Final edition of the report

Coryab/code

.clang-format

@@ -0,0 +1,44 @@
+# Set the language to C++
+Language: Cpp
+
+# Set the language standard to C++11
+Standard: Cpp11
+
+# Never use tab for indentation
+UseTab: Never
+
+# Set the indent width to be 4 columns
+IndentWidth: 4
+
+# Set tab width to be 4 columns
+TabWidth: 4
+
+# Set access modifier (public, private, protected) offset to indent left
+AccessModifierOffset: -4
+
+# Stop indentation of access modifiers
+IndentAccessModifiers: false
+
+# Don't allow a function to be defined on a single line
+AllowShortFunctionsOnASingleLine: false
+
+# Set the column limit to 80 characters
+ColumnLimit: 80
+
+# If an expression has to be split, then split before binary operators unless
+# it's an assignment operator.
+BreakBeforeBinaryOperators: NonAssignment
+
+# Use a Linux style brace break.
+# Break before braces on function, namespace and class definitions.
+BreakBeforeBraces: Linux
+
+
+# If true, spaces will be inserted after ( and before ).
+SpacesInParentheses: false
+
+# If true, spaces will be inserted after [ and before ].
+SpacesInSquareBrackets: false
+
+# Separate definition blocks (classes, functions, structs, enums)
+SeparateDefinitionBlocks: Always

.gitignore

@@ -35,9 +35,11 @@
 *.aux
 *.log
 *.out
-*.bib
 *.synctex.gz
 *.bbl 
+*.blg
+latex/mainNotes.bib
+
 
 # C++ specifics
 src/*
@@ -46,3 +48,7 @@ src/*
 !src/*.hpp
 !src/*.py
 !src/Doxyfile
+!src/scripts
+
+# Job
+!src/job.script

Doxyfile

@@ -917,7 +917,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = include src README.md
+INPUT                  = include src src/scripts README.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1070,7 +1070,7 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             =
+IMAGE_PATH             = ./images
 
 # 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
@@ -2174,7 +2174,7 @@ RTF_EXTENSIONS_FILE    =
 # classes and files.
 # The default value is: NO.
 
-GENERATE_MAN           = YES
+GENERATE_MAN           = NO
 
 # The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of

README.md

@@ -1,5 +1,119 @@
 # Penning trap simulation
 
+![](./images/100_particles.gif)
+
+[Repo](https://github.uio.no/FYS3150-G2-2023/Project-3)
+
+[Documentation](https://pages.github.uio.no/FYS3150-G2-2023/Project-3/)
+
+## Requirements
+
+### Operating systems
+
+- Linux
+    - Has been tested on [Fedora 38](https://fedoraproject.org/)
+    - Will most likely work on other Linux distributions
+- MacOS
+    - Might work, but hasn't been tested
+- Windows
+    - Will most likely not work
+
+### Tools
+
+- Profiling
+    - [gprof](https://ftp.gnu.org/old-gnu/Manuals/gprof-2.9.1/html_mono/gprof.html)
+    - [scalasca](https://www.scalasca.org/)
+    - [score-p](https://www.vi-hps.org/projects/score-p)
+
+### Libraries
+
+- Python
+    - [matplotlib](https://matplotlib.org/)
+    - [numpy](https://numpy.org/)
+
+- C++
+    - [openmp](https://www.openmp.org/)
+    - [armadillo](https://arma.sourceforge.net/)
+
+
+## Compiling
+
+Compiling is as easy as running this command while being inside the src directory:
+
+```shell
+    make
+```
+
+## Running programs
+
+### C++ binaries
+
+To run **main** or **test_suite**, just run this command while being inside src:
+
+```shell
+    ./<program-name>
+```
+
+### Python scripts
+
+#### Install libraries
+
+Before running the scripts, make sure that all libraries are installed.
+Using pip, you can install all requirements like this:
+
+```shell
+    pip install -r requirements.txt
+```
+
+This recursively install all the packages that are listed in **requirements.txt**.
+
+#### Running scripts
+
+For the Python scripts, run them from the src directory like this:
+
+```shell
+    python scripts/<script-name>
+```
+
+If you have any problems running the scripts, you might have to run this instead:
+
+```shell
+    python3 scripts/<script-name>
+```
+
+## Performance
+
+This section aims to give an idea to the time it takes for the program to
+run so that you know a bit what to expect if you decide to run it for
+yourself.
+
+### CPU
+
+The times mentioned here are times achieved on a computer with these 
+specifications:
+
+- CPU model
+    - Intel i7-9850H
+- Threads
+    - 12
+- Clock speed
+    - 4.6GHz
+
+### Times
+
+All times mentioned use the **evolve_RK4** method.
+
+Running a simulation with 100 particles without particle interactions over
+40000 steps takes around 1.8 seconds. With particle interactions, it takes
+around 4.8 seconds.
+
+**potential_resonance_wide_sweep** takes around 56 seconds to complete.
+
+**potential_resonance_narrow_sweep** takes around 172 seconds to complete.
+
+**potential_resonance_narrow_sweep_interaction** takes around 936 seconds to 
+complete.
+
 ## Credits
 
 The Doxygen theme used here is 

docs/Particle_8cpp.html

@@ -112,8 +112,8 @@ $(document).ready(function(){initNavTree('Particle_8cpp.html',''); initResizable
 <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>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="section version"><dt>Version</dt><dd>1.0</dd></dl>
+<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000007">Bug:</a></b></dt><dd>No known bugs </dd></dl>
 
 <p class="definition">Definition in file <a class="el" href="Particle_8cpp_source.html">Particle.cpp</a>.</p>
 </div></div><!-- contents -->

docs/Particle_8cpp_source.html

@@ -102,24 +102,23 @@ $(document).ready(function(){initNavTree('Particle_8cpp_source.html',''); initRe
 </div><!--header-->
 <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>
-<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="preprocessor">#include &quot;<a class="code" href="Particle_8hpp.html">Particle.hpp</a>&quot;</span></div>
-<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span> </div>
-<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"><a class="line" href="classParticle.html#a00e108823877a25513ccae7cac011b4c">   16</a></span><a class="code hl_function" href="classParticle.html#a00e108823877a25513ccae7cac011b4c">Particle::Particle</a>(<span class="keywordtype">double</span> q, <span class="keywordtype">double</span> m,</div>
-<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span>                   arma::vec::fixed&lt;3&gt; r_vec,</div>
-<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>                   arma::vec::fixed&lt;3&gt; v_vec)</div>
-<div class="line"><a id="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="comment">// Giving the particle its properties</span></div>
-<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>    this-&gt;q = <a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>;</div>
-<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>    this-&gt;m = <a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>;</div>
-<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>    this-&gt;r_vec = <a class="code hl_variable" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a>;</div>
-<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>    this-&gt;v_vec = <a class="code hl_variable" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a>;</div>
-<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</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="l00014" name="l00014"></a><span class="lineno">   14</span> </div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"><a class="line" href="classParticle.html#af1d7535fb8311eaa77d2b7b345882ec4">   15</a></span><a class="code hl_function" href="classParticle.html#af1d7535fb8311eaa77d2b7b345882ec4">Particle::Particle</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r_vec, <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> v_vec, <span class="keywordtype">double</span> q, <span class="keywordtype">double</span> m)</div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span>{</div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span>    <span class="comment">// Giving the particle its properties</span></div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>    this-&gt;r_vec = <a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>;</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>    this-&gt;v_vec = <a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a>;</div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>    this-&gt;q = <a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>;</div>
+<div class="line"><a id="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>}</div>
 <div class="ttc" id="aParticle_8hpp_html"><div class="ttname"><a href="Particle_8hpp.html">Particle.hpp</a></div><div class="ttdoc">A class that holds the properties of a particle.</div></div>
-<div class="ttc" id="aclassParticle_html_a00e108823877a25513ccae7cac011b4c"><div class="ttname"><a href="classParticle.html#a00e108823877a25513ccae7cac011b4c">Particle::Particle</a></div><div class="ttdeci">Particle(double q, double m, arma::vec::fixed&lt; 3 &gt; r_vec, arma::vec::fixed&lt; 3 &gt; v_vec)</div><div class="ttdoc">Initialize the particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8cpp_source.html#l00016">Particle.cpp:16</a></div></div>
-<div class="ttc" id="aclassParticle_html_a4a5d22c7aeca66f67d083f270cba25df"><div class="ttname"><a href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">Particle::v_vec</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; v_vec</div><div class="ttdoc">velocity</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00024">Particle.hpp:24</a></div></div>
-<div class="ttc" id="aclassParticle_html_a566dcc1de4bdc01251776948798ea8e1"><div class="ttname"><a href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">Particle::q</a></div><div class="ttdeci">double q</div><div class="ttdoc">Charge.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00021">Particle.hpp:21</a></div></div>
-<div class="ttc" id="aclassParticle_html_acf1a0f3c978b06d76df5bb4279594467"><div class="ttname"><a href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">Particle::r_vec</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; r_vec</div><div class="ttdoc">position</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00023">Particle.hpp:23</a></div></div>
-<div class="ttc" id="aclassParticle_html_aedcc7e1bc53b0e2b1a4a07c9a1b47563"><div class="ttname"><a href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle::m</a></div><div class="ttdeci">double m</div><div class="ttdoc">Mass.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00022">Particle.hpp:22</a></div></div>
+<div class="ttc" id="aclassParticle_html_a1c59101411db43624828b766f87ad460"><div class="ttname"><a href="classParticle.html#a1c59101411db43624828b766f87ad460">Particle::r_vec</a></div><div class="ttdeci">vec3 r_vec</div><div class="ttdoc">position</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00025">Particle.hpp:25</a></div></div>
+<div class="ttc" id="aclassParticle_html_a3a10400add8dd22b8031330c2aafb6fe"><div class="ttname"><a href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">Particle::v_vec</a></div><div class="ttdeci">vec3 v_vec</div><div class="ttdoc">velocity</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00026">Particle.hpp:26</a></div></div>
+<div class="ttc" id="aclassParticle_html_a566dcc1de4bdc01251776948798ea8e1"><div class="ttname"><a href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">Particle::q</a></div><div class="ttdeci">double q</div><div class="ttdoc">Charge.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00027">Particle.hpp:27</a></div></div>
+<div class="ttc" id="aclassParticle_html_aedcc7e1bc53b0e2b1a4a07c9a1b47563"><div class="ttname"><a href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle::m</a></div><div class="ttdeci">double m</div><div class="ttdoc">Mass.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00028">Particle.hpp:28</a></div></div>
+<div class="ttc" id="aclassParticle_html_af1d7535fb8311eaa77d2b7b345882ec4"><div class="ttname"><a href="classParticle.html#af1d7535fb8311eaa77d2b7b345882ec4">Particle::Particle</a></div><div class="ttdeci">Particle(vec3 r_vec, vec3 v_vec, double q=CA_CHARGE, double m=CA_MASS)</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="atypedefs_8hpp_html_a3bdfb73a02f88ae32b6128ef747c4aea"><div class="ttname"><a href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; vec3</div><div class="ttdoc">Typedef for a fixed 3d arma vector.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00023">typedefs.hpp:23</a></div></div>
 </div><!-- fragment --></div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->

docs/Particle_8hpp.html

@@ -107,6 +107,8 @@ $(document).ready(function(){initNavTree('Particle_8hpp.html',''); initResizable
 <p>A class that holds the properties of a particle.  
 <a href="#details">More...</a></p>
 <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 &quot;<a class="el" href="typedefs_8hpp_source.html">typedefs.hpp</a>&quot;</code><br />
 </div>
 <p><a href="Particle_8hpp_source.html">Go to the source code of this file.</a></p>
 <table class="memberdecls">
@@ -121,7 +123,7 @@ Classes</h2></td></tr>
 <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>0.1</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#_bug000002">Bug:</a></b></dt><dd>No known bugs </dd></dl>
 
 <p class="definition">Definition in file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>

docs/Particle_8hpp_source.html

@@ -107,28 +107,35 @@ $(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="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="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="l00020" name="l00020"></a><span class="lineno">   20</span><span class="keyword">private</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="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="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="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="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="keyword">public</span>:</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="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="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="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="l00041" name="l00041"></a><span class="lineno">   41</span><span class="preprocessor">#endif</span></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_a4a5d22c7aeca66f67d083f270cba25df"><div class="ttname"><a href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">Particle::v_vec</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; v_vec</div><div class="ttdoc">velocity</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00024">Particle.hpp:24</a></div></div>
-<div class="ttc" id="aclassParticle_html_a566dcc1de4bdc01251776948798ea8e1"><div class="ttname"><a href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">Particle::q</a></div><div class="ttdeci">double q</div><div class="ttdoc">Charge.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00021">Particle.hpp:21</a></div></div>
-<div class="ttc" id="aclassParticle_html_acf1a0f3c978b06d76df5bb4279594467"><div class="ttname"><a href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">Particle::r_vec</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; r_vec</div><div class="ttdoc">position</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00023">Particle.hpp:23</a></div></div>
-<div class="ttc" id="aclassParticle_html_aedcc7e1bc53b0e2b1a4a07c9a1b47563"><div class="ttname"><a href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle::m</a></div><div class="ttdeci">double m</div><div class="ttdoc">Mass.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00022">Particle.hpp:22</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="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="l00018" name="l00018"></a><span class="lineno">   18</span><span class="preprocessor">#include &quot;<a class="code" href="typedefs_8hpp.html">typedefs.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span> </div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"><a class="line" href="classParticle.html">   22</a></span><span class="keyword">class </span><a class="code hl_class" href="classParticle.html">Particle</a></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">private</span>:</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"><a class="line" href="classParticle.html#a1c59101411db43624828b766f87ad460">   25</a></span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>; </div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"><a class="line" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">   26</a></span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a>; </div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"><a class="line" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">   27</a></span>    <span class="keywordtype">double</span> <a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>;   </div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"><a class="line" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">   28</a></span>    <span class="keywordtype">double</span> <a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>;   </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">public</span>:</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>    <a class="code hl_class" href="classParticle.html">Particle</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>, <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a> = <a class="code hl_define" href="constants_8hpp.html#af7602a3a314957137ad1cd719aa23789">CA_CHARGE</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a> = <a class="code hl_define" href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">CA_MASS</a>);</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span> </div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"><a class="line" href="classParticle.html#aa797d319549dc2a0beb06cdbfd430232">   45</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="l00046" name="l00046"></a><span class="lineno">   46</span>};</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span> </div>
+<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span><span class="preprocessor">#endif</span></div>
+<div class="ttc" id="aclassParticle_html"><div class="ttname"><a href="classParticle.html">Particle</a></div><div class="ttdoc">A class that holds attributes of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00022">Particle.hpp:23</a></div></div>
+<div class="ttc" id="aclassParticle_html_a1c59101411db43624828b766f87ad460"><div class="ttname"><a href="classParticle.html#a1c59101411db43624828b766f87ad460">Particle::r_vec</a></div><div class="ttdeci">vec3 r_vec</div><div class="ttdoc">position</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00025">Particle.hpp:25</a></div></div>
+<div class="ttc" id="aclassParticle_html_a3a10400add8dd22b8031330c2aafb6fe"><div class="ttname"><a href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">Particle::v_vec</a></div><div class="ttdeci">vec3 v_vec</div><div class="ttdoc">velocity</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00026">Particle.hpp:26</a></div></div>
+<div class="ttc" id="aclassParticle_html_a566dcc1de4bdc01251776948798ea8e1"><div class="ttname"><a href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">Particle::q</a></div><div class="ttdeci">double q</div><div class="ttdoc">Charge.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00027">Particle.hpp:27</a></div></div>
+<div class="ttc" id="aclassParticle_html_aedcc7e1bc53b0e2b1a4a07c9a1b47563"><div class="ttname"><a href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle::m</a></div><div class="ttdeci">double m</div><div class="ttdoc">Mass.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00028">Particle.hpp:28</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00031">PenningTrap.hpp:32</a></div></div>
+<div class="ttc" id="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_a2ff491cc7958ffd5e749c518a4a60ec8"><div class="ttname"><a href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">CA_MASS</a></div><div class="ttdeci">#define CA_MASS</div><div class="ttdoc">Mass of a single calcium ion. unit: amu.</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00029">constants.hpp:29</a></div></div>
+<div class="ttc" id="aconstants_8hpp_html_af7602a3a314957137ad1cd719aa23789"><div class="ttname"><a href="constants_8hpp.html#af7602a3a314957137ad1cd719aa23789">CA_CHARGE</a></div><div class="ttdeci">#define CA_CHARGE</div><div class="ttdoc">Charge of a singly charged calcium ion. unit: e.</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00033">constants.hpp:33</a></div></div>
+<div class="ttc" id="atypedefs_8hpp_html"><div class="ttname"><a href="typedefs_8hpp.html">typedefs.hpp</a></div><div class="ttdoc">Useful typedefs for cleaner code.</div></div>
+<div class="ttc" id="atypedefs_8hpp_html_a3bdfb73a02f88ae32b6128ef747c4aea"><div class="ttname"><a href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; vec3</div><div class="ttdoc">Typedef for a fixed 3d arma vector.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00023">typedefs.hpp:23</a></div></div>
 </div><!-- fragment --></div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->

docs/PenningTrap_8cpp.html

@@ -105,6 +105,11 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp.html',''); initResiza
 <p>The implementation of the <a class="el" href="classPenningTrap.html" title="A class that simulates a Penning trap.">PenningTrap</a> class.  
 <a href="#details">More...</a></p>
 <div class="textblock"><code>#include &quot;<a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="typedefs_8hpp_source.html">typedefs.hpp</a>&quot;</code><br />
+<code>#include &lt;algorithm&gt;</code><br />
+<code>#include &lt;functional&gt;</code><br />
+<code>#include &lt;sys/types.h&gt;</code><br />
+<code>#include &lt;vector&gt;</code><br />
 </div>
 <p><a href="PenningTrap_8cpp_source.html">Go to the source code of this file.</a></p>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
@@ -112,19 +117,8 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp.html',''); initResiza
 <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>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="todo"><dt><b><a class="el" href="todo.html#_todo000001">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>
+<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
+<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000008">Bug:</a></b></dt><dd>No known bugs </dd></dl>
 
 <p class="definition">Definition in file <a class="el" href="PenningTrap_8cpp_source.html">PenningTrap.cpp</a>.</p>
 </div></div><!-- contents -->

