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coryab merged 59 commits from develop into main 2023-10-14 01:13:56 +00:00
Conversation 0 Commits 59 Files Changed 132 +5911 -795
132 changed files with 5911 additions and 795 deletions
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@ -68,7 +68,7 @@ PROJECT_LOGO =
# entered, it will be relative to the location where doxygen was started. If # entered, it will be relative to the location where doxygen was started. If
# left blank the current directory will be used. # left blank the current directory will be used.
OUTPUT_DIRECTORY = docs OUTPUT_DIRECTORY =
# If the CREATE_SUBDIRS tag is set to YES then doxygen will create up to 4096 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create up to 4096
# sub-directories (in 2 levels) under the output directory of each output format # sub-directories (in 2 levels) under the output directory of each output format
@ -1070,7 +1070,7 @@ EXAMPLE_RECURSIVE = NO
# that contain images that are to be included in the documentation (see the # that contain images that are to be included in the documentation (see the
# \image command). # \image command).
IMAGE_PATH = IMAGE_PATH = ./images
# The INPUT_FILTER tag can be used to specify a program that doxygen should # The INPUT_FILTER tag can be used to specify a program that doxygen should
# invoke to filter for each input file. Doxygen will invoke the filter program # invoke to filter for each input file. Doxygen will invoke the filter program
@ -1303,7 +1303,7 @@ GENERATE_HTML = YES
# The default directory is: html. # The default directory is: html.
# This tag requires that the tag GENERATE_HTML is set to YES. # This tag requires that the tag GENERATE_HTML is set to YES.
HTML_OUTPUT = html HTML_OUTPUT = docs
# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each # The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
# generated HTML page (for example: .htm, .php, .asp). # generated HTML page (for example: .htm, .php, .asp).
@ -2183,7 +2183,7 @@ GENERATE_MAN = YES
# The default directory is: man. # The default directory is: man.
# This tag requires that the tag GENERATE_MAN is set to YES. # This tag requires that the tag GENERATE_MAN is set to YES.
MAN_OUTPUT = man MAN_OUTPUT = man_pages
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# man pages. In case the manual section does not start with a number, the number # man pages. In case the manual section does not start with a number, the number

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@ -1,5 +1,8 @@
# Penning trap simulation # Penning trap simulation
![](./images/100_particles.gif)
## Credits ## Credits
The Doxygen theme used here is The Doxygen theme used here is

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@ -113,8 +113,7 @@ $(document).ready(function(){initNavTree('Particle_8cpp.html',''); initResizable
<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>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000001">Todo:</a></b></dt><dd>Implement constructor </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>
</div></div><!-- contents --> </div></div><!-- contents -->

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@ -102,16 +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="l00015" name="l00015"></a><span class="lineno"> 15</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="l00016" name="l00016"></a><span class="lineno"> 16</span> </div> <div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> </div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"><a class="line" href="classParticle.html#a00e108823877a25513ccae7cac011b4c"> 17</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="l00018" name="l00018"></a><span class="lineno"> 18</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="l00019" name="l00019"></a><span class="lineno"> 19</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="l00020" name="l00020"></a><span class="lineno"> 20</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"> 21</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="l00022" name="l00022"></a><span class="lineno"> 22</span>}</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="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="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="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="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#l00017">Particle.cpp:17</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_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_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><!-- fragment --></div><!-- contents --> </div><!-- fragment --></div><!-- contents -->
</div><!-- doc-content --> </div><!-- doc-content -->
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@ -107,6 +107,7 @@ $(document).ready(function(){initNavTree('Particle_8hpp.html',''); initResizable
<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>
<table class="memberdecls"> <table class="memberdecls">

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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#l00025">PenningTrap.hpp:25</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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@ -105,6 +105,9 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp.html',''); initResiza
<p>The implementation of the <a class="el" href="classPenningTrap.html" title="A class that simulates a Penning trap.">PenningTrap</a> class. <p>The implementation of the <a class="el" href="classPenningTrap.html" title="A class that simulates a Penning trap.">PenningTrap</a> class.
<a href="#details">More...</a></p> <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="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 />
</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>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
@ -113,18 +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#_todo000002">Todo:</a></b></dt><dd><p class="startdd">Implement constructor </p>
<p class="interdd">Implement add_particle </p>
<p class="interdd">Implement external_E_field </p>
<p class="interdd">Implement external_B_field </p>
<p class="interdd">Implement force_on_particle </p>
<p class="interdd">Implement total_force_external </p>
<p class="interdd">Implement total_force_particles </p>
<p class="interdd">Implement total_force </p>
<p class="interdd">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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@ -102,69 +102,311 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp_source.html',''); ini
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<div class="contents"> <div class="contents">
<a href="PenningTrap_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span> </div> <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="l00024" name="l00024"></a><span class="lineno"> 24</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="l00025" name="l00025"></a><span class="lineno"> 25</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="l00026" name="l00026"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560"> 26</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="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="l00027" name="l00027"></a><span class="lineno"> 27</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="l00028" name="l00028"></a><span class="lineno"> 28</span> </div> <div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> </div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</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="l00030" name="l00030"></a><span class="lineno"> 30</span> </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="l00031" name="l00031"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8"> 31</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="l00020" name="l00020"></a><span class="lineno"> 20</span>{</div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span>{</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="l00033" name="l00033"></a><span class="lineno"> 33</span> </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="l00034" name="l00034"></a><span class="lineno"> 34</span>}</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="l00035" name="l00035"></a><span class="lineno"> 35</span> </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="l00036" name="l00036"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b"> 36</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="l00025" name="l00025"></a><span class="lineno"> 25</span>}</div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</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#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> 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> : <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="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"> 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> 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> 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> 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> }</div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span>}</div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> </div> <div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> </div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 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> </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"><a class="line" href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784"> 41</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="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"> 43</span> </div> <div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> this-&gt;particles = <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span>}</div> <div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span>}</div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> </div> <div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> </div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182"> 46</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="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>{</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"> 