Merge pull request #16 from FYS3150-G2-2023/develop

Develop

.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 +1,142 @@
 # 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>
+```
+
+### Batch system
+
+For the **frequency_narrow_sweeps_long** program, the is a script called 
+**job.script** that comes along with it. This is to be able to run it on a
+batch system using Slurm if you have access to one. 
+This is the recommended way to use this program as it takes approximately 90 
+minutes to complete when using 16 cores.
+
+If you happen to have such a system available to you, then you should clone
+this repo on that system, then compile it by running:
+
+```shell
+    make frequency_narrow_sweeps_long
+```
+
+You might have to load the Armadillo library before compiling.
+
+After compiling, you can schedule it by running:
+
+```shell
+    sbatch job.script
+```
+
+## 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#_bug000008">Bug:</a></b></dt><dd>No known bugs </dd></dl>
 
 <p class="definition">Definition in file <a class="el" href="Particle_8cpp_source.html">Particle.cpp</a>.</p>
 </div></div><!-- contents -->

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

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

docs/PenningTrap_8cpp_source.html

@@ -102,69 +102,377 @@ $(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="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="l00013" name="l00013"></a><span class="lineno">   13</span><span class="preprocessor">#include &lt;algorithm&gt;</span></div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="preprocessor">#include &lt;functional&gt;</span></div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="preprocessor">#include &lt;sys/types.h&gt;</span></div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span> </div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span><span class="preprocessor">#include &quot;<a class="code" href="typedefs_8hpp.html">typedefs.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span> </div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">   21</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap::v_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt)</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>{</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>    <span class="keywordflow">switch</span> (i) {</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>    <span class="keywordflow">case</span> 0:</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>        <span class="keywordflow">return</span> .5 * dt * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>[0][j];</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>    <span class="keywordflow">case</span> 1:</div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span>        <span class="keywordflow">return</span> .5 * dt * this-&gt;k_v[1][j];</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>    <span class="keywordflow">case</span> 2:</div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span>        <span class="keywordflow">return</span> dt * this-&gt;k_v[2][j];</div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span>    <span class="keywordflow">case</span> 3:</div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span>        <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((dt / 6.)</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>                    * (this-&gt;k_v[0][j] + 2. * this-&gt;k_v[1][j]</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span>                       + 2. * this-&gt;k_v[2][j] + this-&gt;k_v[3][j]));</div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span>    <span class="keywordflow">default</span>:</div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span>        abort();</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span>    }</div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>}</div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span> </div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">   40</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">PenningTrap::r_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt)</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>{</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>    <span class="keywordflow">switch</span> (i) {</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>    <span class="keywordflow">case</span> 0:</div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span>        <span class="keywordflow">return</span> .5 * dt * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>[0][j];</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span>    <span class="keywordflow">case</span> 1:</div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>        <span class="keywordflow">return</span> .5 * dt * this-&gt;k_r[1][j];</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>    <span class="keywordflow">case</span> 2:</div>
+<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span>        <span class="keywordflow">return</span> dt * this-&gt;k_r[2][j];</div>
+<div class="line"><a id="l00049" name="l00049"></a><span class="lineno">   49</span>    <span class="keywordflow">case</span> 3:</div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span>        <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((dt / 6.)</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span>                    * (this-&gt;k_r[0][j] + 2. * this-&gt;k_r[1][j]</div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span>                       + 2. * this-&gt;k_r[2][j] + this-&gt;k_r[3][j]));</div>
+<div class="line"><a id="l00053" name="l00053"></a><span class="lineno">   53</span>    <span class="keywordflow">default</span>:</div>
+<div class="line"><a id="l00054" name="l00054"></a><span class="lineno">   54</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Not valid!&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00055" name="l00055"></a><span class="lineno">   55</span>        abort();</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno">   56</span>    }</div>
+<div class="line"><a id="l00057" name="l00057"></a><span class="lineno">   57</span>}</div>
 <div class="line"><a id="l00058" name="l00058"></a><span class="lineno">   58</span> </div>
-<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   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="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="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="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="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="l00059" name="l00059"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">   59</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">PenningTrap::external_E_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r)</div>
+<div class="line"><a id="l00060" name="l00060"></a><span class="lineno">   60</span>{</div>
+<div class="line"><a id="l00061" name="l00061"></a><span class="lineno">   61</span>    r(2) *= -2.;</div>
+<div class="line"><a id="l00062" name="l00062"></a><span class="lineno">   62</span> </div>
+<div class="line"><a id="l00063" name="l00063"></a><span class="lineno">   63</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(</div>
+<div class="line"><a id="l00064" name="l00064"></a><span class="lineno">   64</span>        ((this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</a>(this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>)) / (this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>)) * r);</div>
+<div class="line"><a id="l00065" name="l00065"></a><span class="lineno">   65</span>}</div>
+<div class="line"><a id="l00066" name="l00066"></a><span class="lineno">   66</span> </div>
+<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">   67</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">PenningTrap::external_B_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r)</div>
+<div class="line"><a id="l00068" name="l00068"></a><span class="lineno">   68</span>{</div>
+<div class="line"><a id="l00069" name="l00069"></a><span class="lineno">   69</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 0., this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>};</div>
+<div class="line"><a id="l00070" name="l00070"></a><span class="lineno">   70</span>}</div>
+<div class="line"><a id="l00071" name="l00071"></a><span class="lineno">   71</span> </div>
+<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">   72</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap::force_on_particle</a>(uint i, uint j)</div>
+<div class="line"><a id="l00073" name="l00073"></a><span class="lineno">   73</span>{</div>
+<div class="line"><a id="l00074" name="l00074"></a><span class="lineno">   74</span>    <span class="comment">// Calculate the difference between the particles&#39; position</span></div>
+<div class="line"><a id="l00075" name="l00075"></a><span class="lineno">   75</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec - this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].r_vec;</div>
+<div class="line"><a id="l00076" name="l00076"></a><span class="lineno">   76</span> </div>
+<div class="line"><a id="l00077" name="l00077"></a><span class="lineno">   77</span>    <span class="comment">// Get the distance between the particles</span></div>
+<div class="line"><a id="l00078" name="l00078"></a><span class="lineno">   78</span>    <span class="keywordtype">double</span> norm = arma::norm(res, 2);</div>
+<div class="line"><a id="l00079" name="l00079"></a><span class="lineno">   79</span> </div>
+<div class="line"><a id="l00080" name="l00080"></a><span class="lineno">   80</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>((this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].q / (norm * norm * norm)) * res);</div>
+<div class="line"><a id="l00081" name="l00081"></a><span class="lineno">   81</span>}</div>
+<div class="line"><a id="l00082" name="l00082"></a><span class="lineno">   82</span> </div>
+<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">   83</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap::total_force_external</a>(uint i)</div>
+<div class="line"><a id="l00084" name="l00084"></a><span class="lineno">   84</span>{</div>
+<div class="line"><a id="l00085" name="l00085"></a><span class="lineno">   85</span>    <a class="code hl_class" href="classParticle.html">Particle</a> *p = &amp;this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i];</div>
+<div class="line"><a id="l00086" name="l00086"></a><span class="lineno">   86</span> </div>
+<div class="line"><a id="l00087" name="l00087"></a><span class="lineno">   87</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(p-&gt;<a class="code hl_variable" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a></div>
+<div class="line"><a id="l00088" name="l00088"></a><span class="lineno">   88</span>                * (this-&gt;external_E_field(p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>)</div>
+<div class="line"><a id="l00089" name="l00089"></a><span class="lineno">   89</span>                   + arma::cross(p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a>, this-&gt;external_B_field(p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>))));</div>
+<div class="line"><a id="l00090" name="l00090"></a><span class="lineno">   90</span>}</div>
+<div class="line"><a id="l00091" name="l00091"></a><span class="lineno">   91</span> </div>
+<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">   92</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap::total_force_particles</a>(uint i)</div>
+<div class="line"><a id="l00093" name="l00093"></a><span class="lineno">   93</span>{</div>
+<div class="line"><a id="l00094" name="l00094"></a><span class="lineno">   94</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res;</div>
+<div class="line"><a id="l00095" name="l00095"></a><span class="lineno">   95</span> </div>
+<div class="line"><a id="l00096" name="l00096"></a><span class="lineno">   96</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); j++) {</div>
+<div class="line"><a id="l00097" name="l00097"></a><span class="lineno">   97</span>        <span class="keywordflow">if</span> (i != j)</div>
+<div class="line"><a id="l00098" name="l00098"></a><span class="lineno">   98</span>            res += this-&gt;<a class="code hl_function" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">force_on_particle</a>(i, j);</div>
+<div class="line"><a id="l00099" name="l00099"></a><span class="lineno">   99</span>    }</div>
+<div class="line"><a id="l00100" name="l00100"></a><span class="lineno">  100</span> </div>
+<div class="line"><a id="l00101" name="l00101"></a><span class="lineno">  101</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(res * (<a class="code hl_define" href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">K_E</a> * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].q));</div>
+<div class="line"><a id="l00102" name="l00102"></a><span class="lineno">  102</span>}</div>
+<div class="line"><a id="l00103" name="l00103"></a><span class="lineno">  103</span> </div>
+<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">  104</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a>(uint i)</div>
+<div class="line"><a id="l00105" name="l00105"></a><span class="lineno">  105</span>{</div>
+<div class="line"><a id="l00106" name="l00106"></a><span class="lineno">  106</span>    <span class="keywordflow">if</span> (arma::norm(this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec) &gt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>) {</div>
+<div class="line"><a id="l00107" name="l00107"></a><span class="lineno">  107</span>        <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 0., 0.};</div>
+<div class="line"><a id="l00108" name="l00108"></a><span class="lineno">  108</span>    }</div>
+<div class="line"><a id="l00109" name="l00109"></a><span class="lineno">  109</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(this-&gt;<a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">total_force_external</a>(i) - this-&gt;<a class="code hl_function" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">total_force_particles</a>(i));</div>
+<div class="line"><a id="l00110" name="l00110"></a><span class="lineno">  110</span>}</div>
+<div class="line"><a id="l00111" name="l00111"></a><span class="lineno">  111</span> </div>
+<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">  112</a></span><a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap::total_force_no_interaction</a>(uint i)</div>
+<div class="line"><a id="l00113" name="l00113"></a><span class="lineno">  113</span>{</div>
+<div class="line"><a id="l00114" name="l00114"></a><span class="lineno">  114</span>    <span class="keywordflow">if</span> (arma::norm(this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec) &gt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>) {</div>
+<div class="line"><a id="l00115" name="l00115"></a><span class="lineno">  115</span>        <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>{0., 0., 0.};</div>
+<div class="line"><a id="l00116" name="l00116"></a><span class="lineno">  116</span>    }</div>
+<div class="line"><a id="l00117" name="l00117"></a><span class="lineno">  117</span>    <span class="keywordflow">return</span> <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(this-&gt;<a class="code hl_function" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">total_force_external</a>(i));</div>
+<div class="line"><a id="l00118" name="l00118"></a><span class="lineno">  118</span>}</div>
+<div class="line"><a id="l00119" name="l00119"></a><span class="lineno">  119</span> </div>
+<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">  120</a></span><a class="code hl_function" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a>(<span class="keywordtype">double</span> B_0, <span class="keywordtype">double</span> V_0, <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</div>
+<div class="line"><a id="l00121" name="l00121"></a><span class="lineno">  121</span>{</div>
+<div class="line"><a id="l00122" name="l00122"></a><span class="lineno">  122</span>    this-&gt;B_0 = <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a>;</div>
+<div class="line"><a id="l00123" name="l00123"></a><span class="lineno">  123</span>    this-&gt;V_0 = <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a>;</div>
+<div class="line"><a id="l00124" name="l00124"></a><span class="lineno">  124</span>    this-&gt;d = <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</div>
+<div class="line"><a id="l00125" name="l00125"></a><span class="lineno">  125</span>    this-&gt;t = <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>;</div>
+<div class="line"><a id="l00126" name="l00126"></a><span class="lineno">  126</span>    this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</a> = [](<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>) { <span class="keywordflow">return</span> 1.; };</div>
+<div class="line"><a id="l00127" name="l00127"></a><span class="lineno">  127</span>}</div>
+<div class="line"><a id="l00128" name="l00128"></a><span class="lineno">  128</span> </div>
+<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a830be1b8cbf59664e060b6edbeaa302f">  129</a></span><a class="code hl_function" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a>(uint i, <span class="keywordtype">double</span> B_0, <span class="keywordtype">double</span> V_0, <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</div>
+<div class="line"><a id="l00130" name="l00130"></a><span class="lineno">  130</span>    : <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(B_0, V_0, d)</div>
+<div class="line"><a id="l00131" name="l00131"></a><span class="lineno">  131</span>{</div>
+<div class="line"><a id="l00132" name="l00132"></a><span class="lineno">  132</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; i; j++) {</div>
+<div class="line"><a id="l00133" name="l00133"></a><span class="lineno">  133</span>        this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(</div>
+<div class="line"><a id="l00134" name="l00134"></a><span class="lineno">  134</span>            <a class="code hl_class" href="classParticle.html">Particle</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>().randn() * .1 * this-&gt;d),</div>
+<div class="line"><a id="l00135" name="l00135"></a><span class="lineno">  135</span>                     <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>().randn() * .1 * this-&gt;d)));</div>
+<div class="line"><a id="l00136" name="l00136"></a><span class="lineno">  136</span>    }</div>
+<div class="line"><a id="l00137" name="l00137"></a><span class="lineno">  137</span>}</div>
+<div class="line"><a id="l00138" name="l00138"></a><span class="lineno">  138</span> </div>
+<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"><a class="line" href="classPenningTrap.html#addc96789dcfec07b75156e19fee82f4f">  139</a></span><a class="code hl_function" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a>(std::vector&lt;Particle&gt; particles, <span class="keywordtype">double</span> B_0,</div>
+<div class="line"><a id="l00140" name="l00140"></a><span class="lineno">  140</span>                         <span class="keywordtype">double</span> V_0, <span class="keywordtype">double</span> d, <span class="keywordtype">double</span> t)</div>
+<div class="line"><a id="l00141" name="l00141"></a><span class="lineno">  141</span>    : <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(B_0, V_0, d)</div>
+<div class="line"><a id="l00142" name="l00142"></a><span class="lineno">  142</span>{</div>
+<div class="line"><a id="l00143" name="l00143"></a><span class="lineno">  143</span>    this-&gt;particles = <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
+<div class="line"><a id="l00144" name="l00144"></a><span class="lineno">  144</span>}</div>
+<div class="line"><a id="l00145" name="l00145"></a><span class="lineno">  145</span> </div>
+<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">  146</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">PenningTrap::set_pertubation</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V)</div>
+<div class="line"><a id="l00147" name="l00147"></a><span class="lineno">  147</span>{</div>
+<div class="line"><a id="l00148" name="l00148"></a><span class="lineno">  148</span>    this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</a> = [f, omega_V](<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>) {</div>
+<div class="line"><a id="l00149" name="l00149"></a><span class="lineno">  149</span>        <span class="keywordflow">return</span> 1 + f * std::cos(omega_V * <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>);</div>
+<div class="line"><a id="l00150" name="l00150"></a><span class="lineno">  150</span>    };</div>
+<div class="line"><a id="l00151" name="l00151"></a><span class="lineno">  151</span>}</div>
+<div class="line"><a id="l00152" name="l00152"></a><span class="lineno">  152</span> </div>
+<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"><a class="line" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">  153</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap::reinitialize</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V, <span class="keywordtype">double</span> t)</div>
+<div class="line"><a id="l00154" name="l00154"></a><span class="lineno">  154</span>{</div>
+<div class="line"><a id="l00155" name="l00155"></a><span class="lineno">  155</span>    this-&gt;t = <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a>;</div>
+<div class="line"><a id="l00156" name="l00156"></a><span class="lineno">  156</span>    this-&gt;<a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">set_pertubation</a>(f, omega_V);</div>
+<div class="line"><a id="l00157" name="l00157"></a><span class="lineno">  157</span>    <a class="code hl_class" href="classParticle.html">Particle</a> *p;</div>
+<div class="line"><a id="l00158" name="l00158"></a><span class="lineno">  158</span> </div>
+<div class="line"><a id="l00159" name="l00159"></a><span class="lineno">  159</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); i++) {</div>
+<div class="line"><a id="l00160" name="l00160"></a><span class="lineno">  160</span>        p = &amp;this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i];</div>
+<div class="line"><a id="l00161" name="l00161"></a><span class="lineno">  161</span>        p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a> = <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>().randn() * .1 * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</div>
+<div class="line"><a id="l00162" name="l00162"></a><span class="lineno">  162</span>        p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a> = <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>().randn() * .1 * this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>;</div>
+<div class="line"><a id="l00163" name="l00163"></a><span class="lineno">  163</span>    }</div>
+<div class="line"><a id="l00164" name="l00164"></a><span class="lineno">  164</span>}</div>
+<div class="line"><a id="l00165" name="l00165"></a><span class="lineno">  165</span> </div>
+<div class="line"><a id="l00166" name="l00166"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">  166</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap::add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a> particle)</div>
+<div class="line"><a id="l00167" name="l00167"></a><span class="lineno">  167</span>{</div>
+<div class="line"><a id="l00168" name="l00168"></a><span class="lineno">  168</span>    this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.push_back(particle);</div>
+<div class="line"><a id="l00169" name="l00169"></a><span class="lineno">  169</span>}</div>
+<div class="line"><a id="l00170" name="l00170"></a><span class="lineno">  170</span> </div>
+<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">  171</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction)</div>
+<div class="line"><a id="l00172" name="l00172"></a><span class="lineno">  172</span>{</div>
+<div class="line"><a id="l00173" name="l00173"></a><span class="lineno">  173</span>    <a class="code hl_class" href="classParticle.html">Particle</a> *p;</div>
+<div class="line"><a id="l00174" name="l00174"></a><span class="lineno">  174</span> </div>
+<div class="line"><a id="l00175" name="l00175"></a><span class="lineno">  175</span>    <span class="comment">// Keep original particles</span></div>
+<div class="line"><a id="l00176" name="l00176"></a><span class="lineno">  176</span>    std::vector&lt;Particle&gt; original_particles = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
+<div class="line"><a id="l00177" name="l00177"></a><span class="lineno">  177</span>    std::vector&lt;Particle&gt; tmp_particles = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>;</div>
+<div class="line"><a id="l00178" name="l00178"></a><span class="lineno">  178</span> </div>
+<div class="line"><a id="l00179" name="l00179"></a><span class="lineno">  179</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*force)(uint) =</div>
+<div class="line"><a id="l00180" name="l00180"></a><span class="lineno">  180</span>        particle_interaction ? &amp;<a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div>
+<div class="line"><a id="l00181" name="l00181"></a><span class="lineno">  181</span>                             : &amp;<a class="code hl_function" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap::total_force_no_interaction</a>;</div>
+<div class="line"><a id="l00182" name="l00182"></a><span class="lineno">  182</span> </div>
+<div class="line"><a id="l00183" name="l00183"></a><span class="lineno">  183</span>    <span class="keywordtype">size_t</span> size = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div>
+<div class="line"><a id="l00184" name="l00184"></a><span class="lineno">  184</span> </div>
+<div class="line"><a id="l00185" name="l00185"></a><span class="lineno">  185</span>    <span class="comment">// Allocating takes a long time, so reuse sim_arr if possible</span></div>
+<div class="line"><a id="l00186" name="l00186"></a><span class="lineno">  186</span>    <span class="keywordflow">if</span> (this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>.size() != 4 || this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>.size() != 4</div>
+<div class="line"><a id="l00187" name="l00187"></a><span class="lineno">  187</span>        || this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>[0].size() != size || this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>[0].size() != size) {</div>
+<div class="line"><a id="l00188" name="l00188"></a><span class="lineno">  188</span>        this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a> = <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(4, <a class="code hl_typedef" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a>(size));</div>
+<div class="line"><a id="l00189" name="l00189"></a><span class="lineno">  189</span>        this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a> = <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(4, <a class="code hl_typedef" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a>(size));</div>
+<div class="line"><a id="l00190" name="l00190"></a><span class="lineno">  190</span>    }</div>
+<div class="line"><a id="l00191" name="l00191"></a><span class="lineno">  191</span> </div>
+<div class="line"><a id="l00192" name="l00192"></a><span class="lineno">  192</span>    <span class="comment">// Each k_{i+1} is dependent on k_i, so outer loop is not parallelizable</span></div>
+<div class="line"><a id="l00193" name="l00193"></a><span class="lineno">  193</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 4; i++) {</div>
+<div class="line"><a id="l00194" name="l00194"></a><span class="lineno">  194</span>        <span class="comment">// Inner loop is able to be parallelized</span></div>
+<div class="line"><a id="l00195" name="l00195"></a><span class="lineno">  195</span><span class="preprocessor">#pragma omp parallel for private(p)</span></div>
+<div class="line"><a id="l00196" name="l00196"></a><span class="lineno">  196</span>        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; size; j++) {</div>
+<div class="line"><a id="l00197" name="l00197"></a><span class="lineno">  197</span>            this-&gt;<a class="code hl_variable" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">k_v</a>[i][j] = (this-&gt;*force)(j) / this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].m;</div>
+<div class="line"><a id="l00198" name="l00198"></a><span class="lineno">  198</span>            this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">k_r</a>[i][j] = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[j].v_vec;</div>
+<div class="line"><a id="l00199" name="l00199"></a><span class="lineno">  199</span> </div>
+<div class="line"><a id="l00200" name="l00200"></a><span class="lineno">  200</span>            p = &amp;tmp_particles[j];</div>
+<div class="line"><a id="l00201" name="l00201"></a><span class="lineno">  201</span> </div>
+<div class="line"><a id="l00202" name="l00202"></a><span class="lineno">  202</span>            p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a> = original_particles[j].v_vec + this-&gt;<a class="code hl_function" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">v_func</a>(i, j, dt);</div>
+<div class="line"><a id="l00203" name="l00203"></a><span class="lineno">  203</span>            p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a> = original_particles[j].r_vec + this-&gt;<a class="code hl_function" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">r_func</a>(i, j, dt);</div>
+<div class="line"><a id="l00204" name="l00204"></a><span class="lineno">  204</span>        }</div>
+<div class="line"><a id="l00205" name="l00205"></a><span class="lineno">  205</span>        this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a> = tmp_particles;</div>
+<div class="line"><a id="l00206" name="l00206"></a><span class="lineno">  206</span>    }</div>
+<div class="line"><a id="l00207" name="l00207"></a><span class="lineno">  207</span> </div>
+<div class="line"><a id="l00208" name="l00208"></a><span class="lineno">  208</span>    this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> += dt;</div>
+<div class="line"><a id="l00209" name="l00209"></a><span class="lineno">  209</span>}</div>
+<div class="line"><a id="l00210" name="l00210"></a><span class="lineno">  210</span> </div>
+<div class="line"><a id="l00211" name="l00211"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">  211</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction)</div>
+<div class="line"><a id="l00212" name="l00212"></a><span class="lineno">  212</span>{</div>
+<div class="line"><a id="l00213" name="l00213"></a><span class="lineno">  213</span>    <span class="keywordtype">size_t</span> size = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div>
+<div class="line"><a id="l00214" name="l00214"></a><span class="lineno">  214</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> force_res[size];</div>
+<div class="line"><a id="l00215" name="l00215"></a><span class="lineno">  215</span>    <a class="code hl_class" href="classParticle.html">Particle</a> *p;</div>
+<div class="line"><a id="l00216" name="l00216"></a><span class="lineno">  216</span> </div>
+<div class="line"><a id="l00217" name="l00217"></a><span class="lineno">  217</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*force)(uint) =</div>
+<div class="line"><a id="l00218" name="l00218"></a><span class="lineno">  218</span>        particle_interaction ? &amp;<a class="code hl_function" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div>
+<div class="line"><a id="l00219" name="l00219"></a><span class="lineno">  219</span>                             : &amp;<a class="code hl_function" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap::total_force_no_interaction</a>;</div>
+<div class="line"><a id="l00220" name="l00220"></a><span class="lineno">  220</span> </div>
+<div class="line"><a id="l00221" name="l00221"></a><span class="lineno">  221</span>    <span class="comment">// Calculating the force for each particle is independent and therefore</span></div>
+<div class="line"><a id="l00222" name="l00222"></a><span class="lineno">  222</span>    <span class="comment">// a good candidate for parallel execution</span></div>
+<div class="line"><a id="l00223" name="l00223"></a><span class="lineno">  223</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00224" name="l00224"></a><span class="lineno">  224</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; size; i++) {</div>
+<div class="line"><a id="l00225" name="l00225"></a><span class="lineno">  225</span>        force_res[i] = (this-&gt;*force)(i);</div>
+<div class="line"><a id="l00226" name="l00226"></a><span class="lineno">  226</span>    }</div>
+<div class="line"><a id="l00227" name="l00227"></a><span class="lineno">  227</span> </div>
+<div class="line"><a id="l00228" name="l00228"></a><span class="lineno">  228</span>    <span class="comment">// Updating the particles is also independent, so we can parallelize</span></div>
+<div class="line"><a id="l00229" name="l00229"></a><span class="lineno">  229</span>    <span class="comment">// this as well</span></div>
+<div class="line"><a id="l00230" name="l00230"></a><span class="lineno">  230</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00231" name="l00231"></a><span class="lineno">  231</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; size; i++) {</div>
+<div class="line"><a id="l00232" name="l00232"></a><span class="lineno">  232</span>        p = &amp;this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i];</div>
+<div class="line"><a id="l00233" name="l00233"></a><span class="lineno">  233</span>        p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a> += dt * p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a>;</div>
+<div class="line"><a id="l00234" name="l00234"></a><span class="lineno">  234</span>        p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a> += dt * force_res[i] / p-&gt;<a class="code hl_variable" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>;</div>
+<div class="line"><a id="l00235" name="l00235"></a><span class="lineno">  235</span>    }</div>
+<div class="line"><a id="l00236" name="l00236"></a><span class="lineno">  236</span> </div>
+<div class="line"><a id="l00237" name="l00237"></a><span class="lineno">  237</span>    this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> += dt;</div>
+<div class="line"><a id="l00238" name="l00238"></a><span class="lineno">  238</span>}</div>
+<div class="line"><a id="l00239" name="l00239"></a><span class="lineno">  239</span> </div>
+<div class="line"><a id="l00240" name="l00240"></a><span class="lineno"><a class="line" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">  240</a></span><a class="code hl_struct" href="structsimulation.html">simulation_t</a> <a class="code hl_function" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap::simulate</a>(<span class="keywordtype">double</span> time, uint steps, std::string method,</div>
+<div class="line"><a id="l00241" name="l00241"></a><span class="lineno">  241</span>                                   <span class="keywordtype">bool</span> particle_interaction)</div>
+<div class="line"><a id="l00242" name="l00242"></a><span class="lineno">  242</span>{</div>
+<div class="line"><a id="l00243" name="l00243"></a><span class="lineno">  243</span>    <a class="code hl_class" href="classParticle.html">Particle</a> *p;</div>
+<div class="line"><a id="l00244" name="l00244"></a><span class="lineno">  244</span>    <span class="keywordtype">double</span> dt = time / (double)steps;</div>
+<div class="line"><a id="l00245" name="l00245"></a><span class="lineno">  245</span> </div>
+<div class="line"><a id="l00246" name="l00246"></a><span class="lineno">  246</span>    uint size = this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div>
+<div class="line"><a id="l00247" name="l00247"></a><span class="lineno">  247</span> </div>
+<div class="line"><a id="l00248" name="l00248"></a><span class="lineno">  248</span>    <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res{<a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(size, <a class="code hl_typedef" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a>(steps)),</div>
+<div class="line"><a id="l00249" name="l00249"></a><span class="lineno">  249</span>                     <a class="code hl_typedef" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">sim_arr</a>(size, <a class="code hl_typedef" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">sim_cols</a>(steps))};</div>
+<div class="line"><a id="l00250" name="l00250"></a><span class="lineno">  250</span> </div>
+<div class="line"><a id="l00251" name="l00251"></a><span class="lineno">  251</span>    void (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*func)(double, bool);</div>
+<div class="line"><a id="l00252" name="l00252"></a><span class="lineno">  252</span>    <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;rk4&quot;</span>) {</div>
+<div class="line"><a id="l00253" name="l00253"></a><span class="lineno">  253</span>        func = &amp;<a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a>;</div>
+<div class="line"><a id="l00254" name="l00254"></a><span class="lineno">  254</span>    } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;euler&quot;</span>) {</div>
+<div class="line"><a id="l00255" name="l00255"></a><span class="lineno">  255</span>        func = &amp;<a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>;</div>
+<div class="line"><a id="l00256" name="l00256"></a><span class="lineno">  256</span>    } <span class="keywordflow">else</span> {</div>
+<div class="line"><a id="l00257" name="l00257"></a><span class="lineno">  257</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Not a valid method!&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00258" name="l00258"></a><span class="lineno">  258</span>        abort();</div>
+<div class="line"><a id="l00259" name="l00259"></a><span class="lineno">  259</span>    }</div>
+<div class="line"><a id="l00260" name="l00260"></a><span class="lineno">  260</span> </div>
+<div class="line"><a id="l00261" name="l00261"></a><span class="lineno">  261</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; steps; j++) {</div>
+<div class="line"><a id="l00262" name="l00262"></a><span class="lineno">  262</span>        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; size; i++) {</div>
+<div class="line"><a id="l00263" name="l00263"></a><span class="lineno">  263</span>            p = &amp;this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i];</div>
+<div class="line"><a id="l00264" name="l00264"></a><span class="lineno">  264</span>            res.r_vecs[i][j] = p-&gt;<a class="code hl_variable" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a>;</div>
+<div class="line"><a id="l00265" name="l00265"></a><span class="lineno">  265</span>            res.v_vecs[i][j] = p-&gt;<a class="code hl_variable" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a>;</div>
+<div class="line"><a id="l00266" name="l00266"></a><span class="lineno">  266</span>        }</div>
+<div class="line"><a id="l00267" name="l00267"></a><span class="lineno">  267</span>        (this-&gt;*func)(dt, particle_interaction);</div>
+<div class="line"><a id="l00268" name="l00268"></a><span class="lineno">  268</span>    }</div>
+<div class="line"><a id="l00269" name="l00269"></a><span class="lineno">  269</span> </div>
+<div class="line"><a id="l00270" name="l00270"></a><span class="lineno">  270</span>    <span class="keywordflow">return</span> res;</div>
+<div class="line"><a id="l00271" name="l00271"></a><span class="lineno">  271</span>}</div>
+<div class="line"><a id="l00272" name="l00272"></a><span class="lineno">  272</span> </div>
+<div class="line"><a id="l00273" name="l00273"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">  273</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap::write_simulation_to_dir</a>(std::string path, <span class="keywordtype">double</span> time,</div>
+<div class="line"><a id="l00274" name="l00274"></a><span class="lineno">  274</span>                                          uint steps, std::string method,</div>
+<div class="line"><a id="l00275" name="l00275"></a><span class="lineno">  275</span>                                          <span class="keywordtype">bool</span> particle_interaction)</div>
+<div class="line"><a id="l00276" name="l00276"></a><span class="lineno">  276</span>{</div>
+<div class="line"><a id="l00277" name="l00277"></a><span class="lineno">  277</span>    <span class="keywordflow">if</span> (path.back() != <span class="charliteral">&#39;/&#39;</span>) {</div>
+<div class="line"><a id="l00278" name="l00278"></a><span class="lineno">  278</span>        path += <span class="charliteral">&#39;/&#39;</span>;</div>
+<div class="line"><a id="l00279" name="l00279"></a><span class="lineno">  279</span>    }</div>
+<div class="line"><a id="l00280" name="l00280"></a><span class="lineno">  280</span>    <span class="keywordflow">if</span> (<a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path, 0777) != 0) {</div>
+<div class="line"><a id="l00281" name="l00281"></a><span class="lineno">  281</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Failed to make path&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00282" name="l00282"></a><span class="lineno">  282</span>        abort();</div>
+<div class="line"><a id="l00283" name="l00283"></a><span class="lineno">  283</span>    }</div>
+<div class="line"><a id="l00284" name="l00284"></a><span class="lineno">  284</span> </div>
+<div class="line"><a id="l00285" name="l00285"></a><span class="lineno">  285</span>    <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res =</div>
+<div class="line"><a id="l00286" name="l00286"></a><span class="lineno">  286</span>        this-&gt;<a class="code hl_function" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">simulate</a>(time, steps, method, particle_interaction);</div>
+<div class="line"><a id="l00287" name="l00287"></a><span class="lineno">  287</span> </div>
+<div class="line"><a id="l00288" name="l00288"></a><span class="lineno">  288</span>    std::ofstream ofile;</div>
+<div class="line"><a id="l00289" name="l00289"></a><span class="lineno">  289</span> </div>
+<div class="line"><a id="l00290" name="l00290"></a><span class="lineno">  290</span>    <span class="comment">// Writing each particle to its own file is independent and can be run in</span></div>
+<div class="line"><a id="l00291" name="l00291"></a><span class="lineno">  291</span>    <span class="comment">// parallel.</span></div>
+<div class="line"><a id="l00292" name="l00292"></a><span class="lineno">  292</span><span class="preprocessor">#pragma omp parallel for private(ofile)</span></div>
+<div class="line"><a id="l00293" name="l00293"></a><span class="lineno">  293</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); i++) {</div>
+<div class="line"><a id="l00294" name="l00294"></a><span class="lineno">  294</span>        ofile.open(path + <span class="stringliteral">&quot;particle_&quot;</span> + std::to_string(i) + <span class="stringliteral">&quot;_r.txt&quot;</span>);</div>
+<div class="line"><a id="l00295" name="l00295"></a><span class="lineno">  295</span>        <span class="keywordflow">for</span> (<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> &amp;vec : res.r_vecs[i]) {</div>
+<div class="line"><a id="l00296" name="l00296"></a><span class="lineno">  296</span>            ofile &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(0), 10, 8) &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00297" name="l00297"></a><span class="lineno">  297</span>                  &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(1), 10, 8) &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00298" name="l00298"></a><span class="lineno">  298</span>                  &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(2), 10, 8) &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00299" name="l00299"></a><span class="lineno">  299</span>        }</div>
+<div class="line"><a id="l00300" name="l00300"></a><span class="lineno">  300</span>        ofile.close();</div>
+<div class="line"><a id="l00301" name="l00301"></a><span class="lineno">  301</span>        ofile.open(path + <span class="stringliteral">&quot;particle_&quot;</span> + std::to_string(i) + <span class="stringliteral">&quot;_v.txt&quot;</span>);</div>
+<div class="line"><a id="l00302" name="l00302"></a><span class="lineno">  302</span>        <span class="keywordflow">for</span> (<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> &amp;vec : res.v_vecs[i]) {</div>
+<div class="line"><a id="l00303" name="l00303"></a><span class="lineno">  303</span>            ofile &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(0), 10, 8) &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00304" name="l00304"></a><span class="lineno">  304</span>                  &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(1), 10, 8) &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00305" name="l00305"></a><span class="lineno">  305</span>                  &lt;&lt; <a class="code hl_function" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">scientific_format</a>(vec(2), 10, 8) &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00306" name="l00306"></a><span class="lineno">  306</span>        }</div>
+<div class="line"><a id="l00307" name="l00307"></a><span class="lineno">  307</span>        ofile.close();</div>
+<div class="line"><a id="l00308" name="l00308"></a><span class="lineno">  308</span>    }</div>
+<div class="line"><a id="l00309" name="l00309"></a><span class="lineno">  309</span>}</div>
+<div class="line"><a id="l00310" name="l00310"></a><span class="lineno">  310</span> </div>
+<div class="line"><a id="l00311" name="l00311"></a><span class="lineno"><a class="line" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">  311</a></span><span class="keywordtype">double</span> <a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap::fraction_of_particles_left</a>(<span class="keywordtype">double</span> time, uint steps,</div>
+<div class="line"><a id="l00312" name="l00312"></a><span class="lineno">  312</span>                                               std::string method,</div>
+<div class="line"><a id="l00313" name="l00313"></a><span class="lineno">  313</span>                                               <span class="keywordtype">bool</span> particle_interaction)</div>
+<div class="line"><a id="l00314" name="l00314"></a><span class="lineno">  314</span>{</div>
+<div class="line"><a id="l00315" name="l00315"></a><span class="lineno">  315</span>    <span class="keywordtype">double</span> dt = time / (double)steps;</div>
+<div class="line"><a id="l00316" name="l00316"></a><span class="lineno">  316</span> </div>
+<div class="line"><a id="l00317" name="l00317"></a><span class="lineno">  317</span>    void (<a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>::*func)(double, bool);</div>
+<div class="line"><a id="l00318" name="l00318"></a><span class="lineno">  318</span>    <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;rk4&quot;</span>) {</div>
+<div class="line"><a id="l00319" name="l00319"></a><span class="lineno">  319</span>        func = &amp;<a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a>;</div>
+<div class="line"><a id="l00320" name="l00320"></a><span class="lineno">  320</span>    } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (method == <span class="stringliteral">&quot;euler&quot;</span>) {</div>
+<div class="line"><a id="l00321" name="l00321"></a><span class="lineno">  321</span>        func = &amp;<a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a>;</div>
+<div class="line"><a id="l00322" name="l00322"></a><span class="lineno">  322</span>    } <span class="keywordflow">else</span> {</div>
+<div class="line"><a id="l00323" name="l00323"></a><span class="lineno">  323</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Not a valid method!&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00324" name="l00324"></a><span class="lineno">  324</span>        abort();</div>
+<div class="line"><a id="l00325" name="l00325"></a><span class="lineno">  325</span>    }</div>
+<div class="line"><a id="l00326" name="l00326"></a><span class="lineno">  326</span> </div>
+<div class="line"><a id="l00327" name="l00327"></a><span class="lineno">  327</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; steps; j++) {</div>
+<div class="line"><a id="l00328" name="l00328"></a><span class="lineno">  328</span>        (this-&gt;*func)(dt, particle_interaction);</div>
+<div class="line"><a id="l00329" name="l00329"></a><span class="lineno">  329</span>    }</div>
+<div class="line"><a id="l00330" name="l00330"></a><span class="lineno">  330</span> </div>
+<div class="line"><a id="l00331" name="l00331"></a><span class="lineno">  331</span>    <span class="keywordtype">int</span> particles_left = 0;</div>
+<div class="line"><a id="l00332" name="l00332"></a><span class="lineno">  332</span> </div>
+<div class="line"><a id="l00333" name="l00333"></a><span class="lineno">  333</span>    <span class="comment">// A reduction is perfect here</span></div>
+<div class="line"><a id="l00334" name="l00334"></a><span class="lineno">  334</span><span class="preprocessor">#pragma omp parallel for reduction(+ : particles_left)</span></div>
+<div class="line"><a id="l00335" name="l00335"></a><span class="lineno">  335</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size(); i++) {</div>
+<div class="line"><a id="l00336" name="l00336"></a><span class="lineno">  336</span>        <span class="keywordflow">if</span> (arma::norm(this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>[i].r_vec) &lt; this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a>) {</div>
+<div class="line"><a id="l00337" name="l00337"></a><span class="lineno">  337</span>            particles_left++;</div>
+<div class="line"><a id="l00338" name="l00338"></a><span class="lineno">  338</span>        }</div>
+<div class="line"><a id="l00339" name="l00339"></a><span class="lineno">  339</span>    }</div>
+<div class="line"><a id="l00340" name="l00340"></a><span class="lineno">  340</span> </div>
+<div class="line"><a id="l00341" name="l00341"></a><span class="lineno">  341</span>    <span class="keywordflow">return</span> (<span class="keywordtype">double</span>)particles_left / (double)this-&gt;<a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>.size();</div>
+<div class="line"><a id="l00342" name="l00342"></a><span class="lineno">  342</span>}</div>
 <div class="ttc" id="aPenningTrap_8hpp_html"><div class="ttname"><a href="PenningTrap_8hpp.html">PenningTrap.hpp</a></div><div class="ttdoc">A class for simulating a Penning trap.</div></div>
-<div class="ttc" id="aclassParticle_html"><div class="ttname"><a href="classParticle.html">Particle</a></div><div class="ttdoc">A class that holds attributes of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#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="aclassParticle_html_aedcc7e1bc53b0e2b1a4a07c9a1b47563"><div class="ttname"><a href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle::m</a></div><div class="ttdeci">double m</div><div class="ttdoc">Mass.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00028">Particle.hpp:28</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00031">PenningTrap.hpp:32</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a0112525d9e79a472e761f8ef402a339f"><div class="ttname"><a href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">PenningTrap::particles</a></div><div class="ttdeci">std::vector&lt; Particle &gt; particles</div><div class="ttdoc">The particles in the Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00042">PenningTrap.hpp:42</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a0cac3509aa96e71a26d3b2c902e27716"><div class="ttname"><a href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">PenningTrap::B_0</a></div><div class="ttdeci">double B_0</div><div class="ttdoc">Magnetic field strength.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00037">PenningTrap.hpp:37</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a2c01108b52c8e2a003cf9170da9e7682"><div class="ttname"><a href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap::total_force_external</a></div><div class="ttdeci">vec3 total_force_external(uint i)</div><div class="ttdoc">Calculate the total external force on a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00083">PenningTrap.cpp:83</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a2f168622587709b9e3c49077f0b9a640"><div class="ttname"><a href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">PenningTrap::k_r</a></div><div class="ttdeci">sim_arr k_r</div><div class="ttdoc">A 2D vector containing all  where  is the index of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00052">PenningTrap.hpp:52</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a2fe1cefbae18fa5808155ee0d2df713c"><div class="ttname"><a href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap::total_force_particles</a></div><div class="ttdeci">vec3 total_force_particles(uint i)</div><div class="ttdoc">Calculate the total force on a particle p_i from other particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00092">PenningTrap.cpp:92</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a361f2c4862c90b5e8e2a2f50c6a95655"><div class="ttname"><a href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">PenningTrap::external_B_field</a></div><div class="ttdeci">vec3 external_B_field(vec3 r)</div><div class="ttdoc">Calculate B at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00067">PenningTrap.cpp:67</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a36946152fd951b1f7c346c51ff900d8e"><div class="ttname"><a href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a></div><div class="ttdeci">void evolve_RK4(double dt, bool particle_interaction=true)</div><div class="ttdoc">Go forward one timestep using the RK4 method.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00171">PenningTrap.cpp:171</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a3c0a44e4e0a94366ff609e81fe463fa2"><div class="ttname"><a href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap::v_func</a></div><div class="ttdeci">vec3 v_func(uint i, uint j, double dt)</div><div class="ttdoc">Helper for evolve_RK4 when calculating  values.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00021">PenningTrap.cpp:21</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a5846c8f75cdc543fd9cf0b2185a3ef22"><div class="ttname"><a href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">PenningTrap::external_E_field</a></div><div class="ttdeci">vec3 external_E_field(vec3 r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00059">PenningTrap.cpp:59</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a5b6c6d4636f3a6e279ccde59d4a345e8"><div class="ttname"><a href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap::PenningTrap</a></div><div class="ttdeci">PenningTrap(double B_0=T, double V_0=(25. *V)/1000., double d=500., double t=0.)</div><div class="ttdoc">Constructor for the PenningTrap class.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00120">PenningTrap.cpp:120</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a6069f82d8dbc7cadaebd228dbcd95018"><div class="ttname"><a href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap::total_force_no_interaction</a></div><div class="ttdeci">vec3 total_force_no_interaction(uint i)</div><div class="ttdoc">calculate the total force on a particle p_i without interaction</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00112">PenningTrap.cpp:112</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a66dfe89c68716b9502927b97f59c27d2"><div class="ttname"><a href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">PenningTrap::d</a></div><div class="ttdeci">double d</div><div class="ttdoc">Characteristic dimension.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00040">PenningTrap.hpp:40</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a6e9776ff5b149f01080800716455d7c8"><div class="ttname"><a href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap::add_particle</a></div><div class="ttdeci">void add_particle(Particle particle)</div><div class="ttdoc">Add a particle to the system.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00166">PenningTrap.cpp:166</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a715329844d75ec4c04f8391421fb4e89"><div class="ttname"><a href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">PenningTrap::V_0</a></div><div class="ttdeci">double V_0</div><div class="ttdoc">Applied potential.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00038">PenningTrap.hpp:38</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a7a1d9f0528a12308de25bc30718da20a"><div class="ttname"><a href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap::simulate</a></div><div class="ttdeci">simulation_t simulate(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate the particle system inside the Penning trap over a certain amount of time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00240">PenningTrap.cpp:240</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a7f210bb2768a5d79ced4b0df0df97598"><div class="ttname"><a href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap::force_on_particle</a></div><div class="ttdeci">vec3 force_on_particle(uint i, uint j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00072">PenningTrap.cpp:72</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a826b7fa8e709d481eb1dee7d0c2cdc08"><div class="ttname"><a href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">PenningTrap::r_func</a></div><div class="ttdeci">vec3 r_func(uint i, uint j, double dt)</div><div class="ttdoc">Helper for evolve_RK4 when calculating  values.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00040">PenningTrap.cpp:40</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a8ca4e21291f60fde619c14099d8c4e8e"><div class="ttname"><a href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">PenningTrap::t</a></div><div class="ttdeci">double t</div><div class="ttdoc">Current time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00041">PenningTrap.hpp:41</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a9a301b0540078c36697880ef204afdf3"><div class="ttname"><a href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div><div class="ttdeci">vec3 total_force(uint i)</div><div class="ttdoc">calculate the total force on a particle p_i.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00104">PenningTrap.cpp:104</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a9d1d8e90ca839b928aee1ad0cd4aff43"><div class="ttname"><a href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">PenningTrap::set_pertubation</a></div><div class="ttdeci">void set_pertubation(double f, double omega_V)</div><div class="ttdoc">Time dependent perturbation to V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00146">PenningTrap.cpp:146</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_aaee129f177657455348d0c8ae1441dea"><div class="ttname"><a href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap::reinitialize</a></div><div class="ttdeci">void reinitialize(double f, double omega_V, double t=0.)</div><div class="ttdoc">Give all particles new positions and velocities, and change t and V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00153">PenningTrap.cpp:153</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ab9ea97a406534bbe621a95215144875e"><div class="ttname"><a href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a></div><div class="ttdeci">void evolve_forward_euler(double dt, bool particle_interaction=true)</div><div class="ttdoc">Go forward one timestep using the forward Euler method.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00211">PenningTrap.cpp:211</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ac529aa26c288f34eae184a67e6bac41f"><div class="ttname"><a href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap::fraction_of_particles_left</a></div><div class="ttdeci">double fraction_of_particles_left(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and calculate what fraction of particles are still left inside the Penning trap after the si...</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00311">PenningTrap.cpp:311</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ad8bc4df7ab3eed53b16cfdff38e7760b"><div class="ttname"><a href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap::write_simulation_to_dir</a></div><div class="ttdeci">void write_simulation_to_dir(std::string path, double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and write the displacement of all particles to files.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00273">PenningTrap.cpp:273</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ae915f6ad0eef1fb46530e836b6e071e5"><div class="ttname"><a href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">PenningTrap::perturbation</a></div><div class="ttdeci">std::function&lt; double(double)&gt; perturbation</div><div class="ttdoc">Time-dependent perturbation.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00039">PenningTrap.hpp:39</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ae9b5afdaa5cd366e94bd294452a1eed4"><div class="ttname"><a href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">PenningTrap::k_v</a></div><div class="ttdeci">sim_arr k_v</div><div class="ttdoc">A 2D vector containing all  where  is the index of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00047">PenningTrap.hpp:47</a></div></div>
+<div class="ttc" id="aconstants_8hpp_html_a4e451456ad7e9276ed0afa42826e7ccb"><div class="ttname"><a href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">K_E</a></div><div class="ttdeci">#define K_E</div><div class="ttdoc">Coulomb constant. unit: .</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00017">constants.hpp:17</a></div></div>
+<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 +106,120 @@ $(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>
+<div class="line"><a id="l00065" name="l00065"></a><span class="lineno">   65</span> </div>
+<div class="line"><a id="l00076" name="l00076"></a><span class="lineno">   76</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">r_func</a>(uint i, uint j, <span class="keywordtype">double</span> dt);</div>
+<div class="line"><a id="l00077" name="l00077"></a><span class="lineno">   77</span> </div>
+<div class="line"><a id="l00084" name="l00084"></a><span class="lineno">   84</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">external_E_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r);</div>
+<div class="line"><a id="l00085" name="l00085"></a><span class="lineno">   85</span> </div>
+<div class="line"><a id="l00092" name="l00092"></a><span class="lineno">   92</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">external_B_field</a>(<a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> r);</div>
+<div class="line"><a id="l00093" name="l00093"></a><span class="lineno">   93</span> </div>
+<div class="line"><a id="l00104" name="l00104"></a><span class="lineno">  104</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">force_on_particle</a>(uint i, uint j);</div>
+<div class="line"><a id="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="l00140" name="l00140"></a><span class="lineno">  140</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> <a class="code hl_function" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">total_force_no_interaction</a>(uint i);</div>
+<div class="line"><a id="l00141" name="l00141"></a><span class="lineno">  141</span> </div>
+<div class="line"><a id="l00142" name="l00142"></a><span class="lineno">  142</span><span class="keyword">public</span>:</div>
+<div class="line"><a id="l00150" name="l00150"></a><span class="lineno">  150</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(<span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a> = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> = (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>) / 1000., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> = 500.,</div>
+<div class="line"><a id="l00151" name="l00151"></a><span class="lineno">  151</span>                <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
+<div class="line"><a id="l00152" name="l00152"></a><span class="lineno">  152</span> </div>
+<div class="line"><a id="l00161" name="l00161"></a><span class="lineno">  161</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(uint i, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a> = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> = (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>) / 1000.,</div>
+<div class="line"><a id="l00162" name="l00162"></a><span class="lineno">  162</span>                <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> = 500., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
+<div class="line"><a id="l00163" name="l00163"></a><span class="lineno">  163</span> </div>
+<div class="line"><a id="l00172" name="l00172"></a><span class="lineno">  172</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a>(std::vector&lt;Particle&gt; <a class="code hl_variable" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a>, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">B_0</a> = <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>,</div>
+<div class="line"><a id="l00173" name="l00173"></a><span class="lineno">  173</span>                <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a> = (25. * <a class="code hl_define" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>) / 1000., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">d</a> = 500., <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
+<div class="line"><a id="l00174" name="l00174"></a><span class="lineno">  174</span> </div>
+<div class="line"><a id="l00180" name="l00180"></a><span class="lineno">  180</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">set_pertubation</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V);</div>
+<div class="line"><a id="l00181" name="l00181"></a><span class="lineno">  181</span> </div>
+<div class="line"><a id="l00188" name="l00188"></a><span class="lineno">  188</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(<span class="keywordtype">double</span> f, <span class="keywordtype">double</span> omega_V, <span class="keywordtype">double</span> <a class="code hl_variable" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">t</a> = 0.);</div>
+<div class="line"><a id="l00189" name="l00189"></a><span class="lineno">  189</span> </div>
+<div class="line"><a id="l00194" name="l00194"></a><span class="lineno">  194</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(<a class="code hl_class" href="classParticle.html">Particle</a> particle);</div>
+<div class="line"><a id="l00195" name="l00195"></a><span class="lineno">  195</span> </div>
+<div class="line"><a id="l00201" name="l00201"></a><span class="lineno">  201</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">evolve_RK4</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
+<div class="line"><a id="l00202" name="l00202"></a><span class="lineno">  202</span> </div>
+<div class="line"><a id="l00208" name="l00208"></a><span class="lineno">  208</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">evolve_forward_euler</a>(<span class="keywordtype">double</span> dt, <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
+<div class="line"><a id="l00209" name="l00209"></a><span class="lineno">  209</span> </div>
+<div class="line"><a id="l00220" name="l00220"></a><span class="lineno">  220</span>    <a class="code hl_struct" href="structsimulation.html">simulation_t</a> <a class="code hl_function" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">simulate</a>(<span class="keywordtype">double</span> time, uint steps, std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
+<div class="line"><a id="l00221" name="l00221"></a><span class="lineno">  221</span>                          <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
+<div class="line"><a id="l00222" name="l00222"></a><span class="lineno">  222</span> </div>
+<div class="line"><a id="l00231" name="l00231"></a><span class="lineno">  231</span>    <span class="keywordtype">void</span> <a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(std::string path, <span class="keywordtype">double</span> time, uint steps,</div>
+<div class="line"><a id="l00232" name="l00232"></a><span class="lineno">  232</span>                                 std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
+<div class="line"><a id="l00233" name="l00233"></a><span class="lineno">  233</span>                                 <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
+<div class="line"><a id="l00234" name="l00234"></a><span class="lineno">  234</span> </div>
+<div class="line"><a id="l00245" name="l00245"></a><span class="lineno">  245</span>    <span class="keywordtype">double</span> <a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(<span class="keywordtype">double</span> time, uint steps,</div>
+<div class="line"><a id="l00246" name="l00246"></a><span class="lineno">  246</span>                                      std::string method = <span class="stringliteral">&quot;rk4&quot;</span>,</div>
+<div class="line"><a id="l00247" name="l00247"></a><span class="lineno">  247</span>                                      <span class="keywordtype">bool</span> particle_interaction = <span class="keyword">true</span>);</div>
+<div class="line"><a id="l00248" name="l00248"></a><span class="lineno">  248</span> </div>
+<div class="line"><a id="l00249" name="l00249"></a><span class="lineno">  249</span>};</div>
+<div class="line"><a id="l00250" name="l00250"></a><span class="lineno">  250</span> </div>
+<div class="line"><a id="l00251" name="l00251"></a><span class="lineno">  251</span><span class="preprocessor">#endif</span></div>
 <div class="ttc" id="aParticle_8hpp_html"><div class="ttname"><a href="Particle_8hpp.html">Particle.hpp</a></div><div class="ttdoc">A class that holds the properties of a particle.</div></div>
-<div class="ttc" id="aclassParticle_html"><div class="ttname"><a href="classParticle.html">Particle</a></div><div class="ttdoc">A class that holds attributes of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#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#l00083">PenningTrap.cpp:83</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a2f168622587709b9e3c49077f0b9a640"><div class="ttname"><a href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">PenningTrap::k_r</a></div><div class="ttdeci">sim_arr k_r</div><div class="ttdoc">A 2D vector containing all  where  is the index of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00052">PenningTrap.hpp:52</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a2fe1cefbae18fa5808155ee0d2df713c"><div class="ttname"><a href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap::total_force_particles</a></div><div class="ttdeci">vec3 total_force_particles(uint i)</div><div class="ttdoc">Calculate the total force on a particle p_i from other particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00092">PenningTrap.cpp:92</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a361f2c4862c90b5e8e2a2f50c6a95655"><div class="ttname"><a href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">PenningTrap::external_B_field</a></div><div class="ttdeci">vec3 external_B_field(vec3 r)</div><div class="ttdoc">Calculate B at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00067">PenningTrap.cpp:67</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a36946152fd951b1f7c346c51ff900d8e"><div class="ttname"><a href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap::evolve_RK4</a></div><div class="ttdeci">void evolve_RK4(double dt, bool particle_interaction=true)</div><div class="ttdoc">Go forward one timestep using the RK4 method.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00171">PenningTrap.cpp:171</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a3c0a44e4e0a94366ff609e81fe463fa2"><div class="ttname"><a href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap::v_func</a></div><div class="ttdeci">vec3 v_func(uint i, uint j, double dt)</div><div class="ttdoc">Helper for evolve_RK4 when calculating  values.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00021">PenningTrap.cpp:21</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a5846c8f75cdc543fd9cf0b2185a3ef22"><div class="ttname"><a href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">PenningTrap::external_E_field</a></div><div class="ttdeci">vec3 external_E_field(vec3 r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00059">PenningTrap.cpp:59</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a6069f82d8dbc7cadaebd228dbcd95018"><div class="ttname"><a href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap::total_force_no_interaction</a></div><div class="ttdeci">vec3 total_force_no_interaction(uint i)</div><div class="ttdoc">calculate the total force on a particle p_i without interaction</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00112">PenningTrap.cpp:112</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a66dfe89c68716b9502927b97f59c27d2"><div class="ttname"><a href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">PenningTrap::d</a></div><div class="ttdeci">double d</div><div class="ttdoc">Characteristic dimension.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00040">PenningTrap.hpp:40</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a6e9776ff5b149f01080800716455d7c8"><div class="ttname"><a href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap::add_particle</a></div><div class="ttdeci">void add_particle(Particle particle)</div><div class="ttdoc">Add a particle to the system.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00166">PenningTrap.cpp:166</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a715329844d75ec4c04f8391421fb4e89"><div class="ttname"><a href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">PenningTrap::V_0</a></div><div class="ttdeci">double V_0</div><div class="ttdoc">Applied potential.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00038">PenningTrap.hpp:38</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a7a1d9f0528a12308de25bc30718da20a"><div class="ttname"><a href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap::simulate</a></div><div class="ttdeci">simulation_t simulate(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate the particle system inside the Penning trap over a certain amount of time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00240">PenningTrap.cpp:240</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a7f210bb2768a5d79ced4b0df0df97598"><div class="ttname"><a href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap::force_on_particle</a></div><div class="ttdeci">vec3 force_on_particle(uint i, uint j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00072">PenningTrap.cpp:72</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a826b7fa8e709d481eb1dee7d0c2cdc08"><div class="ttname"><a href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">PenningTrap::r_func</a></div><div class="ttdeci">vec3 r_func(uint i, uint j, double dt)</div><div class="ttdoc">Helper for evolve_RK4 when calculating  values.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00040">PenningTrap.cpp:40</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a8ca4e21291f60fde619c14099d8c4e8e"><div class="ttname"><a href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">PenningTrap::t</a></div><div class="ttdeci">double t</div><div class="ttdoc">Current time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00041">PenningTrap.hpp:41</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a9a301b0540078c36697880ef204afdf3"><div class="ttname"><a href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap::total_force</a></div><div class="ttdeci">vec3 total_force(uint i)</div><div class="ttdoc">calculate the total force on a particle p_i.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00104">PenningTrap.cpp:104</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a9d1d8e90ca839b928aee1ad0cd4aff43"><div class="ttname"><a href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">PenningTrap::set_pertubation</a></div><div class="ttdeci">void set_pertubation(double f, double omega_V)</div><div class="ttdoc">Time dependent perturbation to V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00146">PenningTrap.cpp:146</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_aaee129f177657455348d0c8ae1441dea"><div class="ttname"><a href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap::reinitialize</a></div><div class="ttdeci">void reinitialize(double f, double omega_V, double t=0.)</div><div class="ttdoc">Give all particles new positions and velocities, and change t and V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00153">PenningTrap.cpp:153</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ab9ea97a406534bbe621a95215144875e"><div class="ttname"><a href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap::evolve_forward_euler</a></div><div class="ttdeci">void evolve_forward_euler(double dt, bool particle_interaction=true)</div><div class="ttdoc">Go forward one timestep using the forward Euler method.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00211">PenningTrap.cpp:211</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ac529aa26c288f34eae184a67e6bac41f"><div class="ttname"><a href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap::fraction_of_particles_left</a></div><div class="ttdeci">double fraction_of_particles_left(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and calculate what fraction of particles are still left inside the Penning trap after the si...</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00311">PenningTrap.cpp:311</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ad8bc4df7ab3eed53b16cfdff38e7760b"><div class="ttname"><a href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap::write_simulation_to_dir</a></div><div class="ttdeci">void write_simulation_to_dir(std::string path, double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and write the displacement of all particles to files.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00273">PenningTrap.cpp:273</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ae915f6ad0eef1fb46530e836b6e071e5"><div class="ttname"><a href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">PenningTrap::perturbation</a></div><div class="ttdeci">std::function&lt; double(double)&gt; perturbation</div><div class="ttdoc">Time-dependent perturbation.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00039">PenningTrap.hpp:39</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ae9b5afdaa5cd366e94bd294452a1eed4"><div class="ttname"><a href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">PenningTrap::k_v</a></div><div class="ttdeci">sim_arr k_v</div><div class="ttdoc">A 2D vector containing all  where  is the index of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00047">PenningTrap.hpp:47</a></div></div>
 <div class="ttc" id="aconstants_8hpp_html"><div class="ttname"><a href="constants_8hpp.html">constants.hpp</a></div><div class="ttdoc">Library of constants.</div></div>
-<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>
 </div><!-- fragment --></div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->

