
.ad l .ad l
.nh .nh
.SH NAME .SH NAME
@ -9,6 +9,8 @@ include/Particle.hpp \- A class that holds the properties of a particle\&.
.PP .PP
\fC#include <armadillo>\fP \fC#include <armadillo>\fP
.br .br
\fC#include 'typedefs\&.hpp'\fP
.br
.SS "Classes" .SS "Classes"

400
man_pages/man3/PenningTrap.3
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@ -1,4 +1,4 @@
.TH "PenningTrap" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- .TH "PenningTrap" 3 "Sat Oct 14 2023" "Penning Trap Simulation" \" -*- nroff -*-
.ad l .ad l
.nh .nh
.SH NAME .SH NAME
@ -13,51 +13,77 @@ PenningTrap \- A class that simulates a Penning trap\&.
.in +1c .in +1c
.ti -1c .ti -1c
.RI "\fBPenningTrap\fP (double \fBB_0\fP=\fBT\fP, double \fBV_0\fP=25\&.*\fBV\fP/1000\&., double \fBd\fP=500\&.)" .RI "\fBPenningTrap\fP (double \fBB_0\fP=\fBT\fP, std::function< double(double)> \fBV_0\fP=[](double \fBt\fP) { return 25\&. *\fBV\fP/1000\&.;}, double \fBd\fP=500\&., double \fBt\fP=0\&.)"
.br .br
.RI "Set B_0, V_0 and d\&. " .RI "Constructor for the \fBPenningTrap\fP class\&. "
.ti -1c
.RI "\fBPenningTrap\fP (unsigned int i, double \fBB_0\fP=\fBT\fP, std::function< double(double)> \fBV_0\fP=[](double \fBt\fP) { return 25\&. *\fBV\fP/1000\&.;}, double \fBd\fP=500\&., double \fBt\fP=0\&.)"
.br
.RI "Constructor for the \fBPenningTrap\fP class\&. "
.ti -1c
.RI "\fBPenningTrap\fP (std::vector< \fBParticle\fP > \fBparticles\fP, double \fBB_0\fP=\fBT\fP, std::function< double(double)> \fBV_0\fP=[](double \fBt\fP) { return 25\&. *\fBV\fP/1000\&.;}, double \fBd\fP=500\&., double \fBt\fP=0\&.)"
.br
.RI "Constructor for the \fBPenningTrap\fP class\&. "
.ti -1c .ti -1c
.RI "void \fBadd_particle\fP (\fBParticle\fP particle)" .RI "void \fBadd_particle\fP (\fBParticle\fP particle)"
.br .br
.RI "Add a particle to the system\&. " .RI "Add a particle to the system\&. "
.ti -1c .ti -1c
.RI "arma::vec \fBexternal_E_field\fP (arma::vec r)" .RI "\fBvec_3d\fP \fBexternal_E_field\fP (\fBvec_3d\fP r)"
.br .br
.RI "Calculate E at point r\&. " .RI "Calculate E at point r\&. "
.ti -1c .ti -1c
.RI "arma::vec \fBexternal_B_field\fP (arma::vec r)" .RI "\fBvec_3d\fP \fBexternal_B_field\fP (\fBvec_3d\fP r)"
.br .br
.RI "Calculate B at point r\&. " .RI "Calculate B at point r\&. "
.ti -1c .ti -1c
.RI "arma::vec \fBforce_on_particle\fP (int i, int j)" .RI "\fBvec_3d\fP \fBforce_on_particle\fP (unsigned int i, unsigned int j)"
.br .br
.RI "Calculate the force between 2 particles\&. " .RI "Calculate the force between 2 particles\&. "
.ti -1c .ti -1c
.RI "arma::vec \fBtotal_force_external\fP (int i)" .RI "\fBvec_3d\fP \fBtotal_force_external\fP (unsigned int i)"
.br .br
.RI "Calculate the total external force on a particle\&. " .RI "Calculate the total external force on a particle\&. "
.ti -1c .ti -1c
.RI "arma::vec \fBtotal_force_particles\fP (int i)" .RI "\fBvec_3d\fP \fBtotal_force_particles\fP (unsigned int i)"
.br .br
.RI "Calculate the total force on a particle from other particles\&. " .RI "Calculate the total force on a particle p_i from other particles\&. "