50</span> </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"><a class="line" href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee"> 51</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="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>{</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> </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>}</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"><a class="line" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d"> 56</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="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>{</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>}</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> </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"><a class="line" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be"> 61</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="l00061" name="l00061"></a><span class="lineno"> 61</span> }</div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span>{</div> <div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span>}</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"> 65</span> </div> <div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span>{</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9"> 66</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="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>{</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>}</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"><a class="line" href="classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965"> 71</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="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>{</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> </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> 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> <span class="keywordflow">default</span>:</div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> abort();</div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> }</div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span>}</div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> </div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"><a class="line" href="classPenningTrap.html#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="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="l00086" name="l00086"></a><span class="lineno"> 86</span> </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>{</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> <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> </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="l00094" name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"><a class="line" href="classPenningTrap.html#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>{</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="l00099" name="l00099"></a><span class="lineno"> 99</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>{</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> <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"> 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="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> <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> </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="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="l00113" name="l00113"></a><span class="lineno"> 113</span> </div>
<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"><a class="line" href="classPenningTrap.html#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>{</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="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> <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="l00121" name="l00121"></a><span class="lineno"> 121</span> </div>
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> force =</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> 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="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>}</div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> </div>
<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"><a class="line" href="classPenningTrap.html#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="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> </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> </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> <span class="keywordflow">if</span> (i == j) {</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> }</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> 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="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> <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>}</div>
<div class="line"><a id="l00145" name="l00145"></a><span class="lineno"> 145</span> </div>
<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"><a class="line" href="classPenningTrap.html#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>{</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="l00150" name="l00150"></a><span class="lineno"> 150</span> </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>{</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> 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> 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> </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> <span class="keywordflow">if</span> (particle_interaction) {</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> }</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> 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> }</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> <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="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> 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> </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><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> <span class="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> 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> 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> </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> </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> 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> }</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="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="l00185" name="l00185"></a><span class="lineno"> 185</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="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="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="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="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#l00051">PenningTrap.cpp:51</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_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#l00056">PenningTrap.cpp:56</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="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#l00041">PenningTrap.cpp:41</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="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#l00046">PenningTrap.cpp:46</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_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#l00071">PenningTrap.cpp:71</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#l00031">PenningTrap.cpp:31</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_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#l00026">PenningTrap.cpp:26</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_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#l00061">PenningTrap.cpp:61</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_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#l00036">PenningTrap.cpp:36</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_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#l00066">PenningTrap.cpp:66</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_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_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_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_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_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_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_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_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_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_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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@ -107,8 +107,10 @@ $(document).ready(function(){initNavTree('PenningTrap_8hpp.html',''); initResiza
<p>A class for simulating a Penning trap. <p>A class for simulating a Penning trap.
<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="constants_8hpp_source.html">constants.hpp</a>&quot;</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="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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@ -106,59 +106,110 @@ $(document).ready(function(){initNavTree('PenningTrap_8hpp_source.html',''); ini