docs/PenningTrap_8cpp_source.html

@@ -102,69 +102,361 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp_source.html',''); ini
 </div><!--header-->
 <div class="contents">
 <a href="PenningTrap_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span> </div>
-<div class="line"><a id="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="l00025" name="l00025"></a><span class="lineno">   25</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="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>}</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"><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="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>}</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"><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="l00037" name="l00037"></a><span class="lineno">   37</span>{</div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="preprocessor">#include &quot;<a class="code" href="typedefs_8hpp.html">typedefs.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="preprocessor">#include &lt;algorithm&gt;</span></div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span><span class="preprocessor">#include &lt;functional&gt;</span></div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span><span class="preprocessor">#include &lt;sys/types.h&gt;</span></div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span> </div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">   20</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap::v_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt)</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>{</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>    <span class="keywordflow">switch</span> (i) {</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>    <span class="keywordflow">case</span> 0:</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>        <span class="keywordflow">return</span> .5 * dt * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>[0][j];</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>    <span class="keywordflow">case</span> 1:</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>        <span class="keywordflow">return</span> .5 * dt * this-&gt;k_v[1][j];</div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span>    <span class="keywordflow">case</span> 2:</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>        <span class="keywordflow">return</span> dt * this-&gt;k_v[2][j];</div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span>    <span class="keywordflow">case</span> 3:</div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span>        <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((dt / 6.)</div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span>                    * (this-&gt;k_v[0][j] + 2. * this-&gt;k_v[1][j]</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>                       + 2. * this-&gt;k_v[2][j] + this-&gt;k_v[3][j]));</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span>    <span class="keywordflow">default</span>:</div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span>        abort();</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span>    }</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span>}</div>
 <div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span> </div>
-<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</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"><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="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="l00044" name="l00044"></a><span class="lineno">   44</span>}</div>
-<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span> </div>
-<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"><a class="line" href="classPenningTrap.html#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="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="l00049" name="l00049"></a><span class="lineno">   49</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"><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="l00052" name="l00052"></a><span class="lineno">   52</span>{</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> </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="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>}</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"><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="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="l00039" name="l00039"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">   39</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">PenningTrap::r_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt)</div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>{</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>    <span class="keywordflow">switch</span> (i) {</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>    <span class="keywordflow">case</span> 0:</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>        <span class="keywordflow">return</span> .5 * dt * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>[0][j];</div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span>    <span class="keywordflow">case</span> 1:</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span>        <span class="keywordflow">return</span> .5 * dt * this-&gt;k_r[1][j];</div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>    <span class="keywordflow">case</span> 2:</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>        <span class="keywordflow">return</span> dt * this-&gt;k_r[2][j];</div>
+<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span>    <span class="keywordflow">case</span> 3:</div>
+<div class="line"><a id="l00049" name="l00049"></a><span class="lineno">   49</span>        <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((dt / 6.)</div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span>                    * (this-&gt;k_r[0][j] + 2. * this-&gt;k_r[1][j]</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span>                       + 2. * this-&gt;k_r[2][j] + this-&gt;k_r[3][j]));</div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span>    <span class="keywordflow">default</span>:</div>
+<div class="line"><a id="l00053" name="l00053"></a><span class="lineno">   53</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00054" name="l00054"></a><span class="lineno">   54</span>        abort();</div>
+<div class="line"><a id="l00055" name="l00055"></a><span class="lineno">   55</span>    }</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno">   56</span>}</div>
+<div class="line"><a id="l00057" name="l00057"></a><span class="lineno">   57</span> </div>
+<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">   58</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">PenningTrap::external_E_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r)</div>
+<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   59</span>{</div>
+<div class="line"><a id="l00060" name="l00060"></a><span class="lineno">   60</span>    r(2) *= -2.;</div>
+<div class="line"><a id="l00061" name="l00061"></a><span class="lineno">   61</span> </div>
+<div class="line"><a id="l00062" name="l00062"></a><span class="lineno">   62</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</a>(this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>) / (this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>))</div>
+<div class="line"><a id="l00063" name="l00063"></a><span class="lineno">   63</span>                * r);</div>
 <div class="line"><a id="l00064" name="l00064"></a><span class="lineno">   64</span>}</div>
 <div class="line"><a id="l00065" name="l00065"></a><span class="lineno">   65</span> </div>
-<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"><a class="line" href="classPenningTrap.html#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"><a class="line" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">   66</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">PenningTrap::external_B_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r)</div>
 <div class="line"><a id="l00067" name="l00067"></a><span class="lineno">   67</span>{</div>
-<div class="line"><a id="l00068" name="l00068"></a><span class="lineno">   68</span> </div>
+<div class="line"><a id="l00068" name="l00068"></a><span class="lineno">   68</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 0., this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>};</div>
 <div class="line"><a id="l00069" name="l00069"></a><span class="lineno">   69</span>}</div>
 <div class="line"><a id="l00070" name="l00070"></a><span class="lineno">   70</span> </div>
-<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"><a class="line" href="classPenningTrap.html#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"><a class="line" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">   71</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap::force_on_particle</a>(uint i, uint j)</div>
 <div class="line"><a id="l00072" name="l00072"></a><span class="lineno">   72</span>{</div>
-<div class="line"><a id="l00073" name="l00073"></a><span class="lineno">   73</span> </div>
-<div class="line"><a id="l00074" name="l00074"></a><span class="lineno">   74</span>}</div>
+<div class="line"><a id="l00073" name="l00073"></a><span class="lineno">   73</span>    <span class="comment">// Calculate the difference between the particles&#39; position</span></div>
+<div class="line"><a id="l00074" name="l00074"></a><span class="lineno">   74</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec - this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].r_vec;</div>
+<div class="line"><a id="l00075" name="l00075"></a><span class="lineno">   75</span> </div>
+<div class="line"><a id="l00076" name="l00076"></a><span class="lineno">   76</span>    <span class="comment">// Get the distance between the particles</span></div>
+<div class="line"><a id="l00077" name="l00077"></a><span class="lineno">   77</span>    <span class="keywordtype">double</span> norm = arma::norm(res, 2);</div>
+<div class="line"><a id="l00078" name="l00078"></a><span class="lineno">   78</span> </div>
+<div class="line"><a id="l00079" name="l00079"></a><span class="lineno">   79</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].q / (norm * norm * norm)) * res);</div>
+<div class="line"><a id="l00080" name="l00080"></a><span class="lineno">   80</span>}</div>
+<div class="line"><a id="l00081" name="l00081"></a><span class="lineno">   81</span> </div>
+<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">   82</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap::total_force_external</a>(uint i)</div>
+<div class="line"><a id="l00083" name="l00083"></a><span class="lineno">   83</span>{</div>
+<div class="line"><a id="l00084" name="l00084"></a><span class="lineno">   84</span>    <a class="code hl_class" href="classParticle.html">Particle</a> *p = &amp;this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i];</div>
+<div class="line"><a id="l00085" name="l00085"></a><span class="lineno">   85</span> </div>
+<div class="line"><a id="l00086" name="l00086"></a><span class="lineno">   86</span>    <span class="keywordflow">if</span> (arma::norm(p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>) &gt; this-&gt;d) {</div>
+<div class="line"><a id="l00087" name="l00087"></a><span class="lineno">   87</span>        <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 0., 0.};</div>
+<div class="line"><a id="l00088" name="l00088"></a><span class="lineno">   88</span>    }</div>
+<div class="line"><a id="l00089" name="l00089"></a><span class="lineno">   89</span> </div>
+<div class="line"><a id="l00090" name="l00090"></a><span class="lineno">   90</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(p-&gt;<a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a></div>
+<div class="line"><a id="l00091" name="l00091"></a><span class="lineno">   91</span>                * (this-&gt;external_E_field(p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>)</div>
+<div class="line"><a id="l00092" name="l00092"></a><span class="lineno">   92</span>                   + arma::cross(p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a>, this-&gt;external_B_field(p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>))));</div>
+<div class="line"><a id="l00093" name="l00093"></a><span class="lineno">   93</span>}</div>
+<div class="line"><a id="l00094" name="l00094"></a><span class="lineno">   94</span> </div>
+<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">   95</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap::total_force_particles</a>(uint i)</div>
+<div class="line"><a id="l00096" name="l00096"></a><span class="lineno">   96</span>{</div>
+<div class="line"><a id="l00097" name="l00097"></a><span class="lineno">   97</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res;</div>
+<div class="line"><a id="l00098" name="l00098"></a><span class="lineno">   98</span> </div>
+<div class="line"><a id="l00099" name="l00099"></a><span class="lineno">   99</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); j++) {</div>
+<div class="line"><a id="l00100" name="l00100"></a><span class="lineno">  100</span>        <span class="keywordflow">if</span> (i != j)</div>
+<div class="line"><a id="l00101" name="l00101"></a><span class="lineno">  101</span>            res += this-&gt;<a class="code hl_function" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">force_on_particle</a>(i, j);</div>
+<div class="line"><a id="l00102" name="l00102"></a><span class="lineno">  102</span>    }</div>
+<div class="line"><a id="l00103" name="l00103"></a><span class="lineno">  103</span> </div>
+<div class="line"><a id="l00104" name="l00104"></a><span class="lineno">  104</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(res * (<a class="code hl_define" href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">K_E</a> * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].q));</div>
+<div class="line"><a id="l00105" name="l00105"></a><span class="lineno">  105</span>}</div>
+<div class="line"><a id="l00106" name="l00106"></a><span class="lineno">  106</span> </div>
+<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">  107</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a>(uint i)</div>
+<div class="line"><a id="l00108" name="l00108"></a><span class="lineno">  108</span>{</div>
+<div class="line"><a id="l00109" name="l00109"></a><span class="lineno">  109</span>    <span class="keywordflow">if</span> (arma::norm(this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec) &gt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>) {</div>
+<div class="line"><a id="l00110" name="l00110"></a><span class="lineno">  110</span>        <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 0., 0.};</div>
+<div class="line"><a id="l00111" name="l00111"></a><span class="lineno">  111</span>    }</div>
+<div class="line"><a id="l00112" name="l00112"></a><span class="lineno">  112</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(this-&gt;<a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">total_force_external</a>(i) - this-&gt;<a class="code hl_function" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">total_force_particles</a>(i));</div>
+<div class="line"><a id="l00113" name="l00113"></a><span class="lineno">  113</span>}</div>
+<div class="line"><a id="l00114" name="l00114"></a><span class="lineno">  114</span> </div>
+<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">  115</a></span><a class="code hl_function" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a>(<span class="keywordtype">double</span> B_0, <span class="keywordtype">double</span> V_0, <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</div>
+<div class="line"><a id="l00116" name="l00116"></a><span class="lineno">  116</span>{</div>
+<div class="line"><a id="l00117" name="l00117"></a><span class="lineno">  117</span>    this-&gt;B_0 = <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>;</div>
+<div class="line"><a id="l00118" name="l00118"></a><span class="lineno">  118</span>    this-&gt;V_0 = <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a>;</div>
+<div class="line"><a id="l00119" name="l00119"></a><span class="lineno">  119</span>    this-&gt;d = <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</div>
+<div class="line"><a id="l00120" name="l00120"></a><span class="lineno">  120</span>    this-&gt;t = <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>;</div>
+<div class="line"><a id="l00121" name="l00121"></a><span class="lineno">  121</span>    this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</a> = [](<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>) { <span class="keywordflow">return</span> 1.; };</div>
+<div class="line"><a id="l00122" name="l00122"></a><span class="lineno">  122</span>}</div>
+<div class="line"><a id="l00123" name="l00123"></a><span class="lineno">  123</span> </div>
+<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a830be1b8cbf59664e060b6edbeaa302f">  124</a></span><a class="code hl_function" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a>(uint i, <span class="keywordtype">double</span> B_0, <span class="keywordtype">double</span> V_0, <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</div>
+<div class="line"><a id="l00125" name="l00125"></a><span class="lineno">  125</span>    : <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(B_0, V_0, d)</div>
+<div class="line"><a id="l00126" name="l00126"></a><span class="lineno">  126</span>{</div>
+<div class="line"><a id="l00127" name="l00127"></a><span class="lineno">  127</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; i; j++) {</div>
+<div class="line"><a id="l00128" name="l00128"></a><span class="lineno">  128</span>        this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(</div>
+<div class="line"><a id="l00129" name="l00129"></a><span class="lineno">  129</span>            <a class="code hl_class" href="classParticle.html">Particle</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>().randn() * .1 * this-&gt;d),</div>
+<div class="line"><a id="l00130" name="l00130"></a><span class="lineno">  130</span>                     <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>().randn() * .1 * this-&gt;d)));</div>
+<div class="line"><a id="l00131" name="l00131"></a><span class="lineno">  131</span>    }</div>
+<div class="line"><a id="l00132" name="l00132"></a><span class="lineno">  132</span>}</div>
+<div class="line"><a id="l00133" name="l00133"></a><span class="lineno">  133</span> </div>
+<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"><a class="line" href="classPenningTrap.html#addc96789dcfec07b75156e19fee82f4f">  134</a></span><a class="code hl_function" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a>(std::vector&lt;Particle&gt; particles, <span class="keywordtype">double</span> B_0,</div>
+<div class="line"><a id="l00135" name="l00135"></a><span class="lineno">  135</span>                         <span class="keywordtype">double</span> V_0, <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</div>
+<div class="line"><a id="l00136" name="l00136"></a><span class="lineno">  136</span>    : <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(B_0, V_0, d)</div>
+<div class="line"><a id="l00137" name="l00137"></a><span class="lineno">  137</span>{</div>
+<div class="line"><a id="l00138" name="l00138"></a><span class="lineno">  138</span>    this-&gt;particles = <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
+<div class="line"><a id="l00139" name="l00139"></a><span class="lineno">  139</span>}</div>
+<div class="line"><a id="l00140" name="l00140"></a><span class="lineno">  140</span> </div>
+<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">  141</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">PenningTrap::set_pertubation</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V)</div>
+<div class="line"><a id="l00142" name="l00142"></a><span class="lineno">  142</span>{</div>
+<div class="line"><a id="l00143" name="l00143"></a><span class="lineno">  143</span>    this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</a> = [f, omega_V](<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>) {</div>
+<div class="line"><a id="l00144" name="l00144"></a><span class="lineno">  144</span>        <span class="keywordflow">return</span> 1 + f * std::cos(omega_V * <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>);</div>
+<div class="line"><a id="l00145" name="l00145"></a><span class="lineno">  145</span>    };</div>
+<div class="line"><a id="l00146" name="l00146"></a><span class="lineno">  146</span>}</div>
+<div class="line"><a id="l00147" name="l00147"></a><span class="lineno">  147</span> </div>
+<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"><a class="line" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">  148</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap::reinitialize</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V, <span class="keywordtype">double</span> t)</div>
+<div class="line"><a id="l00149" name="l00149"></a><span class="lineno">  149</span>{</div>
+<div class="line"><a id="l00150" name="l00150"></a><span class="lineno">  150</span>    this-&gt;t = <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>;</div>
+<div class="line"><a id="l00151" name="l00151"></a><span class="lineno">  151</span>    this-&gt;<a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">set_pertubation</a>(f, omega_V);</div>
+<div class="line"><a id="l00152" name="l00152"></a><span class="lineno">  152</span> </div>
+<div class="line"><a id="l00153" name="l00153"></a><span class="lineno">  153</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); i++) {</div>
+<div class="line"><a id="l00154" name="l00154"></a><span class="lineno">  154</span>        this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec = <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>().randn() * .1 * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</div>
+<div class="line"><a id="l00155" name="l00155"></a><span class="lineno">  155</span>    }</div>
+<div class="line"><a id="l00156" name="l00156"></a><span class="lineno">  156</span>}</div>
+<div class="line"><a id="l00157" name="l00157"></a><span class="lineno">  157</span> </div>
+<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">  158</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap::add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a> particle)</div>
+<div class="line"><a id="l00159" name="l00159"></a><span class="lineno">  159</span>{</div>
+<div class="line"><a id="l00160" name="l00160"></a><span class="lineno">  160</span>    this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(particle);</div>
+<div class="line"><a id="l00161" name="l00161"></a><span class="lineno">  161</span>}</div>
+<div class="line"><a id="l00162" name="l00162"></a><span class="lineno">  162</span> </div>
+<div class="line"><a id="l00163" name="l00163"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">  163</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction)</div>
+<div class="line"><a id="l00164" name="l00164"></a><span class="lineno">  164</span>{</div>
+<div class="line"><a id="l00165" name="l00165"></a><span class="lineno">  165</span> </div>
+<div class="line"><a id="l00166" name="l00166"></a><span class="lineno">  166</span>    std::vector&lt;Particle&gt; original_particles = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
+<div class="line"><a id="l00167" name="l00167"></a><span class="lineno">  167</span>    std::vector&lt;Particle&gt; tmp_particles = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
+<div class="line"><a id="l00168" name="l00168"></a><span class="lineno">  168</span> </div>
+<div class="line"><a id="l00169" name="l00169"></a><span class="lineno">  169</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*force)(uint) = particle_interaction</div>
+<div class="line"><a id="l00170" name="l00170"></a><span class="lineno">  170</span>                                           ? &amp;<a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div>
+<div class="line"><a id="l00171" name="l00171"></a><span class="lineno">  171</span>                                           : &amp;<a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap::total_force_external</a>;</div>
+<div class="line"><a id="l00172" name="l00172"></a><span class="lineno">  172</span> </div>
+<div class="line"><a id="l00173" name="l00173"></a><span class="lineno">  173</span>    <span class="keywordtype">size_t</span> size = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div>
+<div class="line"><a id="l00174" name="l00174"></a><span class="lineno">  174</span> </div>
+<div class="line"><a id="l00175" name="l00175"></a><span class="lineno">  175</span>    <span class="comment">// Allocating takes a long time, so reuse sim_arr if possible</span></div>
+<div class="line"><a id="l00176" name="l00176"></a><span class="lineno">  176</span>    <span class="keywordflow">if</span> (this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>.size() != 4 || this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>.size() != 4</div>
+<div class="line"><a id="l00177" name="l00177"></a><span class="lineno">  177</span>        || this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>[0].size() != size || this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>[0].size() != size) {</div>
+<div class="line"><a id="l00178" name="l00178"></a><span class="lineno">  178</span>        this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a> = <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(4, <a class="code hl_typedef" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a>(size));</div>
+<div class="line"><a id="l00179" name="l00179"></a><span class="lineno">  179</span>        this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a> = <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(4, <a class="code hl_typedef" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a>(size));</div>
+<div class="line"><a id="l00180" name="l00180"></a><span class="lineno">  180</span>    }</div>
+<div class="line"><a id="l00181" name="l00181"></a><span class="lineno">  181</span> </div>
+<div class="line"><a id="l00182" name="l00182"></a><span class="lineno">  182</span>    <span class="comment">// Each k_{i+1} is dependent on k_i, so outer loop is not parallelizable</span></div>
+<div class="line"><a id="l00183" name="l00183"></a><span class="lineno">  183</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 4; i++) {</div>
+<div class="line"><a id="l00184" name="l00184"></a><span class="lineno">  184</span>        <span class="comment">// Inner loop is able to be parallelized</span></div>
+<div class="line"><a id="l00185" name="l00185"></a><span class="lineno">  185</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00186" name="l00186"></a><span class="lineno">  186</span>        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; size; j++) {</div>
+<div class="line"><a id="l00187" name="l00187"></a><span class="lineno">  187</span>            this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>[i][j] = (this-&gt;*force)(j) / this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].m;</div>
+<div class="line"><a id="l00188" name="l00188"></a><span class="lineno">  188</span>            this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>[i][j] = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].v_vec;</div>
+<div class="line"><a id="l00189" name="l00189"></a><span class="lineno">  189</span> </div>
+<div class="line"><a id="l00190" name="l00190"></a><span class="lineno">  190</span>            tmp_particles[j].v_vec =</div>
+<div class="line"><a id="l00191" name="l00191"></a><span class="lineno">  191</span>                original_particles[j].v_vec + this-&gt;<a class="code hl_function" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">v_func</a>(i, j, dt);</div>
+<div class="line"><a id="l00192" name="l00192"></a><span class="lineno">  192</span>            tmp_particles[j].r_vec =</div>
+<div class="line"><a id="l00193" name="l00193"></a><span class="lineno">  193</span>                original_particles[j].r_vec + this-&gt;<a class="code hl_function" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">r_func</a>(i, j, dt);</div>
+<div class="line"><a id="l00194" name="l00194"></a><span class="lineno">  194</span>        }</div>
+<div class="line"><a id="l00195" name="l00195"></a><span class="lineno">  195</span>        this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a> = tmp_particles;</div>
+<div class="line"><a id="l00196" name="l00196"></a><span class="lineno">  196</span>    }</div>
+<div class="line"><a id="l00197" name="l00197"></a><span class="lineno">  197</span> </div>
+<div class="line"><a id="l00198" name="l00198"></a><span class="lineno">  198</span>    this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> += dt;</div>
+<div class="line"><a id="l00199" name="l00199"></a><span class="lineno">  199</span>}</div>
+<div class="line"><a id="l00200" name="l00200"></a><span class="lineno">  200</span> </div>
+<div class="line"><a id="l00201" name="l00201"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">  201</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction)</div>
+<div class="line"><a id="l00202" name="l00202"></a><span class="lineno">  202</span>{</div>
+<div class="line"><a id="l00203" name="l00203"></a><span class="lineno">  203</span>    <span class="keywordtype">size_t</span> size = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div>
+<div class="line"><a id="l00204" name="l00204"></a><span class="lineno">  204</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> force_res[size];</div>
+<div class="line"><a id="l00205" name="l00205"></a><span class="lineno">  205</span> </div>
+<div class="line"><a id="l00206" name="l00206"></a><span class="lineno">  206</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*force)(uint) = particle_interaction</div>
+<div class="line"><a id="l00207" name="l00207"></a><span class="lineno">  207</span>                                           ? &amp;<a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div>
+<div class="line"><a id="l00208" name="l00208"></a><span class="lineno">  208</span>                                           : &amp;<a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap::total_force_external</a>;</div>
+<div class="line"><a id="l00209" name="l00209"></a><span class="lineno">  209</span> </div>
+<div class="line"><a id="l00210" name="l00210"></a><span class="lineno">  210</span>    <span class="comment">// Calculating the force for each particle is independent and therefore</span></div>
+<div class="line"><a id="l00211" name="l00211"></a><span class="lineno">  211</span>    <span class="comment">// a good candidate for parallel execution</span></div>
+<div class="line"><a id="l00212" name="l00212"></a><span class="lineno">  212</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00213" name="l00213"></a><span class="lineno">  213</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; size; i++) {</div>
+<div class="line"><a id="l00214" name="l00214"></a><span class="lineno">  214</span>        force_res[i] = (this-&gt;*force)(i);</div>
+<div class="line"><a id="l00215" name="l00215"></a><span class="lineno">  215</span>    }</div>
+<div class="line"><a id="l00216" name="l00216"></a><span class="lineno">  216</span> </div>
+<div class="line"><a id="l00217" name="l00217"></a><span class="lineno">  217</span>    <span class="comment">// Updating the particles is also independent, so we can parallelize</span></div>
