diff --git a/.clang-format b/.clang-format index d4d13ad..aa36097 100644 --- a/.clang-format +++ b/.clang-format @@ -8,3 +8,5 @@ BreakBeforeBraces: Custom BraceWrapping: AfterFunction: true BeforeElse: true +BreakBeforeBinaryOperators: All +ColumnLimit: 79 diff --git a/Doxyfile b/Doxyfile index 7b951c6..61d59dd 100644 --- a/Doxyfile +++ b/Doxyfile @@ -917,7 +917,7 @@ WARN_LOGFILE = # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING # Note: If this tag is empty the current directory is searched. -INPUT = include src README.md +INPUT = include src src/scripts README.md # This tag can be used to specify the character encoding of the source files # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses diff --git a/README.md b/README.md index 254c153..f404967 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,78 @@ ![](./images/100_particles.gif) +[Repo](https://github.uio.no/FYS3150-G2-2023/Project-3) + +[Documentation](https://pages.github.uio.no/FYS3150-G2-2023/Project-3/) + +## Requirements + +### Operating systems + +- Linux + - Has been tested on [Fedora 38](https://fedoraproject.org/) + - Will most likely work on other Linux distributions +- MacOS + - Might work, but hasn't been tested +- Windows + - Will most likely not work + +### Libraries + +- Python + - [matplotlib](https://matplotlib.org/) + - [numpy](https://numpy.org/) + +- C++ + - [openmp](https://www.openmp.org/) + - [armadillo](https://arma.sourceforge.net/) + + +## Compiling + +Compiling is as easy as running this command while being inside the src directory: + +```shell + make +``` + +## Running programs + +### C++ binaries + +To run **main** or **test_suite**, just run this command while being inside src: + +```shell + ./ +``` + +### Python scripts + +#### Install libraries + +Before running the scripts, make sure that all libraries are installed. +Using pip, you can install all requirements like this: + +```shell + pip install -r requirements.txt +``` + +This recursively install all the packages that are listed in **requirements.txt**. + +#### Running scripts + +For the Python scripts, run them from the src directory like this: + +```shell + python scripts/ +``` + +If you have any problems running the scripts, you might have to run this instead: + +```shell + python3 scripts/ +``` + ## Credits diff --git a/docs/100_particles.gif b/docs/100_particles.gif index 337c6e5..53eb275 100644 Binary files a/docs/100_particles.gif and b/docs/100_particles.gif differ diff --git a/docs/Particle_8cpp_source.html b/docs/Particle_8cpp_source.html index 13c1950..cac8cb5 100644 --- a/docs/Particle_8cpp_source.html +++ b/docs/Particle_8cpp_source.html @@ -105,8 +105,8 @@ $(document).ready(function(){initNavTree('Particle_8cpp_source.html',''); initRe
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)
+
16 vec_3d r_vec,
+
17 vec_3d v_vec)
18{
19 // Giving the particle its properties
20 this->q = q;
@@ -120,6 +120,7 @@ $(document).ready(function(){initNavTree('Particle_8cpp_source.html',''); initRe
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
+
vec_3d
arma::vec::fixed< 3 > vec_3d
Typedef for a fixed 3d arma vector.
Definition: typedefs.hpp:36
diff --git a/docs/Particle_8hpp_source.html b/docs/Particle_8hpp_source.html index f3339f5..98ff655 100644 --- a/docs/Particle_8hpp_source.html +++ b/docs/Particle_8hpp_source.html @@ -128,7 +128,7 @@ $(document).ready(function(){initNavTree('Particle_8hpp_source.html',''); initRe
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
A class that simulates a Penning trap.
Definition: PenningTrap.hpp:31
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 5817ff6..81ea9db 100644 --- a/docs/PenningTrap_8cpp.html +++ b/docs/PenningTrap_8cpp.html @@ -105,9 +105,6 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp.html',''); initResiza

The implementation of the PenningTrap class. More...

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

Go to the source code of this file.

Detailed Description

diff --git a/docs/PenningTrap_8cpp_source.html b/docs/PenningTrap_8cpp_source.html index 282e5c2..fab32cb 100644 --- a/docs/PenningTrap_8cpp_source.html +++ b/docs/PenningTrap_8cpp_source.html @@ -103,310 +103,336 @@ $(document).ready(function(){initNavTree('PenningTrap_8cpp_source.html',''); ini
Go to the documentation of this file.