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#define __PENNING_TRAP__</span></div> <div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="preprocessor">#define __PENNING_TRAP__</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"> 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><span class="preprocessor">#include &lt;omp.h&gt;</span></div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="preprocessor">#include &quot;<a class="code" href="constants_8hpp.html">constants.hpp</a>&quot;</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> </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="l00025" name="l00025"></a><span class="lineno"><a class="line" href="classPenningTrap.html"> 25</a></span><span class="keyword">class </span><a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> {</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="l00026" name="l00026"></a><span class="lineno"> 26</span><span class="keyword">private</span>:</div> <div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span> </div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716"> 27</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="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="l00028" name="l00028"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89"> 28</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="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#a66dfe89c68716b9502927b97f59c27d2"> 29</a></span> <span class="keywordtype">double</span> <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> </div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f"> 30</a></span> std::vector&lt;Particle&gt; <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>; </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"> 31</span> </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"> 32</span><span class="keyword">public</span>:</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="l00035" name="l00035"></a><span class="lineno"> 35</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="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="l00036" name="l00036"></a><span class="lineno"> 36</span> </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="l00039" name="l00039"></a><span class="lineno"> 39</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="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="l00040" name="l00040"></a><span class="lineno"> 40</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="l00043" name="l00043"></a><span class="lineno"> 43</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="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="l00044" name="l00044"></a><span class="lineno"> 44</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="l00047" name="l00047"></a><span class="lineno"> 47</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="l00041" name="l00041"></a><span class="lineno"> 41</span> </div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</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="l00054" name="l00054"></a><span class="lineno"> 54</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="l00053" name="l00053"></a><span class="lineno"> 53</span> </div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</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="l00061" name="l00061"></a><span class="lineno"> 61</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="l00065" name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</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="l00065" name="l00065"></a><span class="lineno"> 65</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="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="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">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="l00069" name="l00069"></a><span class="lineno"> 69</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="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="l00070" name="l00070"></a><span class="lineno"> 70</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="l00073" name="l00073"></a><span class="lineno"> 73</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="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="l00074" name="l00074"></a><span class="lineno"> 74</span> </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#a56544b6f4befb42984e9650cf2a40965">evolve_forward_euler</a>(<span class="keywordtype">double</span> dt);</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span>};</div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> </div> <div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span><span class="preprocessor">#endif</span></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="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="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="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="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="l00093" name="l00093"></a><span class="lineno"> 93</span> </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="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="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="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="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="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#l00025">PenningTrap.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="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#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#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#l00051">PenningTrap.cpp:51</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#l00027">PenningTrap.hpp:27</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#l00056">PenningTrap.cpp:56</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#l00041">PenningTrap.cpp:41</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#l00046">PenningTrap.cpp:46</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#l00071">PenningTrap.cpp:71</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#l00029">PenningTrap.hpp:29</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#l00031">PenningTrap.cpp:31</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#l00028">PenningTrap.hpp:28</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#l00061">PenningTrap.cpp:61</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#l00036">PenningTrap.cpp:36</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#l00066">PenningTrap.cpp:66</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="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> 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="l00006" name="l00006"></a><span class="lineno"> 6</span> </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> res = []</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> arr = [[], [], []]</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> lines = f.readlines()</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> line <span class="keywordflow">in</span> lines:</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[0].append(xi)</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> arr[2].append(zi)</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> </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> </div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> </div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span><span class="keyword">def </span>update(num, lines, arr):</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> line.set_data(a[:2, num - 1 : num])</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="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="keyword">def </span>animate():</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> fig = plt.figure()</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="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="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="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="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="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> plt.figtext(</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> 0.01,</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> <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> fontsize=12,</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="l00052" name="l00052"></a><span class="lineno"> 52</span> </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> 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="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> 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> </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> 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> </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> 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="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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1
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@ -105,6 +105,7 @@ $(document).ready(function(){initNavTree('annotated.html',''); initResizable();
<table class="directory"> <table class="directory">
<tr id="row_0_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classParticle.html" target="_self">Particle</a></td><td class="desc">A class that holds attributes of a particle </td></tr> <tr id="row_0_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classParticle.html" target="_self">Particle</a></td><td class="desc">A class that holds attributes of a particle </td></tr>
<tr id="row_1_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classPenningTrap.html" target="_self">PenningTrap</a></td><td class="desc">A class that simulates a Penning trap </td></tr> <tr id="row_1_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classPenningTrap.html" target="_self">PenningTrap</a></td><td class="desc">A class that simulates a Penning trap </td></tr>
<tr id="row_2_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classPenningTrapTest.html" target="_self">PenningTrapTest</a></td><td class="desc"></td></tr>
</table> </table>
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3
docs/annotated_dup.js
View File

@ -1,5 +1,6 @@
var annotated_dup = var annotated_dup =
[ [
[ "Particle", "classParticle.html", "classParticle" ], [ "Particle", "classParticle.html", "classParticle" ],
[ "PenningTrap", "classPenningTrap.html", "classPenningTrap" ] [ "PenningTrap", "classPenningTrap.html", "classPenningTrap" ],
[ "PenningTrapTest", "classPenningTrapTest.html", null ]
]; ];

14
docs/bug.html
View File

@ -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>
<dd><a class="anchor" id="_bug000005"></a>No known bugs </dd>
<dt>File <a class="el" href="Particle_8cpp.html">Particle.cpp</a> </dt>
<dd><a class="anchor" id="_bug000006"></a>No known bugs </dd> <dd><a class="anchor" id="_bug000006"></a>No known bugs </dd>
<dt>File <a class="el" href="Particle_8cpp.html">Particle.cpp</a> </dt>
<dd><a class="anchor" id="_bug000007"></a>No known bugs </dd>
<dt>File <a class="el" href="Particle_8hpp.html">Particle.hpp</a> </dt> <dt>File <a class="el" href="Particle_8hpp.html">Particle.hpp</a> </dt>
<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>