.ti -1c .ti -1c
.RI "arma::vec \fBtotal_force\fP (int i)" .RI "\fBvec_3d\fP \fBtotal_force\fP (unsigned int i)"
.br .br
.RI "calculate the total force on a particle\&. " .RI "calculate the total force on a particle p_i\&. "
.ti -1c .ti -1c
.RI "void \fBevolve_RK4\fP (double dt)" .RI "void \fBevolve_RK4\fP (double dt, bool particle_interaction=true)"
.br .br
.RI "Go forward one timestep using the RK4 method\&. " .RI "Go forward one timestep using the RK4 method\&. "
.ti -1c .ti -1c
.RI "void \fBevolve_forward_euler\fP (double dt)" .RI "void \fBevolve_forward_euler\fP (double dt, bool particle_interaction=true)"
.br .br
.RI "Go forward one timestep using the forward Euler method\&. " .RI "Go forward one timestep using the forward Euler method\&. "
.ti -1c .ti -1c
.RI "arma::vec \fBget_particle\fP (int i)" .RI "\fBsim_arr\fP \fBsimulate\fP (double time, unsigned int steps, std::string method='rk4', bool particle_interaction=true)"
.br .br
.RI "Simulate the particle system inside the Penning trap over a certain amount of time\&. "
.ti -1c .ti -1c
.RI "double \fBget_d\fP ()" .RI "void \fBwrite_simulation_to_dir\fP (std::string path, double time, unsigned int steps, std::string method='rk4', bool particle_interaction=true)"
.br .br
.RI "Simulate and write the displacement of all particles to files\&. "
.ti -1c
.RI "double \fBfraction_of_particles_left\fP (double time, unsigned int steps, std::string method='rk4', bool particle_interaction=true)"
.br
.RI "Simulate and calculate what fraction of particles are still left inside the Penning trap after the simulation\&. "
.in -1c
.SS "Private Member Functions"
.in +1c
.ti -1c
.RI "\fBvec_3d\fP \fBv_func\fP (unsigned int i, unsigned int j, double dt)"
.br
.RI "Helper for evolve_RK4 when calculating $k_{v,i,j}$ values\&. "
.ti -1c
.RI "\fBvec_3d\fP \fBr_func\fP (unsigned int i, unsigned int j, double dt)"
.br
.RI "Helper for evolve_RK4 when calculating $k_{r,i,j}$ values\&. "
.in -1c .in -1c
.SS "Private Attributes" .SS "Private Attributes"
@ -67,7 +93,7 @@ PenningTrap \- A class that simulates a Penning trap\&.
.br .br
.RI "Magnetic field strength\&. " .RI "Magnetic field strength\&. "
.ti -1c .ti -1c
.RI "double \fBV_0\fP" .RI "std::function< double(double)> \fBV_0\fP"
.br .br
.RI "Applied potential\&. " .RI "Applied potential\&. "
.ti -1c .ti -1c
@ -75,9 +101,19 @@ PenningTrap \- A class that simulates a Penning trap\&.
.br .br
.RI "Characteristic dimension\&. " .RI "Characteristic dimension\&. "
.ti -1c .ti -1c
.RI "double \fBt\fP"
.br
.RI "Current time\&. "
.ti -1c
.RI "std::vector< \fBParticle\fP > \fBparticles\fP" .RI "std::vector< \fBParticle\fP > \fBparticles\fP"
.br .br
.RI "The particles in the Penning trap\&. " .RI "The particles in the Penning trap\&. "
.ti -1c
.RI "\fBsim_arr\fP \fBk_v\fP"
.br
.ti -1c
.RI "\fBsim_arr\fP \fBk_r\fP"
.br
.in -1c .in -1c
.SH "Detailed Description" .SH "Detailed Description"
.PP .PP
@ -85,15 +121,70 @@ A class that simulates a Penning trap\&.
