diff --git a/.gitignore b/.gitignore index 5f54c8c..17c5519 100644 --- a/.gitignore +++ b/.gitignore @@ -47,3 +47,4 @@ src/* !src/*.hpp !src/*.py !src/Doxyfile +!src/scripts diff --git a/Doxyfile b/Doxyfile index eeba27f..7b951c6 100644 --- a/Doxyfile +++ b/Doxyfile @@ -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 diff --git a/docs/100_particles.gif b/docs/100_particles.gif index 3dde053..337c6e5 100644 Binary files a/docs/100_particles.gif and b/docs/100_particles.gif differ diff --git a/docs/Particle_8cpp.html b/docs/Particle_8cpp.html index 98aaf8d..b3fd0e9 100644 --- a/docs/Particle_8cpp.html +++ b/docs/Particle_8cpp.html @@ -113,7 +113,7 @@ $(document).ready(function(){initNavTree('Particle_8cpp.html',''); initResizable
Janita Ovidie Sandtrøen Willumsen (janitaws)
Version
0.1
-
Bug:
No known bugs
+
Bug:
No known bugs

Definition in file Particle.cpp.

diff --git a/docs/Particle_8cpp_source.html b/docs/Particle_8cpp_source.html index 2eaf72e..13c1950 100644 --- a/docs/Particle_8cpp_source.html +++ b/docs/Particle_8cpp_source.html @@ -102,24 +102,24 @@ $(document).ready(function(){initNavTree('Particle_8cpp_source.html',''); initRe
Go to the documentation of this file.
1
-
14#include "Particle.hpp"
-
15
-
16Particle::Particle(double q, double m,
-
17 arma::vec::fixed<3> r_vec,
-
18 arma::vec::fixed<3> v_vec)
-
19{
-
20 // Giving the particle its properties
-
21 this->q = q;
-
22 this->m = m;
-
23 this->r_vec = r_vec;
-
24 this->v_vec = v_vec;
-
25}
+
13#include "Particle.hpp"
+
14
+
15Particle::Particle(double q, double m,
+
16 arma::vec::fixed<3> r_vec,
+
17 arma::vec::fixed<3> v_vec)
+
18{
+
19 // Giving the particle its properties
+
20 this->q = q;
+
21 this->m = m;
+
22 this->r_vec = r_vec;
+
23 this->v_vec = v_vec;
+
24}
Particle.hpp
A class that holds the properties of a particle.
-
Particle::Particle
Particle(double q, double m, arma::vec::fixed< 3 > r_vec, arma::vec::fixed< 3 > v_vec)
Initialize the particle.
Definition: Particle.cpp:16
-
Particle::v_vec
arma::vec::fixed< 3 > v_vec
velocity
Definition: Particle.hpp:24
-
Particle::q
double q
Charge.
Definition: Particle.hpp:21
-
Particle::r_vec
arma::vec::fixed< 3 > r_vec
position
Definition: Particle.hpp:23
-
Particle::m
double m
Mass.
Definition: Particle.hpp:22
+
Particle::q
double q
Charge.
Definition: Particle.hpp:23
+
Particle::Particle
Particle(double q, double m, vec_3d r_vec, vec_3d v_vec)
Initialize the particle.
Definition: Particle.cpp:15
+
Particle::v_vec
vec_3d v_vec
velocity
Definition: Particle.hpp:26
+
Particle::m
double m
Mass.
Definition: Particle.hpp:24
+
Particle::r_vec
vec_3d r_vec
position
Definition: Particle.hpp:25
diff --git a/docs/Particle_8hpp.html b/docs/Particle_8hpp.html index 3516260..00fc0e2 100644 --- a/docs/Particle_8hpp.html +++ b/docs/Particle_8hpp.html @@ -107,6 +107,7 @@ $(document).ready(function(){initNavTree('Particle_8hpp.html',''); initResizable

A class that holds the properties of a particle. More...

#include <armadillo>
+#include "typedefs.hpp"

Go to the source code of this file.

diff --git a/docs/Particle_8hpp_source.html b/docs/Particle_8hpp_source.html index dbb28de..f3339f5 100644 --- a/docs/Particle_8hpp_source.html +++ b/docs/Particle_8hpp_source.html @@ -107,28 +107,30 @@ $(document).ready(function(){initNavTree('Particle_8hpp_source.html',''); initRe
14
15#include <armadillo>
16
-
19class Particle {
-
20private:
-
21 double q;
-
22 double m;
-
23 arma::vec::fixed<3> r_vec;
-
24 arma::vec::fixed<3> v_vec;
-
25
-
26public:
-
32 Particle(double q, double m,
-
33 arma::vec::fixed<3> r_vec,
-
34 arma::vec::fixed<3> v_vec);
-
35
-
38 friend class PenningTrap;
-
39};
+
17#include "typedefs.hpp"
+
18
+
21class Particle {
+
22private:
+
23 double q;
+
24 double m;
+
25 vec_3d r_vec;
+
26 vec_3d v_vec;
+
27
+
28public:
+
39 Particle(double q, double m, vec_3d r_vec, vec_3d v_vec);
40
-
41#endif
-
Particle
A class that holds attributes of a particle.
Definition: Particle.hpp:19
-
Particle::v_vec
arma::vec::fixed< 3 > v_vec
velocity
Definition: Particle.hpp:24
-
Particle::q
double q
Charge.
Definition: Particle.hpp:21
-
Particle::r_vec
arma::vec::fixed< 3 > r_vec
position
Definition: Particle.hpp:23
-
Particle::m
double m
Mass.
Definition: Particle.hpp:22
-
PenningTrap
A class that simulates a Penning trap.
Definition: PenningTrap.hpp:29
+
43 friend class PenningTrap;
+
44};
+
45
+
46#endif
+
Particle
A class that holds attributes of a particle.
Definition: Particle.hpp:21
+
Particle::q
double q
Charge.
Definition: Particle.hpp:23
+
Particle::v_vec
vec_3d v_vec
velocity
Definition: Particle.hpp:26
+
Particle::m
double m
Mass.
Definition: Particle.hpp:24
+
Particle::r_vec
vec_3d r_vec
position
Definition: Particle.hpp:25
+
PenningTrap
A class that simulates a Penning trap.
Definition: PenningTrap.hpp:30
+
typedefs.hpp
Useful typedefs for cleaner code.
+
vec_3d
arma::vec::fixed< 3 > vec_3d
Typedef for a fixed 3d arma vector.
Definition: typedefs.hpp:36
diff --git a/docs/PenningTrap_8cpp.html b/docs/PenningTrap_8cpp.html index 62355e1..5817ff6 100644 --- a/docs/PenningTrap_8cpp.html +++ b/docs/PenningTrap_8cpp.html @@ -106,6 +106,7 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp.html',''); initResiza More...

#include "PenningTrap.hpp"
#include "constants.hpp"
+#include "typedefs.hpp"
#include "utils.hpp"

Go to the source code of this file.

@@ -115,10 +116,7 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp.html',''); initResiza
Janita Ovidie Sandtrøen Willumsen (janitaws)
Version
0.1
-
Bug:
No known bugs
-
Todo:

Implement evolve_RK4

-

Implement evolve_forward_euler

-
+
Bug:
No known bugs

Definition in file PenningTrap.cpp.

diff --git a/docs/PenningTrap_8cpp_source.html b/docs/PenningTrap_8cpp_source.html index 993de8e..282e5c2 100644 --- a/docs/PenningTrap_8cpp_source.html +++ b/docs/PenningTrap_8cpp_source.html @@ -102,205 +102,311 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp_source.html',''); ini
Go to the documentation of this file.
1
-
16#include "PenningTrap.hpp"
-
17#include "constants.hpp"
-
18#include "utils.hpp"
-
19
-
20PenningTrap::PenningTrap(double B_0, double V_0, double d)
-
21{
-
22 this->B_0 = B_0;
-
23 this->V_0 = V_0;
-
24 this->d = d;
+
13#include "PenningTrap.hpp"
+
14#include "constants.hpp"
+
15#include "typedefs.hpp"
+
16#include "utils.hpp"
+
17
+
18PenningTrap::PenningTrap(double B_0, std::function<double(double)> V_0,
+
19 double d, double t)
+
20{
+
21 this->B_0 = B_0;
+
22 this->V_0 = V_0;
+
23 this->d = d;
+
24 this->t = t;
25}
26
-
27void PenningTrap::add_particle(Particle particle)
-
28{
-
29 this->particles.push_back(particle);
-
30}
-
31
-
32arma::vec PenningTrap::external_E_field(arma::vec r)
-
33{
-
34 arma::vec::fixed<3> res;
-
35 double f = this->V_0 / (this->d * this->d);
-
36 res(0) = r(0);
-
37 res(1) = r(1);
-
38 res(2) = -2. * r(2);
-
39
-
40 return f * res;
-
41}
-
42
-
43arma::vec PenningTrap::external_B_field(arma::vec r)
-
44{
-
45 arma::vec::fixed<3> res{0., 0., this->B_0};
-
46
-
47 return res;
-
48}
-
49
-
50arma::vec PenningTrap::force_on_particle(int i, int j)
-
51{
-
52 // Calculate the difference between the particles' position
-
53 arma::vec::fixed<3> res =
-
54 this->particles.at(i).r_vec - this->particles.at(j).r_vec;
-
55
-
56 // Get the distance between the particles
-
57 double norm = arma::norm(res);
-
58
-
59 // Multiply res with p_j's charge divided by the norm cubed
-
60 res *= this->particles.at(j).q / (norm * norm * norm);
-
61
-
62 return res;
-
63}
-
64
-
65arma::vec PenningTrap::total_force_external(int i)
-
66{
-
67 Particle p = this->particles.at(i);
-
68
-
69 arma::vec::fixed<3> B = this->external_B_field(p.r_vec);
-
70
-
71 arma::vec::fixed<3> v_cross_B{p.v_vec(1) * B(2) - p.v_vec(2) * B(1),
-
72 p.v_vec(2) * B(0) - p.v_vec(0) * B(2),
-
73 p.v_vec(0) * B(1) - p.v_vec(1) * B(0)};
-
74
-
75 arma::vec force = p.q * (this->external_E_field(p.r_vec) + v_cross_B);
-
76
-
77 return force;
-
78}
-
79
-
80arma::vec PenningTrap::total_force_particles(int i)
-
81{
-
82 Particle p = this->particles.at(i);
-
83
-
84 arma::vec res(3);
-
85
-
86 for (int j = 0; j < this->particles.size(); j++) {
-
87 if (i == j) {
-
88 continue;
-
89 }
-
90
-
91 res += this->force_on_particle(i, j);
-
92 }
-
93
-
94 res *= K_E * (p.q / p.m);
-
95
-
96 return res;
-
97}
-
98
-
99arma::vec PenningTrap::total_force(int i)
-
100{
-
101 return this->total_force_external(i) - this->total_force_particles(i);
-
102}
-
103
-
104void PenningTrap::evolve_RK4(double dt)
-
105{
-
106 std::vector<Particle> tmp_particles = this->particles;
-
107
-
108 arma::vec::fixed<3> *k_v = new arma::vec::fixed<3>[this->particles.size()*4];
-
109 arma::vec::fixed<3> *k_r = new arma::vec::fixed<3>[this->particles.size()*4];
+
27PenningTrap::PenningTrap(unsigned int i, double B_0,
+
28 std::function<double(double)> V_0, double d, double t)
+
29 : PenningTrap::PenningTrap(B_0, V_0, d)
+
30{
+
31 vec_3d r, v;
+
32 for (size_t j = 0; j < i; j++) {
+
33 r = vec_3d().randn() * .1 * this->d;
+
34 v = vec_3d().randn() * .1 * this->d;
+
35 this->add_particle(Particle(1., 40., r, v));
+
36 }
+
37}
+
38
+
39PenningTrap::PenningTrap(std::vector<Particle> particles, double B_0,
+
40 std::function<double(double)> V_0, double d, double t)
+
41 : PenningTrap::PenningTrap(B_0, V_0, d)
+
42{
+
43 this->particles = particles;
+
44}
+
45
+
46vec_3d PenningTrap::v_func(unsigned int i, unsigned int j, double dt)
+
47{
+
48 switch (i) {
+
49 case 0:
+
50 return .5 * dt * this->k_v[0][j];
+
51 case 1:
+
52 return .5 * dt * this->k_v[1][j];
+
53 case 2:
+
54 return dt * this->k_v[2][j];
+
55 case 3:
+
56 return (dt / 6.) * (this->k_v[0][j].eval() + this->k_v[1][j].eval() +
+
57 this->k_v[2][j].eval() + this->k_v[3][j].eval());
+
58 default:
+
59 std::cout << "Not valid!" << std::endl;
+
60 abort();
+
61 }
+
62}
+
63
+
64vec_3d PenningTrap::r_func(unsigned int i, unsigned int j, double dt)
+
65{
+
66 switch (i) {
+
67 case 0:
+
68 return .5 * dt * this->k_r[0][j];
+
69 case 1:
+
70 return .5 * dt * this->k_r[1][j];
+
71 case 2:
+
72 return dt * this->k_r[2][j];
+
73 case 3:
+
74 return (dt / 6.) * (this->k_r[0][j].eval() + this->k_r[1][j].eval() +
+
75 this->k_r[2][j].eval() + this->k_r[3][j].eval());
+
76 default:
+
77 std::cout << "Not valid!" << std::endl;
+
78 abort();
+
79 }
+
80}
+
81
+
82void PenningTrap::add_particle(Particle particle)
+
83{
+
84 this->particles.push_back(particle);
+
85}
+
86
+
87vec_3d PenningTrap::external_E_field(vec_3d r)
+
88{
+
89 r(2) *= -2.;
+
90 double f = this->V_0(this->t) / (this->d * this->d);
+
91
+
92 return f * r;
+
93}
+
94
+
95vec_3d PenningTrap::external_B_field(vec_3d r)
+
96{
+
97 return vec_3d{0., 0., this->B_0};
+
98}
+
99
+
100vec_3d PenningTrap::force_on_particle(unsigned int i, unsigned int j)
+
101{
+
102 Particle p_j = this->particles[j];
+
103 // Calculate the difference between the particles' position
+
104 vec_3d res = this->particles[i].r_vec - p_j.r_vec;
+
105
+
106 // Get the distance between the particles
+
107 double norm = arma::norm(res, 2);
+
108
+
109 // Multiply res with p_j's charge divided by the norm cubed
110
-
111 int size = this->particles.size();
-
112
-
113 for (int i=0; i<size; i++) {
-
114 k_v[i] = this->total_force(i)/this->particles.at(i).m;
-
115 k_r[i] = this->particles.at(i).v_vec;
-
116 }
+
111 return vec_3d(res * p_j.q / (norm * norm * norm));
+
112}
+
113
+
114vec_3d PenningTrap::total_force_external(unsigned int i)
+
115{
+
116 Particle p = this->particles[i];
117
-
118 for (int i=0; i<size; i++) {
-
119 Particle *p = &this->particles.at(i);
-
120
-
121 p->v_vec = tmp_particles.at(i).v_vec + (dt/2)*k_v[i];
-
122 p->r_vec = tmp_particles.at(i).r_vec + (dt/2)*k_r[i];
-
123 }
-
124
+
118 if (arma::norm(p.r_vec) > this->d) {
+
119 return vec_3d{0., 0., 0.};
+
120 }
+
121
+
122 vec_3d force =
+
123 p.q * (this->external_E_field(p.r_vec) +
+
124 arma::cross(p.v_vec, this->external_B_field(p.r_vec)));
125
-
126 for (int i=0; i<size; i++) {
-
127 k_v[1*size + i] = this->total_force(i)/this->particles.at(i).m;
-
128 k_r[1*size + i] = this->particles.at(i).v_vec;
-
129 }
-
130
-
131 for (int i=0; i<size; i++) {
-
132 Particle *p = &this->particles.at(i);
-
133
-
134 p->v_vec = tmp_particles.at(i).v_vec + (dt/2)*k_v[1*size + i];
-
135 p->r_vec = tmp_particles.at(i).r_vec + (dt/2)*k_r[1*size + i];
-
136 }
-
137
-
138 for (int i=0; i<size; i++) {
-
139 k_v[2*size + i] = this->total_force(i)/this->particles.at(i).m;
-
140 k_r[2*size + i] = this->particles.at(i).v_vec;
+
126 return force;
+
127}
+
128
+
129vec_3d PenningTrap::total_force_particles(unsigned int i)
+
130{
+
131 Particle p = this->particles[i];
+
132
+
133 vec_3d res;
+
134
+
135 for (size_t j = 0; j < this->particles.size(); j++) {
+
136 if (i == j) {
+
137 continue;
+
138 }
+
139
+
140 res += this->force_on_particle(i, j);
141 }
142
-
143 for (int i=0; i<size; i++) {
-
144 Particle *p = &this->particles.at(i);
+
143 return vec_3d(res * K_E * (p.q / p.m));
+
144}
145
-
146 p->v_vec = tmp_particles.at(i).v_vec + dt*k_v[2*size + i];
-
147 p->r_vec = tmp_particles.at(i).r_vec + dt*k_r[2*size + i];
-
148 }
-
149
+
146vec_3d PenningTrap::total_force(unsigned int i)
+
147{
+
148 return this->total_force_external(i) - this->total_force_particles(i);
+
149}
150
-
151 for (int i=0; i<size; i++) {
-
152 k_v[3*size + i] = this->total_force(i)/this->particles.at(i).m;
-
153 k_r[3*size + i] = this->particles.at(i).v_vec;
-
154 }
-
155
-
156 for (int i=0; i<size; i++) {
-
157 Particle *p = &this->particles.at(i);
-
158
-
159 p->v_vec = tmp_particles.at(i).v_vec + dt*(k_v[i] + k_v[size + i] + k_v[2*size + i] + k_v[3*size + i])/6;
-
160 p->r_vec = tmp_particles.at(i).r_vec + dt*(k_r[i] + k_r[size + i] + k_r[2*size + i] + k_r[3*size + i])/6;
-
161 }
-
162
-
163 delete [] k_v;
-
164 delete [] k_r;
-
165}
+
151void PenningTrap::evolve_RK4(double dt, bool particle_interaction)
+
152{
+
153
+
154 std::vector<Particle> original_particles = this->particles;
+
155 std::vector<Particle> tmp_particles = this->particles;
+
156
+
157 vec_3d (PenningTrap::*force)(unsigned int);
+
158 if (particle_interaction) {
+
159 force = &PenningTrap::total_force;
+
160 }
+
161 else {
+
162 force = &PenningTrap::total_force_external;
+
163 }
+
164
+
165 size_t size = this->particles.size();
166
-
167void PenningTrap::evolve_forward_euler(double dt)
-
168{
-
169 std::vector<Particle> new_state = this->particles;
-
170
-
171 Particle *p;
-
172
-
173#pragma omp parallel for private(p)
-
174 for (int i = 0; i < this->particles.size(); i++) {
-
175 p = &new_state.at(i);
-
176 p->v_vec += dt * this->total_force(i) / new_state.at(i).m;
-
177 p->r_vec += dt * this->particles.at(i).v_vec;
-
178 }
-
179
-
180 this->particles = new_state;
-
181}
-
182
-
183arma::vec PenningTrap::get_particle(int i)
-
184{
-
185 return this->particles.at(i).r_vec;
-
186}
-
187
-
188double PenningTrap::get_d()
-
189{
-
190 return this->d;
-
191}
+
167 this->k_v = sim_arr(4, sim_cols(size));
+
168 this->k_r = sim_arr(4, sim_cols(size));
+
169
+
170 for (size_t i = 0; i < 4; i++) {
+
171#pragma omp parallel for
+
172 for (size_t j = 0; j < this->particles.size(); j++) {
+
173 this->k_v[i][j] = (this->*force)(j) / this->particles[j].m;
+
174 this->k_r[i][j] = this->particles[j].v_vec;
+
175
+
176 Particle *p = &tmp_particles[j];
+
177
+
178 p->v_vec = original_particles[j].v_vec + this->v_func(i, j, dt);
+
179 p->r_vec = original_particles[j].r_vec + this->r_func(i, j, dt);
+
180 }
+
181 this->particles = tmp_particles;
+
182 }
+
183 this->t += dt;
+
184}
+
185
+
186void PenningTrap::evolve_forward_euler(double dt, bool particle_interaction)
+
187{
+
188 std::vector<Particle> new_state = this->particles;
+
189
+
190 Particle *p;
+
191
+
192 vec_3d (PenningTrap::*force)(unsigned int);
+
193 if (particle_interaction) {
+
194 force = &PenningTrap::total_force;
+
195 }
+
196 else {
+
197 force = &PenningTrap::total_force_external;
+
198 }
+
199
+
200#pragma omp parallel for private(p)
+
201 for (size_t i = 0; i < this->particles.size(); i++) {
+
202 p = &new_state[i];
+
203 p->v_vec += dt * (this->*force)(i) / p->m;
+
204 p->r_vec += dt * this->particles[i].v_vec;
+
205 }
+
206
+
207 this->particles = new_state;
+
208 this->t += dt;
+
209}
+
210
+
211sim_arr PenningTrap::simulate(double time, unsigned int steps,
+
212 std::string method, bool particle_interaction)
+
213{
+
214 double dt = time / (double)steps;
+
215
+
216 sim_arr res(this->particles.size(), sim_cols(steps));
+
217
+
218 void (PenningTrap::*func)(double, bool);
+
219 if (method == "rk4") {
+
220 func = &PenningTrap::evolve_RK4;
+
221 }
+
222 else if (method == "euler") {
+
223 func = &PenningTrap::evolve_forward_euler;
+
224 }
+
225 else {
+
226 std::cout << "Not a valid method!" << std::endl;
+
227 abort();
+
228 }
+
229
+
230 for (size_t j = 0; j < steps; j++) {
+
231 for (size_t i = 0; i < this->particles.size(); i++) {
+
232 res[i][j] = this->particles[i].r_vec;
+
233 }
+
234 (this->*func)(dt, particle_interaction);
+
235 }
+
236
+
237 return res;
+
238}
+
239
+
240void PenningTrap::write_simulation_to_dir(std::string path, double time,
+
241 int steps, std::string method,
+
242 bool particle_interaction)
+
243{
+
244 if (path.back() != '/') {
+
245 path += '/';
+
246 }
+
247 if (mkpath(path, 0777) != 0) {
+
248 std::cout << "Hello" << std::endl;
+
249 return;
+
250 }
+
251
+
252 sim_arr res = this->simulate(time, steps, method, particle_interaction);
+
253
+
254 std::ofstream ofile;
+
255
+
256#pragma omp parallel for private(ofile)
+
257 for (size_t i = 0; i < this->particles.size(); i++) {
+
258 ofile.open(path + "particle_" + std::to_string(i) + ".txt");
+
259 for (vec_3d &vec : res[i]) {
+
260 ofile << vec(0) << "," << vec(1) << "," << vec(2) << "\n";
+
261 }
+
262 ofile.close();
+
263 }
+
264}
+
265
+
266double PenningTrap::fraction_of_particles_left(double time, unsigned int steps, std::string method, bool particle_interaction)
+
267{
+
268 sim_arr res = this->simulate(time, steps, method, particle_interaction);
+
269
+
270 int particles_left = 0;
+
271
+
272 for (Particle p : this->particles) {
+
273 if (arma::norm(p.r_vec) < this->d) {
+
274 particles_left++;
+
275 }
+
276 }
+
277
+
278 return (double) particles_left / (double) this->particles.size();
+
279}
+
280
PenningTrap.hpp
A class for simulating a Penning trap.
-
Particle
A class that holds attributes of a particle.
Definition: Particle.hpp:19
-
Particle::v_vec
arma::vec::fixed< 3 > v_vec
velocity
Definition: Particle.hpp:24
-
Particle::q
double q
Charge.
Definition: Particle.hpp:21
-
Particle::r_vec
arma::vec::fixed< 3 > r_vec
position
Definition: Particle.hpp:23
-
Particle::m
double m
Mass.
Definition: Particle.hpp:22
-
PenningTrap::particles
std::vector< Particle > particles
The particles in the Penning trap.
Definition: PenningTrap.hpp:34
-
PenningTrap::total_force_external
arma::vec total_force_external(int i)
Calculate the total external force on a particle.
Definition: PenningTrap.cpp:65
-
PenningTrap::B_0
double B_0
Magnetic field strength.
Definition: PenningTrap.hpp:31
-
PenningTrap::total_force_particles
arma::vec total_force_particles(int i)
Calculate the total force on a particle from other particles.
Definition: PenningTrap.cpp:80
-
PenningTrap::external_B_field
arma::vec external_B_field(arma::vec r)
Calculate B at point r.
Definition: PenningTrap.cpp:43
-
PenningTrap::force_on_particle
arma::vec force_on_particle(int i, int j)
Calculate the force between 2 particles.
Definition: PenningTrap.cpp:50
-
PenningTrap::evolve_forward_euler
void evolve_forward_euler(double dt)
Go forward one timestep using the forward Euler method.
Definition: PenningTrap.cpp:167
-
PenningTrap::d
double d
Characteristic dimension.
Definition: PenningTrap.hpp:33
-
PenningTrap::add_particle
void add_particle(Particle particle)
Add a particle to the system.
Definition: PenningTrap.cpp:27
-
PenningTrap::V_0
double V_0
Applied potential.
Definition: PenningTrap.hpp:32
-
PenningTrap::PenningTrap
PenningTrap(double B_0=T, double V_0=25.*V/1000., double d=500.)
Set B_0, V_0 and d.
Definition: PenningTrap.cpp:20
-
PenningTrap::total_force
arma::vec total_force(int i)
calculate the total force on a particle.
Definition: PenningTrap.cpp:99
-
PenningTrap::external_E_field
arma::vec external_E_field(arma::vec r)
Calculate E at point r.
Definition: PenningTrap.cpp:32
-
PenningTrap::evolve_RK4
void evolve_RK4(double dt)
Go forward one timestep using the RK4 method.
Definition: PenningTrap.cpp:104
+
Particle
A class that holds attributes of a particle.
Definition: Particle.hpp:21
+
Particle::q
double q
Charge.
Definition: Particle.hpp:23
+
Particle::v_vec
vec_3d v_vec
velocity
Definition: Particle.hpp:26
+
Particle::m
double m
Mass.
Definition: Particle.hpp:24
+
Particle::r_vec
vec_3d r_vec
position
Definition: Particle.hpp:25
+
PenningTrap
A class that simulates a Penning trap.
Definition: PenningTrap.hpp:30
+
PenningTrap::particles
std::vector< Particle > particles
The particles in the Penning trap.
Definition: PenningTrap.hpp:36
+
PenningTrap::fraction_of_particles_left
double fraction_of_particles_left(double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)
Simulate and calculate what fraction of particles are still left inside the Penning trap after the si...
Definition: PenningTrap.cpp:266
+
PenningTrap::B_0
double B_0
Magnetic field strength.
Definition: PenningTrap.hpp:32
+
PenningTrap::external_E_field
vec_3d external_E_field(vec_3d r)
Calculate E at point r.
Definition: PenningTrap.cpp:87
+
PenningTrap::total_force
vec_3d total_force(unsigned int i)
calculate the total force on a particle p_i.
Definition: PenningTrap.cpp:146
+
PenningTrap::k_r
sim_arr k_r
Definition: PenningTrap.hpp:39
+
PenningTrap::evolve_RK4
void evolve_RK4(double dt, bool particle_interaction=true)
Go forward one timestep using the RK4 method.
Definition: PenningTrap.cpp:151
+
PenningTrap::r_func
vec_3d r_func(unsigned int i, unsigned int j, double dt)
Helper for evolve_RK4 when calculating values.
Definition: PenningTrap.cpp:64
+
PenningTrap::total_force_particles
vec_3d total_force_particles(unsigned int i)
Calculate the total force on a particle p_i from other particles.
Definition: PenningTrap.cpp:129
+
PenningTrap::simulate
sim_arr simulate(double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)
Simulate the particle system inside the Penning trap over a certain amount of time.
Definition: PenningTrap.cpp:211
+
PenningTrap::d
double d
Characteristic dimension.
Definition: PenningTrap.hpp:34
+
PenningTrap::add_particle
void add_particle(Particle particle)
Add a particle to the system.
Definition: PenningTrap.cpp:82
+
PenningTrap::t
double t
Current time.
Definition: PenningTrap.hpp:35
+
PenningTrap::force_on_particle
vec_3d force_on_particle(unsigned int i, unsigned int j)
Calculate the force between 2 particles.
Definition: PenningTrap.cpp:100
+
PenningTrap::V_0
std::function< double(double)> V_0
Applied potential.
Definition: PenningTrap.hpp:33
+
PenningTrap::evolve_forward_euler
void evolve_forward_euler(double dt, bool particle_interaction=true)
Go forward one timestep using the forward Euler method.
Definition: PenningTrap.cpp:186
+
PenningTrap::write_simulation_to_dir
void write_simulation_to_dir(std::string path, double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)
Simulate and write the displacement of all particles to files.
Definition: PenningTrap.cpp:240
+
PenningTrap::external_B_field
vec_3d external_B_field(vec_3d r)
Calculate B at point r.
Definition: PenningTrap.cpp:95
+
PenningTrap::PenningTrap
PenningTrap(double B_0=T, std::function< double(double)> V_0=[](double t) { return 25. *V/1000.;}, double d=500., double t=0.)
Constructor for the PenningTrap class.
Definition: PenningTrap.cpp:18
+
PenningTrap::total_force_external
vec_3d total_force_external(unsigned int i)
Calculate the total external force on a particle.
Definition: PenningTrap.cpp:114
+
PenningTrap::k_v
sim_arr k_v
Definition: PenningTrap.hpp:37
+
PenningTrap::v_func
vec_3d v_func(unsigned int i, unsigned int j, double dt)
Helper for evolve_RK4 when calculating values.
Definition: PenningTrap.cpp:46
constants.hpp
Library of constants.
K_E
#define K_E
Coulomb constant. unit: .
Definition: constants.hpp:15
+
typedefs.hpp
Useful typedefs for cleaner code.
+
sim_cols
std::vector< arma::vec::fixed< 3 > > sim_cols
Typedef for the column of the result vector from simulating particles.
Definition: typedefs.hpp:24
+
vec_3d
arma::vec::fixed< 3 > vec_3d
Typedef for a fixed 3d arma vector.
Definition: typedefs.hpp:36
+
sim_arr
std::vector< sim_cols > sim_arr
Typedef for the result of the simulate method.
Definition: typedefs.hpp:32
utils.hpp
Function prototypes and macros that are useful.
+
mkpath
bool mkpath(std::string path, int mode=0777)
Make path given.
Definition: utils.cpp:76
diff --git a/docs/PenningTrap_8hpp.html b/docs/PenningTrap_8hpp.html index 306bc89..5f6ee45 100644 --- a/docs/PenningTrap_8hpp.html +++ b/docs/PenningTrap_8hpp.html @@ -110,6 +110,7 @@ $(document).ready(function(){initNavTree('PenningTrap_8hpp.html',''); initResiza #include <omp.h>
#include "Particle.hpp"
#include "constants.hpp"
+#include "typedefs.hpp"