docs/animate__100__particles_8py.html

@@ -0,0 +1,216 @@
+<!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/animate_100_particles.py File Reference</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('animate__100__particles_8py.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="summary">
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle"><div class="title">animate_100_particles.py File Reference</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>Animate 100 particles.  
+<a href="#details">More...</a></p>
+
+<p><a href="animate__100__particles_8py_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:a88563d050144188c2c625a1063f9b4f8"><td class="memItemLeft" align="right" valign="top">def&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="animate__100__particles_8py.html#a88563d050144188c2c625a1063f9b4f8">animate_100_particles.get_data</a> (files)</td></tr>
+<tr class="separator:a88563d050144188c2c625a1063f9b4f8"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a8b3fbca78794cb9cd04d6059d8b63624"><td class="memItemLeft" align="right" valign="top">def&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="animate__100__particles_8py.html#a8b3fbca78794cb9cd04d6059d8b63624">animate_100_particles.update</a> (num, lines, arr)</td></tr>
+<tr class="separator:a8b3fbca78794cb9cd04d6059d8b63624"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ab5a461adc32af6d9bc9475cd6be309ca"><td class="memItemLeft" align="right" valign="top">def&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="animate__100__particles_8py.html#ab5a461adc32af6d9bc9475cd6be309ca">animate_100_particles.animate</a> ()</td></tr>
+<tr class="separator:ab5a461adc32af6d9bc9475cd6be309ca"><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>Animate 100 particles. </p>
+<dl class="section author"><dt>Author</dt><dd>Cory Alexander Balaton (coryab) </dd>
+<dd>
+Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
+<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
+<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000012">Bug:</a></b></dt><dd>No known bugs </dd></dl>
+
+<p class="definition">Definition in file <a class="el" href="animate__100__particles_8py_source.html">animate_100_particles.py</a>.</p>
+</div><h2 class="groupheader">Function Documentation</h2>
+<a id="ab5a461adc32af6d9bc9475cd6be309ca" name="ab5a461adc32af6d9bc9475cd6be309ca"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ab5a461adc32af6d9bc9475cd6be309ca">&#9670;&#160;</a></span>animate()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">def animate_100_particles.animate </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="animate__100__particles_8py_source.html#l00041">41</a> of file <a class="el" href="animate__100__particles_8py_source.html">animate_100_particles.py</a>.</p>
+
+</div>
+</div>
+<a id="a88563d050144188c2c625a1063f9b4f8" name="a88563d050144188c2c625a1063f9b4f8"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a88563d050144188c2c625a1063f9b4f8">&#9670;&#160;</a></span>get_data()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">def animate_100_particles.get_data </td>
+          <td>(</td>
+          <td class="paramtype">&#160;</td>
+          <td class="paramname"><em>files</em></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="animate__100__particles_8py_source.html#l00018">18</a> of file <a class="el" href="animate__100__particles_8py_source.html">animate_100_particles.py</a>.</p>
+
+</div>
+</div>
+<a id="a8b3fbca78794cb9cd04d6059d8b63624" name="a8b3fbca78794cb9cd04d6059d8b63624"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a8b3fbca78794cb9cd04d6059d8b63624">&#9670;&#160;</a></span>update()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">def animate_100_particles.update </td>
+          <td>(</td>
+          <td class="paramtype">&#160;</td>
+          <td class="paramname"><em>num</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">&#160;</td>
+          <td class="paramname"><em>lines</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">&#160;</td>
+          <td class="paramname"><em>arr</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="animate__100__particles_8py_source.html#l00035">35</a> of file <a class="el" href="animate__100__particles_8py_source.html">animate_100_particles.py</a>.</p>
+
+</div>
+</div>
+</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"><a class="el" href="animate__100__particles_8py.html">animate_100_particles.py</a></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/animate__100__particles_8py_source.html

@@ -0,0 +1,186 @@
+<!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/animate_100_particles.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('animate__100__particles_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">animate_100_particles.py</div></div>
+</div><!--header-->
+<div class="contents">
+<a href="animate__100__particles_8py.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="l00011" name="l00011"></a><span class="lineno">   11</span> </div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span><span class="keyword">import</span> matplotlib.pyplot <span class="keyword">as</span> plt</div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="keyword">import</span> numpy <span class="keyword">as</span> np</div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="keyword">from</span> matplotlib <span class="keyword">import</span> animation</div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="keyword">from</span> mpl_toolkits.mplot3d <span class="keyword">import</span> Axes3D</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> </div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span><span class="keyword">def </span>get_data(files):</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>    res = []</div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>    <span class="keywordflow">for</span> file <span class="keywordflow">in</span> files:</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>        arr = [[], [], []]</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</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="l00023" name="l00023"></a><span class="lineno">   23</span>            lines = f.readlines()</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>            <span class="keywordflow">for</span> line <span class="keywordflow">in</span> lines:</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>                xi, yi, zi = map(float, line.strip().split(<span class="stringliteral">&quot;,&quot;</span>))</div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span>                arr[0].append(xi)</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>                arr[1].append(yi)</div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span>                arr[2].append(zi)</div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span>        res.append(arr)</div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span> </div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>    <span class="keywordflow">return</span> np.array(res)</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><span class="keyword">def </span>update(num, lines, arr):</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span>    <span class="keywordflow">for</span> line, a <span class="keywordflow">in</span> zip(lines, arr):</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span>        line.set_data(a[:2, num - 1 : num])</div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>        line.set_3d_properties(a[2, num])</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="keyword">def </span>animate():</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>    plt.style.use(<span class="stringliteral">&quot;dark_background&quot;</span>)</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>    fig = plt.figure()</div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span>    ax = fig.add_subplot(projection=<span class="stringliteral">&quot;3d&quot;</span>)</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span> </div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>    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="l00047" name="l00047"></a><span class="lineno">   47</span> </div>
+<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span>    arr = arr[:, :, ::40]</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>    N = len(arr[0][0])</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>    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="l00053" name="l00053"></a><span class="lineno">   53</span> </div>
+<div class="line"><a id="l00054" name="l00054"></a><span class="lineno">   54</span>    ax.set_title(<span class="stringliteral">&quot;100 particles inside a Penning trap&quot;</span>)</div>
+<div class="line"><a id="l00055" name="l00055"></a><span class="lineno">   55</span>    plt.figtext(</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno">   56</span>        0.5,</div>
+<div class="line"><a id="l00057" name="l00057"></a><span class="lineno">   57</span>        0.01,</div>
+<div class="line"><a id="l00058" name="l00058"></a><span class="lineno">   58</span>        <span class="stringliteral">&quot;100 randomly generated particles &quot;</span></div>
+<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   59</span>        <span class="stringliteral">&quot;evolving over a time of 50 microseconds.&quot;</span>,</div>
+<div class="line"><a id="l00060" name="l00060"></a><span class="lineno">   60</span>        fontsize=12,</div>
+<div class="line"><a id="l00061" name="l00061"></a><span class="lineno">   61</span>        horizontalalignment=<span class="stringliteral">&quot;center&quot;</span>,</div>
+<div class="line"><a id="l00062" name="l00062"></a><span class="lineno">   62</span>    )</div>
+<div class="line"><a id="l00063" name="l00063"></a><span class="lineno">   63</span> </div>
+<div class="line"><a id="l00064" name="l00064"></a><span class="lineno">   64</span>    ax.set_xlim3d([-500.0, 500.0])</div>
+<div class="line"><a id="l00065" name="l00065"></a><span class="lineno">   65</span>    ax.set_xlabel(<span class="stringliteral">&quot;X (micrometers)&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>    ax.set_ylim3d([-500.0, 500.0])</div>
+<div class="line"><a id="l00068" name="l00068"></a><span class="lineno">   68</span>    ax.set_ylabel(<span class="stringliteral">&quot;Y (micrometers)&quot;</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>    ax.set_zlim3d([-500.0, 500.0])</div>
+<div class="line"><a id="l00071" name="l00071"></a><span class="lineno">   71</span>    ax.set_zlabel(<span class="stringliteral">&quot;Z (micrometers)&quot;</span>)</div>
+<div class="line"><a id="l00072" name="l00072"></a><span class="lineno">   72</span> </div>
+<div class="line"><a id="l00073" name="l00073"></a><span class="lineno">   73</span>    ani = animation.FuncAnimation(</div>
+<div class="line"><a id="l00074" name="l00074"></a><span class="lineno">   74</span>        fig, update, N, fargs=(lines, arr), interval=1, blit=<span class="keyword">False</span></div>
+<div class="line"><a id="l00075" name="l00075"></a><span class="lineno">   75</span>    )</div>
+<div class="line"><a id="l00076" name="l00076"></a><span class="lineno">   76</span> </div>
+<div class="line"><a id="l00077" name="l00077"></a><span class="lineno">   77</span>    ani.save(<span class="stringliteral">&quot;../images/100_particles.gif&quot;</span>, writer=animation.FFMpegFileWriter(fps=50))</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="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
+<div class="line"><a id="l00081" name="l00081"></a><span class="lineno">   81</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"><a class="el" href="animate__100__particles_8py.html">animate_100_particles.py</a></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

@@ -102,24 +102,42 @@ $(document).ready(function(){initNavTree('bug.html',''); initResizable(); });
 </div><!--header-->
 <div class="contents">
 <div class="textblock"><dl class="reflist">
+<dt>File <a class="el" href="animate__100__particles_8py.html">animate_100_particles.py</a>  </dt>
+<dd><a class="anchor" id="_bug000012"></a>No known bugs  </dd>
 <dt>File <a class="el" href="constants_8hpp.html">constants.hpp</a>  </dt>
 <dd><a class="anchor" id="_bug000001"></a>No known bugs  </dd>
-<dt>File <a class="el" href="main_8cpp.html">main.cpp</a>  </dt>
-<dd><a class="anchor" id="_bug000005"></a>No known bugs  </dd>
-<dt>File <a class="el" href="Particle_8cpp.html">Particle.cpp</a>  </dt>
+<dt>File <a class="el" href="frequency__narrow__sweeps__long_8cpp.html">frequency_narrow_sweeps_long.cpp</a>  </dt>
 <dd><a class="anchor" id="_bug000006"></a>No known bugs  </dd>
+<dt>File <a class="el" href="main_8cpp.html">main.cpp</a>  </dt>
+<dd><a class="anchor" id="_bug000007"></a>No known bugs  </dd>
+<dt>File <a class="el" href="Particle_8cpp.html">Particle.cpp</a>  </dt>
+<dd><a class="anchor" id="_bug000008"></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="_bug000009"></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="plot__2__particles_8py.html">plot_2_particles.py</a>  </dt>
+<dd><a class="anchor" id="_bug000013"></a>No known bugs  </dd>
+<dt>File <a class="el" href="plot__3d_8py.html">plot_3d.py</a>  </dt>
+<dd><a class="anchor" id="_bug000014"></a>No known bugs  </dd>
+<dt>File <a class="el" href="plot__particles__left_8py.html">plot_particles_left.py</a>  </dt>
+<dd><a class="anchor" id="_bug000015"></a>No known bugs  </dd>
+<dt>File <a class="el" href="plot__phase__space_8py.html">plot_phase_space.py</a>  </dt>
+<dd><a class="anchor" id="_bug000016"></a>No known bugs  </dd>
+<dt>File <a class="el" href="plot__relative__error_8py.html">plot_relative_error.py</a>  </dt>
+<dd><a class="anchor" id="_bug000017"></a>No known bugs  </dd>
+<dt>File <a class="el" href="plot__single__particle_8py.html">plot_single_particle.py</a>  </dt>
+<dd><a class="anchor" id="_bug000018"></a>No known bugs  </dd>
 <dt>File <a class="el" href="test__suite_8cpp.html">test_suite.cpp</a>  </dt>
-<dd><a class="anchor" id="_bug000008"></a>No known bugs  </dd>
-<dt>File <a class="el" href="utils_8cpp.html">utils.cpp</a>  </dt>
-<dd><a class="anchor" id="_bug000009"></a>No known bugs  </dd>
-<dt>File <a class="el" href="utils_8hpp.html">utils.hpp</a>  </dt>
+<dd><a class="anchor" id="_bug000010"></a>No known bugs  </dd>
+<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="_bug000011"></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
 <p>This is the complete list of members for <a class="el" href="classParticle.html">Particle</a>, including all inherited members.</p>
 <table class="directory">
   <tr class="even"><td class="entry"><a class="el" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a></td><td class="entry"><a class="el" href="classParticle.html">Particle</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="odd"><td class="entry"><a class="el" href="classParticle.html#a00e108823877a25513ccae7cac011b4c">Particle</a>(double q, double m, arma::vec::fixed&lt; 3 &gt; r_vec, arma::vec::fixed&lt; 3 &gt; v_vec)</td><td class="entry"><a class="el" href="classParticle.html">Particle</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classParticle.html#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>
   <tr class="even"><td class="entry"><a class="el" href="classParticle.html#aa797d319549dc2a0beb06cdbfd430232">PenningTrap</a></td><td class="entry"><a class="el" href="classParticle.html">Particle</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
   <tr class="odd"><td class="entry"><a class="el" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a></td><td class="entry"><a class="el" href="classParticle.html">Particle</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">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#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a></td><td class="entry"><a class="el" href="classParticle.html">Particle</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="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 -->
 <!-- start footer part -->

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>
 Public Member Functions</h2></td></tr>
-<tr class="memitem:a00e108823877a25513ccae7cac011b4c"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#a00e108823877a25513ccae7cac011b4c">Particle</a> (double <a class="el" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a>, double <a class="el" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a>, arma::vec::fixed&lt; 3 &gt; <a class="el" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a>, arma::vec::fixed&lt; 3 &gt; <a class="el" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a>)</td></tr>
-<tr class="memdesc:a00e108823877a25513ccae7cac011b4c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Initialize the particle.  <br /></td></tr>
-<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>
+<tr class="separator:af1d7535fb8311eaa77d2b7b345882ec4"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </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>
+<tr class="memitem:a1c59101411db43624828b766f87ad460"><td class="memItemLeft" align="right" valign="top"><a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#a1c59101411db43624828b766f87ad460">r_vec</a></td></tr>
+<tr class="memdesc:a1c59101411db43624828b766f87ad460"><td class="mdescLeft">&#160;</td><td class="mdescRight">position  <br /></td></tr>
+<tr class="separator:a1c59101411db43624828b766f87ad460"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a3a10400add8dd22b8031330c2aafb6fe"><td class="memItemLeft" align="right" valign="top"><a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">v_vec</a></td></tr>
+<tr class="memdesc:a3a10400add8dd22b8031330c2aafb6fe"><td class="mdescLeft">&#160;</td><td class="mdescRight">velocity  <br /></td></tr>
+<tr class="separator:a3a10400add8dd22b8031330c2aafb6fe"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a566dcc1de4bdc01251776948798ea8e1"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">q</a></td></tr>
 <tr class="memdesc:a566dcc1de4bdc01251776948798ea8e1"><td class="mdescLeft">&#160;</td><td class="mdescRight">Charge.  <br /></td></tr>
 <tr class="separator:a566dcc1de4bdc01251776948798ea8e1"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:aedcc7e1bc53b0e2b1a4a07c9a1b47563"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">m</a></td></tr>
 <tr class="memdesc:aedcc7e1bc53b0e2b1a4a07c9a1b47563"><td class="mdescLeft">&#160;</td><td class="mdescRight">Mass.  <br /></td></tr>
 <tr class="separator:aedcc7e1bc53b0e2b1a4a07c9a1b47563"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:acf1a0f3c978b06d76df5bb4279594467"><td class="memItemLeft" align="right" valign="top">arma::vec::fixed&lt; 3 &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">r_vec</a></td></tr>
-<tr class="memdesc:acf1a0f3c978b06d76df5bb4279594467"><td class="mdescLeft">&#160;</td><td class="mdescRight">position  <br /></td></tr>
-<tr class="separator:acf1a0f3c978b06d76df5bb4279594467"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:a4a5d22c7aeca66f67d083f270cba25df"><td class="memItemLeft" align="right" valign="top">arma::vec::fixed&lt; 3 &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">v_vec</a></td></tr>
-<tr class="memdesc:a4a5d22c7aeca66f67d083f270cba25df"><td class="mdescLeft">&#160;</td><td class="mdescRight">velocity  <br /></td></tr>
-<tr class="separator:a4a5d22c7aeca66f67d083f270cba25df"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="friends" name="friends"></a>
 Friends</h2></td></tr>
@@ -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>
 
-<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00019">19</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00022">22</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
 </div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
-<a id="a00e108823877a25513ccae7cac011b4c" name="a00e108823877a25513ccae7cac011b4c"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a00e108823877a25513ccae7cac011b4c">&#9670;&#160;</a></span>Particle()</h2>
+<a id="af1d7535fb8311eaa77d2b7b345882ec4" name="af1d7535fb8311eaa77d2b7b345882ec4"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#af1d7535fb8311eaa77d2b7b345882ec4">&#9670;&#160;</a></span>Particle()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -153,26 +153,26 @@ Friends</h2></td></tr>
         <tr>
           <td class="memname">Particle::Particle </td>
           <td>(</td>
-          <td class="paramtype">double&#160;</td>
-          <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>
         </tr>
         <tr>
           <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>
         </tr>
         <tr>
           <td></td>
@@ -184,8 +184,17 @@ Friends</h2></td></tr>
 