<dt>File <a class="el" href="test__suite_8cpp.html">test_suite.cpp</a> </dt> <dt>File <a class="el" href="test__suite_8cpp.html">test_suite.cpp</a> </dt>
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<dt>File <a class="el" href="utils_8hpp.html">utils.hpp</a> </dt> <dt>File <a class="el" href="typedefs_8hpp.html">typedefs.hpp</a> </dt>
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<dt>File <a class="el" href="utils_8hpp.html">utils.hpp</a> </dt>
<dd><a class="anchor" id="_bug000005"></a>No known bugs </dd>
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6
docs/classParticle-members.html
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@ -105,11 +105,11 @@ $(document).ready(function(){initNavTree('classParticle.html',''); initResizable
<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">
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<tr class="odd"><td class="entry"><a class="el" href="classParticle.html#a00e108823877a25513ccae7cac011b4c">Particle</a>(double q, double m, arma::vec::fixed&lt; 3 &gt; r_vec, arma::vec::fixed&lt; 3 &gt; v_vec)</td><td class="entry"><a class="el" href="classParticle.html">Particle</a></td><td class="entry"></td></tr> <tr class="odd"><td class="entry"><a class="el" href="classParticle.html#a7af9f8d1fef63dd7643b06629ac7bef4">Particle</a>(double q, double m, vec_3d r_vec, vec_3d v_vec)</td><td class="entry"><a class="el" href="classParticle.html">Particle</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classParticle.html#aa797d319549dc2a0beb06cdbfd430232">PenningTrap</a></td><td class="entry"><a class="el" href="classParticle.html">Particle</a></td><td class="entry"><span class="mlabel">friend</span></td></tr> <tr class="even"><td class="entry"><a class="el" href="classParticle.html#aa797d319549dc2a0beb06cdbfd430232">PenningTrap</a></td><td class="entry"><a class="el" href="classParticle.html">Particle</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</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="odd"><td class="entry"><a class="el" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</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="odd"><td class="entry"><a class="el" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</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="odd"><td class="entry"><a class="el" href="classParticle.html#a879692772803d6ab65fa4993b54aea6e">v_vec</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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63
docs/classParticle.html
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@ -114,9 +114,9 @@ $(document).ready(function(){initNavTree('classParticle.html',''); initResizable
<table class="memberdecls"> <table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a> <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
Public Member Functions</h2></td></tr> Public Member Functions</h2></td></tr>
<tr class="memitem:a00e108823877a25513ccae7cac011b4c"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#a00e108823877a25513ccae7cac011b4c">Particle</a> (double <a class="el" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>, double <a class="el" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>, arma::vec::fixed&lt; 3 &gt; <a class="el" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a>, arma::vec::fixed&lt; 3 &gt; <a class="el" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a>)</td></tr> <tr class="memitem:a7af9f8d1fef63dd7643b06629ac7bef4"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#a7af9f8d1fef63dd7643b06629ac7bef4">Particle</a> (double <a class="el" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>, double <a class="el" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>, <a class="el" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="el" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">r_vec</a>, <a class="el" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a> <a class="el" href="classParticle.html#a879692772803d6ab65fa4993b54aea6e">v_vec</a>)</td></tr>
<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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@ -126,12 +126,12 @@ Private Attributes</h2></td></tr>
<tr class="memitem:aedcc7e1bc53b0e2b1a4a07c9a1b47563"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a></td></tr> <tr class="memitem:aedcc7e1bc53b0e2b1a4a07c9a1b47563"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a></td></tr>
<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>
<tr class="separator:aedcc7e1bc53b0e2b1a4a07c9a1b47563"><td class="memSeparator" colspan="2">&#160;</td></tr> <tr class="separator:aedcc7e1bc53b0e2b1a4a07c9a1b47563"><td class="memSeparator" colspan="2">&#160;</td></tr>
<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>
<tr class="memdesc:acf1a0f3c978b06d76df5bb4279594467"><td class="mdescLeft">&#160;</td><td class="mdescRight">position <br /></td></tr> <tr class="memdesc:af9497cd8f2dcad0fad54f571ddb383e6"><td class="mdescLeft">&#160;</td><td class="mdescRight">position <br /></td></tr>
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<tr class="memitem:a4a5d22c7aeca66f67d083f270cba25df"><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#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a></td></tr> <tr class="memitem:a879692772803d6ab65fa4993b54aea6e"><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#a879692772803d6ab65fa4993b54aea6e">v_vec</a></td></tr>
<tr class="memdesc:a4a5d22c7aeca66f67d083f270cba25df"><td class="mdescLeft">&#160;</td><td class="mdescRight">velocity <br /></td></tr> <tr class="memdesc:a879692772803d6ab65fa4993b54aea6e"><td class="mdescLeft">&#160;</td><td class="mdescRight">velocity <br /></td></tr>
<tr class="separator:a4a5d22c7aeca66f67d083f270cba25df"><td class="memSeparator" colspan="2">&#160;</td></tr> <tr class="separator:a879692772803d6ab65fa4993b54aea6e"><td class="memSeparator" colspan="2">&#160;</td></tr>
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Friends</h2></td></tr> Friends</h2></td></tr>
@ -142,10 +142,10 @@ Friends</h2></td></tr>
<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>
<a id="a00e108823877a25513ccae7cac011b4c" name="a00e108823877a25513ccae7cac011b4c"></a> <a id="a7af9f8d1fef63dd7643b06629ac7bef4" name="a7af9f8d1fef63dd7643b06629ac7bef4"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a00e108823877a25513ccae7cac011b4c">&#9670;&#160;</a></span>Particle()</h2> <h2 class="memtitle"><span class="permalink"><a href="#a7af9f8d1fef63dd7643b06629ac7bef4">&#9670;&#160;</a></span>Particle()</h2>
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<td class="paramname"><em>r_vec</em>, </td> <td class="paramname"><em>r_vec</em>, </td>
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<td class="paramkey"></td> <td class="paramkey"></td>
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<td class="paramtype">arma::vec::fixed&lt; 3 &gt;&#160;</td> <td class="paramtype"><a class="el" href="typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df">vec_3d</a>&#160;</td>
<td class="paramname"><em>v_vec</em>&#160;</td> <td class="paramname"><em>v_vec</em>&#160;</td>
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@ -183,9 +183,18 @@ Friends</h2></td></tr>
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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>
<tr><td class="paramname">v_vec</td><td>The initial velocity of the particle </td></tr>
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<p class="definition">Definition at line <a class="el" href="Particle_8cpp_source.html#l00017">17</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>
<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00038">38</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#l00043">43</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
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<p>Mass. </p> <p>Mass. </p>
<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00022">22</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#l00024">24</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
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<p>Charge. </p> <p>Charge. </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> <p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00023">23</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
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@ -279,7 +288,7 @@ Friends</h2></td></tr>
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@ -291,12 +300,12 @@ Friends</h2></td></tr>
<p>position </p> <p>position </p>
<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00023">23</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#l00025">25</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
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@ -317,7 +326,7 @@ Friends</h2></td></tr>
<p>velocity </p> <p>velocity </p>
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<tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>test_external_B_field</b>() (defined in <a class="el" href="classPenningTrapTest.html">PenningTrapTest</a>)</td><td class="entry"><a class="el" href="classPenningTrapTest.html">PenningTrapTest</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">static</span></td></tr>
<tr bgcolor="#f0f0f0" class="odd"><td class="entry"><b>test_external_E_field</b>() (defined in <a class="el" href="classPenningTrapTest.html">PenningTrapTest</a>)</td><td class="entry"><a class="el" href="classPenningTrapTest.html">PenningTrapTest</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">static</span></td></tr>
<tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>test_force_on_particle</b>() (defined in <a class="el" href="classPenningTrapTest.html">PenningTrapTest</a>)</td><td class="entry"><a class="el" href="classPenningTrapTest.html">PenningTrapTest</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">static</span></td></tr>
<tr bgcolor="#f0f0f0" class="odd"><td class="entry"><b>test_total_force_external</b>() (defined in <a class="el" href="classPenningTrapTest.html">PenningTrapTest</a>)</td><td class="entry"><a class="el" href="classPenningTrapTest.html">PenningTrapTest</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">static</span></td></tr>
<tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>test_total_force_particles</b>() (defined in <a class="el" href="classPenningTrapTest.html">PenningTrapTest</a>)</td><td class="entry"><a class="el" href="classPenningTrapTest.html">PenningTrapTest</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">static</span></td></tr>
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<a href="#pub-static-methods">Static Public Member Functions</a> &#124;
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<div class="headertitle"><div class="title">PenningTrapTest Class Reference</div></div>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-static-methods" name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr class="memitem:a542996d72c713636b95e0aa9118f7901"><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPenningTrapTest.html#a542996d72c713636b95e0aa9118f7901">test_external_E_field</a> ()</td></tr>
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<tr class="memitem:acb806e49a688424588e0c501bc57a230"><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPenningTrapTest.html#acb806e49a688424588e0c501bc57a230">test_external_B_field</a> ()</td></tr>
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<tr class="memitem:addf81fa5692d8146cce5571ccdc5999b"><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPenningTrapTest.html#addf81fa5692d8146cce5571ccdc5999b">test_force_on_particle</a> ()</td></tr>
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<tr class="memitem:ae104e04dcd21ac63281c908132fdf255"><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPenningTrapTest.html#ae104e04dcd21ac63281c908132fdf255">test_total_force_external</a> ()</td></tr>
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<tr class="memitem:a0ee2bbf5e26c115164208b89c5a29e3d"><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPenningTrapTest.html#a0ee2bbf5e26c115164208b89c5a29e3d">test_total_force_particles</a> ()</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock">
<p class="definition">Definition at line <a class="el" href="test__suite_8cpp_source.html#l00020">20</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
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<a id="acb806e49a688424588e0c501bc57a230" name="acb806e49a688424588e0c501bc57a230"></a>
<h2 class="memtitle"><span class="permalink"><a href="#acb806e49a688424588e0c501bc57a230">&#9670;&#160;</a></span>test_external_B_field()</h2>
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<td class="memname">static void PenningTrapTest::test_external_B_field </td>
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<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">static</span></span> </td>
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<p class="definition">Definition at line <a class="el" href="test__suite_8cpp_source.html#l00059">59</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
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<a id="a542996d72c713636b95e0aa9118f7901" name="a542996d72c713636b95e0aa9118f7901"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a542996d72c713636b95e0aa9118f7901">&#9670;&#160;</a></span>test_external_E_field()</h2>
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<td class="memname">static void PenningTrapTest::test_external_E_field </td>
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<p class="definition">Definition at line <a class="el" href="test__suite_8cpp_source.html#l00022">22</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
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<a id="addf81fa5692d8146cce5571ccdc5999b" name="addf81fa5692d8146cce5571ccdc5999b"></a>
<h2 class="memtitle"><span class="permalink"><a href="#addf81fa5692d8146cce5571ccdc5999b">&#9670;&#160;</a></span>test_force_on_particle()</h2>
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<div class="memproto">
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<td class="memname">static void PenningTrapTest::test_force_on_particle </td>
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<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">static</span></span> </td>
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<p class="definition">Definition at line <a class="el" href="test__suite_8cpp_source.html#l00070">70</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ae104e04dcd21ac63281c908132fdf255">&#9670;&#160;</a></span>test_total_force_external()</h2>
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<td class="memname">static void PenningTrapTest::test_total_force_external </td>
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<p class="definition">Definition at line <a class="el" href="test__suite_8cpp_source.html#l00095">95</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a0ee2bbf5e26c115164208b89c5a29e3d">&#9670;&#160;</a></span>test_total_force_particles()</h2>
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<td class="memname">static void PenningTrapTest::test_total_force_particles </td>
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<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">static</span></span> </td>
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<li>total_force()&#160;:&#160;<a class="el" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">PenningTrap</a></li> <li>r_vec&#160;:&#160;<a class="el" href="classParticle.html#af9497cd8f2dcad0fad54f571ddb383e6">Particle</a></li>
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<li>v_vec&#160;:&#160;<a class="el" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">Particle</a></li> <li>total_force_external()&#160;:&#160;<a class="el" href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">PenningTrap</a></li>
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<li>V_0&#160;:&#160;<a class="el" href="classPenningTrap.html#aaf105828121c4a33cc2b217453c20317">PenningTrap</a></li>
<li>v_func()&#160;:&#160;<a class="el" href="classPenningTrap.html#af98a720da60b0e1a62aefa5f5cb37c1e">PenningTrap</a></li>
<li>v_vec&#160;:&#160;<a class="el" href="classParticle.html#a879692772803d6ab65fa4993b54aea6e">Particle</a></li>
<li>write_simulation_to_dir()&#160;:&#160;<a class="el" href="classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57">PenningTrap</a></li>
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25
docs/functions_func.html
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&#160;<ul> &#160;<ul>
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<li>external_E_field()&#160;:&#160;<a class="el" href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">PenningTrap</a></li> <li>external_E_field()&#160;:&#160;<a class="el" href="classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9">PenningTrap</a></li>
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<li>PenningTrap()&#160;:&#160;<a class="el" href="classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560">PenningTrap</a></li> <li>Particle()&#160;:&#160;<a class="el" href="classParticle.html#a7af9f8d1fef63dd7643b06629ac7bef4">Particle</a></li>
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<li>k_v&#160;:&#160;<a class="el" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">PenningTrap</a></li>
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docs/globals.html
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2
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3
docs/globals_func.html
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&#160;<ul> &#160;<ul>
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<div class="headertitle"><div class="title">Penning trap simulation </div></div> <div class="headertitle"><div class="title">Penning trap simulation </div></div>
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Credits</h1> Credits</h1>
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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;cmath&gt;</code><br />
<code>#include &lt;fstream&gt;</code><br />
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Macros</h2></td></tr>
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Functions</h2></td></tr> Functions</h2></td></tr>
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<tr class="memitem:ac67e0d59227856c4d42e7d01c75e0ad2"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a> ()</td></tr>
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<tr class="memitem:ae66f6b31b5ad750f1fe042a706a4e3d4"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html#ae66f6b31b5ad750f1fe042a706a4e3d4">main</a> ()</td></tr> <tr class="memitem:ae66f6b31b5ad750f1fe042a706a4e3d4"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html#ae66f6b31b5ad750f1fe042a706a4e3d4">main</a> ()</td></tr>
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Variables</h2></td></tr>
<tr class="memitem:a87da4ef9f2cd753579484824310467b8"><td class="memItemLeft" align="right" valign="top"><a id="a87da4ef9f2cd753579484824310467b8" name="a87da4ef9f2cd753579484824310467b8"></a>
<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>
@ -120,10 +160,75 @@ 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">Function Documentation</h2> </div><h2 class="groupheader">Macro Definition Documentation</h2>
<a id="a16cdf08eafbd529171c64d69a0ec02b3" name="a16cdf08eafbd529171c64d69a0ec02b3"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a16cdf08eafbd529171c64d69a0ec02b3">&#9670;&#160;</a></span>CHARGE</h2>
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<td class="memname">#define CHARGE&#160;&#160;&#160;1.</td>
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<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>
</div>
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<a id="ad96793de0cc60529a6b01040c0cd8033" name="ad96793de0cc60529a6b01040c0cd8033"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ad96793de0cc60529a6b01040c0cd8033">&#9670;&#160;</a></span>MASS</h2>
<div class="memitem">
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<td class="memname">#define MASS&#160;&#160;&#160;40.</td>
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<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>
</div>
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<h2 class="memtitle"><span class="permalink"><a href="#a0240ac851181b84ac374872dc5434ee4">&#9670;&#160;</a></span>N</h2>