Go to the source code of this file.

diff --git a/docs/PenningTrap_8hpp_source.html b/docs/PenningTrap_8hpp_source.html index 02b2aed..dfdddbe 100644 --- a/docs/PenningTrap_8hpp_source.html +++ b/docs/PenningTrap_8hpp_source.html @@ -110,63 +110,106 @@ $(document).ready(function(){initNavTree('PenningTrap_8hpp_source.html',''); ini
17
18#include "Particle.hpp"
19#include "constants.hpp"
-
20
-
21#pragma omp declare reduction( + : arma::vec : omp_out += omp_in ) \
-
22 initializer( omp_priv = omp_orig )
-
23
-
29class PenningTrap {
-
30private:
-
31 double B_0;
-
32 double V_0;
-
33 double d;
-
34 std::vector<Particle> particles;
-
35
-
36public:
-
39 PenningTrap(double B_0 = T, double V_0 = 25.*V/1000., double d = 500.);
-
40
-
43 void add_particle(Particle particle);
-
44
-
47 arma::vec external_E_field(arma::vec r);
-
48
-
51 arma::vec external_B_field(arma::vec r);
-
52
-
58 arma::vec force_on_particle(int i, int j);
-
59
-
65 arma::vec total_force_external(int i);
-
66
-
69 arma::vec total_force_particles(int i);
-
70
-
73 arma::vec total_force(int i);
-
74
-
77 void evolve_RK4(double dt);
-
78
-
81 void evolve_forward_euler(double dt);
-
82
-
83 arma::vec get_particle(int i);
-
84
-
85 double get_d();
-
86};
-
87
-
88#endif
+
20#include "typedefs.hpp"
+
21
+
22#pragma omp declare reduction(+ : vec_3d : omp_out += omp_in) \
+
23 initializer(omp_priv = omp_orig)
+
24
+
30class PenningTrap {
+
31private:
+
32 double B_0;
+
33 std::function<double(double)> V_0;
+
34 double d;
+
35 double t;
+
36 std::vector<Particle> particles;
+
37 sim_arr k_v;
+
39 sim_arr k_r;
+
41
+
52 vec_3d v_func(unsigned int i, unsigned int j, double dt);
+
53
+
64 vec_3d r_func(unsigned int i, unsigned int j, double dt);
+
65
+
66public:
+
74 PenningTrap(
+
75 double B_0 = T,
+
76 std::function<double(double)> V_0 =
+
77 [](double t) { return 25. * V / 1000.; },
+
78 double d = 500., double t = 0.);
+
79
+
88 PenningTrap(
+
89 unsigned int i, double B_0 = T,
+
90 std::function<double(double)> V_0 =
+
91 [](double t) { return 25. * V / 1000.; },
+
92 double d = 500., double t = 0.);
+
93
+
102 PenningTrap(
+
103 std::vector<Particle> particles, double B_0 = T,
+
104 std::function<double(double)> V_0 =
+
105 [](double t) { return 25. * V / 1000.; },
+
106 double d = 500., double t = 0.);
+
107
+
112 void add_particle(Particle particle);
+
113
+
120 vec_3d external_E_field(vec_3d r);
+
121
+
128 vec_3d external_B_field(vec_3d r);
+
129
+
140 vec_3d force_on_particle(unsigned int i, unsigned int j);
+
141
+
151 vec_3d total_force_external(unsigned int i);
+
152
+
159 vec_3d total_force_particles(unsigned int i);
+
160
+
167 vec_3d total_force(unsigned int i);
+
168
+
174 void evolve_RK4(double dt, bool particle_interaction = true);
+
175
+
181 void evolve_forward_euler(double dt, bool particle_interaction = true);
+
182
+
191 sim_arr simulate(double time, unsigned int steps,
+
192 std::string method = "rk4",
+
193 bool particle_interaction = true);
+
194
+
203 void write_simulation_to_dir(std::string path, double time,
+
204 unsigned int steps, std::string method = "rk4",
+
205 bool particle_interaction = true);
+
206
+
217 double fraction_of_particles_left(double time, unsigned int steps,
+
218 std::string method = "rk4",
+
219 bool particle_interaction = true);
+
220};
+
221
+
222#endif
Particle.hpp
A class that holds the properties of a particle.
-
Particle
A class that holds attributes of a particle.
Definition: Particle.hpp:19
-
PenningTrap
A class that simulates a Penning trap.
Definition: PenningTrap.hpp:29
-
PenningTrap::particles
std::vector< Particle > particles
The particles in the Penning trap.
Definition: PenningTrap.hpp:34
-
PenningTrap::total_force_external
arma::vec total_force_external(int i)
Calculate the total external force on a particle.
Definition: PenningTrap.cpp:65
-
PenningTrap::B_0
double B_0
Magnetic field strength.
Definition: PenningTrap.hpp:31
-
PenningTrap::total_force_particles
arma::vec total_force_particles(int i)
Calculate the total force on a particle from other particles.
Definition: PenningTrap.cpp:80
-
PenningTrap::external_B_field
arma::vec external_B_field(arma::vec r)
Calculate B at point r.
Definition: PenningTrap.cpp:43
-
PenningTrap::force_on_particle
arma::vec force_on_particle(int i, int j)
Calculate the force between 2 particles.
Definition: PenningTrap.cpp:50
-
PenningTrap::evolve_forward_euler
void evolve_forward_euler(double dt)
Go forward one timestep using the forward Euler method.
Definition: PenningTrap.cpp:167
-
PenningTrap::d
double d
Characteristic dimension.
Definition: PenningTrap.hpp:33
-
PenningTrap::add_particle
void add_particle(Particle particle)
Add a particle to the system.
Definition: PenningTrap.cpp:27
-
PenningTrap::V_0
double V_0
Applied potential.
Definition: PenningTrap.hpp:32
-
PenningTrap::total_force
arma::vec total_force(int i)
calculate the total force on a particle.
Definition: PenningTrap.cpp:99
-
PenningTrap::external_E_field
arma::vec external_E_field(arma::vec r)
Calculate E at point r.
Definition: PenningTrap.cpp:32
-
PenningTrap::evolve_RK4
void evolve_RK4(double dt)
Go forward one timestep using the RK4 method.
Definition: PenningTrap.cpp:104
+
Particle
A class that holds attributes of a particle.
Definition: Particle.hpp:21
+
PenningTrap
A class that simulates a Penning trap.
Definition: PenningTrap.hpp:30
+
PenningTrap::particles
std::vector< Particle > particles
The particles in the Penning trap.
Definition: PenningTrap.hpp:36
+
PenningTrap::fraction_of_particles_left
double fraction_of_particles_left(double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)
Simulate and calculate what fraction of particles are still left inside the Penning trap after the si...
Definition: PenningTrap.cpp:266
+
PenningTrap::B_0
double B_0
Magnetic field strength.
Definition: PenningTrap.hpp:32
+
PenningTrap::external_E_field
vec_3d external_E_field(vec_3d r)
Calculate E at point r.
Definition: PenningTrap.cpp:87
+
PenningTrap::total_force
vec_3d total_force(unsigned int i)
calculate the total force on a particle p_i.
Definition: PenningTrap.cpp:146
+
PenningTrap::k_r
sim_arr k_r
Definition: PenningTrap.hpp:39
+
PenningTrap::evolve_RK4
void evolve_RK4(double dt, bool particle_interaction=true)
Go forward one timestep using the RK4 method.
Definition: PenningTrap.cpp:151
+
PenningTrap::r_func
vec_3d r_func(unsigned int i, unsigned int j, double dt)
Helper for evolve_RK4 when calculating values.
Definition: PenningTrap.cpp:64
+
PenningTrap::total_force_particles
vec_3d total_force_particles(unsigned int i)
Calculate the total force on a particle p_i from other particles.
Definition: PenningTrap.cpp:129
+
PenningTrap::simulate
sim_arr simulate(double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)
Simulate the particle system inside the Penning trap over a certain amount of time.
Definition: PenningTrap.cpp:211
+
PenningTrap::d
double d
Characteristic dimension.
Definition: PenningTrap.hpp:34
+
PenningTrap::add_particle
void add_particle(Particle particle)
Add a particle to the system.
Definition: PenningTrap.cpp:82
+
PenningTrap::t
double t
Current time.
Definition: PenningTrap.hpp:35
+
PenningTrap::force_on_particle
vec_3d force_on_particle(unsigned int i, unsigned int j)
Calculate the force between 2 particles.
Definition: PenningTrap.cpp:100
+
PenningTrap::V_0
std::function< double(double)> V_0
Applied potential.
Definition: PenningTrap.hpp:33
+
PenningTrap::evolve_forward_euler
void evolve_forward_euler(double dt, bool particle_interaction=true)
Go forward one timestep using the forward Euler method.
Definition: PenningTrap.cpp:186
+
PenningTrap::write_simulation_to_dir
void write_simulation_to_dir(std::string path, double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)
Simulate and write the displacement of all particles to files.
Definition: PenningTrap.cpp:240
+
PenningTrap::external_B_field
vec_3d external_B_field(vec_3d r)
Calculate B at point r.
Definition: PenningTrap.cpp:95
+
PenningTrap::total_force_external
vec_3d total_force_external(unsigned int i)
Calculate the total external force on a particle.
Definition: PenningTrap.cpp:114
+
PenningTrap::k_v
sim_arr k_v
Definition: PenningTrap.hpp:37
+
PenningTrap::v_func
vec_3d v_func(unsigned int i, unsigned int j, double dt)
Helper for evolve_RK4 when calculating values.
Definition: PenningTrap.cpp:46
constants.hpp
Library of constants.
T
#define T
1 Tesla. unit:
Definition: constants.hpp:17
V
#define V
1 Volt. unit:
Definition: constants.hpp:19
+
typedefs.hpp
Useful typedefs for cleaner code.
+
vec_3d
arma::vec::fixed< 3 > vec_3d
Typedef for a fixed 3d arma vector.
Definition: typedefs.hpp:36
+
sim_arr
std::vector< sim_cols > sim_arr
Typedef for the result of the simulate method.
Definition: typedefs.hpp:32
diff --git a/docs/animate__100__particles_8py_source.html b/docs/animate__100__particles_8py_source.html index 80feb43..af734ca 100644 --- a/docs/animate__100__particles_8py_source.html +++ b/docs/animate__100__particles_8py_source.html @@ -103,68 +103,75 @@ $(document).ready(function(){initNavTree('animate__100__particles_8py_source.htm
1import matplotlib.pyplot as plt
2import numpy as np
-
3from mpl_toolkits.mplot3d import Axes3D
-
4from matplotlib import animation
+
3from matplotlib import animation
+
4from mpl_toolkits.mplot3d import Axes3D
5
-
6def get_data(files):
-
7 res = []
-
8 for file in files:
-
9 arr = [[], [], []]
-
10 with open(file, encoding="utf8") as f:
-
11 lines = f.readlines()
-
12
-
13 for line in lines:
-
14 xi,yi,zi = map(float, line.strip().split(","))
-
15 arr[0].append(xi)
-
16 arr[1].append(yi)
-
17 arr[2].append(zi)
-
18 res.append(arr)
-
19
-
20 return np.array(res)
-
21
-
22def update(num, lines, arr):
-
23 for line, a in zip(lines, arr):
-
24 line.set_data(a[:2, num])
-
25 line.set_3d_properties(a[2, num])
-
26
-
27
+
6
+
7def get_data(files):
+
8 res = []
+
9 for file in files:
+
10 arr = [[], [], []]
+
11 with open(file, encoding="utf8") as f:
+
12 lines = f.readlines()
+
13
+
14 for line in lines:
+
15 xi, yi, zi = map(float, line.strip().split(","))
+
16 arr[0].append(xi)
+
17 arr[1].append(yi)
+
18 arr[2].append(zi)
+
19 res.append(arr)
+
20
+
21 return np.array(res)
+
22
+
23
+
24def update(num, lines, arr):
+
25 for line, a in zip(lines, arr):
+
26 line.set_data(a[:2, num - 1 : num])
+
27 line.set_3d_properties(a[2, num])
28
-
29def animate():
-
30 plt.style.use("dark_background")
-
31 fig = plt.figure()
-
32 ax = fig.add_subplot(projection="3d")
-
33
+
29
+
30def animate():
+
31 plt.style.use("dark_background")
+
32 fig = plt.figure()
+
33 ax = fig.add_subplot(projection="3d")
34
-
35 arr = get_data([f"output/p{i}_RK4.txt" for i in range(100)])
+
35 arr = get_data([f"output/simulate_100_particles/particle_{i}.txt" for i in range(100)])
36
-
37 arr = arr[:,:,::10]
+
37 arr = arr[:, :, ::10]
38
39 N = len(arr[0][0])
40
-
41 lines = [ax.plot(*a[:,1], "o")[0] for a in arr]
+
41 lines = [ax.plot(*a[:, 1], "o")[0] for a in arr]
42
-
43 ax.set_xlim3d([-500.0, 500.0])
-
44 ax.set_xlabel('X')
-
45
-
46 ax.set_ylim3d([-500.0, 500.0])
-
47 ax.set_ylabel('Y')
-
48
-
49 ax.set_zlim3d([-500.0, 500.0])
-
50 ax.set_zlabel('Z')
-
51
-
52 ani = animation.FuncAnimation(fig, update, N, fargs=(lines, arr),
-
53 interval=1,
-
54 blit=False)
+
43 ax.set_title("100 particles inside a Penning trap")
+
44 plt.figtext(
+
45 0.5,
+
46 0.01,
+
47 "100 randomly generated particles "
+
48 "evolving over a time of 50 microseconds.",
+
49 fontsize=12,
+
50 horizontalalignment="center",
+
51 )
+
52
+
53 ax.set_xlim3d([-500.0, 500.0])
+
54 ax.set_xlabel("X (micrometers)")
55
-
56
-
57 ani.save("100_particles.gif", writer=animation.FFMpegFileWriter(fps=30))
-
58 plt.show()
-
59
-
60
-
61if __name__ == "__main__":
-
62 animate()
-
63
-
64
+
56 ax.set_ylim3d([-500.0, 500.0])
+
57 ax.set_ylabel("Y (micrometers)")
+
58
+
59 ax.set_zlim3d([-500.0, 500.0])
+
60 ax.set_zlabel("Z (micrometers)")
+
61
+
62 ani = animation.FuncAnimation(
+
63 fig, update, N, fargs=(lines, arr), interval=1, blit=False
+
64 )
+
65
+
66 # ani.save("../images/100_particles.gif", writer=animation.FFMpegFileWriter(fps=50))
+
67 plt.show()
+
68
+
69
+
70if __name__ == "__main__":
+
71 animate()
diff --git a/docs/bug.html b/docs/bug.html index bbcbbea..8ed5241 100644 --- a/docs/bug.html +++ b/docs/bug.html @@ -105,21 +105,23 @@ $(document).ready(function(){initNavTree('bug.html',''); initResizable(); });
File constants.hpp
No known bugs
File main.cpp
-
No known bugs
+
No known bugs
File Particle.cpp
-
No known bugs
+
No known bugs
File Particle.hpp
No known bugs
File PenningTrap.cpp
-
No known bugs
+
No known bugs
File PenningTrap.hpp
No known bugs
File test_suite.cpp
-
No known bugs
-
File utils.cpp
No known bugs
+
File typedefs.hpp
+
No known bugs
+
File utils.cpp
+
No known bugs
File utils.hpp
-
No known bugs
+
No known bugs
diff --git a/docs/classParticle-members.html b/docs/classParticle-members.html index 02f2b23..b3fc92b 100644 --- a/docs/classParticle-members.html +++ b/docs/classParticle-members.html @@ -105,11 +105,11 @@ $(document).ready(function(){initNavTree('classParticle.html',''); initResizable

This is the complete list of members for Particle, including all inherited members.

- + - - + +
mParticleprivate
Particle(double q, double m, arma::vec::fixed< 3 > r_vec, arma::vec::fixed< 3 > v_vec)Particle
Particle(double q, double m, vec_3d r_vec, vec_3d v_vec)Particle
PenningTrapParticlefriend
qParticleprivate
r_vecParticleprivate
v_vecParticleprivate
r_vecParticleprivate
v_vecParticleprivate
diff --git a/docs/classParticle.html b/docs/classParticle.html index 997eb37..271a213 100644 --- a/docs/classParticle.html +++ b/docs/classParticle.html @@ -114,9 +114,9 @@ $(document).ready(function(){initNavTree('classParticle.html',''); initResizable - - - + + +

Public Member Functions

 Particle (double q, double m, arma::vec::fixed< 3 > r_vec, arma::vec::fixed< 3 > v_vec)
 Initialize the particle.
 
 Particle (double q, double m, vec_3d r_vec, vec_3d v_vec)
 Initialize the particle.
 
@@ -126,12 +126,12 @@ Private Attributes - - - - - - + + + + + +

Private Attributes

double m
 Mass.
 
arma::vec::fixed< 3 > r_vec
 position
 
arma::vec::fixed< 3 > v_vec
 velocity
 
vec_3d r_vec
 position
 
vec_3d v_vec
 velocity
 
@@ -142,10 +142,10 @@ Friends

Detailed Description

A class that holds attributes of a particle.

-

Definition at line 19 of file Particle.hpp.

+

Definition at line 21 of file Particle.hpp.

Constructor & Destructor Documentation

- -

◆ Particle()

+ +

◆ Particle()

@@ -165,13 +165,13 @@ Friends
- + - + @@ -183,9 +183,18 @@ Friends

Initialize the particle.

-

Initialize the particle with a charge, mass, position and velocity.

+

Initialize the particle with a charge, mass, position and velocity.

+
Parameters
+

Friends

arma::vec::fixed< 3 > vec_3d  r_vec,
arma::vec::fixed< 3 > vec_3d  v_vec 
+ + + + +
qThe charge of the particle
mThe mass of the particle
r_vecThe initial position of the particle
v_vecThe initial velocity of the particle
+ + -

Definition at line 16 of file Particle.cpp.

+

Definition at line 15 of file Particle.cpp.

@@ -212,7 +221,7 @@ Friends

Make private attributes available for PenningTrap.

-

Definition at line 38 of file Particle.hpp.

+

Definition at line 43 of file Particle.hpp.

@@ -239,7 +248,7 @@ Friends

Mass.

-

Definition at line 22 of file Particle.hpp.

+

Definition at line 24 of file Particle.hpp.

@@ -265,12 +274,12 @@ Friends

Charge.

-

Definition at line 21 of file Particle.hpp.

+

Definition at line 23 of file Particle.hpp.

- -

◆ r_vec

+ +

◆ r_vec

@@ -279,7 +288,7 @@ Friends - +
arma::vec::fixed<3> Particle::r_vecvec_3d Particle::r_vec
@@ -291,12 +300,12 @@ Friends

position

-

Definition at line 23 of file Particle.hpp.

+

Definition at line 25 of file Particle.hpp.

- -

◆ v_vec

+ +

◆ v_vec

@@ -305,7 +314,7 @@ Friends - +
arma::vec::fixed<3> Particle::v_vecvec_3d Particle::v_vec
@@ -317,7 +326,7 @@ Friends

velocity

-

Definition at line 24 of file Particle.hpp.

+

Definition at line 26 of file Particle.hpp.

diff --git a/docs/classParticle.js b/docs/classParticle.js index 113132c..71255c1 100644 --- a/docs/classParticle.js +++ b/docs/classParticle.js @@ -1,9 +1,9 @@ var classParticle = [ - [ "Particle", "classParticle.html#a00e108823877a25513ccae7cac011b4c", null ], + [ "Particle", "classParticle.html#a7af9f8d1fef63dd7643b06629ac7bef4", 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#af9497cd8f2dcad0fad54f571ddb383e6", null ], + [ "v_vec", "classParticle.html#a879692772803d6ab65fa4993b54aea6e", null ] ]; \ No newline at end of file diff --git a/docs/classPenningTrap-members.html b/docs/classPenningTrap-members.html index 5a26d52..859c052 100644 --- a/docs/classPenningTrap-members.html +++ b/docs/classPenningTrap-members.html @@ -107,19 +107,27 @@ $(document).ready(function(){initNavTree('classPenningTrap.html',''); initResiza add_particle(Particle particle)PenningTrap B_0PenningTrapprivate dPenningTrapprivate - evolve_forward_euler(double dt)PenningTrap - evolve_RK4(double dt)PenningTrap - external_B_field(arma::vec r)PenningTrap - external_E_field(arma::vec r)PenningTrap - force_on_particle(int i, int j)PenningTrap - get_d() (defined in PenningTrap)PenningTrap - get_particle(int i) (defined in PenningTrap)PenningTrap - particlesPenningTrapprivate - PenningTrap(double B_0=T, double V_0=25.*V/1000., double d=500.)PenningTrap - total_force(int i)PenningTrap - total_force_external(int i)PenningTrap - total_force_particles(int i)PenningTrap - V_0PenningTrapprivate + evolve_forward_euler(double dt, bool particle_interaction=true)PenningTrap + evolve_RK4(double dt, bool particle_interaction=true)PenningTrap + external_B_field(vec_3d r)PenningTrap + external_E_field(vec_3d r)PenningTrap + force_on_particle(unsigned int i, unsigned int j)PenningTrap + fraction_of_particles_left(double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)PenningTrap + k_rPenningTrapprivate + k_vPenningTrapprivate + particlesPenningTrapprivate + PenningTrap(double B_0=T, std::function< double(double)> V_0=[](double t) { return 25. *V/1000.;}, double d=500., double t=0.)PenningTrap + PenningTrap(unsigned int i, double B_0=T, std::function< double(double)> V_0=[](double t) { return 25. *V/1000.;}, double d=500., double t=0.)PenningTrap + PenningTrap(std::vector< Particle > particles, double B_0=T, std::function< double(double)> V_0=[](double t) { return 25. *V/1000.;}, double d=500., double t=0.)PenningTrap + r_func(unsigned int i, unsigned int j, double dt)PenningTrapprivate + simulate(double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)PenningTrap + tPenningTrapprivate + total_force(unsigned int i)PenningTrap + total_force_external(unsigned int i)PenningTrap + total_force_particles(unsigned int i)PenningTrap + V_0PenningTrapprivate + v_func(unsigned int i, unsigned int j, double dt)PenningTrapprivate + write_simulation_to_dir(std::string path, double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)PenningTrap diff --git a/docs/classPenningTrap.html b/docs/classPenningTrap.html index af62e25..9afb617 100644 --- a/docs/classPenningTrap.html +++ b/docs/classPenningTrap.html @@ -100,6 +100,7 @@ $(document).ready(function(){initNavTree('classPenningTrap.html',''); initResiza
Public Member Functions | +Private Member Functions | Private Attributes | List of all members
PenningTrap Class Reference
@@ -113,64 +114,91 @@ $(document).ready(function(){initNavTree('classPenningTrap.html',''); initResiza - - - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Public Member Functions

 PenningTrap (double B_0=T, double V_0=25.*V/1000., double d=500.)
 Set B_0, V_0 and d.
 
 PenningTrap (double B_0=T, std::function< double(double)> V_0=[](double t) { return 25. *V/1000.;}, double d=500., double t=0.)
 Constructor for the PenningTrap class.
 
 PenningTrap (unsigned int i, double B_0=T, std::function< double(double)> V_0=[](double t) { return 25. *V/1000.;}, double d=500., double t=0.)
 Constructor for the PenningTrap class.
 
 PenningTrap (std::vector< Particle > particles, double B_0=T, std::function< double(double)> V_0=[](double t) { return 25. *V/1000.;}, double d=500., double t=0.)
 Constructor for the PenningTrap class.
 
void add_particle (Particle particle)
 Add a particle to the system.
 
arma::vec external_E_field (arma::vec r)
 Calculate E at point r.
 
arma::vec external_B_field (arma::vec r)
 Calculate B at point r.
 
arma::vec force_on_particle (int i, int j)
 Calculate the force between 2 particles.
 
arma::vec total_force_external (int i)
 Calculate the total external force on a particle.
 
arma::vec total_force_particles (int i)
 Calculate the total force on a particle from other particles.
 
arma::vec total_force (int i)
 calculate the total force on a particle.
 
void evolve_RK4 (double dt)
 Go forward one timestep using the RK4 method.
 
void evolve_forward_euler (double dt)
 Go forward one timestep using the forward Euler method.
 
arma::vec get_particle (int i)
 
double get_d ()
 
vec_3d external_E_field (vec_3d r)
 Calculate E at point r.
 
vec_3d external_B_field (vec_3d r)
 Calculate B at point r.
 
vec_3d force_on_particle (unsigned int i, unsigned int j)
 Calculate the force between 2 particles.
 
vec_3d total_force_external (unsigned int i)
 Calculate the total external force on a particle.
 
vec_3d total_force_particles (unsigned int i)
 Calculate the total force on a particle p_i from other particles.
 
vec_3d total_force (unsigned int i)
 calculate the total force on a particle p_i.
 
void evolve_RK4 (double dt, bool particle_interaction=true)
 Go forward one timestep using the RK4 method.
 
void evolve_forward_euler (double dt, bool particle_interaction=true)
 Go forward one timestep using the forward Euler method.
 
sim_arr simulate (double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)
 Simulate the particle system inside the Penning trap over a certain amount of time.
 
void write_simulation_to_dir (std::string path, double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)
 Simulate and write the displacement of all particles to files.
 
double fraction_of_particles_left (double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)
 Simulate and calculate what fraction of particles are still left inside the Penning trap after the simulation.
 
+ + + + + + +

+Private Member Functions

vec_3d v_func (unsigned int i, unsigned int j, double dt)
 Helper for evolve_RK4 when calculating \(k_{v,i,j}\) values.
 
vec_3d r_func (unsigned int i, unsigned int j, double dt)
 Helper for evolve_RK4 when calculating \(k_{r,i,j}\) values.
 
- - - + + + + + + + + + +

Private Attributes

double B_0
 Magnetic field strength.
 
double V_0
 Applied potential.
 
std::function< double(double)> V_0
 Applied potential.
 
double d
 Characteristic dimension.
 
double t
 Current time.
 
std::vector< Particle > particles
 The particles in the Penning trap.
 
sim_arr k_v
 
sim_arr k_r
 

Detailed Description

A class that simulates a Penning trap.

This class simulates a Penning trap. It can take in a number of particles and simulate how they would behave inside a Penning trap.

-

Definition at line 29 of file PenningTrap.hpp.

+

Definition at line 30 of file PenningTrap.hpp.

Constructor & Destructor Documentation

- -

◆ PenningTrap()

+ +

◆ PenningTrap() [1/3]

@@ -184,14 +212,20 @@ Private Attributes - double  - V_0 = 25.*V/1000., + std::function< double(double)>  + V_0 = [](double t) { return 25. * V / 1000.; }, double  - d = 500.  + d = 500., + + + + + double  + t = 0.  @@ -201,9 +235,138 @@ Private Attributes
-

Set B_0, V_0 and d.