+<div class="line"><a id="l00218" name="l00218"></a><span class="lineno">  218</span>    <span class="comment">// this as well</span></div>
+<div class="line"><a id="l00219" name="l00219"></a><span class="lineno">  219</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00220" name="l00220"></a><span class="lineno">  220</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; size; i++) {</div>
+<div class="line"><a id="l00221" name="l00221"></a><span class="lineno">  221</span>        this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec += dt * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].v_vec;</div>
+<div class="line"><a id="l00222" name="l00222"></a><span class="lineno">  222</span>        this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].v_vec += dt * force_res[i] / this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].m;</div>
+<div class="line"><a id="l00223" name="l00223"></a><span class="lineno">  223</span>    }</div>
+<div class="line"><a id="l00224" name="l00224"></a><span class="lineno">  224</span> </div>
+<div class="line"><a id="l00225" name="l00225"></a><span class="lineno">  225</span>    this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> += dt;</div>
+<div class="line"><a id="l00226" name="l00226"></a><span class="lineno">  226</span>}</div>
+<div class="line"><a id="l00227" name="l00227"></a><span class="lineno">  227</span> </div>
+<div class="line"><a id="l00228" name="l00228"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">  228</a></span><a class="code hl_struct" href="structsimulation.html">simulation_t</a> <a class="code hl_function" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap::simulate</a>(<span class="keywordtype">double</span> time, uint steps, std::string method,</div>
+<div class="line"><a id="l00229" name="l00229"></a><span class="lineno">  229</span>                                   <span class="keywordtype">bool</span> particle_interaction)</div>
+<div class="line"><a id="l00230" name="l00230"></a><span class="lineno">  230</span>{</div>
+<div class="line"><a id="l00231" name="l00231"></a><span class="lineno">  231</span>    <span class="keywordtype">double</span> dt = time / (double)steps;</div>
+<div class="line"><a id="l00232" name="l00232"></a><span class="lineno">  232</span> </div>
+<div class="line"><a id="l00233" name="l00233"></a><span class="lineno">  233</span>    uint size = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div>
+<div class="line"><a id="l00234" name="l00234"></a><span class="lineno">  234</span> </div>
+<div class="line"><a id="l00235" name="l00235"></a><span class="lineno">  235</span>    <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res{<a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(size, <a class="code hl_typedef" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a>(steps)),</div>
+<div class="line"><a id="l00236" name="l00236"></a><span class="lineno">  236</span>                     <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(size, <a class="code hl_typedef" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a>(steps))};</div>
+<div class="line"><a id="l00237" name="l00237"></a><span class="lineno">  237</span> </div>
+<div class="line"><a id="l00238" name="l00238"></a><span class="lineno">  238</span>    void (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*func)(double, bool);</div>
+<div class="line"><a id="l00239" name="l00239"></a><span class="lineno">  239</span>    <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;rk4&quot;</span>) {</div>
+<div class="line"><a id="l00240" name="l00240"></a><span class="lineno">  240</span>        func = &amp;<a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a>;</div>
+<div class="line"><a id="l00241" name="l00241"></a><span class="lineno">  241</span>    } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;euler&quot;</span>) {</div>
+<div class="line"><a id="l00242" name="l00242"></a><span class="lineno">  242</span>        func = &amp;<a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>;</div>
+<div class="line"><a id="l00243" name="l00243"></a><span class="lineno">  243</span>    } <span class="keywordflow">else</span> {</div>
+<div class="line"><a id="l00244" name="l00244"></a><span class="lineno">  244</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Not a valid method!&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00245" name="l00245"></a><span class="lineno">  245</span>        abort();</div>
+<div class="line"><a id="l00246" name="l00246"></a><span class="lineno">  246</span>    }</div>
+<div class="line"><a id="l00247" name="l00247"></a><span class="lineno">  247</span> </div>
+<div class="line"><a id="l00248" name="l00248"></a><span class="lineno">  248</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; steps; j++) {</div>
+<div class="line"><a id="l00249" name="l00249"></a><span class="lineno">  249</span>        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; size; i++) {</div>
+<div class="line"><a id="l00250" name="l00250"></a><span class="lineno">  250</span>            res.r_vecs[i][j] = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec;</div>
+<div class="line"><a id="l00251" name="l00251"></a><span class="lineno">  251</span>            res.v_vecs[i][j] = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].v_vec;</div>
+<div class="line"><a id="l00252" name="l00252"></a><span class="lineno">  252</span>        }</div>
+<div class="line"><a id="l00253" name="l00253"></a><span class="lineno">  253</span>        (this-&gt;*func)(dt, particle_interaction);</div>
+<div class="line"><a id="l00254" name="l00254"></a><span class="lineno">  254</span>    }</div>
+<div class="line"><a id="l00255" name="l00255"></a><span class="lineno">  255</span> </div>
+<div class="line"><a id="l00256" name="l00256"></a><span class="lineno">  256</span>    <span class="keywordflow">return</span> res;</div>
+<div class="line"><a id="l00257" name="l00257"></a><span class="lineno">  257</span>}</div>
+<div class="line"><a id="l00258" name="l00258"></a><span class="lineno">  258</span> </div>
+<div class="line"><a id="l00259" name="l00259"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">  259</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap::write_simulation_to_dir</a>(std::string path, <span class="keywordtype">double</span> time,</div>
+<div class="line"><a id="l00260" name="l00260"></a><span class="lineno">  260</span>                                          uint steps, std::string method,</div>
+<div class="line"><a id="l00261" name="l00261"></a><span class="lineno">  261</span>                                          <span class="keywordtype">bool</span> particle_interaction)</div>
+<div class="line"><a id="l00262" name="l00262"></a><span class="lineno">  262</span>{</div>
+<div class="line"><a id="l00263" name="l00263"></a><span class="lineno">  263</span>    <span class="keywordflow">if</span> (path.back() != <span class="charliteral">&#39;/&#39;</span>) {</div>
+<div class="line"><a id="l00264" name="l00264"></a><span class="lineno">  264</span>        path += <span class="charliteral">&#39;/&#39;</span>;</div>
+<div class="line"><a id="l00265" name="l00265"></a><span class="lineno">  265</span>    }</div>
+<div class="line"><a id="l00266" name="l00266"></a><span class="lineno">  266</span>    <span class="keywordflow">if</span> (<a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path, 0777) != 0) {</div>
+<div class="line"><a id="l00267" name="l00267"></a><span class="lineno">  267</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Failed to make path&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00268" name="l00268"></a><span class="lineno">  268</span>        abort();</div>
+<div class="line"><a id="l00269" name="l00269"></a><span class="lineno">  269</span>    }</div>
+<div class="line"><a id="l00270" name="l00270"></a><span class="lineno">  270</span> </div>
+<div class="line"><a id="l00271" name="l00271"></a><span class="lineno">  271</span>    <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res =</div>
+<div class="line"><a id="l00272" name="l00272"></a><span class="lineno">  272</span>        this-&gt;<a class="code hl_function" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">simulate</a>(time, steps, method, particle_interaction);</div>
+<div class="line"><a id="l00273" name="l00273"></a><span class="lineno">  273</span> </div>
+<div class="line"><a id="l00274" name="l00274"></a><span class="lineno">  274</span>    std::ofstream ofile;</div>
+<div class="line"><a id="l00275" name="l00275"></a><span class="lineno">  275</span> </div>
+<div class="line"><a id="l00276" name="l00276"></a><span class="lineno">  276</span>    <span class="comment">// Writing each particle to its own file is independent and can be run in</span></div>
+<div class="line"><a id="l00277" name="l00277"></a><span class="lineno">  277</span>    <span class="comment">// parallel.</span></div>
+<div class="line"><a id="l00278" name="l00278"></a><span class="lineno">  278</span><span class="preprocessor">#pragma omp parallel for private(ofile)</span></div>
+<div class="line"><a id="l00279" name="l00279"></a><span class="lineno">  279</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); i++) {</div>
+<div class="line"><a id="l00280" name="l00280"></a><span class="lineno">  280</span>        ofile.open(path + <span class="stringliteral">&quot;particle_&quot;</span> + std::to_string(i) + <span class="stringliteral">&quot;_r.txt&quot;</span>);</div>
+<div class="line"><a id="l00281" name="l00281"></a><span class="lineno">  281</span>        <span class="keywordflow">for</span> (<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> &amp;vec : res.r_vecs[i]) {</div>
+<div class="line"><a id="l00282" name="l00282"></a><span class="lineno">  282</span>            ofile &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(0), 10, 8) &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00283" name="l00283"></a><span class="lineno">  283</span>                  &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(1), 10, 8) &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00284" name="l00284"></a><span class="lineno">  284</span>                  &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(2), 10, 8) &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00285" name="l00285"></a><span class="lineno">  285</span>        }</div>
+<div class="line"><a id="l00286" name="l00286"></a><span class="lineno">  286</span>        ofile.close();</div>
+<div class="line"><a id="l00287" name="l00287"></a><span class="lineno">  287</span>        ofile.open(path + <span class="stringliteral">&quot;particle_&quot;</span> + std::to_string(i) + <span class="stringliteral">&quot;_v.txt&quot;</span>);</div>
+<div class="line"><a id="l00288" name="l00288"></a><span class="lineno">  288</span>        <span class="keywordflow">for</span> (<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> &amp;vec : res.v_vecs[i]) {</div>
+<div class="line"><a id="l00289" name="l00289"></a><span class="lineno">  289</span>            ofile &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(0), 10, 8) &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00290" name="l00290"></a><span class="lineno">  290</span>                  &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(1), 10, 8) &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00291" name="l00291"></a><span class="lineno">  291</span>                  &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(2), 10, 8) &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00292" name="l00292"></a><span class="lineno">  292</span>        }</div>
+<div class="line"><a id="l00293" name="l00293"></a><span class="lineno">  293</span>        ofile.close();</div>
+<div class="line"><a id="l00294" name="l00294"></a><span class="lineno">  294</span>    }</div>
+<div class="line"><a id="l00295" name="l00295"></a><span class="lineno">  295</span>}</div>
+<div class="line"><a id="l00296" name="l00296"></a><span class="lineno">  296</span> </div>
+<div class="line"><a id="l00297" name="l00297"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">  297</a></span><span class="keywordtype">double</span> <a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap::fraction_of_particles_left</a>(<span class="keywordtype">double</span> time, uint steps,</div>
+<div class="line"><a id="l00298" name="l00298"></a><span class="lineno">  298</span>                                               std::string method,</div>
+<div class="line"><a id="l00299" name="l00299"></a><span class="lineno">  299</span>                                               <span class="keywordtype">bool</span> particle_interaction)</div>
+<div class="line"><a id="l00300" name="l00300"></a><span class="lineno">  300</span>{</div>
+<div class="line"><a id="l00301" name="l00301"></a><span class="lineno">  301</span>    <span class="keywordtype">double</span> dt = time / (double)steps;</div>
+<div class="line"><a id="l00302" name="l00302"></a><span class="lineno">  302</span> </div>
+<div class="line"><a id="l00303" name="l00303"></a><span class="lineno">  303</span>    void (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*func)(double, bool);</div>
+<div class="line"><a id="l00304" name="l00304"></a><span class="lineno">  304</span>    <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;rk4&quot;</span>) {</div>
+<div class="line"><a id="l00305" name="l00305"></a><span class="lineno">  305</span>        func = &amp;<a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a>;</div>
+<div class="line"><a id="l00306" name="l00306"></a><span class="lineno">  306</span>    } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;euler&quot;</span>) {</div>
+<div class="line"><a id="l00307" name="l00307"></a><span class="lineno">  307</span>        func = &amp;<a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>;</div>
+<div class="line"><a id="l00308" name="l00308"></a><span class="lineno">  308</span>    } <span class="keywordflow">else</span> {</div>
+<div class="line"><a id="l00309" name="l00309"></a><span class="lineno">  309</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Not a valid method!&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00310" name="l00310"></a><span class="lineno">  310</span>        abort();</div>
+<div class="line"><a id="l00311" name="l00311"></a><span class="lineno">  311</span>    }</div>
+<div class="line"><a id="l00312" name="l00312"></a><span class="lineno">  312</span> </div>
+<div class="line"><a id="l00313" name="l00313"></a><span class="lineno">  313</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; steps; j++) {</div>
+<div class="line"><a id="l00314" name="l00314"></a><span class="lineno">  314</span>        (this-&gt;*func)(dt, particle_interaction);</div>
+<div class="line"><a id="l00315" name="l00315"></a><span class="lineno">  315</span>    }</div>
+<div class="line"><a id="l00316" name="l00316"></a><span class="lineno">  316</span> </div>
+<div class="line"><a id="l00317" name="l00317"></a><span class="lineno">  317</span>    <span class="keywordtype">int</span> particles_left = 0;</div>
+<div class="line"><a id="l00318" name="l00318"></a><span class="lineno">  318</span> </div>
+<div class="line"><a id="l00319" name="l00319"></a><span class="lineno">  319</span>    <span class="comment">// A reduction is perfect here</span></div>
+<div class="line"><a id="l00320" name="l00320"></a><span class="lineno">  320</span><span class="preprocessor">#pragma omp parallel for reduction(+ : particles_left)</span></div>
+<div class="line"><a id="l00321" name="l00321"></a><span class="lineno">  321</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); i++) {</div>
+<div class="line"><a id="l00322" name="l00322"></a><span class="lineno">  322</span>        <span class="keywordflow">if</span> (arma::norm(this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec) &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>) {</div>
+<div class="line"><a id="l00323" name="l00323"></a><span class="lineno">  323</span>            particles_left++;</div>
+<div class="line"><a id="l00324" name="l00324"></a><span class="lineno">  324</span>        }</div>
+<div class="line"><a id="l00325" name="l00325"></a><span class="lineno">  325</span>    }</div>
+<div class="line"><a id="l00326" name="l00326"></a><span class="lineno">  326</span> </div>
+<div class="line"><a id="l00327" name="l00327"></a><span class="lineno">  327</span>    <span class="keywordflow">return</span> (<span class="keywordtype">double</span>)particles_left / (double)this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div>
+<div class="line"><a id="l00328" name="l00328"></a><span class="lineno">  328</span>}</div>
 <div class="ttc" id="aPenningTrap_8hpp_html"><div class="ttname"><a href="PenningTrap_8hpp.html">PenningTrap.hpp</a></div><div class="ttdoc">A class for simulating a Penning trap.</div></div>
-<div class="ttc" id="aclassParticle_html"><div class="ttname"><a href="classParticle.html">Particle</a></div><div class="ttdoc">A class that holds attributes of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00019">Particle.hpp:19</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_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_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_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_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_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_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_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_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_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="aclassParticle_html"><div class="ttname"><a href="classParticle.html">Particle</a></div><div class="ttdoc">A class that holds attributes of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00022">Particle.hpp:23</a></div></div>
+<div class="ttc" id="aclassParticle_html_a1c59101411db43624828b766f87ad460"><div class="ttname"><a href="classParticle.html#a1c59101411db43624828b766f87ad460">Particle::r_vec</a></div><div class="ttdeci">vec3 r_vec</div><div class="ttdoc">position</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00025">Particle.hpp:25</a></div></div>
+<div class="ttc" id="aclassParticle_html_a3a10400add8dd22b8031330c2aafb6fe"><div class="ttname"><a href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">Particle::v_vec</a></div><div class="ttdeci">vec3 v_vec</div><div class="ttdoc">velocity</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00026">Particle.hpp:26</a></div></div>
+<div class="ttc" id="aclassParticle_html_a566dcc1de4bdc01251776948798ea8e1"><div class="ttname"><a href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">Particle::q</a></div><div class="ttdeci">double q</div><div class="ttdoc">Charge.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00027">Particle.hpp:27</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00031">PenningTrap.hpp:32</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a0112525d9e79a472e761f8ef402a339f"><div class="ttname"><a href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">PenningTrap::particles</a></div><div class="ttdeci">std::vector&lt; Particle &gt; particles</div><div class="ttdoc">The particles in the Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00042">PenningTrap.hpp:42</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a0cac3509aa96e71a26d3b2c902e27716"><div class="ttname"><a href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">PenningTrap::B_0</a></div><div class="ttdeci">double B_0</div><div class="ttdoc">Magnetic field strength.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00037">PenningTrap.hpp:37</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a2c01108b52c8e2a003cf9170da9e7682"><div class="ttname"><a href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap::total_force_external</a></div><div class="ttdeci">vec3 total_force_external(uint i)</div><div class="ttdoc">Calculate the total external force on a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00082">PenningTrap.cpp:82</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a2f168622587709b9e3c49077f0b9a640"><div class="ttname"><a href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">PenningTrap::k_r</a></div><div class="ttdeci">sim_arr k_r</div><div class="ttdoc">A 2D vector containing all  where  is the index of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00052">PenningTrap.hpp:52</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a2fe1cefbae18fa5808155ee0d2df713c"><div class="ttname"><a href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap::total_force_particles</a></div><div class="ttdeci">vec3 total_force_particles(uint i)</div><div class="ttdoc">Calculate the total force on a particle p_i from other particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00095">PenningTrap.cpp:95</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a361f2c4862c90b5e8e2a2f50c6a95655"><div class="ttname"><a href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">PenningTrap::external_B_field</a></div><div class="ttdeci">vec3 external_B_field(vec3 r)</div><div class="ttdoc">Calculate B at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00066">PenningTrap.cpp:66</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a36946152fd951b1f7c346c51ff900d8e"><div class="ttname"><a href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a></div><div class="ttdeci">void evolve_RK4(double dt, bool particle_interaction=true)</div><div class="ttdoc">Go forward one timestep using the RK4 method.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00163">PenningTrap.cpp:163</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a3c0a44e4e0a94366ff609e81fe463fa2"><div class="ttname"><a href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap::v_func</a></div><div class="ttdeci">vec3 v_func(uint i, uint j, double dt)</div><div class="ttdoc">Helper for evolve_RK4 when calculating  values.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00020">PenningTrap.cpp:20</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a5846c8f75cdc543fd9cf0b2185a3ef22"><div class="ttname"><a href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">PenningTrap::external_E_field</a></div><div class="ttdeci">vec3 external_E_field(vec3 r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00058">PenningTrap.cpp:58</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a5b6c6d4636f3a6e279ccde59d4a345e8"><div class="ttname"><a href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a></div><div class="ttdeci">PenningTrap(double B_0=T, double V_0=(25. *V)/1000., double d=500., double t=0.)</div><div class="ttdoc">Constructor for the PenningTrap class.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00115">PenningTrap.cpp:115</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a66dfe89c68716b9502927b97f59c27d2"><div class="ttname"><a href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">PenningTrap::d</a></div><div class="ttdeci">double d</div><div class="ttdoc">Characteristic dimension.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00040">PenningTrap.hpp:40</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a6e9776ff5b149f01080800716455d7c8"><div class="ttname"><a href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap::add_particle</a></div><div class="ttdeci">void add_particle(Particle particle)</div><div class="ttdoc">Add a particle to the system.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00158">PenningTrap.cpp:158</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a715329844d75ec4c04f8391421fb4e89"><div class="ttname"><a href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">PenningTrap::V_0</a></div><div class="ttdeci">double V_0</div><div class="ttdoc">Applied potential.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00038">PenningTrap.hpp:38</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a7a1d9f0528a12308de25bc30718da20a"><div class="ttname"><a href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap::simulate</a></div><div class="ttdeci">simulation_t simulate(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate the particle system inside the Penning trap over a certain amount of time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00228">PenningTrap.cpp:228</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a7f210bb2768a5d79ced4b0df0df97598"><div class="ttname"><a href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap::force_on_particle</a></div><div class="ttdeci">vec3 force_on_particle(uint i, uint j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00071">PenningTrap.cpp:71</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a826b7fa8e709d481eb1dee7d0c2cdc08"><div class="ttname"><a href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">PenningTrap::r_func</a></div><div class="ttdeci">vec3 r_func(uint i, uint j, double dt)</div><div class="ttdoc">Helper for evolve_RK4 when calculating  values.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00039">PenningTrap.cpp:39</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a8ca4e21291f60fde619c14099d8c4e8e"><div class="ttname"><a href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">PenningTrap::t</a></div><div class="ttdeci">double t</div><div class="ttdoc">Current time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00041">PenningTrap.hpp:41</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a9a301b0540078c36697880ef204afdf3"><div class="ttname"><a href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div><div class="ttdeci">vec3 total_force(uint i)</div><div class="ttdoc">calculate the total force on a particle p_i.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00107">PenningTrap.cpp:107</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a9d1d8e90ca839b928aee1ad0cd4aff43"><div class="ttname"><a href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">PenningTrap::set_pertubation</a></div><div class="ttdeci">void set_pertubation(double f, double omega_V)</div><div class="ttdoc">Time dependent perturbation to V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00141">PenningTrap.cpp:141</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_aaee129f177657455348d0c8ae1441dea"><div class="ttname"><a href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap::reinitialize</a></div><div class="ttdeci">void reinitialize(double f, double omega_V, double t=0.)</div><div class="ttdoc">Give all particles new positions and velocities, and change t and V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00148">PenningTrap.cpp:148</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ab9ea97a406534bbe621a95215144875e"><div class="ttname"><a href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a></div><div class="ttdeci">void evolve_forward_euler(double dt, bool particle_interaction=true)</div><div class="ttdoc">Go forward one timestep using the forward Euler method.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00201">PenningTrap.cpp:201</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ac529aa26c288f34eae184a67e6bac41f"><div class="ttname"><a href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap::fraction_of_particles_left</a></div><div class="ttdeci">double fraction_of_particles_left(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and calculate what fraction of particles are still left inside the Penning trap after the si...</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00297">PenningTrap.cpp:297</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ad8bc4df7ab3eed53b16cfdff38e7760b"><div class="ttname"><a href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap::write_simulation_to_dir</a></div><div class="ttdeci">void write_simulation_to_dir(std::string path, double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and write the displacement of all particles to files.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00259">PenningTrap.cpp:259</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ae915f6ad0eef1fb46530e836b6e071e5"><div class="ttname"><a href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">PenningTrap::perturbation</a></div><div class="ttdeci">std::function&lt; double(double)&gt; perturbation</div><div class="ttdoc">Time-dependent perturbation.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00039">PenningTrap.hpp:39</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ae9b5afdaa5cd366e94bd294452a1eed4"><div class="ttname"><a href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">PenningTrap::k_v</a></div><div class="ttdeci">sim_arr k_v</div><div class="ttdoc">A 2D vector containing all  where  is the index of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00047">PenningTrap.hpp:47</a></div></div>
+<div class="ttc" id="aconstants_8hpp_html_a4e451456ad7e9276ed0afa42826e7ccb"><div class="ttname"><a href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">K_E</a></div><div class="ttdeci">#define K_E</div><div class="ttdoc">Coulomb constant. unit: .</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00017">constants.hpp:17</a></div></div>
+<div class="ttc" id="astructsimulation_html"><div class="ttname"><a href="structsimulation.html">simulation</a></div><div class="ttdoc">Typedef for PenningTrap::simulation return value.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00040">typedefs.hpp:40</a></div></div>
+<div class="ttc" id="atypedefs_8hpp_html"><div class="ttname"><a href="typedefs_8hpp.html">typedefs.hpp</a></div><div class="ttdoc">Useful typedefs for cleaner code.</div></div>
+<div class="ttc" id="atypedefs_8hpp_html_a3bdfb73a02f88ae32b6128ef747c4aea"><div class="ttname"><a href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; vec3</div><div class="ttdoc">Typedef for a fixed 3d arma vector.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00023">typedefs.hpp:23</a></div></div>
+<div class="ttc" id="atypedefs_8hpp_html_a46482a2697556c00556c9d73f461784f"><div class="ttname"><a href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a></div><div class="ttdeci">std::vector&lt; vec3 &gt; sim_cols</div><div class="ttdoc">Typedef for the column of the result vector from simulating particles.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00028">typedefs.hpp:28</a></div></div>
+<div class="ttc" id="atypedefs_8hpp_html_aec69d34220fff45de238b9e01f2686af"><div class="ttname"><a href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a></div><div class="ttdeci">std::vector&lt; sim_cols &gt; sim_arr</div><div class="ttdoc">Typedef for the result of the simulate method.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00036">typedefs.hpp:36</a></div></div>
+<div class="ttc" id="autils_8hpp_html_a6fdd7217b750aff5b6295ece7cbdeffa"><div class="ttname"><a href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a></div><div class="ttdeci">bool mkpath(std::string path, int mode=0777)</div><div class="ttdoc">Make path given.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00072">utils.cpp:72</a></div></div>
+<div class="ttc" id="autils_8hpp_html_adfb618b2fdff47ef30a4a2b62c04f384"><div class="ttname"><a href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a></div><div class="ttdeci">std::string scientific_format(double d, int width=20, int prec=10)</div><div class="ttdoc">Turns a double into a string written in scientific format.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00015">utils.cpp:15</a></div></div>
 </div><!-- fragment --></div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->