1
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
-
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);
+
14
+
15PenningTrap::PenningTrap(double B_0, std::function<double(double)> V_0,
+
16 double d, double t)
+
17{
+
18 this->B_0 = B_0;
+
19 this->V_0 = V_0;
+
20 this->d = d;
+
21 this->t = t;
+
22}
+
23
+
24PenningTrap::PenningTrap(unsigned int i, double B_0,
+
25 std::function<double(double)> V_0, double d, double t)
+
26 : PenningTrap::PenningTrap(B_0, V_0, d)
+
27{
+
28 vec_3d r, v;
+
29 for (size_t j = 0; j < i; j++) {
+
30 r = vec_3d().randn() * .1 * this->d;
+
31 v = vec_3d().randn() * .1 * this->d;
+
32 this->add_particle(Particle(1., 40., r, v));
+
33 }
+
34}
+
35
+
36PenningTrap::PenningTrap(std::vector<Particle> particles, double B_0,
+
37 std::function<double(double)> V_0, double d, double t)
+
38 : PenningTrap::PenningTrap(B_0, V_0, d)
+
39{
+
40 this->particles = particles;
+
41}
+
42
+
43vec_3d PenningTrap::v_func(unsigned int i, unsigned int j, double dt)
+
44{
+
45 switch (i) {
+
46 case 0:
+
47 return .5 * dt * this->k_v[0][j];
+
48 case 1:
+
49 return .5 * dt * this->k_v[1][j];
+
50 case 2:
+
51 return dt * this->k_v[2][j];
+
52 case 3:
+
53 return (dt / 6.) * (this->k_v[0][j] + 2. * this->k_v[1][j] +
+
54 2. * this->k_v[2][j] + this->k_v[3][j]);
+
55 default:
+
56 std::cout << "Not valid!" << std::endl;
+
57 abort();
+
58 }
+
59}
+
60
+
61vec_3d PenningTrap::r_func(unsigned int i, unsigned int j, double dt)
+
62{
+
63 switch (i) {
+
64 case 0:
+
65 return .5 * dt * this->k_r[0][j];
+
66 case 1:
+
67 return .5 * dt * this->k_r[1][j];
+
68 case 2:
+
69 return dt * this->k_r[2][j];
+
70 case 3:
+
71 return (dt / 6.) * (this->k_r[0][j] + 2. * this->k_r[1][j] +
+
72 2. * this->k_r[2][j] + this->k_r[3][j]);
+
73 default:
+
74 std::cout << "Not valid!" << std::endl;
+
75 abort();
+
76 }
+
77}
+
78
+
79void PenningTrap::add_particle(Particle particle)
+
80{
+
81 this->particles.push_back(particle);
+
82}
+
83
+
84vec_3d PenningTrap::external_E_field(vec_3d r)
+
85{
+
86 r(2) *= -2.;
+
87 double f = this->V_0(this->t) / (this->d * this->d);
+
88
+
89 return f * r;
+
90}
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 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 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 return force;
-
127}
+
92vec_3d PenningTrap::external_B_field(vec_3d r)
+
93{
+
94 return vec_3d{0., 0., this->B_0};
+
95}
+
96
+
97vec_3d PenningTrap::force_on_particle(unsigned int i, unsigned int j)
+
98{
+
99 // Calculate the difference between the particles' position
+
100 vec_3d res = this->particles[i].r_vec - this->particles[j].r_vec;
+
101
+
102 // Get the distance between the particles
+
103 double norm = arma::norm(res, 2);
+
104
+
105 return vec_3d(res * this->particles[j].q / (norm * norm * norm));
+
106}
+
107
+
108vec_3d PenningTrap::total_force_external(unsigned int i)
+
109{
+
110 Particle p = this->particles[i];
+
111
+
112 if (arma::norm(p.r_vec) > this->d) {
+
113 return vec_3d{0., 0., 0.};
+
114 }
+
115
+
116 vec_3d force =
+
117 p.q * (this->external_E_field(p.r_vec) +
+
118 arma::cross(p.v_vec, this->external_B_field(p.r_vec)));
+
119
+
120 return force;
+
121}
+
122
+
123vec_3d PenningTrap::total_force_particles(unsigned int i)
+
124{
+
125 Particle p = this->particles[i];
+
126
+
127 vec_3d res;
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 }
+
129 for (size_t j = 0; j < this->particles.size(); j++) {
+
130 if (i == j) {
+
131 continue;
+
132 }
+
133
+
134 res += this->force_on_particle(i, j);
+
135 }
+
136
+
137 return vec_3d(res * K_E * (p.q / p.m));
+
138}
139
-
140 res += this->force_on_particle(i, j);
-
141 }
-
142
-
143 return vec_3d(res * K_E * (p.q / p.m));
-
144}
-
145
-