+

Constructor for the PenningTrap class.

+
Parameters
+ + + + + +
B_0The magnetic field strength
V_0The time dependent applied potential
dThe characteristic dimension
tThe starting time
+
+
-

Definition at line 20 of file PenningTrap.cpp.

+

Definition at line 18 of file PenningTrap.cpp.

+ +
+
+ +

◆ PenningTrap() [2/3]

+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
PenningTrap::PenningTrap (unsigned int i,
double B_0 = T,
std::function< double(double)> V_0 = [](double t) { return 25. * V / 1000.; },
double d = 500.,
double t = 0. 
)
+
+ +

Constructor for the PenningTrap class.

+
Parameters
+ + + + + + +
iThe number of particles to generate
B_0The magnetic field strength
V_0The time dependent applied potential
dThe characteristic dimension
tThe starting time
+
+
+ +

Definition at line 27 of file PenningTrap.cpp.

+ +
+
+ +

◆ PenningTrap() [3/3]

+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
PenningTrap::PenningTrap (std::vector< Particle > particles,
double B_0 = T,
std::function< double(double)> V_0 = [](double t) { return 25. * V / 1000.; },
double d = 500.,
double t = 0. 
)
+
+ +

Constructor for the PenningTrap class.

+
Parameters
+ + + + + + +
particlesThe starting particles
B_0The magnetic field strength
V_0The time dependent applied potential
dThe characteristic dimension
tThe starting time
+
+
+ +

Definition at line 39 of file PenningTrap.cpp.

@@ -225,13 +388,19 @@ Private Attributes

Add a particle to the system.

+
Parameters
+ + +
particleThe particle to add to the Penning trap
+
+
-

Definition at line 27 of file PenningTrap.cpp.

+

Definition at line 82 of file PenningTrap.cpp.

- -

◆ evolve_forward_euler()

+ +

◆ evolve_forward_euler()

@@ -240,20 +409,37 @@ Private Attributes void PenningTrap::evolve_forward_euler ( double  - dt) + dt, + + + + bool  + particle_interaction = true  + + + + ) +

Go forward one timestep using the forward Euler method.

+
Parameters
+ + + +
dtThe step length
particle_interactionTurn particle interactions on/off
+
+
-

Definition at line 167 of file PenningTrap.cpp.

+

Definition at line 186 of file PenningTrap.cpp.

- -

◆ evolve_RK4()

+ +

◆ evolve_RK4()

@@ -262,28 +448,45 @@ Private Attributes void PenningTrap::evolve_RK4 ( double  - dt) + dt, + + + + bool  + particle_interaction = true  + + + + ) +

Go forward one timestep using the RK4 method.

+
Parameters
+ + + +
dtThe step length
particle_interactionTurn particle interactions on/off
+
+
-

Definition at line 104 of file PenningTrap.cpp.

+

Definition at line 151 of file PenningTrap.cpp.

- -

◆ external_B_field()

+ +

◆ external_B_field()

- + - + @@ -291,21 +494,28 @@ Private Attributes

Calculate B at point r.

+
Parameters
+
arma::vec PenningTrap::external_B_field vec_3d PenningTrap::external_B_field (arma::vec vec_3d  r)
+ +
rThe position where we want to calculate the B field
+ + +
Returns
vec_3d
-

Definition at line 43 of file PenningTrap.cpp.

+

Definition at line 95 of file PenningTrap.cpp.

- -

◆ external_E_field()

+ +

◆ external_E_field()

- + - + @@ -313,27 +523,34 @@ Private Attributes

Calculate E at point r.

+
Parameters
+
arma::vec PenningTrap::external_E_field vec_3d PenningTrap::external_E_field (arma::vec vec_3d  r)
+ +
rThe position where we want to calculate the E field
+ + +
Returns
vec_3d
-

Definition at line 32 of file PenningTrap.cpp.

+

Definition at line 87 of file PenningTrap.cpp.

- -

◆ force_on_particle()

+ +

◆ force_on_particle()

- + - + - + @@ -345,83 +562,222 @@ Private Attributes

Calculate the force between 2 particles.

-

Calculate the force exhibited on particle p_i from particle p_j.

+

Calculate the force exhibited on particle p_i from particle p_j.

+
Parameters
+
arma::vec PenningTrap::force_on_particle vec_3d PenningTrap::force_on_particle (int unsigned int  i,
int unsigned int  j 
+ + +
iThe index of particle p_i
jThe index of particle p_j
+ + +
Returns
vec_3d
-

Definition at line 50 of file PenningTrap.cpp.

+

Definition at line 100 of file PenningTrap.cpp.

- -

◆ get_d()

+ +

◆ fraction_of_particles_left()

- + - + + + + + + + + + + + + + + + + + + + + + + + +
double PenningTrap::get_d double PenningTrap::fraction_of_particles_left ()double time,
unsigned int steps,
std::string method = "rk4",
bool particle_interaction = true 
)
-

Definition at line 188 of file PenningTrap.cpp.

+

Simulate and calculate what fraction of particles are still left inside the Penning trap after the simulation.

+
Parameters
+ + + + + +
timeThe time to simulate in microseconds
stepsThe amount of steps for the whole simulation
methodThe method to use when moving forward a timestep
particle_interactionTurn particle interactions on/off
+
+
+
Returns
double
+ +

Definition at line 266 of file PenningTrap.cpp.

- -

◆ get_particle()

+ +

◆ r_func()

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + +
vec_3d PenningTrap::r_func (unsigned int i,
unsigned int j,
double dt 
)
+ 		+private
+
+ +

Helper for evolve_RK4 when calculating \(k_{r,i,j}\) values.

+

Something

+
Parameters
+ + + + +
iIndex i for \(k_{r,i,j}\)
jIndex j for \(k_{r,i,j}\)
dtthe step length (delta time)
+
+
+
Returns
vec_3d
+ +

Definition at line 64 of file PenningTrap.cpp.

+ +
+
+ +

◆ simulate()

- + - + + + + + + + + + + + + + + + + + + + + + + + + + + +
arma::vec PenningTrap::get_particle sim_arr PenningTrap::simulate (int double time,
unsigned int steps,
std::string method = "rk4",
bool particle_interaction = true 
)
+
+ +

Simulate the particle system inside the Penning trap over a certain amount of time.

+
Parameters
+ + + + + +
timeThe time to simulate in microseconds
stepsThe amount of steps for the whole simulation
methodThe method to use when moving forward a timestep
particle_interactionTurn particle interactions on/off
+
+
+ +

Definition at line 211 of file PenningTrap.cpp.

+ +
+
+ +

◆ total_force()

+ +
+
+ + + + +
vec_3d PenningTrap::total_force (unsigned int  i)
-

Definition at line 183 of file PenningTrap.cpp.

+

calculate the total force on a particle p_i.

+
Parameters
+ + +
iThe index of particle p_i
+
+
+
Returns
vec_3d
+ +

Definition at line 146 of file PenningTrap.cpp.

- -

◆ total_force()

+ +

◆ total_force_external()

- + - - - - -
arma::vec PenningTrap::total_force vec_3d PenningTrap::total_force_external (int i)
-
- -

calculate the total force on a particle.

- -

Definition at line 99 of file PenningTrap.cpp.

- -
-
- -

◆ total_force_external()

- -
-
- - - - - + @@ -429,31 +785,161 @@ Private Attributes

Calculate the total external force on a particle.

-

Calculate the total amount of force that E and B exhibits on particle p_i.

+

Calculate the total amount of force that E and B exhibits on particle p_i.

+
Parameters
+
arma::vec PenningTrap::total_force_external (int unsigned int  i)
+ +
iThe index of particle p_i
+ + +
Returns
vec_3d
-

Definition at line 65 of file PenningTrap.cpp.

+

Definition at line 114 of file PenningTrap.cpp.

- -

◆ total_force_particles()

+ +

◆ total_force_particles()

- + - +
arma::vec PenningTrap::total_force_particles vec_3d PenningTrap::total_force_particles (int unsigned int  i)
-

Calculate the total force on a particle from other particles.

+

Calculate the total force on a particle p_i from other particles.

+
Parameters
+ + +
iThe index of particle p_i
+
+
+
Returns
vec_3d
-

Definition at line 80 of file PenningTrap.cpp.

+

Definition at line 129 of file PenningTrap.cpp.

+ +
+
+ +

◆ v_func()

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + +
vec_3d PenningTrap::v_func (unsigned int i,
unsigned int j,
double dt 
)
+ 		+private
+
+ +

Helper for evolve_RK4 when calculating \(k_{v,i,j}\) values.

+

Something

+
Parameters
+ + + + +
iIndex i for \(k_{v,i,j}\)
jIndex j for \(k_{v,i,j}\)
dtthe step length (delta time)
+
+
+
Returns
vec_3d
+ +

Definition at line 46 of file PenningTrap.cpp.

+ +
+
+ +

◆ write_simulation_to_dir()

+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
void PenningTrap::write_simulation_to_dir (std::string path,
double time,
unsigned int steps,
std::string method = "rk4",
bool particle_interaction = true 
)
+
+ +

Simulate and write the displacement of all particles to files.

+
Parameters
+ + + + + + +
pathThe directory to save the data
timeThe time to simulate in microseconds
stepsThe amount of steps for the whole simulation
methodThe method to use when moving forward a timestep
particle_interactionTurn particle interactions on/off
+
+
+ +

Definition at line 240 of file PenningTrap.cpp.

@@ -480,7 +966,7 @@ Private Attributes

Magnetic field strength.

-

Definition at line 31 of file PenningTrap.hpp.

+

Definition at line 32 of file PenningTrap.hpp.

@@ -506,7 +992,57 @@ Private Attributes

Characteristic dimension.

-

Definition at line 33 of file PenningTrap.hpp.

+

Definition at line 34 of file PenningTrap.hpp.

+ + + + +

◆ k_r

+ +
+
+ + + + + +
+ + + + +
sim_arr PenningTrap::k_r
+ 		+private
+
+

A 2D vector containing all \(k_{i,j}\) where \(j\) is the index of a particle

+ +

Definition at line 39 of file PenningTrap.hpp.

+ +
+
+ +

◆ k_v

+ +
+
+ + + + + +
+ + + + +
sim_arr PenningTrap::k_v
+ 		+private
+
+

A 2D vector containing all \(k_{i,j}\) where \(j\) is the index of a particle

+ +

Definition at line 37 of file PenningTrap.hpp.

@@ -532,12 +1068,12 @@ Private Attributes

The particles in the Penning trap.

-

Definition at line 34 of file PenningTrap.hpp.

+

Definition at line 36 of file PenningTrap.hpp.

- -

◆ V_0

+ +

◆ t

@@ -546,7 +1082,33 @@ Private Attributes - + + +
double PenningTrap::V_0double PenningTrap::t
+ + +private + + +
+ +

Current time.

+ +

Definition at line 35 of file PenningTrap.hpp.

+ +
+
+ +

◆ V_0

+ +
+
+ + + @@ -558,7 +1120,7 @@ Private Attributes

Applied potential.

-

Definition at line 32 of file PenningTrap.hpp.

+

Definition at line 33 of file PenningTrap.hpp.

diff --git a/docs/classPenningTrap.js b/docs/classPenningTrap.js index 743d3ea..0fd7f36 100644 --- a/docs/classPenningTrap.js +++ b/docs/classPenningTrap.js @@ -1,17 +1,27 @@ var classPenningTrap = [ - [ "PenningTrap", "classPenningTrap.html#a81add5063bd5f29d77f0b5c299c6c560", null ], + [ "PenningTrap", "classPenningTrap.html#ae670d7de621acdb343b01af098086f63", null ], + [ "PenningTrap", "classPenningTrap.html#a763700316b502d5900e587c1f61e6bf1", null ], + [ "PenningTrap", "classPenningTrap.html#a67139e04ef69c0bcffde8f30f67cbf73", 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#acbf065c9c125682329ad82a8d166554c", null ], + [ "external_E_field", "classPenningTrap.html#a1d58feaa2c9e34cbf26b1c5ed75ca9d9", null ], + [ "force_on_particle", "classPenningTrap.html#a9ae34ad740a230e667e96bc6ee8730ce", null ], + [ "fraction_of_particles_left", "classPenningTrap.html#a0194be61c956a9259c747c23e4163c5b", null ], + [ "r_func", "classPenningTrap.html#a43e74792ab4b3f9299f35cb64bdb2648", null ], + [ "simulate", "classPenningTrap.html#a5331837e6dd7bce807a99edd2ba7e854", null ], + [ "total_force", "classPenningTrap.html#a1f668c4433421136ad51741741aa1bc8", null ], + [ "total_force_external", "classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56", null ], + [ "total_force_particles", "classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b", null ], + [ "v_func", "classPenningTrap.html#af98a720da60b0e1a62aefa5f5cb37c1e", null ], + [ "write_simulation_to_dir", "classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57", 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 ], - [ "V_0", "classPenningTrap.html#a715329844d75ec4c04f8391421fb4e89", null ] + [ "t", "classPenningTrap.html#a8ca4e21291f60fde619c14099d8c4e8e", null ], + [ "V_0", "classPenningTrap.html#aaf105828121c4a33cc2b217453c20317", null ] ]; \ No newline at end of file diff --git a/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html b/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html index 81efd6b..4313bbd 100644 --- a/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html +++ b/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html @@ -115,6 +115,8 @@ Files + + diff --git a/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.js b/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.js index 13a8a58..64ce7a5 100644 --- a/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.js +++ b/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.js @@ -4,6 +4,7 @@ var dir_68267d1309a1af8e8297ef4c3efbcdba = [ "main.cpp", "main_8cpp.html", null ], [ "Particle.cpp", "Particle_8cpp.html", null ], [ "PenningTrap.cpp", "PenningTrap_8cpp.html", null ], + [ "plot_particles_left.py", "plot__particles__left_8py_source.html", null ], [ "test_suite.cpp", "test__suite_8cpp.html", "test__suite_8cpp" ], [ "utils.cpp", "utils_8cpp.html", "utils_8cpp" ] ]; \ No newline at end of file diff --git a/docs/dir_d44c64559bbebec7f509842c48db8b23.html b/docs/dir_d44c64559bbebec7f509842c48db8b23.html index 21e883c..289eee3 100644 --- a/docs/dir_d44c64559bbebec7f509842c48db8b23.html +++ b/docs/dir_d44c64559bbebec7f509842c48db8b23.html @@ -113,6 +113,9 @@ Files + + + diff --git a/docs/dir_d44c64559bbebec7f509842c48db8b23.js b/docs/dir_d44c64559bbebec7f509842c48db8b23.js index 48feb88..192eaa8 100644 --- a/docs/dir_d44c64559bbebec7f509842c48db8b23.js +++ b/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" ] ]; \ No newline at end of file diff --git a/docs/files.html b/docs/files.html index b07cc8d..e842a47 100644 --- a/docs/files.html +++ b/docs/files.html @@ -107,14 +107,16 @@ $(document).ready(function(){initNavTree('files.html',''); initResizable(); }); - - - - - - - - + + + + + + + + + +
+ + +
std::function<double(double)> PenningTrap::V_0
file  PenningTrap.cpp [code]
 The implementation of the PenningTrap class.
 
file  plot_particles_left.py [code]
 
file  test_suite.cpp [code]
 The test suite for the project.
 
file  PenningTrap.hpp [code]
 A class for simulating a Penning trap.
 
file  typedefs.hpp [code]
 Useful typedefs for cleaner code.
 
file  utils.hpp [code]
 Function prototypes and macros that are useful.
 
 constants.hppLibrary of constants
 Particle.hppA class that holds the properties of a particle
 PenningTrap.hppA class for simulating a Penning trap
 utils.hppFunction prototypes and macros that are useful
 ▼ src
 animate_100_particles.py
 main.cppThe main program for this project
 Particle.cppThe implementation of the Particle class
 PenningTrap.cppThe implementation of the PenningTrap class
 test_suite.cppThe test suite for the project
 utils.cppImplementation of the utils
 typedefs.hppUseful typedefs for cleaner code
 utils.hppFunction prototypes and macros that are useful
 ▼ src
 animate_100_particles.py
 main.cppThe main program for this project
 Particle.cppThe implementation of the Particle class
 PenningTrap.cppThe implementation of the PenningTrap class
 plot_particles_left.py
 test_suite.cppThe test suite for the project
 utils.cppImplementation of the utils
diff --git a/docs/functions.html b/docs/functions.html index eb473bb..a2f04ea 100644 --- a/docs/functions.html +++ b/docs/functions.html @@ -102,22 +102,30 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
  • add_particle() : PenningTrap
  • B_0 : PenningTrap
  • d : PenningTrap
    • -
  • evolve_forward_euler() : PenningTrap
    • -
  • evolve_RK4() : PenningTrap
    • -
  • external_B_field() : PenningTrap
    • -
  • external_E_field() : PenningTrap
    • -
  • force_on_particle() : PenningTrap
    • +
  • evolve_forward_euler() : PenningTrap
    • +
  • evolve_RK4() : PenningTrap
    • +
  • external_B_field() : PenningTrap
    • +
  • external_E_field() : PenningTrap
    • +
  • force_on_particle() : PenningTrap
    • +
  • fraction_of_particles_left() : PenningTrap
    • +
  • k_r : PenningTrap
    • +
  • k_v : PenningTrap
  • m : Particle
    • -
  • Particle() : Particle
    • +
  • Particle() : Particle
  • particles : PenningTrap
    • -
  • PenningTrap : Particle, PenningTrap
    • +
  • PenningTrap : Particle, PenningTrap
  • q : Particle
    • -
  • r_vec : Particle
    • -
  • total_force() : PenningTrap
    • -
  • total_force_external() : PenningTrap
    • -
  • total_force_particles() : PenningTrap
    • -
  • V_0 : PenningTrap
    • -
  • v_vec : Particle
    • +
  • r_func() : PenningTrap
    • +
  • r_vec : Particle
    • +
  • simulate() : PenningTrap
    • +
  • t : PenningTrap
    • +
  • total_force() : PenningTrap
    • +
  • total_force_external() : PenningTrap
    • +
  • total_force_particles() : PenningTrap
    • +
  • V_0 : PenningTrap
    • +
  • v_func() : PenningTrap
    • +
  • v_vec : Particle
    • +
  • write_simulation_to_dir() : PenningTrap
    • diff --git a/docs/functions_func.html b/docs/functions_func.html index 4a36dd3..1182b1d 100644 --- a/docs/functions_func.html +++ b/docs/functions_func.html @@ -100,16 +100,21 @@ $(document).ready(function(){initNavTree('functions_func.html',''); initResizabl
     
    diff --git a/docs/functions_vars.html b/docs/functions_vars.html index 8c0729a..3ca2e5b 100644 --- a/docs/functions_vars.html +++ b/docs/functions_vars.html @@ -101,12 +101,15 @@ $(document).ready(function(){initNavTree('functions_vars.html',''); initResizabl   diff --git a/docs/globals.html b/docs/globals.html index 9107eef..19a9638 100644 --- a/docs/globals.html +++ b/docs/globals.html @@ -99,14 +99,20 @@ $(document).ready(function(){initNavTree('globals.html',''); initResizable(); })
    Here is a list of all documented file members with links to the documentation:
    diff --git a/docs/globals_defs.html b/docs/globals_defs.html index 332fce0..c7eb483 100644 --- a/docs/globals_defs.html +++ b/docs/globals_defs.html @@ -99,6 +99,7 @@ $(document).ready(function(){initNavTree('globals_defs.html',''); initResizable(
     
    diff --git a/docs/globals_type.html b/docs/globals_type.html new file mode 100644 index 0000000..b7735cc --- /dev/null +++ b/docs/globals_type.html @@ -0,0 +1,116 @@ + + + + + + + +Penning Trap Simulation: File Members + + + + + + + + + + + + + + + + +
    +
    + + + + + + +
    +
    Penning Trap Simulation +
    +
    Simulate particle behavior inside a Penning Trap
    +
    +
    + + + + + + + +
    +
    + +
    +
    +
    + +
    + +
    +
    + + +
    +
    +
    +
    +
    +
    Loading...
    +
    Searching...
    +
    No Matches
    +
    +
    +
    +
    + +
    +  +
    +
    + + + + diff --git a/docs/main_8cpp.html b/docs/main_8cpp.html index 5e67722..b83f224 100644 --- a/docs/main_8cpp.html +++ b/docs/main_8cpp.html @@ -100,17 +100,22 @@ $(document).ready(function(){initNavTree('main_8cpp.html',''); initResizable();
    Macros | -Functions
    +Functions | +Variables
    main.cpp File Reference

    The main program for this project. More...

    -
    #include <fstream>
    +
    #include <cmath>
    +#include <fstream>
    #include <omp.h>
    +#include <string>
    #include <sys/stat.h>
    +#include <vector>
    #include "PenningTrap.hpp"
    +#include "utils.hpp"

    Go to the source code of this file.

    @@ -127,10 +132,27 @@ Macros
    + + + + + + + + +

    Functions

    void simulate_single_particle ()
     
    void simulate_two_particles ()
     
    void simulate_single_particle_with_different_steps ()
     
    void simulate_100_particles ()
     
    void simulate_100_particles_with_time_potential ()
     
    int main ()
     
    + + + + +

    +Variables

    +Particle p1 (CHARGE, MASS, vec_3d{20., 0., 20.}, vec_3d{0., 25., 0.})
     
    +Particle p2 (CHARGE, MASS, vec_3d{25., 25., 0.}, vec_3d{0., 40., 5.})
     

    Detailed Description

    The main program for this project.

    @@ -138,7 +160,7 @@ Functions
    Janita Ovidie Sandtrøen Willumsen (janitaws)
    Version
    0.1
    -
    Bug:
    No known bugs
    +
    Bug:
    No known bugs

    Definition in file main.cpp.

    Macro Definition Documentation

    @@ -154,7 +176,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 21 of file main.cpp.

    +

    Definition at line 25 of file main.cpp.

    @@ -170,7 +192,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 22 of file main.cpp.

    +

    Definition at line 26 of file main.cpp.

    @@ -186,7 +208,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 20 of file main.cpp.

    +

    Definition at line 24 of file main.cpp.

    @@ -202,7 +224,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 19 of file main.cpp.

    +

    Definition at line 23 of file main.cpp.

    @@ -222,7 +244,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 77 of file main.cpp.

    +

    Definition at line 124 of file main.cpp.

    @@ -241,7 +263,83 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 24 of file main.cpp.

    +

    Definition at line 77 of file main.cpp.

    + +
    + + +

    ◆ simulate_100_particles_with_time_potential()

    + +
    +
    + + + + + + + +
    void simulate_100_particles_with_time_potential ()
    +
    + +

    Definition at line 91 of file main.cpp.

    + +
    +
    + +

    ◆ simulate_single_particle()

    + +
    +
    + + + + + + + +
    void simulate_single_particle ()
    +
    + +

    Definition at line 31 of file main.cpp.

    + +
    +
    + +

    ◆ simulate_single_particle_with_different_steps()

    + +
    +
    + + + + + + + +
    void simulate_single_particle_with_different_steps ()
    +
    + +

    Definition at line 55 of file main.cpp.

    + +
    +
    + +

    ◆ simulate_two_particles()

    + +
    +
    + + + + + + + +
    void simulate_two_particles ()
    +
    + +

    Definition at line 42 of file main.cpp.