 <p>Initialize the particle. </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>
 </div>
@@ -212,7 +221,7 @@ Friends</h2></td></tr>
 
 <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>
 
 </div>
 </div>
@@ -239,7 +248,7 @@ Friends</h2></td></tr>
 
 <p>Mass. </p>
 
-<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00022">22</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00028">28</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
 
 </div>
 </div>
@@ -265,12 +274,12 @@ Friends</h2></td></tr>
 
 <p>Charge. </p>
 
-<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00021">21</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00027">27</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
 
 </div>
 </div>
-<a id="acf1a0f3c978b06d76df5bb4279594467" name="acf1a0f3c978b06d76df5bb4279594467"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#acf1a0f3c978b06d76df5bb4279594467">&#9670;&#160;</a></span>r_vec</h2>
+<a id="a1c59101411db43624828b766f87ad460" name="a1c59101411db43624828b766f87ad460"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a1c59101411db43624828b766f87ad460">&#9670;&#160;</a></span>r_vec</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -279,7 +288,7 @@ Friends</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">arma::vec::fixed&lt;3&gt; Particle::r_vec</td>
+          <td class="memname"><a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> Particle::r_vec</td>
         </tr>
       </table>
   </td>
@@ -291,12 +300,12 @@ Friends</h2></td></tr>
 
 <p>position </p>
 
-<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00023">23</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00025">25</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
 
 </div>
 </div>
-<a id="a4a5d22c7aeca66f67d083f270cba25df" name="a4a5d22c7aeca66f67d083f270cba25df"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a4a5d22c7aeca66f67d083f270cba25df">&#9670;&#160;</a></span>v_vec</h2>
+<a id="a3a10400add8dd22b8031330c2aafb6fe" name="a3a10400add8dd22b8031330c2aafb6fe"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a3a10400add8dd22b8031330c2aafb6fe">&#9670;&#160;</a></span>v_vec</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -305,7 +314,7 @@ Friends</h2></td></tr>
   <td class="mlabels-left">
       <table class="memname">
         <tr>
-          <td class="memname">arma::vec::fixed&lt;3&gt; Particle::v_vec</td>
+          <td class="memname"><a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> Particle::v_vec</td>
         </tr>
       </table>
   </td>
@@ -317,7 +326,7 @@ Friends</h2></td></tr>
 
 <p>velocity </p>
 
-<p class="definition">Definition at line <a class="el" href="Particle_8hpp_source.html#l00024">24</a> of file <a class="el" href="Particle_8hpp_source.html">Particle.hpp</a>.</p>
+<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>
 
 </div>
 </div>

docs/classParticle.js

@@ -1,9 +1,9 @@
 var classParticle =
 [
-    [ "Particle", "classParticle.html#a00e108823877a25513ccae7cac011b4c", null ],
+    [ "Particle", "classParticle.html#af1d7535fb8311eaa77d2b7b345882ec4", null ],
     [ "PenningTrap", "classParticle.html#aa797d319549dc2a0beb06cdbfd430232", null ],
     [ "m", "classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563", null ],
     [ "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

@@ -107,17 +107,32 @@ $(document).ready(function(){initNavTree('classPenningTrap.html',''); initResiza
   <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">add_particle</a>(Particle particle)</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#a0cac3509aa96e71a26d3b2c902e27716">B_0</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#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#a715329844d75ec4c04f8391421fb4e89">V_0</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#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>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">particles</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap</a>(double B_0=T, double V_0=(25. *V)/1000., double d=500., double t=0.)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a830be1b8cbf59664e060b6edbeaa302f">PenningTrap</a>(uint i, double B_0=T, double V_0=(25. *V)/1000., double d=500., double t=0.)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#addc96789dcfec07b75156e19fee82f4f">PenningTrap</a>(std::vector&lt; Particle &gt; particles, double B_0=T, double V_0=(25. *V)/1000., double d=500., double t=0.)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae">PenningTrapTest</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">perturbation</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#a826b7fa8e709d481eb1dee7d0c2cdc08">r_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>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(double f, double omega_V, double t=0.)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">set_pertubation</a>(double f, double omega_V)</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#a7a1d9f0528a12308de25bc30718da20a">simulate</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#a8ca4e21291f60fde619c14099d8c4e8e">t</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">total_force</a>(uint i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">total_force_external</a>(uint i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">total_force_no_interaction</a>(uint i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">total_force_particles</a>(uint i)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">V_0</a></td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrap.html#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>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(std::string path, double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</td><td class="entry"><a class="el" href="classPenningTrap.html">PenningTrap</a></td><td class="entry"></td></tr>
 </table></div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->

docs/classPenningTrap.js

@@ -1,17 +1,32 @@
 var classPenningTrap =
 [
-    [ "PenningTrap", "classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560", null ],
+    [ "PenningTrap", "classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8", null ],
+    [ "PenningTrap", "classPenningTrap.html#a830be1b8cbf59664e060b6edbeaa302f", null ],
+    [ "PenningTrap", "classPenningTrap.html#addc96789dcfec07b75156e19fee82f4f", null ],
     [ "add_particle", "classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8", null ],
-    [ "evolve_forward_euler", "classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965", null ],
-    [ "evolve_RK4", "classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9", null ],
-    [ "external_B_field", "classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784", null ],
-    [ "external_E_field", "classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b", null ],
-    [ "force_on_particle", "classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182", null ],
-    [ "total_force", "classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be", null ],
-    [ "total_force_external", "classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee", null ],
-    [ "total_force_particles", "classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d", null ],
+    [ "evolve_forward_euler", "classPenningTrap.html#ab9ea97a406534bbe621a95215144875e", null ],
+    [ "evolve_RK4", "classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e", null ],
+    [ "external_B_field", "classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655", null ],
+    [ "external_E_field", "classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22", null ],
+    [ "force_on_particle", "classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598", null ],
+    [ "fraction_of_particles_left", "classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f", null ],
+    [ "r_func", "classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08", null ],
+    [ "reinitialize", "classPenningTrap.html#aaee129f177657455348d0c8ae1441dea", null ],
+    [ "set_pertubation", "classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43", null ],
+    [ "simulate", "classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a", null ],
+    [ "total_force", "classPenningTrap.html#a9a301b0540078c36697880ef204afdf3", null ],
+    [ "total_force_external", "classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682", null ],
+    [ "total_force_no_interaction", "classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018", null ],
+    [ "total_force_particles", "classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c", null ],
+    [ "v_func", "classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2", null ],
+    [ "write_simulation_to_dir", "classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b", null ],
+    [ "PenningTrapTest", "classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae", null ],
     [ "B_0", "classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716", null ],
     [ "d", "classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2", null ],
+    [ "k_r", "classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640", null ],
+    [ "k_v", "classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4", null ],
     [ "particles", "classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f", null ],
+    [ "perturbation", "classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5", null ],
+    [ "t", "classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e", null ],
     [ "V_0", "classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89", null ]
 ];

docs/classPenningTrapTest-members.html

@@ -0,0 +1,121 @@
+<!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: Member List</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('classPenningTrapTest.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">PenningTrapTest Member List</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="classPenningTrapTest.html">PenningTrapTest</a>, including all inherited members.</p>
+<table class="directory">
+  <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>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrapTest.html#a6a303be62039ca2ecccd8252744d4dc8">test_external_E_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>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrapTest.html#a5f4f0b150e54ce463bb29f76d49883f9">test_force_on_particle</a>()</td><td class="entry"><a class="el" href="classPenningTrapTest.html">PenningTrapTest</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="odd"><td class="entry"><a class="el" href="classPenningTrapTest.html#ae6d0c8e0d80338fb7c7edefc97331046">test_total_force_external</a>()</td><td class="entry"><a class="el" href="classPenningTrapTest.html">PenningTrapTest</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classPenningTrapTest.html#a68449d508e66205bc8b27fa5f60db508">test_total_force_particles</a>()</td><td class="entry"><a class="el" href="classPenningTrapTest.html">PenningTrapTest</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <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/classPenningTrapTest.html

@@ -0,0 +1,292 @@
+<!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: PenningTrapTest Class Reference</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('classPenningTrapTest.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="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>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a6a303be62039ca2ecccd8252744d4dc8"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPenningTrapTest.html#a6a303be62039ca2ecccd8252744d4dc8">test_external_E_field</a> ()</td></tr>
+<tr class="memdesc:a6a303be62039ca2ecccd8252744d4dc8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Test that the external E field gives correct values.  <br /></td></tr>
+<tr class="separator:a6a303be62039ca2ecccd8252744d4dc8"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ad668d7d875bdc1909a42426bf9dead9e"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classPenningTrapTest.html#ad668d7d875bdc1909a42426bf9dead9e">test_external_B_field</a> ()</td></tr>
+<tr class="memdesc:ad668d7d875bdc1909a42426bf9dead9e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Test that the external B field gives correct values.  <br /></td></tr>
+<tr class="separator:ad668d7d875bdc1909a42426bf9dead9e"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<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">
+<div class="memproto">
+<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>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<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! -->
+  <ul>
+    <li class="navelem"><a class="el" href="classPenningTrapTest.html">PenningTrapTest</a></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/classPenningTrapTest.js

@@ -0,0 +1,8 @@
+var classPenningTrapTest =
+[
+    [ "test_external_B_field", "classPenningTrapTest.html#ad668d7d875bdc1909a42426bf9dead9e", null ],
+    [ "test_external_E_field", "classPenningTrapTest.html#a6a303be62039ca2ecccd8252744d4dc8", null ],
+    [ "test_force_on_particle", "classPenningTrapTest.html#a5f4f0b150e54ce463bb29f76d49883f9", null ],
+    [ "test_total_force_external", "classPenningTrapTest.html#ae6d0c8e0d80338fb7c7edefc97331046", null ],
+    [ "test_total_force_particles", "classPenningTrapTest.html#a68449d508e66205bc8b27fa5f60db508", null ]
+];

docs/classes.html

@@ -101,11 +101,14 @@ $(document).ready(function(){initNavTree('classes.html',''); initResizable(); })
   <div class="headertitle"><div class="title">Class Index</div></div>
 </div><!--header-->
 <div class="contents">
-<div class="qindex"><a class="qindex" href="#letter_P">P</a></div>
+<div class="qindex"><a class="qindex" href="#letter_P">P</a>&#160;|&#160;<a class="qindex" href="#letter_S">S</a></div>
 <div class="classindex">
 <dl class="classindex even">
 <dt class="alphachar"><a id="letter_P" name="letter_P">P</a></dt>
-<dd><a class="el" href="classParticle.html">Particle</a></dd><dd><a class="el" href="classPenningTrap.html">PenningTrap</a></dd></dl>
+<dd><a class="el" href="classParticle.html">Particle</a></dd><dd><a class="el" href="classPenningTrap.html">PenningTrap</a></dd><dd><a class="el" href="classPenningTrapTest.html">PenningTrapTest</a></dd></dl>
+<dl class="classindex odd">
+<dt class="alphachar"><a id="letter_S" name="letter_S">S</a></dt>
+<dd><a class="el" href="structsimulation.html">simulation</a></dd></dl>
 </div>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/constants_8hpp.html

@@ -111,26 +111,68 @@ $(document).ready(function(){initNavTree('constants_8hpp.html',''); initResizabl
 <table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="define-members" name="define-members"></a>
 Macros</h2></td></tr>
-<tr class="memitem:a4e451456ad7e9276ed0afa42826e7ccb"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">K_E</a>&#160;&#160;&#160;138935.333</td></tr>
+<tr class="memitem:a4e451456ad7e9276ed0afa42826e7ccb"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">K_E</a>&#160;&#160;&#160;1.38935333 * 1e5</td></tr>
 <tr class="memdesc:a4e451456ad7e9276ed0afa42826e7ccb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Coulomb constant. unit: \(\frac{u(\mu m)^3}{(\mu s)^2 e^2}\).  <br /></td></tr>
 <tr class="separator:a4e451456ad7e9276ed0afa42826e7ccb"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:a0acb682b8260ab1c60b918599864e2e5"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>&#160;&#160;&#160;96.4852558</td></tr>
+<tr class="memitem:a0acb682b8260ab1c60b918599864e2e5"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>&#160;&#160;&#160;9.64852558 * 1e1</td></tr>
 <tr class="memdesc:a0acb682b8260ab1c60b918599864e2e5"><td class="mdescLeft">&#160;</td><td class="mdescRight">1 Tesla. unit: \( \frac{u}{(\mu s) e} \)  <br /></td></tr>
 <tr class="separator:a0acb682b8260ab1c60b918599864e2e5"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:af40a326b23c68a27cebe60f16634a2cb"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>&#160;&#160;&#160;96485255.8</td></tr>
+<tr class="memitem:af40a326b23c68a27cebe60f16634a2cb"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a>&#160;&#160;&#160;9.64852558 * 1e7</td></tr>
 <tr class="memdesc:af40a326b23c68a27cebe60f16634a2cb"><td class="mdescLeft">&#160;</td><td class="mdescRight">1 Volt. unit: \( \frac{u (\mu m)^2}{(\mu s)^2 e} \)  <br /></td></tr>
 <tr class="separator:af40a326b23c68a27cebe60f16634a2cb"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a2ff491cc7958ffd5e749c518a4a60ec8"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">CA_MASS</a>&#160;&#160;&#160;40.078</td></tr>
+<tr class="memdesc:a2ff491cc7958ffd5e749c518a4a60ec8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Mass of a single calcium ion. unit: amu.  <br /></td></tr>
+<tr class="separator:a2ff491cc7958ffd5e749c518a4a60ec8"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:af7602a3a314957137ad1cd719aa23789"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="constants_8hpp.html#af7602a3a314957137ad1cd719aa23789">CA_CHARGE</a>&#160;&#160;&#160;1.</td></tr>
+<tr class="memdesc:af7602a3a314957137ad1cd719aa23789"><td class="mdescLeft">&#160;</td><td class="mdescRight">Charge of a singly charged calcium ion. unit: e.  <br /></td></tr>
+<tr class="separator:af7602a3a314957137ad1cd719aa23789"><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>Library of constants. </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="section version"><dt>Version</dt><dd>1.0</dd></dl>
 <dl class="bug"><dt><b><a class="el" href="bug.html#_bug000001">Bug:</a></b></dt><dd>No known bugs </dd></dl>
 
 <p class="definition">Definition in file <a class="el" href="constants_8hpp_source.html">constants.hpp</a>.</p>
 </div><h2 class="groupheader">Macro Definition Documentation</h2>
+<a id="af7602a3a314957137ad1cd719aa23789" name="af7602a3a314957137ad1cd719aa23789"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#af7602a3a314957137ad1cd719aa23789">&#9670;&#160;</a></span>CA_CHARGE</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define CA_CHARGE&#160;&#160;&#160;1.</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Charge of a singly charged calcium ion. unit: e. </p>
+
+<p class="definition">Definition at line <a class="el" href="constants_8hpp_source.html#l00033">33</a> of file <a class="el" href="constants_8hpp_source.html">constants.hpp</a>.</p>
+
+</div>
+</div>
+<a id="a2ff491cc7958ffd5e749c518a4a60ec8" name="a2ff491cc7958ffd5e749c518a4a60ec8"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a2ff491cc7958ffd5e749c518a4a60ec8">&#9670;&#160;</a></span>CA_MASS</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define CA_MASS&#160;&#160;&#160;40.078</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Mass of a single calcium ion. unit: amu. </p>
+
+<p class="definition">Definition at line <a class="el" href="constants_8hpp_source.html#l00029">29</a> of file <a class="el" href="constants_8hpp_source.html">constants.hpp</a>.</p>
+
+</div>
+</div>
 <a id="a4e451456ad7e9276ed0afa42826e7ccb" name="a4e451456ad7e9276ed0afa42826e7ccb"></a>
 <h2 class="memtitle"><span class="permalink"><a href="#a4e451456ad7e9276ed0afa42826e7ccb">&#9670;&#160;</a></span>K_E</h2>
 
@@ -138,14 +180,14 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
 <div class="memproto">
       <table class="memname">
         <tr>
-          <td class="memname">#define K_E&#160;&#160;&#160;138935.333</td>
+          <td class="memname">#define K_E&#160;&#160;&#160;1.38935333 * 1e5</td>
         </tr>
       </table>
 </div><div class="memdoc">
 
 <p>Coulomb constant. unit: \(\frac{u(\mu m)^3}{(\mu s)^2 e^2}\). </p>
 
-<p class="definition">Definition at line <a class="el" href="constants_8hpp_source.html#l00015">15</a> of file <a class="el" href="constants_8hpp_source.html">constants.hpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="constants_8hpp_source.html#l00017">17</a> of file <a class="el" href="constants_8hpp_source.html">constants.hpp</a>.</p>
 
 </div>
 </div>
@@ -156,14 +198,14 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
 <div class="memproto">
       <table class="memname">
         <tr>
-          <td class="memname">#define T&#160;&#160;&#160;96.4852558</td>
+          <td class="memname">#define T&#160;&#160;&#160;9.64852558 * 1e1</td>
         </tr>
       </table>
 </div><div class="memdoc">
 
 <p>1 Tesla. unit: \( \frac{u}{(\mu s) e} \) </p>
 
-<p class="definition">Definition at line <a class="el" href="constants_8hpp_source.html#l00017">17</a> of file <a class="el" href="constants_8hpp_source.html">constants.hpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="constants_8hpp_source.html#l00021">21</a> of file <a class="el" href="constants_8hpp_source.html">constants.hpp</a>.</p>
 
 </div>
 </div>
@@ -174,14 +216,14 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
 <div class="memproto">
       <table class="memname">
         <tr>
-          <td class="memname">#define V&#160;&#160;&#160;96485255.8</td>
+          <td class="memname">#define V&#160;&#160;&#160;9.64852558 * 1e7</td>
         </tr>
       </table>
 </div><div class="memdoc">
 
 <p>1 Volt. unit: \( \frac{u (\mu m)^2}{(\mu s)^2 e} \) </p>
 
-<p class="definition">Definition at line <a class="el" href="constants_8hpp_source.html#l00019">19</a> of file <a class="el" href="constants_8hpp_source.html">constants.hpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="constants_8hpp_source.html#l00025">25</a> of file <a class="el" href="constants_8hpp_source.html">constants.hpp</a>.</p>
 
 </div>
 </div>

docs/constants_8hpp.js

@@ -1,5 +1,7 @@
 var constants_8hpp =
 [
+    [ "CA_CHARGE", "constants_8hpp.html#af7602a3a314957137ad1cd719aa23789", null ],
+    [ "CA_MASS", "constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8", null ],
     [ "K_E", "constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb", null ],
     [ "T", "constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5", null ],
     [ "V", "constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb", null ]

docs/constants_8hpp_source.html

@@ -105,13 +105,17 @@ $(document).ready(function(){initNavTree('constants_8hpp_source.html',''); initR
 <div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span><span class="preprocessor">#ifndef __CONST__</span></div>
 <div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="preprocessor">#define __CONST__</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="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">   15</a></span><span class="preprocessor">#define K_E 138935.333 </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"><a class="line" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">   17</a></span><span class="preprocessor">#define T 96.4852558 </span></div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"><a class="line" href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">   17</a></span><span class="preprocessor">#define K_E 1.38935333 * 1e5</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"><a class="line" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">   19</a></span><span class="preprocessor">#define V 96485255.8 </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><span class="preprocessor">#endif</span></div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"><a class="line" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">   21</a></span><span class="preprocessor">#define T 9.64852558 * 1e1</span></div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span> </div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"><a class="line" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">   25</a></span><span class="preprocessor">#define V 9.64852558 * 1e7</span></div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span> </div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"><a class="line" href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">   29</a></span><span class="preprocessor">#define CA_MASS 40.078</span></div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span> </div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"><a class="line" href="constants_8hpp.html#af7602a3a314957137ad1cd719aa23789">   33</a></span><span class="preprocessor">#define CA_CHARGE 1.</span></div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span> </div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span><span class="preprocessor">#endif</span></div>
 </div><!-- fragment --></div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->

docs/dir_634e799a3947388232110823971192a8.html

@@ -0,0 +1,139 @@
+<!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 Directory Reference</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('dir_634e799a3947388232110823971192a8.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">scripts Directory Reference</div></div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="files" name="files"></a>
+Files</h2></td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="animate__100__particles_8py.html">animate_100_particles.py</a> <a href="animate__100__particles_8py_source.html">[code]</a></td></tr>
+<tr class="memdesc:animate__100__particles_8py"><td class="mdescLeft">&#160;</td><td class="mdescRight">Animate 100 particles. <br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__2__particles_8py.html">plot_2_particles.py</a> <a href="plot__2__particles_8py_source.html">[code]</a></td></tr>
+<tr class="memdesc:plot__2__particles_8py"><td class="mdescLeft">&#160;</td><td class="mdescRight">Plot 2 particles with and without particle interactions in the xy-plane. <br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__3d_8py.html">plot_3d.py</a> <a href="plot__3d_8py_source.html">[code]</a></td></tr>
+<tr class="memdesc:plot__3d_8py"><td class="mdescLeft">&#160;</td><td class="mdescRight">Plot 2 particles with and without particle interactions in 3D. <br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__particles__left_8py.html">plot_particles_left.py</a> <a href="plot__particles__left_8py_source.html">[code]</a></td></tr>
+<tr class="memdesc:plot__particles__left_8py"><td class="mdescLeft">&#160;</td><td class="mdescRight">Plot how many particles are left after 500 microseconds using different angular frequencies. <br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__phase__space_8py.html">plot_phase_space.py</a> <a href="plot__phase__space_8py_source.html">[code]</a></td></tr>
+<tr class="memdesc:plot__phase__space_8py"><td class="mdescLeft">&#160;</td><td class="mdescRight">Plot the phase space for 2 particles in the x and z direction, with and without particle interactions. <br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__relative__error_8py.html">plot_relative_error.py</a> <a href="plot__relative__error_8py_source.html">[code]</a></td></tr>
+<tr class="memdesc:plot__relative__error_8py"><td class="mdescLeft">&#160;</td><td class="mdescRight">Plot the relative error for forward Euler and RK4 method. <br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__single__particle_8py.html">plot_single_particle.py</a> <a href="plot__single__particle_8py_source.html">[code]</a></td></tr>
+<tr class="memdesc:plot__single__particle_8py"><td class="mdescLeft">&#160;</td><td class="mdescRight">Plot the approximation and analytical solution for one particle in the z axis. <br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+</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="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/dir_634e799a3947388232110823971192a8.js

@@ -0,0 +1,10 @@
+var dir_634e799a3947388232110823971192a8 =
+[
+    [ "animate_100_particles.py", "animate__100__particles_8py.html", null ],
+    [ "plot_2_particles.py", "plot__2__particles_8py.html", null ],
+    [ "plot_3d.py", "plot__3d_8py.html", null ],
+    [ "plot_particles_left.py", "plot__particles__left_8py.html", null ],
+    [ "plot_phase_space.py", "plot__phase__space_8py.html", null ],
+    [ "plot_relative_error.py", "plot__relative__error_8py.html", null ],
+    [ "plot_single_particle.py", "plot__single__particle_8py.html", null ]
+];

docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html

@@ -102,8 +102,16 @@ $(document).ready(function(){initNavTree('dir_68267d1309a1af8e8297ef4c3efbcdba.h
 </div><!--header-->
 <div class="contents">
 <table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="subdirs" name="subdirs"></a>
+Directories</h2></td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">directory &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="dir_634e799a3947388232110823971192a8.html">scripts</a></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="files" name="files"></a>
 Files</h2></td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="frequency__narrow__sweeps__long_8cpp.html">frequency_narrow_sweeps_long.cpp</a> <a href="frequency__narrow__sweeps__long_8cpp_source.html">[code]</a></td></tr>
+<tr class="memdesc:frequency__narrow__sweeps__long_8cpp"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sweep of the frequencies from 1.1 to 1.7 using a small time step. <br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html">main.cpp</a> <a href="main_8cpp_source.html">[code]</a></td></tr>
 <tr class="memdesc:main_8cpp"><td class="mdescLeft">&#160;</td><td class="mdescRight">The main program for this project. <br /></td></tr>
 <tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>

docs/dir_68267d1309a1af8e8297ef4c3efbcdba.js

@@ -1,8 +1,10 @@
 var dir_68267d1309a1af8e8297ef4c3efbcdba =
 [
-    [ "main.cpp", "main_8cpp.html", null ],
+    [ "scripts", "dir_634e799a3947388232110823971192a8.html", "dir_634e799a3947388232110823971192a8" ],
+    [ "frequency_narrow_sweeps_long.cpp", "frequency__narrow__sweeps__long_8cpp.html", "frequency__narrow__sweeps__long_8cpp" ],
+    [ "main.cpp", "main_8cpp.html", "main_8cpp" ],
     [ "Particle.cpp", "Particle_8cpp.html", null ],
     [ "PenningTrap.cpp", "PenningTrap_8cpp.html", null ],
-    [ "test_suite.cpp", "test__suite_8cpp.html", null ],
+    [ "test_suite.cpp", "test__suite_8cpp.html", "test__suite_8cpp" ],
     [ "utils.cpp", "utils_8cpp.html", "utils_8cpp" ]
 ];

docs/dir_d44c64559bbebec7f509842c48db8b23.html

@@ -113,6 +113,9 @@ Files</h2></td></tr>
 <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="PenningTrap_8hpp.html">PenningTrap.hpp</a> <a href="PenningTrap_8hpp_source.html">[code]</a></td></tr>
 <tr class="memdesc:PenningTrap_8hpp"><td class="mdescLeft">&#160;</td><td class="mdescRight">A class for simulating a Penning trap. <br /></td></tr>
 <tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="typedefs_8hpp.html">typedefs.hpp</a> <a href="typedefs_8hpp_source.html">[code]</a></td></tr>
+<tr class="memdesc:typedefs_8hpp"><td class="mdescLeft">&#160;</td><td class="mdescRight">Useful typedefs for cleaner code. <br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="utils_8hpp.html">utils.hpp</a> <a href="utils_8hpp_source.html">[code]</a></td></tr>
 <tr class="memdesc:utils_8hpp"><td class="mdescLeft">&#160;</td><td class="mdescRight">Function prototypes and macros that are useful. <br /></td></tr>
 <tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>

docs/dir_d44c64559bbebec7f509842c48db8b23.js

@@ -3,5 +3,6 @@ var dir_d44c64559bbebec7f509842c48db8b23 =
     [ "constants.hpp", "constants_8hpp.html", "constants_8hpp" ],
     [ "Particle.hpp", "Particle_8hpp.html", "Particle_8hpp" ],
     [ "PenningTrap.hpp", "PenningTrap_8hpp.html", "PenningTrap_8hpp" ],
+    [ "typedefs.hpp", "typedefs_8hpp.html", "typedefs_8hpp" ],
     [ "utils.hpp", "utils_8hpp.html", "utils_8hpp" ]
 ];

docs/files.html

@@ -102,18 +102,28 @@ $(document).ready(function(){initNavTree('files.html',''); initResizable(); });
 </div><!--header-->
 <div class="contents">
 <div class="textblock">Here is a list of all documented files with brief descriptions:</div><div class="directory">
-<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span>]</div><table class="directory">
+<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span><span onclick="javascript:toggleLevel(3);">3</span>]</div><table class="directory">
 <tr id="row_0_" class="even"><td class="entry"><span style="width:0px;display:inline-block;">&#160;</span><span id="arr_0_" class="arrow" onclick="toggleFolder('0_')">&#9660;</span><span id="img_0_" class="iconfopen" onclick="toggleFolder('0_')">&#160;</span><a class="el" href="dir_d44c64559bbebec7f509842c48db8b23.html" target="_self">include</a></td><td class="desc"></td></tr>
 <tr id="row_0_0_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="constants_8hpp_source.html"><span class="icondoc"></span></a><a class="el" href="constants_8hpp.html" target="_self">constants.hpp</a></td><td class="desc">Library of constants </td></tr>
 <tr id="row_0_1_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="Particle_8hpp_source.html"><span class="icondoc"></span></a><a class="el" href="Particle_8hpp.html" target="_self">Particle.hpp</a></td><td class="desc">A class that holds the properties of a particle </td></tr>
 <tr id="row_0_2_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="PenningTrap_8hpp_source.html"><span class="icondoc"></span></a><a class="el" href="PenningTrap_8hpp.html" target="_self">PenningTrap.hpp</a></td><td class="desc">A class for simulating a Penning trap </td></tr>
-<tr id="row_0_3_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="utils_8hpp_source.html"><span class="icondoc"></span></a><a class="el" href="utils_8hpp.html" target="_self">utils.hpp</a></td><td class="desc">Function prototypes and macros that are useful </td></tr>
-<tr id="row_1_" class="odd"><td class="entry"><span style="width:0px;display:inline-block;">&#160;</span><span id="arr_1_" class="arrow" onclick="toggleFolder('1_')">&#9660;</span><span id="img_1_" class="iconfopen" onclick="toggleFolder('1_')">&#160;</span><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html" target="_self">src</a></td><td class="desc"></td></tr>
-<tr id="row_1_0_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="main_8cpp_source.html"><span class="icondoc"></span></a><a class="el" href="main_8cpp.html" target="_self">main.cpp</a></td><td class="desc">The main program for this project </td></tr>
-<tr id="row_1_1_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="Particle_8cpp_source.html"><span class="icondoc"></span></a><a class="el" href="Particle_8cpp.html" target="_self">Particle.cpp</a></td><td class="desc">The implementation of the <a class="el" href="classParticle.html" title="A class that holds attributes of a particle.">Particle</a> class </td></tr>
-<tr id="row_1_2_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="PenningTrap_8cpp_source.html"><span class="icondoc"></span></a><a class="el" href="PenningTrap_8cpp.html" target="_self">PenningTrap.cpp</a></td><td class="desc">The implementation of the <a class="el" href="classPenningTrap.html" title="A class that simulates a Penning trap.">PenningTrap</a> class </td></tr>
-<tr id="row_1_3_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="test__suite_8cpp_source.html"><span class="icondoc"></span></a><a class="el" href="test__suite_8cpp.html" target="_self">test_suite.cpp</a></td><td class="desc">The test suite for the project </td></tr>
-<tr id="row_1_4_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="utils_8cpp_source.html"><span class="icondoc"></span></a><a class="el" href="utils_8cpp.html" target="_self">utils.cpp</a></td><td class="desc">Implementation of the utils </td></tr>
+<tr id="row_0_3_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="typedefs_8hpp_source.html"><span class="icondoc"></span></a><a class="el" href="typedefs_8hpp.html" target="_self">typedefs.hpp</a></td><td class="desc">Useful typedefs for cleaner code </td></tr>
+<tr id="row_0_4_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="utils_8hpp_source.html"><span class="icondoc"></span></a><a class="el" href="utils_8hpp.html" target="_self">utils.hpp</a></td><td class="desc">Function prototypes and macros that are useful </td></tr>
+<tr id="row_1_" class="even"><td class="entry"><span style="width:0px;display:inline-block;">&#160;</span><span id="arr_1_" class="arrow" onclick="toggleFolder('1_')">&#9660;</span><span id="img_1_" class="iconfopen" onclick="toggleFolder('1_')">&#160;</span><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html" target="_self">src</a></td><td class="desc"></td></tr>
+<tr id="row_1_0_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_1_0_" class="arrow" onclick="toggleFolder('1_0_')">&#9660;</span><span id="img_1_0_" class="iconfopen" onclick="toggleFolder('1_0_')">&#160;</span><a class="el" href="dir_634e799a3947388232110823971192a8.html" target="_self">scripts</a></td><td class="desc"></td></tr>
+<tr id="row_1_0_0_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><a href="animate__100__particles_8py_source.html"><span class="icondoc"></span></a><a class="el" href="animate__100__particles_8py.html" target="_self">animate_100_particles.py</a></td><td class="desc">Animate 100 particles </td></tr>
+<tr id="row_1_0_1_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><a href="plot__2__particles_8py_source.html"><span class="icondoc"></span></a><a class="el" href="plot__2__particles_8py.html" target="_self">plot_2_particles.py</a></td><td class="desc">Plot 2 particles with and without particle interactions in the xy-plane </td></tr>
+<tr id="row_1_0_2_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><a href="plot__3d_8py_source.html"><span class="icondoc"></span></a><a class="el" href="plot__3d_8py.html" target="_self">plot_3d.py</a></td><td class="desc">Plot 2 particles with and without particle interactions in 3D </td></tr>
+<tr id="row_1_0_3_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><a href="plot__particles__left_8py_source.html"><span class="icondoc"></span></a><a class="el" href="plot__particles__left_8py.html" target="_self">plot_particles_left.py</a></td><td class="desc">Plot how many particles are left after 500 microseconds using different angular frequencies </td></tr>
+<tr id="row_1_0_4_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><a href="plot__phase__space_8py_source.html"><span class="icondoc"></span></a><a class="el" href="plot__phase__space_8py.html" target="_self">plot_phase_space.py</a></td><td class="desc">Plot the phase space for 2 particles in the x and z direction, with and without particle interactions </td></tr>
+<tr id="row_1_0_5_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><a href="plot__relative__error_8py_source.html"><span class="icondoc"></span></a><a class="el" href="plot__relative__error_8py.html" target="_self">plot_relative_error.py</a></td><td class="desc">Plot the relative error for forward Euler and RK4 method </td></tr>
+<tr id="row_1_0_6_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><a href="plot__single__particle_8py_source.html"><span class="icondoc"></span></a><a class="el" href="plot__single__particle_8py.html" target="_self">plot_single_particle.py</a></td><td class="desc">Plot the approximation and analytical solution for one particle in the z axis </td></tr>
+<tr id="row_1_1_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="frequency__narrow__sweeps__long_8cpp_source.html"><span class="icondoc"></span></a><a class="el" href="frequency__narrow__sweeps__long_8cpp.html" target="_self">frequency_narrow_sweeps_long.cpp</a></td><td class="desc">Sweep of the frequencies from 1.1 to 1.7 using a small time step </td></tr>
+<tr id="row_1_2_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="main_8cpp_source.html"><span class="icondoc"></span></a><a class="el" href="main_8cpp.html" target="_self">main.cpp</a></td><td class="desc">The main program for this project </td></tr>
+<tr id="row_1_3_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="Particle_8cpp_source.html"><span class="icondoc"></span></a><a class="el" href="Particle_8cpp.html" target="_self">Particle.cpp</a></td><td class="desc">The implementation of the <a class="el" href="classParticle.html" title="A class that holds attributes of a particle.">Particle</a> class </td></tr>
+<tr id="row_1_4_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="PenningTrap_8cpp_source.html"><span class="icondoc"></span></a><a class="el" href="PenningTrap_8cpp.html" target="_self">PenningTrap.cpp</a></td><td class="desc">The implementation of the <a class="el" href="classPenningTrap.html" title="A class that simulates a Penning trap.">PenningTrap</a> class </td></tr>
+<tr id="row_1_5_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="test__suite_8cpp_source.html"><span class="icondoc"></span></a><a class="el" href="test__suite_8cpp.html" target="_self">test_suite.cpp</a></td><td class="desc">The test suite for the project </td></tr>
+<tr id="row_1_6_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><a href="utils_8cpp_source.html"><span class="icondoc"></span></a><a class="el" href="utils_8cpp.html" target="_self">utils.cpp</a></td><td class="desc">Implementation of the utils </td></tr>
 </table>
 </div><!-- directory -->
 </div><!-- contents -->

docs/frequency__narrow__sweeps__long_8cpp.html

@@ -0,0 +1,256 @@
+<!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/frequency_narrow_sweeps_long.cpp File Reference</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('frequency__narrow__sweeps__long_8cpp.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="summary">
+<a href="#define-members">Macros</a> &#124;
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle"><div class="title">frequency_narrow_sweeps_long.cpp File Reference</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>Sweep of the frequencies from 1.1 to 1.7 using a small time step.  
+<a href="#details">More...</a></p>
+<div class="textblock"><code>#include &lt;cmath&gt;</code><br />
+<code>#include &lt;complex&gt;</code><br />
+<code>#include &lt;fstream&gt;</code><br />
+<code>#include &lt;omp.h&gt;</code><br />
+<code>#include &lt;string&gt;</code><br />
+<code>#include &lt;vector&gt;</code><br />
+<code>#include &quot;<a class="el" href="PenningTrap_8hpp_source.html">PenningTrap.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="constants_8hpp_source.html">constants.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="utils_8hpp_source.html">utils.hpp</a>&quot;</code><br />
+</div>
+<p><a href="frequency__narrow__sweeps__long_8cpp_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="define-members" name="define-members"></a>
+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="frequency__narrow__sweeps__long_8cpp.html#a7b24a37e8ce9d243351bfc9b24945e63">PARTICLES</a>&#160;&#160;&#160;100</td></tr>
+<tr class="separator:a7b24a37e8ce9d243351bfc9b24945e63"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a0240ac851181b84ac374872dc5434ee4"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="frequency__narrow__sweeps__long_8cpp.html#a0240ac851181b84ac374872dc5434ee4">N</a>&#160;&#160;&#160;40000</td></tr>
+<tr class="separator:a0240ac851181b84ac374872dc5434ee4"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:a33d9b1c76c3c80902f89a58b1a6d96ea"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a> ()</td></tr>
+<tr class="memdesc:a33d9b1c76c3c80902f89a58b1a6d96ea"><td class="mdescLeft">&#160;</td><td class="mdescRight">Simulate 100 particles over 500 \( \mu s \) using a time dependent potential.  <br /></td></tr>
+<tr class="separator:a33d9b1c76c3c80902f89a58b1a6d96ea"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ac1816f70ec612edc27848ef7f0875fdb"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a> ()</td></tr>
+<tr class="memdesc:ac1816f70ec612edc27848ef7f0875fdb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Simulate 100 particles over 500 \( \mu s \) using a time dependent potential.  <br /></td></tr>
+<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="frequency__narrow__sweeps__long_8cpp.html#ae66f6b31b5ad750f1fe042a706a4e3d4">main</a> ()</td></tr>
+<tr class="separator:ae66f6b31b5ad750f1fe042a706a4e3d4"><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>Sweep of the frequencies from 1.1 to 1.7 using a small time step. </p>
+<dl class="section author"><dt>Author</dt><dd>Cory Alexander Balaton (coryab) </dd>
+<dd>
+Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
+<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
+<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000006">Bug:</a></b></dt><dd>No known bugs </dd></dl>
+
+<p class="definition">Definition in file <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html">frequency_narrow_sweeps_long.cpp</a>.</p>
+</div><h2 class="groupheader">Macro Definition Documentation</h2>
+<a id="a0240ac851181b84ac374872dc5434ee4" name="a0240ac851181b84ac374872dc5434ee4"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a0240ac851181b84ac374872dc5434ee4">&#9670;&#160;</a></span>N</h2>
+
+<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="frequency__narrow__sweeps__long_8cpp_source.html#l00025">25</a> of file <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html">frequency_narrow_sweeps_long.cpp</a>.</p>
+
+</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="frequency__narrow__sweeps__long_8cpp_source.html#l00024">24</a> of file <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html">frequency_narrow_sweeps_long.cpp</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Function Documentation</h2>
+<a id="ae66f6b31b5ad750f1fe042a706a4e3d4" name="ae66f6b31b5ad750f1fe042a706a4e3d4"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ae66f6b31b5ad750f1fe042a706a4e3d4">&#9670;&#160;</a></span>main()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int main </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html#l00139">139</a> of file <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html">frequency_narrow_sweeps_long.cpp</a>.</p>
+
+</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="frequency__narrow__sweeps__long_8cpp_source.html#l00034">34</a> of file <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html">frequency_narrow_sweeps_long.cpp</a>.</p>
+
+</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="frequency__narrow__sweeps__long_8cpp_source.html#l00091">91</a> of file <a class="el" href="frequency__narrow__sweeps__long_8cpp_source.html">frequency_narrow_sweeps_long.cpp</a>.</p>
+
+</div>
+</div>
+</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="frequency__narrow__sweeps__long_8cpp.html">frequency_narrow_sweeps_long.cpp</a></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/frequency__narrow__sweeps__long_8cpp.js