docs/PenningTrap_8hpp.html

@@ -107,8 +107,11 @@ $(document).ready(function(){initNavTree('PenningTrap_8hpp.html',''); initResiza
 <p>A class for simulating a Penning trap.  
 <a href="#details">More...</a></p>
 <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="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>
 <p><a href="PenningTrap_8hpp_source.html">Go to the source code of this file.</a></p>
 <table class="memberdecls">
@@ -123,7 +126,7 @@ Classes</h2></td></tr>
 <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>0.1</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#_bug000003">Bug:</a></b></dt><dd>No known bugs </dd></dl>
 
 <p class="definition">Definition in file <a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>.</p>

docs/PenningTrap_8hpp_source.html

@@ -106,59 +106,117 @@ $(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="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="l00016" name="l00016"></a><span class="lineno">   16</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="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> </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="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="l00026" name="l00026"></a><span class="lineno">   26</span><span class="keyword">private</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="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="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="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="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="keyword">public</span>:</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="l00036" name="l00036"></a><span class="lineno">   36</span> </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="l00040" name="l00040"></a><span class="lineno">   40</span> </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="l00044" name="l00044"></a><span class="lineno">   44</span> </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="l00019" name="l00019"></a><span class="lineno">   19</span><span class="preprocessor">#include &quot;<a class="code" href="constants_8hpp.html">constants.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span><span class="preprocessor">#include &quot;<a class="code" href="typedefs_8hpp.html">typedefs.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span><span class="preprocessor">#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">#pragma omp declare reduction(+ : vec3 : omp_out += omp_in)                    \</span></div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span><span class="preprocessor">    initializer(omp_priv = omp_orig)</span></div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span> </div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"><a class="line" href="classPenningTrap.html">   31</a></span><span class="keyword">class </span><a class="code hl_class" href="classPenningTrap.html">PenningTrap</a></div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>{</div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae">   35</a></span>    <span class="keyword">friend</span> <span class="keyword">class </span><a class="code hl_class" href="classPenningTrapTest.html">PenningTrapTest</a>;</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span><span class="keyword">private</span>:</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">   37</a></span>    <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>;                                 </div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">   38</a></span>    <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a>;                                 </div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">   39</a></span>    std::function&lt;double(<span class="keywordtype">double</span>)&gt; <a class="code hl_variable" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</a>; </div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">   40</a></span>    <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;                                   </div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">   41</a></span>    <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>;                                   </div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">   42</a></span>    std::vector&lt;Particle&gt; <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>; </div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span> </div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">   47</a></span>    <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a> <a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>;</div>
 <div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span> </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="l00055" name="l00055"></a><span class="lineno">   55</span> </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="l00062" name="l00062"></a><span class="lineno">   62</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="l00066" name="l00066"></a><span class="lineno">   66</span> </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="l00070" name="l00070"></a><span class="lineno">   70</span> </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="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="l00080" name="l00080"></a><span class="lineno">   80</span><span class="preprocessor">#endif</span></div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">   52</a></span>    <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a> <a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>;</div>
+<div class="line"><a id="l00053" name="l00053"></a><span class="lineno">   53</span> </div>
+<div class="line"><a id="l00064" name="l00064"></a><span class="lineno">   64</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">v_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt);</div>
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+<div class="line"><a id="l00076" name="l00076"></a><span class="lineno">   76</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">r_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt);</div>
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+<div class="line"><a id="l00085" name="l00085"></a><span class="lineno">   85</span> </div>
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+<div class="line"><a id="l00105" name="l00105"></a><span class="lineno">  105</span> </div>
+<div class="line"><a id="l00115" name="l00115"></a><span class="lineno">  115</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">total_force_external</a>(uint i);</div>
+<div class="line"><a id="l00116" name="l00116"></a><span class="lineno">  116</span> </div>
+<div class="line"><a id="l00124" name="l00124"></a><span class="lineno">  124</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">total_force_particles</a>(uint i);</div>
+<div class="line"><a id="l00125" name="l00125"></a><span class="lineno">  125</span> </div>
+<div class="line"><a id="l00132" name="l00132"></a><span class="lineno">  132</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">total_force</a>(uint i);</div>
+<div class="line"><a id="l00133" name="l00133"></a><span class="lineno">  133</span> </div>
+<div class="line"><a id="l00134" name="l00134"></a><span class="lineno">  134</span><span class="keyword">public</span>:</div>
+<div class="line"><a id="l00142" name="l00142"></a><span class="lineno">  142</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a> = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> = (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>) / 1000., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> = 500.,</div>
+<div class="line"><a id="l00143" name="l00143"></a><span class="lineno">  143</span>                <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
+<div class="line"><a id="l00144" name="l00144"></a><span class="lineno">  144</span> </div>
+<div class="line"><a id="l00153" name="l00153"></a><span class="lineno">  153</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(uint i, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a> = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> = (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>) / 1000.,</div>
+<div class="line"><a id="l00154" name="l00154"></a><span class="lineno">  154</span>                <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> = 500., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
+<div class="line"><a id="l00155" name="l00155"></a><span class="lineno">  155</span> </div>
+<div class="line"><a id="l00164" name="l00164"></a><span class="lineno">  164</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(std::vector&lt;Particle&gt; <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a> = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>,</div>
+<div class="line"><a id="l00165" name="l00165"></a><span class="lineno">  165</span>                <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> = (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>) / 1000., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> = 500., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
+<div class="line"><a id="l00166" name="l00166"></a><span class="lineno">  166</span> </div>
+<div class="line"><a id="l00172" name="l00172"></a><span class="lineno">  172</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">set_pertubation</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V);</div>
+<div class="line"><a id="l00173" name="l00173"></a><span class="lineno">  173</span> </div>
+<div class="line"><a id="l00180" name="l00180"></a><span class="lineno">  180</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
+<div class="line"><a id="l00181" name="l00181"></a><span class="lineno">  181</span> </div>
+<div class="line"><a id="l00186" name="l00186"></a><span class="lineno">  186</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a> particle);</div>
+<div class="line"><a id="l00187" name="l00187"></a><span class="lineno">  187</span> </div>
+<div class="line"><a id="l00193" name="l00193"></a><span class="lineno">  193</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">evolve_RK4</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
+<div class="line"><a id="l00194" name="l00194"></a><span class="lineno">  194</span> </div>
+<div class="line"><a id="l00200" name="l00200"></a><span class="lineno">  200</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">evolve_forward_euler</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
+<div class="line"><a id="l00201" name="l00201"></a><span class="lineno">  201</span> </div>
+<div class="line"><a id="l00212" name="l00212"></a><span class="lineno">  212</span>    <a class="code hl_struct" href="structsimulation.html">simulation_t</a> <a class="code hl_function" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">simulate</a>(<span class="keywordtype">double</span> time, uint steps, std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
+<div class="line"><a id="l00213" name="l00213"></a><span class="lineno">  213</span>                          <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
+<div class="line"><a id="l00214" name="l00214"></a><span class="lineno">  214</span> </div>
+<div class="line"><a id="l00223" name="l00223"></a><span class="lineno">  223</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(std::string path, <span class="keywordtype">double</span> time, uint steps,</div>
+<div class="line"><a id="l00224" name="l00224"></a><span class="lineno">  224</span>                                 std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
+<div class="line"><a id="l00225" name="l00225"></a><span class="lineno">  225</span>                                 <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
+<div class="line"><a id="l00226" name="l00226"></a><span class="lineno">  226</span> </div>
+<div class="line"><a id="l00237" name="l00237"></a><span class="lineno">  237</span>    <span class="keywordtype">double</span> <a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(<span class="keywordtype">double</span> time, uint steps,</div>
+<div class="line"><a id="l00238" name="l00238"></a><span class="lineno">  238</span>                                      std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
+<div class="line"><a id="l00239" name="l00239"></a><span class="lineno">  239</span>                                      <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
+<div class="line"><a id="l00240" name="l00240"></a><span class="lineno">  240</span> </div>
+<div class="line"><a id="l00241" name="l00241"></a><span class="lineno">  241</span>};</div>
+<div class="line"><a id="l00242" name="l00242"></a><span class="lineno">  242</span> </div>
+<div class="line"><a id="l00243" name="l00243"></a><span class="lineno">  243</span><span class="preprocessor">#endif</span></div>
 <div class="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="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_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_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_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_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_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_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_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_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_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_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_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_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_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="aclassParticle_html"><div class="ttname"><a href="classParticle.html">Particle</a></div><div class="ttdoc">A class that holds attributes of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00022">Particle.hpp:23</a></div></div>
+<div class="ttc" id="aclassPenningTrapTest_html"><div class="ttname"><a href="classPenningTrapTest.html">PenningTrapTest</a></div><div class="ttdoc">Test class for the Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="test__suite_8cpp_source.html#l00023">test_suite.cpp:24</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00031">PenningTrap.hpp:32</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a0112525d9e79a472e761f8ef402a339f"><div class="ttname"><a href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">PenningTrap::particles</a></div><div class="ttdeci">std::vector&lt; Particle &gt; particles</div><div class="ttdoc">The particles in the Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00042">PenningTrap.hpp:42</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a0cac3509aa96e71a26d3b2c902e27716"><div class="ttname"><a href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">PenningTrap::B_0</a></div><div class="ttdeci">double B_0</div><div class="ttdoc">Magnetic field strength.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00037">PenningTrap.hpp:37</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a2c01108b52c8e2a003cf9170da9e7682"><div class="ttname"><a href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap::total_force_external</a></div><div class="ttdeci">vec3 total_force_external(uint i)</div><div class="ttdoc">Calculate the total external force on a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00082">PenningTrap.cpp:82</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a2f168622587709b9e3c49077f0b9a640"><div class="ttname"><a href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">PenningTrap::k_r</a></div><div class="ttdeci">sim_arr k_r</div><div class="ttdoc">A 2D vector containing all  where  is the index of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00052">PenningTrap.hpp:52</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a2fe1cefbae18fa5808155ee0d2df713c"><div class="ttname"><a href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap::total_force_particles</a></div><div class="ttdeci">vec3 total_force_particles(uint i)</div><div class="ttdoc">Calculate the total force on a particle p_i from other particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00095">PenningTrap.cpp:95</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a361f2c4862c90b5e8e2a2f50c6a95655"><div class="ttname"><a href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">PenningTrap::external_B_field</a></div><div class="ttdeci">vec3 external_B_field(vec3 r)</div><div class="ttdoc">Calculate B at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00066">PenningTrap.cpp:66</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a36946152fd951b1f7c346c51ff900d8e"><div class="ttname"><a href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a></div><div class="ttdeci">void evolve_RK4(double dt, bool particle_interaction=true)</div><div class="ttdoc">Go forward one timestep using the RK4 method.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00163">PenningTrap.cpp:163</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a3c0a44e4e0a94366ff609e81fe463fa2"><div class="ttname"><a href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap::v_func</a></div><div class="ttdeci">vec3 v_func(uint i, uint j, double dt)</div><div class="ttdoc">Helper for evolve_RK4 when calculating  values.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00020">PenningTrap.cpp:20</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a5846c8f75cdc543fd9cf0b2185a3ef22"><div class="ttname"><a href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">PenningTrap::external_E_field</a></div><div class="ttdeci">vec3 external_E_field(vec3 r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00058">PenningTrap.cpp:58</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a66dfe89c68716b9502927b97f59c27d2"><div class="ttname"><a href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">PenningTrap::d</a></div><div class="ttdeci">double d</div><div class="ttdoc">Characteristic dimension.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00040">PenningTrap.hpp:40</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a6e9776ff5b149f01080800716455d7c8"><div class="ttname"><a href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap::add_particle</a></div><div class="ttdeci">void add_particle(Particle particle)</div><div class="ttdoc">Add a particle to the system.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00158">PenningTrap.cpp:158</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a715329844d75ec4c04f8391421fb4e89"><div class="ttname"><a href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">PenningTrap::V_0</a></div><div class="ttdeci">double V_0</div><div class="ttdoc">Applied potential.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00038">PenningTrap.hpp:38</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a7a1d9f0528a12308de25bc30718da20a"><div class="ttname"><a href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap::simulate</a></div><div class="ttdeci">simulation_t simulate(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate the particle system inside the Penning trap over a certain amount of time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00228">PenningTrap.cpp:228</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a7f210bb2768a5d79ced4b0df0df97598"><div class="ttname"><a href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap::force_on_particle</a></div><div class="ttdeci">vec3 force_on_particle(uint i, uint j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00071">PenningTrap.cpp:71</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a826b7fa8e709d481eb1dee7d0c2cdc08"><div class="ttname"><a href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">PenningTrap::r_func</a></div><div class="ttdeci">vec3 r_func(uint i, uint j, double dt)</div><div class="ttdoc">Helper for evolve_RK4 when calculating  values.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00039">PenningTrap.cpp:39</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a8ca4e21291f60fde619c14099d8c4e8e"><div class="ttname"><a href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">PenningTrap::t</a></div><div class="ttdeci">double t</div><div class="ttdoc">Current time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00041">PenningTrap.hpp:41</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a9a301b0540078c36697880ef204afdf3"><div class="ttname"><a href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div><div class="ttdeci">vec3 total_force(uint i)</div><div class="ttdoc">calculate the total force on a particle p_i.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00107">PenningTrap.cpp:107</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a9d1d8e90ca839b928aee1ad0cd4aff43"><div class="ttname"><a href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">PenningTrap::set_pertubation</a></div><div class="ttdeci">void set_pertubation(double f, double omega_V)</div><div class="ttdoc">Time dependent perturbation to V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00141">PenningTrap.cpp:141</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_aaee129f177657455348d0c8ae1441dea"><div class="ttname"><a href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap::reinitialize</a></div><div class="ttdeci">void reinitialize(double f, double omega_V, double t=0.)</div><div class="ttdoc">Give all particles new positions and velocities, and change t and V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00148">PenningTrap.cpp:148</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ab9ea97a406534bbe621a95215144875e"><div class="ttname"><a href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a></div><div class="ttdeci">void evolve_forward_euler(double dt, bool particle_interaction=true)</div><div class="ttdoc">Go forward one timestep using the forward Euler method.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00201">PenningTrap.cpp:201</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ac529aa26c288f34eae184a67e6bac41f"><div class="ttname"><a href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap::fraction_of_particles_left</a></div><div class="ttdeci">double fraction_of_particles_left(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and calculate what fraction of particles are still left inside the Penning trap after the si...</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00297">PenningTrap.cpp:297</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ad8bc4df7ab3eed53b16cfdff38e7760b"><div class="ttname"><a href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap::write_simulation_to_dir</a></div><div class="ttdeci">void write_simulation_to_dir(std::string path, double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and write the displacement of all particles to files.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00259">PenningTrap.cpp:259</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ae915f6ad0eef1fb46530e836b6e071e5"><div class="ttname"><a href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">PenningTrap::perturbation</a></div><div class="ttdeci">std::function&lt; double(double)&gt; perturbation</div><div class="ttdoc">Time-dependent perturbation.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00039">PenningTrap.hpp:39</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ae9b5afdaa5cd366e94bd294452a1eed4"><div class="ttname"><a href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">PenningTrap::k_v</a></div><div class="ttdeci">sim_arr k_v</div><div class="ttdoc">A 2D vector containing all  where  is the index of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00047">PenningTrap.hpp:47</a></div></div>
 <div class="ttc" id="aconstants_8hpp_html"><div class="ttname"><a href="constants_8hpp.html">constants.hpp</a></div><div class="ttdoc">Library of constants.</div></div>
-<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_a0acb682b8260ab1c60b918599864e2e5"><div class="ttname"><a href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a></div><div class="ttdeci">#define T</div><div class="ttdoc">1 Tesla. unit:</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00021">constants.hpp:21</a></div></div>
+<div class="ttc" id="aconstants_8hpp_html_af40a326b23c68a27cebe60f16634a2cb"><div class="ttname"><a href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a></div><div class="ttdeci">#define V</div><div class="ttdoc">1 Volt. unit:</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00025">constants.hpp:25</a></div></div>
+<div class="ttc" id="astructsimulation_html"><div class="ttname"><a href="structsimulation.html">simulation</a></div><div class="ttdoc">Typedef for PenningTrap::simulation return value.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00040">typedefs.hpp:40</a></div></div>
+<div class="ttc" id="atypedefs_8hpp_html"><div class="ttname"><a href="typedefs_8hpp.html">typedefs.hpp</a></div><div class="ttdoc">Useful typedefs for cleaner code.</div></div>
+<div class="ttc" id="atypedefs_8hpp_html_a3bdfb73a02f88ae32b6128ef747c4aea"><div class="ttname"><a href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; vec3</div><div class="ttdoc">Typedef for a fixed 3d arma vector.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00023">typedefs.hpp:23</a></div></div>
+<div class="ttc" id="atypedefs_8hpp_html_aec69d34220fff45de238b9e01f2686af"><div class="ttname"><a href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a></div><div class="ttdeci">std::vector&lt; sim_cols &gt; sim_arr</div><div class="ttdoc">Typedef for the result of the simulate method.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00036">typedefs.hpp:36</a></div></div>
+<div class="ttc" id="autils_8hpp_html"><div class="ttname"><a href="utils_8hpp.html">utils.hpp</a></div><div class="ttdoc">Function prototypes and macros that are useful.</div></div>
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+  <td id="projectalign">
+   <div id="projectname">Penning Trap Simulation
+   </div>
+   <div id="projectbrief">Simulate particle behavior inside a Penning Trap</div>
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+  <div class="headertitle"><div class="title">animate_100_particles.py</div></div>
+</div><!--header-->
+<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><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}_r.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>
+</div><!-- fragment --></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_634e799a3947388232110823971192a8.html">scripts</a></li><li class="navelem"><b>animate_100_particles.py</b></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.6 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/annotated.html

@@ -105,6 +105,8 @@ $(document).ready(function(){initNavTree('annotated.html',''); initResizable();
 <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_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">Test class for the Penning trap </td></tr>
+<tr id="row_3_" 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="structsimulation.html" target="_self">simulation</a></td><td class="desc">Typedef for PenningTrap::simulation return value </td></tr>
 </table>
 </div><!-- directory -->
 </div><!-- contents -->

docs/annotated_dup.js

@@ -1,5 +1,7 @@
 var annotated_dup =
 [
     [ "Particle", "classParticle.html", "classParticle" ],
-    [ "PenningTrap", "classPenningTrap.html", "classPenningTrap" ]
+    [ "PenningTrap", "classPenningTrap.html", "classPenningTrap" ],
+    [ "PenningTrapTest", "classPenningTrapTest.html", "classPenningTrapTest" ],
+    [ "simulation", "structsimulation.html", null ]
 ];

docs/bug.html

@@ -105,21 +105,23 @@ $(document).ready(function(){initNavTree('bug.html',''); initResizable(); });
 <dt>File <a class="el" href="constants_8hpp.html">constants.hpp</a>  </dt>
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 <dt>File <a class="el" href="main_8cpp.html">main.cpp</a>  </dt>
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-<dt>File <a class="el" href="Particle_8cpp.html">Particle.cpp</a>  </dt>
 <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>
 <dd><a class="anchor" id="_bug000002"></a>No known bugs  </dd>
 <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>
 <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>
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 <dd><a class="anchor" id="_bug000009"></a>No known bugs  </dd>
-<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>
 <dd><a class="anchor" id="_bug000004"></a>No known bugs  </dd>
+<dt>File <a class="el" href="utils_8cpp.html">utils.cpp</a>  </dt>
+<dd><a class="anchor" id="_bug000010"></a>No known bugs  </dd>
+<dt>File <a class="el" href="utils_8hpp.html">utils.hpp</a>  </dt>
+<dd><a class="anchor" id="_bug000005"></a>No known bugs </dd>
 </dl>
 </div></div><!-- contents -->
 </div><!-- PageDoc -->

docs/classParticle-members.html

@@ -105,11 +105,11 @@ $(document).ready(function(){initNavTree('classParticle.html',''); initResizable
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+  <tr class="odd"><td class="entry"><a class="el" href="classParticle.html#af1d7535fb8311eaa77d2b7b345882ec4">Particle</a>(vec3 r_vec, vec3 v_vec, double q=CA_CHARGE, double m=CA_MASS)</td><td class="entry"><a class="el" href="classParticle.html">Particle</a></td><td class="entry"></td></tr>
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+  <tr class="even"><td class="entry"><a class="el" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_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#a3a10400add8dd22b8031330c2aafb6fe">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>
 </table></div><!-- contents -->
 </div><!-- doc-content -->
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docs/classParticle.html

@@ -114,24 +114,24 @@ $(document).ready(function(){initNavTree('classParticle.html',''); initResizable
 <table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
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-<tr class="separator:a00e108823877a25513ccae7cac011b4c"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:af1d7535fb8311eaa77d2b7b345882ec4"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#af1d7535fb8311eaa77d2b7b345882ec4">Particle</a> (<a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="el" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>, <a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="el" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a>, double <a class="el" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>=<a class="el" href="constants_8hpp.html#af7602a3a314957137ad1cd719aa23789">CA_CHARGE</a>, double <a class="el" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>=<a class="el" href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">CA_MASS</a>)</td></tr>
+<tr class="memdesc:af1d7535fb8311eaa77d2b7b345882ec4"><td class="mdescLeft">&#160;</td><td class="mdescRight">Initialize the particle.  <br /></td></tr>
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 </table><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pri-attribs" name="pri-attribs"></a>
 Private Attributes</h2></td></tr>
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+<tr class="memdesc:a1c59101411db43624828b766f87ad460"><td class="mdescLeft">&#160;</td><td class="mdescRight">position  <br /></td></tr>
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+<tr class="memdesc:a3a10400add8dd22b8031330c2aafb6fe"><td class="mdescLeft">&#160;</td><td class="mdescRight">velocity  <br /></td></tr>
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@@ -142,10 +142,10 @@ Friends</h2></td></tr>
 <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>
 
