Update docs
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@ -136,9 +136,9 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
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<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> arma::vec result;</div>
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<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> arma::vec v;</div>
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<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> std::stringstream msg;</div>
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<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < tests.size(); i++) {</div>
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<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < tests.size(); i++) {</div>
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<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> v = tests.at(i).first;</div>
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<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> result = trap.<a class="code hl_function" href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">external_E_field</a>(v);</div>
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<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> result = trap.<a class="code hl_function" href="classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9">external_E_field</a>(v);</div>
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<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> </div>
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<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> msg.str(<span class="stringliteral">""</span>);</div>
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<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> msg << <span class="stringliteral">"Testing the external E field at ("</span> << std::setprecision(2)</div>
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@ -154,7 +154,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
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<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> <span class="comment">// on position.</span></div>
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<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> <a class="code hl_class" href="classPenningTrap.html">PenningTrap</a> trap;</div>
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<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> arma::vec expected{0., 0., <a class="code hl_define" href="constants_8hpp.html#a0acb682b8260ab1c60b918599864e2e5">T</a>};</div>
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<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">external_B_field</a>(arma::vec{0., 0., 0.});</div>
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<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#acbf065c9c125682329ad82a8d166554c">external_B_field</a>(arma::vec{0., 0., 0.});</div>
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<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div>
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<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> <span class="stringliteral">"Testing the external B field at (0,0,0)"</span>);</div>
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<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> }</div>
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@ -171,14 +171,14 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
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<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> </div>
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<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> <span class="comment">// Test p0 and p1</span></div>
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<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> arma::vec expected{-1., 0., 0.};</div>
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<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">force_on_particle</a>(0, 1);</div>
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<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce">force_on_particle</a>(0, 1);</div>
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<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div>
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<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> <span class="stringliteral">"Testing the force on a particle at (0,0,0) from a "</span></div>
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<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> <span class="stringliteral">"particle at (1,0,0)."</span>);</div>
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<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> </div>
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<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> <span class="comment">// Test p0 and p2</span></div>
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<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span> expected = arma::vec{0, -.024, -.032};</div>
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<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> result = trap.<a class="code hl_function" href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">force_on_particle</a>(0, 2);</div>
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<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> result = trap.<a class="code hl_function" href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce">force_on_particle</a>(0, 2);</div>
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<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div>
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<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> <span class="stringliteral">"Testing the force on a particle at (0,0,0) from a "</span></div>
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<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> <span class="stringliteral">"particle at (0,3,4)."</span>);</div>
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@ -191,7 +191,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
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<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> <a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{1., 2., 3.}, arma::vec{3., 4., 5.}));</div>
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<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> </div>
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<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> arma::vec expected{395.58954878, -270.15871624, -57.89115348};</div>
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<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">total_force_external</a>(0);</div>
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<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">total_force_external</a>(0);</div>
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<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div>
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<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> <span class="stringliteral">"Testing the total external force on a particle at "</span></div>
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<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> <span class="stringliteral">"(1,2,3) with velocity (3,4,5)"</span>);</div>
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@ -204,7 +204,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
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<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span> <a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{0., 0., 0.}, arma::vec{0., 0., 0.}));</div>
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<div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span> </div>
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<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span> arma::vec expected{0., 0., 0.};</div>
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<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">total_force_particles</a>(0);</div>
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<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> arma::vec result = trap.<a class="code hl_function" href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b">total_force_particles</a>(0);</div>
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<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div>
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<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> <span class="stringliteral">"Testing the total force of all particles on particle 0 "</span></div>
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<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> <span class="stringliteral">"with only a single particle"</span>);</div>
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@ -217,7 +217,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
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<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> <a class="code hl_class" href="classParticle.html">Particle</a>(1., 40., arma::vec{0., 0., 1.}, arma::vec{0., 0., 0.}));</div>
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<div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</span> </div>
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<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span> expected = arma::vec(3, arma::fill::value(-3473.383325));</div>