This class simulates a Penning trap\&. It can take in a number of particles and simulate how they would behave inside a Penning trap\&. This class simulates a Penning trap\&. It can take in a number of particles and simulate how they would behave inside a Penning trap\&.
.PP .PP
Definition at line \fB29\fP of file \fBPenningTrap\&.hpp\fP\&. Definition at line \fB30\fP of file \fBPenningTrap\&.hpp\fP\&.
.SH "Constructor & Destructor Documentation" .SH "Constructor & Destructor Documentation"
.PP .PP
.SS "PenningTrap::PenningTrap (double B_0 = \fC\fBT\fP\fP, double V_0 = \fC25\&.*\fBV\fP/1000\&.\fP, double d = \fC500\&.\fP)" .SS "PenningTrap::PenningTrap (double B_0 = \fC\fBT\fP\fP, std::function< double(double)> V_0 = \fC[](double \fBt\fP) { return 25\&. * \fBV\fP / 1000\&.; }\fP, double d = \fC500\&.\fP, double t = \fC0\&.\fP)"
.PP .PP
Set B_0, V_0 and d\&. Constructor for the \fBPenningTrap\fP class\&.
.PP .PP
Definition at line \fB20\fP of file \fBPenningTrap\&.cpp\fP\&. \fBParameters\fP
.RS 4
\fIB_0\fP The magnetic field strength
.br
\fIV_0\fP The time dependent applied potential
.br
\fId\fP The characteristic dimension
.br
\fIt\fP The starting time
.RE
.PP
.PP
Definition at line \fB18\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "PenningTrap::PenningTrap (unsigned int i, double B_0 = \fC\fBT\fP\fP, std::function< double(double)> V_0 = \fC[](double \fBt\fP) { return 25\&. * \fBV\fP / 1000\&.; }\fP, double d = \fC500\&.\fP, double t = \fC0\&.\fP)"
.PP
Constructor for the \fBPenningTrap\fP class\&.
.PP
\fBParameters\fP
.RS 4
\fIi\fP The number of particles to generate
.br
\fIB_0\fP The magnetic field strength
.br
\fIV_0\fP The time dependent applied potential
.br
\fId\fP The characteristic dimension
.br
\fIt\fP The starting time
.RE
.PP
.PP
Definition at line \fB27\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "PenningTrap::PenningTrap (std::vector< \fBParticle\fP > particles, double B_0 = \fC\fBT\fP\fP, std::function< double(double)> V_0 = \fC[](double \fBt\fP) { return 25\&. * \fBV\fP / 1000\&.; }\fP, double d = \fC500\&.\fP, double t = \fC0\&.\fP)"
.PP
Constructor for the \fBPenningTrap\fP class\&.
.PP
\fBParameters\fP
.RS 4
\fIparticles\fP The starting particles
.br
\fIB_0\fP The magnetic field strength
.br
\fIV_0\fP The time dependent applied potential
.br
\fId\fP The characteristic dimension
.br
\fIt\fP The starting time
.RE
.PP
.PP
Definition at line \fB39\fP of file \fBPenningTrap\&.cpp\fP\&.
.SH "Member Function Documentation" .SH "Member Function Documentation"
.PP .PP
.SS "void PenningTrap::add_particle (\fBParticle\fP particle)" .SS "void PenningTrap::add_particle (\fBParticle\fP particle)"
@ -101,63 +192,262 @@ Definition at line \fB20\fP of file \fBPenningTrap\&.cpp\fP\&.
.PP .PP
Add a particle to the system\&. Add a particle to the system\&.