@@ -0,0 +1,5 @@
+var frequency__narrow__sweeps__long_8cpp =
+[
+    [ "potential_resonance_narrow_sweep", "frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea", null ],
+    [ "potential_resonance_narrow_sweep_interaction", "frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb", null ]
+];

docs/frequency__narrow__sweeps__long_8cpp_source.html

@@ -0,0 +1,252 @@
+<!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/frequency_narrow_sweeps_long.cpp 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('frequency__narrow__sweeps__long_8cpp_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">frequency_narrow_sweeps_long.cpp</div></div>
+</div><!--header-->
+<div class="contents">
+<a href="frequency__narrow__sweeps__long_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span> </div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="preprocessor">#include &lt;cmath&gt;</span></div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="preprocessor">#include &lt;complex&gt;</span></div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="preprocessor">#include &lt;fstream&gt;</span></div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span><span class="preprocessor">#include &lt;omp.h&gt;</span></div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span><span class="preprocessor">#include &lt;string&gt;</span></div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span> </div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span><span class="preprocessor">#include &quot;<a class="code" href="constants_8hpp.html">constants.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span><span class="preprocessor">#include &quot;<a class="code" href="utils_8hpp.html">utils.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span> </div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span><span class="preprocessor">#define PARTICLES 100</span></div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span><span class="preprocessor">#define N 40000</span></div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span> </div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"><a class="line" href="frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">   34</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>()</div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span>{</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span>    <span class="keywordtype">double</span> time = 500.;</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span> </div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>    <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span> </div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>    <span class="keywordtype">double</span> freq_start = 1.1;</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>    <span class="keywordtype">double</span> freq_end = 1.7;</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>    <span class="keywordtype">double</span> freq_increment = .0005;</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>    <span class="keywordtype">size_t</span> freq_iterations =</div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span>        (size_t)((freq_end - freq_start) / freq_increment) + 1;</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span> </div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>    <span class="keywordtype">double</span> res[4][freq_iterations];</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span> </div>
+<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span>    std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
+<div class="line"><a id="l00049" name="l00049"></a><span class="lineno">   49</span>    <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span> </div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span>    std::ofstream ofile;</div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span> </div>
+<div class="line"><a id="l00053" name="l00053"></a><span class="lineno">   53</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00054" name="l00054"></a><span class="lineno">   54</span>    <span class="comment">// Insert frequencies</span></div>
+<div class="line"><a id="l00055" name="l00055"></a><span class="lineno">   55</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno">   56</span>        res[0][i] = freq_start + freq_increment * i;</div>
+<div class="line"><a id="l00057" name="l00057"></a><span class="lineno">   57</span>    }</div>
+<div class="line"><a id="l00058" name="l00058"></a><span class="lineno">   58</span> </div>
+<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   59</span><span class="preprocessor">#pragma omp parallel</span></div>
+<div class="line"><a id="l00060" name="l00060"></a><span class="lineno">   60</span>    {</div>
+<div class="line"><a id="l00061" name="l00061"></a><span class="lineno">   61</span>        <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
+<div class="line"><a id="l00062" name="l00062"></a><span class="lineno">   62</span>        <span class="comment">// the sweep.</span></div>
+<div class="line"><a id="l00063" name="l00063"></a><span class="lineno">   63</span>        <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)PARTICLES);</div>
+<div class="line"><a id="l00064" name="l00064"></a><span class="lineno">   64</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
+<div class="line"><a id="l00065" name="l00065"></a><span class="lineno">   65</span>        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
+<div class="line"><a id="l00066" name="l00066"></a><span class="lineno">   66</span>            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
+<div class="line"><a id="l00067" name="l00067"></a><span class="lineno">   67</span>                <span class="comment">// Reset particles and give new time dependent potential.</span></div>
+<div class="line"><a id="l00068" name="l00068"></a><span class="lineno">   68</span>                trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
+<div class="line"><a id="l00069" name="l00069"></a><span class="lineno">   69</span>                res[i + 1][j] =</div>
+<div class="line"><a id="l00070" name="l00070"></a><span class="lineno">   70</span>                    trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00071" name="l00071"></a><span class="lineno">   71</span>            }</div>
+<div class="line"><a id="l00072" name="l00072"></a><span class="lineno">   72</span>        }</div>
+<div class="line"><a id="l00073" name="l00073"></a><span class="lineno">   73</span>    }</div>
+<div class="line"><a id="l00074" name="l00074"></a><span class="lineno">   74</span> </div>
+<div class="line"><a id="l00075" name="l00075"></a><span class="lineno">   75</span>    <span class="comment">// Write results to file</span></div>
+<div class="line"><a id="l00076" name="l00076"></a><span class="lineno">   76</span>    ofile.open(path + <span class="stringliteral">&quot;narrow_sweep_fine.txt&quot;</span>);</div>
+<div class="line"><a id="l00077" name="l00077"></a><span class="lineno">   77</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00078" name="l00078"></a><span class="lineno">   78</span>        ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00079" name="l00079"></a><span class="lineno">   79</span>              &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00080" name="l00080"></a><span class="lineno">   80</span>    }</div>
+<div class="line"><a id="l00081" name="l00081"></a><span class="lineno">   81</span>    ofile.close();</div>
+<div class="line"><a id="l00082" name="l00082"></a><span class="lineno">   82</span>}</div>
+<div class="line"><a id="l00083" name="l00083"></a><span class="lineno">   83</span> </div>
+<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"><a class="line" href="frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">   91</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>()</div>
+<div class="line"><a id="l00092" name="l00092"></a><span class="lineno">   92</span>{</div>
+<div class="line"><a id="l00093" name="l00093"></a><span class="lineno">   93</span>    <span class="keywordtype">double</span> time = 500.;</div>
+<div class="line"><a id="l00094" name="l00094"></a><span class="lineno">   94</span> </div>
+<div class="line"><a id="l00095" name="l00095"></a><span class="lineno">   95</span>    <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
+<div class="line"><a id="l00096" name="l00096"></a><span class="lineno">   96</span> </div>
+<div class="line"><a id="l00097" name="l00097"></a><span class="lineno">   97</span>    <span class="keywordtype">double</span> freq_start = 1.1;</div>
+<div class="line"><a id="l00098" name="l00098"></a><span class="lineno">   98</span>    <span class="keywordtype">double</span> freq_end = 1.7;</div>
+<div class="line"><a id="l00099" name="l00099"></a><span class="lineno">   99</span>    <span class="keywordtype">double</span> freq_increment = .0005;</div>
+<div class="line"><a id="l00100" name="l00100"></a><span class="lineno">  100</span>    <span class="keywordtype">size_t</span> freq_iterations =</div>
+<div class="line"><a id="l00101" name="l00101"></a><span class="lineno">  101</span>        (size_t)((freq_end - freq_start) / freq_increment) + 1;</div>
+<div class="line"><a id="l00102" name="l00102"></a><span class="lineno">  102</span> </div>
+<div class="line"><a id="l00103" name="l00103"></a><span class="lineno">  103</span>    <span class="keywordtype">double</span> res[4][freq_iterations];</div>
+<div class="line"><a id="l00104" name="l00104"></a><span class="lineno">  104</span> </div>
+<div class="line"><a id="l00105" name="l00105"></a><span class="lineno">  105</span>    std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
+<div class="line"><a id="l00106" name="l00106"></a><span class="lineno">  106</span>    <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
+<div class="line"><a id="l00107" name="l00107"></a><span class="lineno">  107</span> </div>
+<div class="line"><a id="l00108" name="l00108"></a><span class="lineno">  108</span>    std::ofstream ofile;</div>
+<div class="line"><a id="l00109" name="l00109"></a><span class="lineno">  109</span> </div>
+<div class="line"><a id="l00110" name="l00110"></a><span class="lineno">  110</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00111" name="l00111"></a><span class="lineno">  111</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00112" name="l00112"></a><span class="lineno">  112</span>        res[0][i] = freq_start + freq_increment * i;</div>
+<div class="line"><a id="l00113" name="l00113"></a><span class="lineno">  113</span>    }</div>
+<div class="line"><a id="l00114" name="l00114"></a><span class="lineno">  114</span> </div>
+<div class="line"><a id="l00115" name="l00115"></a><span class="lineno">  115</span><span class="preprocessor">#pragma omp parallel</span></div>
+<div class="line"><a id="l00116" name="l00116"></a><span class="lineno">  116</span>    {</div>
+<div class="line"><a id="l00117" name="l00117"></a><span class="lineno">  117</span>        <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
+<div class="line"><a id="l00118" name="l00118"></a><span class="lineno">  118</span>        <span class="comment">// the sweep.</span></div>
+<div class="line"><a id="l00119" name="l00119"></a><span class="lineno">  119</span>        <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)PARTICLES);</div>
+<div class="line"><a id="l00120" name="l00120"></a><span class="lineno">  120</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
+<div class="line"><a id="l00121" name="l00121"></a><span class="lineno">  121</span>        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
+<div class="line"><a id="l00122" name="l00122"></a><span class="lineno">  122</span>            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
+<div class="line"><a id="l00123" name="l00123"></a><span class="lineno">  123</span>                <span class="comment">// Reset particles and give new time dependent potential.</span></div>
+<div class="line"><a id="l00124" name="l00124"></a><span class="lineno">  124</span>                trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
+<div class="line"><a id="l00125" name="l00125"></a><span class="lineno">  125</span>                res[i + 1][j] = trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N);</div>
+<div class="line"><a id="l00126" name="l00126"></a><span class="lineno">  126</span>            }</div>
+<div class="line"><a id="l00127" name="l00127"></a><span class="lineno">  127</span>        }</div>
+<div class="line"><a id="l00128" name="l00128"></a><span class="lineno">  128</span>    }</div>
+<div class="line"><a id="l00129" name="l00129"></a><span class="lineno">  129</span> </div>
+<div class="line"><a id="l00130" name="l00130"></a><span class="lineno">  130</span>    <span class="comment">// Write results to file</span></div>
+<div class="line"><a id="l00131" name="l00131"></a><span class="lineno">  131</span>    ofile.open(path + <span class="stringliteral">&quot;narrow_sweep_interactions_fine.txt&quot;</span>);</div>
+<div class="line"><a id="l00132" name="l00132"></a><span class="lineno">  132</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00133" name="l00133"></a><span class="lineno">  133</span>        ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00134" name="l00134"></a><span class="lineno">  134</span>              &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00135" name="l00135"></a><span class="lineno">  135</span>    }</div>
+<div class="line"><a id="l00136" name="l00136"></a><span class="lineno">  136</span>    ofile.close();</div>
+<div class="line"><a id="l00137" name="l00137"></a><span class="lineno">  137</span>}</div>
+<div class="line"><a id="l00138" name="l00138"></a><span class="lineno">  138</span> </div>
+<div class="line"><a id="l00139" name="l00139"></a><span class="lineno">  139</span><span class="keywordtype">int</span> main()</div>
+<div class="line"><a id="l00140" name="l00140"></a><span class="lineno">  140</span>{</div>
+<div class="line"><a id="l00141" name="l00141"></a><span class="lineno">  141</span>    <span class="keywordtype">double</span> start, end;</div>
+<div class="line"><a id="l00142" name="l00142"></a><span class="lineno">  142</span> </div>
+<div class="line"><a id="l00143" name="l00143"></a><span class="lineno">  143</span>    start = omp_get_wtime();</div>
+<div class="line"><a id="l00144" name="l00144"></a><span class="lineno">  144</span> </div>
+<div class="line"><a id="l00145" name="l00145"></a><span class="lineno">  145</span>    <a class="code hl_function" href="frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>();</div>
+<div class="line"><a id="l00146" name="l00146"></a><span class="lineno">  146</span> </div>
+<div class="line"><a id="l00147" name="l00147"></a><span class="lineno">  147</span>    <a class="code hl_function" href="frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>();</div>
+<div class="line"><a id="l00148" name="l00148"></a><span class="lineno">  148</span> </div>
+<div class="line"><a id="l00149" name="l00149"></a><span class="lineno">  149</span>    end = omp_get_wtime();</div>
+<div class="line"><a id="l00150" name="l00150"></a><span class="lineno">  150</span> </div>
+<div class="line"><a id="l00151" name="l00151"></a><span class="lineno">  151</span>    std::cout &lt;&lt; <span class="stringliteral">&quot;Time: &quot;</span> &lt;&lt; end - start &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00152" name="l00152"></a><span class="lineno">  152</span> </div>
+<div class="line"><a id="l00153" name="l00153"></a><span class="lineno">  153</span>    <span class="keywordflow">return</span> 0;</div>
+<div class="line"><a id="l00154" name="l00154"></a><span class="lineno">  154</span>}</div>
+<div class="ttc" id="aPenningTrap_8hpp_html"><div class="ttname"><a href="PenningTrap_8hpp.html">PenningTrap.hpp</a></div><div class="ttdoc">A class for simulating a Penning trap.</div></div>
+<div class="ttc" id="aclassPenningTrap_html"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00031">PenningTrap.hpp:32</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_aaee129f177657455348d0c8ae1441dea"><div class="ttname"><a href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap::reinitialize</a></div><div class="ttdeci">void reinitialize(double f, double omega_V, double t=0.)</div><div class="ttdoc">Give all particles new positions and velocities, and change t and V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00153">PenningTrap.cpp:153</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ac529aa26c288f34eae184a67e6bac41f"><div class="ttname"><a href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap::fraction_of_particles_left</a></div><div class="ttdeci">double fraction_of_particles_left(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and calculate what fraction of particles are still left inside the Penning trap after the si...</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00311">PenningTrap.cpp:311</a></div></div>
+<div class="ttc" id="aconstants_8hpp_html"><div class="ttname"><a href="constants_8hpp.html">constants.hpp</a></div><div class="ttdoc">Library of constants.</div></div>
+<div class="ttc" id="afrequency__narrow__sweeps__long_8cpp_html_a33d9b1c76c3c80902f89a58b1a6d96ea"><div class="ttname"><a href="frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a></div><div class="ttdeci">void potential_resonance_narrow_sweep()</div><div class="ttdoc">Simulate 100 particles over 500  using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="frequency__narrow__sweeps__long_8cpp_source.html#l00034">frequency_narrow_sweeps_long.cpp:34</a></div></div>
+<div class="ttc" id="afrequency__narrow__sweeps__long_8cpp_html_ac1816f70ec612edc27848ef7f0875fdb"><div class="ttname"><a href="frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a></div><div class="ttdeci">void potential_resonance_narrow_sweep_interaction()</div><div class="ttdoc">Simulate 100 particles over 500  using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="frequency__narrow__sweeps__long_8cpp_source.html#l00091">frequency_narrow_sweeps_long.cpp:91</a></div></div>
+<div class="ttc" id="autils_8hpp_html"><div class="ttname"><a href="utils_8hpp.html">utils.hpp</a></div><div class="ttdoc">Function prototypes and macros that are useful.</div></div>
+<div class="ttc" id="autils_8hpp_html_a6fdd7217b750aff5b6295ece7cbdeffa"><div class="ttname"><a href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a></div><div class="ttdeci">bool mkpath(std::string path, int mode=0777)</div><div class="ttdoc">Make path given.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00072">utils.cpp:72</a></div></div>
+</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="frequency__narrow__sweeps__long_8cpp.html">frequency_narrow_sweeps_long.cpp</a></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/functions.html

@@ -98,26 +98,98 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
 </div>
 
 <div class="contents">
-<div class="textblock">Here is a list of all documented class members with links to the class documentation for each member:</div><ul>
+<div class="textblock">Here is a list of all documented class members with links to the class documentation for each member:</div>
+
+<h3><a id="index_a" name="index_a"></a>- a -</h3><ul>
 <li>add_particle()&#160;:&#160;<a class="el" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap</a></li>
+</ul>
+
+
+<h3><a id="index_b" name="index_b"></a>- b -</h3><ul>
 <li>B_0&#160;:&#160;<a class="el" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">PenningTrap</a></li>
+</ul>
+
+
+<h3><a id="index_d" name="index_d"></a>- d -</h3><ul>
 <li>d&#160;:&#160;<a class="el" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">PenningTrap</a></li>
-<li>evolve_forward_euler()&#160;:&#160;<a class="el" href="classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965">PenningTrap</a></li>
-<li>evolve_RK4()&#160;:&#160;<a class="el" href="classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9">PenningTrap</a></li>
-<li>external_B_field()&#160;:&#160;<a class="el" href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">PenningTrap</a></li>
-<li>external_E_field()&#160;:&#160;<a class="el" href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">PenningTrap</a></li>
-<li>force_on_particle()&#160;:&#160;<a class="el" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">PenningTrap</a></li>
+</ul>
+
+
+<h3><a id="index_e" name="index_e"></a>- e -</h3><ul>
+<li>evolve_forward_euler()&#160;:&#160;<a class="el" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap</a></li>
+<li>evolve_RK4()&#160;:&#160;<a class="el" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap</a></li>
+<li>external_B_field()&#160;:&#160;<a class="el" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">PenningTrap</a></li>
+<li>external_E_field()&#160;:&#160;<a class="el" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">PenningTrap</a></li>
+</ul>
+
+
+<h3><a id="index_f" name="index_f"></a>- f -</h3><ul>
+<li>force_on_particle()&#160;:&#160;<a class="el" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap</a></li>
+<li>fraction_of_particles_left()&#160;:&#160;<a class="el" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap</a></li>
+</ul>
+
+
+<h3><a id="index_k" name="index_k"></a>- k -</h3><ul>
+<li>k_r&#160;:&#160;<a class="el" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">PenningTrap</a></li>
+<li>k_v&#160;:&#160;<a class="el" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">PenningTrap</a></li>
+</ul>
+
+
+<h3><a id="index_m" name="index_m"></a>- m -</h3><ul>
 <li>m&#160;:&#160;<a class="el" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle</a></li>
-<li>Particle()&#160;:&#160;<a class="el" href="classParticle.html#a00e108823877a25513ccae7cac011b4c">Particle</a></li>
+</ul>
+
+
+<h3><a id="index_p" name="index_p"></a>- p -</h3><ul>
+<li>Particle()&#160;:&#160;<a class="el" href="classParticle.html#af1d7535fb8311eaa77d2b7b345882ec4">Particle</a></li>
 <li>particles&#160;:&#160;<a class="el" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">PenningTrap</a></li>
-<li>PenningTrap&#160;:&#160;<a class="el" href="classParticle.html#aa797d319549dc2a0beb06cdbfd430232">Particle</a>, <a class="el" href="classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560">PenningTrap</a></li>
+<li>PenningTrap&#160;:&#160;<a class="el" href="classParticle.html#aa797d319549dc2a0beb06cdbfd430232">Particle</a>, <a class="el" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap</a></li>
+<li>PenningTrapTest&#160;:&#160;<a class="el" href="classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae">PenningTrap</a></li>
+<li>perturbation&#160;:&#160;<a class="el" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">PenningTrap</a></li>
+</ul>
+
+
+<h3><a id="index_q" name="index_q"></a>- q -</h3><ul>
 <li>q&#160;:&#160;<a class="el" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">Particle</a></li>
-<li>r_vec&#160;:&#160;<a class="el" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">Particle</a></li>
-<li>total_force()&#160;:&#160;<a class="el" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">PenningTrap</a></li>
-<li>total_force_external()&#160;:&#160;<a class="el" href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">PenningTrap</a></li>
-<li>total_force_particles()&#160;:&#160;<a class="el" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">PenningTrap</a></li>
+</ul>
+
+
+<h3><a id="index_r" name="index_r"></a>- r -</h3><ul>
+<li>r_func()&#160;:&#160;<a class="el" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">PenningTrap</a></li>
+<li>r_vec&#160;:&#160;<a class="el" href="classParticle.html#a1c59101411db43624828b766f87ad460">Particle</a></li>
+<li>reinitialize()&#160;:&#160;<a class="el" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap</a></li>
+</ul>
+
+
+<h3><a id="index_s" name="index_s"></a>- s -</h3><ul>
+<li>set_pertubation()&#160;:&#160;<a class="el" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">PenningTrap</a></li>
+<li>simulate()&#160;:&#160;<a class="el" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap</a></li>
+</ul>
+
+
+<h3><a id="index_t" name="index_t"></a>- t -</h3><ul>
+<li>t&#160;:&#160;<a class="el" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">PenningTrap</a></li>
+<li>test_external_B_field()&#160;:&#160;<a class="el" href="classPenningTrapTest.html#ad668d7d875bdc1909a42426bf9dead9e">PenningTrapTest</a></li>
+<li>test_external_E_field()&#160;:&#160;<a class="el" href="classPenningTrapTest.html#a6a303be62039ca2ecccd8252744d4dc8">PenningTrapTest</a></li>
+<li>test_force_on_particle()&#160;:&#160;<a class="el" href="classPenningTrapTest.html#a5f4f0b150e54ce463bb29f76d49883f9">PenningTrapTest</a></li>
+<li>test_total_force_external()&#160;:&#160;<a class="el" href="classPenningTrapTest.html#ae6d0c8e0d80338fb7c7edefc97331046">PenningTrapTest</a></li>
+<li>test_total_force_particles()&#160;:&#160;<a class="el" href="classPenningTrapTest.html#a68449d508e66205bc8b27fa5f60db508">PenningTrapTest</a></li>
+<li>total_force()&#160;:&#160;<a class="el" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap</a></li>
+<li>total_force_external()&#160;:&#160;<a class="el" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap</a></li>
+<li>total_force_no_interaction()&#160;:&#160;<a class="el" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap</a></li>
+<li>total_force_particles()&#160;:&#160;<a class="el" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap</a></li>
+</ul>
+
+
+<h3><a id="index_v" name="index_v"></a>- v -</h3><ul>
 <li>V_0&#160;:&#160;<a class="el" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">PenningTrap</a></li>
-<li>v_vec&#160;:&#160;<a class="el" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">Particle</a></li>
+<li>v_func()&#160;:&#160;<a class="el" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap</a></li>
+<li>v_vec&#160;:&#160;<a class="el" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">Particle</a></li>
+</ul>
+
+
+<h3><a id="index_w" name="index_w"></a>- w -</h3><ul>
+<li>write_simulation_to_dir()&#160;:&#160;<a class="el" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/functions_func.html

@@ -100,16 +100,29 @@ $(document).ready(function(){initNavTree('functions_func.html',''); initResizabl
 <div class="contents">
 &#160;<ul>
 <li>add_particle()&#160;:&#160;<a class="el" href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap</a></li>
-<li>evolve_forward_euler()&#160;:&#160;<a class="el" href="classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965">PenningTrap</a></li>
-<li>evolve_RK4()&#160;:&#160;<a class="el" href="classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9">PenningTrap</a></li>
-<li>external_B_field()&#160;:&#160;<a class="el" href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">PenningTrap</a></li>
-<li>external_E_field()&#160;:&#160;<a class="el" href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">PenningTrap</a></li>
-<li>force_on_particle()&#160;:&#160;<a class="el" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">PenningTrap</a></li>
-<li>Particle()&#160;:&#160;<a class="el" href="classParticle.html#a00e108823877a25513ccae7cac011b4c">Particle</a></li>
-<li>PenningTrap()&#160;:&#160;<a class="el" href="classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560">PenningTrap</a></li>
-<li>total_force()&#160;:&#160;<a class="el" href="classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be">PenningTrap</a></li>
-<li>total_force_external()&#160;:&#160;<a class="el" href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">PenningTrap</a></li>
-<li>total_force_particles()&#160;:&#160;<a class="el" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">PenningTrap</a></li>
+<li>evolve_forward_euler()&#160;:&#160;<a class="el" href="classPenningTrap.html#ab9ea97a406534bbe621a95215144875e">PenningTrap</a></li>
+<li>evolve_RK4()&#160;:&#160;<a class="el" href="classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e">PenningTrap</a></li>
+<li>external_B_field()&#160;:&#160;<a class="el" href="classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655">PenningTrap</a></li>
+<li>external_E_field()&#160;:&#160;<a class="el" href="classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22">PenningTrap</a></li>
+<li>force_on_particle()&#160;:&#160;<a class="el" href="classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598">PenningTrap</a></li>
+<li>fraction_of_particles_left()&#160;:&#160;<a class="el" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap</a></li>
+<li>Particle()&#160;:&#160;<a class="el" href="classParticle.html#af1d7535fb8311eaa77d2b7b345882ec4">Particle</a></li>
+<li>PenningTrap()&#160;:&#160;<a class="el" href="classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8">PenningTrap</a></li>
+<li>r_func()&#160;:&#160;<a class="el" href="classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08">PenningTrap</a></li>
+<li>reinitialize()&#160;:&#160;<a class="el" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap</a></li>
+<li>set_pertubation()&#160;:&#160;<a class="el" href="classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43">PenningTrap</a></li>
+<li>simulate()&#160;:&#160;<a class="el" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap</a></li>
+<li>test_external_B_field()&#160;:&#160;<a class="el" href="classPenningTrapTest.html#ad668d7d875bdc1909a42426bf9dead9e">PenningTrapTest</a></li>
+<li>test_external_E_field()&#160;:&#160;<a class="el" href="classPenningTrapTest.html#a6a303be62039ca2ecccd8252744d4dc8">PenningTrapTest</a></li>
+<li>test_force_on_particle()&#160;:&#160;<a class="el" href="classPenningTrapTest.html#a5f4f0b150e54ce463bb29f76d49883f9">PenningTrapTest</a></li>
+<li>test_total_force_external()&#160;:&#160;<a class="el" href="classPenningTrapTest.html#ae6d0c8e0d80338fb7c7edefc97331046">PenningTrapTest</a></li>
+<li>test_total_force_particles()&#160;:&#160;<a class="el" href="classPenningTrapTest.html#a68449d508e66205bc8b27fa5f60db508">PenningTrapTest</a></li>
+<li>total_force()&#160;:&#160;<a class="el" href="classPenningTrap.html#a9a301b0540078c36697880ef204afdf3">PenningTrap</a></li>
+<li>total_force_external()&#160;:&#160;<a class="el" href="classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682">PenningTrap</a></li>
+<li>total_force_no_interaction()&#160;:&#160;<a class="el" href="classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018">PenningTrap</a></li>
+<li>total_force_particles()&#160;:&#160;<a class="el" href="classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c">PenningTrap</a></li>
+<li>v_func()&#160;:&#160;<a class="el" href="classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2">PenningTrap</a></li>
+<li>write_simulation_to_dir()&#160;:&#160;<a class="el" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/functions_rela.html

@@ -100,6 +100,7 @@ $(document).ready(function(){initNavTree('functions_rela.html',''); initResizabl
 <div class="contents">
 &#160;<ul>
 <li>PenningTrap&#160;:&#160;<a class="el" href="classParticle.html#aa797d319549dc2a0beb06cdbfd430232">Particle</a></li>
+<li>PenningTrapTest&#160;:&#160;<a class="el" href="classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae">PenningTrap</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/functions_vars.html

@@ -101,12 +101,16 @@ $(document).ready(function(){initNavTree('functions_vars.html',''); initResizabl
 &#160;<ul>
 <li>B_0&#160;:&#160;<a class="el" href="classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716">PenningTrap</a></li>
 <li>d&#160;:&#160;<a class="el" href="classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2">PenningTrap</a></li>
+<li>k_r&#160;:&#160;<a class="el" href="classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640">PenningTrap</a></li>
+<li>k_v&#160;:&#160;<a class="el" href="classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4">PenningTrap</a></li>
 <li>m&#160;:&#160;<a class="el" href="classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563">Particle</a></li>
 <li>particles&#160;:&#160;<a class="el" href="classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f">PenningTrap</a></li>
+<li>perturbation&#160;:&#160;<a class="el" href="classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5">PenningTrap</a></li>
 <li>q&#160;:&#160;<a class="el" href="classParticle.html#a566dcc1de4bdc01251776948798ea8e1">Particle</a></li>
-<li>r_vec&#160;:&#160;<a class="el" href="classParticle.html#acf1a0f3c978b06d76df5bb4279594467">Particle</a></li>
+<li>r_vec&#160;:&#160;<a class="el" href="classParticle.html#a1c59101411db43624828b766f87ad460">Particle</a></li>
+<li>t&#160;:&#160;<a class="el" href="classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e">PenningTrap</a></li>
 <li>V_0&#160;:&#160;<a class="el" href="classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89">PenningTrap</a></li>
-<li>v_vec&#160;:&#160;<a class="el" href="classParticle.html#a4a5d22c7aeca66f67d083f270cba25df">Particle</a></li>
+<li>v_vec&#160;:&#160;<a class="el" href="classParticle.html#a3a10400add8dd22b8031330c2aafb6fe">Particle</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/globals.html

@@ -98,12 +98,72 @@ $(document).ready(function(){initNavTree('globals.html',''); initResizable(); })
 </div>
 
 <div class="contents">
-<div class="textblock">Here is a list of all documented file members with links to the documentation:</div><ul>
+<div class="textblock">Here is a list of all documented file members with links to the documentation:</div>
+
+<h3><a id="index__5F" name="index__5F"></a>- _ -</h3><ul>
+<li>__METHOD_NAME__&#160;:&#160;<a class="el" href="utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168">utils.hpp</a></li>
+</ul>
+
+
+<h3><a id="index_a" name="index_a"></a>- a -</h3><ul>
+<li>analytical_solution_particle_1()&#160;:&#160;<a class="el" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">main.cpp</a></li>
+<li>ASSERT&#160;:&#160;<a class="el" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">utils.hpp</a></li>
+</ul>
+
+
+<h3><a id="index_c" name="index_c"></a>- c -</h3><ul>
+<li>CA_CHARGE&#160;:&#160;<a class="el" href="constants_8hpp.html#af7602a3a314957137ad1cd719aa23789">constants.hpp</a></li>
+<li>CA_MASS&#160;:&#160;<a class="el" href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">constants.hpp</a></li>
+<li>close_to()&#160;:&#160;<a class="el" href="utils_8hpp.html#ab3e0cf669bddc59bd53998490ffb68b9">utils.hpp</a>, <a class="el" href="utils_8cpp.html#a6be6f938bcbb235ebb6a2ed9d08411b2">utils.cpp</a></li>
+</ul>
+
+
+<h3><a id="index_d" name="index_d"></a>- d -</h3><ul>
 <li>DEBUG&#160;:&#160;<a class="el" href="utils_8hpp.html#aecc1f7a8a2493b9e021e5bff76a00a5b">utils.hpp</a></li>
+</ul>
+
+
+<h3><a id="index_k" name="index_k"></a>- k -</h3><ul>
 <li>K_E&#160;:&#160;<a class="el" href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">constants.hpp</a></li>
+</ul>
+
+
+<h3><a id="index_m" name="index_m"></a>- m -</h3><ul>
+<li>m_assert()&#160;:&#160;<a class="el" href="utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38">utils.hpp</a>, <a class="el" href="utils_8cpp.html#aff5e07c3c1d321709b0cc38e999f427b">utils.cpp</a></li>
+<li>mkpath()&#160;:&#160;<a class="el" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">utils.hpp</a>, <a class="el" href="utils_8cpp.html#acf13f4e492199cb7231bfa646dbd08de">utils.cpp</a></li>
+</ul>
+
+
+<h3><a id="index_p" name="index_p"></a>- p -</h3><ul>
+<li>p1&#160;:&#160;<a class="el" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">main.cpp</a></li>
+<li>p2&#160;:&#160;<a class="el" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">main.cpp</a></li>
+<li>potential_resonance_narrow_sweep()&#160;:&#160;<a class="el" href="frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">frequency_narrow_sweeps_long.cpp</a>, <a class="el" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">main.cpp</a></li>
+<li>potential_resonance_narrow_sweep_interaction()&#160;:&#160;<a class="el" href="frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">frequency_narrow_sweeps_long.cpp</a>, <a class="el" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">main.cpp</a></li>
+<li>potential_resonance_wide_sweep()&#160;:&#160;<a class="el" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">main.cpp</a></li>
+</ul>
+
+
+<h3><a id="index_s" name="index_s"></a>- s -</h3><ul>
 <li>scientific_format()&#160;:&#160;<a class="el" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">utils.hpp</a>, <a class="el" href="utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746">utils.cpp</a></li>
+<li>sim_arr&#160;:&#160;<a class="el" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">typedefs.hpp</a></li>
+<li>sim_cols&#160;:&#160;<a class="el" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">typedefs.hpp</a></li>
+<li>sim_rows&#160;:&#160;<a class="el" href="typedefs_8hpp.html#a33418f31f28663b8414c8f7182998c22">typedefs.hpp</a></li>
+<li>simulate_100_particles()&#160;:&#160;<a class="el" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">main.cpp</a></li>
+<li>simulate_single_particle()&#160;:&#160;<a class="el" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">main.cpp</a></li>
+<li>simulate_single_particle_with_different_steps()&#160;:&#160;<a class="el" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">main.cpp</a></li>
+<li>simulate_two_particles()&#160;:&#160;<a class="el" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">main.cpp</a></li>
+<li>simulation_t&#160;:&#160;<a class="el" href="typedefs_8hpp.html#a784799c37b5e4fb8bf4f6368e004dec6">typedefs.hpp</a></li>
+</ul>
+
+
+<h3><a id="index_t" name="index_t"></a>- t -</h3><ul>
 <li>T&#160;:&#160;<a class="el" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">constants.hpp</a></li>
+</ul>
+
+
+<h3><a id="index_v" name="index_v"></a>- v -</h3><ul>
 <li>V&#160;:&#160;<a class="el" href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">constants.hpp</a></li>
+<li>vec3&#160;:&#160;<a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">typedefs.hpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/globals_defs.html

@@ -99,6 +99,10 @@ $(document).ready(function(){initNavTree('globals_defs.html',''); initResizable(
 
 <div class="contents">
 &#160;<ul>
+<li>__METHOD_NAME__&#160;:&#160;<a class="el" href="utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168">utils.hpp</a></li>
+<li>ASSERT&#160;:&#160;<a class="el" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">utils.hpp</a></li>
+<li>CA_CHARGE&#160;:&#160;<a class="el" href="constants_8hpp.html#af7602a3a314957137ad1cd719aa23789">constants.hpp</a></li>
+<li>CA_MASS&#160;:&#160;<a class="el" href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">constants.hpp</a></li>
 <li>DEBUG&#160;:&#160;<a class="el" href="utils_8hpp.html#aecc1f7a8a2493b9e021e5bff76a00a5b">utils.hpp</a></li>
 <li>K_E&#160;:&#160;<a class="el" href="constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb">constants.hpp</a></li>
 <li>T&#160;:&#160;<a class="el" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">constants.hpp</a></li>

docs/globals_func.html

@@ -99,7 +99,18 @@ $(document).ready(function(){initNavTree('globals_func.html',''); initResizable(
 
 <div class="contents">
 &#160;<ul>
+<li>analytical_solution_particle_1()&#160;:&#160;<a class="el" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">main.cpp</a></li>
+<li>close_to()&#160;:&#160;<a class="el" href="utils_8hpp.html#ab3e0cf669bddc59bd53998490ffb68b9">utils.hpp</a>, <a class="el" href="utils_8cpp.html#a6be6f938bcbb235ebb6a2ed9d08411b2">utils.cpp</a></li>
+<li>m_assert()&#160;:&#160;<a class="el" href="utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38">utils.hpp</a>, <a class="el" href="utils_8cpp.html#aff5e07c3c1d321709b0cc38e999f427b">utils.cpp</a></li>
+<li>mkpath()&#160;:&#160;<a class="el" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">utils.hpp</a>, <a class="el" href="utils_8cpp.html#acf13f4e492199cb7231bfa646dbd08de">utils.cpp</a></li>
+<li>potential_resonance_narrow_sweep()&#160;:&#160;<a class="el" href="frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">frequency_narrow_sweeps_long.cpp</a>, <a class="el" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">main.cpp</a></li>
+<li>potential_resonance_narrow_sweep_interaction()&#160;:&#160;<a class="el" href="frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">frequency_narrow_sweeps_long.cpp</a>, <a class="el" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">main.cpp</a></li>
+<li>potential_resonance_wide_sweep()&#160;:&#160;<a class="el" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">main.cpp</a></li>
 <li>scientific_format()&#160;:&#160;<a class="el" href="utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384">utils.hpp</a>, <a class="el" href="utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746">utils.cpp</a></li>
+<li>simulate_100_particles()&#160;:&#160;<a class="el" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">main.cpp</a></li>
+<li>simulate_single_particle()&#160;:&#160;<a class="el" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">main.cpp</a></li>
+<li>simulate_single_particle_with_different_steps()&#160;:&#160;<a class="el" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">main.cpp</a></li>
+<li>simulate_two_particles()&#160;:&#160;<a class="el" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">main.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/globals_type.html

@@ -0,0 +1,117 @@
+<!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: File Members</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('globals_type.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="contents">
+&#160;<ul>
+<li>sim_arr&#160;:&#160;<a class="el" href="typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af">typedefs.hpp</a></li>
+<li>sim_cols&#160;:&#160;<a class="el" href="typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f">typedefs.hpp</a></li>
+<li>sim_rows&#160;:&#160;<a class="el" href="typedefs_8hpp.html#a33418f31f28663b8414c8f7182998c22">typedefs.hpp</a></li>
+<li>simulation_t&#160;:&#160;<a class="el" href="typedefs_8hpp.html#a784799c37b5e4fb8bf4f6368e004dec6">typedefs.hpp</a></li>
+<li>vec3&#160;:&#160;<a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">typedefs.hpp</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <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/globals_vars.html