146vec_3d PenningTrap::total_force(unsigned int i)
-
147{
-
148 return this->total_force_external(i) - this->total_force_particles(i);
-
149}
+
140vec_3d PenningTrap::total_force(unsigned int i)
+
141{
+
142 if (arma::norm(this->particles[i].r_vec) > this->d) {
+
143 return vec_3d{0., 0., 0.};
+
144 }
+
145 return this->total_force_external(i) - this->total_force_particles(i);
+
146}
+
147
+
148void PenningTrap::evolve_RK4(double dt, bool particle_interaction)
+
149{
150
-
151void PenningTrap::evolve_RK4(double dt, bool particle_interaction)
-
152{
+
151 std::vector<Particle> original_particles = this->particles;
+
152 std::vector<Particle> tmp_particles = this->particles;
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;
+
154 vec_3d (PenningTrap::*force)(unsigned int);
+
155 if (particle_interaction) {
+
156 force = &PenningTrap::total_force;
+
157 }
+
158 else {
+
159 force = &PenningTrap::total_force_external;
160 }
-
161 else {
-
162 force = &PenningTrap::total_force_external;
-
163 }
-
164
-
165 size_t size = this->particles.size();
+
161
+
162 size_t size = this->particles.size();
+
163
+
164 this->k_v = sim_arr(4, sim_cols(size));
+
165 this->k_r = sim_arr(4, sim_cols(size));
166
-
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;
+
167 for (size_t i = 0; i < 4; i++) {
+
168#pragma omp parallel for
+
169 for (size_t j = 0; j < this->particles.size(); j++) {
+
170 this->k_v[i][j] = (this->*force)(j) / this->particles[j].m;
+
171 this->k_r[i][j] = this->particles[j].v_vec;
+
172
+
173 Particle *p = &tmp_particles[j];
+
174
+
175 p->v_vec = original_particles[j].v_vec + this->v_func(i, j, dt);
+
176 p->r_vec = original_particles[j].r_vec + this->r_func(i, j, dt);
+
177 }
+
178 this->particles.swap(tmp_particles);
+
179 }
+
180 this->t += dt;
+
181}
+
182
+
183void PenningTrap::evolve_forward_euler(double dt, bool particle_interaction)
+
184{
+
185 size_t size = this->particles.size();
+
186 vec_3d force_res[size];
+
187 Particle *p;
+
188
+
189 vec_3d (PenningTrap::*force)(unsigned int);
+
190 if (particle_interaction) {
+
191 force = &PenningTrap::total_force;
+
192 }
+
193 else {
+
194 force = &PenningTrap::total_force_external;
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));
+
196
+
197#pragma omp parallel for
+
198 for (size_t i = 0; i < size; i++) {
+
199 force_res[i] = (this->*force)(i);
+
200 }
+
201
+
202#pragma omp parallel for private(p)
+
203 for (size_t i = 0; i < size; i++) {
+
204 p = &this->particles[i];
+
205 p->r_vec += dt * p->v_vec;
+
206 p->v_vec += dt * force_res[i] / p->m;
+
207 }
+
208
+
209 this->t += dt;
+
210}
+
211
+
212simulation_t PenningTrap::simulate(double time, unsigned int steps,
+
213 std::string method,
+
214 bool particle_interaction)
+
215{
+
216 double dt = time / (double)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();
+
218 unsigned int size = this->particles.size();
+
219
+
220 simulation_t res{sim_arr(size, sim_cols(steps)),
+
221 sim_arr(size, sim_cols(steps))};
+
222
+
223 void (PenningTrap::*func)(double, bool);
+
224 if (method == "rk4") {
+
225 func = &PenningTrap::evolve_RK4;
+
226 }
+
227 else if (method == "euler") {
+
228 func = &PenningTrap::evolve_forward_euler;
+
229 }
+
230 else {
+
231 std::cout << "Not a valid method!" << std::endl;
+
232 abort();
+
233 }
+
234
+
235 for (size_t j = 0; j < steps; j++) {
+
236 for (size_t i = 0; i < size; i++) {
+
237 res.r_vecs[i][j] = this->particles[i].r_vec;
+
238 res.v_vecs[i][j] = this->particles[i].v_vec;
+
239 }
+
240 (this->*func)(dt, particle_interaction);
+
241 }
+
242
+
243 return res;
+
244}
+
245
+
246void PenningTrap::write_simulation_to_dir(std::string path, double time,
+
247 unsigned int steps,
+
248 std::string method,
+
249 bool particle_interaction)