.PP .PP
Definition at line \fB27\fP of file \fBPenningTrap\&.cpp\fP\&. \fBParameters\fP
.SS "void PenningTrap::evolve_forward_euler (double dt)" .RS 4
\fIparticle\fP The particle to add to the Penning trap
.RE
.PP
.PP
Definition at line \fB82\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "void PenningTrap::evolve_forward_euler (double dt, bool particle_interaction = \fCtrue\fP)"
.PP .PP
Go forward one timestep using the forward Euler method\&. Go forward one timestep using the forward Euler method\&.
.PP .PP
Definition at line \fB167\fP of file \fBPenningTrap\&.cpp\fP\&. \fBParameters\fP
.SS "void PenningTrap::evolve_RK4 (double dt)" .RS 4
\fIdt\fP The step length
.br
\fIparticle_interaction\fP Turn particle interactions on/off
.RE
.PP
.PP
Definition at line \fB186\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "void PenningTrap::evolve_RK4 (double dt, bool particle_interaction = \fCtrue\fP)"
.PP .PP
Go forward one timestep using the RK4 method\&. Go forward one timestep using the RK4 method\&.
.PP .PP
Definition at line \fB104\fP of file \fBPenningTrap\&.cpp\fP\&. \fBParameters\fP
.SS "arma::vec PenningTrap::external_B_field (arma::vec r)" .RS 4
\fIdt\fP The step length
.br
\fIparticle_interaction\fP Turn particle interactions on/off
.RE
.PP
.PP
Definition at line \fB151\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "\fBvec_3d\fP PenningTrap::external_B_field (\fBvec_3d\fP r)"
.PP .PP
Calculate B at point r\&. Calculate B at point r\&.
.PP .PP
Definition at line \fB43\fP of file \fBPenningTrap\&.cpp\fP\&. \fBParameters\fP
.SS "arma::vec PenningTrap::external_E_field (arma::vec r)" .RS 4
\fIr\fP The position where we want to calculate the B field
.RE
.PP
\fBReturns\fP
.RS 4
vec_3d
.RE
.PP
.PP
Definition at line \fB95\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "\fBvec_3d\fP PenningTrap::external_E_field (\fBvec_3d\fP r)"
.PP .PP
Calculate E at point r\&. Calculate E at point r\&.
.PP .PP
Definition at line \fB32\fP of file \fBPenningTrap\&.cpp\fP\&. \fBParameters\fP
.SS "arma::vec PenningTrap::force_on_particle (int i, int j)" .RS 4
\fIr\fP The position where we want to calculate the E field
.RE
.PP
\fBReturns\fP
.RS 4
vec_3d
.RE
.PP
.PP
Definition at line \fB87\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "\fBvec_3d\fP PenningTrap::force_on_particle (unsigned int i, unsigned int j)"
.PP .PP
Calculate the force between 2 particles\&. Calculate the force exhibited on particle p_i from particle p_j\&. Calculate the force between 2 particles\&. Calculate the force exhibited on particle p_i from particle p_j\&.
.PP .PP
Definition at line \fB50\fP of file \fBPenningTrap\&.cpp\fP\&. \fBParameters\fP
.SS "double PenningTrap::get_d ()" .RS 4
\fIi\fP The index of particle p_i
.br
\fIj\fP The index of particle p_j
.RE
.PP
\fBReturns\fP
.RS 4
vec_3d
.RE
.PP
.PP .PP
Definition at line \fB188\fP of file \fBPenningTrap\&.cpp\fP\&. Definition at line \fB100\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "arma::vec PenningTrap::get_particle (int i)" .SS "double PenningTrap::fraction_of_particles_left (double time, unsigned int steps, std::string method = \fC'rk4'\fP, bool particle_interaction = \fCtrue\fP)"
.PP .PP
Definition at line \fB183\fP of file \fBPenningTrap\&.cpp\fP\&. Simulate and calculate what fraction of particles are still left inside the Penning trap after the simulation\&.