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+<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>
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-<h2 class="memtitle"><span class="permalink"><a href="#a00e108823877a25513ccae7cac011b4c">&#9670;&#160;</a></span>Particle()</h2>
+<a id="af1d7535fb8311eaa77d2b7b345882ec4" name="af1d7535fb8311eaa77d2b7b345882ec4"></a>
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           <td class="memname">Particle::Particle </td>
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-          <td class="paramname"><em>q</em>, </td>
-        </tr>
-        <tr>
-          <td class="paramkey"></td>
-          <td></td>
-          <td class="paramtype">double&#160;</td>
-          <td class="paramname"><em>m</em>, </td>
-        </tr>
-        <tr>
-          <td class="paramkey"></td>
-          <td></td>
-          <td class="paramtype">arma::vec::fixed&lt; 3 &gt;&#160;</td>
+          <td class="paramtype"><a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>&#160;</td>
           <td class="paramname"><em>r_vec</em>, </td>
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           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">arma::vec::fixed&lt; 3 &gt;&#160;</td>
-          <td class="paramname"><em>v_vec</em>&#160;</td>
+          <td class="paramtype"><a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>&#160;</td>
+          <td class="paramname"><em>v_vec</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double&#160;</td>
+          <td class="paramname"><em>q</em> = <code><a class="el" href="constants_8hpp.html#af7602a3a314957137ad1cd719aa23789">CA_CHARGE</a></code>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">double&#160;</td>
+          <td class="paramname"><em>m</em> = <code><a class="el" href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">CA_MASS</a></code>&#160;</td>
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 <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>
+  </table>
+  </dd>
+</dl>
 
-<p class="definition">Definition at line <a class="el" href="Particle_8cpp_source.html#l00016">16</a> of file <a class="el" href="Particle_8cpp_source.html">Particle.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="Particle_8cpp_source.html#l00015">15</a> of file <a class="el" href="Particle_8cpp_source.html">Particle.cpp</a>.</p>
 
 </div>
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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 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#l00045">45</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
 
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+<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00028">28</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
 
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 <p>Charge. </p>
 
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+<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00027">27</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
 
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 <p>position </p>
 
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+<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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 <p>velocity </p>
 
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+<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00026">26</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
 
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docs/classParticle.js

@@ -1,9 +1,9 @@
 var classParticle =
 [
-    [ "Particle", "classParticle.html#a00e108823877a25513ccae7cac011b4c", null ],
+    [ "Particle", "classParticle.html#af1d7535fb8311eaa77d2b7b345882ec4", null ],
     [ "PenningTrap", "classParticle.html#aa797d319549dc2a0beb06cdbfd430232", null ],
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     [ "q", "classParticle.html#a566dcc1de4bdc01251776948798ea8e1", null ],
-    [ "r_vec", "classParticle.html#acf1a0f3c978b06d76df5bb4279594467", null ],
-    [ "v_vec", "classParticle.html#a4a5d22c7aeca66f67d083f270cba25df", null ]
+    [ "r_vec", "classParticle.html#a1c59101411db43624828b766f87ad460", null ],
+    [ "v_vec", "classParticle.html#a3a10400add8dd22b8031330c2aafb6fe", null ]
 ];

docs/classPenningTrap-members.html

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   <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965">evolve_forward_euler</a>(double dt)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9">evolve_RK4</a>(double dt)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">external_B_field</a>(arma::vec r)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">external_E_field</a>(arma::vec r)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">force_on_particle</a>(int i, int j)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560">PenningTrap</a>(double B_0=T, double V_0=25.*V/1000., double d=500.)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">total_force</a>(int i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">total_force_external</a>(int i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">total_force_particles</a>(int i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">evolve_forward_euler</a>(double dt, bool particle_interaction=true)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">evolve_RK4</a>(double dt, bool particle_interaction=true)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">external_B_field</a>(vec3 r)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">external_E_field</a>(vec3 r)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">force_on_particle</a>(uint i, uint j)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">v_func</a>(uint i, uint j, double dt)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
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docs/classPenningTrap.js

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+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrapTest.html#ad668d7d875bdc1909a42426bf9dead9e">test_external_B_field</a>()</td><td class="entry"><a class="el" href="classPenningTrapTest.html">PenningTrapTest</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
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+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="classPenningTrapTest-members.html">List of all members</a>  </div>
+  <div class="headertitle"><div class="title">PenningTrapTest Class Reference</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>Test class for the Penning trap.  
+ <a href="classPenningTrapTest.html#details">More...</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
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+<tr class="memitem:a5f4f0b150e54ce463bb29f76d49883f9"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPenningTrapTest.html#a5f4f0b150e54ce463bb29f76d49883f9">test_force_on_particle</a> ()</td></tr>
+<tr class="memdesc:a5f4f0b150e54ce463bb29f76d49883f9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Test that the force between particles gives expected results.  <br /></td></tr>
+<tr class="separator:a5f4f0b150e54ce463bb29f76d49883f9"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ae6d0c8e0d80338fb7c7edefc97331046"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPenningTrapTest.html#ae6d0c8e0d80338fb7c7edefc97331046">test_total_force_external</a> ()</td></tr>
+<tr class="memdesc:ae6d0c8e0d80338fb7c7edefc97331046"><td class="mdescLeft">&#160;</td><td class="mdescRight">Test that the total external force returns expected results.  <br /></td></tr>
+<tr class="separator:ae6d0c8e0d80338fb7c7edefc97331046"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a68449d508e66205bc8b27fa5f60db508"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPenningTrapTest.html#a68449d508e66205bc8b27fa5f60db508">test_total_force_particles</a> ()</td></tr>
+<tr class="memdesc:a68449d508e66205bc8b27fa5f60db508"><td class="mdescLeft">&#160;</td><td class="mdescRight">Test that the total force of all particles on a single particle returns expected results.  <br /></td></tr>
+<tr class="separator:a68449d508e66205bc8b27fa5f60db508"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><p>Test class for the Penning trap. </p>
+
+<p class="definition">Definition at line <a class="el" href="test__suite_8cpp_source.html#l00023">23</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
+</div><h2 class="groupheader">Member Function Documentation</h2>
+<a id="ad668d7d875bdc1909a42426bf9dead9e" name="ad668d7d875bdc1909a42426bf9dead9e"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ad668d7d875bdc1909a42426bf9dead9e">&#9670;&#160;</a></span>test_external_B_field()</h2>
+
+<div class="memitem">
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+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">void PenningTrapTest::test_external_B_field </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">inline</span></span>  </td>
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+<p>Test that the external B field gives correct values. </p>
+
+<p class="definition">Definition at line <a class="el" href="test__suite_8cpp_source.html#l00066">66</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a6a303be62039ca2ecccd8252744d4dc8" name="a6a303be62039ca2ecccd8252744d4dc8"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a6a303be62039ca2ecccd8252744d4dc8">&#9670;&#160;</a></span>test_external_E_field()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">void PenningTrapTest::test_external_E_field </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Test that the external E field gives correct values. </p>
+
+<p class="definition">Definition at line <a class="el" href="test__suite_8cpp_source.html#l00028">28</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a5f4f0b150e54ce463bb29f76d49883f9" name="a5f4f0b150e54ce463bb29f76d49883f9"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a5f4f0b150e54ce463bb29f76d49883f9">&#9670;&#160;</a></span>test_force_on_particle()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">void PenningTrapTest::test_force_on_particle </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Test that the force between particles gives expected results. </p>
+
+<p class="definition">Definition at line <a class="el" href="test__suite_8cpp_source.html#l00080">80</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
+
+</div>
+</div>
+<a id="ae6d0c8e0d80338fb7c7edefc97331046" name="ae6d0c8e0d80338fb7c7edefc97331046"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ae6d0c8e0d80338fb7c7edefc97331046">&#9670;&#160;</a></span>test_total_force_external()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">void PenningTrapTest::test_total_force_external </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Test that the total external force returns expected results. </p>
+
+<p class="definition">Definition at line <a class="el" href="test__suite_8cpp_source.html#l00107">107</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a68449d508e66205bc8b27fa5f60db508" name="a68449d508e66205bc8b27fa5f60db508"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a68449d508e66205bc8b27fa5f60db508">&#9670;&#160;</a></span>test_total_force_particles()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">void PenningTrapTest::test_total_force_particles </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Test that the total force of all particles on a single particle returns expected results. </p>
+
+<p class="definition">Definition at line <a class="el" href="test__suite_8cpp_source.html#l00122">122</a> of file <a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>src/<a class="el" href="test__suite_8cpp_source.html">test_suite.cpp</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
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docs/index.html

@@ -101,8 +101,68 @@ $(document).ready(function(){initNavTree('index.html',''); initResizable(); });
   <div class="headertitle"><div class="title">Penning trap simulation </div></div>
 </div><!--header-->
 <div class="contents">
-<div class="textblock"><p><a class="anchor" id="md_README"></a> </p>
+<div class="textblock"><p><a class="anchor" id="md_README"></a> </p><div class="image">
+<img src="100_particles.gif" alt=""/>
+</div>
+    <p><a href="https://github.uio.no/FYS3150-G2-2023/Project-3">Repo</a></p>
+<p><a href="https://pages.github.uio.no/FYS3150-G2-2023/Project-3/">Documentation</a></p>
 <h1><a class="anchor" id="autotoc_md1"></a>
+Requirements</h1>
+<h2><a class="anchor" id="autotoc_md2"></a>
+Operating systems</h2>
+<ul>
+<li>Linux<ul>
+<li>Has been tested on <a href="https://fedoraproject.org/">Fedora 38</a></li>
+<li>Will most likely work on other Linux distributions</li>
+</ul>
+</li>
+<li>MacOS<ul>
+<li>Might work, but hasn't been tested</li>
+</ul>
+</li>
+<li>Windows<ul>
+<li>Will most likely not work</li>
+</ul>
+</li>
+</ul>
+<h2><a class="anchor" id="autotoc_md3"></a>
+Libraries</h2>
+<ul>
+<li>Python<ul>
+<li><a href="https://matplotlib.org/">matplotlib</a></li>
+<li><a href="https://numpy.org/">numpy</a></li>
+</ul>
+</li>
+<li>C++<ul>
+<li><a href="https://www.openmp.org/">openmp</a></li>
+<li><a href="https://arma.sourceforge.net/">armadillo</a></li>
+</ul>
+</li>
+</ul>
+<h1><a class="anchor" id="autotoc_md4"></a>
+Compiling</h1>
+<p>Compiling is as easy as running this command while being inside the src directory:</p>
+<div class="fragment"><div class="line">make</div>
+</div><!-- fragment --><h1><a class="anchor" id="autotoc_md5"></a>
+Running programs</h1>
+<h2><a class="anchor" id="autotoc_md6"></a>
+C++ binaries</h2>
+<p>To run <b>main</b> or <b>test_suite</b>, just run this command while being inside src:</p>
+<div class="fragment"><div class="line">./&lt;program-name&gt;</div>
+</div><!-- fragment --><h2><a class="anchor" id="autotoc_md7"></a>
+Python scripts</h2>
+<h3><a class="anchor" id="autotoc_md8"></a>
+Install libraries</h3>
+<p>Before running the scripts, make sure that all libraries are installed. Using pip, you can install all requirements like this:</p>
+<div class="fragment"><div class="line">pip install -r requirements.txt</div>
+</div><!-- fragment --><p>This recursively install all the packages that are listed in <b>requirements.txt</b>.</p>
+<h3><a class="anchor" id="autotoc_md9"></a>
+Running scripts</h3>
+<p>For the Python scripts, run them from the src directory like this:</p>
+<div class="fragment"><div class="line">python scripts/&lt;script-name&gt;</div>
+</div><!-- fragment --><p>If you have any problems running the scripts, you might have to run this instead:</p>
+<div class="fragment"><div class="line">python3 scripts/&lt;script-name&gt;</div>
+</div><!-- fragment --><h1><a class="anchor" id="autotoc_md10"></a>
 Credits</h1>
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+<a href="#func-members">Functions</a> &#124;
+<a href="#var-members">Variables</a>  </div>
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 <div class="contents">
 
 <p>The main program for this project.  
 <a href="#details">More...</a></p>
-
+<div class="textblock"><code>#include &lt;cmath&gt;</code><br />
+<code>#include &lt;complex&gt;</code><br />
+<code>#include &lt;fstream&gt;</code><br />
+<code>#include &lt;omp.h&gt;</code><br />
+<code>#include &lt;string&gt;</code><br />
+<code>#include &lt;vector&gt;</code><br />
+<code>#include &quot;<a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="constants_8hpp_source.html">constants.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="utils_8hpp_source.html">utils.hpp</a>&quot;</code><br />
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+Macros</h2></td></tr>
+<tr class="memitem:a7b24a37e8ce9d243351bfc9b24945e63"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html#a7b24a37e8ce9d243351bfc9b24945e63">PARTICLES</a>&#160;&#160;&#160;100</td></tr>
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+<tr class="memdesc:a8d92fb2ad085065fbd14718647551657"><td class="mdescLeft">&#160;</td><td class="mdescRight">The analytical solution for particle p1.  <br /></td></tr>
+<tr class="separator:a8d92fb2ad085065fbd14718647551657"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a8fdbe2d5a872e50ef5ec1263243589d6"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a> ()</td></tr>
+<tr class="memdesc:a8fdbe2d5a872e50ef5ec1263243589d6"><td class="mdescLeft">&#160;</td><td class="mdescRight">Simulate a single particle over the period of 50 \( \mu s \).  <br /></td></tr>
+<tr class="separator:a8fdbe2d5a872e50ef5ec1263243589d6"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a783789519f97c6430081171cacb0ffb1"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a> ()</td></tr>
+<tr class="memdesc:a783789519f97c6430081171cacb0ffb1"><td class="mdescLeft">&#160;</td><td class="mdescRight">Simulate 2 particles over the period of 50 \( \mu s \) with and without particle interactions.  <br /></td></tr>
+<tr class="separator:a783789519f97c6430081171cacb0ffb1"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<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>
+<tr class="memdesc:ac67e0d59227856c4d42e7d01c75e0ad2"><td class="mdescLeft">&#160;</td><td class="mdescRight">Simulate a single particle over 50 \( \mu s \) using different amount of steps and different methods.  <br /></td></tr>
+<tr class="separator:ac67e0d59227856c4d42e7d01c75e0ad2"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a213713d6ecc02a32b588ffd179dc7513"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a> ()</td></tr>
+<tr class="memdesc:a213713d6ecc02a32b588ffd179dc7513"><td class="mdescLeft">&#160;</td><td class="mdescRight">Simulate 100 particles over 50 \( \mu s \).  <br /></td></tr>
+<tr class="separator:a213713d6ecc02a32b588ffd179dc7513"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a6b38b477c18e2f4268779751a88edab1"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a> ()</td></tr>
+<tr class="memdesc:a6b38b477c18e2f4268779751a88edab1"><td class="mdescLeft">&#160;</td><td class="mdescRight">Simulate 100 particles over 500 \( \mu s \) using a time dependent potential.  <br /></td></tr>
+<tr class="separator:a6b38b477c18e2f4268779751a88edab1"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a33d9b1c76c3c80902f89a58b1a6d96ea"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a> ()</td></tr>
+<tr class="memdesc:a33d9b1c76c3c80902f89a58b1a6d96ea"><td class="mdescLeft">&#160;</td><td class="mdescRight">Simulate 100 particles over 500 \( \mu s \) using a time dependent potential.  <br /></td></tr>
+<tr class="separator:a33d9b1c76c3c80902f89a58b1a6d96ea"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ac1816f70ec612edc27848ef7f0875fdb"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a> ()</td></tr>
+<tr class="memdesc:ac1816f70ec612edc27848ef7f0875fdb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Simulate 100 particles over 500 \( \mu s \) using a time dependent potential.  <br /></td></tr>
+<tr class="separator:ac1816f70ec612edc27848ef7f0875fdb"><td class="memSeparator" colspan="2">&#160;</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>
 <tr class="separator:ae66f6b31b5ad750f1fe042a706a4e3d4"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="var-members" name="var-members"></a>
+Variables</h2></td></tr>
+<tr class="memitem:a2efa69bb9d93049429ce4637075f1d30"><td class="memItemLeft" align="right" valign="top"><a id="a2efa69bb9d93049429ce4637075f1d30" name="a2efa69bb9d93049429ce4637075f1d30"></a>
+<a class="el" href="classParticle.html">Particle</a>&#160;</td><td class="memItemRight" valign="bottom"><b>p1</b> (<a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{20., 0., 20.}, <a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 25., 0.})</td></tr>
+<tr class="memdesc:a2efa69bb9d93049429ce4637075f1d30"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classParticle.html" title="A class that holds attributes of a particle.">Particle</a> 1. <br /></td></tr>
+<tr class="separator:a2efa69bb9d93049429ce4637075f1d30"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ac70b61df65f4336f57ea9b4c35250df7"><td class="memItemLeft" align="right" valign="top"><a id="ac70b61df65f4336f57ea9b4c35250df7" name="ac70b61df65f4336f57ea9b4c35250df7"></a>
+<a class="el" href="classParticle.html">Particle</a>&#160;</td><td class="memItemRight" valign="bottom"><b>p2</b> (<a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{25., 25., 0.}, <a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 40., 5.})</td></tr>
+<tr class="memdesc:ac70b61df65f4336f57ea9b4c35250df7"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classParticle.html" title="A class that holds attributes of a particle.">Particle</a> 2. <br /></td></tr>
+<tr class="separator:ac70b61df65f4336f57ea9b4c35250df7"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>The main program for this project. </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>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="section version"><dt>Version</dt><dd>1.0</dd></dl>
+<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000006">Bug:</a></b></dt><dd>No known bugs </dd></dl>
 
 <p class="definition">Definition in file <a class="el" href="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="a0240ac851181b84ac374872dc5434ee4" name="a0240ac851181b84ac374872dc5434ee4"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a0240ac851181b84ac374872dc5434ee4">&#9670;&#160;</a></span>N</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define N&#160;&#160;&#160;40000</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<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>
+</div>
+<a id="a7b24a37e8ce9d243351bfc9b24945e63" name="a7b24a37e8ce9d243351bfc9b24945e63"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a7b24a37e8ce9d243351bfc9b24945e63">&#9670;&#160;</a></span>PARTICLES</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define PARTICLES&#160;&#160;&#160;100</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<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>
+<h2 class="groupheader">Function Documentation</h2>
+<a id="a8d92fb2ad085065fbd14718647551657" name="a8d92fb2ad085065fbd14718647551657"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a8d92fb2ad085065fbd14718647551657">&#9670;&#160;</a></span>analytical_solution_particle_1()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> analytical_solution_particle_1 </td>
+          <td>(</td>
+          <td class="paramtype">double&#160;</td>
+          <td class="paramname"><em>t</em></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>The analytical solution for particle p1. </p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">t</td><td>Time</td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns</dt><dd>vec3 </dd></dl>
+
+<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00037">37</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
+
+</div>
+</div>
 <a id="ae66f6b31b5ad750f1fe042a706a4e3d4" name="ae66f6b31b5ad750f1fe042a706a4e3d4"></a>
 <h2 class="memtitle"><span class="permalink"><a href="#ae66f6b31b5ad750f1fe042a706a4e3d4">&#9670;&#160;</a></span>main()</h2>
 
@@ -139,7 +254,157 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
       </table>
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-<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#l00309">309</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a33d9b1c76c3c80902f89a58b1a6d96ea" name="a33d9b1c76c3c80902f89a58b1a6d96ea"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a33d9b1c76c3c80902f89a58b1a6d96ea">&#9670;&#160;</a></span>potential_resonance_narrow_sweep()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void potential_resonance_narrow_sweep </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Simulate 100 particles over 500 \( \mu s \) using a time dependent potential. </p>
+<p>The simulation sweeps over different frequencies in [1., 1.7] MHz. </p>
+
+<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00206">206</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
+
+</div>
+</div>
+<a id="ac1816f70ec612edc27848ef7f0875fdb" name="ac1816f70ec612edc27848ef7f0875fdb"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ac1816f70ec612edc27848ef7f0875fdb">&#9670;&#160;</a></span>potential_resonance_narrow_sweep_interaction()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void potential_resonance_narrow_sweep_interaction </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Simulate 100 particles over 500 \( \mu s \) using a time dependent potential. </p>
+<p>The simulation sweeps over different frequencies in [1., 1.7] MHz. </p>
+
+<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00262">262</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a6b38b477c18e2f4268779751a88edab1" name="a6b38b477c18e2f4268779751a88edab1"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a6b38b477c18e2f4268779751a88edab1">&#9670;&#160;</a></span>potential_resonance_wide_sweep()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void potential_resonance_wide_sweep </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Simulate 100 particles over 500 \( \mu s \) using a time dependent potential. </p>
+<p>The simulation sweeps over different frequencies in [0.2, 2.5] MHz. </p>
+
+<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00149">149</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a213713d6ecc02a32b588ffd179dc7513" name="a213713d6ecc02a32b588ffd179dc7513"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a213713d6ecc02a32b588ffd179dc7513">&#9670;&#160;</a></span>simulate_100_particles()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void simulate_100_particles </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Simulate 100 particles over 50 \( \mu s \). </p>
+
+<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00132">132</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a8fdbe2d5a872e50ef5ec1263243589d6" name="a8fdbe2d5a872e50ef5ec1263243589d6"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a8fdbe2d5a872e50ef5ec1263243589d6">&#9670;&#160;</a></span>simulate_single_particle()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void simulate_single_particle </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Simulate a single particle over the period of 50 \( \mu s \). </p>
+
+<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00054">54</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
+
+</div>
+</div>
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+<h2 class="memtitle"><span class="permalink"><a href="#ac67e0d59227856c4d42e7d01c75e0ad2">&#9670;&#160;</a></span>simulate_single_particle_with_different_steps()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void simulate_single_particle_with_different_steps </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Simulate a single particle over 50 \( \mu s \) using different amount of steps and different methods. </p>
+
+<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00087">87</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
+
+</div>
+</div>
+<a id="a783789519f97c6430081171cacb0ffb1" name="a783789519f97c6430081171cacb0ffb1"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a783789519f97c6430081171cacb0ffb1">&#9670;&#160;</a></span>simulate_two_particles()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void simulate_two_particles </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Simulate 2 particles over the period of 50 \( \mu s \) with and without particle interactions. </p>
+
+<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00069">69</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
 