+
250{
+
251 if (path.back() != '/') {
+
252 path += '/';
+
253 }
+
254 if (mkpath(path, 0777) != 0) {
+
255 std::cout << "Hello" << std::endl;
+
256 return;
+
257 }
+
258
+
259 simulation_t res =
+
260 this->simulate(time, steps, method, particle_interaction);
+
261
+
262 std::ofstream ofile;
+
263
+
264#pragma omp parallel for private(ofile)
+
265 for (size_t i = 0; i < this->particles.size(); i++) {
+
266 ofile.open(path + "particle_" + std::to_string(i) + "_r.txt");
+
267 for (vec_3d &vec : res.r_vecs[i]) {
+
268 ofile << vec(0) << "," << vec(1) << "," << vec(2) << "\n";
+
269 }
+
270 ofile.close();
+
271 ofile.open(path + "particle_" + std::to_string(i) + "_v.txt");
+
272 for (vec_3d &vec : res.v_vecs[i]) {
+
273 ofile << scientific_format(vec(0), 10, 8) << ","
+
274 << scientific_format(vec(1), 8, 10) << ","
+
275 << scientific_format(vec(2), 8, 10) << "\n";
+
276 }
+
277 ofile.close();
+
278 }
279}
280
+
281double PenningTrap::fraction_of_particles_left(double time, unsigned int steps,
+
282 std::string method,
+
283 bool particle_interaction)
+
284{
+
285 simulation_t res =
+
286 this->simulate(time, steps, method, particle_interaction);
+
287
+
288 int particles_left = 0;
+
289
+
290 for (Particle p : this->particles) {
+
291 if (arma::norm(p.r_vec) < this->d) {
+
292 particles_left++;
+
293 }
+
294 }
+
295
+
296 return (double)particles_left / (double)this->particles.size();
+
297}
+
298
+
299vec_3d PenningTrap::get_r(int i)
+
300{
+
301 return this->particles[i].r_vec;
+
302}
+
303
+
304double PenningTrap::get_t()
+
305{
+
306 return this->t;
+
307}
PenningTrap.hpp
A class for simulating a Penning trap.
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.
+
PenningTrap
A class that simulates a Penning trap.
Definition: PenningTrap.hpp:31
+
PenningTrap::particles
std::vector< Particle > particles
The particles in the Penning trap.
Definition: PenningTrap.hpp:37
+
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:281
+
PenningTrap::B_0
double B_0
Magnetic field strength.
Definition: PenningTrap.hpp:33
+
PenningTrap::external_E_field
vec_3d external_E_field(vec_3d r)
Calculate E at point r.
Definition: PenningTrap.cpp:84
+
PenningTrap::total_force
vec_3d total_force(unsigned int i)
calculate the total force on a particle p_i.
Definition: PenningTrap.cpp:140
+
PenningTrap::k_r
sim_arr k_r
Definition: PenningTrap.hpp:40
+
PenningTrap::evolve_RK4
void evolve_RK4(double dt, bool particle_interaction=true)
Go forward one timestep using the RK4 method.
Definition: PenningTrap.cpp:148
+
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:61
+
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:123
+
PenningTrap::d
double d
Characteristic dimension.
Definition: PenningTrap.hpp:35
+
PenningTrap::add_particle
void add_particle(Particle particle)
Add a particle to the system.
Definition: PenningTrap.cpp:79
+
PenningTrap::t
double t
Current time.
Definition: PenningTrap.hpp:36
+
PenningTrap::force_on_particle
vec_3d force_on_particle(unsigned int i, unsigned int j)
Calculate the force between 2 particles.
Definition: PenningTrap.cpp:97
+
PenningTrap::V_0
std::function< double(double)> V_0
Applied potential.
Definition: PenningTrap.hpp:34
+
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:183
+
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:246
+
PenningTrap::external_B_field
vec_3d external_B_field(vec_3d r)
Calculate B at point r.
Definition: PenningTrap.cpp:92
+
PenningTrap::simulate
simulation_t 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:212
+
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:15
+
PenningTrap::total_force_external
vec_3d total_force_external(unsigned int i)
Calculate the total external force on a particle.