.SS "arma::vec PenningTrap::total_force (int i)" .PP
\fBParameters\fP
.RS 4
\fItime\fP The time to simulate in microseconds
.br
\fIsteps\fP The amount of steps for the whole simulation
.br
\fImethod\fP The method to use when moving forward a timestep
.br
\fIparticle_interaction\fP Turn particle interactions on/off
.RE
.PP
\fBReturns\fP
.RS 4
double
.RE
.PP
.PP .PP
calculate the total force on a particle\&. Definition at line \fB266\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "\fBvec_3d\fP PenningTrap::r_func (unsigned int i, unsigned int j, double dt)\fC [private]\fP"
.PP .PP
Definition at line \fB99\fP of file \fBPenningTrap\&.cpp\fP\&. Helper for evolve_RK4 when calculating $k_{r,i,j}$ values\&. Something
.SS "arma::vec PenningTrap::total_force_external (int i)" .PP
\fBParameters\fP
.RS 4
\fIi\fP Index i for $k_{r,i,j}$
.br
\fIj\fP Index j for $k_{r,i,j}$
.br
\fIdt\fP the step length (delta time)
.RE
.PP
\fBReturns\fP
.RS 4
vec_3d
.RE
.PP
.PP
Definition at line \fB64\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "\fBsim_arr\fP PenningTrap::simulate (double time, unsigned int steps, std::string method = \fC'rk4'\fP, bool particle_interaction = \fCtrue\fP)"
.PP
Simulate the particle system inside the Penning trap over a certain amount of time\&.
.PP
\fBParameters\fP
.RS 4
\fItime\fP The time to simulate in microseconds
.br
\fIsteps\fP The amount of steps for the whole simulation
.br
\fImethod\fP The method to use when moving forward a timestep
.br
\fIparticle_interaction\fP Turn particle interactions on/off
.RE
.PP
.PP
Definition at line \fB211\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "\fBvec_3d\fP PenningTrap::total_force (unsigned int i)"
.PP
calculate the total force on a particle p_i\&.
.PP
\fBParameters\fP
.RS 4
\fIi\fP The index of particle p_i
.RE
.PP
\fBReturns\fP
.RS 4
vec_3d
.RE
.PP
.PP
Definition at line \fB146\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "\fBvec_3d\fP PenningTrap::total_force_external (unsigned int i)"
.PP .PP
Calculate the total external force on a particle\&. Calculate the total amount of force that E and B exhibits on particle p_i\&. Calculate the total external force on a particle\&. Calculate the total amount of force that E and B exhibits on particle p_i\&.
.PP .PP
Definition at line \fB65\fP of file \fBPenningTrap\&.cpp\fP\&. \fBParameters\fP
.SS "arma::vec PenningTrap::total_force_particles (int i)" .RS 4
\fIi\fP The index of particle p_i
.RE
.PP
\fBReturns\fP
.RS 4
vec_3d
.RE
.PP
.PP .PP
Calculate the total force on a particle from other particles\&. Definition at line \fB114\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "\fBvec_3d\fP PenningTrap::total_force_particles (unsigned int i)"
.PP .PP
Definition at line \fB80\fP of file \fBPenningTrap\&.cpp\fP\&. Calculate the total force on a particle p_i from other particles\&.
.PP
\fBParameters\fP
.RS 4
\fIi\fP The index of particle p_i
.RE
.PP
\fBReturns\fP
.RS 4
vec_3d
.RE
.PP
.PP
Definition at line \fB129\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "\fBvec_3d\fP PenningTrap::v_func (unsigned int i, unsigned int j, double dt)\fC [private]\fP"
.PP
Helper for evolve_RK4 when calculating $k_{v,i,j}$ values\&. Something
.PP
\fBParameters\fP
.RS 4
\fIi\fP Index i for $k_{v,i,j}$
.br
\fIj\fP Index j for $k_{v,i,j}$
.br
\fIdt\fP the step length (delta time)
.RE
.PP
\fBReturns\fP
.RS 4
vec_3d
.RE
.PP
.PP
Definition at line \fB46\fP of file \fBPenningTrap\&.cpp\fP\&.