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+    [ "potential_resonance_wide_sweep", "main_8cpp.html#a6b38b477c18e2f4268779751a88edab1", null ],
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+    [ "simulate_two_particles", "main_8cpp.html#a783789519f97c6430081171cacb0ffb1", null ],
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+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="preprocessor">#include &lt;cmath&gt;</span></div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="preprocessor">#include &lt;complex&gt;</span></div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="preprocessor">#include &lt;fstream&gt;</span></div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span><span class="preprocessor">#include &lt;omp.h&gt;</span></div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span><span class="preprocessor">#include &lt;string&gt;</span></div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span> </div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div>
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+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span> </div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span><span class="preprocessor">#define PARTICLES 100</span></div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span><span class="preprocessor">#define N 40000</span></div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span> </div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span><span class="comment">// Particles used for testing</span></div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"><a class="line" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">   28</a></span><a class="code hl_class" href="classParticle.html">Particle</a> <a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{20., 0., 20.}, <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 25., 0.}); </div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"><a class="line" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">   29</a></span><a class="code hl_class" href="classParticle.html">Particle</a> <a class="code hl_variable" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">p2</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{25., 25., 0.}, <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</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="l00037" name="l00037"></a><span class="lineno"><a class="line" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">   37</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a>(<span class="keywordtype">double</span> t)</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>    <span class="keywordtype">double</span> w_0 = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a> / <a class="code hl_define" href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">CA_MASS</a>;</div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>    <span class="keywordtype">double</span> w_z2 = (50. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a> / 1000.) / (<a class="code hl_define" href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">CA_MASS</a> * 500. * 500.);</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>    <span class="keywordtype">double</span> w_p = (w_0 + std::sqrt(w_0 * w_0 - 2. * w_z2)) / 2.;</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>    <span class="keywordtype">double</span> w_n = (w_0 - std::sqrt(w_0 * w_0 - 2. * w_z2)) / 2.;</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>    <span class="keywordtype">double</span> A_p = (25. + w_n * 20.) / (w_n - w_p);</div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span>    <span class="keywordtype">double</span> A_n = -(25. + w_p * 20.) / (w_n - w_p);</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span>    std::complex&lt;double&gt; f =</div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>        A_p * std::exp(std::complex&lt;double&gt;(0., -w_p * t))</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>        + A_n * std::exp(std::complex&lt;double&gt;(0., -w_n * t));</div>
+<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res{std::real(f), std::imag(f), 20. * std::cos(std::sqrt(w_z2) * t)};</div>
+<div class="line"><a id="l00049" name="l00049"></a><span class="lineno">   49</span>    <span class="keywordflow">return</span> res;</div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span>}</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span> </div>
+<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"><a class="line" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">   54</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a>()</div>
+<div class="line"><a id="l00055" name="l00055"></a><span class="lineno">   55</span>{</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno">   56</span>    <span class="comment">// Initialize trap with particle 1</span></div>
+<div class="line"><a id="l00057" name="l00057"></a><span class="lineno">   57</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>});</div>
+<div class="line"><a id="l00058" name="l00058"></a><span class="lineno">   58</span> </div>
+<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   59</span>    <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
+<div class="line"><a id="l00060" name="l00060"></a><span class="lineno">   60</span> </div>
+<div class="line"><a id="l00061" name="l00061"></a><span class="lineno">   61</span>    <span class="comment">// Simulate and write results to file</span></div>
+<div class="line"><a id="l00062" name="l00062"></a><span class="lineno">   62</span>    trap.<a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(<span class="stringliteral">&quot;output/simulate_single_particle&quot;</span>, time, N,</div>
+<div class="line"><a id="l00063" name="l00063"></a><span class="lineno">   63</span>                                 <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00064" name="l00064"></a><span class="lineno">   64</span>}</div>
+<div class="line"><a id="l00065" name="l00065"></a><span class="lineno">   65</span> </div>
+<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"><a class="line" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">   69</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a>()</div>
+<div class="line"><a id="l00070" name="l00070"></a><span class="lineno">   70</span>{</div>
+<div class="line"><a id="l00071" name="l00071"></a><span class="lineno">   71</span>    <span class="comment">// Initialize traps with particles</span></div>
+<div class="line"><a id="l00072" name="l00072"></a><span class="lineno">   72</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap_no_interaction(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>, <a class="code hl_variable" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">p2</a>});</div>
+<div class="line"><a id="l00073" name="l00073"></a><span class="lineno">   73</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap_with_interaction(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>, <a class="code hl_variable" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">p2</a>});</div>
+<div class="line"><a id="l00074" name="l00074"></a><span class="lineno">   74</span> </div>
+<div class="line"><a id="l00075" name="l00075"></a><span class="lineno">   75</span>    <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
+<div class="line"><a id="l00076" name="l00076"></a><span class="lineno">   76</span> </div>
+<div class="line"><a id="l00077" name="l00077"></a><span class="lineno">   77</span>    <span class="comment">// Simulate and write results to files</span></div>
+<div class="line"><a id="l00078" name="l00078"></a><span class="lineno">   78</span>    trap_no_interaction.<a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(</div>
+<div class="line"><a id="l00079" name="l00079"></a><span class="lineno">   79</span>        <span class="stringliteral">&quot;output/simulate_2_particles/no_interaction&quot;</span>, time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00080" name="l00080"></a><span class="lineno">   80</span>    trap_with_interaction.write_simulation_to_dir(</div>
+<div class="line"><a id="l00081" name="l00081"></a><span class="lineno">   81</span>        <span class="stringliteral">&quot;output/simulate_2_particles/with_interaction&quot;</span>, time, N);</div>
+<div class="line"><a id="l00082" name="l00082"></a><span class="lineno">   82</span>}</div>
+<div class="line"><a id="l00083" name="l00083"></a><span class="lineno">   83</span> </div>
+<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"><a class="line" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">   87</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a>()</div>
+<div class="line"><a id="l00088" name="l00088"></a><span class="lineno">   88</span>{</div>
+<div class="line"><a id="l00089" name="l00089"></a><span class="lineno">   89</span>    <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
+<div class="line"><a id="l00090" name="l00090"></a><span class="lineno">   90</span> </div>
+<div class="line"><a id="l00091" name="l00091"></a><span class="lineno">   91</span>    std::ofstream ofile;</div>
+<div class="line"><a id="l00092" name="l00092"></a><span class="lineno">   92</span> </div>
+<div class="line"><a id="l00093" name="l00093"></a><span class="lineno">   93</span>    <span class="comment">// Calculate relative error for RK4</span></div>
+<div class="line"><a id="l00094" name="l00094"></a><span class="lineno">   94</span>    std::string path = <span class="stringliteral">&quot;output/relative_error/RK4/&quot;</span>;</div>
+<div class="line"><a id="l00095" name="l00095"></a><span class="lineno">   95</span>    <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
+<div class="line"><a id="l00096" name="l00096"></a><span class="lineno">   96</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00097" name="l00097"></a><span class="lineno">   97</span>    <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; 4; i++) {</div>
+<div class="line"><a id="l00098" name="l00098"></a><span class="lineno">   98</span>        <span class="keywordtype">int</span> steps = 4000 * std::pow(2, i);</div>
+<div class="line"><a id="l00099" name="l00099"></a><span class="lineno">   99</span>        <span class="keywordtype">double</span> dt = time / (double)steps;</div>
+<div class="line"><a id="l00100" name="l00100"></a><span class="lineno">  100</span>        ofile.open(path + std::to_string(steps) + <span class="stringliteral">&quot;_steps.txt&quot;</span>);</div>
+<div class="line"><a id="l00101" name="l00101"></a><span class="lineno">  101</span>        <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>});</div>
+<div class="line"><a id="l00102" name="l00102"></a><span class="lineno">  102</span>        <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res = trap.simulate(time, steps, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00103" name="l00103"></a><span class="lineno">  103</span>        <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; steps; i++) {</div>
+<div class="line"><a id="l00104" name="l00104"></a><span class="lineno">  104</span>            ofile &lt;&lt; arma::norm(res.r_vecs[0][i]</div>
+<div class="line"><a id="l00105" name="l00105"></a><span class="lineno">  105</span>                                - <a class="code hl_function" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a>(dt * i))</div>
+<div class="line"><a id="l00106" name="l00106"></a><span class="lineno">  106</span>                  &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00107" name="l00107"></a><span class="lineno">  107</span>        }</div>
+<div class="line"><a id="l00108" name="l00108"></a><span class="lineno">  108</span>        ofile.close();</div>
+<div class="line"><a id="l00109" name="l00109"></a><span class="lineno">  109</span>    }</div>
+<div class="line"><a id="l00110" name="l00110"></a><span class="lineno">  110</span> </div>
+<div class="line"><a id="l00111" name="l00111"></a><span class="lineno">  111</span>    <span class="comment">// Calculate relative error for forward Euler</span></div>
+<div class="line"><a id="l00112" name="l00112"></a><span class="lineno">  112</span>    path = <span class="stringliteral">&quot;output/relative_error/euler/&quot;</span>;</div>
+<div class="line"><a id="l00113" name="l00113"></a><span class="lineno">  113</span>    <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
+<div class="line"><a id="l00114" name="l00114"></a><span class="lineno">  114</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00115" name="l00115"></a><span class="lineno">  115</span>    <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; 4; i++) {</div>
+<div class="line"><a id="l00116" name="l00116"></a><span class="lineno">  116</span>        <span class="keywordtype">int</span> steps = 4000 * std::pow(2, i);</div>
+<div class="line"><a id="l00117" name="l00117"></a><span class="lineno">  117</span>        <span class="keywordtype">double</span> dt = time / (double)steps;</div>
+<div class="line"><a id="l00118" name="l00118"></a><span class="lineno">  118</span>        ofile.open(path + std::to_string(steps) + <span class="stringliteral">&quot;_steps.txt&quot;</span>);</div>
+<div class="line"><a id="l00119" name="l00119"></a><span class="lineno">  119</span>        <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>});</div>
+<div class="line"><a id="l00120" name="l00120"></a><span class="lineno">  120</span>        <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res = trap.simulate(time, steps, <span class="stringliteral">&quot;euler&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00121" name="l00121"></a><span class="lineno">  121</span>        <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; steps; i++) {</div>
+<div class="line"><a id="l00122" name="l00122"></a><span class="lineno">  122</span>            ofile &lt;&lt; arma::norm(res.r_vecs[0][i]</div>
+<div class="line"><a id="l00123" name="l00123"></a><span class="lineno">  123</span>                                - <a class="code hl_function" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a>(dt * i))</div>
+<div class="line"><a id="l00124" name="l00124"></a><span class="lineno">  124</span>                  &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00125" name="l00125"></a><span class="lineno">  125</span>        }</div>
+<div class="line"><a id="l00126" name="l00126"></a><span class="lineno">  126</span>        ofile.close();</div>
+<div class="line"><a id="l00127" name="l00127"></a><span class="lineno">  127</span>    }</div>
+<div class="line"><a id="l00128" name="l00128"></a><span class="lineno">  128</span>}</div>
+<div class="line"><a id="l00129" name="l00129"></a><span class="lineno">  129</span> </div>
+<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"><a class="line" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">  132</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a>()</div>
+<div class="line"><a id="l00133" name="l00133"></a><span class="lineno">  133</span>{</div>
+<div class="line"><a id="l00134" name="l00134"></a><span class="lineno">  134</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((<span class="keywordtype">unsigned</span>)100);</div>
+<div class="line"><a id="l00135" name="l00135"></a><span class="lineno">  135</span> </div>
+<div class="line"><a id="l00136" name="l00136"></a><span class="lineno">  136</span>    <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
+<div class="line"><a id="l00137" name="l00137"></a><span class="lineno">  137</span> </div>
+<div class="line"><a id="l00138" name="l00138"></a><span class="lineno">  138</span>    trap.<a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(<span class="stringliteral">&quot;output/simulate_100_particles&quot;</span>, time, N,</div>
+<div class="line"><a id="l00139" name="l00139"></a><span class="lineno">  139</span>                                 <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00140" name="l00140"></a><span class="lineno">  140</span>}</div>
+<div class="line"><a id="l00141" name="l00141"></a><span class="lineno">  141</span> </div>
+<div class="line"><a id="l00149" name="l00149"></a><span class="lineno"><a class="line" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">  149</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a>()</div>
+<div class="line"><a id="l00150" name="l00150"></a><span class="lineno">  150</span>{</div>
+<div class="line"><a id="l00151" name="l00151"></a><span class="lineno">  151</span>    <span class="keywordtype">double</span> time = 500.;</div>
+<div class="line"><a id="l00152" name="l00152"></a><span class="lineno">  152</span> </div>
+<div class="line"><a id="l00153" name="l00153"></a><span class="lineno">  153</span>    <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
+<div class="line"><a id="l00154" name="l00154"></a><span class="lineno">  154</span> </div>
+<div class="line"><a id="l00155" name="l00155"></a><span class="lineno">  155</span>    <span class="keywordtype">double</span> freq_start = .2;</div>
+<div class="line"><a id="l00156" name="l00156"></a><span class="lineno">  156</span>    <span class="keywordtype">double</span> freq_end = 2.5;</div>
+<div class="line"><a id="l00157" name="l00157"></a><span class="lineno">  157</span>    <span class="keywordtype">double</span> freq_increment = .02;</div>
+<div class="line"><a id="l00158" name="l00158"></a><span class="lineno">  158</span>    <span class="keywordtype">size_t</span> freq_iterations =</div>
+<div class="line"><a id="l00159" name="l00159"></a><span class="lineno">  159</span>        (size_t)((freq_end - freq_start) / freq_increment) + 1;</div>
+<div class="line"><a id="l00160" name="l00160"></a><span class="lineno">  160</span> </div>
+<div class="line"><a id="l00161" name="l00161"></a><span class="lineno">  161</span>    <span class="keywordtype">double</span> res[4][freq_iterations];</div>
+<div class="line"><a id="l00162" name="l00162"></a><span class="lineno">  162</span> </div>
+<div class="line"><a id="l00163" name="l00163"></a><span class="lineno">  163</span>    std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
+<div class="line"><a id="l00164" name="l00164"></a><span class="lineno">  164</span>    <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
+<div class="line"><a id="l00165" name="l00165"></a><span class="lineno">  165</span> </div>
+<div class="line"><a id="l00166" name="l00166"></a><span class="lineno">  166</span>    std::ofstream ofile;</div>
+<div class="line"><a id="l00167" name="l00167"></a><span class="lineno">  167</span> </div>
+<div class="line"><a id="l00168" name="l00168"></a><span class="lineno">  168</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00169" name="l00169"></a><span class="lineno">  169</span>    <span class="comment">// Insert frequencies</span></div>
+<div class="line"><a id="l00170" name="l00170"></a><span class="lineno">  170</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00171" name="l00171"></a><span class="lineno">  171</span>        res[0][i] = freq_start + freq_increment * i;</div>
+<div class="line"><a id="l00172" name="l00172"></a><span class="lineno">  172</span>    }</div>
+<div class="line"><a id="l00173" name="l00173"></a><span class="lineno">  173</span> </div>
+<div class="line"><a id="l00174" name="l00174"></a><span class="lineno">  174</span><span class="preprocessor">#pragma omp parallel</span></div>
+<div class="line"><a id="l00175" name="l00175"></a><span class="lineno">  175</span>    {</div>
+<div class="line"><a id="l00176" name="l00176"></a><span class="lineno">  176</span>        <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
+<div class="line"><a id="l00177" name="l00177"></a><span class="lineno">  177</span>        <span class="comment">// the sweep.</span></div>
+<div class="line"><a id="l00178" name="l00178"></a><span class="lineno">  178</span>        <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)100);</div>
+<div class="line"><a id="l00179" name="l00179"></a><span class="lineno">  179</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
+<div class="line"><a id="l00180" name="l00180"></a><span class="lineno">  180</span>        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
+<div class="line"><a id="l00181" name="l00181"></a><span class="lineno">  181</span>            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
+<div class="line"><a id="l00182" name="l00182"></a><span class="lineno">  182</span>                <span class="comment">// Reset particles and give new time dependent potential.</span></div>
+<div class="line"><a id="l00183" name="l00183"></a><span class="lineno">  183</span>                trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
+<div class="line"><a id="l00184" name="l00184"></a><span class="lineno">  184</span>                res[i + 1][j] =</div>
+<div class="line"><a id="l00185" name="l00185"></a><span class="lineno">  185</span>                    trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00186" name="l00186"></a><span class="lineno">  186</span>            }</div>
+<div class="line"><a id="l00187" name="l00187"></a><span class="lineno">  187</span>        }</div>
+<div class="line"><a id="l00188" name="l00188"></a><span class="lineno">  188</span>    }</div>
+<div class="line"><a id="l00189" name="l00189"></a><span class="lineno">  189</span> </div>
+<div class="line"><a id="l00190" name="l00190"></a><span class="lineno">  190</span>    <span class="comment">// Write results to file</span></div>
+<div class="line"><a id="l00191" name="l00191"></a><span class="lineno">  191</span>    ofile.open(path + <span class="stringliteral">&quot;wide_sweep.txt&quot;</span>);</div>
+<div class="line"><a id="l00192" name="l00192"></a><span class="lineno">  192</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00193" name="l00193"></a><span class="lineno">  193</span>        ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00194" name="l00194"></a><span class="lineno">  194</span>              &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00195" name="l00195"></a><span class="lineno">  195</span>    }</div>
+<div class="line"><a id="l00196" name="l00196"></a><span class="lineno">  196</span>    ofile.close();</div>
+<div class="line"><a id="l00197" name="l00197"></a><span class="lineno">  197</span>}</div>
+<div class="line"><a id="l00198" name="l00198"></a><span class="lineno">  198</span> </div>
+<div class="line"><a id="l00206" name="l00206"></a><span class="lineno"><a class="line" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">  206</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>()</div>
+<div class="line"><a id="l00207" name="l00207"></a><span class="lineno">  207</span>{</div>
+<div class="line"><a id="l00208" name="l00208"></a><span class="lineno">  208</span>    <span class="keywordtype">double</span> time = 500.;</div>
+<div class="line"><a id="l00209" name="l00209"></a><span class="lineno">  209</span> </div>
+<div class="line"><a id="l00210" name="l00210"></a><span class="lineno">  210</span>    <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
+<div class="line"><a id="l00211" name="l00211"></a><span class="lineno">  211</span> </div>
+<div class="line"><a id="l00212" name="l00212"></a><span class="lineno">  212</span>    <span class="keywordtype">double</span> freq_start = 1.;</div>
+<div class="line"><a id="l00213" name="l00213"></a><span class="lineno">  213</span>    <span class="keywordtype">double</span> freq_end = 1.7;</div>
+<div class="line"><a id="l00214" name="l00214"></a><span class="lineno">  214</span>    <span class="keywordtype">double</span> freq_increment = .002;</div>
+<div class="line"><a id="l00215" name="l00215"></a><span class="lineno">  215</span>    <span class="keywordtype">size_t</span> freq_iterations = (size_t)((freq_end - freq_start) / freq_increment);</div>
+<div class="line"><a id="l00216" name="l00216"></a><span class="lineno">  216</span> </div>
+<div class="line"><a id="l00217" name="l00217"></a><span class="lineno">  217</span>    <span class="keywordtype">double</span> res[4][freq_iterations];</div>
+<div class="line"><a id="l00218" name="l00218"></a><span class="lineno">  218</span> </div>
+<div class="line"><a id="l00219" name="l00219"></a><span class="lineno">  219</span>    std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
+<div class="line"><a id="l00220" name="l00220"></a><span class="lineno">  220</span>    <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
+<div class="line"><a id="l00221" name="l00221"></a><span class="lineno">  221</span> </div>
+<div class="line"><a id="l00222" name="l00222"></a><span class="lineno">  222</span>    std::ofstream ofile;</div>
+<div class="line"><a id="l00223" name="l00223"></a><span class="lineno">  223</span> </div>
+<div class="line"><a id="l00224" name="l00224"></a><span class="lineno">  224</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00225" name="l00225"></a><span class="lineno">  225</span>    <span class="comment">// Insert frequencies</span></div>
+<div class="line"><a id="l00226" name="l00226"></a><span class="lineno">  226</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00227" name="l00227"></a><span class="lineno">  227</span>        res[0][i] = freq_start + freq_increment * i;</div>
+<div class="line"><a id="l00228" name="l00228"></a><span class="lineno">  228</span>    }</div>
+<div class="line"><a id="l00229" name="l00229"></a><span class="lineno">  229</span> </div>
+<div class="line"><a id="l00230" name="l00230"></a><span class="lineno">  230</span><span class="preprocessor">#pragma omp parallel</span></div>
+<div class="line"><a id="l00231" name="l00231"></a><span class="lineno">  231</span>    {</div>
+<div class="line"><a id="l00232" name="l00232"></a><span class="lineno">  232</span>        <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
+<div class="line"><a id="l00233" name="l00233"></a><span class="lineno">  233</span>        <span class="comment">// the sweep.</span></div>
+<div class="line"><a id="l00234" name="l00234"></a><span class="lineno">  234</span>        <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)100);</div>
+<div class="line"><a id="l00235" name="l00235"></a><span class="lineno">  235</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
+<div class="line"><a id="l00236" name="l00236"></a><span class="lineno">  236</span>        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
+<div class="line"><a id="l00237" name="l00237"></a><span class="lineno">  237</span>            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
+<div class="line"><a id="l00238" name="l00238"></a><span class="lineno">  238</span>                <span class="comment">// Reset particles and give new time dependent potential.</span></div>
+<div class="line"><a id="l00239" name="l00239"></a><span class="lineno">  239</span>                trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
+<div class="line"><a id="l00240" name="l00240"></a><span class="lineno">  240</span>                res[i + 1][j] =</div>
+<div class="line"><a id="l00241" name="l00241"></a><span class="lineno">  241</span>                    trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00242" name="l00242"></a><span class="lineno">  242</span>            }</div>
+<div class="line"><a id="l00243" name="l00243"></a><span class="lineno">  243</span>        }</div>
+<div class="line"><a id="l00244" name="l00244"></a><span class="lineno">  244</span>    }</div>
+<div class="line"><a id="l00245" name="l00245"></a><span class="lineno">  245</span> </div>
+<div class="line"><a id="l00246" name="l00246"></a><span class="lineno">  246</span>    <span class="comment">// Write results to file</span></div>
+<div class="line"><a id="l00247" name="l00247"></a><span class="lineno">  247</span>    ofile.open(path + <span class="stringliteral">&quot;narrow_sweep.txt&quot;</span>);</div>
+<div class="line"><a id="l00248" name="l00248"></a><span class="lineno">  248</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00249" name="l00249"></a><span class="lineno">  249</span>        ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00250" name="l00250"></a><span class="lineno">  250</span>              &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00251" name="l00251"></a><span class="lineno">  251</span>    }</div>
+<div class="line"><a id="l00252" name="l00252"></a><span class="lineno">  252</span>    ofile.close();</div>
+<div class="line"><a id="l00253" name="l00253"></a><span class="lineno">  253</span>}</div>
+<div class="line"><a id="l00254" name="l00254"></a><span class="lineno">  254</span> </div>
+<div class="line"><a id="l00262" name="l00262"></a><span class="lineno"><a class="line" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">  262</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>()</div>
+<div class="line"><a id="l00263" name="l00263"></a><span class="lineno">  263</span>{</div>
+<div class="line"><a id="l00264" name="l00264"></a><span class="lineno">  264</span>    <span class="keywordtype">double</span> time = 500.;</div>
+<div class="line"><a id="l00265" name="l00265"></a><span class="lineno">  265</span> </div>
+<div class="line"><a id="l00266" name="l00266"></a><span class="lineno">  266</span>    <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
+<div class="line"><a id="l00267" name="l00267"></a><span class="lineno">  267</span> </div>
+<div class="line"><a id="l00268" name="l00268"></a><span class="lineno">  268</span>    <span class="keywordtype">double</span> freq_start = 1.;</div>
+<div class="line"><a id="l00269" name="l00269"></a><span class="lineno">  269</span>    <span class="keywordtype">double</span> freq_end = 1.7;</div>
+<div class="line"><a id="l00270" name="l00270"></a><span class="lineno">  270</span>    <span class="keywordtype">double</span> freq_increment = .002;</div>
+<div class="line"><a id="l00271" name="l00271"></a><span class="lineno">  271</span>    <span class="keywordtype">size_t</span> freq_iterations = (size_t)((freq_end - freq_start) / freq_increment);</div>
+<div class="line"><a id="l00272" name="l00272"></a><span class="lineno">  272</span> </div>
+<div class="line"><a id="l00273" name="l00273"></a><span class="lineno">  273</span>    <span class="keywordtype">double</span> res[4][freq_iterations];</div>
+<div class="line"><a id="l00274" name="l00274"></a><span class="lineno">  274</span> </div>
+<div class="line"><a id="l00275" name="l00275"></a><span class="lineno">  275</span>    std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
+<div class="line"><a id="l00276" name="l00276"></a><span class="lineno">  276</span>    <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
+<div class="line"><a id="l00277" name="l00277"></a><span class="lineno">  277</span> </div>
+<div class="line"><a id="l00278" name="l00278"></a><span class="lineno">  278</span>    std::ofstream ofile;</div>
+<div class="line"><a id="l00279" name="l00279"></a><span class="lineno">  279</span> </div>
+<div class="line"><a id="l00280" name="l00280"></a><span class="lineno">  280</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00281" name="l00281"></a><span class="lineno">  281</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00282" name="l00282"></a><span class="lineno">  282</span>        res[0][i] = freq_start + freq_increment * i;</div>
+<div class="line"><a id="l00283" name="l00283"></a><span class="lineno">  283</span>    }</div>
+<div class="line"><a id="l00284" name="l00284"></a><span class="lineno">  284</span> </div>
+<div class="line"><a id="l00285" name="l00285"></a><span class="lineno">  285</span><span class="preprocessor">#pragma omp parallel</span></div>
+<div class="line"><a id="l00286" name="l00286"></a><span class="lineno">  286</span>    {</div>
+<div class="line"><a id="l00287" name="l00287"></a><span class="lineno">  287</span>        <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
+<div class="line"><a id="l00288" name="l00288"></a><span class="lineno">  288</span>        <span class="comment">// the sweep.</span></div>
+<div class="line"><a id="l00289" name="l00289"></a><span class="lineno">  289</span>        <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)100);</div>
+<div class="line"><a id="l00290" name="l00290"></a><span class="lineno">  290</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
+<div class="line"><a id="l00291" name="l00291"></a><span class="lineno">  291</span>        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
+<div class="line"><a id="l00292" name="l00292"></a><span class="lineno">  292</span>            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
+<div class="line"><a id="l00293" name="l00293"></a><span class="lineno">  293</span>                <span class="comment">// Reset particles and give new time dependent potential.</span></div>
+<div class="line"><a id="l00294" name="l00294"></a><span class="lineno">  294</span>                trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
+<div class="line"><a id="l00295" name="l00295"></a><span class="lineno">  295</span>                res[i + 1][j] = trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N);</div>
+<div class="line"><a id="l00296" name="l00296"></a><span class="lineno">  296</span>            }</div>
+<div class="line"><a id="l00297" name="l00297"></a><span class="lineno">  297</span>        }</div>
+<div class="line"><a id="l00298" name="l00298"></a><span class="lineno">  298</span>    }</div>
+<div class="line"><a id="l00299" name="l00299"></a><span class="lineno">  299</span> </div>
+<div class="line"><a id="l00300" name="l00300"></a><span class="lineno">  300</span>    <span class="comment">// Write results to file</span></div>
+<div class="line"><a id="l00301" name="l00301"></a><span class="lineno">  301</span>    ofile.open(path + <span class="stringliteral">&quot;narrow_sweep_interactions.txt&quot;</span>);</div>
+<div class="line"><a id="l00302" name="l00302"></a><span class="lineno">  302</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00303" name="l00303"></a><span class="lineno">  303</span>        ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00304" name="l00304"></a><span class="lineno">  304</span>              &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00305" name="l00305"></a><span class="lineno">  305</span>    }</div>
+<div class="line"><a id="l00306" name="l00306"></a><span class="lineno">  306</span>    ofile.close();</div>
+<div class="line"><a id="l00307" name="l00307"></a><span class="lineno">  307</span>}</div>
+<div class="line"><a id="l00308" name="l00308"></a><span class="lineno">  308</span> </div>
+<div class="line"><a id="l00309" name="l00309"></a><span class="lineno">  309</span><span class="keywordtype">int</span> main()</div>
+<div class="line"><a id="l00310" name="l00310"></a><span class="lineno">  310</span>{</div>
+<div class="line"><a id="l00311" name="l00311"></a><span class="lineno">  311</span>    <span class="keywordtype">double</span> start, end, t1, t2;</div>
+<div class="line"><a id="l00312" name="l00312"></a><span class="lineno">  312</span>    start = omp_get_wtime();</div>
+<div class="line"><a id="l00313" name="l00313"></a><span class="lineno">  313</span> </div>
+<div class="line"><a id="l00314" name="l00314"></a><span class="lineno">  314</span>    <a class="code hl_function" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a>();</div>
+<div class="line"><a id="l00315" name="l00315"></a><span class="lineno">  315</span> </div>
+<div class="line"><a id="l00316" name="l00316"></a><span class="lineno">  316</span>    <a class="code hl_function" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a>();</div>
+<div class="line"><a id="l00317" name="l00317"></a><span class="lineno">  317</span> </div>
+<div class="line"><a id="l00318" name="l00318"></a><span class="lineno">  318</span>    <a class="code hl_function" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a>();</div>
+<div class="line"><a id="l00319" name="l00319"></a><span class="lineno">  319</span> </div>
+<div class="line"><a id="l00320" name="l00320"></a><span class="lineno">  320</span>    t2 = omp_get_wtime();</div>
+<div class="line"><a id="l00321" name="l00321"></a><span class="lineno">  321</span> </div>
+<div class="line"><a id="l00322" name="l00322"></a><span class="lineno">  322</span>    std::cout &lt;&lt; <span class="stringliteral">&quot;Time single and double            : &quot;</span> &lt;&lt; (t2 - start)</div>
+<div class="line"><a id="l00323" name="l00323"></a><span class="lineno">  323</span>              &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00324" name="l00324"></a><span class="lineno">  324</span> </div>
+<div class="line"><a id="l00325" name="l00325"></a><span class="lineno">  325</span>    t1 = omp_get_wtime();</div>
+<div class="line"><a id="l00326" name="l00326"></a><span class="lineno">  326</span> </div>
+<div class="line"><a id="l00327" name="l00327"></a><span class="lineno">  327</span>    <a class="code hl_function" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a>();</div>
+<div class="line"><a id="l00328" name="l00328"></a><span class="lineno">  328</span> </div>
+<div class="line"><a id="l00329" name="l00329"></a><span class="lineno">  329</span>    t2 = omp_get_wtime();</div>
+<div class="line"><a id="l00330" name="l00330"></a><span class="lineno">  330</span> </div>
+<div class="line"><a id="l00331" name="l00331"></a><span class="lineno">  331</span>    std::cout &lt;&lt; <span class="stringliteral">&quot;Time 100 particles                : &quot;</span> &lt;&lt; (t2 - t1)</div>
+<div class="line"><a id="l00332" name="l00332"></a><span class="lineno">  332</span>              &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00333" name="l00333"></a><span class="lineno">  333</span> </div>
+<div class="line"><a id="l00334" name="l00334"></a><span class="lineno">  334</span>    t1 = omp_get_wtime();</div>
+<div class="line"><a id="l00335" name="l00335"></a><span class="lineno">  335</span> </div>
+<div class="line"><a id="l00336" name="l00336"></a><span class="lineno">  336</span>    <a class="code hl_function" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a>();</div>
+<div class="line"><a id="l00337" name="l00337"></a><span class="lineno">  337</span> </div>
+<div class="line"><a id="l00338" name="l00338"></a><span class="lineno">  338</span>    t2 = omp_get_wtime();</div>
+<div class="line"><a id="l00339" name="l00339"></a><span class="lineno">  339</span> </div>
+<div class="line"><a id="l00340" name="l00340"></a><span class="lineno">  340</span>    std::cout &lt;&lt; <span class="stringliteral">&quot;Time wide sweep                   : &quot;</span> &lt;&lt; (t2 - t1)</div>
+<div class="line"><a id="l00341" name="l00341"></a><span class="lineno">  341</span>              &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00342" name="l00342"></a><span class="lineno">  342</span> </div>
+<div class="line"><a id="l00343" name="l00343"></a><span class="lineno">  343</span>    t1 = omp_get_wtime();</div>
+<div class="line"><a id="l00344" name="l00344"></a><span class="lineno">  344</span> </div>
+<div class="line"><a id="l00345" name="l00345"></a><span class="lineno">  345</span>    <a class="code hl_function" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>();</div>
+<div class="line"><a id="l00346" name="l00346"></a><span class="lineno">  346</span> </div>
+<div class="line"><a id="l00347" name="l00347"></a><span class="lineno">  347</span>    t2 = omp_get_wtime();</div>
+<div class="line"><a id="l00348" name="l00348"></a><span class="lineno">  348</span> </div>
+<div class="line"><a id="l00349" name="l00349"></a><span class="lineno">  349</span>    std::cout &lt;&lt; <span class="stringliteral">&quot;Time narrow sweep no interaction  : &quot;</span> &lt;&lt; (t2 - t1)</div>
+<div class="line"><a id="l00350" name="l00350"></a><span class="lineno">  350</span>              &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00351" name="l00351"></a><span class="lineno">  351</span> </div>
+<div class="line"><a id="l00352" name="l00352"></a><span class="lineno">  352</span>    t1 = omp_get_wtime();</div>
+<div class="line"><a id="l00353" name="l00353"></a><span class="lineno">  353</span> </div>
+<div class="line"><a id="l00354" name="l00354"></a><span class="lineno">  354</span>    <a class="code hl_function" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>();</div>
+<div class="line"><a id="l00355" name="l00355"></a><span class="lineno">  355</span> </div>
+<div class="line"><a id="l00356" name="l00356"></a><span class="lineno">  356</span>    t2 = omp_get_wtime();</div>
+<div class="line"><a id="l00357" name="l00357"></a><span class="lineno">  357</span> </div>
+<div class="line"><a id="l00358" name="l00358"></a><span class="lineno">  358</span>    std::cout &lt;&lt; <span class="stringliteral">&quot;Time narrow sweep with interaction: &quot;</span> &lt;&lt; (t2 - t1)</div>
+<div class="line"><a id="l00359" name="l00359"></a><span class="lineno">  359</span>              &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00360" name="l00360"></a><span class="lineno">  360</span> </div>
+<div class="line"><a id="l00361" name="l00361"></a><span class="lineno">  361</span>    end = omp_get_wtime();</div>
+<div class="line"><a id="l00362" name="l00362"></a><span class="lineno">  362</span> </div>
+<div class="line"><a id="l00363" name="l00363"></a><span class="lineno">  363</span>    std::cout &lt;&lt; <span class="stringliteral">&quot;Time                              : &quot;</span> &lt;&lt; (end - start)</div>
+<div class="line"><a id="l00364" name="l00364"></a><span class="lineno">  364</span>              &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00365" name="l00365"></a><span class="lineno">  365</span> </div>
+<div class="line"><a id="l00366" name="l00366"></a><span class="lineno">  366</span>    <span class="keywordflow">return</span> 0;</div>
+<div class="line"><a id="l00367" name="l00367"></a><span class="lineno">  367</span>}</div>
+<div class="ttc" id="aPenningTrap_8hpp_html"><div class="ttname"><a href="PenningTrap_8hpp.html">PenningTrap.hpp</a></div><div class="ttdoc">A class for simulating a Penning trap.</div></div>
+<div class="ttc" id="aclassParticle_html"><div class="ttname"><a href="classParticle.html">Particle</a></div><div class="ttdoc">A class that holds attributes of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00022">Particle.hpp:23</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00031">PenningTrap.hpp:32</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_aaee129f177657455348d0c8ae1441dea"><div class="ttname"><a href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap::reinitialize</a></div><div class="ttdeci">void reinitialize(double f, double omega_V, double t=0.)</div><div class="ttdoc">Give all particles new positions and velocities, and change t and V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00148">PenningTrap.cpp:148</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ac529aa26c288f34eae184a67e6bac41f"><div class="ttname"><a href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap::fraction_of_particles_left</a></div><div class="ttdeci">double fraction_of_particles_left(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and calculate what fraction of particles are still left inside the Penning trap after the si...</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00297">PenningTrap.cpp:297</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ad8bc4df7ab3eed53b16cfdff38e7760b"><div class="ttname"><a href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap::write_simulation_to_dir</a></div><div class="ttdeci">void write_simulation_to_dir(std::string path, double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and write the displacement of all particles to files.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00259">PenningTrap.cpp:259</a></div></div>
+<div class="ttc" id="aconstants_8hpp_html"><div class="ttname"><a href="constants_8hpp.html">constants.hpp</a></div><div class="ttdoc">Library of constants.</div></div>
+<div class="ttc" id="aconstants_8hpp_html_a0acb682b8260ab1c60b918599864e2e5"><div class="ttname"><a href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a></div><div class="ttdeci">#define T</div><div class="ttdoc">1 Tesla. unit:</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00021">constants.hpp:21</a></div></div>
+<div class="ttc" id="aconstants_8hpp_html_a2ff491cc7958ffd5e749c518a4a60ec8"><div class="ttname"><a href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">CA_MASS</a></div><div class="ttdeci">#define CA_MASS</div><div class="ttdoc">Mass of a single calcium ion. unit: amu.</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00029">constants.hpp:29</a></div></div>
+<div class="ttc" id="aconstants_8hpp_html_af40a326b23c68a27cebe60f16634a2cb"><div class="ttname"><a href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a></div><div class="ttdeci">#define V</div><div class="ttdoc">1 Volt. unit:</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00025">constants.hpp:25</a></div></div>
+<div class="ttc" id="amain_8cpp_html_a213713d6ecc02a32b588ffd179dc7513"><div class="ttname"><a href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a></div><div class="ttdeci">void simulate_100_particles()</div><div class="ttdoc">Simulate 100 particles over 50 .</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00132">main.cpp:132</a></div></div>
+<div class="ttc" id="amain_8cpp_html_a2efa69bb9d93049429ce4637075f1d30"><div class="ttname"><a href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a></div><div class="ttdeci">Particle p1(vec3{20., 0., 20.}, vec3{0., 25., 0.})</div><div class="ttdoc">Particle 1.</div></div>
+<div class="ttc" id="amain_8cpp_html_a33d9b1c76c3c80902f89a58b1a6d96ea"><div class="ttname"><a href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a></div><div class="ttdeci">void potential_resonance_narrow_sweep()</div><div class="ttdoc">Simulate 100 particles over 500  using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00206">main.cpp:206</a></div></div>
+<div class="ttc" id="amain_8cpp_html_a6b38b477c18e2f4268779751a88edab1"><div class="ttname"><a href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a></div><div class="ttdeci">void potential_resonance_wide_sweep()</div><div class="ttdoc">Simulate 100 particles over 500  using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00149">main.cpp:149</a></div></div>
+<div class="ttc" id="amain_8cpp_html_a783789519f97c6430081171cacb0ffb1"><div class="ttname"><a href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a></div><div class="ttdeci">void simulate_two_particles()</div><div class="ttdoc">Simulate 2 particles over the period of 50  with and without particle interactions.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00069">main.cpp:69</a></div></div>
+<div class="ttc" id="amain_8cpp_html_a8d92fb2ad085065fbd14718647551657"><div class="ttname"><a href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a></div><div class="ttdeci">vec3 analytical_solution_particle_1(double t)</div><div class="ttdoc">The analytical solution for particle p1.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00037">main.cpp:37</a></div></div>
+<div class="ttc" id="amain_8cpp_html_a8fdbe2d5a872e50ef5ec1263243589d6"><div class="ttname"><a href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a></div><div class="ttdeci">void simulate_single_particle()</div><div class="ttdoc">Simulate a single particle over the period of 50 .</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00054">main.cpp:54</a></div></div>
+<div class="ttc" id="amain_8cpp_html_ac1816f70ec612edc27848ef7f0875fdb"><div class="ttname"><a href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a></div><div class="ttdeci">void potential_resonance_narrow_sweep_interaction()</div><div class="ttdoc">Simulate 100 particles over 500  using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00262">main.cpp:262</a></div></div>
+<div class="ttc" id="amain_8cpp_html_ac67e0d59227856c4d42e7d01c75e0ad2"><div class="ttname"><a href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a></div><div class="ttdeci">void simulate_single_particle_with_different_steps()</div><div class="ttdoc">Simulate a single particle over 50  using different amount of steps and different methods.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00087">main.cpp:87</a></div></div>
+<div class="ttc" id="amain_8cpp_html_ac70b61df65f4336f57ea9b4c35250df7"><div class="ttname"><a href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">p2</a></div><div class="ttdeci">Particle p2(vec3{25., 25., 0.}, vec3{0., 40., 5.})</div><div class="ttdoc">Particle 2.</div></div>
+<div class="ttc" id="astructsimulation_html"><div class="ttname"><a href="structsimulation.html">simulation</a></div><div class="ttdoc">Typedef for PenningTrap::simulation return value.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00040">typedefs.hpp:40</a></div></div>
+<div class="ttc" id="atypedefs_8hpp_html_a3bdfb73a02f88ae32b6128ef747c4aea"><div class="ttname"><a href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a></div><div class="ttdeci">arma::vec::fixed&lt; 3 &gt; vec3</div><div class="ttdoc">Typedef for a fixed 3d arma vector.</div><div class="ttdef"><b>Definition:</b> <a href="typedefs_8hpp_source.html#l00023">typedefs.hpp:23</a></div></div>
+<div class="ttc" id="autils_8hpp_html"><div class="ttname"><a href="utils_8hpp.html">utils.hpp</a></div><div class="ttdoc">Function prototypes and macros that are useful.</div></div>
+<div class="ttc" id="autils_8hpp_html_a6fdd7217b750aff5b6295ece7cbdeffa"><div class="ttname"><a href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a></div><div class="ttdeci">bool mkpath(std::string path, int mode=0777)</div><div class="ttdoc">Make path given.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00072">utils.cpp:72</a></div></div>
 </div><!-- fragment --></div><!-- contents -->
 </div><!-- doc-content -->
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docs/menudata.js