    diff --git a/docs/main_8cpp_source.html b/docs/main_8cpp_source.html index 5542b5a..d437689 100644 --- a/docs/main_8cpp_source.html +++ b/docs/main_8cpp_source.html @@ -102,87 +102,149 @@ $(document).ready(function(){initNavTree('main_8cpp_source.html',''); initResiza
    Go to the documentation of this file.
    1
    -
    13#include <fstream>
    -
    14#include <omp.h>
    -
    15#include <sys/stat.h>
    -
    16
    -
    17#include "PenningTrap.hpp"
    -
    18
    -
    19#define PARTICLES 100
    -
    20#define N 10000
    -
    21#define CHARGE 1.
    -
    22#define MASS 40. // unit: amu
    -
    23
    -
    24void simulate_100_particles()
    -
    25{
    -
    26 PenningTrap trap;
    +
    13#include <cmath>
    +
    14#include <fstream>
    +
    15#include <omp.h>
    +
    16#include <string>
    +
    17#include <sys/stat.h>
    +
    18#include <vector>
    +
    19
    +
    20#include "PenningTrap.hpp"
    +
    21#include "utils.hpp"
    +
    22
    +
    23#define PARTICLES 100
    +
    24#define N 10000
    +
    25#define CHARGE 1.
    +
    26#define MASS 40. // unit: amu
    27
    -
    28 // Add particles inside trap
    -
    29 for (int i = 0; i < PARTICLES; i++) {
    -
    30 arma::vec r = arma::vec(3).randn() * 0.1 *
    -
    31 trap.get_d(); // random initial position
    -
    32 arma::vec v = arma::vec(3).randn() * 0.1 *
    -
    33 trap.get_d(); // random initial velocity
    -
    34 trap.add_particle(Particle(CHARGE, MASS, r, v));
    -
    35 }
    -
    36
    -
    37 double time = 50.; // microseconds
    -
    38 double dt = time / (double)N;
    -
    39
    -
    40 auto res = new arma::vec::fixed<3>[PARTICLES][N];
    +
    28Particle p1(CHARGE, MASS, vec_3d{20., 0., 20.}, vec_3d{0., 25., 0.});
    +
    29Particle p2(CHARGE, MASS, vec_3d{25., 25., 0.}, vec_3d{0., 40., 5.});
    +
    30
    +
    31void simulate_single_particle()
    +
    32{
    +
    33 DEBUG("Inside single particle sim");
    +
    34 PenningTrap trap(std::vector<Particle>{p1});
    +
    35
    +
    36 double time = 50.; // microseconds
    +
    37
    +
    38 DEBUG("Write to dir");
    +
    39 trap.write_simulation_to_dir("output/simulate_single_particle", time, N);
    +
    40}
    41
    -
    42 int counter = 0;
    -
    43
    -
    44 // Get the path of all particles
    -
    45 for (int j = 0; j < N; j++) {
    -
    46#pragma omp parallel for
    -
    47 for (int i = 0; i < PARTICLES; i++) {
    -
    48 res[i][j] = trap.get_particle(i);
    -
    49 }
    -
    50 trap.evolve_RK4(dt);
    -
    51 }
    -
    52
    -
    53 std::cout << counter << std::endl;
    +
    42void simulate_two_particles()
    +
    43{
    +
    44 PenningTrap trap_no_interaction(std::vector<Particle>{p1, p2});
    +
    45 PenningTrap trap_with_interaction(std::vector<Particle>{p1, p2});
    +
    46
    +
    47 double time = 50.; // microseconds
    +
    48
    +
    49 trap_no_interaction.write_simulation_to_dir(
    +
    50 "output/simulate_2_particles/no_interaction", time, N, "rk4", false);
    +
    51 trap_with_interaction.write_simulation_to_dir(
    +
    52 "output/simulate_2_particles/with_interaction", time, N);
    +
    53}
    54
    -
    55 arma::vec::fixed<3> *cur_row;
    -
    56 arma::vec::fixed<3> cur_elem;
    +
    55void simulate_single_particle_with_different_steps()
    +
    56{
    57
    -
    58 mkdir("output", 0777);
    -
    59 mkdir("output/simulate_100_particles", 0777);
    -
    60
    -
    61 std::ofstream ofile;
    -
    62
    -
    63// Write particle paths to file
    -
    64#pragma omp parallel for private(cur_row, cur_elem, ofile)
    -
    65 for (int i = 0; i < PARTICLES; i++) {
    -
    66 cur_row = res[i];
    -
    67 ofile.open("output/simulate_100_particles/p" + std::to_string(i) + ".txt");
    -
    68 for (int j = 0; j < N; j++) {
    -
    69 cur_elem = cur_row[j];
    -
    70 ofile << cur_elem(0) << "," << cur_elem(1) << "," << cur_elem(2)
    -
    71 << "\n";
    -
    72 }
    -
    73 ofile.close();
    +
    58 double time = 50; // microseconds
    +
    59
    +
    60 for (int i = 0; i < 4; i++) {
    +
    61 int steps = 4000 * (i + 1);
    +
    62 PenningTrap trap(std::vector<Particle>{p1});
    +
    63 trap.write_simulation_to_dir("output/N_steps/RK4/" +
    +
    64 std::to_string(steps) + "_steps",
    +
    65 time, steps, "rk4", false);
    +
    66 }
    +
    67
    +
    68 for (int i = 0; i < 4; i++) {
    +
    69 int steps = 4000 * (i + 1);
    +
    70 PenningTrap trap(std::vector<Particle>{p1});
    +
    71 trap.write_simulation_to_dir("output/N_steps/euler/" +
    +
    72 std::to_string(steps) + "_steps",
    +
    73 time, steps, "euler", false);
    74 }
    75}
    76
    -
    77int main()
    +
    77void simulate_100_particles()
    78{
    -
    79 double start = omp_get_wtime();
    -
    80
    -
    81 simulate_100_particles();
    -
    82
    -
    83 double end = omp_get_wtime();
    -
    84
    -
    85 std::cout << "Time: " << end - start << " seconds" << std::endl;
    -
    86
    -
    87 return 0;
    -
    88}
    +
    79 PenningTrap trap((unsigned)100, T,
    +
    80 [](double t) {
    +
    81 return 25. * V / 1000. *
    +
    82 (1. + .4 * std::cos(1.5 * t));
    +
    83 },
    +
    84 500., 0);
    +
    85
    +
    86 double time = 500.; // microseconds
    +
    87
    +
    88 trap.write_simulation_to_dir("output/simulate_100_particles", time, N*5);
    +
    89}
    +
    90
    +
    91void simulate_100_particles_with_time_potential()
    +
    92{
    +
    93 double amplitudes[]{.1, .4, .7};
    +
    94
    +
    95 double freq_start = .2;
    +
    96 double freq_end = 2.5;
    +
    97 double freq_increment = .02;
    +
    98 size_t freq_iterations = (size_t) ((freq_end - freq_start) / freq_increment);
    +
    99
    +
    100 std::string path = "output/time_dependent_potential/";
    +
    101 mkpath(path);
    +
    102
    +
    103 std::ofstream ofile;
    +
    104
    +
    105 for (double f : amplitudes) {
    +
    106 ofile.open(path + "f_" + std::to_string(f) + ".txt");
    +
    107 #pragma omp parallel for ordered schedule(static, 1)
    +
    108 for (size_t i=0; i < freq_iterations; i++) {
    +
    109 double freq = freq_start + i*freq_increment;
    +
    110 PenningTrap trap((unsigned)100, T,
    +
    111 [f, freq](double t) {
    +
    112 return (25. * V / 1000.) *
    +
    113 (1. + f * std::cos(freq * t));
    +
    114 },
    +
    115 500., 0.);
    +
    116 double res = trap.fraction_of_particles_left(500., 40000, "rk4", true);
    +
    117 #pragma omp ordered
    +
    118 ofile << freq << "," << res << "\n";
    +
    119 }
    +
    120 ofile.close();
    +
    121 }
    +
    122}
    +
    123
    +
    124int main()
    +
    125{
    +
    126
    +
    127 simulate_single_particle();
    +
    128
    +
    129 simulate_two_particles();
    +
    130
    +
    131 simulate_single_particle_with_different_steps();
    +
    132
    +
    133 double start = omp_get_wtime();
    +
    134
    +
    135 //simulate_100_particles();
    +
    136
    +
    137 simulate_100_particles_with_time_potential();
    +
    138
    +
    139 double end = omp_get_wtime();
    +
    140
    +
    141 std::cout << "Time: " << end - start << " seconds" << std::endl;
    +
    142
    +
    143 return 0;
    +
    144}
    PenningTrap.hpp
    A class for simulating a Penning trap.
    -
    Particle
    A class that holds attributes of a particle.
    Definition: Particle.hpp:19
    -
    PenningTrap
    A class that simulates a Penning trap.
    Definition: PenningTrap.hpp:29
    -
    PenningTrap::add_particle
    void add_particle(Particle particle)
    Add a particle to the system.
    Definition: PenningTrap.cpp:27
    -
    PenningTrap::evolve_RK4
    void evolve_RK4(double dt)
    Go forward one timestep using the RK4 method.
    Definition: PenningTrap.cpp:104
    +
    Particle
    A class that holds attributes of a particle.
    Definition: Particle.hpp:21
    +
    PenningTrap
    A class that simulates a Penning trap.
    Definition: PenningTrap.hpp:30
    +
    PenningTrap::fraction_of_particles_left
    double fraction_of_particles_left(double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)
    Simulate and calculate what fraction of particles are still left inside the Penning trap after the si...
    Definition: PenningTrap.cpp:266
    +
    PenningTrap::write_simulation_to_dir
    void write_simulation_to_dir(std::string path, double time, unsigned int steps, std::string method="rk4", bool particle_interaction=true)
    Simulate and write the displacement of all particles to files.
    Definition: PenningTrap.cpp:240
    +
    T
    #define T
    1 Tesla. unit:
    Definition: constants.hpp:17
    +
    V
    #define V
    1 Volt. unit:
    Definition: constants.hpp:19
    +
    vec_3d
    arma::vec::fixed< 3 > vec_3d
    Typedef for a fixed 3d arma vector.
    Definition: typedefs.hpp:36
    +
    utils.hpp
    Function prototypes and macros that are useful.
    +
    mkpath
    bool mkpath(std::string path, int mode=0777)
    Make path given.
    Definition: utils.cpp:76
    +
    DEBUG
    #define DEBUG(msg)
    Writes a debug message.
    Definition: utils.hpp:36
    diff --git a/docs/menudata.js b/docs/menudata.js index 88ec31f..74c1d7b 100644 --- a/docs/menudata.js +++ b/docs/menudata.js @@ -38,4 +38,5 @@ var menudata={children:[ {text:"File Members",url:"globals.html",children:[ {text:"All",url:"globals.html"}, {text:"Functions",url:"globals_func.html"}, +{text:"Typedefs",url:"globals_type.html"}, {text:"Macros",url:"globals_defs.html"}]}]}]} diff --git a/docs/navtreedata.js b/docs/navtreedata.js index 10ee5ad..9640812 100644 --- a/docs/navtreedata.js +++ b/docs/navtreedata.js @@ -27,7 +27,6 @@ var NAVTREE = [ "Penning Trap Simulation", "index.html", [ [ "Credits", "index.html#autotoc_md1", 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 +42,7 @@ var NAVTREE = [ "File Members", "globals.html", [ [ "All", "globals.html", null ], [ "Functions", "globals_func.html", null ], + [ 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$(document).ready(function(){initNavTree('pages.html',''); initResizable(); });
    Here is a list of all related documentation pages:
    -
     Bug List
     Todo List
    diff --git a/docs/plot__particles__left_8py_source.html b/docs/plot__particles__left_8py_source.html new file mode 100644 index 0000000..c9ab258 --- /dev/null +++ b/docs/plot__particles__left_8py_source.html @@ -0,0 +1,147 @@ + + + + + + + +Penning Trap Simulation: src/plot_particles_left.py Source File + + + + + + + + + + + + + + + + +
    +
    + + + + + + +
    +
    Penning Trap Simulation +
    +
    Simulate particle behavior inside a Penning Trap
    +
    +
    + + + + + + + +
    +
    + +
    +
    +
    + +
    + +
    +
    + + +
    +
    +
    +
    +
    +
    Loading...
    +
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    +
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    +
    +
    +
    +
    + +
    +
    plot_particles_left.py
    +
    +
    +
    1import matplotlib.pyplot as plt
    +
    2
    +
    3def main():
    +
    4 files = [
    +
    5 "output/time_dependent_potential/f_0.100000.txt",
    +
    6 "output/time_dependent_potential/f_0.400000.txt",
    +
    7 "output/time_dependent_potential/f_0.700000.txt",
    +
    8 ]
    +
    9 vals = [
    +
    10 .1,
    +
    11 .4,
    +
    12 .7
    +
    13 ]
    +
    14 for i in range(3):
    +
    15 with open(files[i]) as f:
    +
    16 lines = f.readlines()
    +
    17 x = []
    +
    18 y = []
    +
    19 for line in lines:
    +
    20 a,b = line.strip().split(",")
    +
    21 x.append(float(a))
    +
    22 y.append(float(b))
    +
    23 plt.plot(x,y,label=f"amplitude: {vals[i]}")
    +
    24
    +
    25 plt.xlabel(r"$\omega_V$")
    +
    26 plt.ylabel(r"Fraction of particles left")
    +
    27 plt.title(r"The fraction of particles left in the Penning trap "
    +
    28 "after 500 microseconds for different amplitudes and frequencies")
    +
    29 plt.legend()
    +
    30 plt.show()
    +
    31
    +
    32if __name__ == "__main__":
    +
    33 main()
    +
    +
    + + + + diff --git a/docs/search/all_0.js b/docs/search/all_0.js index 4fc815a..1e5c227 100644 --- a/docs/search/all_0.js +++ b/docs/search/all_0.js @@ -1,6 +1,4 @@ var searchData= [ - ['add_5fparticle_0',['add_particle',['../classPenningTrap.html#a6e9776ff5b149f01080800716455d7c8',1,'PenningTrap']]], - ['arma_5fvector_5fclose_5fto_1',['arma_vector_close_to',['../utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772',1,'arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8): utils.cpp'],['../utils_8cpp.html#a5d2e1e032fd19614f2fbb58149a7b02a',1,'arma_vector_close_to(arma::vec &a, arma::vec &b, double tol): utils.cpp']]], - ['assert_2',['ASSERT',['../utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9',1,'utils.hpp']]] + ['_5f_5fmethod_5fname_5f_5f_0',['__METHOD_NAME__',['../utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168',1,'utils.hpp']]] ]; diff --git a/docs/search/all_1.js b/docs/search/all_1.js index 80ed042..4fc815a 100644 --- a/docs/search/all_1.js +++ b/docs/search/all_1.js @@ -1,5 +1,6 @@ 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']]], + ['arma_5fvector_5fclose_5fto_1',['arma_vector_close_to',['../utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772',1,'arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8): utils.cpp'],['../utils_8cpp.html#a5d2e1e032fd19614f2fbb58149a7b02a',1,'arma_vector_close_to(arma::vec &a, arma::vec &b, double tol): utils.cpp']]], + ['assert_2',['ASSERT',['../utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9',1,'utils.hpp']]] ]; 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    Janita Ovidie Sandtrøen Willumsen (janitaws)
    Version
    0.1
    -
    Bug:
    No known bugs
    +
    Bug:
    No known bugs

    Definition in file test_suite.cpp.

    Function Documentation

    diff --git a/docs/test__suite_8cpp_source.html b/docs/test__suite_8cpp_source.html index 3fab92c..b317c82 100644 --- a/docs/test__suite_8cpp_source.html +++ b/docs/test__suite_8cpp_source.html @@ -136,9 +136,9 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
    44 arma::vec result;
    45 arma::vec v;
    46 std::stringstream msg;
    -
    47 for (int i = 0; i < tests.size(); i++) {
    +
    47 for (size_t i = 0; i < tests.size(); i++) {
    48 v = tests.at(i).first;
    -
    49 result = trap.external_E_field(v);
    +
    49 result = trap.external_E_field(v);
    50
    51 msg.str("");
    52 msg << "Testing the external E field at (" << std::setprecision(2)
    @@ -154,7 +154,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
    62 // on position.
    63 PenningTrap trap;
    64 arma::vec expected{0., 0., T};
    -
    65 arma::vec result = trap.external_B_field(arma::vec{0., 0., 0.});
    +
    65 arma::vec result = trap.external_B_field(arma::vec{0., 0., 0.});
    66 ASSERT(arma_vector_close_to(expected, result),
    67 "Testing the external B field at (0,0,0)");
    68 }
    @@ -171,14 +171,14 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
    79
    80 // Test p0 and p1
    81 arma::vec expected{-1., 0., 0.};
    -
    82 arma::vec result = trap.force_on_particle(0, 1);
    +
    82 arma::vec result = trap.force_on_particle(0, 1);
    83 ASSERT(arma_vector_close_to(expected, result),
    84 "Testing the force on a particle at (0,0,0) from a "
    85 "particle at (1,0,0).");
    86
    87 // Test p0 and p2
    88 expected = arma::vec{0, -.024, -.032};
    -
    89 result = trap.force_on_particle(0, 2);
    +
    89 result = trap.force_on_particle(0, 2);
    90 ASSERT(arma_vector_close_to(expected, result),
    91 "Testing the force on a particle at (0,0,0) from a "
    92 "particle at (0,3,4).");
    @@ -191,7 +191,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
    99 Particle(1., 40., arma::vec{1., 2., 3.}, arma::vec{3., 4., 5.}));
    100
    101 arma::vec expected{395.58954878, -270.15871624, -57.89115348};
    -
    102 arma::vec result = trap.total_force_external(0);
    +
    102 arma::vec result = trap.total_force_external(0);
    103 ASSERT(arma_vector_close_to(expected, result),
    104 "Testing the total external force on a particle at "
    105 "(1,2,3) with velocity (3,4,5)");
    @@ -204,7 +204,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
    112 Particle(1., 40., arma::vec{0., 0., 0.}, arma::vec{0., 0., 0.}));
    113
    114 arma::vec expected{0., 0., 0.};
    -
    115 arma::vec result = trap.total_force_particles(0);
    +
    115 arma::vec result = trap.total_force_particles(0);
    116 ASSERT(arma_vector_close_to(expected, result),
    117 "Testing the total force of all particles on particle 0 "
    118 "with only a single particle");
    @@ -217,7 +217,7 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
    125 Particle(1., 40., arma::vec{0., 0., 1.}, arma::vec{0., 0., 0.}));
    126
    127 expected = arma::vec(3, arma::fill::value(-3473.383325));
    -
    128 result = trap.total_force_particles(0);
    +
    128 result = trap.total_force_particles(0);
    129 ASSERT(arma_vector_close_to(expected, result),
    130 "Testing the total force of all particles on particle 0 "
    131 "with 3 other particles.");
    @@ -234,18 +234,18 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
    142 return 0;
    143}
    PenningTrap.hpp
    A class for simulating a Penning trap.
    -
    Particle
    A class that holds attributes of a particle.
    Definition: Particle.hpp:19
    +
    Particle
    A class that holds attributes of a particle.
    Definition: Particle.hpp:21
    PenningTrapTest
    Definition: test_suite.cpp:20
    -
    PenningTrap
    A class that simulates a Penning trap.
    Definition: PenningTrap.hpp:29
    -
    PenningTrap::total_force_external
    arma::vec total_force_external(int i)
    Calculate the total external force on a particle.
    Definition: PenningTrap.cpp:65
    -
    PenningTrap::total_force_particles
    arma::vec total_force_particles(int i)
    Calculate the total force on a particle from other particles.
    Definition: PenningTrap.cpp:80
    -
    PenningTrap::external_B_field
    arma::vec external_B_field(arma::vec r)
    Calculate B at point r.
    Definition: PenningTrap.cpp:43
    -
    PenningTrap::force_on_particle
    arma::vec force_on_particle(int i, int j)
    Calculate the force between 2 particles.
    Definition: PenningTrap.cpp:50
    -
    PenningTrap::add_particle
    void add_particle(Particle particle)
    Add a particle to the system.
    Definition: PenningTrap.cpp:27
    -
    PenningTrap::external_E_field
    arma::vec external_E_field(arma::vec r)
    Calculate E at point r.
    Definition: PenningTrap.cpp:32
    +
    PenningTrap
    A class that simulates a Penning trap.
    Definition: PenningTrap.hpp:30
    +
    PenningTrap::external_E_field
    vec_3d external_E_field(vec_3d r)
    Calculate E at point r.
    Definition: PenningTrap.cpp:87
    +
    PenningTrap::total_force_particles
    vec_3d total_force_particles(unsigned int i)
    Calculate the total force on a particle p_i from other particles.
    Definition: PenningTrap.cpp:129
    +
    PenningTrap::add_particle
    void add_particle(Particle particle)
    Add a particle to the system.
    Definition: PenningTrap.cpp:82
    +
    PenningTrap::force_on_particle
    vec_3d force_on_particle(unsigned int i, unsigned int j)
    Calculate the force between 2 particles.
    Definition: PenningTrap.cpp:100
    +
    PenningTrap::external_B_field
    vec_3d external_B_field(vec_3d r)
    Calculate B at point r.
    Definition: PenningTrap.cpp:95
    +
    PenningTrap::total_force_external
    vec_3d total_force_external(unsigned int i)
    Calculate the total external force on a particle.
    Definition: PenningTrap.cpp:114
    T
    #define T
    1 Tesla. unit:
    Definition: constants.hpp:17
    utils.hpp
    Function prototypes and macros that are useful.
    -
    arma_vector_close_to
    bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8)
    Test if two armadillo vectors are close to each other.
    Definition: utils.cpp:59
    +
    arma_vector_close_to
    bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8)
    Test if two armadillo vectors are close to each other.
    Definition: utils.cpp:62
    ASSERT
    #define ASSERT(expr, msg)
    A prettier assertion function.
    Definition: utils.hpp:45
    diff --git a/docs/typedefs_8hpp.html b/docs/typedefs_8hpp.html new file mode 100644 index 0000000..1f2eedb --- /dev/null +++ b/docs/typedefs_8hpp.html @@ -0,0 +1,222 @@ + + + + + + + +Penning Trap Simulation: include/typedefs.hpp File Reference + + + + + + + + + + + + + + + + +
    +
    + + + + + + +
    +
    Penning Trap Simulation +
    +
    Simulate particle behavior inside a Penning Trap
    +
    +
    + + + + + + + +
    +
    + +
    +
    +
    + +
    + +
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    + + +
    +
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    +
    +
    Loading...
    +
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    +
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    +
    +
    +
    +
    + +
    +
    +Typedefs
    +
    typedefs.hpp File Reference
    +
    +
    + +

    Useful typedefs for cleaner code. +More...

    +
    #include <vector>
    +#include <armadillo>
    +
    +

    Go to the source code of this file.

    + + + + + + + + + + + + + + +

    +Typedefs

    typedef std::vector< arma::vec::fixed< 3 > > sim_cols
     Typedef for the column of the result vector from simulating particles.
     
    typedef std::vector< arma::vec::fixed< 3 > > sim_rows
     Typedef for the row of the result vector from simulating particles.
     
    typedef std::vector< sim_cols > sim_arr
     Typedef for the result of the simulate method.
     
    typedef arma::vec::fixed< 3 > vec_3d
     Typedef for a fixed 3d arma vector.
     
    +

    Detailed Description

    +

    Useful typedefs for cleaner code.

    +
    Author
    Cory Alexander Balaton (coryab)
    +
    +Janita Ovidie Sandtrøen Willumsen (janitaws)
    +
    Version
    1.0
    +

    These typedefs make the code more readable and easy to follow along.

    +
    Bug:
    No known bugs
    + +

    Definition in file typedefs.hpp.

    +

    Typedef Documentation

    + +

    ◆ sim_arr

    + +
    +
    + + + + +
    typedef std::vector<sim_cols> sim_arr
    +
    + +

    Typedef for the result of the simulate method.

    + +

    Definition at line 32 of file typedefs.hpp.

    + +
    +
    + +

    ◆ sim_cols

    + +
    +
    + + + + +
    typedef std::vector<arma::vec::fixed<3> > sim_cols
    +
    + +

    Typedef for the column of the result vector from simulating particles.

    + +

    Definition at line 24 of file typedefs.hpp.

    + +
    +
    + +

    ◆ sim_rows

    + +
    +
    + + + + +
    typedef std::vector<arma::vec::fixed<3> > sim_rows
    +
    + +

    Typedef for the row of the result vector from simulating particles.

    + +

    Definition at line 28 of file typedefs.hpp.

    + +
    +
    + +

    ◆ vec_3d

    + +
    +
    + + + + +
    typedef arma::vec::fixed<3> vec_3d
    +
    + +

    Typedef for a fixed 3d arma vector.

    + +

    Definition at line 36 of file typedefs.hpp.

    + +
    +
    +
    +
    + + + + diff --git a/docs/typedefs_8hpp.js b/docs/typedefs_8hpp.js new file mode 100644 index 0000000..d014844 --- /dev/null +++ b/docs/typedefs_8hpp.js @@ -0,0 +1,7 @@ +var typedefs_8hpp = +[ + [ "sim_arr", "typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af", null ], + [ "sim_cols", "typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23", null ], + [ "sim_rows", "typedefs_8hpp.html#a8502989b1b361725834fc185bd575f66", null ], + [ "vec_3d", "typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df", null ] +]; \ No newline at end of file diff --git a/docs/typedefs_8hpp_source.html b/docs/typedefs_8hpp_source.html new file mode 100644 index 0000000..475ff07 --- /dev/null +++ b/docs/typedefs_8hpp_source.html @@ -0,0 +1,134 @@ + + + + + + + +Penning Trap Simulation: include/typedefs.hpp Source File + + + + + + + + + + + + + + + + +
    +
    + + + + + + +
    +
    Penning Trap Simulation +
    +
    Simulate particle behavior inside a Penning Trap
    +
    +
    + + + + + + + +
    +
    + +
    +
    +
    + +
    + +
    +
    + + +
    +
    +
    +
    +
    +
    Loading...
    +
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    +
    No Matches
    +
    +
    +
    +
    + +
    +
    typedefs.hpp
    +
    +
    +Go to the documentation of this file.
    1
    +
    15#ifndef __TYPEDEFS__
    +
    16#define __TYPEDEFS__
    +
    17
    +
    18#include <vector>
    +
    19#include <armadillo>
    +
    20
    +
    24typedef std::vector<arma::vec::fixed<3>> sim_cols;
    +
    25
    +
    28typedef std::vector<arma::vec::fixed<3>> sim_rows;
    +
    29
    +
    32typedef std::vector<sim_cols> sim_arr;
    +
    33
    +
    36typedef arma::vec::fixed<3> vec_3d;
    +
    37
    +
    38#endif
    +
    sim_cols
    std::vector< arma::vec::fixed< 3 > > sim_cols
    Typedef for the column of the result vector from simulating particles.
    Definition: typedefs.hpp:24
    +
    sim_rows
    std::vector< arma::vec::fixed< 3 > > sim_rows
    Typedef for the row of the result vector from simulating particles.
    Definition: typedefs.hpp:28
    +
    vec_3d
    arma::vec::fixed< 3 > vec_3d
    Typedef for a fixed 3d arma vector.
    Definition: typedefs.hpp:36
    +
    sim_arr
    std::vector< sim_cols > sim_arr
    Typedef for the result of the simulate method.
    Definition: typedefs.hpp:32
    +
    +
    + + + + diff --git a/docs/utils_8cpp.html b/docs/utils_8cpp.html index c2ffd2e..9401b51 100644 --- a/docs/utils_8cpp.html +++ b/docs/utils_8cpp.html @@ -106,7 +106,8 @@ $(document).ready(function(){initNavTree('utils_8cpp.html',''); initResizable();

    Implementation of the utils. More...

    -
    #include "utils.hpp"
    +
    #include <sys/stat.h>
    +#include "utils.hpp"

    Go to the source code of this file.

    @@ -124,6 +125,9 @@ Functions + + +
    bool arma_vector_close_to (arma::vec &a, arma::vec &b, double tol)
     Test if two armadillo vectors are close to each other.
     
    bool mkpath (std::string path, int mode)
     Make path given.
     

    Detailed Description

    Implementation of the utils.

    @@ -131,7 +135,7 @@ Functions
    Janita Ovidie Sandtrøen Willumsen (janitaws)
    Version
    1.0
    -
    Bug:
    No known bugs
    +
    Bug:
    No known bugs

    Definition in file utils.cpp.

    Function Documentation

    @@ -177,9 +181,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws) -
    Returns
    Boolean
    +
    Returns
    bool
    -

    Definition at line 59 of file utils.cpp.

    +

    Definition at line 62 of file utils.cpp.

    @@ -247,7 +251,48 @@ Janita Ovidie Sandtrøen Willumsen (janitaws) -

    Definition at line 40 of file utils.cpp.

    +

    Definition at line 43 of file utils.cpp.

    + + + + +

    ◆ mkpath()

    + +
    +
    + + + + + + + + + + + + + + + + + + +
    bool mkpath (std::string path,
    int mode = 0777 
    )
    +
    + +

    Make path given.

    +

    This tries to be the equivalent to "mkdir -p" and creates a new directory whenever it needs to.

    +
    Parameters
    + + + +
    pathThe path to be created
    modeThe mode/permissions for all the new directories
    +
    +
    +
    Returns
    bool
    + +

    Definition at line 76 of file utils.cpp.

    @@ -284,6 +329,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)

    Turns a vector of doubles into a string written in scientific format.

    +

    The code is stolen from https://github.com/anderkve/FYS3150.

    Parameters
    @@ -292,9 +338,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    vThe vector to stringify
    -
    Returns
    String
    +
    Returns
    std::string
    -

    Definition at line 21 of file utils.cpp.

    +

    Definition at line 24 of file utils.cpp.

    @@ -331,7 +377,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)

    Turns a double into a string written in scientific format.

    -

    Code stolen from https://github.com/anderkve/FYS3150 Header: https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/include/utils.hpp Source: https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/src/utils.cpp

    +

    The code is stolen from https://github.com/anderkve/FYS3150.

    Parameters
    @@ -340,9 +386,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    dThe number to stringify
    -
    Returns
    String
    +
    Returns
    std::string
    -

    Definition at line 14 of file utils.cpp.

    +

    Definition at line 17 of file utils.cpp.

    diff --git a/docs/utils_8cpp.js b/docs/utils_8cpp.js index 36c50fa..362b36a 100644 --- a/docs/utils_8cpp.js +++ b/docs/utils_8cpp.js @@ -2,6 +2,7 @@ var utils_8cpp = [ [ "arma_vector_close_to", "utils_8cpp.html#a5d2e1e032fd19614f2fbb58149a7b02a", null ], [ "m_assert", "utils_8cpp.html#aff5e07c3c1d321709b0cc38e999f427b", null ], + [ "mkpath", "utils_8cpp.html#acf13f4e492199cb7231bfa646dbd08de", null ], [ "scientific_format", "utils_8cpp.html#a58565270b643b24e3132f38c653e0199", null ], [ "scientific_format", "utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746", null ] ]; \ No newline at end of file diff --git a/docs/utils_8cpp_source.html b/docs/utils_8cpp_source.html index 069cd7c..5ed9571 100644 --- a/docs/utils_8cpp_source.html +++ b/docs/utils_8cpp_source.html @@ -102,69 +102,97 @@ $(document).ready(function(){initNavTree('utils_8cpp_source.html',''); initResiz
    Go to the documentation of this file.
    1
    -
    12#include "utils.hpp"
    -
    13
    -
    14std::string scientific_format(double d, int width, int prec)
    -
    15{
    -
    16 std::stringstream ss;
    -
    17 ss << std::setw(width) << std::setprecision(prec) << std::scientific << d;
    -
    18 return ss.str();
    -
    19}
    -
    20
    -
    21std::string scientific_format(const std::vector<double> &v, int width, int prec)
    -
    22{
    -
    23 std::stringstream ss;
    -
    24 for (double elem : v) {
    -
    25 ss << scientific_format(elem, width, prec);
    -
    26 }
    -
    27 return ss.str();
    -
    28}
    -
    29
    -
    30static void print_message(std::string msg)
    -
    31{
    -
    32 if (msg.size() > 0) {
    -
    33 std::cout << "message: " << msg << "\n\n";
    -
    34 }
    -
    35 else {
    -
    36 std::cout << "\n";
    +
    13#include <sys/stat.h>
    +
    14
    +
    15#include "utils.hpp"
    +
    16
    +
    17std::string scientific_format(double d, int width, int prec)
    +
    18{
    +
    19 std::stringstream ss;
    +
    20 ss << std::setw(width) << std::setprecision(prec) << std::scientific << d;
    +
    21 return ss.str();
    +
    22}
    +
    23
    +
    24std::string scientific_format(const std::vector<double> &v, int width, int prec)
    +
    25{
    +
    26 std::stringstream ss;
    +
    27 for (double elem : v) {
    +
    28 ss << scientific_format(elem, width, prec);
    +
    29 }
    +
    30 return ss.str();
    +
    31}
    +
    32
    +
    33static void print_message(std::string msg)
    +
    34{
    +
    35 if (msg.size() > 0) {
    +
    36 std::cout << "message: " << msg << "\n\n";
    37 }
    -
    38}
    -
    39
    -
    40void m_assert(bool expr, std::string expr_str, std::string f, std::string file,
    -
    41 int line, std::string msg)
    -
    42{
    -
    43 std::string new_assert(f.size() + (expr ? 4 : 6), '-');
    -
    44 std::cout << "\x1B[36m" << new_assert << "\033[0m\n";
    -
    45 std::cout << f << ": ";
    -
    46 if (expr) {
    -
    47 std::cout << "\x1B[32mOK\033[0m\n";
    -
    48 print_message(msg);
    -
    49 }
    -
    50 else {
    -
    51 std::cout << "\x1B[31mFAIL\033[0m\n";
    -
    52 print_message(msg);
    -
    53 std::cout << file << " " << line << ": Assertion \"" << expr_str
    -
    54 << "\" Failed\n\n";
    -
    55 abort();
    -
    56 }
    -
    57}
    -
    58
    -
    59bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol)
    -
    60{
    -
    61 if (a.n_elem != b.n_elem) {
    -
    62 return false;
    -
    63 }
    -
    64
    -
    65 for (int i = 0; i < a.n_elem; i++) {
    -
    66 if (std::abs(a(i) - b(i)) >= tol) {
    -
    67 return false;
    -
    68 }
    -
    69 }
    -
    70 return true;
    -
    71}
    -
    arma_vector_close_to
    bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol)
    Test if two armadillo vectors are close to each other.
    Definition: utils.cpp:59
    -
    scientific_format
    std::string scientific_format(double d, int width, int prec)
    Turns a double into a string written in scientific format.
    Definition: utils.cpp:14
    -
    m_assert
    void m_assert(bool expr, std::string expr_str, std::string f, std::string file, int line, std::string msg)
    Test an expression, confirm that test is ok, or abort execution.
    Definition: utils.cpp:40
    +
    38 else {
    +
    39 std::cout << "\n";
    +
    40 }
    +
    41}
    +
    42
    +
    43void m_assert(bool expr, std::string expr_str, std::string f, std::string file,
    +
    44 int line, std::string msg)
    +
    45{
    +
    46 std::string new_assert(f.size() + (expr ? 4 : 6), '-');
    +
    47 std::cout << "\x1B[36m" << new_assert << "\033[0m\n";
    +
    48 std::cout << f << ": ";
    +
    49 if (expr) {
    +
    50 std::cout << "\x1B[32mOK\033[0m\n";
    +
    51 print_message(msg);
    +
    52 }
    +
    53 else {
    +
    54 std::cout << "\x1B[31mFAIL\033[0m\n";
    +
    55 print_message(msg);
    +
    56 std::cout << file << " " << line << ": Assertion \"" << expr_str
    +
    57 << "\" Failed\n\n";
    +
    58 abort();
    +
    59 }
    +
    60}
    +
    61
    +
    62bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol)
    +
    63{
    +
    64 if (a.n_elem != b.n_elem) {
    +
    65 return false;
    +
    66 }
    +
    67
    +
    68 for (size_t i = 0; i < a.n_elem; i++) {
    +
    69 if (std::abs(a(i) - b(i)) >= tol) {
    +
    70 return false;
    +
    71 }
    +
    72 }
    +
    73 return true;
    +
    74}
    +
    75
    +
    76bool mkpath(std::string path, int mode)
    +
    77{
    +
    78 std::string cur_dir;
    +
    79 std::string::size_type pos = -1;
    +
    80 struct stat buf;
    +
    81
    +
    82 if (path.back() != '/') {
    +
    83 path += '/';
    +
    84 }
    +
    85 while (true) {
    +
    86 pos++;
    +
    87 pos = path.find('/', pos);
    +
    88 if (pos != std::string::npos) {
    +
    89 cur_dir = path.substr(0, pos);
    +
    90 if (mkdir(cur_dir.c_str(), mode) != 0 && stat(cur_dir.c_str(), &buf) != 0) {
    +
    91 return -1;
    +
    92 }
    +
    93 }
    +
    94 else {
    +
    95 break;
    +
    96 }
    +
    97 }
    +
    98 return 0;
    +
    99}
    +
    arma_vector_close_to
    bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol)
    Test if two armadillo vectors are close to each other.
    Definition: utils.cpp:62
    +
    scientific_format
    std::string scientific_format(double d, int width, int prec)
    Turns a double into a string written in scientific format.
    Definition: utils.cpp:17
    +
    mkpath
    bool mkpath(std::string path, int mode)
    Make path given.
    Definition: utils.cpp:76
    +
    m_assert
    void m_assert(bool expr, std::string expr_str, std::string f, std::string file, int line, std::string msg)
    Test an expression, confirm that test is ok, or abort execution.
    Definition: utils.cpp:43
    utils.hpp
    Function prototypes and macros that are useful.
    diff --git a/docs/utils_8hpp.html b/docs/utils_8hpp.html index dea4601..2866ae0 100644 --- a/docs/utils_8hpp.html +++ b/docs/utils_8hpp.html @@ -124,6 +124,7 @@ Macros  A prettier assertion function.
      #define __METHOD_NAME__   methodName(__PRETTY_FUNCTION__) + Get the name of the current method/function.
      + + +

    @@ -140,6 +141,9 @@ Functions

    bool arma_vector_close_to (arma::vec &a, arma::vec &b, double tol=1e-8)
     Test if two armadillo vectors are close to each other.
     
    bool mkpath (std::string path, int mode=0777)
     Make path given.
     