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<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> result = trap.<a class="code hl_function" href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">total_force_particles</a>(0);</div>
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<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> result = trap.<a class="code hl_function" href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b">total_force_particles</a>(0);</div>
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<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> <a class="code hl_define" href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a>(<a class="code hl_function" href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a>(expected, result),</div>
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<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> <span class="stringliteral">"Testing the total force of all particles on particle 0 "</span></div>
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<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> <span class="stringliteral">"with 3 other particles."</span>);</div>
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@ -234,18 +234,18 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
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<div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span> <span class="keywordflow">return</span> 0;</div>
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<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span>}</div>
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<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>
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<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>
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<div class="ttc" id="aclassParticle_html"><div class="ttname"><a href="classParticle.html">Particle</a></div><div class="ttdoc">A class that holds attributes of a particle.</div><div class="ttdef"><b>Definition:</b> <a href="Particle_8hpp_source.html#l00021">Particle.hpp:21</a></div></div>
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<div class="ttc" id="aclassPenningTrapTest_html"><div class="ttname"><a href="classPenningTrapTest.html">PenningTrapTest</a></div><div class="ttdef"><b>Definition:</b> <a href="test__suite_8cpp_source.html#l00020">test_suite.cpp:20</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00029">PenningTrap.hpp:29</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html_a045adb85e97a8e0c38fb36d2fd74eeee"><div class="ttname"><a href="classPenningTrap.html#a045adb85e97a8e0c38fb36d2fd74eeee">PenningTrap::total_force_external</a></div><div class="ttdeci">arma::vec total_force_external(int i)</div><div class="ttdoc">Calculate the total external force on a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00065">PenningTrap.cpp:65</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html_a135db7d991d9b88b00fde4edee71f78d"><div class="ttname"><a href="classPenningTrap.html#a135db7d991d9b88b00fde4edee71f78d">PenningTrap::total_force_particles</a></div><div class="ttdeci">arma::vec total_force_particles(int i)</div><div class="ttdoc">Calculate the total force on a particle from other particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00080">PenningTrap.cpp:80</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html_a2a3e7f480ba52e9f24d4c50c3981a784"><div class="ttname"><a href="classPenningTrap.html#a2a3e7f480ba52e9f24d4c50c3981a784">PenningTrap::external_B_field</a></div><div class="ttdeci">arma::vec external_B_field(arma::vec r)</div><div class="ttdoc">Calculate B at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00043">PenningTrap.cpp:43</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html_a4790f41e4fbc6ede4991aa7bbda92182"><div class="ttname"><a href="classPenningTrap.html#a4790f41e4fbc6ede4991aa7bbda92182">PenningTrap::force_on_particle</a></div><div class="ttdeci">arma::vec force_on_particle(int i, int j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00050">PenningTrap.cpp:50</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html_a6e9776ff5b149f01080800716455d7c8"><div class="ttname"><a href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap::add_particle</a></div><div class="ttdeci">void add_particle(Particle particle)</div><div class="ttdoc">Add a particle to the system.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00027">PenningTrap.cpp:27</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html_a978a2e2026a4b5308d5184712f81704b"><div class="ttname"><a href="classPenningTrap.html#a978a2e2026a4b5308d5184712f81704b">PenningTrap::external_E_field</a></div><div class="ttdeci">arma::vec external_E_field(arma::vec r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00032">PenningTrap.cpp:32</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html"><div class="ttname"><a href="classPenningTrap.html">PenningTrap</a></div><div class="ttdoc">A class that simulates a Penning trap.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8hpp_source.html#l00030">PenningTrap.hpp:30</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html_a1d58feaa2c9e34cbf26b1c5ed75ca9d9"><div class="ttname"><a href="classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9">PenningTrap::external_E_field</a></div><div class="ttdeci">vec_3d external_E_field(vec_3d r)</div><div class="ttdoc">Calculate E at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00087">PenningTrap.cpp:87</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html_a46a954a0946def199e30fb300ba1c47b"><div class="ttname"><a href="classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b">PenningTrap::total_force_particles</a></div><div class="ttdeci">vec_3d total_force_particles(unsigned int i)</div><div class="ttdoc">Calculate the total force on a particle p_i from other particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00129">PenningTrap.cpp:129</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html_a6e9776ff5b149f01080800716455d7c8"><div class="ttname"><a href="classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8">PenningTrap::add_particle</a></div><div class="ttdeci">void add_particle(Particle particle)</div><div class="ttdoc">Add a particle to the system.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00082">PenningTrap.cpp:82</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html_a9ae34ad740a230e667e96bc6ee8730ce"><div class="ttname"><a href="classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce">PenningTrap::force_on_particle</a></div><div class="ttdeci">vec_3d force_on_particle(unsigned int i, unsigned int j)</div><div class="ttdoc">Calculate the force between 2 particles.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00100">PenningTrap.cpp:100</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html_acbf065c9c125682329ad82a8d166554c"><div class="ttname"><a href="classPenningTrap.html#acbf065c9c125682329ad82a8d166554c">PenningTrap::external_B_field</a></div><div class="ttdeci">vec_3d external_B_field(vec_3d r)</div><div class="ttdoc">Calculate B at point r.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00095">PenningTrap.cpp:95</a></div></div>
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<div class="ttc" id="aclassPenningTrap_html_ae72d203b0bfa1b9e72bea28cb2863c56"><div class="ttname"><a href="classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56">PenningTrap::total_force_external</a></div><div class="ttdeci">vec_3d total_force_external(unsigned int i)</div><div class="ttdoc">Calculate the total external force on a particle.</div><div class="ttdef"><b>Definition:</b> <a href="PenningTrap_8cpp_source.html#l00114">PenningTrap.cpp:114</a></div></div>
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<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>
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<div class="ttc" id="autils_8hpp_html"><div class="ttname"><a href="utils_8hpp.html">utils.hpp</a></div><div class="ttdoc">Function prototypes and macros that are useful.</div></div>
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<div class="ttc" id="autils_8hpp_html_a0c95c4791692b06f8811905a76dbd772"><div class="ttname"><a href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a></div><div class="ttdeci">bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8)</div><div class="ttdoc">Test if two armadillo vectors are close to each other.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00059">utils.cpp:59</a></div></div>
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<div class="ttc" id="autils_8hpp_html_a0c95c4791692b06f8811905a76dbd772"><div class="ttname"><a href="utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772">arma_vector_close_to</a></div><div class="ttdeci">bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8)</div><div class="ttdoc">Test if two armadillo vectors are close to each other.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8cpp_source.html#l00062">utils.cpp:62</a></div></div>
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<div class="ttc" id="autils_8hpp_html_a73d4f21ad937dbc50a0c0538c78fd4f9"><div class="ttname"><a href="utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9">ASSERT</a></div><div class="ttdeci">#define ASSERT(expr, msg)</div><div class="ttdoc">A prettier assertion function.</div><div class="ttdef"><b>Definition:</b> <a href="utils_8hpp_source.html#l00045">utils.hpp:45</a></div></div>
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