@@ -0,0 +1,114 @@
+<!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: File Members</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('globals_vars.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="contents">
+&#160;<ul>
+<li>p1&#160;:&#160;<a class="el" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">main.cpp</a></li>
+<li>p2&#160;:&#160;<a class="el" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">main.cpp</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <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/index.html

@@ -101,8 +101,113 @@ $(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>
+Tools</h2>
+<ul>
+<li>Profiling<ul>
+<li><a href="https://ftp.gnu.org/old-gnu/Manuals/gprof-2.9.1/html_mono/gprof.html">gprof</a></li>
+<li><a href="https://www.scalasca.org/">scalasca</a></li>
+<li><a href="https://www.vi-hps.org/projects/score-p">score-p</a></li>
+</ul>
+</li>
+</ul>
+<h2><a class="anchor" id="autotoc_md4"></a>
+Libraries</h2>
+<ul>
+<li>Python<ul>
+<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_md5"></a>
+Compiling</h1>
+<p>Compiling is as easy as running this command while being inside the src directory:</p>
+<div class="fragment"><div class="line">make</div>
+</div><!-- fragment --><h1><a class="anchor" id="autotoc_md6"></a>
+Running programs</h1>
+<h2><a class="anchor" id="autotoc_md7"></a>
+C++ binaries</h2>
+<p>To run <b>main</b> or <b>test_suite</b>, just run this command while being inside src:</p>
+<div class="fragment"><div class="line">./&lt;program-name&gt;</div>
+</div><!-- fragment --><h2><a class="anchor" id="autotoc_md8"></a>
+Python scripts</h2>
+<h3><a class="anchor" id="autotoc_md9"></a>
+Install libraries</h3>
+<p>Before running the scripts, make sure that all libraries are installed. Using pip, you can install all requirements like this:</p>
+<div class="fragment"><div class="line">pip install -r requirements.txt</div>
+</div><!-- fragment --><p>This recursively install all the packages that are listed in <b>requirements.txt</b>.</p>
+<h3><a class="anchor" id="autotoc_md10"></a>
+Running scripts</h3>
+<p>For the Python scripts, run them from the src directory like this:</p>
+<div class="fragment"><div class="line">python scripts/&lt;script-name&gt;</div>
+</div><!-- fragment --><p>If you have any problems running the scripts, you might have to run this instead:</p>
+<div class="fragment"><div class="line">python3 scripts/&lt;script-name&gt;</div>
+</div><!-- fragment --><h2><a class="anchor" id="autotoc_md11"></a>
+Batch system</h2>
+<p>For the <b>frequency_narrow_sweeps_long</b> program, the is a script called <b>job.script</b> that comes along with it. This is to be able to run it on a batch system using Slurm if you have access to one. This is the recommended way to use this program as it takes approximately 90 minutes to complete when using 16 cores.</p>
+<p>If you happen to have such a system available to you, then you should clone this repo on that system, then compile it by running:</p>
+<div class="fragment"><div class="line">make frequency_narrow_sweeps_long</div>
+</div><!-- fragment --><p>You might have to load the Armadillo library before compiling.</p>
+<p>After compiling, you can schedule it by running:</p>
+<div class="fragment"><div class="line">sbatch job.script</div>
+</div><!-- fragment --><h1><a class="anchor" id="autotoc_md12"></a>
+Performance</h1>
+<p>This section aims to give an idea to the time it takes for the program to run so that you know a bit what to expect if you decide to run it for yourself.</p>
+<h2><a class="anchor" id="autotoc_md13"></a>
+CPU</h2>
+<p>The times mentioned here are times achieved on a computer with these specifications:</p>
+<ul>
+<li>CPU model<ul>
+<li>Intel i7-9850H</li>
+</ul>
+</li>
+<li>Threads<ul>
+<li>12</li>
+</ul>
+</li>
+<li>Clock speed<ul>
+<li>4.6GHz</li>
+</ul>
+</li>
+</ul>
+<h2><a class="anchor" id="autotoc_md14"></a>
+Times</h2>
+<p>All times mentioned use the <b>evolve_RK4</b> method.</p>
+<p>Running a simulation with 100 particles without particle interactions over 40000 steps takes around 1.8 seconds. With particle interactions, it takes around 4.8 seconds.</p>
+<p><b>potential_resonance_wide_sweep</b> takes around 56 seconds to complete.</p>
+<p><b>potential_resonance_narrow_sweep</b> takes around 172 seconds to complete.</p>
+<p><b>potential_resonance_narrow_sweep_interaction</b> takes around 936 seconds to complete.</p>
+<h1><a class="anchor" id="autotoc_md15"></a>
 Credits</h1>
 <p>The Doxygen theme used here is <a href="https://github.com/jothepro/doxygen-awesome-css">doxygen-awesome-css</a>. </p>
 </div></div><!-- PageDoc -->

docs/main_8cpp.html

@@ -99,31 +99,146 @@ $(document).ready(function(){initNavTree('main_8cpp.html',''); initResizable();
 
 <div class="header">
   <div class="summary">
-<a href="#func-members">Functions</a>  </div>
+<a href="#define-members">Macros</a> &#124;
+<a href="#func-members">Functions</a> &#124;
+<a href="#var-members">Variables</a>  </div>
   <div class="headertitle"><div class="title">main.cpp File Reference</div></div>
 </div><!--header-->
 <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 />
+</div>
 <p><a href="main_8cpp_source.html">Go to the source code of this file.</a></p>
 <table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="define-members" name="define-members"></a>
+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>
+<tr class="separator:a7b24a37e8ce9d243351bfc9b24945e63"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a0240ac851181b84ac374872dc5434ee4"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html#a0240ac851181b84ac374872dc5434ee4">N</a>&#160;&#160;&#160;40000</td></tr>
+<tr class="separator:a0240ac851181b84ac374872dc5434ee4"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
 Functions</h2></td></tr>
+<tr class="memitem:a8d92fb2ad085065fbd14718647551657"><td class="memItemLeft" align="right" valign="top"><a class="el" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a> (double t)</td></tr>
+<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#_bug000007">Bug:</a></b></dt><dd>No known bugs </dd></dl>
 
 <p class="definition">Definition in file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
-</div><h2 class="groupheader">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>
 </div><div class="memdoc">
 
-<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00013">13</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
+<p class="definition">Definition at line <a class="el" href="main_8cpp_source.html#l00314">314</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#l00209">209</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#l00266">266</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#l00152">152</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#l00134">134</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#l00055">55</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
+
+</div>
+</div>
+<a id="ac67e0d59227856c4d42e7d01c75e0ad2" name="ac67e0d59227856c4d42e7d01c75e0ad2"></a>
+<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#l00088">88</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#l00070">70</a> of file <a class="el" href="main_8cpp_source.html">main.cpp</a>.</p>
 
 </div>
 </div>

docs/main_8cpp.js

@@ -0,0 +1,13 @@
+var main_8cpp =
+[
+    [ "analytical_solution_particle_1", "main_8cpp.html#a8d92fb2ad085065fbd14718647551657", null ],
+    [ "potential_resonance_narrow_sweep", "main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea", null ],
+    [ "potential_resonance_narrow_sweep_interaction", "main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb", null ],
+    [ "potential_resonance_wide_sweep", "main_8cpp.html#a6b38b477c18e2f4268779751a88edab1", null ],
+    [ "simulate_100_particles", "main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513", null ],
+    [ "simulate_single_particle", "main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6", null ],
+    [ "simulate_single_particle_with_different_steps", "main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2", null ],
+    [ "simulate_two_particles", "main_8cpp.html#a783789519f97c6430081171cacb0ffb1", null ],
+    [ "p1", "main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30", null ],
+    [ "p2", "main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7", null ]
+];

docs/main_8cpp_source.html

@@ -102,10 +102,398 @@ $(document).ready(function(){initNavTree('main_8cpp_source.html',''); initResiza
 </div><!--header-->
 <div class="contents">
 <a href="main_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span> </div>
-<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="keywordtype">int</span> main() </div>
-<div class="line"><a id="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="keywordflow">return</span> 0;</div>
-<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span>}</div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="preprocessor">#include &lt;cmath&gt;</span></div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="preprocessor">#include &lt;complex&gt;</span></div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="preprocessor">#include &lt;fstream&gt;</span></div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span><span class="preprocessor">#include &lt;omp.h&gt;</span></div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span><span class="preprocessor">#include &lt;string&gt;</span></div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span><span class="preprocessor">#include &lt;vector&gt;</span></div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span> </div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span><span class="preprocessor">#include &quot;<a class="code" href="PenningTrap_8hpp.html">PenningTrap.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span><span class="preprocessor">#include &quot;<a class="code" href="constants_8hpp.html">constants.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span><span class="preprocessor">#include &quot;<a class="code" href="utils_8hpp.html">utils.hpp</a>&quot;</span></div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span> </div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span><span class="preprocessor">#define PARTICLES 100</span></div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span><span class="preprocessor">#define N 40000</span></div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span> </div>
+<div class="line"><a id="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::cout &lt;&lt; A_p &lt;&lt; <span class="stringliteral">&quot;,&quot;</span> &lt;&lt; A_n &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>    std::complex&lt;double&gt; f =</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>        A_p * std::exp(std::complex&lt;double&gt;(0., -w_p * t))</div>
+<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span>        + A_n * std::exp(std::complex&lt;double&gt;(0., -w_n * t));</div>
+<div class="line"><a id="l00049" name="l00049"></a><span class="lineno">   49</span>    <a class="code hl_typedef" href="typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea">vec3</a> res{std::real(f), std::imag(f), 20. * std::cos(std::sqrt(w_z2) * t)};</div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span>    <span class="keywordflow">return</span> res;</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span>}</div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span> </div>
+<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"><a class="line" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">   55</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a>()</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno">   56</span>{</div>
+<div class="line"><a id="l00057" name="l00057"></a><span class="lineno">   57</span>    <span class="comment">// Initialize trap with particle 1</span></div>
+<div class="line"><a id="l00058" name="l00058"></a><span class="lineno">   58</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>});</div>
+<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   59</span> </div>
+<div class="line"><a id="l00060" name="l00060"></a><span class="lineno">   60</span>    <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
+<div class="line"><a id="l00061" name="l00061"></a><span class="lineno">   61</span> </div>
+<div class="line"><a id="l00062" name="l00062"></a><span class="lineno">   62</span>    <span class="comment">// Simulate and write results to file</span></div>
+<div class="line"><a id="l00063" name="l00063"></a><span class="lineno">   63</span>    trap.<a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(<span class="stringliteral">&quot;output/simulate_single_particle&quot;</span>, time, N,</div>
+<div class="line"><a id="l00064" name="l00064"></a><span class="lineno">   64</span>                                 <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00065" name="l00065"></a><span class="lineno">   65</span>}</div>
+<div class="line"><a id="l00066" name="l00066"></a><span class="lineno">   66</span> </div>
+<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"><a class="line" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">   70</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a>()</div>
+<div class="line"><a id="l00071" name="l00071"></a><span class="lineno">   71</span>{</div>
+<div class="line"><a id="l00072" name="l00072"></a><span class="lineno">   72</span>    <span class="comment">// Initialize traps with particles</span></div>
+<div class="line"><a id="l00073" name="l00073"></a><span class="lineno">   73</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap_no_interaction(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>, <a class="code hl_variable" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">p2</a>});</div>
+<div class="line"><a id="l00074" name="l00074"></a><span class="lineno">   74</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap_with_interaction(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>, <a class="code hl_variable" href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">p2</a>});</div>
+<div class="line"><a id="l00075" name="l00075"></a><span class="lineno">   75</span> </div>
+<div class="line"><a id="l00076" name="l00076"></a><span class="lineno">   76</span>    <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
+<div class="line"><a id="l00077" name="l00077"></a><span class="lineno">   77</span> </div>
+<div class="line"><a id="l00078" name="l00078"></a><span class="lineno">   78</span>    <span class="comment">// Simulate and write results to files</span></div>
+<div class="line"><a id="l00079" name="l00079"></a><span class="lineno">   79</span>    trap_no_interaction.<a class="code hl_function" href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">write_simulation_to_dir</a>(</div>
+<div class="line"><a id="l00080" name="l00080"></a><span class="lineno">   80</span>        <span class="stringliteral">&quot;output/simulate_2_particles/no_interaction&quot;</span>, time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00081" name="l00081"></a><span class="lineno">   81</span>    trap_with_interaction.write_simulation_to_dir(</div>
+<div class="line"><a id="l00082" name="l00082"></a><span class="lineno">   82</span>        <span class="stringliteral">&quot;output/simulate_2_particles/with_interaction&quot;</span>, time, N);</div>
+<div class="line"><a id="l00083" name="l00083"></a><span class="lineno">   83</span>}</div>
+<div class="line"><a id="l00084" name="l00084"></a><span class="lineno">   84</span> </div>
+<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"><a class="line" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">   88</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a>()</div>
+<div class="line"><a id="l00089" name="l00089"></a><span class="lineno">   89</span>{</div>
+<div class="line"><a id="l00090" name="l00090"></a><span class="lineno">   90</span>    <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
+<div class="line"><a id="l00091" name="l00091"></a><span class="lineno">   91</span> </div>
+<div class="line"><a id="l00092" name="l00092"></a><span class="lineno">   92</span>    std::ofstream ofile;</div>
+<div class="line"><a id="l00093" name="l00093"></a><span class="lineno">   93</span> </div>
+<div class="line"><a id="l00094" name="l00094"></a><span class="lineno">   94</span>    <span class="comment">// Calculate relative error for RK4</span></div>
+<div class="line"><a id="l00095" name="l00095"></a><span class="lineno">   95</span>    std::string path = <span class="stringliteral">&quot;output/relative_error/RK4/&quot;</span>;</div>
+<div class="line"><a id="l00096" name="l00096"></a><span class="lineno">   96</span>    <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
+<div class="line"><a id="l00097" name="l00097"></a><span class="lineno">   97</span><span class="preprocessor">#pragma omp parallel for private(ofile)</span></div>
+<div class="line"><a id="l00098" name="l00098"></a><span class="lineno">   98</span>    <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; 4; i++) {</div>
+<div class="line"><a id="l00099" name="l00099"></a><span class="lineno">   99</span>        <span class="keywordtype">int</span> steps = 4000 * std::pow(2, i);</div>
+<div class="line"><a id="l00100" name="l00100"></a><span class="lineno">  100</span>        std::cout &lt;&lt; steps &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00101" name="l00101"></a><span class="lineno">  101</span>        <span class="keywordtype">double</span> dt = time / (double)steps;</div>
+<div class="line"><a id="l00102" name="l00102"></a><span class="lineno">  102</span>        ofile.open(path + std::to_string(steps) + <span class="stringliteral">&quot;_steps.txt&quot;</span>);</div>
+<div class="line"><a id="l00103" name="l00103"></a><span class="lineno">  103</span>        <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>});</div>
+<div class="line"><a id="l00104" name="l00104"></a><span class="lineno">  104</span>        <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res = trap.simulate(time, steps, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00105" name="l00105"></a><span class="lineno">  105</span>        <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; steps; i++) {</div>
+<div class="line"><a id="l00106" name="l00106"></a><span class="lineno">  106</span>            ofile &lt;&lt; arma::norm(res.r_vecs[0][i]</div>
+<div class="line"><a id="l00107" name="l00107"></a><span class="lineno">  107</span>                                - <a class="code hl_function" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a>(dt * i))</div>
+<div class="line"><a id="l00108" name="l00108"></a><span class="lineno">  108</span>                  &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00109" name="l00109"></a><span class="lineno">  109</span>        }</div>
+<div class="line"><a id="l00110" name="l00110"></a><span class="lineno">  110</span>        ofile.close();</div>
+<div class="line"><a id="l00111" name="l00111"></a><span class="lineno">  111</span>    }</div>
+<div class="line"><a id="l00112" name="l00112"></a><span class="lineno">  112</span> </div>
+<div class="line"><a id="l00113" name="l00113"></a><span class="lineno">  113</span>    <span class="comment">// Calculate relative error for forward Euler</span></div>
+<div class="line"><a id="l00114" name="l00114"></a><span class="lineno">  114</span>    path = <span class="stringliteral">&quot;output/relative_error/euler/&quot;</span>;</div>
+<div class="line"><a id="l00115" name="l00115"></a><span class="lineno">  115</span>    <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
+<div class="line"><a id="l00116" name="l00116"></a><span class="lineno">  116</span><span class="preprocessor">#pragma omp parallel for private(ofile)</span></div>
+<div class="line"><a id="l00117" name="l00117"></a><span class="lineno">  117</span>    <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; 4; i++) {</div>
+<div class="line"><a id="l00118" name="l00118"></a><span class="lineno">  118</span>        <span class="keywordtype">int</span> steps = 4000 * std::pow(2, i);</div>
+<div class="line"><a id="l00119" name="l00119"></a><span class="lineno">  119</span>        <span class="keywordtype">double</span> dt = time / (double)steps;</div>
+<div class="line"><a id="l00120" name="l00120"></a><span class="lineno">  120</span>        ofile.open(path + std::to_string(steps) + <span class="stringliteral">&quot;_steps.txt&quot;</span>);</div>
+<div class="line"><a id="l00121" name="l00121"></a><span class="lineno">  121</span>        <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap(std::vector&lt;Particle&gt;{<a class="code hl_variable" href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a>});</div>
+<div class="line"><a id="l00122" name="l00122"></a><span class="lineno">  122</span>        <a class="code hl_struct" href="structsimulation.html">simulation_t</a> res = trap.simulate(time, steps, <span class="stringliteral">&quot;euler&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00123" name="l00123"></a><span class="lineno">  123</span>        <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i &lt; steps; i++) {</div>
+<div class="line"><a id="l00124" name="l00124"></a><span class="lineno">  124</span>            ofile &lt;&lt; arma::norm(res.r_vecs[0][i]</div>
+<div class="line"><a id="l00125" name="l00125"></a><span class="lineno">  125</span>                                - <a class="code hl_function" href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a>(dt * i))</div>
+<div class="line"><a id="l00126" name="l00126"></a><span class="lineno">  126</span>                  &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00127" name="l00127"></a><span class="lineno">  127</span>        }</div>
+<div class="line"><a id="l00128" name="l00128"></a><span class="lineno">  128</span>        ofile.close();</div>
+<div class="line"><a id="l00129" name="l00129"></a><span class="lineno">  129</span>    }</div>
+<div class="line"><a id="l00130" name="l00130"></a><span class="lineno">  130</span>}</div>
+<div class="line"><a id="l00131" name="l00131"></a><span class="lineno">  131</span> </div>
+<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"><a class="line" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">  134</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a>()</div>
+<div class="line"><a id="l00135" name="l00135"></a><span class="lineno">  135</span>{</div>
+<div class="line"><a id="l00136" name="l00136"></a><span class="lineno">  136</span>    <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((<span class="keywordtype">unsigned</span>)100);</div>
+<div class="line"><a id="l00137" name="l00137"></a><span class="lineno">  137</span> </div>
+<div class="line"><a id="l00138" name="l00138"></a><span class="lineno">  138</span>    <span class="keywordtype">double</span> time = 50.; <span class="comment">// microseconds</span></div>
+<div class="line"><a id="l00139" name="l00139"></a><span class="lineno">  139</span> </div>
+<div class="line"><a id="l00140" name="l00140"></a><span class="lineno">  140</span>    <span class="comment">// trap.write_simulation_to_dir(&quot;output/simulate_100_particles&quot;, time, N,</span></div>
+<div class="line"><a id="l00141" name="l00141"></a><span class="lineno">  141</span>    <span class="comment">//&quot;rk4&quot;, false);</span></div>
+<div class="line"><a id="l00142" name="l00142"></a><span class="lineno">  142</span>    trap.<a class="code hl_function" href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">simulate</a>(time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">true</span>);</div>
+<div class="line"><a id="l00143" name="l00143"></a><span class="lineno">  143</span>}</div>
+<div class="line"><a id="l00144" name="l00144"></a><span class="lineno">  144</span> </div>
+<div class="line"><a id="l00152" name="l00152"></a><span class="lineno"><a class="line" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">  152</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a>()</div>
+<div class="line"><a id="l00153" name="l00153"></a><span class="lineno">  153</span>{</div>
+<div class="line"><a id="l00154" name="l00154"></a><span class="lineno">  154</span>    <span class="keywordtype">double</span> time = 500.;</div>
+<div class="line"><a id="l00155" name="l00155"></a><span class="lineno">  155</span> </div>
+<div class="line"><a id="l00156" name="l00156"></a><span class="lineno">  156</span>    <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
+<div class="line"><a id="l00157" name="l00157"></a><span class="lineno">  157</span> </div>
+<div class="line"><a id="l00158" name="l00158"></a><span class="lineno">  158</span>    <span class="keywordtype">double</span> freq_start = .2;</div>
+<div class="line"><a id="l00159" name="l00159"></a><span class="lineno">  159</span>    <span class="keywordtype">double</span> freq_end = 2.5;</div>
+<div class="line"><a id="l00160" name="l00160"></a><span class="lineno">  160</span>    <span class="keywordtype">double</span> freq_increment = .02;</div>
+<div class="line"><a id="l00161" name="l00161"></a><span class="lineno">  161</span>    <span class="keywordtype">size_t</span> freq_iterations =</div>
+<div class="line"><a id="l00162" name="l00162"></a><span class="lineno">  162</span>        (size_t)((freq_end - freq_start) / freq_increment) + 1;</div>
+<div class="line"><a id="l00163" name="l00163"></a><span class="lineno">  163</span> </div>
+<div class="line"><a id="l00164" name="l00164"></a><span class="lineno">  164</span>    <span class="keywordtype">double</span> res[4][freq_iterations];</div>
+<div class="line"><a id="l00165" name="l00165"></a><span class="lineno">  165</span> </div>
+<div class="line"><a id="l00166" name="l00166"></a><span class="lineno">  166</span>    std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
+<div class="line"><a id="l00167" name="l00167"></a><span class="lineno">  167</span>    <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
+<div class="line"><a id="l00168" name="l00168"></a><span class="lineno">  168</span> </div>
+<div class="line"><a id="l00169" name="l00169"></a><span class="lineno">  169</span>    std::ofstream ofile;</div>
+<div class="line"><a id="l00170" name="l00170"></a><span class="lineno">  170</span> </div>
+<div class="line"><a id="l00171" name="l00171"></a><span class="lineno">  171</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00172" name="l00172"></a><span class="lineno">  172</span>    <span class="comment">// Insert frequencies</span></div>
+<div class="line"><a id="l00173" name="l00173"></a><span class="lineno">  173</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00174" name="l00174"></a><span class="lineno">  174</span>        res[0][i] = freq_start + freq_increment * i;</div>
+<div class="line"><a id="l00175" name="l00175"></a><span class="lineno">  175</span>    }</div>
+<div class="line"><a id="l00176" name="l00176"></a><span class="lineno">  176</span> </div>
+<div class="line"><a id="l00177" name="l00177"></a><span class="lineno">  177</span><span class="preprocessor">#pragma omp parallel</span></div>
+<div class="line"><a id="l00178" name="l00178"></a><span class="lineno">  178</span>    {</div>
+<div class="line"><a id="l00179" name="l00179"></a><span class="lineno">  179</span>        <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
+<div class="line"><a id="l00180" name="l00180"></a><span class="lineno">  180</span>        <span class="comment">// the sweep.</span></div>
+<div class="line"><a id="l00181" name="l00181"></a><span class="lineno">  181</span>        <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)100);</div>
+<div class="line"><a id="l00182" name="l00182"></a><span class="lineno">  182</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
+<div class="line"><a id="l00183" name="l00183"></a><span class="lineno">  183</span>        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
+<div class="line"><a id="l00184" name="l00184"></a><span class="lineno">  184</span>            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
+<div class="line"><a id="l00185" name="l00185"></a><span class="lineno">  185</span>                <span class="comment">// Reset particles and give new time dependent potential.</span></div>
+<div class="line"><a id="l00186" name="l00186"></a><span class="lineno">  186</span>                trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
+<div class="line"><a id="l00187" name="l00187"></a><span class="lineno">  187</span>                res[i + 1][j] =</div>
+<div class="line"><a id="l00188" name="l00188"></a><span class="lineno">  188</span>                    trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00189" name="l00189"></a><span class="lineno">  189</span>            }</div>
+<div class="line"><a id="l00190" name="l00190"></a><span class="lineno">  190</span>        }</div>
+<div class="line"><a id="l00191" name="l00191"></a><span class="lineno">  191</span>    }</div>
+<div class="line"><a id="l00192" name="l00192"></a><span class="lineno">  192</span> </div>
+<div class="line"><a id="l00193" name="l00193"></a><span class="lineno">  193</span>    <span class="comment">// Write results to file</span></div>
+<div class="line"><a id="l00194" name="l00194"></a><span class="lineno">  194</span>    ofile.open(path + <span class="stringliteral">&quot;wide_sweep.txt&quot;</span>);</div>
+<div class="line"><a id="l00195" name="l00195"></a><span class="lineno">  195</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00196" name="l00196"></a><span class="lineno">  196</span>        ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00197" name="l00197"></a><span class="lineno">  197</span>              &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00198" name="l00198"></a><span class="lineno">  198</span>    }</div>
+<div class="line"><a id="l00199" name="l00199"></a><span class="lineno">  199</span>    ofile.close();</div>
+<div class="line"><a id="l00200" name="l00200"></a><span class="lineno">  200</span>}</div>
+<div class="line"><a id="l00201" name="l00201"></a><span class="lineno">  201</span> </div>
+<div class="line"><a id="l00209" name="l00209"></a><span class="lineno"><a class="line" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">  209</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>()</div>
+<div class="line"><a id="l00210" name="l00210"></a><span class="lineno">  210</span>{</div>
+<div class="line"><a id="l00211" name="l00211"></a><span class="lineno">  211</span>    <span class="keywordtype">double</span> time = 500.;</div>
+<div class="line"><a id="l00212" name="l00212"></a><span class="lineno">  212</span> </div>
+<div class="line"><a id="l00213" name="l00213"></a><span class="lineno">  213</span>    <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
+<div class="line"><a id="l00214" name="l00214"></a><span class="lineno">  214</span> </div>
+<div class="line"><a id="l00215" name="l00215"></a><span class="lineno">  215</span>    <span class="keywordtype">double</span> freq_start = 1.1;</div>
+<div class="line"><a id="l00216" name="l00216"></a><span class="lineno">  216</span>    <span class="keywordtype">double</span> freq_end = 1.7;</div>
+<div class="line"><a id="l00217" name="l00217"></a><span class="lineno">  217</span>    <span class="keywordtype">double</span> freq_increment = .002;</div>
+<div class="line"><a id="l00218" name="l00218"></a><span class="lineno">  218</span>    <span class="keywordtype">size_t</span> freq_iterations =</div>
+<div class="line"><a id="l00219" name="l00219"></a><span class="lineno">  219</span>        (size_t)((freq_end - freq_start) / freq_increment) + 1;</div>
+<div class="line"><a id="l00220" name="l00220"></a><span class="lineno">  220</span> </div>
+<div class="line"><a id="l00221" name="l00221"></a><span class="lineno">  221</span>    <span class="keywordtype">double</span> res[4][freq_iterations];</div>
+<div class="line"><a id="l00222" name="l00222"></a><span class="lineno">  222</span> </div>
+<div class="line"><a id="l00223" name="l00223"></a><span class="lineno">  223</span>    std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
+<div class="line"><a id="l00224" name="l00224"></a><span class="lineno">  224</span>    <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
+<div class="line"><a id="l00225" name="l00225"></a><span class="lineno">  225</span> </div>
+<div class="line"><a id="l00226" name="l00226"></a><span class="lineno">  226</span>    std::ofstream ofile;</div>
+<div class="line"><a id="l00227" name="l00227"></a><span class="lineno">  227</span> </div>
+<div class="line"><a id="l00228" name="l00228"></a><span class="lineno">  228</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00229" name="l00229"></a><span class="lineno">  229</span>    <span class="comment">// Insert frequencies</span></div>
+<div class="line"><a id="l00230" name="l00230"></a><span class="lineno">  230</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00231" name="l00231"></a><span class="lineno">  231</span>        res[0][i] = freq_start + freq_increment * i;</div>
+<div class="line"><a id="l00232" name="l00232"></a><span class="lineno">  232</span>    }</div>
+<div class="line"><a id="l00233" name="l00233"></a><span class="lineno">  233</span> </div>
+<div class="line"><a id="l00234" name="l00234"></a><span class="lineno">  234</span><span class="preprocessor">#pragma omp parallel</span></div>
+<div class="line"><a id="l00235" name="l00235"></a><span class="lineno">  235</span>    {</div>
+<div class="line"><a id="l00236" name="l00236"></a><span class="lineno">  236</span>        <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
+<div class="line"><a id="l00237" name="l00237"></a><span class="lineno">  237</span>        <span class="comment">// the sweep.</span></div>
+<div class="line"><a id="l00238" name="l00238"></a><span class="lineno">  238</span>        <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)100);</div>
+<div class="line"><a id="l00239" name="l00239"></a><span class="lineno">  239</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
+<div class="line"><a id="l00240" name="l00240"></a><span class="lineno">  240</span>        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
+<div class="line"><a id="l00241" name="l00241"></a><span class="lineno">  241</span>            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
+<div class="line"><a id="l00242" name="l00242"></a><span class="lineno">  242</span>                <span class="comment">// Reset particles and give new time dependent potential.</span></div>
+<div class="line"><a id="l00243" name="l00243"></a><span class="lineno">  243</span>                trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
+<div class="line"><a id="l00244" name="l00244"></a><span class="lineno">  244</span>                res[i + 1][j] =</div>
+<div class="line"><a id="l00245" name="l00245"></a><span class="lineno">  245</span>                    trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N, <span class="stringliteral">&quot;rk4&quot;</span>, <span class="keyword">false</span>);</div>
+<div class="line"><a id="l00246" name="l00246"></a><span class="lineno">  246</span>            }</div>
+<div class="line"><a id="l00247" name="l00247"></a><span class="lineno">  247</span>        }</div>
+<div class="line"><a id="l00248" name="l00248"></a><span class="lineno">  248</span>    }</div>
+<div class="line"><a id="l00249" name="l00249"></a><span class="lineno">  249</span> </div>
+<div class="line"><a id="l00250" name="l00250"></a><span class="lineno">  250</span>    <span class="comment">// Write results to file</span></div>
+<div class="line"><a id="l00251" name="l00251"></a><span class="lineno">  251</span>    ofile.open(path + <span class="stringliteral">&quot;narrow_sweep.txt&quot;</span>);</div>
+<div class="line"><a id="l00252" name="l00252"></a><span class="lineno">  252</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00253" name="l00253"></a><span class="lineno">  253</span>        ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00254" name="l00254"></a><span class="lineno">  254</span>              &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00255" name="l00255"></a><span class="lineno">  255</span>    }</div>
+<div class="line"><a id="l00256" name="l00256"></a><span class="lineno">  256</span>    ofile.close();</div>
+<div class="line"><a id="l00257" name="l00257"></a><span class="lineno">  257</span>}</div>
+<div class="line"><a id="l00258" name="l00258"></a><span class="lineno">  258</span> </div>
+<div class="line"><a id="l00266" name="l00266"></a><span class="lineno"><a class="line" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">  266</a></span><span class="keywordtype">void</span> <a class="code hl_function" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>()</div>
+<div class="line"><a id="l00267" name="l00267"></a><span class="lineno">  267</span>{</div>
+<div class="line"><a id="l00268" name="l00268"></a><span class="lineno">  268</span>    <span class="keywordtype">double</span> time = 500.;</div>
+<div class="line"><a id="l00269" name="l00269"></a><span class="lineno">  269</span> </div>
+<div class="line"><a id="l00270" name="l00270"></a><span class="lineno">  270</span>    <span class="keywordtype">double</span> amplitudes[]{.1, .4, .7};</div>
+<div class="line"><a id="l00271" name="l00271"></a><span class="lineno">  271</span> </div>
+<div class="line"><a id="l00272" name="l00272"></a><span class="lineno">  272</span>    <span class="keywordtype">double</span> freq_start = 1.1;</div>
+<div class="line"><a id="l00273" name="l00273"></a><span class="lineno">  273</span>    <span class="keywordtype">double</span> freq_end = 1.7;</div>
+<div class="line"><a id="l00274" name="l00274"></a><span class="lineno">  274</span>    <span class="keywordtype">double</span> freq_increment = .002;</div>
+<div class="line"><a id="l00275" name="l00275"></a><span class="lineno">  275</span>    <span class="keywordtype">size_t</span> freq_iterations =</div>
+<div class="line"><a id="l00276" name="l00276"></a><span class="lineno">  276</span>        (size_t)((freq_end - freq_start) / freq_increment) + 1;</div>
+<div class="line"><a id="l00277" name="l00277"></a><span class="lineno">  277</span> </div>
+<div class="line"><a id="l00278" name="l00278"></a><span class="lineno">  278</span>    <span class="keywordtype">double</span> res[4][freq_iterations];</div>
+<div class="line"><a id="l00279" name="l00279"></a><span class="lineno">  279</span> </div>
+<div class="line"><a id="l00280" name="l00280"></a><span class="lineno">  280</span>    std::string path = <span class="stringliteral">&quot;output/time_dependent_potential/&quot;</span>;</div>
+<div class="line"><a id="l00281" name="l00281"></a><span class="lineno">  281</span>    <a class="code hl_function" href="utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa">mkpath</a>(path);</div>
+<div class="line"><a id="l00282" name="l00282"></a><span class="lineno">  282</span> </div>
+<div class="line"><a id="l00283" name="l00283"></a><span class="lineno">  283</span>    std::ofstream ofile;</div>
+<div class="line"><a id="l00284" name="l00284"></a><span class="lineno">  284</span> </div>
+<div class="line"><a id="l00285" name="l00285"></a><span class="lineno">  285</span><span class="preprocessor">#pragma omp parallel for</span></div>
+<div class="line"><a id="l00286" name="l00286"></a><span class="lineno">  286</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00287" name="l00287"></a><span class="lineno">  287</span>        res[0][i] = freq_start + freq_increment * i;</div>
+<div class="line"><a id="l00288" name="l00288"></a><span class="lineno">  288</span>    }</div>
+<div class="line"><a id="l00289" name="l00289"></a><span class="lineno">  289</span> </div>
+<div class="line"><a id="l00290" name="l00290"></a><span class="lineno">  290</span><span class="preprocessor">#pragma omp parallel</span></div>
+<div class="line"><a id="l00291" name="l00291"></a><span class="lineno">  291</span>    {</div>
+<div class="line"><a id="l00292" name="l00292"></a><span class="lineno">  292</span>        <span class="comment">// Each thread creates a PenningTrap instance and reuses it throughout</span></div>
+<div class="line"><a id="l00293" name="l00293"></a><span class="lineno">  293</span>        <span class="comment">// the sweep.</span></div>
+<div class="line"><a id="l00294" name="l00294"></a><span class="lineno">  294</span>        <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap((uint)100);</div>
+<div class="line"><a id="l00295" name="l00295"></a><span class="lineno">  295</span><span class="preprocessor">#pragma omp for collapse(2)</span></div>
+<div class="line"><a id="l00296" name="l00296"></a><span class="lineno">  296</span>        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; 3; i++) {</div>
+<div class="line"><a id="l00297" name="l00297"></a><span class="lineno">  297</span>            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> j = 0; j &lt; freq_iterations; j++) {</div>
+<div class="line"><a id="l00298" name="l00298"></a><span class="lineno">  298</span>                <span class="comment">// Reset particles and give new time dependent potential.</span></div>
+<div class="line"><a id="l00299" name="l00299"></a><span class="lineno">  299</span>                trap.<a class="code hl_function" href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">reinitialize</a>(amplitudes[i], res[0][j]);</div>
+<div class="line"><a id="l00300" name="l00300"></a><span class="lineno">  300</span>                res[i + 1][j] = trap.<a class="code hl_function" href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">fraction_of_particles_left</a>(time, N);</div>
+<div class="line"><a id="l00301" name="l00301"></a><span class="lineno">  301</span>            }</div>
+<div class="line"><a id="l00302" name="l00302"></a><span class="lineno">  302</span>        }</div>
+<div class="line"><a id="l00303" name="l00303"></a><span class="lineno">  303</span>    }</div>
+<div class="line"><a id="l00304" name="l00304"></a><span class="lineno">  304</span> </div>
+<div class="line"><a id="l00305" name="l00305"></a><span class="lineno">  305</span>    <span class="comment">// Write results to file</span></div>
+<div class="line"><a id="l00306" name="l00306"></a><span class="lineno">  306</span>    ofile.open(path + <span class="stringliteral">&quot;narrow_sweep_interactions.txt&quot;</span>);</div>
+<div class="line"><a id="l00307" name="l00307"></a><span class="lineno">  307</span>    <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; freq_iterations; i++) {</div>
+<div class="line"><a id="l00308" name="l00308"></a><span class="lineno">  308</span>        ofile &lt;&lt; res[0][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[1][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span> &lt;&lt; res[2][i] &lt;&lt; <span class="charliteral">&#39;,&#39;</span></div>
+<div class="line"><a id="l00309" name="l00309"></a><span class="lineno">  309</span>              &lt;&lt; res[3][i] &lt;&lt; <span class="charliteral">&#39;\n&#39;</span>;</div>
+<div class="line"><a id="l00310" name="l00310"></a><span class="lineno">  310</span>    }</div>
+<div class="line"><a id="l00311" name="l00311"></a><span class="lineno">  311</span>    ofile.close();</div>
+<div class="line"><a id="l00312" name="l00312"></a><span class="lineno">  312</span>}</div>
+<div class="line"><a id="l00313" name="l00313"></a><span class="lineno">  313</span> </div>
+<div class="line"><a id="l00314" name="l00314"></a><span class="lineno">  314</span><span class="keywordtype">int</span> main()</div>
+<div class="line"><a id="l00315" name="l00315"></a><span class="lineno">  315</span>{</div>
+<div class="line"><a id="l00316" name="l00316"></a><span class="lineno">  316</span>    <span class="keywordtype">int</span> option = 1;</div>
+<div class="line"><a id="l00317" name="l00317"></a><span class="lineno">  317</span>    <span class="keywordtype">bool</span> chosen = <span class="keyword">false</span>;</div>
+<div class="line"><a id="l00318" name="l00318"></a><span class="lineno">  318</span> </div>
+<div class="line"><a id="l00319" name="l00319"></a><span class="lineno">  319</span>    system(<span class="stringliteral">&quot;clear&quot;</span>);</div>
+<div class="line"><a id="l00320" name="l00320"></a><span class="lineno">  320</span>    std::cout &lt;&lt; <span class="stringliteral">&quot;(1) All (default)\n&quot;</span></div>
+<div class="line"><a id="l00321" name="l00321"></a><span class="lineno">  321</span>              &lt;&lt; <span class="stringliteral">&quot;(2) Simulate single particle\n&quot;</span></div>
+<div class="line"><a id="l00322" name="l00322"></a><span class="lineno">  322</span>              &lt;&lt; <span class="stringliteral">&quot;(3) simulate 2 particles\n&quot;</span></div>
+<div class="line"><a id="l00323" name="l00323"></a><span class="lineno">  323</span>              &lt;&lt; <span class="stringliteral">&quot;(4) Simulate single particle with different time steps\n&quot;</span></div>
+<div class="line"><a id="l00324" name="l00324"></a><span class="lineno">  324</span>              &lt;&lt; <span class="stringliteral">&quot;(5) Simulate 100 particles\n&quot;</span></div>
+<div class="line"><a id="l00325" name="l00325"></a><span class="lineno">  325</span>              &lt;&lt; <span class="stringliteral">&quot;(6) Potential resonance wide sweep\n&quot;</span></div>
+<div class="line"><a id="l00326" name="l00326"></a><span class="lineno">  326</span>              &lt;&lt; <span class="stringliteral">&quot;(7) Potential resonance narrow sweep without particle &quot;</span></div>
+<div class="line"><a id="l00327" name="l00327"></a><span class="lineno">  327</span>                 <span class="stringliteral">&quot;interactions\n&quot;</span></div>
+<div class="line"><a id="l00328" name="l00328"></a><span class="lineno">  328</span>              &lt;&lt; <span class="stringliteral">&quot;(8) Potential resonance narrow sweep with particle &quot;</span></div>
+<div class="line"><a id="l00329" name="l00329"></a><span class="lineno">  329</span>                 <span class="stringliteral">&quot;interaction\n&quot;</span></div>
+<div class="line"><a id="l00330" name="l00330"></a><span class="lineno">  330</span>              &lt;&lt; <span class="stringliteral">&quot;Select what to run: &quot;</span>;</div>
+<div class="line"><a id="l00331" name="l00331"></a><span class="lineno">  331</span>    std::cin &gt;&gt; std::noskipws;</div>
+<div class="line"><a id="l00332" name="l00332"></a><span class="lineno">  332</span>    <span class="keywordflow">do</span> {</div>
+<div class="line"><a id="l00333" name="l00333"></a><span class="lineno">  333</span>        <span class="keywordflow">if</span> (!(std::cin &gt;&gt; option) || option &lt; 1 || option &gt; 8) {</div>
+<div class="line"><a id="l00334" name="l00334"></a><span class="lineno">  334</span>            std::cin.clear();</div>
+<div class="line"><a id="l00335" name="l00335"></a><span class="lineno">  335</span>            std::cin.ignore(std::numeric_limits&lt;std::streamsize&gt;::max(), <span class="charliteral">&#39;\n&#39;</span>);</div>
+<div class="line"><a id="l00336" name="l00336"></a><span class="lineno">  336</span>            system(<span class="stringliteral">&quot;clear&quot;</span>);</div>
+<div class="line"><a id="l00337" name="l00337"></a><span class="lineno">  337</span>            std::cout</div>
+<div class="line"><a id="l00338" name="l00338"></a><span class="lineno">  338</span>                &lt;&lt; <span class="stringliteral">&quot;(1) All (default)\n&quot;</span></div>
+<div class="line"><a id="l00339" name="l00339"></a><span class="lineno">  339</span>                &lt;&lt; <span class="stringliteral">&quot;(2) Simulate single particle\n&quot;</span></div>
+<div class="line"><a id="l00340" name="l00340"></a><span class="lineno">  340</span>                &lt;&lt; <span class="stringliteral">&quot;(3) simulate 2 particles\n&quot;</span></div>
+<div class="line"><a id="l00341" name="l00341"></a><span class="lineno">  341</span>                &lt;&lt; <span class="stringliteral">&quot;(4) Simulate single particle with different time steps\n&quot;</span></div>
+<div class="line"><a id="l00342" name="l00342"></a><span class="lineno">  342</span>                &lt;&lt; <span class="stringliteral">&quot;(5) Simulate 100 particles\n&quot;</span></div>
+<div class="line"><a id="l00343" name="l00343"></a><span class="lineno">  343</span>                &lt;&lt; <span class="stringliteral">&quot;(6) Potential resonance wide sweep\n&quot;</span></div>
+<div class="line"><a id="l00344" name="l00344"></a><span class="lineno">  344</span>                &lt;&lt; <span class="stringliteral">&quot;(7) Potential resonance narrow sweep without particle &quot;</span></div>
+<div class="line"><a id="l00345" name="l00345"></a><span class="lineno">  345</span>                   <span class="stringliteral">&quot;interactions\n&quot;</span></div>
+<div class="line"><a id="l00346" name="l00346"></a><span class="lineno">  346</span>                &lt;&lt; <span class="stringliteral">&quot;(8) Potential resonance narrow sweep with particle &quot;</span></div>
+<div class="line"><a id="l00347" name="l00347"></a><span class="lineno">  347</span>                   <span class="stringliteral">&quot;interaction\n&quot;</span></div>
+<div class="line"><a id="l00348" name="l00348"></a><span class="lineno">  348</span>                &lt;&lt; <span class="stringliteral">&quot;Not a valid option, please enter a valid number: &quot;</span>;</div>
+<div class="line"><a id="l00349" name="l00349"></a><span class="lineno">  349</span>        } <span class="keywordflow">else</span> {</div>
+<div class="line"><a id="l00350" name="l00350"></a><span class="lineno">  350</span>            chosen = <span class="keyword">true</span>;</div>
+<div class="line"><a id="l00351" name="l00351"></a><span class="lineno">  351</span>        }</div>
+<div class="line"><a id="l00352" name="l00352"></a><span class="lineno">  352</span>    } <span class="keywordflow">while</span> (!chosen);</div>
+<div class="line"><a id="l00353" name="l00353"></a><span class="lineno">  353</span> </div>
+<div class="line"><a id="l00354" name="l00354"></a><span class="lineno">  354</span>    <span class="keywordtype">double</span> start, end;</div>
+<div class="line"><a id="l00355" name="l00355"></a><span class="lineno">  355</span> </div>
+<div class="line"><a id="l00356" name="l00356"></a><span class="lineno">  356</span>    system(<span class="stringliteral">&quot;clear&quot;</span>);</div>
+<div class="line"><a id="l00357" name="l00357"></a><span class="lineno">  357</span> </div>
+<div class="line"><a id="l00358" name="l00358"></a><span class="lineno">  358</span>    start = omp_get_wtime();</div>
+<div class="line"><a id="l00359" name="l00359"></a><span class="lineno">  359</span>    <span class="keywordflow">switch</span> (option) {</div>
+<div class="line"><a id="l00360" name="l00360"></a><span class="lineno">  360</span>    <span class="keywordflow">case</span> 1:</div>
+<div class="line"><a id="l00361" name="l00361"></a><span class="lineno">  361</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_single_particle\n&quot;</span>;</div>
+<div class="line"><a id="l00362" name="l00362"></a><span class="lineno">  362</span>        <a class="code hl_function" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a>();</div>
+<div class="line"><a id="l00363" name="l00363"></a><span class="lineno">  363</span> </div>
+<div class="line"><a id="l00364" name="l00364"></a><span class="lineno">  364</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_two_particles\n&quot;</span>;</div>
+<div class="line"><a id="l00365" name="l00365"></a><span class="lineno">  365</span>        <a class="code hl_function" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a>();</div>
+<div class="line"><a id="l00366" name="l00366"></a><span class="lineno">  366</span> </div>
+<div class="line"><a id="l00367" name="l00367"></a><span class="lineno">  367</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_single_particle_with_different_steps\n&quot;</span>;</div>
+<div class="line"><a id="l00368" name="l00368"></a><span class="lineno">  368</span>        <a class="code hl_function" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a>();</div>
+<div class="line"><a id="l00369" name="l00369"></a><span class="lineno">  369</span> </div>
+<div class="line"><a id="l00370" name="l00370"></a><span class="lineno">  370</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_100_particles\n&quot;</span>;</div>
+<div class="line"><a id="l00371" name="l00371"></a><span class="lineno">  371</span>        <a class="code hl_function" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a>();</div>
+<div class="line"><a id="l00372" name="l00372"></a><span class="lineno">  372</span> </div>
+<div class="line"><a id="l00373" name="l00373"></a><span class="lineno">  373</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running potential_resonance_wide_sweep\n&quot;</span>;</div>
+<div class="line"><a id="l00374" name="l00374"></a><span class="lineno">  374</span>        <a class="code hl_function" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a>();</div>
+<div class="line"><a id="l00375" name="l00375"></a><span class="lineno">  375</span> </div>
+<div class="line"><a id="l00376" name="l00376"></a><span class="lineno">  376</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running potential_resonance_narrow_sweep\n&quot;</span>;</div>
+<div class="line"><a id="l00377" name="l00377"></a><span class="lineno">  377</span>        <a class="code hl_function" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>();</div>
+<div class="line"><a id="l00378" name="l00378"></a><span class="lineno">  378</span> </div>
+<div class="line"><a id="l00379" name="l00379"></a><span class="lineno">  379</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running potential_resonance_narrow_sweep_interaction\n&quot;</span>;</div>
+<div class="line"><a id="l00380" name="l00380"></a><span class="lineno">  380</span>        <a class="code hl_function" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>();</div>
+<div class="line"><a id="l00381" name="l00381"></a><span class="lineno">  381</span>        <span class="keywordflow">break</span>;</div>
+<div class="line"><a id="l00382" name="l00382"></a><span class="lineno">  382</span>    <span class="keywordflow">case</span> 2:</div>
+<div class="line"><a id="l00383" name="l00383"></a><span class="lineno">  383</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_single_particle\n&quot;</span>;</div>
+<div class="line"><a id="l00384" name="l00384"></a><span class="lineno">  384</span>        <a class="code hl_function" href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a>();</div>
+<div class="line"><a id="l00385" name="l00385"></a><span class="lineno">  385</span>        <span class="keywordflow">break</span>;</div>
+<div class="line"><a id="l00386" name="l00386"></a><span class="lineno">  386</span>    <span class="keywordflow">case</span> 3:</div>
+<div class="line"><a id="l00387" name="l00387"></a><span class="lineno">  387</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_two_particles\n&quot;</span>;</div>
+<div class="line"><a id="l00388" name="l00388"></a><span class="lineno">  388</span>        <a class="code hl_function" href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a>();</div>
+<div class="line"><a id="l00389" name="l00389"></a><span class="lineno">  389</span>        <span class="keywordflow">break</span>;</div>
+<div class="line"><a id="l00390" name="l00390"></a><span class="lineno">  390</span>    <span class="keywordflow">case</span> 4:</div>
+<div class="line"><a id="l00391" name="l00391"></a><span class="lineno">  391</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_single_particle_with_different_steps\n&quot;</span>;</div>
+<div class="line"><a id="l00392" name="l00392"></a><span class="lineno">  392</span>        <a class="code hl_function" href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a>();</div>
+<div class="line"><a id="l00393" name="l00393"></a><span class="lineno">  393</span>        <span class="keywordflow">break</span>;</div>
+<div class="line"><a id="l00394" name="l00394"></a><span class="lineno">  394</span>    <span class="keywordflow">case</span> 5:</div>
+<div class="line"><a id="l00395" name="l00395"></a><span class="lineno">  395</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running simulate_100_particles\n&quot;</span>;</div>
+<div class="line"><a id="l00396" name="l00396"></a><span class="lineno">  396</span>        <a class="code hl_function" href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a>();</div>
+<div class="line"><a id="l00397" name="l00397"></a><span class="lineno">  397</span>        <span class="keywordflow">break</span>;</div>
+<div class="line"><a id="l00398" name="l00398"></a><span class="lineno">  398</span>    <span class="keywordflow">case</span> 6:</div>
+<div class="line"><a id="l00399" name="l00399"></a><span class="lineno">  399</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running potential_resonance_wide_sweep\n&quot;</span>;</div>
+<div class="line"><a id="l00400" name="l00400"></a><span class="lineno">  400</span>        <a class="code hl_function" href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a>();</div>
+<div class="line"><a id="l00401" name="l00401"></a><span class="lineno">  401</span>        <span class="keywordflow">break</span>;</div>
+<div class="line"><a id="l00402" name="l00402"></a><span class="lineno">  402</span>    <span class="keywordflow">case</span> 7:</div>
+<div class="line"><a id="l00403" name="l00403"></a><span class="lineno">  403</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running potential_resonance_narrow_sweep\n&quot;</span>;</div>
+<div class="line"><a id="l00404" name="l00404"></a><span class="lineno">  404</span>        <a class="code hl_function" href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a>();</div>
+<div class="line"><a id="l00405" name="l00405"></a><span class="lineno">  405</span>        <span class="keywordflow">break</span>;</div>
+<div class="line"><a id="l00406" name="l00406"></a><span class="lineno">  406</span>    <span class="keywordflow">case</span> 8:</div>
+<div class="line"><a id="l00407" name="l00407"></a><span class="lineno">  407</span>        std::cout &lt;&lt; <span class="stringliteral">&quot;Running potential_resonance_narrow_sweep_interaction\n&quot;</span>;</div>
+<div class="line"><a id="l00408" name="l00408"></a><span class="lineno">  408</span>        <a class="code hl_function" href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a>();</div>
+<div class="line"><a id="l00409" name="l00409"></a><span class="lineno">  409</span>        <span class="keywordflow">break</span>;</div>
+<div class="line"><a id="l00410" name="l00410"></a><span class="lineno">  410</span>    }</div>
+<div class="line"><a id="l00411" name="l00411"></a><span class="lineno">  411</span>    end = omp_get_wtime();</div>
+<div class="line"><a id="l00412" name="l00412"></a><span class="lineno">  412</span> </div>
+<div class="line"><a id="l00413" name="l00413"></a><span class="lineno">  413</span>    std::cout &lt;&lt; <span class="stringliteral">&quot;Time: &quot;</span> &lt;&lt; end - start &lt;&lt; <span class="stringliteral">&quot; seconds&quot;</span> &lt;&lt; std::endl;</div>
+<div class="line"><a id="l00414" name="l00414"></a><span class="lineno">  414</span> </div>
+<div class="line"><a id="l00415" name="l00415"></a><span class="lineno">  415</span>    <span class="keywordflow">return</span> 0;</div>
+<div class="line"><a id="l00416" name="l00416"></a><span class="lineno">  416</span>}</div>
+<div class="ttc" id="aPenningTrap_8hpp_html"><div class="ttname"><a href="PenningTrap_8hpp.html">PenningTrap.hpp</a></div><div class="ttdoc">A class for simulating a Penning trap.</div></div>
+<div class="ttc" id="aclassParticle_html"><div class="ttname"><a href="classParticle.html">Particle</a></div><div class="ttdoc">A class that holds attributes of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00022">Particle.hpp:23</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00031">PenningTrap.hpp:32</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_a7a1d9f0528a12308de25bc30718da20a"><div class="ttname"><a href="classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a">PenningTrap::simulate</a></div><div class="ttdeci">simulation_t simulate(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate the particle system inside the Penning trap over a certain amount of time.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00240">PenningTrap.cpp:240</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_aaee129f177657455348d0c8ae1441dea"><div class="ttname"><a href="classPenningTrap.html#aaee129f177657455348d0c8ae1441dea">PenningTrap::reinitialize</a></div><div class="ttdeci">void reinitialize(double f, double omega_V, double t=0.)</div><div class="ttdoc">Give all particles new positions and velocities, and change t and V_0.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00153">PenningTrap.cpp:153</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ac529aa26c288f34eae184a67e6bac41f"><div class="ttname"><a href="classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f">PenningTrap::fraction_of_particles_left</a></div><div class="ttdeci">double fraction_of_particles_left(double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and calculate what fraction of particles are still left inside the Penning trap after the si...</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00311">PenningTrap.cpp:311</a></div></div>
+<div class="ttc" id="aclassPenningTrap_html_ad8bc4df7ab3eed53b16cfdff38e7760b"><div class="ttname"><a href="classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b">PenningTrap::write_simulation_to_dir</a></div><div class="ttdeci">void write_simulation_to_dir(std::string path, double time, uint steps, std::string method=&quot;rk4&quot;, bool particle_interaction=true)</div><div class="ttdoc">Simulate and write the displacement of all particles to files.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00273">PenningTrap.cpp:273</a></div></div>
+<div class="ttc" id="aconstants_8hpp_html"><div class="ttname"><a href="constants_8hpp.html">constants.hpp</a></div><div class="ttdoc">Library of constants.</div></div>
+<div class="ttc" id="aconstants_8hpp_html_a0acb682b8260ab1c60b918599864e2e5"><div class="ttname"><a href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a></div><div class="ttdeci">#define T</div><div class="ttdoc">1 Tesla. unit:</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00021">constants.hpp:21</a></div></div>
+<div class="ttc" id="aconstants_8hpp_html_a2ff491cc7958ffd5e749c518a4a60ec8"><div class="ttname"><a href="constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8">CA_MASS</a></div><div class="ttdeci">#define CA_MASS</div><div class="ttdoc">Mass of a single calcium ion. unit: amu.</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00029">constants.hpp:29</a></div></div>
+<div class="ttc" id="aconstants_8hpp_html_af40a326b23c68a27cebe60f16634a2cb"><div class="ttname"><a href="constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb">V</a></div><div class="ttdeci">#define V</div><div class="ttdoc">1 Volt. unit:</div><div class="ttdef"><b>Definition:</b> <a href="constants_8hpp_source.html#l00025">constants.hpp:25</a></div></div>
+<div class="ttc" id="amain_8cpp_html_a213713d6ecc02a32b588ffd179dc7513"><div class="ttname"><a href="main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513">simulate_100_particles</a></div><div class="ttdeci">void simulate_100_particles()</div><div class="ttdoc">Simulate 100 particles over 50 .</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00134">main.cpp:134</a></div></div>
+<div class="ttc" id="amain_8cpp_html_a2efa69bb9d93049429ce4637075f1d30"><div class="ttname"><a href="main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30">p1</a></div><div class="ttdeci">Particle p1(vec3{20., 0., 20.}, vec3{0., 25., 0.})</div><div class="ttdoc">Particle 1.</div></div>
+<div class="ttc" id="amain_8cpp_html_a33d9b1c76c3c80902f89a58b1a6d96ea"><div class="ttname"><a href="main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea">potential_resonance_narrow_sweep</a></div><div class="ttdeci">void potential_resonance_narrow_sweep()</div><div class="ttdoc">Simulate 100 particles over 500  using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00209">main.cpp:209</a></div></div>
+<div class="ttc" id="amain_8cpp_html_a6b38b477c18e2f4268779751a88edab1"><div class="ttname"><a href="main_8cpp.html#a6b38b477c18e2f4268779751a88edab1">potential_resonance_wide_sweep</a></div><div class="ttdeci">void potential_resonance_wide_sweep()</div><div class="ttdoc">Simulate 100 particles over 500  using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00152">main.cpp:152</a></div></div>
+<div class="ttc" id="amain_8cpp_html_a783789519f97c6430081171cacb0ffb1"><div class="ttname"><a href="main_8cpp.html#a783789519f97c6430081171cacb0ffb1">simulate_two_particles</a></div><div class="ttdeci">void simulate_two_particles()</div><div class="ttdoc">Simulate 2 particles over the period of 50  with and without particle interactions.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00070">main.cpp:70</a></div></div>
+<div class="ttc" id="amain_8cpp_html_a8d92fb2ad085065fbd14718647551657"><div class="ttname"><a href="main_8cpp.html#a8d92fb2ad085065fbd14718647551657">analytical_solution_particle_1</a></div><div class="ttdeci">vec3 analytical_solution_particle_1(double t)</div><div class="ttdoc">The analytical solution for particle p1.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00037">main.cpp:37</a></div></div>
+<div class="ttc" id="amain_8cpp_html_a8fdbe2d5a872e50ef5ec1263243589d6"><div class="ttname"><a href="main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6">simulate_single_particle</a></div><div class="ttdeci">void simulate_single_particle()</div><div class="ttdoc">Simulate a single particle over the period of 50 .</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00055">main.cpp:55</a></div></div>
+<div class="ttc" id="amain_8cpp_html_ac1816f70ec612edc27848ef7f0875fdb"><div class="ttname"><a href="main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb">potential_resonance_narrow_sweep_interaction</a></div><div class="ttdeci">void potential_resonance_narrow_sweep_interaction()</div><div class="ttdoc">Simulate 100 particles over 500  using a time dependent potential.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00266">main.cpp:266</a></div></div>
+<div class="ttc" id="amain_8cpp_html_ac67e0d59227856c4d42e7d01c75e0ad2"><div class="ttname"><a href="main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2">simulate_single_particle_with_different_steps</a></div><div class="ttdeci">void simulate_single_particle_with_different_steps()</div><div class="ttdoc">Simulate a single particle over 50  using different amount of steps and different methods.</div><div class="ttdef"><b>Definition:</b> <a href="main_8cpp_source.html#l00088">main.cpp:88</a></div></div>
+<div class="ttc" id="amain_8cpp_html_ac70b61df65f4336f57ea9b4c35250df7"><div class="ttname"><a href="main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7">p2</a></div><div class="ttdeci">Particle p2(vec3{25., 25., 0.}, vec3{0., 40., 5.})</div><div class="ttdoc">Particle 2.</div></div>
+<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 -->
 <!-- start footer part -->