    Detailed Description

    Function prototypes and macros that are useful.

    @@ -148,7 +152,7 @@ Functions Janita Ovidie Sandtrøen Willumsen (janitaws)
    Version
    1.0

    These utility function are mainly for convenience and aren't directly related to the project.

    -
    Bug:
    No known bugs
    +
    Bug:
    No known bugs

    Definition in file utils.hpp.

    Macro Definition Documentation

    @@ -164,7 +168,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 48 of file utils.hpp.

    +

    Get the name of the current method/function.

    + +

    Definition at line 51 of file utils.hpp.

    @@ -193,9 +199,10 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -Value:
    m_assert(expr, #expr, __METHOD_NAME__, __FILE__, \
    +Value:
    m_assert(expr, #expr, __METHOD_NAME__, __FILE__, \
    __LINE__, msg)
    -
    m_assert
    void m_assert(bool expr, std::string expr_str, std::string func, std::string file, int line, std::string msg)
    Test an expression, confirm that test is ok, or abort execution.
    Definition: utils.cpp:40
    +
    m_assert
    void m_assert(bool expr, std::string expr_str, std::string func, std::string file, int line, std::string msg)
    Test an expression, confirm that test is ok, or abort execution.
    Definition: utils.cpp:43
    +
    __METHOD_NAME__
    #define __METHOD_NAME__
    Get the name of the current method/function.
    Definition: utils.hpp:51

    A prettier assertion function.

    This macro calls the m_assert function which is a more informative assertion function than the regular assert function from cassert.

    @@ -270,9 +277,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws) -
    Returns
    Boolean
    +
    Returns
    bool
    -

    Definition at line 59 of file utils.cpp.

    +

    Definition at line 62 of file utils.cpp.

    @@ -340,7 +347,48 @@ Janita Ovidie Sandtrøen Willumsen (janitaws) -

    Definition at line 40 of file utils.cpp.

    +

    Definition at line 43 of file utils.cpp.

    + + + + +

    ◆ mkpath()

    + +
    +
    + + + + + + + + + + + + + + + + + + +
    bool mkpath (std::string path,
    int mode = 0777 
    )
    +
    + +

    Make path given.

    +

    This tries to be the equivalent to "mkdir -p" and creates a new directory whenever it needs to.

    +
    Parameters
    + + + +
    pathThe path to be created
    modeThe mode/permissions for all the new directories
    +
    +
    +
    Returns
    bool
    + +

    Definition at line 76 of file utils.cpp.

    @@ -377,6 +425,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)

    Turns a vector of doubles into a string written in scientific format.

    +

    The code is stolen from https://github.com/anderkve/FYS3150.

    Parameters
    @@ -385,9 +434,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    vThe vector to stringify
    -
    Returns
    String
    +
    Returns
    std::string
    -

    Definition at line 21 of file utils.cpp.

    +

    Definition at line 24 of file utils.cpp.

    @@ -424,7 +473,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)

    Turns a double into a string written in scientific format.

    -

    Code stolen from https://github.com/anderkve/FYS3150 Header: https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/include/utils.hpp Source: https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/src/utils.cpp

    +

    The code is stolen from https://github.com/anderkve/FYS3150.

    Parameters
    @@ -433,9 +482,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    dThe number to stringify
    -
    Returns
    String
    +
    Returns
    std::string
    -

    Definition at line 14 of file utils.cpp.

    +

    Definition at line 17 of file utils.cpp.