.SS "void PenningTrap::write_simulation_to_dir (std::string path, double time, unsigned int steps, std::string method = \fC'rk4'\fP, bool particle_interaction = \fCtrue\fP)"
.PP
Simulate and write the displacement of all particles to files\&.
.PP
\fBParameters\fP
.RS 4
\fIpath\fP The directory to save the data
.br
\fItime\fP The time to simulate in microseconds
.br
\fIsteps\fP The amount of steps for the whole simulation
.br
\fImethod\fP The method to use when moving forward a timestep
.br
\fIparticle_interaction\fP Turn particle interactions on/off
.RE
.PP
.PP
Definition at line \fB240\fP of file \fBPenningTrap\&.cpp\fP\&.
.SH "Member Data Documentation" .SH "Member Data Documentation"
.PP .PP
.SS "double PenningTrap::B_0\fC [private]\fP" .SS "double PenningTrap::B_0\fC [private]\fP"
@ -165,25 +455,39 @@ Definition at line \fB80\fP of file \fBPenningTrap\&.cpp\fP\&.
.PP .PP
Magnetic field strength\&. Magnetic field strength\&.
.PP .PP
Definition at line \fB31\fP of file \fBPenningTrap\&.hpp\fP\&. Definition at line \fB32\fP of file \fBPenningTrap\&.hpp\fP\&.
.SS "double PenningTrap::d\fC [private]\fP" .SS "double PenningTrap::d\fC [private]\fP"
.PP .PP
Characteristic dimension\&. Characteristic dimension\&.
.PP .PP
Definition at line \fB33\fP of file \fBPenningTrap\&.hpp\fP\&. Definition at line \fB34\fP of file \fBPenningTrap\&.hpp\fP\&.
.SS "\fBsim_arr\fP PenningTrap::k_r\fC [private]\fP"
A 2D vector containing all $k_{i,j}$ where $j$ is the index of a particle
.PP
Definition at line \fB39\fP of file \fBPenningTrap\&.hpp\fP\&.
.SS "\fBsim_arr\fP PenningTrap::k_v\fC [private]\fP"
A 2D vector containing all $k_{i,j}$ where $j$ is the index of a particle
.PP
Definition at line \fB37\fP of file \fBPenningTrap\&.hpp\fP\&.
.SS "std::vector<\fBParticle\fP> PenningTrap::particles\fC [private]\fP" .SS "std::vector<\fBParticle\fP> PenningTrap::particles\fC [private]\fP"
.PP .PP
The particles in the Penning trap\&. The particles in the Penning trap\&.
.PP .PP
Definition at line \fB34\fP of file \fBPenningTrap\&.hpp\fP\&. Definition at line \fB36\fP of file \fBPenningTrap\&.hpp\fP\&.
.SS "double PenningTrap::V_0\fC [private]\fP" .SS "double PenningTrap::t\fC [private]\fP"
.PP
Current time\&.
.PP
Definition at line \fB35\fP of file \fBPenningTrap\&.hpp\fP\&.
.SS "std::function<double(double)> PenningTrap::V_0\fC [private]\fP"
.PP .PP
Applied potential\&. Applied potential\&.
.PP .PP
Definition at line \fB32\fP of file \fBPenningTrap\&.hpp\fP\&. Definition at line \fB33\fP of file \fBPenningTrap\&.hpp\fP\&.
.SH "Author" .SH "Author"
.PP .PP

12
man_pages/man3/PenningTrap.cpp.3
View File

@ -1,4 +1,4 @@
.TH "src/PenningTrap.cpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- .TH "src/PenningTrap.cpp" 3 "Sat Oct 14 2023" "Penning Trap Simulation" \" -*- nroff -*-
.ad l .ad l
.nh .nh
.SH NAME .SH NAME
@ -11,6 +11,8 @@ src/PenningTrap.cpp \- The implementation of the \fBPenningTrap\fP class\&.