docs/menudata.js

@@ -29,13 +29,39 @@ var menudata={children:[
 {text:"Class List",url:"annotated.html"},
 {text:"Class Index",url:"classes.html"},
 {text:"Class Members",url:"functions.html",children:[
-{text:"All",url:"functions.html"},
+{text:"All",url:"functions.html",children:[
+{text:"a",url:"functions.html#index_a"},
+{text:"b",url:"functions.html#index_b"},
+{text:"d",url:"functions.html#index_d"},
+{text:"e",url:"functions.html#index_e"},
+{text:"f",url:"functions.html#index_f"},
+{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"},
+{text:"v",url:"functions.html#index_v"},
+{text:"w",url:"functions.html#index_w"}]},
 {text:"Functions",url:"functions_func.html"},
 {text:"Variables",url:"functions_vars.html"},
 {text:"Related Functions",url:"functions_rela.html"}]}]},
 {text:"Files",url:"files.html",children:[
 {text:"File List",url:"files.html"},
 {text:"File Members",url:"globals.html",children:[
-{text:"All",url:"globals.html"},
+{text:"All",url:"globals.html",children:[
+{text:"_",url:"globals.html#index__5F"},
+{text:"a",url:"globals.html#index_a"},
+{text:"c",url:"globals.html#index_c"},
+{text:"d",url:"globals.html#index_d"},
+{text:"k",url:"globals.html#index_k"},
+{text:"m",url:"globals.html#index_m"},
+{text:"p",url:"globals.html#index_p"},
+{text:"s",url:"globals.html#index_s"},
+{text:"t",url:"globals.html#index_t"},
+{text:"v",url:"globals.html#index_v"}]},
 {text:"Functions",url:"globals_func.html"},
+{text:"Variables",url:"globals_vars.html"},
+{text:"Typedefs",url:"globals_type.html"},
 {text:"Macros",url:"globals_defs.html"}]}]}]}

docs/namespaceplot__3d.html

@@ -0,0 +1,177 @@
+<!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: plot_3d Namespace Reference</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('namespaceplot__3d.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="summary">
+<a href="#func-members">Functions</a> &#124;
+<a href="#var-members">Variables</a>  </div>
+  <div class="headertitle"><div class="title">plot_3d Namespace Reference</div></div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:adb8902df55180f4ad62fb3799bc5c5a8"><td class="memItemLeft" align="right" valign="top">def&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceplot__3d.html#adb8902df55180f4ad62fb3799bc5c5a8">main</a> ()</td></tr>
+<tr class="separator:adb8902df55180f4ad62fb3799bc5c5a8"><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:a7026cb07859df7ff6b3fb60453573467"><td class="memItemLeft" align="right" valign="top">dict&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceplot__3d.html#a7026cb07859df7ff6b3fb60453573467">params</a></td></tr>
+<tr class="separator:a7026cb07859df7ff6b3fb60453573467"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><pre class="fragment"> @package plot_3d</pre> </div><h2 class="groupheader">Function Documentation</h2>
+<a id="adb8902df55180f4ad62fb3799bc5c5a8" name="adb8902df55180f4ad62fb3799bc5c5a8"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#adb8902df55180f4ad62fb3799bc5c5a8">&#9670;&#160;</a></span>main()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">def plot_3d.main </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="plot__3d_8py_source.html#l00022">22</a> of file <a class="el" href="plot__3d_8py_source.html">plot_3d.py</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Variable Documentation</h2>
+<a id="a7026cb07859df7ff6b3fb60453573467" name="a7026cb07859df7ff6b3fb60453573467"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a7026cb07859df7ff6b3fb60453573467">&#9670;&#160;</a></span>params</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">dict plot_3d.params</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<b>Initial value:</b><div class="fragment"><div class="line"><span class="lineno">    1</span>=  {</div>
+<div class="line"><span class="lineno">    2</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><span class="lineno">    3</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>, </div>
+<div class="line"><span class="lineno">    4</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><span class="lineno">    5</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    6</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    7</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    8</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    9</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</span>,</div>
+<div class="line"><span class="lineno">   10</span>    <span class="stringliteral">&quot;figure.autolayout&quot;</span>: <span class="keyword">True</span></div>
+<div class="line"><span class="lineno">   11</span>}</div>
+</div><!-- fragment -->
+<p class="definition">Definition at line <a class="el" href="plot__3d_8py_source.html#l00009">9</a> of file <a class="el" href="plot__3d_8py_source.html">plot_3d.py</a>.</p>
+
+</div>
+</div>
+</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="namespaceplot__3d.html">plot_3d</a></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/namespaces.html

@@ -0,0 +1,118 @@
+<!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: Namespace List</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('namespaces.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">Namespace List</div></div>
+</div><!--header-->
+<div class="contents">
+<div class="textblock">Here is a list of all documented namespaces with brief descriptions:</div><div class="directory">
+<table class="directory">
+<tr id="row_0_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespaceplot__3d.html" target="_self">plot_3d</a></td><td class="desc"></td></tr>
+</table>
+</div><!-- directory -->
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <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/namespaces_dup.js

@@ -0,0 +1,4 @@
+var namespaces_dup =
+[
+    [ "plot_3d", "namespaceplot__3d.html", null ]
+];

docs/navtreedata.js

@@ -25,9 +25,26 @@
 var NAVTREE =
 [
   [ "Penning Trap Simulation", "index.html", [
-    [ "Credits", "index.html#autotoc_md1", null ],
+    [ "Requirements", "index.html#autotoc_md1", [
+      [ "Operating systems", "index.html#autotoc_md2", null ],
+      [ "Tools", "index.html#autotoc_md3", null ],
+      [ "Libraries", "index.html#autotoc_md4", null ]
+    ] ],
+    [ "Compiling", "index.html#autotoc_md5", null ],
+    [ "Running programs", "index.html#autotoc_md6", [
+      [ "C++ binaries", "index.html#autotoc_md7", null ],
+      [ "Python scripts", "index.html#autotoc_md8", [
+        [ "Install libraries", "index.html#autotoc_md9", null ],
+        [ "Running scripts", "index.html#autotoc_md10", null ]
+      ] ],
+      [ "Batch system", "index.html#autotoc_md11", null ]
+    ] ],
+    [ "Performance", "index.html#autotoc_md12", [
+      [ "CPU", "index.html#autotoc_md13", null ],
+      [ "Times", "index.html#autotoc_md14", null ]
+    ] ],
+    [ "Credits", "index.html#autotoc_md15", null ],
     [ "Bug List", "bug.html", null ],
-    [ "Todo List", "todo.html", null ],
     [ "Classes", "annotated.html", [
       [ "Class List", "annotated.html", "annotated_dup" ],
       [ "Class Index", "classes.html", null ],
@@ -43,6 +60,8 @@ var NAVTREE =
       [ "File Members", "globals.html", [
         [ "All", "globals.html", null ],
         [ "Functions", "globals_func.html", null ],
+        [ "Variables", "globals_vars.html", null ],
+        [ "Typedefs", "globals_type.html", null ],
         [ "Macros", "globals_defs.html", null ]
       ] ]
     ] ]

docs/navtreeindex0.js

@@ -1,68 +1,151 @@
 var NAVTREEINDEX0 =
 {
-"Particle_8cpp.html":[4,0,1,1],
-"Particle_8cpp_source.html":[4,0,1,1],
-"Particle_8hpp.html":[4,0,0,1],
-"Particle_8hpp_source.html":[4,0,0,1],
-"PenningTrap_8cpp.html":[4,0,1,2],
-"PenningTrap_8cpp_source.html":[4,0,1,2],
-"PenningTrap_8hpp.html":[4,0,0,2],
-"PenningTrap_8hpp_source.html":[4,0,0,2],
-"annotated.html":[3,0],
-"bug.html":[1],
-"classParticle.html":[3,0,0],
-"classParticle.html#a00e108823877a25513ccae7cac011b4c":[3,0,0,0],
-"classParticle.html#a4a5d22c7aeca66f67d083f270cba25df":[3,0,0,5],
-"classParticle.html#a566dcc1de4bdc01251776948798ea8e1":[3,0,0,3],
-"classParticle.html#aa797d319549dc2a0beb06cdbfd430232":[3,0,0,1],
-"classParticle.html#acf1a0f3c978b06d76df5bb4279594467":[3,0,0,4],
-"classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563":[3,0,0,2],
-"classPenningTrap.html":[3,0,1],
-"classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f":[3,0,1,12],
-"classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee":[3,0,1,8],
-"classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716":[3,0,1,10],
-"classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d":[3,0,1,9],
-"classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784":[3,0,1,4],
-"classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182":[3,0,1,6],
-"classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965":[3,0,1,2],
-"classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2":[3,0,1,11],
-"classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8":[3,0,1,1],
-"classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89":[3,0,1,13],
-"classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560":[3,0,1,0],
-"classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be":[3,0,1,7],
-"classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b":[3,0,1,5],
-"classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9":[3,0,1,3],
-"classes.html":[3,1],
-"constants_8hpp.html":[4,0,0,0],
-"constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5":[4,0,0,0,1],
-"constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb":[4,0,0,0,0],
-"constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb":[4,0,0,0,2],
-"constants_8hpp_source.html":[4,0,0,0],
-"dir_68267d1309a1af8e8297ef4c3efbcdba.html":[4,0,1],
-"dir_d44c64559bbebec7f509842c48db8b23.html":[4,0,0],
-"files.html":[4,0],
-"functions.html":[3,2,0],
-"functions_func.html":[3,2,1],
-"functions_rela.html":[3,2,3],
-"functions_vars.html":[3,2,2],
-"globals.html":[4,1,0],
-"globals_defs.html":[4,1,2],
-"globals_func.html":[4,1,1],
+"Particle_8cpp.html":[7,0,1,3],
+"Particle_8cpp_source.html":[7,0,1,3],
+"Particle_8hpp.html":[7,0,0,1],
+"Particle_8hpp_source.html":[7,0,0,1],
+"PenningTrap_8cpp.html":[7,0,1,4],
+"PenningTrap_8cpp_source.html":[7,0,1,4],
+"PenningTrap_8hpp.html":[7,0,0,2],
+"PenningTrap_8hpp_source.html":[7,0,0,2],
+"animate__100__particles_8py.html":[7,0,1,0,0],
+"animate__100__particles_8py_source.html":[7,0,1,0,0],
+"annotated.html":[6,0],
+"bug.html":[5],
+"classParticle.html":[6,0,0],
+"classParticle.html#a1c59101411db43624828b766f87ad460":[6,0,0,4],
+"classParticle.html#a3a10400add8dd22b8031330c2aafb6fe":[6,0,0,5],
+"classParticle.html#a566dcc1de4bdc01251776948798ea8e1":[6,0,0,3],
+"classParticle.html#aa797d319549dc2a0beb06cdbfd430232":[6,0,0,1],
+"classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563":[6,0,0,2],
+"classParticle.html#af1d7535fb8311eaa77d2b7b345882ec4":[6,0,0,0],
+"classPenningTrap.html":[6,0,1],
+"classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f":[6,0,1,25],
+"classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716":[6,0,1,21],
+"classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682":[6,0,1,15],
+"classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640":[6,0,1,23],
+"classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c":[6,0,1,17],
+"classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655":[6,0,1,6],
+"classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e":[6,0,1,5],
+"classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2":[6,0,1,18],
+"classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22":[6,0,1,7],
+"classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8":[6,0,1,0],
+"classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018":[6,0,1,16],
+"classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2":[6,0,1,22],
+"classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8":[6,0,1,3],
+"classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89":[6,0,1,28],
+"classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a":[6,0,1,13],
+"classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598":[6,0,1,8],
+"classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08":[6,0,1,10],
+"classPenningTrap.html#a830be1b8cbf59664e060b6edbeaa302f":[6,0,1,1],
+"classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae":[6,0,1,20],
+"classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e":[6,0,1,27],
+"classPenningTrap.html#a9a301b0540078c36697880ef204afdf3":[6,0,1,14],
+"classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43":[6,0,1,12],
+"classPenningTrap.html#aaee129f177657455348d0c8ae1441dea":[6,0,1,11],
+"classPenningTrap.html#ab9ea97a406534bbe621a95215144875e":[6,0,1,4],
+"classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f":[6,0,1,9],
+"classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b":[6,0,1,19],
+"classPenningTrap.html#addc96789dcfec07b75156e19fee82f4f":[6,0,1,2],
+"classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5":[6,0,1,26],
+"classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4":[6,0,1,24],
+"classPenningTrapTest.html":[6,0,2],
+"classPenningTrapTest.html#a5f4f0b150e54ce463bb29f76d49883f9":[6,0,2,2],
+"classPenningTrapTest.html#a68449d508e66205bc8b27fa5f60db508":[6,0,2,4],
+"classPenningTrapTest.html#a6a303be62039ca2ecccd8252744d4dc8":[6,0,2,1],
+"classPenningTrapTest.html#ad668d7d875bdc1909a42426bf9dead9e":[6,0,2,0],
+"classPenningTrapTest.html#ae6d0c8e0d80338fb7c7edefc97331046":[6,0,2,3],
+"classes.html":[6,1],
+"constants_8hpp.html":[7,0,0,0],
+"constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5":[7,0,0,0,3],
+"constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8":[7,0,0,0,1],
+"constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb":[7,0,0,0,2],
+"constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb":[7,0,0,0,4],
+"constants_8hpp.html#af7602a3a314957137ad1cd719aa23789":[7,0,0,0,0],
+"constants_8hpp_source.html":[7,0,0,0],
+"dir_634e799a3947388232110823971192a8.html":[7,0,1,0],
+"dir_68267d1309a1af8e8297ef4c3efbcdba.html":[7,0,1],
+"dir_d44c64559bbebec7f509842c48db8b23.html":[7,0,0],
+"files.html":[7,0],
+"frequency__narrow__sweeps__long_8cpp.html":[7,0,1,1],
+"frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea":[7,0,1,1,0],
+"frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb":[7,0,1,1,1],
+"frequency__narrow__sweeps__long_8cpp_source.html":[7,0,1,1],
+"functions.html":[6,2,0],
+"functions_func.html":[6,2,1],
+"functions_rela.html":[6,2,3],
+"functions_vars.html":[6,2,2],
+"globals.html":[7,1,0],
+"globals_defs.html":[7,1,4],
+"globals_func.html":[7,1,1],
+"globals_type.html":[7,1,3],
+"globals_vars.html":[7,1,2],
 "index.html":[],
 "index.html#autotoc_md1":[0],
-"main_8cpp.html":[4,0,1,0],
-"main_8cpp_source.html":[4,0,1,0],
+"index.html#autotoc_md10":[2,1,1],
+"index.html#autotoc_md11":[2,2],
+"index.html#autotoc_md12":[3],
+"index.html#autotoc_md13":[3,0],
+"index.html#autotoc_md14":[3,1],
+"index.html#autotoc_md15":[4],
+"index.html#autotoc_md2":[0,0],
+"index.html#autotoc_md3":[0,1],
+"index.html#autotoc_md4":[0,2],
+"index.html#autotoc_md5":[1],
+"index.html#autotoc_md6":[2],
+"index.html#autotoc_md7":[2,0],
+"index.html#autotoc_md8":[2,1],
+"index.html#autotoc_md9":[2,1,0],
+"main_8cpp.html":[7,0,1,2],
+"main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513":[7,0,1,2,4],
+"main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30":[7,0,1,2,8],
+"main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea":[7,0,1,2,1],
+"main_8cpp.html#a6b38b477c18e2f4268779751a88edab1":[7,0,1,2,3],
+"main_8cpp.html#a783789519f97c6430081171cacb0ffb1":[7,0,1,2,7],
+"main_8cpp.html#a8d92fb2ad085065fbd14718647551657":[7,0,1,2,0],
+"main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6":[7,0,1,2,5],
+"main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb":[7,0,1,2,2],
+"main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2":[7,0,1,2,6],
+"main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7":[7,0,1,2,9],
+"main_8cpp_source.html":[7,0,1,2],
 "pages.html":[],
-"test__suite_8cpp.html":[4,0,1,3],
-"test__suite_8cpp_source.html":[4,0,1,3],
-"todo.html":[2],
-"utils_8cpp.html":[4,0,1,4],
-"utils_8cpp.html#a58565270b643b24e3132f38c653e0199":[4,0,1,4,0],
-"utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746":[4,0,1,4,1],
-"utils_8cpp_source.html":[4,0,1,4],
-"utils_8hpp.html":[4,0,0,3],
-"utils_8hpp.html#ad54b96a1074f9df4dc892a41d115b72d":[4,0,0,3,1],
-"utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384":[4,0,0,3,2],
-"utils_8hpp.html#aecc1f7a8a2493b9e021e5bff76a00a5b":[4,0,0,3,0],
-"utils_8hpp_source.html":[4,0,0,3]
+"plot__2__particles_8py.html":[7,0,1,0,1],
+"plot__2__particles_8py_source.html":[7,0,1,0,1],
+"plot__3d_8py.html":[7,0,1,0,2],
+"plot__3d_8py_source.html":[7,0,1,0,2],
+"plot__particles__left_8py.html":[7,0,1,0,3],
+"plot__particles__left_8py_source.html":[7,0,1,0,3],
+"plot__phase__space_8py.html":[7,0,1,0,4],
+"plot__phase__space_8py_source.html":[7,0,1,0,4],
+"plot__relative__error_8py.html":[7,0,1,0,5],
+"plot__relative__error_8py_source.html":[7,0,1,0,5],
+"plot__single__particle_8py.html":[7,0,1,0,6],
+"plot__single__particle_8py_source.html":[7,0,1,0,6],
+"structsimulation.html":[6,0,3],
+"test__suite_8cpp.html":[7,0,1,5],
+"test__suite_8cpp_source.html":[7,0,1,5],
+"typedefs_8hpp.html":[7,0,0,3],
+"typedefs_8hpp.html#a33418f31f28663b8414c8f7182998c22":[7,0,0,3,3],
+"typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea":[7,0,0,3,5],
+"typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f":[7,0,0,3,2],
+"typedefs_8hpp.html#a784799c37b5e4fb8bf4f6368e004dec6":[7,0,0,3,4],
+"typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af":[7,0,0,3,1],
+"typedefs_8hpp_source.html":[7,0,0,3],
+"utils_8cpp.html":[7,0,1,6],
+"utils_8cpp.html#a58565270b643b24e3132f38c653e0199":[7,0,1,6,3],
+"utils_8cpp.html#a6be6f938bcbb235ebb6a2ed9d08411b2":[7,0,1,6,0],
+"utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746":[7,0,1,6,4],
+"utils_8cpp.html#acf13f4e492199cb7231bfa646dbd08de":[7,0,1,6,2],
+"utils_8cpp.html#aff5e07c3c1d321709b0cc38e999f427b":[7,0,1,6,1],
+"utils_8cpp_source.html":[7,0,1,6],
+"utils_8hpp.html":[7,0,0,4],
+"utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38":[7,0,0,4,4],
+"utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168":[7,0,0,4,0],
+"utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa":[7,0,0,4,5],
+"utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9":[7,0,0,4,1],
+"utils_8hpp.html#ab3e0cf669bddc59bd53998490ffb68b9":[7,0,0,4,3],
+"utils_8hpp.html#ad54b96a1074f9df4dc892a41d115b72d":[7,0,0,4,6],
+"utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384":[7,0,0,4,7],
+"utils_8hpp.html#aecc1f7a8a2493b9e021e5bff76a00a5b":[7,0,0,4,2],
+"utils_8hpp_source.html":[7,0,0,4]
 };

docs/pages.html

@@ -104,7 +104,6 @@ $(document).ready(function(){initNavTree('pages.html',''); initResizable(); });
 <div class="textblock">Here is a list of all related documentation pages:</div><div class="directory">
 <table class="directory">
 <tr id="row_0_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><a class="el" href="bug.html" target="_self">Bug List</a></td><td class="desc"></td></tr>
-<tr id="row_1_" class="odd"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><a class="el" href="todo.html" target="_self">Todo List</a></td><td class="desc"></td></tr>
 </table>
 </div><!-- directory -->
 </div><!-- contents -->

docs/plot__2__particles_8py.html

@@ -0,0 +1,189 @@
+<!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_2_particles.py File Reference</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__2__particles_8py.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="summary">
+<a href="#func-members">Functions</a> &#124;
+<a href="#var-members">Variables</a>  </div>
+  <div class="headertitle"><div class="title">plot_2_particles.py File Reference</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>Plot 2 particles with and without particle interactions in the xy-plane.  
+<a href="#details">More...</a></p>
+
+<p><a href="plot__2__particles_8py_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:a8863a67cb3a33d1a522efae56b05d37d"><td class="memItemLeft" align="right" valign="top">def&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__2__particles_8py.html#a8863a67cb3a33d1a522efae56b05d37d">plot_2_particles.main</a> ()</td></tr>
+<tr class="separator:a8863a67cb3a33d1a522efae56b05d37d"><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:a65096b5c625338aed999b0be51846e3a"><td class="memItemLeft" align="right" valign="top">dict&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__2__particles_8py.html#a65096b5c625338aed999b0be51846e3a">plot_2_particles.params</a></td></tr>
+<tr class="separator:a65096b5c625338aed999b0be51846e3a"><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>Plot 2 particles with and without particle interactions in the xy-plane. </p>
+<dl class="section author"><dt>Author</dt><dd>Cory Alexander Balaton (coryab) </dd>
+<dd>
+Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
+<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
+<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000013">Bug:</a></b></dt><dd>No known bugs </dd></dl>
+
+<p class="definition">Definition in file <a class="el" href="plot__2__particles_8py_source.html">plot_2_particles.py</a>.</p>
+</div><h2 class="groupheader">Function Documentation</h2>
+<a id="a8863a67cb3a33d1a522efae56b05d37d" name="a8863a67cb3a33d1a522efae56b05d37d"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a8863a67cb3a33d1a522efae56b05d37d">&#9670;&#160;</a></span>main()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">def plot_2_particles.main </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="plot__2__particles_8py_source.html#l00030">30</a> of file <a class="el" href="plot__2__particles_8py_source.html">plot_2_particles.py</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Variable Documentation</h2>
+<a id="a65096b5c625338aed999b0be51846e3a" name="a65096b5c625338aed999b0be51846e3a"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a65096b5c625338aed999b0be51846e3a">&#9670;&#160;</a></span>params</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">dict plot_2_particles.params</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<b>Initial value:</b><div class="fragment"><div class="line"><span class="lineno">    1</span>=  {</div>
+<div class="line"><span class="lineno">    2</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><span class="lineno">    3</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>, </div>
+<div class="line"><span class="lineno">    4</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><span class="lineno">    5</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    6</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    7</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    8</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    9</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</span></div>
+<div class="line"><span class="lineno">   10</span>}</div>
+</div><!-- fragment -->
+<p class="definition">Definition at line <a class="el" href="plot__2__particles_8py_source.html#l00018">18</a> of file <a class="el" href="plot__2__particles_8py_source.html">plot_2_particles.py</a>.</p>
+
+</div>
+</div>
+</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"><a class="el" href="plot__2__particles_8py.html">plot_2_particles.py</a></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__2__particles_8py_source.html