    diff --git a/docs/utils_8hpp.js b/docs/utils_8hpp.js index 34c7b36..68951df 100644 --- a/docs/utils_8hpp.js +++ b/docs/utils_8hpp.js @@ -1,9 +1,11 @@ var utils_8hpp = [ + [ "__METHOD_NAME__", "utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168", null ], [ "ASSERT", "utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9", null ], [ "DEBUG", "utils_8hpp.html#aecc1f7a8a2493b9e021e5bff76a00a5b", null ], [ "arma_vector_close_to", "utils_8hpp.html#a0c95c4791692b06f8811905a76dbd772", null ], [ "m_assert", "utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38", null ], + [ "mkpath", "utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa", null ], [ "scientific_format", "utils_8hpp.html#ad54b96a1074f9df4dc892a41d115b72d", null ], [ "scientific_format", "utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384", null ] ]; \ No newline at end of file diff --git a/docs/utils_8hpp_source.html b/docs/utils_8hpp_source.html index 33ddc52..1c7052d 100644 --- a/docs/utils_8hpp_source.html +++ b/docs/utils_8hpp_source.html @@ -121,39 +121,45 @@ $(document).ready(function(){initNavTree('utils_8hpp_source.html',''); initResiz
    45#define ASSERT(expr, msg) m_assert(expr, #expr, __METHOD_NAME__, __FILE__, \
    46 __LINE__, msg)
    47
    -
    48#define __METHOD_NAME__ methodName(__PRETTY_FUNCTION__)
    -
    49
    -
    50
    +
    51#define __METHOD_NAME__ methodName(__PRETTY_FUNCTION__)
    +
    52
    +
    53
    64std::string scientific_format(double d, int width=20, int prec=10);
    65
    -
    74std::string scientific_format(const std::vector<double>& v,
    -
    75 int width=20,
    -
    76 int prec=10);
    -
    77
    -
    90void m_assert(bool expr,
    -
    91 std::string expr_str,
    -
    92 std::string func,
    -
    93 std::string file,
    -
    94 int line,
    -
    95 std::string msg);
    -
    96
    -
    97
    -
    109bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8);
    -
    110
    -
    111
    -
    112static inline std::string methodName(const std::string& prettyFunction)
    -
    113{
    -
    114 size_t colons = prettyFunction.find("::");
    -
    115 size_t begin = prettyFunction.substr(0,colons).rfind(" ") + 1;
    -
    116 size_t end = prettyFunction.rfind("(") - begin;
    -
    117
    -
    118 return prettyFunction.substr(begin,end) + "()";
    -
    119}
    -
    120
    -
    121#endif
    -
    arma_vector_close_to
    bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8)
    Test if two armadillo vectors are close to each other.
    Definition: utils.cpp:59
    -
    m_assert
    void m_assert(bool expr, std::string expr_str, std::string func, std::string file, int line, std::string msg)
    Test an expression, confirm that test is ok, or abort execution.
    Definition: utils.cpp:40
    -
    scientific_format
    std::string scientific_format(double d, int width=20, int prec=10)
    Turns a double into a string written in scientific format.
    Definition: utils.cpp:14
    +
    66
    +
    77std::string scientific_format(const std::vector<double>& v,
    +
    78 int width=20,
    +
    79 int prec=10);
    +
    80
    +
    81
    +
    94void m_assert(bool expr,
    +
    95 std::string expr_str,
    +
    96 std::string func,
    +
    97 std::string file,
    +
    98 int line,
    +
    99 std::string msg);
    +
    100
    +
    101
    +
    113bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8);
    +
    114
    +
    115
    +
    126static inline std::string methodName(const std::string& pretty_function)
    +
    127{
    +
    128 size_t colons = pretty_function.find("::");
    +
    129 size_t begin = pretty_function.substr(0,colons).rfind(" ") + 1;
    +
    130 size_t end = pretty_function.rfind("(") - begin;
    +
    131
    +
    132 return pretty_function.substr(begin,end) + "()";
    +
    133}
    +
    134
    +
    135
    +
    146bool mkpath(std::string path, int mode = 0777);
    +
    147
    +
    148#endif
    +
    arma_vector_close_to
    bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8)
    Test if two armadillo vectors are close to each other.
    Definition: utils.cpp:62
    +
    m_assert
    void m_assert(bool expr, std::string expr_str, std::string func, std::string file, int line, std::string msg)
    Test an expression, confirm that test is ok, or abort execution.
    Definition: utils.cpp:43
    +
    mkpath
    bool mkpath(std::string path, int mode=0777)
    Make path given.
    Definition: utils.cpp:76
    +
    scientific_format
    std::string scientific_format(double d, int width=20, int prec=10)
    Turns a double into a string written in scientific format.
    Definition: utils.cpp:17
    diff --git a/include/Particle.hpp b/include/Particle.hpp index 29b4ccb..4b5e716 100644 --- a/include/Particle.hpp +++ b/include/Particle.hpp @@ -14,24 +14,29 @@ #include +#include "typedefs.hpp" + /** @brief A class that holds attributes of a particle * */ class Particle { private: - double q; ///< Charge - double m; ///< Mass - arma::vec::fixed<3> r_vec; ///< position - arma::vec::fixed<3> v_vec; ///< velocity + double q; ///< Charge + double m; ///< Mass + vec_3d r_vec; ///< position + vec_3d v_vec; ///< velocity public: /** @brief Initialize the particle. * * @details Initialize the particle with a charge, mass, position and * velocity. + * + * @param q The charge of the particle + * @param m The mass of the particle + * @param r_vec The initial position of the particle + * @param v_vec The initial velocity of the particle * */ - Particle(double q, double m, - arma::vec::fixed<3> r_vec, - arma::vec::fixed<3> v_vec); + Particle(double q, double m, vec_3d r_vec, vec_3d v_vec); /** @brief Make private attributes available for PenningTrap. * */ diff --git a/include/PenningTrap.hpp b/include/PenningTrap.hpp index 3601634..9a78784 100644 --- a/include/PenningTrap.hpp +++ b/include/PenningTrap.hpp @@ -17,9 +17,15 @@ #include "Particle.hpp" #include "constants.hpp" +#include "typedefs.hpp" -#pragma omp declare reduction( + : arma::vec : omp_out += omp_in ) \ - initializer( omp_priv = omp_orig ) +#pragma omp declare reduction(+ : vec_3d : omp_out += omp_in) \ + initializer(omp_priv = omp_orig) + +typedef struct simulation { + sim_arr r_vecs; + sim_arr v_vecs; +} simulation_t; /** @brief A class that simulates a Penning trap. * @@ -28,61 +34,197 @@ * */ class PenningTrap { private: - double B_0; ///< Magnetic field strength - double V_0; ///< Applied potential - double d; ///< Characteristic dimension - std::vector particles; ///< The particles in the Penning trap + double B_0; ///< Magnetic field strength + std::function V_0; ///< Applied potential + double d; ///< Characteristic dimension + double t; ///< Current time + std::vector particles; ///< The particles in the Penning trap + sim_arr k_v; ///< A 2D vector containing all \f$k_{i,j}\f$ where \f$j\f$ is + ///< the index of a particle + sim_arr k_r; ///< A 2D vector containing all \f$k_{i,j}\f$ where \f$j\f$ is + ///< the index of a particle + + /** @brief Helper for evolve_RK4 when calculating \f$k_{v,i,j}\f$ values + * + * @details Something + * + * @param i Index i for \f$k_{v,i,j}\f$ + * @param j Index j for \f$k_{v,i,j}\f$ + * @param dt the step length (delta time) + * + * @return vec_3d + * */ + vec_3d v_func(unsigned int i, unsigned int j, double dt); + + /** @brief Helper for evolve_RK4 when calculating \f$k_{r,i,j}\f$ values + * + * @details Something + * + * @param i Index i for \f$k_{r,i,j}\f$ + * @param j Index j for \f$k_{r,i,j}\f$ + * @param dt the step length (delta time) + * + * @return vec_3d + * */ + vec_3d r_func(unsigned int i, unsigned int j, double dt); public: - /** @brief Set B_0, V_0 and d. + /** @brief Constructor for the PenningTrap class + * + * @param B_0 The magnetic field strength + * @param V_0 The time dependent applied potential + * @param d The characteristic dimension + * @param t The starting time * */ - PenningTrap(double B_0 = T, double V_0 = 25.*V/1000., double d = 500.); + PenningTrap( + double B_0 = T, + std::function V_0 = + [](double t) { return 25. * V / 1000.; }, + double d = 500., double t = 0.); + + /** @brief Constructor for the PenningTrap class + * + * @param i The number of particles to generate + * @param B_0 The magnetic field strength + * @param V_0 The time dependent applied potential + * @param d The characteristic dimension + * @param t The starting time + * */ + PenningTrap( + unsigned int i, double B_0 = T, + std::function V_0 = + [](double t) { return 25. * V / 1000.; }, + double d = 500., double t = 0.); + + /** @brief Constructor for the PenningTrap class + * + * @param particles The starting particles + * @param B_0 The magnetic field strength + * @param V_0 The time dependent applied potential + * @param d The characteristic dimension + * @param t The starting time + * */ + PenningTrap( + std::vector particles, double B_0 = T, + std::function V_0 = + [](double t) { return 25. * V / 1000.; }, + double d = 500., double t = 0.); /** @brief Add a particle to the system + * + * @param particle The particle to add to the Penning trap * */ void add_particle(Particle particle); /** @brief Calculate E at point r + * + * @param r The position where we want to calculate the E field + * + * @return vec_3d * */ - arma::vec external_E_field(arma::vec r); + vec_3d external_E_field(vec_3d r); /** @brief Calculate B at point r + * + * @param r The position where we want to calculate the B field + * + * @return vec_3d * */ - arma::vec external_B_field(arma::vec r); + vec_3d external_B_field(vec_3d r); /** @brief Calculate the force between 2 particles. * - * @details Calculate the force exhibited on particle p_i from + * @details Calculate the force exhibited on particle p_i from * particle p_j. + * + * @param i The index of particle p_i + * @param j The index of particle p_j + * + * @return vec_3d * */ - arma::vec force_on_particle(int i, int j); + vec_3d force_on_particle(unsigned int i, unsigned int j); /** @brief Calculate the total external force on a particle. * * @details Calculate the total amount of force that E and B exhibits * on particle p_i. + * + * @param i The index of particle p_i + * + * @return vec_3d * */ - arma::vec total_force_external(int i); + vec_3d total_force_external(unsigned int i); - /** @brief Calculate the total force on a particle from other particles. + /** @brief Calculate the total force on a particle p_i from other particles. + * + * @param i The index of particle p_i + * + * @return vec_3d * */ - arma::vec total_force_particles(int i); + vec_3d total_force_particles(unsigned int i); - /** @brief calculate the total force on a particle. - * */ - arma::vec total_force(int i); + /** @brief calculate the total force on a particle p_i. + * + * @param i The index of particle p_i + * + * @return vec_3d + * */ + vec_3d total_force(unsigned int i); /** @brief Go forward one timestep using the RK4 method + * + * @param dt The step length + * @param particle_interaction Turn particle interactions on/off * */ - void evolve_RK4(double dt); + void evolve_RK4(double dt, bool particle_interaction = true); /** @brief Go forward one timestep using the forward Euler method + * + * @param dt The step length + * @param particle_interaction Turn particle interactions on/off * */ - void evolve_forward_euler(double dt); + void evolve_forward_euler(double dt, bool particle_interaction = true); - arma::vec get_particle(int i); + /** @brief Simulate the particle system inside the Penning trap over + * a certain amount of time. + * + * @param time The time to simulate in microseconds + * @param steps The amount of steps for the whole simulation + * @param method The method to use when moving forward a timestep + * @param particle_interaction Turn particle interactions on/off + * */ + simulation_t simulate(double time, unsigned int steps, + std::string method = "rk4", + bool particle_interaction = true); - double get_d(); + /** @brief Simulate and write the displacement of all particles to files. + * + * @param path The directory to save the data + * @param time The time to simulate in microseconds + * @param steps The amount of steps for the whole simulation + * @param method The method to use when moving forward a timestep + * @param particle_interaction Turn particle interactions on/off + * */ + void write_simulation_to_dir(std::string path, double time, + unsigned int steps, std::string method = "rk4", + bool particle_interaction = true); + + /** @brief Simulate and calculate what fraction of particles are still + * left inside the Penning trap after the simulation. + * + * @param time The time to simulate in microseconds + * @param steps The amount of steps for the whole simulation + * @param method The method to use when moving forward a timestep + * @param particle_interaction Turn particle interactions on/off + * + * @return double + * */ + double fraction_of_particles_left(double time, unsigned int steps, + std::string method = "rk4", + bool particle_interaction = true); + + vec_3d get_r(int i); + double get_t(); }; #endif diff --git a/include/typedefs.hpp b/include/typedefs.hpp new file mode 100644 index 0000000..f0ceca2 --- /dev/null +++ b/include/typedefs.hpp @@ -0,0 +1,38 @@ +/** @file typedefs.hpp + * + * @author Cory Alexander Balaton (coryab) + * @author Janita Ovidie Sandtrøen Willumsen (janitaws) + * + * @version 1.0 + * + * @brief Useful typedefs for cleaner code. + * + * @details These typedefs make the code more readable and easy to follow + * along. + * + * @bug No known bugs + * */ +#ifndef __TYPEDEFS__ +#define __TYPEDEFS__ + +#include +#include + +/** @brief Typedef for the column of the result vector from simulating + * particles. + * */ +typedef std::vector> sim_cols; + +/** @brief Typedef for the row of the result vector from simulating particles. + * */ +typedef std::vector> sim_rows; + +/** @brief Typedef for the result of the simulate method. + * */ +typedef std::vector sim_arr; + +/** @brief Typedef for a fixed 3d arma vector. + * */ +typedef arma::vec::fixed<3> vec_3d; + +#endif diff --git a/include/utils.hpp b/include/utils.hpp index 7a03149..c9c9485 100644 --- a/include/utils.hpp +++ b/include/utils.hpp @@ -45,40 +45,44 @@ #define ASSERT(expr, msg) m_assert(expr, #expr, __METHOD_NAME__, __FILE__, \ __LINE__, msg) +/** @def __METHOD_NAME__ + * @brief Get the name of the current method/function. + * */ #define __METHOD_NAME__ methodName(__PRETTY_FUNCTION__) -/** Code stolen from https://github.com/anderkve/FYS3150 - * Header: https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/include/utils.hpp - * Source: https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/src/utils.cpp - * */ - /** @brief Turns a double into a string written in scientific format. + * + * @details The code is stolen from https://github.com/anderkve/FYS3150. * * @param d The number to stringify * @param width The reserved width of the string * @param prec The precision of the stringified number * - * @return String + * @return std::string * */ std::string scientific_format(double d, int width=20, int prec=10); + /** @brief Turns a vector of doubles into a string written in scientific format. + * + * @details The code is stolen from https://github.com/anderkve/FYS3150. * * @param v The vector to stringify * @param width The reserved width of the string * @param prec The precision of the stringified number * - * @return String + * @return std::string * */ std::string scientific_format(const std::vector& v, int width=20, int prec=10); + /** @brief Test an expression, confirm that test is ok, or abort execution. * - * This function takes in an expression and prints an OK message if it's - * true, or it prints a fail message and aborts execution if it fails. + * @details This function takes in an expression and prints an OK message if + * it's true, or it prints a fail message and aborts execution if it fails. * * @param expr The expression to be evaluated * @param expr_str The stringified version of the expression @@ -97,25 +101,48 @@ void m_assert(bool expr, /** @brief Test if two armadillo vectors are close to each other. * - * This function takes in 2 vectors and checks if they are approximately - * equal to each other given a tolerance. + * @details This function takes in 2 vectors and checks if they are + * approximately equal to each other given a tolerance. * * @param a Vector a * @param b Vector b * @param tol The tolerance * - * @return Boolean + * @return bool * */ bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8); -static inline std::string methodName(const std::string& prettyFunction) +/** @brief Takes in the __PRETTY_FUNCTION__ string and removes the return type. + * + * @details This function should only be used for the __METHOD_NAME__ macro, + * since it takes the output from __PRETTY_FUNCTION__ and strips the return + * type. + * + * @param pretty_function The string from __PRETTY_FUNCTION__ + * + * @return std::string + * */ +static inline std::string methodName(const std::string& pretty_function) { - size_t colons = prettyFunction.find("::"); - size_t begin = prettyFunction.substr(0,colons).rfind(" ") + 1; - size_t end = prettyFunction.rfind("(") - begin; + size_t colons = pretty_function.find("::"); + size_t begin = pretty_function.substr(0,colons).rfind(" ") + 1; + size_t end = pretty_function.rfind("(") - begin; - return prettyFunction.substr(begin,end) + "()"; + return pretty_function.substr(begin,end) + "()"; } + +/** @brief Make path given. + * + * @details This tries to be the equivalent to "mkdir -p" and creates a new + * directory whenever it needs to. + * + * @param path The path to be created + * @param mode The mode/permissions for all the new directories + * + * @return bool + * */ +bool mkpath(std::string path, int mode = 0777); + #endif diff --git a/latex/images/3d_plot.pdf b/latex/images/3d_plot.pdf new file mode 100644 index 0000000..78b115e Binary files /dev/null and b/latex/images/3d_plot.pdf differ diff --git a/latex/images/particles_left.pdf b/latex/images/particles_left.pdf new file mode 100644 index 0000000..cc065d4 Binary files /dev/null and b/latex/images/particles_left.pdf differ diff --git a/latex/images/phase_space_2_particles.pdf b/latex/images/phase_space_2_particles.pdf new file mode 100644 index 0000000..6c006d4 Binary files /dev/null and b/latex/images/phase_space_2_particles.pdf differ diff --git a/latex/images/phase_space_2_particles_x.pdf b/latex/images/phase_space_2_particles_x.pdf new file mode 100644 index 0000000..7af3a9c Binary files /dev/null and b/latex/images/phase_space_2_particles_x.pdf differ diff --git a/latex/images/phase_space_2_particles_z.pdf b/latex/images/phase_space_2_particles_z.pdf new file mode 100644 index 0000000..86fe6c3 Binary files /dev/null and b/latex/images/phase_space_2_particles_z.pdf differ diff --git a/latex/images/plot_2_particles_xy.pdf b/latex/images/plot_2_particles_xy.pdf new file mode 100644 index 0000000..8e44ccd Binary files /dev/null and b/latex/images/plot_2_particles_xy.pdf differ diff --git a/latex/images/single_particle.pdf b/latex/images/single_particle.pdf new file mode 100644 index 0000000..cf0ee5a Binary files /dev/null and b/latex/images/single_particle.pdf differ diff --git a/latex/main.tex b/latex/main.tex index 4bd63f2..f9c63f7 100644 --- a/latex/main.tex +++ b/latex/main.tex @@ -63,6 +63,9 @@ % Introduction \subfile{sections/introduction} +% Theory +\subfile{sections/theory} + % Methods \subfile{sections/methods} diff --git a/latex/references/references.bib b/latex/references/references.bib index b8d6413..6a49b46 100644 --- a/latex/references/references.bib +++ b/latex/references/references.bib @@ -74,4 +74,14 @@ publisher = {Farleia Forlag}, year = {2018}, pages = {162--163} -} \ No newline at end of file +} + + +@article{rk4_method, + author = "Morten Hjorth-Jensen", + title = "Computational Physics, Lecture Notes Fall 2015", + journal = "Department of Physics, University of Oslo", + year = "2015", + chapter = "8.4", + pages = "250--252", +} diff --git a/latex/sections/methods.tex b/latex/sections/methods.tex index 409b5bc..125bd37 100644 --- a/latex/sections/methods.tex +++ b/latex/sections/methods.tex @@ -3,67 +3,234 @@ \begin{document} \section{Methods} -% problem 1 -When we study the Penning traps effect on a particle with a charge $q$, we need to consider the forces acting on the particle. The sum of all forces acting on the particle, is given by the Lorentz force \eqref{eq:lorentz_force}. -\begin{equation}\label{eq:lorentz_force} - \mathbf{F} = q \mathbf{E} + q \mathbf{v} \times \mathbf{B}, + +\subsection{Units and constants} + +Before continuing, we need to define the units we'll be working with. +Since we are working with particles, we need small units to work with so the +numbers we are working with aren't so small that they could potentially lead +to large round-off errors in our simulation. The units that we will use are listed in Table~\ref{tab:units}. +\begin{table}[H] + \begin{center} + \begin{tabular}[c]{lll} + Dimension & Unit & Symbol \\ + \hline + Length & micrometer & $\mu m$ \\ + Time & microseconds & $\mu s$ \\ + Mass & atomic mass unit & $u$ \\ + Charge & the elementary charge & $e$ \\ + \hline + \end{tabular} + \end{center} + \caption{The set of units we'll be working with.}\label{tab:units} +\end{table} +With these base units, we get +\begin{equation} + k_e = 1.3893533 \cdot 10^5 \frac{u(\mu m)^3}{(\mu s)^2 e}, \end{equation} -We can use Newton's second law \eqref{eq:newton_second} to determine this sum by -\begin{align*} - \ddot{\mathbf{r}} &= \frac{1}{m} \sum_{i} \mathbf{F}_{i} \\ - &= \frac{1}{m} (q \mathbf{E} + q \mathbf{v} \times \mathbf{B}) \\ - &= \frac{q}{m} \big(\frac{V_{0}}{d^{2}} (x, y, -2z) + (B_{0}\dot{y}, -B_{0}\dot{x}, 0) \big), -\end{align*} -where the complete derivation can be found in \ref{sec:appendix_b}. We can now write the particle's position as -\begin{align} - \label{eq:motion_x} - \ddot{x} - \omega_{0} \dot{y} - \frac{1}{2} \omega_{z}^{2} x &= 0, \\ - \label{eq:motion_y} - \ddot{y} + \omega_{0} \dot{x} - \frac{1}{2} \omega_{z}^{2} y &= 0, \\ - \label{eq:motion_z} - \ddot{z} + \omega_{z}^{2} z &= 0, -\end{align} -% define w_0 og w_z i appendix? -In addition, we can find the general solution for eq. \eqref{eq:motion_z}, when we consider the characteristic equation of a second order differential equation \cite{lindstrom:2016:ch10:5}. -\begin{align*} - r^{2} + \omega_{z}^{2} &= 0 \\ - r &= \pm \sqrt{- \omega_{z}^{2}} = \mp i \omega_{z}, -\end{align*} -two complex roots which gives us solutions in the form of -\begin{equation}\label{eq:all_diff_sol} - z = c_{1} e^{i \omega_{z} t} + c_{2} e^{-i \omega_{z} t}, +and we get that the unit for magnetic field strength (Tesla, $T$) and electric potential (Volt, $V$) are +\begin{equation} + \begin{split} + T &= 9.64852558 \cdot 10^1 \frac{u}{(\mu s) e} \\ + V &= 9.64852558 \cdot 10^7 \frac{u (\mu m)^2}{(\mu s)^2 e}. \\ + \end{split} + \label{eq:} \end{equation} -For a complex number $z = a + ib$, we can define $e^{z} \equiv e^{a} (\cos{b} + i \sin{b})$ \cite{lindstrom:2016:ch3}. We can rewrite \eqref{eq:all_diff_sol} as -\begin{align*} - c_{1} e^{i \omega_{z} t} + c_{2} e^{-i \omega_{z} t} &= c_{1} (\cos{\omega_{z} t} + i \sin{\omega_{z} t}) + c_{2} (\cos{\omega_{z} t} - i \sin{\omega_{z} t} \\ - &= E \cos{\omega_{z} t} + i F \sin{\omega_{z} t} -\end{align*} -% -Since \eqref{eq:motion_x} and \eqref{eq:motion_y} are coupled, we want to rewrite it as a single differential equation. We can obtain this by introducing $f(t) = x(t) + iy(t)$, -\begin{align*} - (\ddot{x} - \omega_{0} \dot{y} - \frac{1}{2} \omega_{z}^{2} x) + i (\ddot{y} + \omega_{0} \dot{x} - \frac{1}{2} \omega_{z}^{2} y) &= 0 \\ - \ddot{x} - \omega_{0} \dot{y} - \frac{1}{2} \omega_{z}^{2} x + i\ddot{y} + i\omega_{0} \dot{x} - i \frac{1}{2} \omega_{z}^{2} y &= 0 \\ - \ddot{x} + i\ddot{y} + i\omega_{0} \dot{x} - \omega_{0} \dot{y} - \frac{1}{2} \omega_{z}^{2} x - i \frac{1}{2} \omega_{z}^{2} y &= 0 \\ - \ddot{x} + i\ddot{y} + i\omega_{0} (\dot{x} + i \dot{y}) - \frac{1}{2} \omega_{z}^{2} x - i \frac{1}{2} \omega_{z}^{2} y &= 0 \text{where $i \omega_{0} \dot{x} + (-1) \omega_{0} \dot{y} = i \omega_{0} \dot{x} + i^{2} \omega_{0} \dot{y}$} \\ - \ddot{f} + i \omega_{0} \dot{f} - \frac{1}{2} \omega_{z}^{2} f &= 0 -\end{align*} - +\subsection{Dealing with a multi--particle system} - - - - -Physical properties given by newtons second law \eqref{eq:newton_second} -\begin{equation}\label{eq:general_solution} - f(t) = A_{+}e^{-i(\omega_{+} t + \phi_{+})} + A_{-}e^{-i(\omega_{-} t + \phi_{-})} +For a multi-particles system, we need to modify $\vb{F}$ to account for the +force of other particles in the system acting upon each other. To do that, we +add another term to $\vb{F}$ +\begin{equation} + \vb{F}_i(t, \vb{v}_i, \vb{r}_i) = q_i \vb{E}(t, \vb{r}_i) + q_i \vb{v}_i \cross \vb{B} - \vb{E}_p(t, \vb{r}_i), +\end{equation} +where $i$ and $j$ are particle indices and +\begin{equation} + \vb{E}_p(t, \vb{r}_i) = q_i k_e \sum_{j \neq i} + q_j \frac{\vb{r_i} - \vb{r_j}}{\left| \vb{r_i} - \vb{r_j} \right|^3}. + \label{eq:} \end{equation} -The particle moves and its position can be determined using newton. where the electric field -\subsection*{Algorithm} +Newton's second law for a particle $i$ is then +\begin{equation} + \frac{d^2\vb{r}_i}{dt^2} = \frac{\vb{F}_i\left(t, \frac{d\vb{r}_i}{dt}, \vb{r_i}\right)}{m_i}, + \label{eq:newtonlaw2} +\end{equation} +We can then rewrite the second order ODE from equation~\ref{eq:newtonlaw2} +into a set of coupled first order ODEs. +We now rewrite Newton's second law of motion as +\begin{equation} + \begin{split} + \frac{d\vb{r}_i}{dt} &= \vb{v}_i \\ + \frac{d\vb{v}_i}{dt} &= \frac{\vb{F}_i(t, \vb{v}_i, \vb{r}_i)}{m_i}. + \end{split} + \label{eq:coupled} +\end{equation} + +\subsection{Forward Euler} + +For a particle $i$, the forward Euler method for a coupled system is +expressed as +\begin{equation} + \begin{split} + \vb{r}_{i,j+1} &= \vb{r}_{i,j} + h \cdot \frac{d\vb{r}_{i,j}}{dt} = \vb{r}_{i,j} + h \cdot \vb{v}_{i,j} \\ + \vb{v}_{i,j+1} &= \vb{v}_{i,j} + h \cdot \frac{\vb{v}_{i,j}}{dt} = \vb{v}_{i,j} + h \cdot \frac{\vb{F}\left( t_{j}, \vb{v}_{i,j}, \vb{r}_{i,j} \right)}{m}, + \end{split} +\end{equation} +for particle $i$ where $j$ is the current time step of the particle, +$m$ is the mass of the particle, and $h$ is the step length. + +When dealing with a multi-particle system, we need to ensure that we do not +update the position of any particles until every particle has calculated their +next step. An easy way of doing this is to create a copy of all the particles, +then update the copy, and when all the particles have calculated their next +step, simply replace the particles with the copies. +Algorithm~\ref{algo:forwardeuler} provides an overview on how that can be achieved. % Make this better + +\begin{figure}[H] + \begin{algorithm}[H] + \caption{Forward Euler method} + \label{algo:forwardeuler} + \begin{algorithmic} + \Procedure{Evolve forward Euler}{$particles, dt$} + \State $N \leftarrow \text{Number of particles in } particles$ + \State $a \leftarrow \text{Calculate } \frac{\vb{F_i}}{m_i} \text{ for each particle in } particles$ + \For{ $i = 1, 2, \ldots , N$ } + \State $particles_i.\vb{r} \leftarrow particles_i.\vb{r} + dt \cdot particles_i.\vb{v}$ + \State $particles_i.\vb{v} \leftarrow particles_i.\vb{v} + dt \cdot a_i$ + \EndFor + \EndProcedure + \end{algorithmic} + \end{algorithm} +\end{figure} + +\subsection{4th order Runge-Kutta} + +For a particle $i$, we can express the 4th order Runge-Kutta (RK4) method as +\begin{equation} + \begin{split} + \vb{v}_{i,j+1} &= \vb{v}_{i,j} + \frac{h}{6} \left( \vb{k}_{\vb{v},1,i} + + 2\vb{k}_{\vb{v},2,i} + 2\vb{k}_{\vb{v},3,i} + \vb{k}_{\vb{v},4,i} + \right) \\ + \vb{r}_{i,j+1} &= \vb{r}_{i,j} + \frac{h}{6} \left( \vb{k}_{\vb{r},1,i} + + 2\vb{k}_{\vb{r},2,i} + 2\vb{k}_{\vb{r},3,i} + \vb{k}_{\vb{r},4,i} + \right), + \end{split} +\end{equation} +where +\begin{equation} + \begin{split} + \vb{k}_{\vb{v},1,i} &= \frac{\vb{F}_i(t_j, \vb{v}_{i,j}, + \vb{r}_{i,j})}{m} \\ + \vb{k}_{\vb{r},1,i} &= \vb{v}_{i,j} \\ + \vb{k}_{\vb{v},2,i} &= \frac{\vb{F}_i(t_j+\frac{h}{2}, \vb{v}_{i,j} + + h \cdot \frac{\vb{k}_{\vb{v},1,i}}{2}, \vb{r}_{i,j} + + h \cdot \frac{\vb{k}_{\vb{r},1,i}}{2})}{m} \\ + \vb{k}_{\vb{r},2,i} &= \vb{v}_{i,j} + + h \cdot \frac{\vb{k}_{\vb{v},1,i}}{2} \\ + \vb{k}_{\vb{v},3,i} &= \frac{\vb{F}_i(t_j+\frac{h}{2}, \vb{v}_{i,j} + + h \cdot \frac{\vb{k}_{\vb{v},2,i}}{2}, \vb{r}_{i,j} + + h \frac{\cdot \vb{k}_{\vb{r},2,i}}{2})}{m} \\ + \vb{k}_{\vb{r},3,i} &= \vb{v}_{i,j} + + h \cdot \frac{\vb{k}_{\vb{v},2,i}}{2} \\ + \vb{k}_{\vb{v},4,i} &= \frac{\vb{F}_i(t_j+h, \vb{v}_{i,j} + + h \cdot \vb{k}_{\vb{v},3,i}, \vb{r}_{i,j} + + h \cdot \vb{k}_{\vb{r},3,i})}{m} \\ + \vb{k}_{\vb{r},4,i} &= \vb{v}_{i,j} + + h \cdot \frac{\vb{k}_{\vb{v},1,i}}{2}. + \end{split} +\end{equation} + +In order to find each $\vb{k}_{\vb{r},i}$ and $\vb{k}_{\vb{v},i}$, +we need to first compute all $\vb{k}_{\vb{r},i}$ and $\vb{k}_{\vb{v},i}$ +for all particles, then we can update the particles in order to compute +$\vb{k}_{\vb{r},i+1}$ and $\vb{k}_{\vb{v},i+1}$. In order for the algorithm +to work, we need to save a copy of each particle before starting so that we +can update the particles correctly for each step. + +This approach would require 8 loops to be able to complete the calculation since +we cannot update the particles until after all $\vb{k}$ values have been +computed, however if we create a temporary array that holds particles, we can +put the updated particles in there, and then use that array in the next loop, +and would reduce the required amount of loops down to 4. + +\begin{figure} + \begin{algorithm}[H] + \caption{RK4 method} + \label{algo:rk4} + \begin{algorithmic} + \Procedure{Evolve RK4}{$particles, dt$} + \State $N \leftarrow \text{Number of particles inside the Penning trap}$ + \State $orig\_p \leftarrow \text{Copy of particles}$ + \State $tmp\_p \leftarrow \text{Array of particles of size }N$ + \State $\vb{k}_{\vb{r}} \leftarrow \text{2D array of vectors of size } 4 \cross N$ + \State $\vb{k}_{\vb{v}} \leftarrow \text{2D array of vectors of size } 4 \cross N$ + + \For{ $i = 1, 2, \ldots, N$ } + \State $\vb{k}_{\vb{r},1,i} \leftarrow particles_i.\vb{v}$ + \State $\vb{k}_{\vb{v},1,i} \leftarrow \frac{\vb{F}_i}{m_i}$ + + \State $tmp\_p_i.\vb{r} \leftarrow orig\_p_i.\vb{r} + + \frac{dt}{2} \cdot \vb{k}_{\vb{r},1,i}$ + \State $tmp\_p_i.\vb{v} \leftarrow orig\_p_i.\vb{v} + + \frac{dt}{2} \cdot \vb{k}_{\vb{v},1,i}$ + \EndFor + + \State $particles \leftarrow tmp\_p$ \Comment{Update particles} + + \For{ $i = 1, 2, \ldots, N$ } + \State $\vb{k}_{\vb{r},2,i} \leftarrow particles_i.