.br .br
\fC#include 'constants\&.hpp'\fP \fC#include 'constants\&.hpp'\fP
.br .br
\fC#include 'typedefs\&.hpp'\fP
.br
\fC#include 'utils\&.hpp'\fP \fC#include 'utils\&.hpp'\fP
.br .br
@ -38,14 +40,6 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
No known bugs No known bugs
.RE .RE
.PP .PP
.PP
\fBTodo\fP
.RS 4
Implement evolve_RK4
.PP
Implement evolve_forward_euler
.RE
.PP
.PP .PP
Definition in file \fBPenningTrap\&.cpp\fP\&. Definition in file \fBPenningTrap\&.cpp\fP\&.

4
man_pages/man3/PenningTrap.hpp.3
View File

@ -1,4 +1,4 @@
.TH "include/PenningTrap.hpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- .TH "include/PenningTrap.hpp" 3 "Sat Oct 14 2023" "Penning Trap Simulation" \" -*- nroff -*-
.ad l .ad l
.nh .nh
.SH NAME .SH NAME
@ -15,6 +15,8 @@ include/PenningTrap.hpp \- A class for simulating a Penning trap\&.
.br .br
\fC#include 'constants\&.hpp'\fP \fC#include 'constants\&.hpp'\fP
.br .br
\fC#include 'typedefs\&.hpp'\fP
.br
.SS "Classes" .SS "Classes"

2
man_pages/man3/PenningTrapTest.3
View File

@ -1,4 +1,4 @@
.TH "PenningTrapTest" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- .TH "PenningTrapTest" 3 "Sat Oct 14 2023" "Penning Trap Simulation" \" -*- nroff -*-
.ad l .ad l
.nh .nh
.SH NAME .SH NAME

4
man_pages/man3/bug.3
View File

@ -1,4 +1,4 @@
.TH "bug" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- .TH "bug" 3 "Sat Oct 14 2023" "Penning Trap Simulation" \" -*- nroff -*-
.ad l .ad l
.nh .nh
.SH NAME .SH NAME
@ -19,6 +19,8 @@ No known bugs
No known bugs No known bugs
.IP "\fBFile \fBtest_suite\&.cpp\fP \fP" 1c .IP "\fBFile \fBtest_suite\&.cpp\fP \fP" 1c
No known bugs No known bugs
.IP "\fBFile \fBtypedefs\&.hpp\fP \fP" 1c
No known bugs
.IP "\fBFile \fButils\&.cpp\fP \fP" 1c .IP "\fBFile \fButils\&.cpp\fP \fP" 1c
No known bugs No known bugs
.IP "\fBFile \fButils\&.hpp\fP \fP" 1c .IP "\fBFile \fButils\&.hpp\fP \fP" 1c

2
man_pages/man3/constants.hpp.3
View File

@ -1,4 +1,4 @@
.TH "include/constants.hpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- .TH "include/constants.hpp" 3 "Sat Oct 14 2023" "Penning Trap Simulation" \" -*- nroff -*-
.ad l .ad l
.nh .nh
.SH NAME .SH NAME

60
man_pages/man3/main.cpp.3
View File

@ -1,4 +1,4 @@
.TH "src/main.cpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- .TH "src/main.cpp" 3 "Sat Oct 14 2023" "Penning Trap Simulation" \" -*- nroff -*-
.ad l .ad l
.nh .nh
.SH NAME .SH NAME
@ -7,14 +7,22 @@ src/main.cpp \- The main program for this project\&.
.SH SYNOPSIS .SH SYNOPSIS
.br .br
.PP .PP
\fC#include <cmath>\fP
.br
\fC#include <fstream>\fP \fC#include <fstream>\fP
.br .br
\fC#include <omp\&.h>\fP \fC#include <omp\&.h>\fP
.br .br
\fC#include <string>\fP
.br
\fC#include <sys/stat\&.h>\fP \fC#include <sys/stat\&.h>\fP
.br .br
\fC#include <vector>\fP
.br
\fC#include 'PenningTrap\&.hpp'\fP \fC#include 'PenningTrap\&.hpp'\fP
.br .br
\fC#include 'utils\&.hpp'\fP
.br
.SS "Macros" .SS "Macros"
@ -36,12 +44,34 @@ src/main.cpp \- The main program for this project\&.