@@ -0,0 +1,179 @@
+<!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_2_particles.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__2__particles_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_2_particles.py</div></div>
+</div><!--header-->
+<div class="contents">
+<a href="plot__2__particles_8py.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span> </div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span> </div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="keyword">import</span> matplotlib.pyplot <span class="keyword">as</span> plt</div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="keyword">import</span> numpy <span class="keyword">as</span> np</div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="keyword">import</span> seaborn <span class="keyword">as</span> sns</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>sns.set_theme()</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>params = {</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>, </div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</span></div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span>}</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>plt.rcParams.update(params)</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>main():</div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span>    directories = {</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>        <span class="stringliteral">&quot;output/simulate_2_particles/no_interaction/&quot;</span>,</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span>        <span class="stringliteral">&quot;output/simulate_2_particles/with_interaction/&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>    files = [</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span>        <span class="stringliteral">&quot;particle_0_r.txt&quot;</span>,</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span>        <span class="stringliteral">&quot;particle_1_r.txt&quot;</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>    outputs = [</div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>        <span class="stringliteral">&quot;../latex/images/simulate_2_particles_no_interaction_xy.pdf&quot;</span>,</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>        <span class="stringliteral">&quot;../latex/images/simulate_2_particles_interaction_xy.pdf&quot;</span>,</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>    ]</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>    labels = [</div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span>        <span class="stringliteral">r&quot;$p_1$&quot;</span>,</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span>        <span class="stringliteral">r&quot;$p_2$&quot;</span>,</div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>        <span class="stringliteral">r&quot;$\hat{p}_1$&quot;</span>,</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>        <span class="stringliteral">r&quot;$\hat{p}_2$&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>    colors = [</div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span>        <span class="stringliteral">&quot;seagreen&quot;</span>,</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span>        <span class="stringliteral">&quot;darkred&quot;</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>    start_pos = set()</div>
+<div class="line"><a id="l00054" name="l00054"></a><span class="lineno">   54</span>    <span class="keywordflow">for</span> dir, output <span class="keywordflow">in</span> zip(directories, outputs):</div>
+<div class="line"><a id="l00055" name="l00055"></a><span class="lineno">   55</span>        fig, ax = plt.subplots()</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno">   56</span>        <span class="keywordflow">for</span> label, color, file <span class="keywordflow">in</span> zip(labels, colors, files):</div>
+<div class="line"><a id="l00057" name="l00057"></a><span class="lineno">   57</span>            <span class="keyword">with</span> open(dir+file) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00058" name="l00058"></a><span class="lineno">   58</span>                lines = f.readlines()</div>
+<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   59</span>                t = np.linspace(0, 50, len(lines))</div>
+<div class="line"><a id="l00060" name="l00060"></a><span class="lineno">   60</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="l00061" name="l00061"></a><span class="lineno">   61</span>                ax.plot(r[:,0], r[:,1], label=label, color=color)</div>
+<div class="line"><a id="l00062" name="l00062"></a><span class="lineno">   62</span>                start_pos.add((r[0,0],r[0,1]))</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="keywordflow">for</span> pos <span class="keywordflow">in</span> start_pos:</div>
+<div class="line"><a id="l00065" name="l00065"></a><span class="lineno">   65</span>            ax.plot(*pos, <span class="stringliteral">&quot;o&quot;</span>, color=<span class="stringliteral">&quot;black&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>        ax.set_xlabel(<span class="stringliteral">r&quot;x $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00068" name="l00068"></a><span class="lineno">   68</span>        ax.set_ylabel(<span class="stringliteral">r&quot;y $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00069" name="l00069"></a><span class="lineno">   69</span>        ax.legend(loc=<span class="stringliteral">&quot;upper right&quot;</span>)</div>
+<div class="line"><a id="l00070" name="l00070"></a><span class="lineno">   70</span>        ax.axis(<span class="stringliteral">&quot;equal&quot;</span>)</div>
+<div class="line"><a id="l00071" name="l00071"></a><span class="lineno">   71</span>        fig.savefig(output, bbox_inches=<span class="stringliteral">&quot;tight&quot;</span>)</div>
+<div class="line"><a id="l00072" name="l00072"></a><span class="lineno">   72</span> </div>
+<div class="line"><a id="l00073" name="l00073"></a><span class="lineno">   73</span> </div>
+<div class="line"><a id="l00074" name="l00074"></a><span class="lineno">   74</span><span class="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
+<div class="line"><a id="l00075" name="l00075"></a><span class="lineno">   75</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"><a class="el" href="plot__2__particles_8py.html">plot_2_particles.py</a></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.html

@@ -0,0 +1,190 @@
+<!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_3d.py File Reference</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__3d_8py.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="summary">
+<a href="#func-members">Functions</a> &#124;
+<a href="#var-members">Variables</a>  </div>
+  <div class="headertitle"><div class="title">plot_3d.py File Reference</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>Plot 2 particles with and without particle interactions in 3D.  
+<a href="#details">More...</a></p>
+
+<p><a href="plot__3d_8py_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:adb8902df55180f4ad62fb3799bc5c5a8"><td class="memItemLeft" align="right" valign="top">def&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__3d_8py.html#adb8902df55180f4ad62fb3799bc5c5a8">plot_3d.main</a> ()</td></tr>
+<tr class="separator:adb8902df55180f4ad62fb3799bc5c5a8"><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:a7026cb07859df7ff6b3fb60453573467"><td class="memItemLeft" align="right" valign="top">dict&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__3d_8py.html#a7026cb07859df7ff6b3fb60453573467">plot_3d.params</a></td></tr>
+<tr class="separator:a7026cb07859df7ff6b3fb60453573467"><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>Plot 2 particles with and without particle interactions in 3D. </p>
+<dl class="section author"><dt>Author</dt><dd>Cory Alexander Balaton (coryab) </dd>
+<dd>
+Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
+<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
+<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000014">Bug:</a></b></dt><dd>No known bugs </dd></dl>
+
+<p class="definition">Definition in file <a class="el" href="plot__3d_8py_source.html">plot_3d.py</a>.</p>
+</div><h2 class="groupheader">Function Documentation</h2>
+<a id="adb8902df55180f4ad62fb3799bc5c5a8" name="adb8902df55180f4ad62fb3799bc5c5a8"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#adb8902df55180f4ad62fb3799bc5c5a8">&#9670;&#160;</a></span>main()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">def plot_3d.main </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="plot__3d_8py_source.html#l00030">30</a> of file <a class="el" href="plot__3d_8py_source.html">plot_3d.py</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Variable Documentation</h2>
+<a id="a7026cb07859df7ff6b3fb60453573467" name="a7026cb07859df7ff6b3fb60453573467"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a7026cb07859df7ff6b3fb60453573467">&#9670;&#160;</a></span>params</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">dict plot_3d.params</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<b>Initial value:</b><div class="fragment"><div class="line"><span class="lineno">    1</span>=  {</div>
+<div class="line"><span class="lineno">    2</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><span class="lineno">    3</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>, </div>
+<div class="line"><span class="lineno">    4</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><span class="lineno">    5</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    6</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    7</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    8</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    9</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</span>,</div>
+<div class="line"><span class="lineno">   10</span>    <span class="stringliteral">&quot;figure.autolayout&quot;</span>: <span class="keyword">True</span></div>
+<div class="line"><span class="lineno">   11</span>}</div>
+</div><!-- fragment -->
+<p class="definition">Definition at line <a class="el" href="plot__3d_8py_source.html#l00017">17</a> of file <a class="el" href="plot__3d_8py_source.html">plot_3d.py</a>.</p>
+
+</div>
+</div>
+</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"><a class="el" href="plot__3d_8py.html">plot_3d.py</a></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 +1,172 @@
+<!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_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>
+<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__3d_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_3d.py</div></div>
+</div><!--header-->
+<div class="contents">
+<a href="plot__3d_8py.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="l00011" name="l00011"></a><span class="lineno">   11</span> </div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span><span class="keyword">import</span> matplotlib.pyplot <span class="keyword">as</span> plt</div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="keyword">import</span> numpy <span class="keyword">as</span> np</div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="keyword">import</span> seaborn <span class="keyword">as</span> sns</div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span> </div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span>sns.set_theme()</div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span>params = {</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>, </div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</span>,</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>    <span class="stringliteral">&quot;figure.autolayout&quot;</span>: <span class="keyword">True</span></div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span>}</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>plt.rcParams.update(params)</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>main():</div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span>    files = [</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>        <span class="stringliteral">&quot;output/simulate_2_particles/no_interaction/particle_0_r.txt&quot;</span>,</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span>        <span class="stringliteral">&quot;output/simulate_2_particles/no_interaction/particle_1_r.txt&quot;</span>,</div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span>        <span class="stringliteral">&quot;output/simulate_2_particles/with_interaction/particle_0_r.txt&quot;</span>,</div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span>        <span class="stringliteral">&quot;output/simulate_2_particles/with_interaction/particle_1_r.txt&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>    labels = [</div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>        <span class="stringliteral">r&quot;$p_1$&quot;</span>,</div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span>        <span class="stringliteral">r&quot;$p_2$&quot;</span>,</div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>        <span class="stringliteral">r&quot;$\hat{p}_1$&quot;</span>,</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>        <span class="stringliteral">r&quot;$\hat{p}_2$&quot;</span>,</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>    ]</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>    colors = [</div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span>        <span class="stringliteral">&quot;mediumaquamarine&quot;</span>,</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span>        <span class="stringliteral">&quot;salmon&quot;</span>,</div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>        <span class="stringliteral">&quot;seagreen&quot;</span>,</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>        <span class="stringliteral">&quot;darkred&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>    ax = plt.figure().add_subplot(projection=<span class="stringliteral">&quot;3d&quot;</span>)</div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span>    <span class="keywordflow">for</span> label, color, file <span class="keywordflow">in</span> zip(labels, colors, files):</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span>        <span class="keyword">with</span> open(file) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span>            lines = f.readlines()</div>
+<div class="line"><a id="l00053" name="l00053"></a><span class="lineno">   53</span>            t = np.linspace(0, 50, len(lines))</div>
+<div class="line"><a id="l00054" name="l00054"></a><span class="lineno">   54</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="l00055" name="l00055"></a><span class="lineno">   55</span>            ax.plot(r[:,0], r[:,1], r[:,2], label=label, color=color)</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>    ax.set_xlabel(<span class="stringliteral">r&quot;x $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00058" name="l00058"></a><span class="lineno">   58</span>    ax.set_ylabel(<span class="stringliteral">r&quot;y $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   59</span>    ax.set_zlabel(<span class="stringliteral">r&quot;z $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00060" name="l00060"></a><span class="lineno">   60</span>    ax.view_init(10,-35)</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>    plt.legend()</div>
+<div class="line"><a id="l00063" name="l00063"></a><span class="lineno">   63</span>    plt.savefig(<span class="stringliteral">&quot;../latex/images/3d_plot.pdf&quot;</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="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
+<div class="line"><a id="l00067" name="l00067"></a><span class="lineno">   67</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"><a class="el" href="plot__3d_8py.html">plot_3d.py</a></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.html

@@ -0,0 +1,189 @@
+<!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 File Reference</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__particles__left_8py.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="summary">
+<a href="#func-members">Functions</a> &#124;
+<a href="#var-members">Variables</a>  </div>
+  <div class="headertitle"><div class="title">plot_particles_left.py File Reference</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>Plot how many particles are left after 500 microseconds using different angular frequencies.  
+<a href="#details">More...</a></p>
+
+<p><a href="plot__particles__left_8py_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:abec6efa92c9e476e2e3a403dac12ea1c"><td class="memItemLeft" align="right" valign="top">def&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__particles__left_8py.html#abec6efa92c9e476e2e3a403dac12ea1c">plot_particles_left.main</a> ()</td></tr>
+<tr class="separator:abec6efa92c9e476e2e3a403dac12ea1c"><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:aad2ff4255461cc187b87065843d0b391"><td class="memItemLeft" align="right" valign="top">dict&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__particles__left_8py.html#aad2ff4255461cc187b87065843d0b391">plot_particles_left.params</a></td></tr>
+<tr class="separator:aad2ff4255461cc187b87065843d0b391"><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>Plot how many particles are left after 500 microseconds using different angular frequencies. </p>
+<dl class="section author"><dt>Author</dt><dd>Cory Alexander Balaton (coryab) </dd>
+<dd>
+Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
+<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
+<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000015">Bug:</a></b></dt><dd>No known bugs </dd></dl>
+
+<p class="definition">Definition in file <a class="el" href="plot__particles__left_8py_source.html">plot_particles_left.py</a>.</p>
+</div><h2 class="groupheader">Function Documentation</h2>
+<a id="abec6efa92c9e476e2e3a403dac12ea1c" name="abec6efa92c9e476e2e3a403dac12ea1c"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#abec6efa92c9e476e2e3a403dac12ea1c">&#9670;&#160;</a></span>main()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">def plot_particles_left.main </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="plot__particles__left_8py_source.html#l00029">29</a> of file <a class="el" href="plot__particles__left_8py_source.html">plot_particles_left.py</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Variable Documentation</h2>
+<a id="aad2ff4255461cc187b87065843d0b391" name="aad2ff4255461cc187b87065843d0b391"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#aad2ff4255461cc187b87065843d0b391">&#9670;&#160;</a></span>params</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">dict plot_particles_left.params</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<b>Initial value:</b><div class="fragment"><div class="line"><span class="lineno">    1</span>=  {</div>
+<div class="line"><span class="lineno">    2</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><span class="lineno">    3</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>, </div>
+<div class="line"><span class="lineno">    4</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><span class="lineno">    5</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    6</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    7</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    8</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    9</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</span></div>
+<div class="line"><span class="lineno">   10</span>}</div>
+</div><!-- fragment -->
+<p class="definition">Definition at line <a class="el" href="plot__particles__left_8py_source.html#l00017">17</a> of file <a class="el" href="plot__particles__left_8py_source.html">plot_particles_left.py</a>.</p>
+
+</div>
+</div>
+</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"><a class="el" href="plot__particles__left_8py.html">plot_particles_left.py</a></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 +1,185 @@
+<!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');
+  $(document).ready(function() { init_search(); });
+});
+/* @license-end */
+</script>
+<div id="main-nav"></div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
+    <div id="nav-tree-contents">
+      <div id="nav-sync" class="sync"></div>
+    </div>
+  </div>
+  <div id="splitbar" style="-moz-user-select:none;" 
+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
+$(document).ready(function(){initNavTree('plot__particles__left_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_particles_left.py</div></div>
+</div><!--header-->
+<div class="contents">
+<a href="plot__particles__left_8py.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span> </div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span> </div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="keyword">import</span> matplotlib.pyplot <span class="keyword">as</span> plt</div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="keyword">import</span> seaborn <span class="keyword">as</span> sns</div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span> </div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span>sns.set_theme()</div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span>params = {</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>, </div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</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>plt.rcParams.update(params)</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span> </div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span><span class="keyword">def </span>main():</div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span>    colors = [</div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span>        <span class="stringliteral">&quot;mediumseagreen&quot;</span>,</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>        <span class="stringliteral">&quot;darkred&quot;</span>,</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span>        <span class="stringliteral">&quot;darkgoldenrod&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>    files = [</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span>        <span class="stringliteral">&quot;output/time_dependent_potential/wide_sweep.txt&quot;</span>,</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span>        <span class="stringliteral">&quot;output/time_dependent_potential/narrow_sweep.txt&quot;</span>,</div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>        <span class="stringliteral">&quot;output/time_dependent_potential/narrow_sweep_fine.txt&quot;</span>,</div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span>        <span class="stringliteral">&quot;output/time_dependent_potential/narrow_sweep_interactions.txt&quot;</span>,</div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>        <span class="stringliteral">&quot;output/time_dependent_potential/narrow_sweep_interactions_fine.txt&quot;</span>,</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>    ]</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>    outputs = [</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>        <span class="stringliteral">&quot;../latex/images/particles_left_wide_sweep.pdf&quot;</span>,</div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span>        <span class="stringliteral">&quot;../latex/images/particles_left_narrow_sweep.pdf&quot;</span>,</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span>        <span class="stringliteral">&quot;../latex/images/particles_left_narrow_sweep_fine.pdf&quot;</span>,</div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>        <span class="stringliteral">&quot;../latex/images/particles_left_narrow_sweep_interactions.pdf&quot;</span>,</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>        <span class="stringliteral">&quot;../latex/images/particles_left_narrow_sweep_interactions_fine.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>    <span class="keywordflow">for</span> file, output <span class="keywordflow">in</span> zip(files, outputs):</div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span>        <span class="keyword">with</span> open(file) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span>            lines = f.readlines()</div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span>            x = []</div>
+<div class="line"><a id="l00053" name="l00053"></a><span class="lineno">   53</span>            y1 = []</div>
+<div class="line"><a id="l00054" name="l00054"></a><span class="lineno">   54</span>            y2 = []</div>
+<div class="line"><a id="l00055" name="l00055"></a><span class="lineno">   55</span>            y3 = []</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno">   56</span>            <span class="keywordflow">for</span> line <span class="keywordflow">in</span> lines:</div>
+<div class="line"><a id="l00057" name="l00057"></a><span class="lineno">   57</span>                l = line.strip().split(<span class="stringliteral">&quot;,&quot;</span>)</div>
+<div class="line"><a id="l00058" name="l00058"></a><span class="lineno">   58</span>                x.append(float(l[0]))</div>
+<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   59</span>                y1.append(float(l[1]))</div>
+<div class="line"><a id="l00060" name="l00060"></a><span class="lineno">   60</span>                y2.append(float(l[2]))</div>
+<div class="line"><a id="l00061" name="l00061"></a><span class="lineno">   61</span>                y3.append(float(l[3]))</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>            fig, ax = plt.subplots()</div>
+<div class="line"><a id="l00064" name="l00064"></a><span class="lineno">   64</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="l00065" name="l00065"></a><span class="lineno">   65</span>            ax.plot(x, y2, label=<span class="stringliteral">r&quot;$f_{2} = 0.4$&quot;</span>, color=colors[1])</div>
+<div class="line"><a id="l00066" name="l00066"></a><span class="lineno">   66</span>            ax.plot(x, y3, label=<span class="stringliteral">r&quot;$f_{3} = 0.7$&quot;</span>, color=colors[2])</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>        ax.set_xlabel(<span class="stringliteral">r&quot;Angular frequency $\omega_V$ (MHz)&quot;</span>)</div>
+<div class="line"><a id="l00069" name="l00069"></a><span class="lineno">   69</span>        <span class="comment"># ax.set_xlim((0, 2.8))</span></div>
+<div class="line"><a id="l00070" name="l00070"></a><span class="lineno">   70</span>        ax.set_ylabel(<span class="stringliteral">r&quot;Fraction of particles left&quot;</span>)</div>
+<div class="line"><a id="l00071" name="l00071"></a><span class="lineno">   71</span>        <span class="comment"># ax.set_ylim((-0.1, 1.1))</span></div>
+<div class="line"><a id="l00072" name="l00072"></a><span class="lineno">   72</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="l00073" name="l00073"></a><span class="lineno">   73</span>        <span class="comment">#           &quot;after 500 microseconds for different amplitudes and frequencies&quot;)</span></div>
+<div class="line"><a id="l00074" name="l00074"></a><span class="lineno">   74</span>        </div>
+<div class="line"><a id="l00075" name="l00075"></a><span class="lineno">   75</span>        ax.legend(loc=<span class="stringliteral">&quot;upper right&quot;</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"># plt.show()</span></div>
+<div class="line"><a id="l00078" name="l00078"></a><span class="lineno">   78</span>        fig.savefig(output, bbox_inches=<span class="stringliteral">&quot;tight&quot;</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="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
+<div class="line"><a id="l00081" name="l00081"></a><span class="lineno">   81</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"><a class="el" href="plot__particles__left_8py.html">plot_particles_left.py</a></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.html

@@ -0,0 +1,189 @@
+<!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 File Reference</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__phase__space_8py.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="summary">
+<a href="#func-members">Functions</a> &#124;
+<a href="#var-members">Variables</a>  </div>
+  <div class="headertitle"><div class="title">plot_phase_space.py File Reference</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>Plot the phase space for 2 particles in the x and z direction, with and without particle interactions.  
+<a href="#details">More...</a></p>
+
+<p><a href="plot__phase__space_8py_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:aa92530b83695dcb6ca6adff74e5088dd"><td class="memItemLeft" align="right" valign="top">def&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__phase__space_8py.html#aa92530b83695dcb6ca6adff74e5088dd">plot_phase_space.main</a> ()</td></tr>
+<tr class="separator:aa92530b83695dcb6ca6adff74e5088dd"><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:ac5425fde52c92b301d6815f3492b713e"><td class="memItemLeft" align="right" valign="top">dict&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__phase__space_8py.html#ac5425fde52c92b301d6815f3492b713e">plot_phase_space.params</a></td></tr>
+<tr class="separator:ac5425fde52c92b301d6815f3492b713e"><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>Plot the phase space for 2 particles in the x and z direction, with and without particle interactions. </p>
+<dl class="section author"><dt>Author</dt><dd>Cory Alexander Balaton (coryab) </dd>
+<dd>
+Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
+<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
+<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000016">Bug:</a></b></dt><dd>No known bugs </dd></dl>
+
+<p class="definition">Definition in file <a class="el" href="plot__phase__space_8py_source.html">plot_phase_space.py</a>.</p>
+</div><h2 class="groupheader">Function Documentation</h2>
+<a id="aa92530b83695dcb6ca6adff74e5088dd" name="aa92530b83695dcb6ca6adff74e5088dd"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#aa92530b83695dcb6ca6adff74e5088dd">&#9670;&#160;</a></span>main()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">def plot_phase_space.main </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="plot__phase__space_8py_source.html#l00031">31</a> of file <a class="el" href="plot__phase__space_8py_source.html">plot_phase_space.py</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Variable Documentation</h2>
+<a id="ac5425fde52c92b301d6815f3492b713e" name="ac5425fde52c92b301d6815f3492b713e"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ac5425fde52c92b301d6815f3492b713e">&#9670;&#160;</a></span>params</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">dict plot_phase_space.params</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<b>Initial value:</b><div class="fragment"><div class="line"><span class="lineno">    1</span>=  {</div>
+<div class="line"><span class="lineno">    2</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><span class="lineno">    3</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>,</div>
+<div class="line"><span class="lineno">    4</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><span class="lineno">    5</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    6</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    7</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    8</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    9</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</span>,</div>
+<div class="line"><span class="lineno">   10</span>}</div>
+</div><!-- fragment -->
+<p class="definition">Definition at line <a class="el" href="plot__phase__space_8py_source.html#l00018">18</a> of file <a class="el" href="plot__phase__space_8py_source.html">plot_phase_space.py</a>.</p>
+
+</div>
+</div>
+</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"><a class="el" href="plot__phase__space_8py.html">plot_phase_space.py</a></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 +1,190 @@
+<!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"/>
+<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__phase__space_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_phase_space.py</div></div>
+</div><!--header-->
+<div class="contents">
+<a href="plot__phase__space_8py.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span> </div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span> </div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="keyword">import</span> matplotlib.pyplot <span class="keyword">as</span> plt</div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="keyword">import</span> numpy <span class="keyword">as</span> np</div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="keyword">import</span> seaborn <span class="keyword">as</span> sns</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>sns.set_theme()</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>params = {</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>,</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</span>,</div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span>}</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>plt.rcParams.update(params)</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">   31</span><span class="keyword">def </span>main():</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>    directories = [</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span>        <span class="stringliteral">&quot;output/simulate_2_particles/no_interaction/&quot;</span>,</div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span>        <span class="stringliteral">&quot;output/simulate_2_particles/with_interaction/&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>    files = [</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span>        <span class="stringliteral">&quot;particle_0&quot;</span>,</div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>        <span class="stringliteral">&quot;particle_1&quot;</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>    labels = [<span class="stringliteral">r&quot;$p_1$&quot;</span>, <span class="stringliteral">r&quot;$p_2$&quot;</span>]</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>    output = [</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>        <span class="stringliteral">&quot;../latex/images/phase_space_no_interaction&quot;</span>,</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>        <span class="stringliteral">&quot;../latex/images/phase_space_interaction&quot;</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>    colors = [</div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>        <span class="stringliteral">&quot;seagreen&quot;</span>,</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>        <span class="stringliteral">&quot;darkred&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">for</span> i, dir <span class="keywordflow">in</span> enumerate(directories):</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span>        fig1, axs1 = plt.subplots(sharex=<span class="keyword">True</span>)</div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span>        fig2, axs2 = plt.subplots(sharex=<span class="keyword">True</span>)</div>
+<div class="line"><a id="l00053" name="l00053"></a><span class="lineno">   53</span>        <span class="keywordflow">for</span> j, (file, label, color) <span class="keywordflow">in</span> enumerate(zip(files, labels, colors)):</div>
+<div class="line"><a id="l00054" name="l00054"></a><span class="lineno">   54</span>            r = []</div>
+<div class="line"><a id="l00055" name="l00055"></a><span class="lineno">   55</span>            v = []</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno">   56</span>            <span class="keyword">with</span> open(dir + file + <span class="stringliteral">&quot;_r.txt&quot;</span>) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00057" name="l00057"></a><span class="lineno">   57</span>                lines = f.readlines()</div>
+<div class="line"><a id="l00058" name="l00058"></a><span class="lineno">   58</span>                r = np.array(</div>
+<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   59</span>                    [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="l00060" name="l00060"></a><span class="lineno">   60</span>                )</div>
+<div class="line"><a id="l00061" name="l00061"></a><span class="lineno">   61</span> </div>
+<div class="line"><a id="l00062" name="l00062"></a><span class="lineno">   62</span>            <span class="keyword">with</span> open(dir + file + <span class="stringliteral">&quot;_v.txt&quot;</span>) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00063" name="l00063"></a><span class="lineno">   63</span>                lines = f.readlines()</div>
+<div class="line"><a id="l00064" name="l00064"></a><span class="lineno">   64</span>                v = np.array(</div>
+<div class="line"><a id="l00065" name="l00065"></a><span class="lineno">   65</span>                    [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="l00066" name="l00066"></a><span class="lineno">   66</span>                )</div>
+<div class="line"><a id="l00067" name="l00067"></a><span class="lineno">   67</span>            axs1.plot(r[:, 0], v[:, 0], label=label, color=color)</div>
+<div class="line"><a id="l00068" name="l00068"></a><span class="lineno">   68</span>            axs1.plot(r[0,0], v[0,0], <span class="stringliteral">&quot;ko&quot;</span>)</div>
+<div class="line"><a id="l00069" name="l00069"></a><span class="lineno">   69</span>            axs2.plot(r[:, 2], v[:, 2], label=label, color=color)</div>
+<div class="line"><a id="l00070" name="l00070"></a><span class="lineno">   70</span>            axs2.plot(r[0,2], v[0,2], <span class="stringliteral">&quot;ko&quot;</span>)</div>
+<div class="line"><a id="l00071" name="l00071"></a><span class="lineno">   71</span>            axs1.axis(<span class="stringliteral">&quot;equal&quot;</span>)</div>
+<div class="line"><a id="l00072" name="l00072"></a><span class="lineno">   72</span>            axs2.axis(<span class="stringliteral">&quot;equal&quot;</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>        axs1.set(xlabel=<span class="stringliteral">r&quot;$x (\mu m)$&quot;</span>, ylabel=<span class="stringliteral">r&quot;$v_x (\mu m / \mu s)$&quot;</span>)</div>
+<div class="line"><a id="l00075" name="l00075"></a><span class="lineno">   75</span>        axs2.set(xlabel=<span class="stringliteral">r&quot;$z (\mu m)$&quot;</span>, ylabel=<span class="stringliteral">r&quot;$v_z (\mu m / \mu s)$&quot;</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>        axs1.legend(loc=<span class="stringliteral">&quot;upper right&quot;</span>)</div>
+<div class="line"><a id="l00078" name="l00078"></a><span class="lineno">   78</span>        axs2.legend(loc=<span class="stringliteral">&quot;upper right&quot;</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>        fig1.savefig(f<span class="stringliteral">&quot;{output[i]}_x.pdf&quot;</span>, bbox_inches=<span class="stringliteral">&quot;tight&quot;</span>)</div>
+<div class="line"><a id="l00081" name="l00081"></a><span class="lineno">   81</span>        fig2.savefig(f<span class="stringliteral">&quot;{output[i]}_z.pdf&quot;</span>, bbox_inches=<span class="stringliteral">&quot;tight&quot;</span>)</div>
+<div class="line"><a id="l00082" name="l00082"></a><span class="lineno">   82</span>    <span class="comment"># plt.show()</span></div>
+<div class="line"><a id="l00083" name="l00083"></a><span class="lineno">   83</span> </div>
+<div class="line"><a id="l00084" name="l00084"></a><span class="lineno">   84</span> </div>
+<div class="line"><a id="l00085" name="l00085"></a><span class="lineno">   85</span><span class="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
+<div class="line"><a id="l00086" name="l00086"></a><span class="lineno">   86</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"><a class="el" href="plot__phase__space_8py.html">plot_phase_space.py</a></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.html