<div class="memitem">
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<td class="memname">#define N&#160;&#160;&#160;10000</td>
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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>
</div>
</div>
<a id="a7b24a37e8ce9d243351bfc9b24945e63" name="a7b24a37e8ce9d243351bfc9b24945e63"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a7b24a37e8ce9d243351bfc9b24945e63">&#9670;&#160;</a></span>PARTICLES</h2>
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<td class="memname">#define PARTICLES&#160;&#160;&#160;100</td>
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<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00023">23</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
</div>
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<h2 class="groupheader">Function Documentation</h2>
<a id="ae66f6b31b5ad750f1fe042a706a4e3d4" name="ae66f6b31b5ad750f1fe042a706a4e3d4"></a> <a id="ae66f6b31b5ad750f1fe042a706a4e3d4" name="ae66f6b31b5ad750f1fe042a706a4e3d4"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ae66f6b31b5ad750f1fe042a706a4e3d4">&#9670;&#160;</a></span>main()</h2> <h2 class="memtitle"><span class="permalink"><a href="#ae66f6b31b5ad750f1fe042a706a4e3d4">&#9670;&#160;</a></span>main()</h2>
@ -139,7 +244,102 @@ 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="main_8cpp_source.html#l00013">13</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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<h2 class="memtitle"><span class="permalink"><a href="#a213713d6ecc02a32b588ffd179dc7513">&#9670;&#160;</a></span>simulate_100_particles()</h2>
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<td class="memname">void simulate_100_particles </td>
<td>(</td>
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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>
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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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<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="keywordtype">int</span> main() </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>{</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="keywordflow">return</span> 0;</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 &lt;sys/stat.h&gt;</span></div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span> </div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span><span class="preprocessor">#include &quot;<a class="code" href="utils_8hpp.html">utils.hpp</a>&quot;</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><span class="preprocessor">#define PARTICLES 100</span></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><span class="preprocessor">#define CHARGE 1.</span></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="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><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> </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>{</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> <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="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> </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> 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>}</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">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="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> <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> </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> </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> <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> trap_with_interaction.write_simulation_to_dir(</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>}</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><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>{</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> <span class="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> </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> <span class="keywordtype">int</span> steps = 4000 * (i + 1);</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> 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> 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> 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> }</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> i = 0; i &lt; 4; i++) {</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> <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> 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> 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> 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="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="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="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> [](<span class="keywordtype">double</span> t) {</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> (1. + .4 * std::cos(1.5 * t));</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> 500., 0);</div>
<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> <span class="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> </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="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#l00030">PenningTrap.hpp:30</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 class="headertitle"><div class="title">plot_particles_left.py</div></div>
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<div class="contents">
<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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<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="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="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="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="l00007" name="l00007"></a><span class="lineno"> 7</span> res = []</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="l00009" name="l00009"></a><span class="lineno"> 9</span> arr = [[], [], []]</div>
<div class="line"><a id="l00010" name="l00010"></a><span class="lineno"> 10</span> <span class="keyword">with</span> open(file) <span class="keyword">as</span> f:</div>
<div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span> lines = f.readlines()</div>
<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span> </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="l00014" name="l00014"></a><span class="lineno"> 14</span> xi,yi,zi = map(<span class="keyword">lambda</span> x: float(x), line.strip().split(<span class="stringliteral">&quot;,&quot;</span>))</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="l00016" name="l00016"></a><span class="lineno"> 16</span> arr[1].append(yi)</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="l00018" name="l00018"></a><span class="lineno"> 18</span> res.append(arr)</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="keywordflow">return</span> np.array(res)</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="keyword">def </span>update(num, lines, arr):</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="l00024" name="l00024"></a><span class="lineno"> 24</span> line.set_data(a[:2, num])</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="l00026" name="l00026"></a><span class="lineno"> 26</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> </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="l00030" name="l00030"></a><span class="lineno"> 30</span> fig = plt.figure()</div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</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> </div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> </div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> arr = get_data([f<span class="stringliteral">&quot;output/p{i}.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> </div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> arr = arr[:,:,::10]</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> N = len(arr[0][0])</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> 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> </div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</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_xlabel(<span class="stringliteral">&#39;X&#39;</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> ax.set_ylim3d([-500.0, 500.0])</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</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> </div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> ax.set_zlim3d([-500.0, 500.0])</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</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> </div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</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> interval=1,</div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> blit=<span class="keyword">False</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> </div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> <span class="comment"># ani.save(&quot;100_particles.gif&quot;, writer=animation.FFMpegFileWriter(fps=30))</span></div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</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="l00060" name="l00060"></a><span class="lineno"> 60</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> animate()</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>
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@ -99,6 +99,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp.html',''); initResiza
<div class="header"> <div class="header">
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<a href="#nested-classes">Classes</a> &#124;
<a href="#func-members">Functions</a> </div> <a href="#func-members">Functions</a> </div>
<div class="headertitle"><div class="title">test_suite.cpp File Reference</div></div> <div class="headertitle"><div class="title">test_suite.cpp File Reference</div></div>
</div><!--header--> </div><!--header-->
@ -106,9 +107,19 @@ $(document).ready(function(){initNavTree('test__suite_8cpp.html',''); initResiza
<p>The test suite for the project. <p>The test suite for the project.