\vb{v}$ + \State $\vb{k}_{\vb{v},2,i} \leftarrow \frac{\vb{F}_i}{m_i}$ + + \State $tmp\_p_i.\vb{r} \leftarrow orig\_p_i.\vb{r} + + \frac{dt}{2} \cdot \vb{k}_{\vb{r},2,i}$ + \State $tmp\_p_i.\vb{v} \leftarrow orig\_p_i.\vb{v} + + \frac{dt}{2} \cdot \vb{k}_{\vb{v},2,i}$ + \EndFor + + \State $particles \leftarrow tmp\_p$ \Comment{Update particles} + + \For{ $i = 1, 2, \ldots, N$ } + \State $\vb{k}_{\vb{r},3,i} \leftarrow particles_i.\vb{v}$ + \State $\vb{k}_{\vb{v},3,i} \leftarrow \frac{\vb{F}_i}{m}$ + + \State $tmp\_p_i.\vb{r} \leftarrow orig\_p_i.\vb{r} + dt \cdot \vb{k}_{\vb{r},3,i}$ + \State $tmp\_p_i.\vb{v} \leftarrow orig\_p_i.\vb{v} + dt \cdot \vb{k}_{\vb{v},3,i}$ + \EndFor + + \State $particles \leftarrow tmp\_p$ \Comment{Update particles} + + \For{ $i = 1, 2, \ldots, N$ } + \State $\vb{k}_{\vb{r},4,i} \leftarrow particles_i.\vb{v}$ + \State $\vb{k}_{\vb{v},4,i} \leftarrow \frac{\vb{F}}{m}$ + + \State $tmp\_p_i.\vb{r} \leftarrow orig\_p_i.\vb{r} + \frac{dt}{6} + \cdot \left( \vb{k}_{\vb{r},1,i} + \vb{k}_{\vb{r},2,i} + + \vb{k}_{\vb{r},3,i} + \vb{k}_{\vb{r},4,i} \right)$ + + \State $tmp\_p_i.\vb{v} \leftarrow orig\_p_i.\vb{v} + \frac{dt}{6} + \cdot \left( \vb{k}_{\vb{v},1,i} + \vb{k}_{\vb{v},2,i} + + \vb{k}_{\vb{v},3,i} + \vb{k}_{\vb{v},4,i} \right)$ + + \EndFor + + \State $particles \leftarrow tmp\_p$ \Comment{Final update} + \EndProcedure + \end{algorithmic} + \end{algorithm} + $\vb{F}$ in the algorithm does not take any arguments as it uses the + velocities and positions of the particles inside the array $particles$ to + calculate the total force acting on particle $i$. +\end{figure} -\subsection*{Tools} +\subsection{Testing the simulation} + +\subsection{Relative error and error convergance rate} + +\subsection{Tools} We used matplotlib -\end{document} \ No newline at end of file +%\biblio +\end{document} diff --git a/latex/sections/theory.tex b/latex/sections/theory.tex new file mode 100644 index 0000000..e8d43c8 --- /dev/null +++ b/latex/sections/theory.tex @@ -0,0 +1,61 @@ +\documentclass[../main.tex]{subfiles} +\graphicspath{{\subfix{../images/}}} + +\begin{document} +\section{Theory} +% problem 1 +When we study the Penning traps effect on a particle with a charge $q$, we need to consider the forces acting on the particle. The sum of all forces acting on the particle, is given by the Lorentz force \eqref{eq:lorentz_force}. +\begin{equation}\label{eq:lorentz_force} + \mathbf{F} = q \mathbf{E} + q \mathbf{v} \times \mathbf{B}, +\end{equation} +We can use Newton's second law \eqref{eq:newton_second} to determine this sum by +\begin{align*} + \ddot{\mathbf{r}} &= \frac{1}{m} \sum_{i} \mathbf{F}_{i} \\ + &= \frac{1}{m} (q \mathbf{E} + q \mathbf{v} \times \mathbf{B}) \\ + &= \frac{q}{m} \big(\frac{V_{0}}{d^{2}} (x, y, -2z) + (B_{0}\dot{y}, -B_{0}\dot{x}, 0) \big), +\end{align*} +where the complete derivation can be found in \ref{sec:appendix_b}. We can now write the particle's position as +\begin{align} + \label{eq:motion_x} + \ddot{x} - \omega_{0} \dot{y} - \frac{1}{2} \omega_{z}^{2} x &= 0, \\ + \label{eq:motion_y} + \ddot{y} + \omega_{0} \dot{x} - \frac{1}{2} \omega_{z}^{2} y &= 0, \\ + \label{eq:motion_z} + \ddot{z} + \omega_{z}^{2} z &= 0, +\end{align} +% define w_0 og w_z i appendix? +In addition, we can find the general solution for eq. \eqref{eq:motion_z}, when we consider the characteristic equation of a second order differential equation \cite{lindstrom:2016:ch10:5}. +\begin{align*} + r^{2} + \omega_{z}^{2} &= 0 \\ + r &= \pm \sqrt{- \omega_{z}^{2}} = \mp i \omega_{z}, +\end{align*} +two complex roots which gives us solutions in the form of +\begin{equation}\label{eq:all_diff_sol} + z = c_{1} e^{i \omega_{z} t} + c_{2} e^{-i \omega_{z} t}, +\end{equation} +For a complex number $z = a + ib$, we can define $e^{z} \equiv e^{a} (\cos{b} + i \sin{b})$ \cite{lindstrom:2016:ch3}. We can rewrite \eqref{eq:all_diff_sol} as +\begin{align*} + c_{1} e^{i \omega_{z} t} + c_{2} e^{-i \omega_{z} t} &= c_{1} (\cos{\omega_{z} t} + i \sin{\omega_{z} t}) + c_{2} (\cos{\omega_{z} t} - i \sin{\omega_{z} t} \\ + &= E \cos{\omega_{z} t} + i F \sin{\omega_{z} t} +\end{align*} +% +Since \eqref{eq:motion_x} and \eqref{eq:motion_y} are coupled, we want to rewrite it as a single differential equation. We can obtain this by introducing $f(t) = x(t) + iy(t)$, +\begin{align*} + (\ddot{x} - \omega_{0} \dot{y} - \frac{1}{2} \omega_{z}^{2} x) + i (\ddot{y} + \omega_{0} \dot{x} - \frac{1}{2} \omega_{z}^{2} y) &= 0 \\ + \ddot{x} - \omega_{0} \dot{y} - \frac{1}{2} \omega_{z}^{2} x + i\ddot{y} + i\omega_{0} \dot{x} - i \frac{1}{2} \omega_{z}^{2} y &= 0 \\ + \ddot{x} + i\ddot{y} + i\omega_{0} \dot{x} - \omega_{0} \dot{y} - \frac{1}{2} \omega_{z}^{2} x - i \frac{1}{2} \omega_{z}^{2} y &= 0 \\ + \ddot{x} + i\ddot{y} + i\omega_{0} (\dot{x} + i \dot{y}) - \frac{1}{2} \omega_{z}^{2} x - i \frac{1}{2} \omega_{z}^{2} y &= 0 \text{where $i \omega_{0} \dot{x} + (-1) \omega_{0} \dot{y} = i \omega_{0} \dot{x} + i^{2} \omega_{0} \dot{y}$} \\ + \ddot{f} + i \omega_{0} \dot{f} - \frac{1}{2} \omega_{z}^{2} f &= 0 +\end{align*} + + +Physical properties given by newtons second law \eqref{eq:newton_second} +\begin{equation}\label{eq:general_solution} + f(t) = A_{+}e^{-i(\omega_{+} t + \phi_{+})} + A_{-}e^{-i(\omega_{-} t + \phi_{-})} +\end{equation} +The particle moves and its position can be determined using newton. where the electric field + + + +%\biblio +\end{document} diff --git a/man_pages/man3/Particle.3 b/man_pages/man3/Particle.3 deleted file mode 100644 index f37639d..0000000 --- a/man_pages/man3/Particle.3 +++ /dev/null @@ -1,98 +0,0 @@ -.TH "Particle" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -Particle \- A class that holds attributes of a particle\&. - -.SH SYNOPSIS -.br -.PP -.PP -\fC#include \fP -.SS "Public Member Functions" - -.in +1c -.ti -1c -.RI "\fBParticle\fP (double \fBq\fP, double \fBm\fP, arma::vec::fixed< 3 > \fBr_vec\fP, arma::vec::fixed< 3 > \fBv_vec\fP)" -.br -.RI "Initialize the particle\&. " -.in -1c -.SS "Private Attributes" - -.in +1c -.ti -1c -.RI "double \fBq\fP" -.br -.RI "Charge\&. " -.ti -1c -.RI "double \fBm\fP" -.br -.RI "Mass\&. " -.ti -1c -.RI "arma::vec::fixed< 3 > \fBr_vec\fP" -.br -.RI "position " -.ti -1c -.RI "arma::vec::fixed< 3 > \fBv_vec\fP" -.br -.RI "velocity " -.in -1c -.SS "Friends" - -.in +1c -.ti -1c -.RI "class \fBPenningTrap\fP" -.br -.RI "Make private attributes available for \fBPenningTrap\fP\&. " -.in -1c -.SH "Detailed Description" -.PP -A class that holds attributes of a particle\&. -.PP -Definition at line \fB19\fP of file \fBParticle\&.hpp\fP\&. -.SH "Constructor & Destructor Documentation" -.PP -.SS "Particle::Particle (double q, double m, arma::vec::fixed< 3 > r_vec, arma::vec::fixed< 3 > v_vec)" - -.PP -Initialize the particle\&. Initialize the particle with a charge, mass, position and velocity\&. -.PP -Definition at line \fB16\fP of file \fBParticle\&.cpp\fP\&. -.SH "Friends And Related Function Documentation" -.PP -.SS "friend class \fBPenningTrap\fP\fC [friend]\fP" - -.PP -Make private attributes available for \fBPenningTrap\fP\&. -.PP -Definition at line \fB38\fP of file \fBParticle\&.hpp\fP\&. -.SH "Member Data Documentation" -.PP -.SS "double Particle::m\fC [private]\fP" - -.PP -Mass\&. -.PP -Definition at line \fB22\fP of file \fBParticle\&.hpp\fP\&. -.SS "double Particle::q\fC [private]\fP" - -.PP -Charge\&. -.PP -Definition at line \fB21\fP of file \fBParticle\&.hpp\fP\&. -.SS "arma::vec::fixed<3> Particle::r_vec\fC [private]\fP" - -.PP -position -.PP -Definition at line \fB23\fP of file \fBParticle\&.hpp\fP\&. -.SS "arma::vec::fixed<3> Particle::v_vec\fC [private]\fP" - -.PP -velocity -.PP -Definition at line \fB24\fP of file \fBParticle\&.hpp\fP\&. - -.SH "Author" -.PP -Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. diff --git a/man_pages/man3/Particle.cpp.3 b/man_pages/man3/Particle.cpp.3 deleted file mode 100644 index 7a93b45..0000000 --- a/man_pages/man3/Particle.cpp.3 +++ /dev/null @@ -1,42 +0,0 @@ -.TH "src/Particle.cpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -src/Particle.cpp \- The implementation of the \fBParticle\fP class\&. - -.SH SYNOPSIS -.br -.PP -\fC#include 'Particle\&.hpp'\fP -.br - -.SH "Detailed Description" -.PP -The implementation of the \fBParticle\fP class\&. - - -.PP -\fBAuthor\fP -.RS 4 -Cory Alexander Balaton (coryab) -.PP -Janita Ovidie Sandtrøen Willumsen (janitaws) -.RE -.PP -\fBVersion\fP -.RS 4 -0\&.1 -.RE -.PP -.PP -\fBBug\fP -.RS 4 -No known bugs -.RE -.PP - -.PP -Definition in file \fBParticle\&.cpp\fP\&. -.SH "Author" -.PP -Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. diff --git a/man_pages/man3/Particle.hpp.3 b/man_pages/man3/Particle.hpp.3 deleted file mode 100644 index abb26a7..0000000 --- a/man_pages/man3/Particle.hpp.3 +++ /dev/null @@ -1,50 +0,0 @@ -.TH "include/Particle.hpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -include/Particle.hpp \- A class that holds the properties of a particle\&. - -.SH SYNOPSIS -.br -.PP -\fC#include \fP -.br - -.SS "Classes" - -.in +1c -.ti -1c -.RI "class \fBParticle\fP" -.br -.RI "A class that holds attributes of a particle\&. " -.in -1c -.SH "Detailed Description" -.PP -A class that holds the properties of a particle\&. - - -.PP -\fBAuthor\fP -.RS 4 -Cory Alexander Balaton (coryab) -.PP -Janita Ovidie Sandtrøen Willumsen (janitaws) -.RE -.PP -\fBVersion\fP -.RS 4 -0\&.1 -.RE -.PP -.PP -\fBBug\fP -.RS 4 -No known bugs -.RE -.PP - -.PP -Definition in file \fBParticle\&.hpp\fP\&. -.SH "Author" -.PP -Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. diff --git a/man_pages/man3/PenningTrap.3 b/man_pages/man3/PenningTrap.3 deleted file mode 100644 index 2087bb5..0000000 --- a/man_pages/man3/PenningTrap.3 +++ /dev/null @@ -1,190 +0,0 @@ -.TH "PenningTrap" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -PenningTrap \- A class that simulates a Penning trap\&. - -.SH SYNOPSIS -.br -.PP -.PP -\fC#include \fP -.SS "Public Member Functions" - -.in +1c -.ti -1c -.RI "\fBPenningTrap\fP (double \fBB_0\fP=\fBT\fP, double \fBV_0\fP=25\&.*\fBV\fP/1000\&., double \fBd\fP=500\&.)" -.br -.RI "Set B_0, V_0 and d\&. " -.ti -1c -.RI "void \fBadd_particle\fP (\fBParticle\fP particle)" -.br -.RI "Add a particle to the system\&. " -.ti -1c -.RI "arma::vec \fBexternal_E_field\fP (arma::vec r)" -.br -.RI "Calculate E at point r\&. " -.ti -1c -.RI "arma::vec \fBexternal_B_field\fP (arma::vec r)" -.br -.RI "Calculate B at point r\&. " -.ti -1c -.RI "arma::vec \fBforce_on_particle\fP (int i, int j)" -.br -.RI "Calculate the force between 2 particles\&. " -.ti -1c -.RI "arma::vec \fBtotal_force_external\fP (int i)" -.br -.RI "Calculate the total external force on a particle\&. " -.ti -1c -.RI "arma::vec \fBtotal_force_particles\fP (int i)" -.br -.RI "Calculate the total force on a particle from other particles\&. " -.ti -1c -.RI "arma::vec \fBtotal_force\fP (int i)" -.br -.RI "calculate the total force on a particle\&. " -.ti -1c -.RI "void \fBevolve_RK4\fP (double dt)" -.br -.RI "Go forward one timestep using the RK4 method\&. " -.ti -1c -.RI "void \fBevolve_forward_euler\fP (double dt)" -.br -.RI "Go forward one timestep using the forward Euler method\&. " -.ti -1c -.RI "arma::vec \fBget_particle\fP (int i)" -.br -.ti -1c -.RI "double \fBget_d\fP ()" -.br -.in -1c -.SS "Private Attributes" - -.in +1c -.ti -1c -.RI "double \fBB_0\fP" -.br -.RI "Magnetic field strength\&. " -.ti -1c -.RI "double \fBV_0\fP" -.br -.RI "Applied potential\&. " -.ti -1c -.RI "double \fBd\fP" -.br -.RI "Characteristic dimension\&. " -.ti -1c -.RI "std::vector< \fBParticle\fP > \fBparticles\fP" -.br -.RI "The particles in the Penning trap\&. " -.in -1c -.SH "Detailed Description" -.PP -A class that simulates a Penning trap\&. - -This class simulates a Penning trap\&. It can take in a number of particles and simulate how they would behave inside a Penning trap\&. -.PP -Definition at line \fB29\fP of file \fBPenningTrap\&.hpp\fP\&. -.SH "Constructor & Destructor Documentation" -.PP -.SS "PenningTrap::PenningTrap (double B_0 = \fC\fBT\fP\fP, double V_0 = \fC25\&.*\fBV\fP/1000\&.\fP, double d = \fC500\&.\fP)" - -.PP -Set B_0, V_0 and d\&. -.PP -Definition at line \fB20\fP of file \fBPenningTrap\&.cpp\fP\&. -.SH "Member Function Documentation" -.PP -.SS "void PenningTrap::add_particle (\fBParticle\fP particle)" - -.PP -Add a particle to the system\&. -.PP -Definition at line \fB27\fP of file \fBPenningTrap\&.cpp\fP\&. -.SS "void PenningTrap::evolve_forward_euler (double dt)" - -.PP -Go forward one timestep using the forward Euler method\&. -.PP -Definition at line \fB167\fP of file \fBPenningTrap\&.cpp\fP\&. -.SS "void PenningTrap::evolve_RK4 (double dt)" - -.PP -Go forward one timestep using the RK4 method\&. -.PP -Definition at line \fB104\fP of file \fBPenningTrap\&.cpp\fP\&. -.SS "arma::vec PenningTrap::external_B_field (arma::vec r)" - -.PP -Calculate B at point r\&. -.PP -Definition at line \fB43\fP of file \fBPenningTrap\&.cpp\fP\&. -.SS "arma::vec PenningTrap::external_E_field (arma::vec r)" - -.PP -Calculate E at point r\&. -.PP -Definition at line \fB32\fP of file \fBPenningTrap\&.cpp\fP\&. -.SS "arma::vec PenningTrap::force_on_particle (int i, int j)" - -.PP -Calculate the force between 2 particles\&. Calculate the force exhibited on particle p_i from particle p_j\&. -.PP -Definition at line \fB50\fP of file \fBPenningTrap\&.cpp\fP\&. -.SS "double PenningTrap::get_d ()" - -.PP -Definition at line \fB188\fP of file \fBPenningTrap\&.cpp\fP\&. -.SS "arma::vec PenningTrap::get_particle (int i)" - -.PP -Definition at line \fB183\fP of file \fBPenningTrap\&.cpp\fP\&. -.SS "arma::vec PenningTrap::total_force (int i)" - -.PP -calculate the total force on a particle\&. -.PP -Definition at line \fB99\fP of file \fBPenningTrap\&.cpp\fP\&. -.SS "arma::vec PenningTrap::total_force_external (int i)" - -.PP -Calculate the total external force on a particle\&. Calculate the total amount of force that E and B exhibits on particle p_i\&. -.PP -Definition at line \fB65\fP of file \fBPenningTrap\&.cpp\fP\&. -.SS "arma::vec PenningTrap::total_force_particles (int i)" - -.PP -Calculate the total force on a particle from other particles\&. -.PP -Definition at line \fB80\fP of file \fBPenningTrap\&.cpp\fP\&. -.SH "Member Data Documentation" -.PP -.SS "double PenningTrap::B_0\fC [private]\fP" - -.PP -Magnetic field strength\&. -.PP -Definition at line \fB31\fP of file \fBPenningTrap\&.hpp\fP\&. -.SS "double PenningTrap::d\fC [private]\fP" - -.PP -Characteristic dimension\&. -.PP -Definition at line \fB33\fP of file \fBPenningTrap\&.hpp\fP\&. -.SS "std::vector<\fBParticle\fP> PenningTrap::particles\fC [private]\fP" - -.PP -The particles in the Penning trap\&. -.PP -Definition at line \fB34\fP of file \fBPenningTrap\&.hpp\fP\&. -.SS "double PenningTrap::V_0\fC [private]\fP" - -.PP -Applied potential\&. -.PP -Definition at line \fB32\fP of file \fBPenningTrap\&.hpp\fP\&. - -.SH "Author" -.PP -Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. diff --git a/man_pages/man3/PenningTrap.cpp.3 b/man_pages/man3/PenningTrap.cpp.3 deleted file mode 100644 index f850299..0000000 --- a/man_pages/man3/PenningTrap.cpp.3 +++ /dev/null @@ -1,54 +0,0 @@ -.TH "src/PenningTrap.cpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -src/PenningTrap.cpp \- The implementation of the \fBPenningTrap\fP class\&. - -.SH SYNOPSIS -.br -.PP -\fC#include 'PenningTrap\&.hpp'\fP -.br -\fC#include 'constants\&.hpp'\fP -.br -\fC#include 'utils\&.hpp'\fP -.br - -.SH "Detailed Description" -.PP -The implementation of the \fBPenningTrap\fP class\&. - - -.PP -\fBAuthor\fP -.RS 4 -Cory Alexander Balaton (coryab) -.PP -Janita Ovidie Sandtrøen Willumsen (janitaws) -.RE -.PP -\fBVersion\fP -.RS 4 -0\&.1 -.RE -.PP -.PP -\fBBug\fP -.RS 4 -No known bugs -.RE -.PP -.PP -\fBTodo\fP -.RS 4 -Implement evolve_RK4 -.PP -Implement evolve_forward_euler -.RE -.PP - -.PP -Definition in file \fBPenningTrap\&.cpp\fP\&. -.SH "Author" -.PP -Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. diff --git a/man_pages/man3/PenningTrap.hpp.3 b/man_pages/man3/PenningTrap.hpp.3 deleted file mode 100644 index c16a94b..0000000 --- a/man_pages/man3/PenningTrap.hpp.3 +++ /dev/null @@ -1,56 +0,0 @@ -.TH "include/PenningTrap.hpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -include/PenningTrap.hpp \- A class for simulating a Penning trap\&. - -.SH SYNOPSIS -.br -.PP -\fC#include \fP -.br -\fC#include \fP -.br -\fC#include 'Particle\&.hpp'\fP -.br -\fC#include 'constants\&.hpp'\fP -.br - -.SS "Classes" - -.in +1c -.ti -1c -.RI "class \fBPenningTrap\fP" -.br -.RI "A class that simulates a Penning trap\&. " -.in -1c -.SH "Detailed Description" -.PP -A class for simulating a Penning trap\&. - - -.PP -\fBAuthor\fP -.RS 4 -Cory Alexander Balaton (coryab) -.PP -Janita Ovidie Sandtrøen Willumsen (janitaws) -.RE -.PP -\fBVersion\fP -.RS 4 -0\&.1 -.RE -.PP -.PP -\fBBug\fP -.RS 4 -No known bugs -.RE -.PP - -.PP -Definition in file \fBPenningTrap\&.hpp\fP\&. -.SH "Author" -.PP -Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. diff --git a/man_pages/man3/PenningTrapTest.3 b/man_pages/man3/PenningTrapTest.3 deleted file mode 100644 index 07c0b75..0000000 --- a/man_pages/man3/PenningTrapTest.3 +++ /dev/null @@ -1,56 +0,0 @@ -.TH "PenningTrapTest" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -PenningTrapTest -.SH SYNOPSIS -.br -.PP -.SS "Static Public Member Functions" - -.in +1c -.ti -1c -.RI "static void \fBtest_external_E_field\fP ()" -.br -.ti -1c -.RI "static void \fBtest_external_B_field\fP ()" -.br -.ti -1c -.RI "static void \fBtest_force_on_particle\fP ()" -.br -.ti -1c -.RI "static void \fBtest_total_force_external\fP ()" -.br -.ti -1c -.RI "static void \fBtest_total_force_particles\fP ()" -.br -.in -1c -.SH "Detailed Description" -.PP -Definition at line \fB20\fP of file \fBtest_suite\&.cpp\fP\&. -.SH "Member Function Documentation" -.PP -.SS "static void PenningTrapTest::test_external_B_field ()\fC [inline]\fP, \fC [static]\fP" - -.PP -Definition at line \fB59\fP of file \fBtest_suite\&.cpp\fP\&. -.SS "static void PenningTrapTest::test_external_E_field ()\fC [inline]\fP, \fC [static]\fP" - -.PP -Definition at line \fB22\fP of file \fBtest_suite\&.cpp\fP\&. -.SS "static void PenningTrapTest::test_force_on_particle ()\fC [inline]\fP, \fC [static]\fP" - -.PP -Definition at line \fB70\fP of file \fBtest_suite\&.cpp\fP\&. -.SS "static void PenningTrapTest::test_total_force_external ()\fC [inline]\fP, \fC [static]\fP" - -.PP -Definition at line \fB95\fP of file \fBtest_suite\&.cpp\fP\&. -.SS "static void PenningTrapTest::test_total_force_particles ()\fC [inline]\fP, \fC [static]\fP" - -.PP -Definition at line \fB108\fP of file \fBtest_suite\&.cpp\fP\&. - -.SH "Author" -.PP -Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. diff --git a/man_pages/man3/bug.3 b/man_pages/man3/bug.3 deleted file mode 100644 index f93d6e3..0000000 --- a/man_pages/man3/bug.3 +++ /dev/null @@ -1,27 +0,0 @@ -.TH "bug" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -bug \- Bug List -.PP - -.IP "\fBFile \fBconstants\&.hpp\fP \fP" 1c -No known bugs -.IP "\fBFile \fBmain\&.cpp\fP \fP" 1c -No known bugs -.IP "\fBFile \fBParticle\&.cpp\fP \fP" 1c -No known bugs -.IP "\fBFile \fBParticle\&.hpp\fP \fP" 1c -No known bugs -.IP "\fBFile \fBPenningTrap\&.cpp\fP \fP" 1c -No known bugs -.IP "\fBFile \fBPenningTrap\&.hpp\fP \fP" 1c -No known bugs -.IP "\fBFile \fBtest_suite\&.cpp\fP \fP" 1c -No known bugs -.IP "\fBFile \fButils\&.cpp\fP \fP" 1c -No known bugs -.IP "\fBFile \fButils\&.hpp\fP \fP" 1c -No known bugs -.PP - diff --git a/man_pages/man3/constants.hpp.3 b/man_pages/man3/constants.hpp.3 deleted file mode 100644 index ed6ff65..0000000 --- a/man_pages/man3/constants.hpp.3 +++ /dev/null @@ -1,75 +0,0 @@ -.TH "include/constants.hpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -include/constants.hpp \- Library of constants\&. - -.SH SYNOPSIS -.br -.PP -.SS "Macros" - -.in +1c -.ti -1c -.RI "#define \fBK_E\fP 138935\&.333" -.br -.RI "Coulomb constant\&. unit: $\frac{u(\mu m)^3}{(\mu s)^2 e^2}$\&. " -.ti -1c -.RI "#define \fBT\fP 96\&.4852558" -.br -.RI "1 Tesla\&. unit: $ \frac{u}{(\mu s) e} $ " -.ti -1c -.RI "#define \fBV\fP 96485255\&.8" -.br -.RI "1 Volt\&. unit: $ \frac{u (\mu m)^2}{(\mu s)^2 e} $ " -.in -1c -.SH "Detailed Description" -.PP -Library of constants\&. - - -.PP -\fBAuthor\fP -.RS 4 -Cory Alexander Balaton (coryab) -.PP -Janita Ovidie Sandtrøen Willumsen (janitaws) -.RE -.PP -\fBVersion\fP -.RS 4 -0\&.1 -.RE -.PP -.PP -\fBBug\fP -.RS 4 -No known bugs -.RE -.PP - -.PP -Definition in file \fBconstants\&.hpp\fP\&. -.SH "Macro Definition Documentation" -.PP -.SS "#define K_E 138935\&.333" - -.PP -Coulomb constant\&. unit: $\frac{u(\mu m)^3}{(\mu s)^2 e^2}$\&. -.PP -Definition at line \fB15\fP of file \fBconstants\&.hpp\fP\&. -.SS "#define T 96\&.4852558" - -.PP -1 Tesla\&. unit: $ \frac{u}{(\mu s) e} $ -.PP -Definition at line \fB17\fP of file \fBconstants\&.hpp\fP\&. -.SS "#define V 96485255\&.8" - -.PP -1 Volt\&. unit: $ \frac{u (\mu m)^2}{(\mu s)^2 e} $ -.PP -Definition at line \fB19\fP of file \fBconstants\&.hpp\fP\&. -.SH "Author" -.PP -Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. diff --git a/man_pages/man3/main.cpp.3 b/man_pages/man3/main.cpp.3 deleted file mode 100644 index e02bbe4..0000000 --- a/man_pages/man3/main.cpp.3 +++ /dev/null @@ -1,102 +0,0 @@ -.TH "src/main.cpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -src/main.cpp \- The main program for this project\&. - -.SH SYNOPSIS -.br -.PP -\fC#include \fP -.br -\fC#include \fP -.br -\fC#include \fP -.br -\fC#include 'PenningTrap\&.hpp'\fP -.br - -.SS "Macros" - -.in +1c -.ti -1c -.RI "#define \fBPARTICLES\fP 100" -.br -.ti -1c -.RI "#define \fBN\fP 10000" -.br -.ti -1c -.RI "#define \fBCHARGE\fP 1\&." -.br -.ti -1c -.RI "#define \fBMASS\fP 40\&." -.br -.in -1c -.SS "Functions" - -.in +1c -.ti -1c -.RI "void \fBsimulate_100_particles\fP ()" -.br -.ti -1c -.RI "int \fBmain\fP ()" -.br -.in -1c -.SH "Detailed Description" -.PP -The main program for this project\&. - - -.PP -\fBAuthor\fP -.RS 4 -Cory Alexander Balaton (coryab) -.PP -Janita Ovidie Sandtrøen Willumsen (janitaws) -.RE -.PP -\fBVersion\fP -.RS 4 -0\&.1 -.RE -.PP -.PP -\fBBug\fP -.RS 4 -No known bugs -.RE -.PP - -.PP -Definition in file \fBmain\&.cpp\fP\&. -.SH "Macro Definition Documentation" -.PP -.SS "#define CHARGE 1\&." - -.PP -Definition at line \fB21\fP of file \fBmain\&.cpp\fP\&. -.SS "#define MASS 40\&." - -.PP -Definition at line \fB22\fP of file \fBmain\&.cpp\fP\&. -.SS "#define N 10000" - -.PP -Definition at line \fB20\fP of file \fBmain\&.cpp\fP\&. -.SS "#define PARTICLES 100" - -.PP -Definition at line \fB19\fP of file \fBmain\&.cpp\fP\&. -.SH "Function Documentation" -.PP -.SS "int main ()" - -.PP -Definition at line \fB77\fP of file \fBmain\&.cpp\fP\&. -.SS "void simulate_100_particles ()" - -.PP -Definition at line \fB24\fP of file \fBmain\&.cpp\fP\&. -.SH "Author" -.PP -Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. diff --git a/man_pages/man3/test_suite.cpp.3 b/man_pages/man3/test_suite.cpp.3 deleted file mode 100644 index fa522ef..0000000 --- a/man_pages/man3/test_suite.cpp.3 +++ /dev/null @@ -1,70 +0,0 @@ -.TH "src/test_suite.cpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -src/test_suite.cpp \- The test suite for the project\&. - -.SH SYNOPSIS -.br -.PP -\fC#include 'PenningTrap\&.hpp'\fP -.br -\fC#include 'utils\&.hpp'\fP -.br -\fC#include \fP -.br -\fC#include \fP -.br -\fC#include \fP -.br - -.SS "Classes" - -.in +1c -.ti -1c -.RI "class \fBPenningTrapTest\fP" -.br -.in -1c -.SS "Functions" - -.in +1c -.ti -1c -.RI "int \fBmain\fP ()" -.br -.in -1c -.SH "Detailed Description" -.PP -The test suite for the project\&. - - -.PP -\fBAuthor\fP -.RS 4 -Cory Alexander Balaton (coryab) -.PP -Janita Ovidie Sandtrøen Willumsen (janitaws) -.RE -.PP -\fBVersion\fP -.RS 4 -0\&.1 -.RE -.PP -.PP -\fBBug\fP -.RS 4 -No known bugs -.RE -.PP - -.PP -Definition in file \fBtest_suite\&.cpp\fP\&. -.SH "Function Documentation" -.PP -.SS "int main ()" - -.PP -Definition at line \fB135\fP of file \fBtest_suite\&.cpp\fP\&. -.SH "Author" -.PP -Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. diff --git a/man_pages/man3/todo.3 b/man_pages/man3/todo.3 deleted file mode 100644 index a66e064..0000000 --- a/man_pages/man3/todo.3 +++ /dev/null @@ -1,14 +0,0 @@ -.TH "todo" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -todo \- Todo List -.PP - -.IP "\fBFile \fBPenningTrap\&.cpp\fP \fP" 1c -Implement evolve_RK4 -.PP -.PP -Implement evolve_forward_euler -.PP - diff --git a/man_pages/man3/utils.cpp.3 b/man_pages/man3/utils.cpp.3 deleted file mode 100644 index 3d60a86..0000000 --- a/man_pages/man3/utils.cpp.3 +++ /dev/null @@ -1,153 +0,0 @@ -.TH "src/utils.cpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -src/utils.cpp \- Implementation of the utils\&. - -.SH SYNOPSIS -.br -.PP -\fC#include 'utils\&.hpp'\fP -.br - -.SS "Functions" - -.in +1c -.ti -1c -.RI "std::string \fBscientific_format\fP (double d, int width, int prec)" -.br -.RI "Turns a double into a string written in scientific format\&. " -.ti -1c -.RI "std::string \fBscientific_format\fP (const std::vector< double > &v, int width, int prec)" -.br -.RI "Turns a vector of doubles into a string written in scientific format\&. " -.ti -1c -.RI "void \fBm_assert\fP (bool expr, std::string expr_str, std::string f, std::string file, int line, std::string msg)" -.br -.RI "Test an expression, confirm that test is ok, or abort execution\&. " -.ti -1c -.RI "bool \fBarma_vector_close_to\fP (arma::vec &a, arma::vec &b, double tol)" -.br -.RI "Test if two armadillo vectors are close to each other\&. " -.in -1c -.SH "Detailed Description" -.PP -Implementation of the utils\&. - - -.PP -\fBAuthor\fP -.RS 4 -Cory Alexander Balaton (coryab) -.PP -Janita Ovidie Sandtrøen Willumsen (janitaws) -.RE -.PP -\fBVersion\fP -.RS 4 -1\&.0 -.RE -.PP -.PP -\fBBug\fP -.RS 4 -No known bugs -.RE -.PP - -.PP -Definition in file \fButils\&.cpp\fP\&. -.SH "Function Documentation" -.PP -.SS "bool arma_vector_close_to (arma::vec & a, arma::vec & b, double tol = \fC1e\-8\fP)" - -.PP -Test if two armadillo vectors are close to each other\&. This function takes in 2 vectors and checks if they are approximately equal to each other given a tolerance\&. -.PP -\fBParameters\fP -.RS 4 -\fIa\fP Vector a -.br -\fIb\fP Vector b -.br -\fItol\fP The tolerance -.RE -.PP -\fBReturns\fP -.RS 4 -Boolean -.RE -.PP - -.PP -Definition at line \fB59\fP of file \fButils\&.cpp\fP\&. -.SS "void m_assert (bool expr, std::string expr_str, std::string func, std::string file, int line, std::string msg)" - -.PP -Test an expression, confirm that test is ok, or abort execution\&. This function takes in an expression and prints an OK message if it's true, or it prints a fail message and aborts execution if it fails\&. -.PP -\fBParameters\fP -.RS 4 -\fIexpr\fP The expression to be evaluated -.br -\fIexpr_str\fP The stringified version of the expression -.br -\fIfunc\fP The function name of the caller -.br -\fIfile\fP The file of the caller -.br -\fIline\fP The line number where this function is called from -.br -\fImsg\fP The message to be displayed -.RE -.PP - -.PP -Definition at line \fB40\fP of file \fButils\&.cpp\fP\&. -.SS "std::string scientific_format (const std::vector< double > & v, int width = \fC20\fP, int prec = \fC10\fP)" - -.PP -Turns a vector of doubles into a string written in scientific format\&. -.PP -\fBParameters\fP -.RS 4 -\fIv\fP The vector to stringify -.br -\fIwidth\fP The reserved width of the string -.br -\fIprec\fP The precision of the stringified number -.RE -.PP -\fBReturns\fP -.RS 4 -String -.RE -.PP - -.PP -Definition at line \fB21\fP of file \fButils\&.cpp\fP\&. -.SS "std::string scientific_format (double d, int width = \fC20\fP, int prec = \fC10\fP)" - -.PP -Turns a double into a string written in scientific format\&. Code stolen from https://github.com/anderkve/FYS3150 Header: https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/include/utils.hpp Source: https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/src/utils.cpp -.PP -\fBParameters\fP -.RS 4 -\fId\fP The number to stringify -.br -\fIwidth\fP The reserved width of the string -.br -\fIprec\fP The precision of the stringified number -.RE -.PP -\fBReturns\fP -.RS 4 -String -.RE -.PP - -.PP -Definition at line \fB14\fP of file \fButils\&.cpp\fP\&. -.SH "Author" -.PP -Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. diff --git a/man_pages/man3/utils.hpp.3 b/man_pages/man3/utils.hpp.3 deleted file mode 100644 index a67beb7..0000000 --- a/man_pages/man3/utils.hpp.3 +++ /dev/null @@ -1,201 +0,0 @@ -.TH "include/utils.hpp" 3 "Sun Oct 8 2023" "Penning Trap Simulation" \" -*- nroff -*- -.ad l -.nh -.SH NAME -include/utils.hpp \- Function prototypes and macros that are useful\&. - -.SH SYNOPSIS -.br -.PP -\fC#include \fP -.br -\fC#include \fP -.br -\fC#include \fP -.br -\fC#include \fP -.br -\fC#include \fP -.br - -.SS "Macros" - -.in +1c -.ti -1c -.RI "#define \fBDEBUG\fP(msg)" -.br -.RI "Writes a debug message\&. " -.ti -1c -.RI "#define \fBASSERT\fP(expr, msg)" -.br -.RI "A prettier assertion function\&. " -.ti -1c -.RI "#define \fB__METHOD_NAME__\fP methodName(__PRETTY_FUNCTION__)" -.br -.in -1c -.SS "Functions" - -.in +1c -.ti -1c -.RI "std::string \fBscientific_format\fP (double d, int width=20, int prec=10)" -.br -.RI "Turns a double into a string written in scientific format\&. " -.ti -1c -.RI "std::string \fBscientific_format\fP (const std::vector< double > &v, int width=20, int prec=10)" -.br -.RI "Turns a vector of doubles into a string written in scientific format\&. " -.ti -1c -.RI "void \fBm_assert\fP (bool expr, std::string expr_str, std::string func, std::string file, int line, std::string msg)" -.br -.RI "Test an expression, confirm that test is ok, or abort execution\&. " -.ti -1c -.RI "bool \fBarma_vector_close_to\fP (arma::vec &a, arma::vec &b, double tol=1e\-8)" -.br -.RI "Test if two armadillo vectors are close to each other\&. " -.in -1c -.SH "Detailed Description" -.PP -Function prototypes and macros that are useful\&. - - -.PP -\fBAuthor\fP -.RS 4 -Cory Alexander Balaton (coryab) -.PP -Janita Ovidie Sandtrøen Willumsen (janitaws) -.RE -.PP -\fBVersion\fP -.RS 4 -1\&.0 -.RE -.PP -.PP -These utility function are mainly for convenience and aren't directly related to the project\&. -.PP -\fBBug\fP -.RS 4 -No known bugs -.RE -.PP - -.PP -Definition in file \fButils\&.hpp\fP\&. -.SH "Macro Definition Documentation" -.PP -.SS "#define __METHOD_NAME__ methodName(__PRETTY_FUNCTION__)" - -.PP -Definition at line \fB48\fP of file \fButils\&.hpp\fP\&. -.SS "#define ASSERT(expr, msg)" -\fBValue:\fP.PP -.nf - m_assert(expr, #expr, __METHOD_NAME__, __FILE__, \\ - __LINE__, msg) -.fi - -.PP -A prettier assertion function\&. This macro calls the m_assert function which is a more informative assertion function than the regular assert function from cassert\&. -.PP -Definition at line \fB45\fP of file \fButils\&.hpp\fP\&. -.SS "#define DEBUG(msg)" - -.PP -Writes a debug message\&. This macro writes a debug message that includes the filename, line number, and a custom message\&. The function is wrapped in an ifdef that checks if DBG is defined, so one can choose to display the debug messages by adding the -DDBG flag when compiling\&. -.PP -Definition at line \fB36\fP of file \fButils\&.hpp\fP\&. -.SH "Function Documentation" -.PP -.SS "bool arma_vector_close_to (arma::vec & a, arma::vec & b, double tol = \fC1e\-8\fP)" - -.PP -Test if two armadillo vectors are close to each other\&. This function takes in 2 vectors and checks if they are approximately equal to each other given a tolerance\&. -.PP -\fBParameters\fP -.RS 4 -\fIa\fP Vector a -.br -\fIb\fP Vector b -.br -\fItol\fP The tolerance -.RE -.PP -\fBReturns\fP -.RS 4 -Boolean -.RE -.PP - -.PP -Definition at line \fB59\fP of file \fButils\&.cpp\fP\&. -.SS "void m_assert (bool expr, std::string expr_str, std::string func, std::string file, int line, std::string msg)" - -.PP -Test an expression, confirm that test is ok, or abort execution\&. This function takes in an expression and prints an OK message if it's true, or it prints a fail message and aborts execution if it fails\&. -.PP -\fBParameters\fP -.RS 4 -\fIexpr\fP The expression to be evaluated -.br -\fIexpr_str\fP The stringified version of the expression -.br -\fIfunc\fP The function name of the caller -.br -\fIfile\fP The file of the caller -.br -\fIline\fP The line number where this function is called from -.br -\fImsg\fP The message to be displayed -.RE -.PP - -.PP -Definition at line \fB40\fP of file \fButils\&.cpp\fP\&. -.SS "std::string scientific_format (const std::vector< double > & v, int width = \fC20\fP, int prec = \fC10\fP)" - -.PP -Turns a vector of doubles into a string written in scientific format\&. -.PP -\fBParameters\fP -.RS 4 -\fIv\fP The vector to stringify -.br -\fIwidth\fP The reserved width of the string -.br -\fIprec\fP The precision of the stringified number -.RE -.PP -\fBReturns\fP -.RS 4 -String -.RE -.PP - -.PP -Definition at line \fB21\fP of file \fButils\&.cpp\fP\&. -.SS "std::string scientific_format (double d, int width = \fC20\fP, int prec = \fC10\fP)" - -.PP -Turns a double into a string written in scientific format\&. Code stolen from https://github.com/anderkve/FYS3150 Header: https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/include/utils.hpp Source: https://github.com/anderkve/FYS3150/blob/master/code_examples/compilation_linking/example_1/src/utils.cpp -.PP -\fBParameters\fP -.RS 4 -\fId\fP The number to stringify -.br -\fIwidth\fP The reserved width of the string -.br -\fIprec\fP The precision of the stringified number -.RE -.PP -\fBReturns\fP -.RS 4 -String -.RE -.PP - -.PP -Definition at line \fB14\fP of file \fButils\&.cpp\fP\&. -.SH "Author" -.PP -Generated automatically by Doxygen for Penning Trap Simulation from the source code\&. diff --git a/src/Makefile b/src/Makefile index 52c16b7..f678e43 100644 --- a/src/Makefile +++ b/src/Makefile @@ -8,7 +8,7 @@ CLASSOBJS=$(CLASSSRCS:.cpp=.o) INCLUDE=../include -CFLAGS=-larmadillo -llapack -std=c++11 -O2 +CFLAGS=-Wall -larmadillo -lblas -llapack -std=c++11 -O3 OPENMP=-fopenmp # Add a debug flag when compiling (For the DEBUG macro in utils.hpp) @@ -19,20 +19,27 @@ else DBGFLAG= endif +PROFILE ?