@@ -29,13 +29,39 @@ var menudata={children:[
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 {text:"Class Index",url:"classes.html"},
 {text:"Class Members",url:"functions.html",children:[
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+{text:"d",url:"functions.html#index_d"},
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+{text:"k",url:"functions.html#index_k"},
+{text:"m",url:"functions.html#index_m"},
+{text:"p",url:"functions.html#index_p"},
+{text:"q",url:"functions.html#index_q"},
+{text:"r",url:"functions.html#index_r"},
+{text:"s",url:"functions.html#index_s"},
+{text:"t",url:"functions.html#index_t"},
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 {text:"File Members",url:"globals.html",children:[
-{text:"All",url:"globals.html"},
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docs/navtreedata.js

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+<div class="line"><a id="l00011" name="l00011"></a><span class="lineno">   11</span>    labels = [</div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span>        <span class="stringliteral">&quot;particle 1 no interaction&quot;</span>,</div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span>        <span class="stringliteral">&quot;particle 2 no interaction&quot;</span>,</div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span>        <span class="stringliteral">&quot;particle 1 with interaction&quot;</span>,</div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span>        <span class="stringliteral">&quot;particle 2 with interaction&quot;</span>,</div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span>    ]</div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span>    colors = [</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>        <span class="stringliteral">&quot;lightskyblue&quot;</span>,</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>        <span class="stringliteral">&quot;lightskyblue&quot;</span>,</div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>        <span class="stringliteral">&quot;salmon&quot;</span>,</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>        <span class="stringliteral">&quot;salmon&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="keywordflow">for</span> label, color, file <span class="keywordflow">in</span> zip(labels, colors, files):</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>        <span class="keyword">with</span> open(file) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>            lines = f.readlines()</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>            t = np.linspace(0, 50, len(lines))</div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span>            r = np.array([list(map(float, line.strip().split(<span class="stringliteral">&quot;,&quot;</span>))) <span class="keywordflow">for</span> line <span class="keywordflow">in</span> lines])</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>            plt.plot(r[:,0], r[:,1], label=label, color=color)</div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span>    </div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span>    plt.xlabel(<span class="stringliteral">r&quot;x $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span>    plt.ylabel(<span class="stringliteral">r&quot;y $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>    plt.title(<span class="stringliteral">r&quot;2 particles with and without interactions.&quot;</span>)</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span>    <span class="comment"># plt.legend()</span></div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span>    <span class="comment"># plt.show()</span></div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span>    plt.savefig(<span class="stringliteral">&quot;../latex/images/plot_2_particles_xy.pdf&quot;</span>)</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span> </div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span> </div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span><span class="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span>    main()</div>
+</div><!-- fragment --></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_634e799a3947388232110823971192a8.html">scripts</a></li><li class="navelem"><b>plot_2_particles.py</b></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.6 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/plot__3d_8py_source.html