<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 />
<code>#include &quot;<a class="el" href="utils_8hpp_source.html">utils.hpp</a>&quot;</code><br />
<code>#include &lt;iomanip&gt;</code><br />
<code>#include &lt;sstream&gt;</code><br />
<code>#include &lt;string&gt;</code><br />
</div>
<p><a href="test__suite_8cpp_source.html">Go to the source code of this file.</a></p> <p><a href="test__suite_8cpp_source.html">Go to the source code of this file.</a></p>
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Classes</h2></td></tr>
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<tr class="memitem:ae66f6b31b5ad750f1fe042a706a4e3d4"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="test__suite_8cpp.html#ae66f6b31b5ad750f1fe042a706a4e3d4">main</a> ()</td></tr> <tr class="memitem:ae66f6b31b5ad750f1fe042a706a4e3d4"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="test__suite_8cpp.html#ae66f6b31b5ad750f1fe042a706a4e3d4">main</a> ()</td></tr>
@ -120,7 +131,7 @@ 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#_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>
</div><h2 class="groupheader">Function Documentation</h2> </div><h2 class="groupheader">Function Documentation</h2>
@ -139,7 +150,7 @@ 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="test__suite_8cpp_source.html#l00012">12</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p> <p class="definition">Definition at line <a class="el" href="test__suite_8cpp_source.html#l00135">135</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
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@ -0,0 +1,4 @@
var test__suite_8cpp =
[
[ "PenningTrapTest", "classPenningTrapTest.html", null ]
];

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@ -102,10 +102,151 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
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<div class="contents"> <div class="contents">
<a href="test__suite_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="test__suite_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="keywordtype">int</span> main() </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="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="preprocessor">#include &quot;<a class="code" href="utils_8hpp.html">utils.hpp</a>&quot;</span></div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span> <span class="keywordflow">return</span> 0;</div> <div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</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><span class="preprocessor">#include &lt;iomanip&gt;</span></div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span><span class="preprocessor">#include &lt;sstream&gt;</span></div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#include &lt;string&gt;</span></div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span> </div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"><a class="line" href="classPenningTrapTest.html"> 20</a></span><span class="keyword">class </span><a class="code hl_class" href="classPenningTrapTest.html">PenningTrapTest</a> {</div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span><span class="keyword">public</span>:</div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> <span class="keyword">static</span> <span class="keywordtype">void</span> test_external_E_field()</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> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap;</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> <span class="comment">// Vector containing inputs and expected results</span></div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span> std::vector&lt;std::pair&lt;arma::vec, arma::vec&gt;&gt; tests;</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> tests.push_back(</div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"> 30</span> std::make_pair(arma::vec{0., 0., 0.}, arma::vec{0., 0., 0.}));</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> tests.push_back(std::make_pair(arma::vec{10., 0., 0.},</div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> arma::vec{96.4852558, 0., 0.}));</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> tests.push_back(std::make_pair(arma::vec{10., 0., 0.},</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> arma::vec{96.4852558, 0., 0.}));</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> tests.push_back(std::make_pair(arma::vec{0., 10., 0.},</div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> arma::vec{0., 96.4852558, 0.}));</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> tests.push_back(std::make_pair(arma::vec{0., 0., 10.},</div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> arma::vec{0., 0., -192.9705116}));</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> arma::vec result;</div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> arma::vec v;</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">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="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="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="l00053" name="l00053"></a><span class="lineno"> 53</span> &lt;&lt; v(0) &lt;&lt; <span class="stringliteral">&quot;,&quot;</span> &lt;&lt; v(1) &lt;&lt; <span class="stringliteral">&quot;,&quot;</span> &lt;&lt; v(2) &lt;&lt; <span class="stringliteral">&quot;).&quot;</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> <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>(result, tests.at(i).second), msg.str());</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> }</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> }</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> </div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> <span class="keyword">static</span> <span class="keywordtype">void</span> test_external_B_field()</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> {</div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> <span class="comment">// No point in testing at different points since it&#39;s not dependent</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="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#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="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="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="keyword">static</span> <span class="keywordtype">void</span> test_force_on_particle()</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> {</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap;</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> arma::vec v{0., 0., 0.};</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> </div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> <span class="comment">// Add particles to test</span></div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> trap.<a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{0., 0., 0.}, v));</div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> trap.<a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{1., 0., 0.}, v));</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> trap.<a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{0., 3., 4.}, v));</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="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#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="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="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="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#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="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="l00093" name="l00093"></a><span class="lineno"> 93</span> }</div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> <span class="keyword">static</span> <span class="keywordtype">void</span> test_total_force_external()</div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> {</div>
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap;</div>
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> trap.<a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(</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="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#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="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="l00106" name="l00106"></a><span class="lineno"> 106</span> }</div>
<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</span> </div>
<div class="line"><a id="l00108" name="l00108"></a><span class="lineno"> 108</span> <span class="keyword">static</span> <span class="keywordtype">void</span> test_total_force_particles()</div>
<div class="line"><a id="l00109" name="l00109"></a><span class="lineno"> 109</span> {</div>
<div class="line"><a id="l00110" name="l00110"></a><span class="lineno"> 110</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap;</div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> trap.<a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(</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="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#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="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="l00119" name="l00119"></a><span class="lineno"> 119</span> </div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span> trap.<a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(</div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> <a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{1., 0., 0.}, arma::vec{0., 0., 0.}));</div>
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> trap.<a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(</div>
<div class="line"><a id="l00123" name="l00123"></a><span class="lineno"> 123</span> <a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{0., 1., 0.}, arma::vec{0., 0., 0.}));</div>