@@ -0,0 +1,189 @@
+<!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 File Reference</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__relative__error_8py.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="summary">
+<a href="#func-members">Functions</a> &#124;
+<a href="#var-members">Variables</a>  </div>
+  <div class="headertitle"><div class="title">plot_relative_error.py File Reference</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>Plot the relative error for forward Euler and RK4 method.  
+<a href="#details">More...</a></p>
+
+<p><a href="plot__relative__error_8py_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:a615fd09c73966d40320e768bed20683c"><td class="memItemLeft" align="right" valign="top">def&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__relative__error_8py.html#a615fd09c73966d40320e768bed20683c">plot_relative_error.main</a> ()</td></tr>
+<tr class="separator:a615fd09c73966d40320e768bed20683c"><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:a5cc494411e5ca543673367a938f5f160"><td class="memItemLeft" align="right" valign="top">dict&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__relative__error_8py.html#a5cc494411e5ca543673367a938f5f160">plot_relative_error.params</a></td></tr>
+<tr class="separator:a5cc494411e5ca543673367a938f5f160"><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>Plot the relative error for forward Euler and RK4 method. </p>
+<dl class="section author"><dt>Author</dt><dd>Cory Alexander Balaton (coryab) </dd>
+<dd>
+Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
+<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
+<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000017">Bug:</a></b></dt><dd>No known bugs </dd></dl>
+
+<p class="definition">Definition in file <a class="el" href="plot__relative__error_8py_source.html">plot_relative_error.py</a>.</p>
+</div><h2 class="groupheader">Function Documentation</h2>
+<a id="a615fd09c73966d40320e768bed20683c" name="a615fd09c73966d40320e768bed20683c"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a615fd09c73966d40320e768bed20683c">&#9670;&#160;</a></span>main()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">def plot_relative_error.main </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="plot__relative__error_8py_source.html#l00029">29</a> of file <a class="el" href="plot__relative__error_8py_source.html">plot_relative_error.py</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Variable Documentation</h2>
+<a id="a5cc494411e5ca543673367a938f5f160" name="a5cc494411e5ca543673367a938f5f160"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a5cc494411e5ca543673367a938f5f160">&#9670;&#160;</a></span>params</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">dict plot_relative_error.params</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<b>Initial value:</b><div class="fragment"><div class="line"><span class="lineno">    1</span>=  {</div>
+<div class="line"><span class="lineno">    2</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><span class="lineno">    3</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>, </div>
+<div class="line"><span class="lineno">    4</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><span class="lineno">    5</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    6</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    7</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    8</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    9</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</span></div>
+<div class="line"><span class="lineno">   10</span>}</div>
+</div><!-- fragment -->
+<p class="definition">Definition at line <a class="el" href="plot__relative__error_8py_source.html#l00017">17</a> of file <a class="el" href="plot__relative__error_8py_source.html">plot_relative_error.py</a>.</p>
+
+</div>
+</div>
+</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"><a class="el" href="plot__relative__error_8py.html">plot_relative_error.py</a></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 +1,188 @@
+<!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>
+<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__relative__error_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_relative_error.py</div></div>
+</div><!--header-->
+<div class="contents">
+<a href="plot__relative__error_8py.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="l00011" name="l00011"></a><span class="lineno">   11</span> </div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span><span class="keyword">import</span> matplotlib.pyplot <span class="keyword">as</span> plt</div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="keyword">import</span> numpy <span class="keyword">as</span> np</div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="keyword">import</span> seaborn <span class="keyword">as</span> sns</div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span> </div>
+<div class="line"><a id="l00016" name="l00016"></a><span class="lineno">   16</span>sns.set_theme()</div>
+<div class="line"><a id="l00017" name="l00017"></a><span class="lineno">   17</span>params = {</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>, </div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</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>plt.rcParams.update(params)</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span> </div>
+<div class="line"><a id="l00029" name="l00029"></a><span class="lineno">   29</span><span class="keyword">def </span>main():</div>
+<div class="line"><a id="l00030" name="l00030"></a><span class="lineno">   30</span>    directories = [</div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span>        <span class="stringliteral">&quot;output/relative_error/RK4/&quot;</span>,</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>        <span class="stringliteral">&quot;output/relative_error/euler/&quot;</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>    files = [</div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span>        <span class="stringliteral">&quot;4000_steps.txt&quot;</span>,</div>
+<div class="line"><a id="l00036" name="l00036"></a><span class="lineno">   36</span>        <span class="stringliteral">&quot;8000_steps.txt&quot;</span>,</div>
+<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span>        <span class="stringliteral">&quot;16000_steps.txt&quot;</span>,</div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>        <span class="stringliteral">&quot;32000_steps.txt&quot;</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>    labels = [</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>        <span class="stringliteral">r&quot;$n_1$&quot;</span>,</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>        <span class="stringliteral">r&quot;$n_2$&quot;</span>,</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span>        <span class="stringliteral">r&quot;$n_3$&quot;</span>,</div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span>        <span class="stringliteral">r&quot;$n_4$&quot;</span>,</div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span>    ]</div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>    titles = [</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>        <span class="stringliteral">&quot;(a)&quot;</span>,</div>
+<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span>        <span class="stringliteral">&quot;(b)&quot;</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>    methods = [</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span>        <span class="stringliteral">&quot;rk4&quot;</span>,</div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span>        <span class="stringliteral">&quot;euler&quot;</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>    colors = [</div>
+<div class="line"><a id="l00055" name="l00055"></a><span class="lineno">   55</span>        <span class="stringliteral">&quot;seagreen&quot;</span>,</div>
+<div class="line"><a id="l00056" name="l00056"></a><span class="lineno">   56</span>        <span class="stringliteral">&quot;darkred&quot;</span>,</div>
+<div class="line"><a id="l00057" name="l00057"></a><span class="lineno">   57</span>        <span class="stringliteral">&quot;darkgoldenrod&quot;</span>,</div>
+<div class="line"><a id="l00058" name="l00058"></a><span class="lineno">   58</span>        <span class="stringliteral">&quot;steelblue&quot;</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>    fig1, axs1 = plt.subplots(2,1)</div>
+<div class="line"><a id="l00061" name="l00061"></a><span class="lineno">   61</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="l00062" name="l00062"></a><span class="lineno">   62</span>        max_err = []</div>
+<div class="line"><a id="l00063" name="l00063"></a><span class="lineno">   63</span>        <span class="keywordflow">for</span> label, file, color <span class="keywordflow">in</span> zip(labels, files, colors):</div>
+<div class="line"><a id="l00064" name="l00064"></a><span class="lineno">   64</span>            <span class="keyword">with</span> open(dir+file) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00065" name="l00065"></a><span class="lineno">   65</span>                lines = f.readlines()</div>
+<div class="line"><a id="l00066" name="l00066"></a><span class="lineno">   66</span>                t = np.linspace(0, 50, len(lines))</div>
+<div class="line"><a id="l00067" name="l00067"></a><span class="lineno">   67</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="l00068" name="l00068"></a><span class="lineno">   68</span>                max_err.append(max(r))</div>
+<div class="line"><a id="l00069" name="l00069"></a><span class="lineno">   69</span>                axs1[i].plot(t, r, label=label, color=color)</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>        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="l00072" name="l00072"></a><span class="lineno">   72</span>        axs1[i].legend()</div>
+<div class="line"><a id="l00073" name="l00073"></a><span class="lineno">   73</span>        axs1[i].set_title(title)</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>        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="l00076" name="l00076"></a><span class="lineno">   76</span>        print(f<span class="stringliteral">&quot;{methods[i]}: {conv_rate}&quot;</span>)</div>
+<div class="line"><a id="l00077" name="l00077"></a><span class="lineno">   77</span> </div>
+<div class="line"><a id="l00078" name="l00078"></a><span class="lineno">   78</span>    plt.tight_layout()</div>
+<div class="line"><a id="l00079" name="l00079"></a><span class="lineno">   79</span>    fig1.savefig(<span class="stringliteral">&quot;../latex/images/relative_error.pdf&quot;</span>, bbox_inches=<span class="stringliteral">&quot;tight&quot;</span>)</div>
+<div class="line"><a id="l00080" name="l00080"></a><span class="lineno">   80</span> </div>
+<div class="line"><a id="l00081" name="l00081"></a><span class="lineno">   81</span> </div>
+<div class="line"><a id="l00082" name="l00082"></a><span class="lineno">   82</span><span class="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
+<div class="line"><a id="l00083" name="l00083"></a><span class="lineno">   83</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"><a class="el" href="plot__relative__error_8py.html">plot_relative_error.py</a></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.html

@@ -0,0 +1,211 @@
+<!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 File Reference</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.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="summary">
+<a href="#func-members">Functions</a> &#124;
+<a href="#var-members">Variables</a>  </div>
+  <div class="headertitle"><div class="title">plot_single_particle.py File Reference</div></div>
+</div><!--header-->
+<div class="contents">
+
+<p>Plot the approximation and analytical solution for one particle in the z axis.  
+<a href="#details">More...</a></p>
+
+<p><a href="plot__single__particle_8py_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:a502c69553dc8b55651b3f0d6d06686ee"><td class="memItemLeft" align="right" valign="top">def&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__single__particle_8py.html#a502c69553dc8b55651b3f0d6d06686ee">plot_single_particle.z</a> (t)</td></tr>
+<tr class="separator:a502c69553dc8b55651b3f0d6d06686ee"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ab0261bc484d15ef01c27420592fadc00"><td class="memItemLeft" align="right" valign="top">def&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__single__particle_8py.html#ab0261bc484d15ef01c27420592fadc00">plot_single_particle.main</a> ()</td></tr>
+<tr class="separator:ab0261bc484d15ef01c27420592fadc00"><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:a631948da2ca2a1f0df71e9ce6b328d71"><td class="memItemLeft" align="right" valign="top">dict&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__single__particle_8py.html#a631948da2ca2a1f0df71e9ce6b328d71">plot_single_particle.params</a></td></tr>
+<tr class="separator:a631948da2ca2a1f0df71e9ce6b328d71"><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>Plot the approximation and analytical solution for one particle in the z axis. </p>
+<dl class="section author"><dt>Author</dt><dd>Cory Alexander Balaton (coryab) </dd>
+<dd>
+Janita Ovidie Sandtrøen Willumsen (janitaws)</dd></dl>
+<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
+<dl class="bug"><dt><b><a class="el" href="bug.html#_bug000018">Bug:</a></b></dt><dd>No known bugs </dd></dl>
+
+<p class="definition">Definition in file <a class="el" href="plot__single__particle_8py_source.html">plot_single_particle.py</a>.</p>
+</div><h2 class="groupheader">Function Documentation</h2>
+<a id="ab0261bc484d15ef01c27420592fadc00" name="ab0261bc484d15ef01c27420592fadc00"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ab0261bc484d15ef01c27420592fadc00">&#9670;&#160;</a></span>main()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">def plot_single_particle.main </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="plot__single__particle_8py_source.html#l00037">37</a> of file <a class="el" href="plot__single__particle_8py_source.html">plot_single_particle.py</a>.</p>
+
+</div>
+</div>
+<a id="a502c69553dc8b55651b3f0d6d06686ee" name="a502c69553dc8b55651b3f0d6d06686ee"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a502c69553dc8b55651b3f0d6d06686ee">&#9670;&#160;</a></span>z()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">def plot_single_particle.z </td>
+          <td>(</td>
+          <td class="paramtype">&#160;</td>
+          <td class="paramname"><em>t</em></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p class="definition">Definition at line <a class="el" href="plot__single__particle_8py_source.html#l00030">30</a> of file <a class="el" href="plot__single__particle_8py_source.html">plot_single_particle.py</a>.</p>
+
+</div>
+</div>
+<h2 class="groupheader">Variable Documentation</h2>
+<a id="a631948da2ca2a1f0df71e9ce6b328d71" name="a631948da2ca2a1f0df71e9ce6b328d71"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a631948da2ca2a1f0df71e9ce6b328d71">&#9670;&#160;</a></span>params</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">dict plot_single_particle.params</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<b>Initial value:</b><div class="fragment"><div class="line"><span class="lineno">    1</span>=  {</div>
+<div class="line"><span class="lineno">    2</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><span class="lineno">    3</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>, </div>
+<div class="line"><span class="lineno">    4</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><span class="lineno">    5</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    6</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    7</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    8</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><span class="lineno">    9</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</span></div>
+<div class="line"><span class="lineno">   10</span>}</div>
+</div><!-- fragment -->
+<p class="definition">Definition at line <a class="el" href="plot__single__particle_8py_source.html#l00018">18</a> of file <a class="el" href="plot__single__particle_8py_source.html">plot_single_particle.py</a>.</p>
+
+</div>
+</div>
+</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"><a class="el" href="plot__single__particle_8py.html">plot_single_particle.py</a></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 +1,163 @@
+<!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">
+<a href="plot__single__particle_8py.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span> </div>
+<div class="line"><a id="l00012" name="l00012"></a><span class="lineno">   12</span> </div>
+<div class="line"><a id="l00013" name="l00013"></a><span class="lineno">   13</span><span class="keyword">import</span> matplotlib.pyplot <span class="keyword">as</span> plt</div>
+<div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="keyword">import</span> numpy <span class="keyword">as</span> np</div>
+<div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span><span class="keyword">import</span> seaborn <span class="keyword">as</span> sns</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>sns.set_theme()</div>
+<div class="line"><a id="l00018" name="l00018"></a><span class="lineno">   18</span>params = {</div>
+<div class="line"><a id="l00019" name="l00019"></a><span class="lineno">   19</span>    <span class="stringliteral">&quot;font.family&quot;</span>: <span class="stringliteral">&quot;Serif&quot;</span>,</div>
+<div class="line"><a id="l00020" name="l00020"></a><span class="lineno">   20</span>    <span class="stringliteral">&quot;font.serif&quot;</span>: <span class="stringliteral">&quot;Roman&quot;</span>, </div>
+<div class="line"><a id="l00021" name="l00021"></a><span class="lineno">   21</span>    <span class="stringliteral">&quot;text.usetex&quot;</span>: <span class="keyword">True</span>,</div>
+<div class="line"><a id="l00022" name="l00022"></a><span class="lineno">   22</span>    <span class="stringliteral">&quot;axes.titlesize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00023" name="l00023"></a><span class="lineno">   23</span>    <span class="stringliteral">&quot;axes.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00024" name="l00024"></a><span class="lineno">   24</span>    <span class="stringliteral">&quot;xtick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00025" name="l00025"></a><span class="lineno">   25</span>    <span class="stringliteral">&quot;ytick.labelsize&quot;</span>: <span class="stringliteral">&quot;large&quot;</span>,</div>
+<div class="line"><a id="l00026" name="l00026"></a><span class="lineno">   26</span>    <span class="stringliteral">&quot;legend.fontsize&quot;</span>: <span class="stringliteral">&quot;medium&quot;</span></div>
+<div class="line"><a id="l00027" name="l00027"></a><span class="lineno">   27</span>}</div>
+<div class="line"><a id="l00028" name="l00028"></a><span class="lineno">   28</span>plt.rcParams.update(params)</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>z(t):</div>
+<div class="line"><a id="l00031" name="l00031"></a><span class="lineno">   31</span>    V_0 = 25.*9.64852558 * 10**4</div>
+<div class="line"><a id="l00032" name="l00032"></a><span class="lineno">   32</span>    m = 40.</div>
+<div class="line"><a id="l00033" name="l00033"></a><span class="lineno">   33</span>    d = 500.</div>
+<div class="line"><a id="l00034" name="l00034"></a><span class="lineno">   34</span>    w_z = np.sqrt((2.*V_0)/(m*d*d))</div>
+<div class="line"><a id="l00035" name="l00035"></a><span class="lineno">   35</span>    <span class="keywordflow">return</span> 20.*np.cos(w_z*t)</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><span class="keyword">def </span>main():</div>
+<div class="line"><a id="l00038" name="l00038"></a><span class="lineno">   38</span>    filename = <span class="stringliteral">&quot;output/simulate_single_particle/particle_0_r.txt&quot;</span></div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span>    r = t = []</div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>    <span class="keyword">with</span> open(filename) <span class="keyword">as</span> f:</div>
+<div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span>        lines = f.readlines()</div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>        t = np.linspace(0, 50, len(lines))</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</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="l00044" name="l00044"></a><span class="lineno">   44</span> </div>
+<div class="line"><a id="l00045" name="l00045"></a><span class="lineno">   45</span>    fig, ax = plt.subplots()</div>
+<div class="line"><a id="l00046" name="l00046"></a><span class="lineno">   46</span>    ax.plot(t, r[:, 2], label=<span class="stringliteral">&quot;approximation&quot;</span>, color=<span class="stringliteral">&quot;mediumseagreen&quot;</span>)</div>
+<div class="line"><a id="l00047" name="l00047"></a><span class="lineno">   47</span>    ax.plot(t, z(t), label=<span class="stringliteral">&quot;analytical&quot;</span>, color=<span class="stringliteral">&quot;black&quot;</span>, linestyle=<span class="stringliteral">&quot;dotted&quot;</span>)</div>
+<div class="line"><a id="l00048" name="l00048"></a><span class="lineno">   48</span>    ax.set_xlabel(<span class="stringliteral">r&quot;t $(\mu s)$&quot;</span>)</div>
+<div class="line"><a id="l00049" name="l00049"></a><span class="lineno">   49</span>    ax.set_xlim((-5, 55))</div>
+<div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span>    ax.set_ylabel(<span class="stringliteral">r&quot;z $(\mu m)$&quot;</span>)</div>
+<div class="line"><a id="l00051" name="l00051"></a><span class="lineno">   51</span>    ax.set_ylim((-25, 25))</div>
+<div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span>    <span class="comment"># plt.title(r&quot;Movement of a single particle in the x direction&quot;)</span></div>
+<div class="line"><a id="l00053" name="l00053"></a><span class="lineno">   53</span>    ax.legend(loc=<span class="stringliteral">&quot;upper right&quot;</span>)</div>
+<div class="line"><a id="l00054" name="l00054"></a><span class="lineno">   54</span>    fig.savefig(<span class="stringliteral">&quot;../latex/images/single_particle.pdf&quot;</span>, bbox_inches=<span class="stringliteral">&quot;tight&quot;</span>)</div>
+<div class="line"><a id="l00055" name="l00055"></a><span class="lineno">   55</span>    <span class="comment"># plt.show()</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">   58</span><span class="keywordflow">if</span> __name__ == <span class="stringliteral">&quot;__main__&quot;</span>:</div>
+<div class="line"><a id="l00059" name="l00059"></a><span class="lineno">   59</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"><a class="el" href="plot__single__particle_8py.html">plot_single_particle.py</a></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/search/all_0.js

@@ -1,4 +1,4 @@
 var searchData=
 [
-  ['add_5fparticle_0',['add_particle',['../classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8',1,'PenningTrap']]]
+  ['_5f_5fmethod_5fname_5f_5f_0',['__METHOD_NAME__',['../utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168',1,'utils.hpp']]]
 ];

docs/search/all_1.js

@@ -1,5 +1,7 @@
 var searchData=
 [
-  ['b_5f0_0',['B_0',['../classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716',1,'PenningTrap']]],
-  ['bug_20list_1',['Bug List',['../bug.html',1,'']]]
+  ['add_5fparticle_0',['add_particle',['../classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8',1,'PenningTrap']]],
+  ['analytical_5fsolution_5fparticle_5f1_1',['analytical_solution_particle_1',['../main_8cpp.html#a8d92fb2ad085065fbd14718647551657',1,'main.cpp']]],
+  ['animate_5f100_5fparticles_2epy_2',['animate_100_particles.py',['../animate__100__particles_8py.html',1,'']]],
+  ['assert_3',['ASSERT',['../utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9',1,'utils.hpp']]]
 ];

docs/search/all_10.js

@@ -0,0 +1,4 @@
+var searchData=
+[
+  ['write_5fsimulation_5fto_5fdir_0',['write_simulation_to_dir',['../classPenningTrap.html#ad8bc4df7ab3eed53b16cfdff38e7760b',1,'PenningTrap']]]
+];

docs/search/all_2.js

@@ -1,4 +1,5 @@
 var searchData=
 [
-  ['constants_2ehpp_0',['constants.hpp',['../constants_8hpp.html',1,'']]]
+  ['b_5f0_0',['B_0',['../classPenningTrap.html#a0cac3509aa96e71a26d3b2c902e27716',1,'PenningTrap']]],
+  ['bug_20list_1',['Bug List',['../bug.html',1,'']]]
 ];

docs/search/all_3.js

@@ -1,5 +1,7 @@
 var searchData=
 [
-  ['d_0',['d',['../classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2',1,'PenningTrap']]],
-  ['debug_1',['DEBUG',['../utils_8hpp.html#aecc1f7a8a2493b9e021e5bff76a00a5b',1,'utils.hpp']]]
+  ['ca_5fcharge_0',['CA_CHARGE',['../constants_8hpp.html#af7602a3a314957137ad1cd719aa23789',1,'constants.hpp']]],
+  ['ca_5fmass_1',['CA_MASS',['../constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8',1,'constants.hpp']]],
+  ['close_5fto_2',['close_to',['../utils_8hpp.html#ab3e0cf669bddc59bd53998490ffb68b9',1,'close_to(arma::vec &a, arma::vec &b, double tol=1e-8): utils.cpp'],['../utils_8cpp.html#a6be6f938bcbb235ebb6a2ed9d08411b2',1,'close_to(arma::vec &a, arma::vec &b, double tol): utils.cpp']]],
+  ['constants_2ehpp_3',['constants.hpp',['../constants_8hpp.html',1,'']]]
 ];

docs/search/all_4.js

@@ -1,7 +1,5 @@
 var searchData=
 [
-  ['evolve_5fforward_5feuler_0',['evolve_forward_euler',['../classPenningTrap.html#a56544b6f4befb42984e9650cf2a40965',1,'PenningTrap']]],
-  ['evolve_5frk4_1',['evolve_RK4',['../classPenningTrap.html#ab891b839c40eeb38d8a2a636c70090a9',1,'PenningTrap']]],
-  ['external_5fb_5ffield_2',['external_B_field',['../classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784',1,'PenningTrap']]],
-  ['external_5fe_5ffield_3',['external_E_field',['../classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b',1,'PenningTrap']]]
+  ['d_0',['d',['../classPenningTrap.html#a66dfe89c68716b9502927b97f59c27d2',1,'PenningTrap']]],
+  ['debug_1',['DEBUG',['../utils_8hpp.html#aecc1f7a8a2493b9e021e5bff76a00a5b',1,'utils.hpp']]]
 ];

docs/search/all_5.js

@@ -1,4 +1,7 @@
 var searchData=
 [
-  ['force_5fon_5fparticle_0',['force_on_particle',['../classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182',1,'PenningTrap']]]
+  ['evolve_5fforward_5feuler_0',['evolve_forward_euler',['../classPenningTrap.html#ab9ea97a406534bbe621a95215144875e',1,'PenningTrap']]],
+  ['evolve_5frk4_1',['evolve_RK4',['../classPenningTrap.html#a36946152fd951b1f7c346c51ff900d8e',1,'PenningTrap']]],
+  ['external_5fb_5ffield_2',['external_B_field',['../classPenningTrap.html#a361f2c4862c90b5e8e2a2f50c6a95655',1,'PenningTrap']]],
+  ['external_5fe_5ffield_3',['external_E_field',['../classPenningTrap.html#a5846c8f75cdc543fd9cf0b2185a3ef22',1,'PenningTrap']]]
 ];

docs/search/all_6.js

@@ -1,4 +1,6 @@
 var searchData=
 [
-  ['k_5fe_0',['K_E',['../constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb',1,'constants.hpp']]]
+  ['force_5fon_5fparticle_0',['force_on_particle',['../classPenningTrap.html#a7f210bb2768a5d79ced4b0df0df97598',1,'PenningTrap']]],
+  ['fraction_5fof_5fparticles_5fleft_1',['fraction_of_particles_left',['../classPenningTrap.html#ac529aa26c288f34eae184a67e6bac41f',1,'PenningTrap']]],
+  ['frequency_5fnarrow_5fsweeps_5flong_2ecpp_2',['frequency_narrow_sweeps_long.cpp',['../frequency__narrow__sweeps__long_8cpp.html',1,'']]]
 ];

docs/search/all_7.js

@@ -1,5 +1,6 @@
 var searchData=
 [
-  ['m_0',['m',['../classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563',1,'Particle']]],
-  ['main_2ecpp_1',['main.cpp',['../main_8cpp.html',1,'']]]
+  ['k_5fe_0',['K_E',['../constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb',1,'constants.hpp']]],
+  ['k_5fr_1',['k_r',['../classPenningTrap.html#a2f168622587709b9e3c49077f0b9a640',1,'PenningTrap']]],
+  ['k_5fv_2',['k_v',['../classPenningTrap.html#ae9b5afdaa5cd366e94bd294452a1eed4',1,'PenningTrap']]]
 ];

docs/search/all_8.js

@@ -1,11 +1,7 @@
 var searchData=
 [
-  ['particle_0',['Particle',['../classParticle.html',1,'Particle'],['../classParticle.html#a00e108823877a25513ccae7cac011b4c',1,'Particle::Particle()']]],
-  ['particle_2ecpp_1',['Particle.cpp',['../Particle_8cpp.html',1,'']]],
-  ['particle_2ehpp_2',['Particle.hpp',['../Particle_8hpp.html',1,'']]],
-  ['particles_3',['particles',['../classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f',1,'PenningTrap']]],
-  ['penning_20trap_20simulation_4',['Penning trap simulation',['../index.html',1,'']]],
-  ['penningtrap_5',['PenningTrap',['../classPenningTrap.html',1,'PenningTrap'],['../classParticle.html#aa797d319549dc2a0beb06cdbfd430232',1,'Particle::PenningTrap()'],['../classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560',1,'PenningTrap::PenningTrap()']]],
-  ['penningtrap_2ecpp_6',['PenningTrap.cpp',['../PenningTrap_8cpp.html',1,'']]],
-  ['penningtrap_2ehpp_7',['PenningTrap.hpp',['../PenningTrap_8hpp.html',1,'']]]
+  ['m_0',['m',['../classParticle.html#aedcc7e1bc53b0e2b1a4a07c9a1b47563',1,'Particle']]],
+  ['m_5fassert_1',['m_assert',['../utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38',1,'m_assert(bool expr, std::string expr_str, std::string func, std::string file, int line, std::string msg): utils.cpp'],['../utils_8cpp.html#aff5e07c3c1d321709b0cc38e999f427b',1,'m_assert(bool expr, std::string expr_str, std::string f, std::string file, int line, std::string msg): utils.cpp']]],
+  ['main_2ecpp_2',['main.cpp',['../main_8cpp.html',1,'']]],
+  ['mkpath_3',['mkpath',['../utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa',1,'mkpath(std::string path, int mode=0777): utils.cpp'],['../utils_8cpp.html#acf13f4e492199cb7231bfa646dbd08de',1,'mkpath(std::string path, int mode): utils.cpp']]]
 ];

docs/search/all_9.js

@@ -1,4 +1,24 @@
 var searchData=
 [
-  ['q_0',['q',['../classParticle.html#a566dcc1de4bdc01251776948798ea8e1',1,'Particle']]]
+  ['p1_0',['p1',['../main_8cpp.html#a2efa69bb9d93049429ce4637075f1d30',1,'main.cpp']]],
+  ['p2_1',['p2',['../main_8cpp.html#ac70b61df65f4336f57ea9b4c35250df7',1,'main.cpp']]],
+  ['particle_2',['Particle',['../classParticle.html',1,'Particle'],['../classParticle.html#af1d7535fb8311eaa77d2b7b345882ec4',1,'Particle::Particle()']]],
+  ['particle_2ecpp_3',['Particle.cpp',['../Particle_8cpp.html',1,'']]],
+  ['particle_2ehpp_4',['Particle.hpp',['../Particle_8hpp.html',1,'']]],
+  ['particles_5',['particles',['../classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f',1,'PenningTrap']]],
+  ['penning_20trap_20simulation_6',['Penning trap simulation',['../index.html',1,'']]],
+  ['penningtrap_7',['PenningTrap',['../classPenningTrap.html#addc96789dcfec07b75156e19fee82f4f',1,'PenningTrap::PenningTrap()'],['../classPenningTrap.html',1,'PenningTrap'],['../classPenningTrap.html#a830be1b8cbf59664e060b6edbeaa302f',1,'PenningTrap::PenningTrap(uint i, double B_0=T, double V_0=(25. *V)/1000., double d=500., double t=0.)'],['../classPenningTrap.html#a5b6c6d4636f3a6e279ccde59d4a345e8',1,'PenningTrap::PenningTrap(double B_0=T, double V_0=(25. *V)/1000., double d=500., double t=0.)'],['../classParticle.html#aa797d319549dc2a0beb06cdbfd430232',1,'Particle::PenningTrap()']]],
+  ['penningtrap_2ecpp_8',['PenningTrap.cpp',['../PenningTrap_8cpp.html',1,'']]],
+  ['penningtrap_2ehpp_9',['PenningTrap.hpp',['../PenningTrap_8hpp.html',1,'']]],
+  ['penningtraptest_10',['PenningTrapTest',['../classPenningTrap.html#a869f032f37d0569ed16f224b4c4356ae',1,'PenningTrap::PenningTrapTest()'],['../classPenningTrapTest.html',1,'PenningTrapTest']]],
+  ['perturbation_11',['perturbation',['../classPenningTrap.html#ae915f6ad0eef1fb46530e836b6e071e5',1,'PenningTrap']]],
+  ['plot_5f2_5fparticles_2epy_12',['plot_2_particles.py',['../plot__2__particles_8py.html',1,'']]],
+  ['plot_5f3d_2epy_13',['plot_3d.py',['../plot__3d_8py.html',1,'']]],
+  ['plot_5fparticles_5fleft_2epy_14',['plot_particles_left.py',['../plot__particles__left_8py.html',1,'']]],
+  ['plot_5fphase_5fspace_2epy_15',['plot_phase_space.py',['../plot__phase__space_8py.html',1,'']]],
+  ['plot_5frelative_5ferror_2epy_16',['plot_relative_error.py',['../plot__relative__error_8py.html',1,'']]],
+  ['plot_5fsingle_5fparticle_2epy_17',['plot_single_particle.py',['../plot__single__particle_8py.html',1,'']]],
+  ['potential_5fresonance_5fnarrow_5fsweep_18',['potential_resonance_narrow_sweep',['../frequency__narrow__sweeps__long_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea',1,'potential_resonance_narrow_sweep(): frequency_narrow_sweeps_long.cpp'],['../main_8cpp.html#a33d9b1c76c3c80902f89a58b1a6d96ea',1,'potential_resonance_narrow_sweep(): main.cpp']]],
+  ['potential_5fresonance_5fnarrow_5fsweep_5finteraction_19',['potential_resonance_narrow_sweep_interaction',['../frequency__narrow__sweeps__long_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb',1,'potential_resonance_narrow_sweep_interaction(): frequency_narrow_sweeps_long.cpp'],['../main_8cpp.html#ac1816f70ec612edc27848ef7f0875fdb',1,'potential_resonance_narrow_sweep_interaction(): main.cpp']]],
+  ['potential_5fresonance_5fwide_5fsweep_20',['potential_resonance_wide_sweep',['../main_8cpp.html#a6b38b477c18e2f4268779751a88edab1',1,'main.cpp']]]
 ];

docs/search/all_a.js

@@ -1,4 +1,4 @@
 var searchData=
 [
-  ['r_5fvec_0',['r_vec',['../classParticle.html#acf1a0f3c978b06d76df5bb4279594467',1,'Particle']]]
+  ['q_0',['q',['../classParticle.html#a566dcc1de4bdc01251776948798ea8e1',1,'Particle']]]
 ];

docs/search/all_b.js

@@ -1,4 +1,6 @@
 var searchData=
 [
-  ['scientific_5fformat_0',['scientific_format',['../utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384',1,'scientific_format(double d, int width=20, int prec=10): utils.cpp'],['../utils_8hpp.html#ad54b96a1074f9df4dc892a41d115b72d',1,'scientific_format(const std::vector< double > &v, int width=20, int prec=10): utils.cpp'],['../utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746',1,'scientific_format(double d, int width, int prec): utils.cpp'],['../utils_8cpp.html#a58565270b643b24e3132f38c653e0199',1,'scientific_format(const std::vector< double > &v, int width, int prec): utils.cpp']]]
+  ['r_5ffunc_0',['r_func',['../classPenningTrap.html#a826b7fa8e709d481eb1dee7d0c2cdc08',1,'PenningTrap']]],
+  ['r_5fvec_1',['r_vec',['../classParticle.html#a1c59101411db43624828b766f87ad460',1,'Particle']]],
+  ['reinitialize_2',['reinitialize',['../classPenningTrap.html#aaee129f177657455348d0c8ae1441dea',1,'PenningTrap']]]
 ];

docs/search/all_c.js

@@ -1,9 +1,15 @@
 var searchData=
 [
-  ['t_0',['T',['../constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5',1,'constants.hpp']]],
-  ['test_5fsuite_2ecpp_1',['test_suite.cpp',['../test__suite_8cpp.html',1,'']]],
-  ['todo_20list_2',['Todo List',['../todo.html',1,'']]],
-  ['total_5fforce_3',['total_force',['../classPenningTrap.html#a83cc7a04dae009ed8e75453c38fdf8be',1,'PenningTrap']]],
-  ['total_5fforce_5fexternal_4',['total_force_external',['../classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee',1,'PenningTrap']]],
-  ['total_5fforce_5fparticles_5',['total_force_particles',['../classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d',1,'PenningTrap']]]
+  ['scientific_5fformat_0',['scientific_format',['../utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384',1,'scientific_format(double d, int width=20, int prec=10): utils.cpp'],['../utils_8hpp.html#ad54b96a1074f9df4dc892a41d115b72d',1,'scientific_format(const std::vector< double > &v, int width=20, int prec=10): utils.cpp'],['../utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746',1,'scientific_format(double d, int width, int prec): utils.cpp'],['../utils_8cpp.html#a58565270b643b24e3132f38c653e0199',1,'scientific_format(const std::vector< double > &v, int width, int prec): utils.cpp']]],
+  ['set_5fpertubation_1',['set_pertubation',['../classPenningTrap.html#a9d1d8e90ca839b928aee1ad0cd4aff43',1,'PenningTrap']]],
+  ['sim_5farr_2',['sim_arr',['../typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af',1,'typedefs.hpp']]],
+  ['sim_5fcols_3',['sim_cols',['../typedefs_8hpp.html#a46482a2697556c00556c9d73f461784f',1,'typedefs.hpp']]],
+  ['sim_5frows_4',['sim_rows',['../typedefs_8hpp.html#a33418f31f28663b8414c8f7182998c22',1,'typedefs.hpp']]],
+  ['simulate_5',['simulate',['../classPenningTrap.html#a7a1d9f0528a12308de25bc30718da20a',1,'PenningTrap']]],
+  ['simulate_5f100_5fparticles_6',['simulate_100_particles',['../main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513',1,'main.cpp']]],
+  ['simulate_5fsingle_5fparticle_7',['simulate_single_particle',['../main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6',1,'main.cpp']]],
+  ['simulate_5fsingle_5fparticle_5fwith_5fdifferent_5fsteps_8',['simulate_single_particle_with_different_steps',['../main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2',1,'main.cpp']]],
+  ['simulate_5ftwo_5fparticles_9',['simulate_two_particles',['../main_8cpp.html#a783789519f97c6430081171cacb0ffb1',1,'main.cpp']]],
+  ['simulation_10',['simulation',['../structsimulation.html',1,'']]],
+  ['simulation_5ft_11',['simulation_t',['../typedefs_8hpp.html#a784799c37b5e4fb8bf4f6368e004dec6',1,'typedefs.hpp']]]
 ];

docs/search/all_d.js

@@ -1,5 +1,16 @@
 var searchData=
 [
-  ['utils_2ecpp_0',['utils.cpp',['../utils_8cpp.html',1,'']]],
-  ['utils_2ehpp_1',['utils.hpp',['../utils_8hpp.html',1,'']]]
+  ['t_0',['t',['../classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e',1,'PenningTrap']]],
+  ['t_1',['T',['../constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5',1,'constants.hpp']]],
+  ['test_5fexternal_5fb_5ffield_2',['test_external_B_field',['../classPenningTrapTest.html#ad668d7d875bdc1909a42426bf9dead9e',1,'PenningTrapTest']]],
+  ['test_5fexternal_5fe_5ffield_3',['test_external_E_field',['../classPenningTrapTest.html#a6a303be62039ca2ecccd8252744d4dc8',1,'PenningTrapTest']]],
+  ['test_5fforce_5fon_5fparticle_4',['test_force_on_particle',['../classPenningTrapTest.html#a5f4f0b150e54ce463bb29f76d49883f9',1,'PenningTrapTest']]],
+  ['test_5fsuite_2ecpp_5',['test_suite.cpp',['../test__suite_8cpp.html',1,'']]],
+  ['test_5ftotal_5fforce_5fexternal_6',['test_total_force_external',['../classPenningTrapTest.html#ae6d0c8e0d80338fb7c7edefc97331046',1,'PenningTrapTest']]],
+  ['test_5ftotal_5fforce_5fparticles_7',['test_total_force_particles',['../classPenningTrapTest.html#a68449d508e66205bc8b27fa5f60db508',1,'PenningTrapTest']]],
+  ['total_5fforce_8',['total_force',['../classPenningTrap.html#a9a301b0540078c36697880ef204afdf3',1,'PenningTrap']]],
+  ['total_5fforce_5fexternal_9',['total_force_external',['../classPenningTrap.html#a2c01108b52c8e2a003cf9170da9e7682',1,'PenningTrap']]],
+  ['total_5fforce_5fno_5finteraction_10',['total_force_no_interaction',['../classPenningTrap.html#a6069f82d8dbc7cadaebd228dbcd95018',1,'PenningTrap']]],
+  ['total_5fforce_5fparticles_11',['total_force_particles',['../classPenningTrap.html#a2fe1cefbae18fa5808155ee0d2df713c',1,'PenningTrap']]],
+  ['typedefs_2ehpp_12',['typedefs.hpp',['../typedefs_8hpp.html',1,'']]]
 ];

docs/search/all_e.js

@@ -1,6 +1,5 @@
 var searchData=
 [
-  ['v_0',['V',['../constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb',1,'constants.hpp']]],
-  ['v_5f0_1',['V_0',['../classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89',1,'PenningTrap']]],
-  ['v_5fvec_2',['v_vec',['../classParticle.html#a4a5d22c7aeca66f67d083f270cba25df',1,'Particle']]]
+  ['utils_2ecpp_0',['utils.cpp',['../utils_8cpp.html',1,'']]],
+  ['utils_2ehpp_1',['utils.hpp',['../utils_8hpp.html',1,'']]]
 ];

docs/search/all_f.js

@@ -0,0 +1,8 @@
+var searchData=
+[
+  ['v_0',['V',['../constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb',1,'constants.hpp']]],
+  ['v_5f0_1',['V_0',['../classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89',1,'PenningTrap']]],
+  ['v_5ffunc_2',['v_func',['../classPenningTrap.html#a3c0a44e4e0a94366ff609e81fe463fa2',1,'PenningTrap']]],
+  ['v_5fvec_3',['v_vec',['../classParticle.html#a3a10400add8dd22b8031330c2aafb6fe',1,'Particle']]],
+  ['vec3_4',['vec3',['../typedefs_8hpp.html#a3bdfb73a02f88ae32b6128ef747c4aea',1,'typedefs.hpp']]]
+];

docs/search/classes_0.js

@@ -1,5 +1,6 @@
 var searchData=
 [
   ['particle_0',['Particle',['../classParticle.html',1,'']]],
-  ['penningtrap_1',['PenningTrap',['../classPenningTrap.html',1,'']]]
+  ['penningtrap_1',['PenningTrap',['../classPenningTrap.html',1,'']]],
+  ['penningtraptest_2',['PenningTrapTest',['../classPenningTrapTest.html',1,'']]]
 ];

docs/search/classes_1.js

@@ -0,0 +1,4 @@
+var searchData=
+[
+  ['simulation_0',['simulation',['../structsimulation.html',1,'']]]
+];

docs/search/defines_0.js

@@ -1,4 +1,4 @@
 var searchData=
 [
-  ['debug_0',['DEBUG',['../utils_8hpp.html#aecc1f7a8a2493b9e021e5bff76a00a5b',1,'utils.hpp']]]
+  ['_5f_5fmethod_5fname_5f_5f_0',['__METHOD_NAME__',['../utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168',1,'utils.hpp']]]
 ];

docs/search/defines_1.js

@@ -1,4 +1,4 @@
 var searchData=
 [
-  ['k_5fe_0',['K_E',['../constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb',1,'constants.hpp']]]
+  ['assert_0',['ASSERT',['../utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9',1,'utils.hpp']]]
 ];

docs/search/defines_2.js

@@ -1,4 +1,5 @@
 var searchData=
 [
-  ['t_0',['T',['../constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5',1,'constants.hpp']]]
+  ['ca_5fcharge_0',['CA_CHARGE',['../constants_8hpp.html#af7602a3a314957137ad1cd719aa23789',1,'constants.hpp']]],
+  ['ca_5fmass_1',['CA_MASS',['../constants_8hpp.html#a2ff491cc7958ffd5e749c518a4a60ec8',1,'constants.hpp']]]
 ];

docs/search/defines_3.js

@@ -1,4 +1,4 @@
 var searchData=
 [
-  ['v_0',['V',['../constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb',1,'constants.hpp']]]
+  ['debug_0',['DEBUG',['../utils_8hpp.html#aecc1f7a8a2493b9e021e5bff76a00a5b',1,'utils.hpp']]]
 ];

docs/search/defines_4.js

@@ -0,0 +1,4 @@
+var searchData=
+[
+  ['k_5fe_0',['K_E',['../constants_8hpp.html#a4e451456ad7e9276ed0afa42826e7ccb',1,'constants.hpp']]]
+];

docs/search/defines_5.js

@@ -0,0 +1,4 @@
+var searchData=
+[
+  ['t_0',['T',['../constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5',1,'constants.hpp']]]
+];

docs/search/defines_6.js

@@ -0,0 +1,4 @@
+var searchData=
+[
+  ['v_0',['V',['../constants_8hpp.html#af40a326b23c68a27cebe60f16634a2cb',1,'constants.hpp']]]
+];

docs/search/files_0.js

@@ -1,4 +1,4 @@
 var searchData=
 [
-  ['constants_2ehpp_0',['constants.hpp',['../constants_8hpp.html',1,'']]]
+  ['animate_5f100_5fparticles_2epy_0',['animate_100_particles.py',['../animate__100__particles_8py.html',1,'']]]
 ];