@@ -0,0 +1,154 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=11"/>
+<meta name="generator" content="Doxygen 1.9.6"/>
+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+<title>Penning Trap Simulation: src/scripts/plot_3d.py Source File</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<script type="text/javascript" src="navtreedata.js"></script>
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+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/x-mathjax-config">
+MathJax.Hub.Config({
+  extensions: ["tex2jax.js"],
+  jax: ["input/TeX","output/HTML-CSS"],
+});
+</script>
+<script type="text/javascript" async="async" src="https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">Penning Trap Simulation
+   </div>
+   <div id="projectbrief">Simulate particle behavior inside a Penning Trap</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.9.6 -->
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+var searchBox = new SearchBox("searchBox", "search/",'.html');
+/* @license-end */
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+<script type="text/javascript">
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+       class="ui-resizable-handle">
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+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+</div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<div id="MSearchResults">
+<div class="SRPage">
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+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">plot_3d.py</div></div>
+</div><!--header-->
+<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><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> </div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span><span class="keyword">def </span>main():</div>
+<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span>    files = [</div>
+<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span>        <span class="stringliteral">&quot;output/simulate_2_particles/no_interaction/particle_0_r.txt&quot;</span>,</div>
+<div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span>        <span class="stringliteral">&quot;output/simulate_2_particles/no_interaction/particle_1_r.txt&quot;</span>,</div>
+<div class="line"><a id="l00008" name="l00008"></a><span class="lineno">    8</span>        <span class="stringliteral">&quot;output/simulate_2_particles/with_interaction/particle_0_r.txt&quot;</span>,</div>
+<div class="line"><a id="l00009" name="l00009"></a><span class="lineno">    9</span>        <span class="stringliteral">&quot;output/simulate_2_particles/with_interaction/particle_1_r.txt&quot;</span></div>
+<div class="line"><a id="l00010" name="l00010"></a><span class="lineno">   10</span>    ]</div>
+<div class="line"><a id="l00011" name="l00011"></a><span class="lineno">   11</span>    labels = [</div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span>        <span class="stringliteral">&quot;particle 1 no interaction&quot;</span>,</div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span>        <span class="stringliteral">&quot;particle 2 no interaction&quot;</span>,</div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span>        <span class="stringliteral">&quot;particle 1 with interaction&quot;</span>,</div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span>        <span class="stringliteral">&quot;particle 2 with interaction&quot;</span>,</div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span>    ]</div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span>    colors = [</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>        <span class="stringliteral">&quot;lightskyblue&quot;</span>,</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>        <span class="stringliteral">&quot;deepskyblue&quot;</span>,</div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>        <span class="stringliteral">&quot;salmon&quot;</span>,</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>        <span class="stringliteral">&quot;darkred&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>    ax = plt.figure().add_subplot(projection=<span class="stringliteral">&quot;3d&quot;</span>)</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>    <span class="keywordflow">for</span> label, color, file <span class="keywordflow">in</span> zip(labels, colors, files):</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>        <span class="keyword">with</span> open(file) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>            lines = f.readlines()</div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span>            t = np.linspace(0, 50, len(lines))</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>            r = np.array([list(map(float, line.strip().split(<span class="stringliteral">&quot;,&quot;</span>))) <span class="keywordflow">for</span> line <span class="keywordflow">in</span> lines])</div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span>            ax.plot(r[:,0], r[:,1], r[:,2], label=label, color=color)</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>    ax.set_xlabel(<span class="stringliteral">r&quot;x $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>    ax.set_ylabel(<span class="stringliteral">r&quot;y $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span>    ax.set_zlabel(<span class="stringliteral">r&quot;z $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span>    plt.title(<span class="stringliteral">r&quot;2 particles with and without interactions.&quot;</span>)</div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span>    plt.legend()</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span>    plt.savefig(<span class="stringliteral">&quot;../latex/images/3d_plot.pdf&quot;</span>)</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span> </div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span> </div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span><span class="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>    main()</div>
+</div><!-- fragment --></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_634e799a3947388232110823971192a8.html">scripts</a></li><li class="navelem"><b>plot_3d.py</b></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.6 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/plot__particles__left_8py_source.html

@@ -0,0 +1,182 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=11"/>
+<meta name="generator" content="Doxygen 1.9.6"/>
+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+<title>Penning Trap Simulation: src/scripts/plot_particles_left.py Source File</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtreedata.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/searchdata.js"></script>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/x-mathjax-config">
+MathJax.Hub.Config({
+  extensions: ["tex2jax.js"],
+  jax: ["input/TeX","output/HTML-CSS"],
+});
+</script>
+<script type="text/javascript" async="async" src="https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">Penning Trap Simulation
+   </div>
+   <div id="projectbrief">Simulate particle behavior inside a Penning Trap</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.9.6 -->
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+var searchBox = new SearchBox("searchBox", "search/",'.html');
+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search');
+  $(document).ready(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
+    <div id="nav-tree-contents">
+      <div id="nav-sync" class="sync"></div>
+    </div>
+  </div>
+  <div id="splitbar" style="-moz-user-select:none;" 
+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+</div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<div id="MSearchResults">
+<div class="SRPage">
+<div id="SRIndex">
+<div id="SRResults"></div>
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">plot_particles_left.py</div></div>
+</div><!--header-->
+<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><span class="keyword">import</span> seaborn <span class="keyword">as</span> sns</div>
+<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span> </div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span>sns.set_theme()</div>
+<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span>params = {</div>
+<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>, </div>
+<div class="line"><a id="l00008" name="l00008"></a><span class="lineno">    8</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><a id="l00009" name="l00009"></a><span class="lineno">    9</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00010" name="l00010"></a><span class="lineno">   10</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00011" name="l00011"></a><span class="lineno">   11</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</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>plt.rcParams.update(params)</div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span> </div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span><span class="keyword">def </span>main():</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>    colors = [</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>        <span class="stringliteral">&quot;lightskyblue&quot;</span>,</div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>        <span class="stringliteral">&quot;deepskyblue&quot;</span>,</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>        <span class="stringliteral">&quot;salmon&quot;</span>,</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>        <span class="stringliteral">&quot;tomato&quot;</span>,</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>        <span class="stringliteral">&quot;mediumaquamarine&quot;</span>,</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>        <span class="stringliteral">&quot;mediumseagreen&quot;</span></div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>    ]</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>    files = [</div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span>        <span class="stringliteral">&quot;output/time_dependent_potential/wide_sweep.txt&quot;</span>,</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>        <span class="stringliteral">&quot;output/time_dependent_potential/narrow_sweep.txt&quot;</span>,</div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span>        <span class="stringliteral">&quot;output/time_dependent_potential/narrow_sweep_interactions.txt&quot;</span>,</div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span>    ]</div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span>    outputs = [</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>        <span class="stringliteral">&quot;../latex/images/wide_sweep.pdf&quot;</span>,</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span>        <span class="stringliteral">&quot;../latex/images/narrow_sweep.pdf&quot;</span>,</div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span>        <span class="stringliteral">&quot;../latex/images/narrow_sweep_interactions.pdf&quot;</span>,</div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span>    ]</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span>    <span class="keywordflow">for</span> file, output <span class="keywordflow">in</span> zip(files, outputs):</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span>        <span class="keyword">with</span> open(file) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>            lines = f.readlines()</div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span>            x = []</div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>            y1 = []</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>            y2 = []</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>            y3 = []</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>            <span class="keywordflow">for</span> line <span class="keywordflow">in</span> lines:</div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span>                l = line.strip().split(<span class="stringliteral">&quot;,&quot;</span>)</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span>                x.append(float(l[0]))</div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>                y1.append(float(l[1]))</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>                y2.append(float(l[2]))</div>
+<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span>                y3.append(float(l[3]))</div>
+<div class="line"><a id="l00049" name="l00049"></a><span class="lineno">   49</span> </div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span>            fig, ax = plt.subplots()</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span>            ax.plot(x, y1, label=<span class="stringliteral">r&quot;$f_{1} = 0.1$&quot;</span>, color=colors[0])</div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span>            ax.plot(x, y2, label=<span class="stringliteral">r&quot;$f_{2} = 0.4$&quot;</span>, color=colors[2])</div>
+<div class="line"><a id="l00053" name="l00053"></a><span class="lineno">   53</span>            ax.plot(x, y3, label=<span class="stringliteral">r&quot;$f_{3} = 0.7$&quot;</span>, color=colors[4])</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>        ax.set_xlabel(<span class="stringliteral">r&quot;Frequency $\omega_V$ (MHz)&quot;</span>)</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno">   56</span>        <span class="comment"># ax.set_xlim((0, 2.8))</span></div>
+<div class="line"><a id="l00057" name="l00057"></a><span class="lineno">   57</span>        ax.set_ylabel(<span class="stringliteral">r&quot;Fraction of particles left&quot;</span>)</div>
+<div class="line"><a id="l00058" name="l00058"></a><span class="lineno">   58</span>        <span class="comment"># ax.set_ylim((-0.1, 1.1))</span></div>
+<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   59</span>        <span class="comment"># plt.title(r&quot;The fraction of particles left in the Penning trap &quot;</span></div>
+<div class="line"><a id="l00060" name="l00060"></a><span class="lineno">   60</span>        <span class="comment">#           &quot;after 500 microseconds for different amplitudes and frequencies&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>        ax.legend(loc=<span class="stringliteral">&quot;upper right&quot;</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>        <span class="comment"># plt.show()</span></div>
+<div class="line"><a id="l00065" name="l00065"></a><span class="lineno">   65</span>        fig.savefig(output, bbox_inches=<span class="stringliteral">&quot;tight&quot;</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><span class="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
+<div class="line"><a id="l00068" name="l00068"></a><span class="lineno">   68</span>    main()</div>
+</div><!-- fragment --></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_634e799a3947388232110823971192a8.html">scripts</a></li><li class="navelem"><b>plot_particles_left.py</b></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.6 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/plot__phase__space_8py_source.html

@@ -0,0 +1,167 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=11"/>
+<meta name="generator" content="Doxygen 1.9.6"/>
+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+<title>Penning Trap Simulation: src/scripts/plot_phase_space.py Source File</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/searchdata.js"></script>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/x-mathjax-config">
+MathJax.Hub.Config({
+  extensions: ["tex2jax.js"],
+  jax: ["input/TeX","output/HTML-CSS"],
+});
+</script>
+<script type="text/javascript" async="async" src="https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">Penning Trap Simulation
+   </div>
+   <div id="projectbrief">Simulate particle behavior inside a Penning Trap</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.9.6 -->
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+var searchBox = new SearchBox("searchBox", "search/",'.html');
+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+</div>
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+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<div id="MSearchResults">
+<div class="SRPage">
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+<div id="SRResults"></div>
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">plot_phase_space.py</div></div>
+</div><!--header-->
+<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><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> </div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span><span class="keyword">def </span>main():</div>
+<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span>    directories = {</div>
+<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span>        <span class="stringliteral">&quot;output/simulate_2_particles/no_interaction/&quot;</span>,</div>
+<div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span>        <span class="stringliteral">&quot;output/simulate_2_particles/with_interaction/&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>    titles = {</div>
+<div class="line"><a id="l00010" name="l00010"></a><span class="lineno">   10</span>        <span class="stringliteral">&quot;particles without interaction&quot;</span>,</div>
+<div class="line"><a id="l00011" name="l00011"></a><span class="lineno">   11</span>        <span class="stringliteral">&quot;particles with interaction&quot;</span></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>    files = [</div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span>        <span class="stringliteral">&quot;particle_0_r.txt&quot;</span>,</div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span>        <span class="stringliteral">&quot;particle_0_v.txt&quot;</span>,</div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span>        <span class="stringliteral">&quot;particle_1_r.txt&quot;</span>,</div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span>        <span class="stringliteral">&quot;particle_1_v.txt&quot;</span>,</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>    ]</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>    labels = [</div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>        <span class="stringliteral">r&quot;particle 1 r&quot;</span>,</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>        <span class="stringliteral">r&quot;particle 1 v&quot;</span>,</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>        <span class="stringliteral">r&quot;particle 2 r&quot;</span>,</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>        <span class="stringliteral">r&quot;particle 2 v&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>    colors = [</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>        <span class="stringliteral">&quot;lightskyblue&quot;</span>,</div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span>        <span class="stringliteral">&quot;deepskyblue&quot;</span>,</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>        <span class="stringliteral">&quot;salmon&quot;</span>,</div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span>        <span class="stringliteral">&quot;tomato&quot;</span>,</div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span>    ]</div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span>    fig1, axs1 = plt.subplots(2,1)</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>    fig2, axs2 = plt.subplots(2,1)</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span>    <span class="keywordflow">for</span> i, (dir, title) <span class="keywordflow">in</span> enumerate(zip(directories, titles)):</div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span>        <span class="keywordflow">for</span> label, color, file <span class="keywordflow">in</span> zip(labels, colors, files):</div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span>            <span class="keyword">with</span> open(dir+file) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span>                lines = f.readlines()</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span>                t = np.linspace(0, 50, len(lines))</div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>                r = np.array([list(map(float, line.strip().split(<span class="stringliteral">&quot;,&quot;</span>))) <span class="keywordflow">for</span> line <span class="keywordflow">in</span> lines])</div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span>                axs1[i].plot(t, r[:,0], label=label, color=color)</div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>                axs2[i].plot(t, r[:,2], label=label, color=color)</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>            axs1[i].set(xlabel=<span class="stringliteral">r&quot;t $(\mu s)$&quot;</span>, ylabel = <span class="stringliteral">r&quot;z $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>        </div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span>        axs1[i].legend()</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span>        axs1[i].set_title(title)</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="comment"># plt.show()</span></div>
+<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span>    fig1.savefig(<span class="stringliteral">&quot;../latex/images/phase_space_2_particles_x.pdf&quot;</span>)</div>
+<div class="line"><a id="l00049" name="l00049"></a><span class="lineno">   49</span>    fig2.savefig(<span class="stringliteral">&quot;../latex/images/phase_space_2_particles_z.pdf&quot;</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> </div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span><span class="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
+<div class="line"><a id="l00053" name="l00053"></a><span class="lineno">   53</span>    main()</div>
+</div><!-- fragment --></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_634e799a3947388232110823971192a8.html">scripts</a></li><li class="navelem"><b>plot_phase_space.py</b></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.6 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/plot__relative__error_8py_source.html

@@ -0,0 +1,165 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=11"/>
+<meta name="generator" content="Doxygen 1.9.6"/>
+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+<title>Penning Trap Simulation: src/scripts/plot_relative_error.py Source File</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
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+MathJax.Hub.Config({
+  extensions: ["tex2jax.js"],
+  jax: ["input/TeX","output/HTML-CSS"],
+});
+</script>
+<script type="text/javascript" async="async" src="https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">Penning Trap Simulation
+   </div>
+   <div id="projectbrief">Simulate particle behavior inside a Penning Trap</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.9.6 -->
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+var searchBox = new SearchBox("searchBox", "search/",'.html');
+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
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+  $(document).ready(function() { init_search(); });
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+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+</div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<div id="MSearchResults">
+<div class="SRPage">
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+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">plot_relative_error.py</div></div>
+</div><!--header-->
+<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><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> </div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span><span class="keyword">def </span>main():</div>
+<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span>    directories = [</div>
+<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span>        <span class="stringliteral">&quot;output/relative_error/RK4/&quot;</span>,</div>
+<div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span>        <span class="stringliteral">&quot;output/relative_error/euler/&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>    files = [</div>
+<div class="line"><a id="l00010" name="l00010"></a><span class="lineno">   10</span>        <span class="stringliteral">&quot;4000_steps.txt&quot;</span>,</div>
+<div class="line"><a id="l00011" name="l00011"></a><span class="lineno">   11</span>        <span class="stringliteral">&quot;8000_steps.txt&quot;</span>,</div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span>        <span class="stringliteral">&quot;16000_steps.txt&quot;</span>,</div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span>        <span class="stringliteral">&quot;32000_steps.txt&quot;</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>    labels = [</div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span>        <span class="stringliteral">r&quot;4000 steps&quot;</span>,</div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span>        <span class="stringliteral">r&quot;8000 steps&quot;</span>,</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>        <span class="stringliteral">r&quot;16000 steps&quot;</span>,</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>        <span class="stringliteral">r&quot;32000 steps&quot;</span>,</div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>    ]</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>    titles = [</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>        <span class="stringliteral">&quot;Relative error for the RK4 method&quot;</span>,</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>        <span class="stringliteral">&quot;Relative error for the forward Euler method&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>    methods = [</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>        <span class="stringliteral">&quot;rk4&quot;</span>,</div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span>        <span class="stringliteral">&quot;euler&quot;</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>    fig1, axs1 = plt.subplots(2,1)</div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span>    <span class="keywordflow">for</span> i, (dir, title) <span class="keywordflow">in</span> enumerate(list(zip(directories, titles))):</div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span>        max_err = []</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>        <span class="keywordflow">for</span> label, file <span class="keywordflow">in</span> zip(labels, files):</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span>            <span class="keyword">with</span> open(dir+file) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span>                lines = f.readlines()</div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span>                t = np.linspace(0, 50, len(lines))</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span>                r = np.array([float(line.strip()) <span class="keywordflow">for</span> line <span class="keywordflow">in</span> lines])</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span>                max_err.append(max(r))</div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>                axs1[i].plot(t, r, label=label)</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>        axs1[i].set(xlabel=<span class="stringliteral">r&quot;t $(\mu s)$&quot;</span>, ylabel = <span class="stringliteral">r&quot;relative_error $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>        axs1[i].legend()</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>        axs1[i].set_title(title)</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>        conv_rate = 1/3 * sum([np.log2(max_err[i+1]/max_err[i])/np.log2(.5) <span class="keywordflow">for</span> i <span class="keywordflow">in</span> range(3)])</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span>        print(f<span class="stringliteral">&quot;{methods[i]}: {conv_rate}&quot;</span>)</div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span> </div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>    fig1.savefig(<span class="stringliteral">&quot;../latex/images/phase_space_2_particles_x.pdf&quot;</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> </div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span><span class="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span>    main()</div>
+</div><!-- fragment --></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_634e799a3947388232110823971192a8.html">scripts</a></li><li class="navelem"><b>plot_relative_error.py</b></li>
+    <li class="footer">Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.6 </li>
+  </ul>
+</div>
+</body>
+</html>

docs/plot__single__particle_8py_source.html

@@ -0,0 +1,144 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=11"/>
+<meta name="generator" content="Doxygen 1.9.6"/>
+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+<title>Penning Trap Simulation: src/scripts/plot_single_particle.py Source File</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtreedata.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/searchdata.js"></script>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/x-mathjax-config">
+MathJax.Hub.Config({
+  extensions: ["tex2jax.js"],
+  jax: ["input/TeX","output/HTML-CSS"],
+});
+</script>
+<script type="text/javascript" async="async" src="https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+<link href="doxygen-awesome.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr id="projectrow">
+  <td id="projectalign">
+   <div id="projectname">Penning Trap Simulation
+   </div>
+   <div id="projectbrief">Simulate particle behavior inside a Penning Trap</div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.9.6 -->
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+var searchBox = new SearchBox("searchBox", "search/",'.html');
+/* @license-end */
+</script>
+<script type="text/javascript" src="menudata.js"></script>
+<script type="text/javascript" src="menu.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(function() {
+  initMenu('',true,false,'search.php','Search');
+  $(document).ready(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
+    <div id="nav-tree-contents">
+      <div id="nav-sync" class="sync"></div>
+    </div>
+  </div>
+  <div id="splitbar" style="-moz-user-select:none;" 
+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(document).ready(function(){initNavTree('plot__single__particle_8py_source.html',''); initResizable(); });
+/* @license-end */
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+</div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<div id="MSearchResults">
+<div class="SRPage">
+<div id="SRIndex">
+<div id="SRResults"></div>
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</div>
+</div>
+</div>
+
+<div class="header">
+  <div class="headertitle"><div class="title">plot_single_particle.py</div></div>
+</div><!--header-->
+<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><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> </div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span><span class="keyword">def </span>z(t):</div>
+<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span>    V_0 = 25.*9.64852558 * 10**4</div>
+<div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span>    m = 40.</div>
+<div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span>    d = 500.</div>
+<div class="line"><a id="l00008" name="l00008"></a><span class="lineno">    8</span>    w_z = np.sqrt((2.*V_0)/(m*d*d))</div>
+<div class="line"><a id="l00009" name="l00009"></a><span class="lineno">    9</span>    <span class="keywordflow">return</span> 20.*np.cos(w_z*t)</div>
+<div class="line"><a id="l00010" name="l00010"></a><span class="lineno">   10</span> </div>
+<div class="line"><a id="l00011" name="l00011"></a><span class="lineno">   11</span><span class="keyword">def </span>main():</div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span>    filename = <span class="stringliteral">&quot;output/simulate_single_particle/particle_0_r.txt&quot;</span></div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span>    r = t = []</div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span>    <span class="keyword">with</span> open(filename) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span>        lines = f.readlines()</div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span>        t = np.linspace(0, 50, len(lines))</div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span>        r = np.array([list(map(float, line.strip().split(<span class="stringliteral">&quot;,&quot;</span>))) <span class="keywordflow">for</span> line <span class="keywordflow">in</span> lines])</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span> </div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>    plt.plot(t, r[:, 2], label=<span class="stringliteral">&quot;approximation&quot;</span>)</div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>    plt.plot(t, z(t), label=<span class="stringliteral">&quot;analytical&quot;</span>)</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>    plt.xlabel(<span class="stringliteral">r&quot;time $(\mu s)$&quot;</span>)</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>    plt.ylabel(<span class="stringliteral">r&quot;z $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>    plt.title(<span class="stringliteral">r&quot;Movement of a single particle in the x direction&quot;</span>)</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>    plt.legend()</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>    <span class="comment"># plt.savefig(&quot;../latex/images/single_particle.pdf&quot;)</span></div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>    plt.show()</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>
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+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span>    main()</div>
+</div><!-- fragment --></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
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