.in +1c .in +1c
.ti -1c .ti -1c
.RI "void \fBsimulate_single_particle\fP ()"
.br
.ti -1c
.RI "void \fBsimulate_two_particles\fP ()"
.br
.ti -1c
.RI "void \fBsimulate_single_particle_with_different_steps\fP ()"
.br
.ti -1c
.RI "void \fBsimulate_100_particles\fP ()" .RI "void \fBsimulate_100_particles\fP ()"
.br .br
.ti -1c .ti -1c
.RI "void \fBsimulate_100_particles_with_time_potential\fP ()"
.br
.ti -1c
.RI "int \fBmain\fP ()" .RI "int \fBmain\fP ()"
.br .br
.in -1c .in -1c
.SS "Variables"
.in +1c
.ti -1c
.RI "\fBParticle\fP \fBp1\fP (CHARGE, MASS, \fBvec_3d\fP{20\&., 0\&., 20\&.}, \fBvec_3d\fP{0\&., 25\&., 0\&.})"
.br
.ti -1c
.RI "\fBParticle\fP \fBp2\fP (CHARGE, MASS, \fBvec_3d\fP{25\&., 25\&., 0\&.}, \fBvec_3d\fP{0\&., 40\&., 5\&.})"
.br
.in -1c
.SH "Detailed Description" .SH "Detailed Description"
.PP .PP
The main program for this project\&. The main program for this project\&.
@ -74,29 +104,45 @@ Definition in file \fBmain\&.cpp\fP\&.
.SS "#define CHARGE 1\&." .SS "#define CHARGE 1\&."
.PP .PP
Definition at line \fB21\fP of file \fBmain\&.cpp\fP\&. Definition at line \fB25\fP of file \fBmain\&.cpp\fP\&.
.SS "#define MASS 40\&." .SS "#define MASS 40\&."
.PP .PP
Definition at line \fB22\fP of file \fBmain\&.cpp\fP\&. Definition at line \fB26\fP of file \fBmain\&.cpp\fP\&.
.SS "#define N 10000" .SS "#define N 10000"
.PP .PP
Definition at line \fB20\fP of file \fBmain\&.cpp\fP\&. Definition at line \fB24\fP of file \fBmain\&.cpp\fP\&.
.SS "#define PARTICLES 100" .SS "#define PARTICLES 100"
.PP .PP
Definition at line \fB19\fP of file \fBmain\&.cpp\fP\&. Definition at line \fB23\fP of file \fBmain\&.cpp\fP\&.
.SH "Function Documentation" .SH "Function Documentation"
.PP .PP
.SS "int main ()" .SS "int main ()"
.PP .PP
Definition at line \fB77\fP of file \fBmain\&.cpp\fP\&. Definition at line \fB124\fP of file \fBmain\&.cpp\fP\&.
.SS "void simulate_100_particles ()" .SS "void simulate_100_particles ()"
.PP .PP
Definition at line \fB24\fP of file \fBmain\&.cpp\fP\&. Definition at line \fB77\fP of file \fBmain\&.cpp\fP\&.
.SS "void simulate_100_particles_with_time_potential ()"
.PP
Definition at line \fB91\fP of file \fBmain\&.cpp\fP\&.
.SS "void simulate_single_particle ()"
.PP
Definition at line \fB31\fP of file \fBmain\&.cpp\fP\&.
.SS "void simulate_single_particle_with_different_steps ()"
.PP
Definition at line \fB55\fP of file \fBmain\&.cpp\fP\&.
.SS "void simulate_two_particles ()"
.PP
Definition at line \fB42\fP of file \fBmain\&.cpp\fP\&.
.SH "Author" .SH "Author"
.PP .PP
Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. Generated automatically by Doxygen for Penning Trap Simulation from the source code\&.

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