<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> trap.<a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(</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="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#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="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="l00132" name="l00132"></a><span class="lineno"> 132</span> }</div>
<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span>};</div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> </div>
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span><span class="keywordtype">int</span> main()</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> PenningTrapTest::test_external_E_field();</div>
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> PenningTrapTest::test_external_B_field();</div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> PenningTrapTest::test_force_on_particle();</div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> PenningTrapTest::test_total_force_external();</div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"> 141</span> PenningTrapTest::test_total_force_particles();</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="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#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="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_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_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_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_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_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="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="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_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_a73d4f21ad937dbc50a0c0538c78fd4f9"><div class="ttname"><a href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a></div><div class="ttdeci">#define ASSERT(expr, msg)</div><div class="ttdoc">A prettier assertion function.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8hpp_source.html#l00045">utils.hpp:45</a></div></div>
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<div class="contents"> <div class="contents">
<div class="textblock"><dl class="reflist"> <div class="textblock"><dl class="reflist">
<dt>File <a class="el" href="Particle_8cpp.html">Particle.cpp</a> </dt>
<dd><a class="anchor" id="_todo000001"></a>Implement constructor </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><p class="startdd"><a class="anchor" id="_todo000002"></a>Implement constructor </p> <dd><p class="startdd"><a class="anchor" id="_todo000001"></a>Implement evolve_RK4 </p>
<p class="interdd"></p>
<p class="interdd">Implement add_particle </p>
<p class="interdd"></p>
<p class="interdd">Implement external_E_field </p>
<p class="interdd"></p>
<p class="interdd">Implement external_B_field </p>
<p class="interdd"></p>
<p class="interdd">Implement force_on_particle </p>
<p class="interdd"></p>
<p class="interdd">Implement total_force_external </p>
<p class="interdd"></p>
<p class="interdd">Implement total_force_particles </p>
<p class="interdd"></p>
<p class="interdd">Implement total_force </p>
<p class="interdd"></p>
<p class="interdd">Implement evolve_RK4 </p>
<p class="interdd"></p> <p class="interdd"></p>
<p class="enddd">Implement evolve_forward_euler </p> <p class="enddd">Implement evolve_forward_euler </p>
</dd> </dd>

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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>
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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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<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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<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>
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<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> </div>
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<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>
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<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">
@ -118,6 +119,15 @@ Functions</h2></td></tr>
<tr class="memitem:a58565270b643b24e3132f38c653e0199"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="utils_8cpp.html#a58565270b643b24e3132f38c653e0199">scientific_format</a> (const std::vector&lt; double &gt; &amp;v, int width, int prec)</td></tr> <tr class="memitem:a58565270b643b24e3132f38c653e0199"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="utils_8cpp.html#a58565270b643b24e3132f38c653e0199">scientific_format</a> (const std::vector&lt; double &gt; &amp;v, int width, int prec)</td></tr>
<tr class="memdesc:a58565270b643b24e3132f38c653e0199"><td class="mdescLeft">&#160;</td><td class="mdescRight">Turns a vector of doubles into a string written in scientific format. <br /></td></tr> <tr class="memdesc:a58565270b643b24e3132f38c653e0199"><td class="mdescLeft">&#160;</td><td class="mdescRight">Turns a vector of doubles into a string written in scientific format. <br /></td></tr>
<tr class="separator:a58565270b643b24e3132f38c653e0199"><td class="memSeparator" colspan="2">&#160;</td></tr> <tr class="separator:a58565270b643b24e3132f38c653e0199"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aff5e07c3c1d321709b0cc38e999f427b"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="utils_8cpp.html#aff5e07c3c1d321709b0cc38e999f427b">m_assert</a> (bool expr, std::string expr_str, std::string f, std::string file, int line, std::string msg)</td></tr>
<tr class="memdesc:aff5e07c3c1d321709b0cc38e999f427b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Test an expression, confirm that test is ok, or abort execution. <br /></td></tr>
<tr class="separator:aff5e07c3c1d321709b0cc38e999f427b"><td class="memSeparator" colspan="2">&#160;</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="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>
@ -125,10 +135,167 @@ 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>
<a id="a5d2e1e032fd19614f2fbb58149a7b02a" name="a5d2e1e032fd19614f2fbb58149a7b02a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a5d2e1e032fd19614f2fbb58149a7b02a">&#9670;&#160;</a></span>arma_vector_close_to()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool arma_vector_close_to </td>
<td>(</td>
<td class="paramtype">arma::vec &amp;&#160;</td>
<td class="paramname"><em>a</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">arma::vec &amp;&#160;</td>
<td class="paramname"><em>b</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double&#160;</td>
<td class="paramname"><em>tol</em> = <code>1e-8</code>&#160;</td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Test if two armadillo vectors are close to each other. </p>
<p>This function takes in 2 vectors and checks if they are approximately equal to each other given a tolerance.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">a</td><td>Vector a </td></tr>
<tr><td class="paramname">b</td><td>Vector b </td></tr>
<tr><td class="paramname">tol</td><td>The tolerance</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#l00062">62</a> of file <a class="el" href="utils_8cpp_source.html">utils.cpp</a>.</p>
</div>
</div>
<a id="aff5e07c3c1d321709b0cc38e999f427b" name="aff5e07c3c1d321709b0cc38e999f427b"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aff5e07c3c1d321709b0cc38e999f427b">&#9670;&#160;</a></span>m_assert()</h2>
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<td class="memname">void m_assert </td>
<td>(</td>
<td class="paramtype">bool&#160;</td>
<td class="paramname"><em>expr</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">std::string&#160;</td>
<td class="paramname"><em>expr_str</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">std::string&#160;</td>
<td class="paramname"><em>func</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">std::string&#160;</td>
<td class="paramname"><em>file</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int&#160;</td>
<td class="paramname"><em>line</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">std::string&#160;</td>
<td class="paramname"><em>msg</em>&#160;</td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Test an expression, confirm that test is ok, or abort execution. </p>
<p>This function takes in an expression and prints an OK message if it's true, or it prints a fail message and aborts execution if it fails.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">expr</td><td>The expression to be evaluated </td></tr>
<tr><td class="paramname">expr_str</td><td>The stringified version of the expression </td></tr>
<tr><td class="paramname">func</td><td>The function name of the caller </td></tr>
<tr><td class="paramname">file</td><td>The file of the caller </td></tr>
<tr><td class="paramname">line</td><td>The line number where this function is called from </td></tr>
<tr><td class="paramname">msg</td><td>The message to be displayed </td></tr>
</table>
</dd>
</dl>
<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>
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<div class="memproto">
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<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>
<a id="a58565270b643b24e3132f38c653e0199" name="a58565270b643b24e3132f38c653e0199"></a> <a id="a58565270b643b24e3132f38c653e0199" name="a58565270b643b24e3132f38c653e0199"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a58565270b643b24e3132f38c653e0199">&#9670;&#160;</a></span>scientific_format() <span class="overload">[1/2]</span></h2> <h2 class="memtitle"><span class="permalink"><a href="#a58565270b643b24e3132f38c653e0199">&#9670;&#160;</a></span>scientific_format() <span class="overload">[1/2]</span></h2>
@ -162,6 +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>
@ -170,9 +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>
@ -209,7 +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>
@ -218,9 +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>
</div> </div>
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@ -1,5 +1,8 @@
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