= 0 +ifeq ($(PROFILE), 1) + PROFFLAG=-pg +else + PROFFLAG= +endif + .PHONY: clean all: test_suite main # Rules for executables main: main.o $(LIBOBJS) $(CLASSOBJS) - $(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) -I$(INCLUDE) $(OPENMP) + $(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP) test_suite: test_suite.o $(LIBOBJS) $(CLASSOBJS) - $(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) -I$(INCLUDE) $(OPENMP) + $(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP) # Rule for object files %.o: %.cpp - $(CC) -c $^ -o $@ $(CFLAGS) $(DBGFLAG) -I$(INCLUDE) $(OPENMP) + $(CC) -c $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP) clean: rm *.o diff --git a/src/Particle.cpp b/src/Particle.cpp index 0ff18e8..2caad68 100644 --- a/src/Particle.cpp +++ b/src/Particle.cpp @@ -8,7 +8,6 @@ * @brief The implementation of the Particle class. * * @bug No known bugs - * * */ #include "Particle.hpp" diff --git a/src/PenningTrap.cpp b/src/PenningTrap.cpp index 5d9a16b..d5a3b16 100644 --- a/src/PenningTrap.cpp +++ b/src/PenningTrap.cpp @@ -8,20 +8,75 @@ * @brief The implementation of the PenningTrap class. * * @bug No known bugs - * - * @todo Implement evolve_RK4 - * @todo Implement evolve_forward_euler * */ #include "PenningTrap.hpp" #include "constants.hpp" +#include "typedefs.hpp" #include "utils.hpp" -PenningTrap::PenningTrap(double B_0, double V_0, double d) +PenningTrap::PenningTrap(double B_0, std::function V_0, + double d, double t) { this->B_0 = B_0; this->V_0 = V_0; this->d = d; + this->t = t; +} + +PenningTrap::PenningTrap(unsigned int i, double B_0, + std::function V_0, double d, double t) + : PenningTrap::PenningTrap(B_0, V_0, d) +{ + vec_3d r, v; + for (size_t j = 0; j < i; j++) { + r = vec_3d().randn() * .1 * this->d; + v = vec_3d().randn() * .1 * this->d; + this->add_particle(Particle(1., 40., r, v)); + } +} + +PenningTrap::PenningTrap(std::vector particles, double B_0, + std::function V_0, double d, double t) + : PenningTrap::PenningTrap(B_0, V_0, d) +{ + this->particles = particles; +} + +vec_3d PenningTrap::v_func(unsigned int i, unsigned int j, double dt) +{ + switch (i) { + case 0: + return .5 * dt * this->k_v[0][j]; + case 1: + return .5 * dt * this->k_v[1][j]; + case 2: + return dt * this->k_v[2][j]; + case 3: + return (dt / 6.) * (this->k_v[0][j] + 2. * this->k_v[1][j] + + 2. * this->k_v[2][j] + this->k_v[3][j]); + default: + std::cout << "Not valid!" << std::endl; + abort(); + } +} + +vec_3d PenningTrap::r_func(unsigned int i, unsigned int j, double dt) +{ + switch (i) { + case 0: + return .5 * dt * this->k_r[0][j]; + case 1: + return .5 * dt * this->k_r[1][j]; + case 2: + return dt * this->k_r[2][j]; + case 3: + return (dt / 6.) * (this->k_r[0][j] + 2. * this->k_r[1][j] + + 2. * this->k_r[2][j] + this->k_r[3][j]); + default: + std::cout << "Not valid!" << std::endl; + abort(); + } } void PenningTrap::add_particle(Particle particle) @@ -29,61 +84,53 @@ void PenningTrap::add_particle(Particle particle) this->particles.push_back(particle); } -arma::vec PenningTrap::external_E_field(arma::vec r) +vec_3d PenningTrap::external_E_field(vec_3d r) { - arma::vec::fixed<3> res; - double f = this->V_0 / (this->d * this->d); - res(0) = r(0); - res(1) = r(1); - res(2) = -2. * r(2); + r(2) *= -2.; + double f = this->V_0(this->t) / (this->d * this->d); - return f * res; + return f * r; } -arma::vec PenningTrap::external_B_field(arma::vec r) +vec_3d PenningTrap::external_B_field(vec_3d r) { - arma::vec::fixed<3> res{0., 0., this->B_0}; - - return res; + return vec_3d{0., 0., this->B_0}; } -arma::vec PenningTrap::force_on_particle(int i, int j) +vec_3d PenningTrap::force_on_particle(unsigned int i, unsigned int j) { + Particle p_j = this->particles[j]; // Calculate the difference between the particles' position - arma::vec::fixed<3> res = - this->particles.at(i).r_vec - this->particles.at(j).r_vec; + vec_3d res = this->particles[i].r_vec - p_j.r_vec; // Get the distance between the particles - double norm = arma::norm(res); + double norm = arma::norm(res, 2); - // Multiply res with p_j's charge divided by the norm cubed - res *= this->particles.at(j).q / (norm * norm * norm); - - return res; + return vec_3d(res * p_j.q / (norm * norm * norm)); } -arma::vec PenningTrap::total_force_external(int i) +vec_3d PenningTrap::total_force_external(unsigned int i) { - Particle p = this->particles.at(i); + Particle p = this->particles[i]; - arma::vec::fixed<3> B = this->external_B_field(p.r_vec); + if (arma::norm(p.r_vec) > this->d) { + return vec_3d{0., 0., 0.}; + } - arma::vec::fixed<3> v_cross_B{p.v_vec(1) * B(2) - p.v_vec(2) * B(1), - p.v_vec(2) * B(0) - p.v_vec(0) * B(2), - p.v_vec(0) * B(1) - p.v_vec(1) * B(0)}; - - arma::vec force = p.q * (this->external_E_field(p.r_vec) + v_cross_B); + vec_3d force = + p.q * (this->external_E_field(p.r_vec) + + arma::cross(p.v_vec, this->external_B_field(p.r_vec))); return force; } -arma::vec PenningTrap::total_force_particles(int i) +vec_3d PenningTrap::total_force_particles(unsigned int i) { - Particle p = this->particles.at(i); + Particle p = this->particles[i]; - arma::vec res(3); + vec_3d res; - for (int j = 0; j < this->particles.size(); j++) { + for (size_t j = 0; j < this->particles.size(); j++) { if (i == j) { continue; } @@ -91,101 +138,171 @@ arma::vec PenningTrap::total_force_particles(int i) res += this->force_on_particle(i, j); } - res *= K_E * (p.q / p.m); - - return res; + return vec_3d(res * K_E * (p.q / p.m)); } -arma::vec PenningTrap::total_force(int i) +vec_3d PenningTrap::total_force(unsigned int i) { return this->total_force_external(i) - this->total_force_particles(i); } -void PenningTrap::evolve_RK4(double dt) +void PenningTrap::evolve_RK4(double dt, bool particle_interaction) { + + std::vector original_particles = this->particles; std::vector tmp_particles = this->particles; - - arma::vec::fixed<3> *k_v = new arma::vec::fixed<3>[this->particles.size()*4]; - arma::vec::fixed<3> *k_r = new arma::vec::fixed<3>[this->particles.size()*4]; - int size = this->particles.size(); - - for (int i=0; itotal_force(i)/this->particles.at(i).m; - k_r[i] = this->particles.at(i).v_vec; + vec_3d (PenningTrap::*force)(unsigned int); + if (particle_interaction) { + force = &PenningTrap::total_force; + } + else { + force = &PenningTrap::total_force_external; } - for (int i=0; iparticles.at(i); + size_t size = this->particles.size(); - p->v_vec = tmp_particles.at(i).v_vec + (dt/2)*k_v[i]; - p->r_vec = tmp_particles.at(i).r_vec + (dt/2)*k_r[i]; + this->k_v = sim_arr(4, sim_cols(size)); + this->k_r = sim_arr(4, sim_cols(size)); + + for (size_t i = 0; i < 4; i++) { +#pragma omp parallel for + for (size_t j = 0; j < this->particles.size(); j++) { + this->k_v[i][j] = (this->*force)(j) / this->particles[j].m; + this->k_r[i][j] = this->particles[j].v_vec; + + Particle *p = &tmp_particles[j]; + + p->v_vec = original_particles[j].v_vec + this->v_func(i, j, dt); + p->r_vec = original_particles[j].r_vec + this->r_func(i, j, dt); + } + this->particles.swap(tmp_particles); } - - - for (int i=0; itotal_force(i)/this->particles.at(i).m; - k_r[1*size + i] = this->particles.at(i).v_vec; - } - - for (int i=0; iparticles.at(i); - - p->v_vec = tmp_particles.at(i).v_vec + (dt/2)*k_v[1*size + i]; - p->r_vec = tmp_particles.at(i).r_vec + (dt/2)*k_r[1*size + i]; - } - - for (int i=0; itotal_force(i)/this->particles.at(i).m; - k_r[2*size + i] = this->particles.at(i).v_vec; - } - - for (int i=0; iparticles.at(i); - - p->v_vec = tmp_particles.at(i).v_vec + dt*k_v[2*size + i]; - p->r_vec = tmp_particles.at(i).r_vec + dt*k_r[2*size + i]; - } - - - for (int i=0; itotal_force(i)/this->particles.at(i).m; - k_r[3*size + i] = this->particles.at(i).v_vec; - } - - for (int i=0; iparticles.at(i); - - p->v_vec = tmp_particles.at(i).v_vec + dt*(k_v[i] + k_v[size + i] + k_v[2*size + i] + k_v[3*size + i])/6; - p->r_vec = tmp_particles.at(i).r_vec + dt*(k_r[i] + k_r[size + i] + k_r[2*size + i] + k_r[3*size + i])/6; - } - - delete [] k_v; - delete [] k_r; + this->t += dt; } -void PenningTrap::evolve_forward_euler(double dt) +void PenningTrap::evolve_forward_euler(double dt, bool particle_interaction) { - std::vector new_state = this->particles; - + size_t size = this->particles.size(); + vec_3d force_res[size]; Particle *p; -#pragma omp parallel for private(p) - for (int i = 0; i < this->particles.size(); i++) { - p = &new_state.at(i); - p->v_vec += dt * this->total_force(i) / new_state.at(i).m; - p->r_vec += dt * this->particles.at(i).v_vec; + vec_3d (PenningTrap::*force)(unsigned int); + if (particle_interaction) { + force = &PenningTrap::total_force; + } + else { + force = &PenningTrap::total_force_external; } - this->particles = new_state; +#pragma omp parallel for + for (size_t i = 0; i < size; i++) { + force_res[i] = (this->*force)(i); + } + +#pragma omp parallel for private(p) + for (size_t i = 0; i < size; i++) { + p = &this->particles[i]; + p->r_vec += dt * p->v_vec; + p->v_vec += dt * force_res[i] / p->m; + } + + this->t += dt; } -arma::vec PenningTrap::get_particle(int i) +simulation_t PenningTrap::simulate(double time, unsigned int steps, + std::string method, + bool particle_interaction) { - return this->particles.at(i).r_vec; + double dt = time / (double)steps; + + unsigned int size = this->particles.size(); + // sim_arr res(this->particles.size(), sim_cols(steps)); + simulation_t res{sim_arr(size, sim_cols(steps)), + sim_arr(size, sim_cols(steps))}; + + void (PenningTrap::*func)(double, bool); + if (method == "rk4") { + func = &PenningTrap::evolve_RK4; + } + else if (method == "euler") { + func = &PenningTrap::evolve_forward_euler; + } + else { + std::cout << "Not a valid method!" << std::endl; + abort(); + } + + for (size_t j = 0; j < steps; j++) { + for (size_t i = 0; i < size; i++) { + res.r_vecs[i][j] = this->particles[i].r_vec; + res.v_vecs[i][j] = this->particles[i].v_vec; + } + (this->*func)(dt, particle_interaction); + } + + return res; } -double PenningTrap::get_d() +void PenningTrap::write_simulation_to_dir(std::string path, double time, + unsigned int steps, + std::string method, + bool particle_interaction) { - return this->d; + if (path.back() != '/') { + path += '/'; + } + if (mkpath(path, 0777) != 0) { + std::cout << "Hello" << std::endl; + return; + } + + simulation_t res = + this->simulate(time, steps, method, particle_interaction); + + std::ofstream ofile; + +#pragma omp parallel for private(ofile) + for (size_t i = 0; i < this->particles.size(); i++) { + ofile.open(path + "particle_" + std::to_string(i) + "_r.txt"); + for (vec_3d &vec : res.r_vecs[i]) { + ofile << vec(0) << "," << vec(1) << "," << vec(2) << "\n"; + } + ofile.close(); + ofile.open(path + "particle_" + std::to_string(i) + "_v.txt"); + for (vec_3d &vec : res.v_vecs[i]) { + ofile << scientific_format(vec(0), 10, 8) << "," + << scientific_format(vec(1), 8, 10) << "," + << scientific_format(vec(2), 8, 10) << "\n"; + } + ofile.close(); + } +} + +double PenningTrap::fraction_of_particles_left(double time, unsigned int steps, + std::string method, + bool particle_interaction) +{ + simulation_t res = + this->simulate(time, steps, method, particle_interaction); + + int particles_left = 0; + + for (Particle p : this->particles) { + if (arma::norm(p.r_vec) < this->d) { + particles_left++; + } + } + + return (double)particles_left / (double)this->particles.size(); +} + +vec_3d PenningTrap::get_r(int i) +{ + return this->particles[i].r_vec; +} + +double PenningTrap::get_t() +{ + return this->t; } diff --git a/src/main.cpp b/src/main.cpp index 1c55279..19ef8fd 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -10,79 +10,181 @@ * @bug No known bugs * */ +#include +#include #include +#include #include +#include #include +#include #include "PenningTrap.hpp" +#include "utils.hpp" #define PARTICLES 100 -#define N 10000 +#define N 40000 #define CHARGE 1. #define MASS 40. // unit: amu -void simulate_100_particles() -{ - PenningTrap trap; +Particle p1(CHARGE, MASS, vec_3d{20., 0., 20.}, vec_3d{0., 25., 0.}); +Particle p2(CHARGE, MASS, vec_3d{25., 25., 0.}, vec_3d{0., 40., 5.}); - // Add particles inside trap - for (int i = 0; i < PARTICLES; i++) { - arma::vec r = arma::vec(3).randn() * 0.1 * - trap.get_d(); // random initial position - arma::vec v = arma::vec(3).randn() * 0.1 * - trap.get_d(); // random initial velocity - trap.add_particle(Particle(CHARGE, MASS, r, v)); - } +vec_3d analytical_solution_particle_1(double t) +{ + double w_0 = T / MASS; + double w_z2 = (50. * V / 1000.) / (MASS * 500. * 500.); + double w_p = (w_0 + std::sqrt(w_0 * w_0 - 2. * w_z2)) / 2.; + double w_n = (w_0 - std::sqrt(w_0 * w_0 - 2. * w_z2)) / 2.; + double A_p = (25. + w_n * 20.) / (w_n - w_p); + double A_n = -(25. + w_p * 20.) / (w_n - w_p); + std::complex f = A_p * std::exp(std::complex(0., -w_p * t)) + + A_n * std::exp(std::complex(0., -w_n * t)); + vec_3d res{std::real(f), std::imag(f), 20. * std::cos(std::sqrt(w_z2) * t)}; + return res; +} + +void simulate_single_particle() +{ + DEBUG("Inside single particle sim"); + PenningTrap trap(std::vector{p1}); double time = 50.; // microseconds - double dt = time / (double)N; - auto res = new arma::vec::fixed<3>[PARTICLES][N]; + DEBUG("Write to dir"); + trap.write_simulation_to_dir("output/simulate_single_particle", time, N, + "rk4", false); +} - int counter = 0; +void simulate_two_particles() +{ + PenningTrap trap_no_interaction(std::vector{p1, p2}); + PenningTrap trap_with_interaction(std::vector{p1, p2}); - // Get the path of all particles - for (int j = 0; j < N; j++) { -#pragma omp parallel for - for (int i = 0; i < PARTICLES; i++) { - res[i][j] = trap.get_particle(i); - } - trap.evolve_RK4(dt); - } + double time = 50.; // microseconds - std::cout << counter << std::endl; + trap_no_interaction.write_simulation_to_dir( + "output/simulate_2_particles/no_interaction", time, N, "rk4", false); + trap_with_interaction.write_simulation_to_dir( + "output/simulate_2_particles/with_interaction", time, N); +} - arma::vec::fixed<3> *cur_row; - arma::vec::fixed<3> cur_elem; +void simulate_single_particle_with_different_steps() +{ - mkdir("output", 0777); - mkdir("output/simulate_100_particles", 0777); + double time = 50.; // microseconds std::ofstream ofile; -// Write particle paths to file -#pragma omp parallel for private(cur_row, cur_elem, ofile) - for (int i = 0; i < PARTICLES; i++) { - cur_row = res[i]; - ofile.open("output/simulate_100_particles/p" + std::to_string(i) + ".txt"); - for (int j = 0; j < N; j++) { - cur_elem = cur_row[j]; - ofile << cur_elem(0) << "," << cur_elem(1) << "," << cur_elem(2) + for (int i = 0; i < 4; i++) { + int steps = 4000 * std::pow(2, i); + double dt = time / (double)steps; + std::string path = "output/relative_error/RK4/"; + mkpath(path); + ofile.open(path + std::to_string(steps) + "_steps.txt"); + PenningTrap trap(std::vector{p1}); + for (int i = 0; i < steps; i++) { + trap.evolve_RK4(dt); + ofile << arma::norm(trap.get_r(0) - + analytical_solution_particle_1(trap.get_t())) + << "\n"; + } + ofile.close(); + } + + for (int i = 0; i < 4; i++) { + int steps = 4000 * std::pow(2, i); + double dt = time / (double)steps; + std::string path = "output/relative_error/euler/"; + mkpath(path); + ofile.open(path + std::to_string(steps) + "_steps.txt"); + PenningTrap trap(std::vector{p1}); + for (int i = 0; i < steps; i++) { + trap.evolve_forward_euler(dt); + ofile << arma::norm(trap.get_r(0) - + analytical_solution_particle_1(trap.get_t())) << "\n"; } ofile.close(); } } +void simulate_100_particles() +{ + PenningTrap trap((unsigned)100, T, + [](double t) { + return 25. * V / 1000. * (1. + .4 * std::cos(1.5 * t)); + }, + 500., 0); + + double time = 500.; // microseconds + + trap.write_simulation_to_dir("output/simulate_100_particles", time, N * 4); +} + +void simulate_100_particles_with_time_potential() +{ + double amplitudes[]{.1, .4, .7}; + + double freq_start = .2; + double freq_end = 2.5; + double freq_increment = .02; + size_t freq_iterations = (size_t)((freq_end - freq_start) / freq_increment); + + double res[4][freq_iterations]; + + std::string path = "output/time_dependent_potential/"; + mkpath(path); + + std::ofstream ofile; + + double freq = freq_start; + for (size_t i = 0; i < freq_iterations; i++) { + res[0][i] = freq; + freq += freq_increment; + } + +#pragma omp parallel for collapse(2) num_threads(4) + for (size_t i = 0; i < 3; i++) { + for (size_t j = 0; j < freq_iterations; j++) { + PenningTrap trap( + (unsigned)100, T, + std::bind( + [](double f, double r, double t) { + return (25. * V / 1000.) * (1. + f * std::cos(r * t)); + }, + amplitudes[i], res[0][j], std::placeholders::_1), + 500., 0.); + res[i + 1][j] = + trap.fraction_of_particles_left(500., 40000, "rk4", false); + } + } + + ofile.open(path + "res.txt"); + for (size_t i = 0; i < freq_iterations; i++) { + ofile << res[0][i] << "," << res[1][i] << "," << res[2][i] << "," + << res[3][i] << "\n"; + } + ofile.close(); +} + int main() { double start = omp_get_wtime(); - simulate_100_particles(); + simulate_single_particle(); + + simulate_two_particles(); + + simulate_single_particle_with_different_steps(); + + // simulate_100_particles(); + + // simulate_100_particles_with_time_potential(); double end = omp_get_wtime(); - std::cout << "Time: " << end - start << " seconds" << std::endl; + std::cout << "Time: " << (end - start) << " seconds" << std::endl; return 0; } diff --git a/src/animate_100_particles.py b/src/scripts/animate_100_particles.py similarity index 88% rename from src/animate_100_particles.py rename to src/scripts/animate_100_particles.py index 19f10ca..0fc0083 100644 --- a/src/animate_100_particles.py +++ b/src/scripts/animate_100_particles.py @@ -32,7 +32,7 @@ def animate(): fig = plt.figure() ax = fig.add_subplot(projection="3d") - arr = get_data([f"output/simulate_100_particles/p{i}.txt" for i in range(100)]) + arr = get_data([f"output/simulate_100_particles/particle_{i}.txt" for i in range(100)]) arr = arr[:, :, ::10] @@ -63,8 +63,8 @@ def animate(): fig, update, N, fargs=(lines, arr), interval=1, blit=False ) - ani.save("../images/100_particles.gif", writer=animation.FFMpegFileWriter(fps=50)) - # plt.show() + # ani.save("../images/100_particles.gif", writer=animation.FFMpegFileWriter(fps=50)) + plt.show() if __name__ == "__main__": diff --git a/src/scripts/plot_2_particles.py b/src/scripts/plot_2_particles.py new file mode 100644 index 0000000..17f327c --- /dev/null +++ b/src/scripts/plot_2_particles.py @@ -0,0 +1,39 @@ +import matplotlib.pyplot as plt +import numpy as np + +def main(): + files = [ + "output/simulate_2_particles/no_interaction/particle_0_r.txt", + "output/simulate_2_particles/no_interaction/particle_1_r.txt", + "output/simulate_2_particles/with_interaction/particle_0_r.txt", + "output/simulate_2_particles/with_interaction/particle_1_r.txt" + ] + labels = [ + "particle 1 no interaction", + "particle 2 no interaction", + "particle 1 with interaction", + "particle 2 with interaction", + ] + colors = [ + "lightskyblue", + "lightskyblue", + "salmon", + "salmon" + ] + for label, color, file in zip(labels, colors, files): + with open(file) as f: + lines = f.readlines() + t = np.linspace(0, 50, len(lines)) + r = np.array([list(map(float, line.strip().split(","))) for line in lines]) + plt.plot(r[:,0], r[:,1], label=label, color=color) + + plt.xlabel(r"x $(\mu m)$") + plt.ylabel(r"y $(\mu m)$") + plt.title(r"2 particles with and without interactions.") + # plt.legend() + # plt.show() + plt.savefig("../latex/images/plot_2_particles_xy.pdf") + + +if __name__ == "__main__": + main() diff --git a/src/scripts/plot_3d.py b/src/scripts/plot_3d.py new file mode 100644 index 0000000..811bf6a --- /dev/null +++ b/src/scripts/plot_3d.py @@ -0,0 +1,40 @@ +import matplotlib.pyplot as plt +import numpy as np + +def main(): + files = [ + "output/simulate_2_particles/no_interaction/particle_0_r.txt", + "output/simulate_2_particles/no_interaction/particle_1_r.txt", + "output/simulate_2_particles/with_interaction/particle_0_r.txt", + "output/simulate_2_particles/with_interaction/particle_1_r.txt" + ] + labels = [ + "particle 1 no interaction", + "particle 2 no interaction", + "particle 1 with interaction", + "particle 2 with interaction", + ] + colors = [ + "lightskyblue", + "deepskyblue", + "salmon", + "darkred" + ] + ax = plt.figure().add_subplot(projection="3d") + for label, color, file in zip(labels, colors, files): + with open(file) as f: + lines = f.readlines() + t = np.linspace(0, 50, len(lines)) + r = np.array([list(map(float, line.strip().split(","))) for line in lines]) + ax.plot(r[:,0], r[:,1], r[:,2], label=label, color=color) + + ax.set_xlabel(r"x $(\mu m)$") + ax.set_ylabel(r"y $(\mu m)$") + ax.set_zlabel(r"z $(\mu m)$") + plt.title(r"2 particles with and without interactions.") + plt.legend() + plt.savefig("../latex/images/3d_plot.pdf") + + +if __name__ == "__main__": + main() diff --git a/src/scripts/plot_particles_left.py b/src/scripts/plot_particles_left.py new file mode 100644 index 0000000..85bfd78 --- /dev/null +++ b/src/scripts/plot_particles_left.py @@ -0,0 +1,30 @@ +import matplotlib.pyplot as plt + +def main(): + with open("output/time_dependent_potential/res.txt") as f: + lines = f.readlines() + x = [] + y1 = [] + y2 = [] + y3 = [] + for line in lines: + l = line.strip().split(",") + x.append(float(l[0])) + y1.append(float(l[1])) + y2.append(float(l[2])) + y3.append(float(l[3])) + + plt.plot(x,y1,label=f"amplitude: 0.1") + plt.plot(x,y2,label=f"amplitude: 0.4") + plt.plot(x,y3,label=f"amplitude: 0.7") + + plt.xlabel(r"$\omega_V$ (MHz)") + plt.ylabel(r"Fraction of particles left") + plt.title(r"The fraction of particles left in the Penning trap " + "after 500 microseconds for different amplitudes and frequencies") + plt.legend() + # plt.show() + plt.savefig("../latex/images/particles_left.pdf") + +if __name__ == "__main__": + main() diff --git a/src/scripts/plot_phase_space.py b/src/scripts/plot_phase_space.py new file mode 100644 index 0000000..5a4c3ac --- /dev/null +++ b/src/scripts/plot_phase_space.py @@ -0,0 +1,53 @@ +import matplotlib.pyplot as plt +import numpy as np + +def main(): + directories = { + "output/simulate_2_particles/no_interaction/", + "output/simulate_2_particles/with_interaction/", + } + titles = { + "particles without interaction", + "particles with interaction" + } + files = [ + "particle_0_r.txt", + "particle_0_v.txt", + "particle_1_r.txt", + "particle_1_v.txt", + ] + labels = [ + r"particle 1 r", + r"particle 1 v", + r"particle 2 r", + r"particle 2 v", + ] + colors = [ + "lightskyblue", + "deepskyblue", + "salmon", + "tomato", + ] + fig1, axs1 = plt.subplots(2,1) + fig2, axs2 = plt.subplots(2,1) + for i, (dir, title) in enumerate(zip(directories, titles)): + for label, color, file in zip(labels, colors, files): + with open(dir+file) as f: + lines = f.readlines() + t = np.linspace(0, 50, len(lines)) + r = np.array([list(map(float, line.strip().split(","))) for line in lines]) + axs1[i].plot(t, r[:,0], label=label, color=color) + axs2[i].plot(t, r[:,2], label=label, color=color) + + axs1[i].set(xlabel=r"t $(\mu s)$", ylabel = r"z $(\mu m)$") + + axs1[i].legend() + axs1[i].set_title(title) + + # plt.show() + fig1.savefig("../latex/images/phase_space_2_particles_x.pdf") + fig2.savefig("../latex/images/phase_space_2_particles_z.pdf") + + +if __name__ == "__main__": + main() diff --git a/src/scripts/plot_relative_error.py b/src/scripts/plot_relative_error.py new file mode 100644 index 0000000..54214c8 --- /dev/null +++ b/src/scripts/plot_relative_error.py @@ -0,0 +1,50 @@ +import matplotlib.pyplot as plt +import numpy as np + +def main(): + directories = { + "output/relative_error/RK4/", + "output/relative_error/euler/", + } + files = [ + "4000_steps.txt", + "8000_steps.txt", + "16000_steps.txt", + "32000_steps.txt", + ] + labels = [ + r"4000 steps", + r"8000 steps", + r"16000 steps", + r"32000 steps", + ] + titles = [ + "Relative error for the RK4 method", + "Relative error for the forward Euler method" + ] + fig1, axs1 = plt.subplots(2,1) + for i, (dir, title) in enumerate(zip(directories, titles)): + max_err = [] + for label, file in zip(labels, files): + with open(dir+file) as f: + lines = f.readlines() + t = np.linspace(0, 50, len(lines)) + r = np.array([float(line.strip()) for line in lines]) + max_err.append(max(r)) + axs1[i].plot(t, r, label=label) + + axs1[i].set(xlabel=r"t $(\mu s)$", ylabel = r"relative_error $(\mu m)$") + + + axs1[i].legend() + axs1[i].set_title(title) + + conv_rate = 1/3 * sum([np.log10(max_err[i+1]/max_err[i])/np.log10(.5) for i in range(3)]) + print(conv_rate) + + plt.show() + # fig1.savefig("../latex/images/phase_space_2_particles_x.pdf") + + +if __name__ == "__main__": + main() diff --git a/src/scripts/plot_single_particle.py b/src/scripts/plot_single_particle.py new file mode 100644 index 0000000..f4bdc6a --- /dev/null +++ b/src/scripts/plot_single_particle.py @@ -0,0 +1,30 @@ +import matplotlib.pyplot as plt +import numpy as np + +def z(t): + V_0 = 25.*9.64852558 * 10**4 + m = 40. + d = 500. + w_z = np.sqrt((2.*V_0)/(m*d*d)) + return 20.*np.cos(w_z*t) + +def main(): + filename = "output/simulate_single_particle/particle_0_r.txt" + r = t = [] + with open(filename) as f: + lines = f.readlines() + t = np.linspace(0, 50, len(lines)) + r = np.array([list(map(float, line.strip().split(","))) for line in lines]) + + plt.plot(t, r[:, 2], label="approximation") + plt.plot(t, z(t), label="analytical") + plt.xlabel(r"time $(\mu s)$") + plt.ylabel(r"z $(\mu m)$") + plt.title(r"Movement of a single particle in the x direction") + plt.legend() + # plt.savefig("../latex/images/single_particle.pdf") + plt.show() + + +if __name__ == "__main__": + main() diff --git a/src/test_suite.cpp b/src/test_suite.cpp index 81ea5c1..cd422c5 100644 --- a/src/test_suite.cpp +++ b/src/test_suite.cpp @@ -44,7 +44,7 @@ public: arma::vec result; arma::vec v; std::stringstream msg; - for (int i = 0; i < tests.size(); i++) { + for (size_t i = 0; i < tests.size(); i++) { v = tests.at(i).first; result = trap.external_E_field(v); diff --git a/src/utils.cpp b/src/utils.cpp index b55fa34..14670f0 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -9,6 +9,9 @@ * * @bug No known bugs * */ + +#include + #include "utils.hpp" std::string scientific_format(double d, int width, int prec) @@ -62,10 +65,35 @@ bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol) return false; } - for (int i = 0; i < a.n_elem; i++) { + for (size_t i = 0; i < a.n_elem; i++) { if (std::abs(a(i) - b(i)) >= tol) { return false; } } return true; } + +bool mkpath(std::string path, int mode) +{ + std::string cur_dir; + std::string::size_type pos = -1; + struct stat buf; + + if (path.back() != '/') { + path += '/'; + } + while (true) { + pos++; + pos = path.find('/', pos); + if (pos != std::string::npos) { + cur_dir = path.substr(0, pos); + if (mkdir(cur_dir.c_str(), mode) != 0 && stat(cur_dir.c_str(), &buf) != 0) { + return -1; + } + } + else { + break; + } + } + return 0; +}