Definition: PenningTrap.cpp:108
+
PenningTrap::k_v
sim_arr k_v
Definition: PenningTrap.hpp:38
+
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:43
K_E
#define K_E
Coulomb constant. unit: .
Definition: constants.hpp:15
-
typedefs.hpp
Useful typedefs for cleaner code.
+
simulation
Typedef for PenningTrap::simulation return value.
Definition: typedefs.hpp:40
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
+
mkpath
bool mkpath(std::string path, int mode=0777)
Make path given.
Definition: utils.cpp:74
+
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:15
diff --git a/docs/PenningTrap_8hpp.html b/docs/PenningTrap_8hpp.html index 5f6ee45..7632939 100644 --- a/docs/PenningTrap_8hpp.html +++ b/docs/PenningTrap_8hpp.html @@ -111,6 +111,7 @@ $(document).ready(function(){initNavTree('PenningTrap_8hpp.html',''); initResiza #include "Particle.hpp"
#include "constants.hpp"
#include "typedefs.hpp"
+#include "utils.hpp"

Go to the source code of this file.

diff --git a/docs/PenningTrap_8hpp_source.html b/docs/PenningTrap_8hpp_source.html index dfdddbe..cc866c3 100644 --- a/docs/PenningTrap_8hpp_source.html +++ b/docs/PenningTrap_8hpp_source.html @@ -111,105 +111,111 @@ $(document).ready(function(){initNavTree('PenningTrap_8hpp_source.html',''); ini
18#include "Particle.hpp"
19#include "constants.hpp"
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
+
21#include "utils.hpp"
+
22
+
23#pragma omp declare reduction(+ : vec_3d : omp_out += omp_in) \
+
24 initializer(omp_priv = omp_orig)
+
25
+
31class PenningTrap {
+
32private:
+
33 double B_0;
+
34 std::function<double(double)> V_0;
+
35 double d;
+
36 double t;
+
37 std::vector<Particle> particles;
+
38 sim_arr k_v;
+
40 sim_arr k_r;
+
42
+
53 vec_3d v_func(unsigned int i, unsigned int j, double dt);
+
54
+
65 vec_3d r_func(unsigned int i, unsigned int j, double dt);
+
66
+
67public:
+
75 PenningTrap(
+
76 double B_0 = T,
+
77 std::function<double(double)> V_0 =
+
78 [](double t) { return 25. * V / 1000.; },
+
79 double d = 500., double t = 0.);
+
80
+
89 PenningTrap(
+
90 unsigned int i, double B_0 = T,
+
91 std::function<double(double)> V_0 =
+
92 [](double t) { return 25. * V / 1000.; },
+
93 double d = 500., double t = 0.);
+
94
+
103 PenningTrap(
+
104 std::vector<Particle> particles, double B_0 = T,
+
105 std::function<double(double)> V_0 =
+
106 [](double t) { return 25. * V / 1000.; },
+
107 double d = 500., double t = 0.);
+
108
+
113 void add_particle(Particle particle);
+
114
+
121 vec_3d external_E_field(vec_3d r);
+
122
+
129 vec_3d external_B_field(vec_3d r);
+
130
+
141 vec_3d force_on_particle(unsigned int i, unsigned int j);
+
142
+
152 vec_3d total_force_external(unsigned int i);
+
153
+
160 vec_3d total_force_particles(unsigned int i);
+
161
+
168 vec_3d total_force(unsigned int i);
+
169
+
175 void evolve_RK4(double dt, bool particle_interaction = true);
+
176
+
182 void evolve_forward_euler(double dt, bool particle_interaction = true);
+
183
+
194 simulation_t simulate(double time, unsigned int steps,
+
195 std::string method = "rk4",
+
196 bool particle_interaction = true);
+
197
+
206 void write_simulation_to_dir(std::string path, double time,
+
207 unsigned int steps, std::string method = "rk4",
+
208 bool particle_interaction = true);
+
209
+
220 double fraction_of_particles_left(double time, unsigned int steps,
+
221 std::string method = "rk4",
+
222 bool particle_interaction = true);
+
223
+
224 vec_3d get_r(int i);
+
225 double get_t();
+
226};
+
227
+
228#endif
Particle.hpp
A class that holds the properties of a particle.
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
+
PenningTrap
A class that simulates a Penning trap.
Definition: PenningTrap.hpp:31
+
PenningTrap::particles
std::vector< Particle > particles
The particles in the Penning trap.
Definition: PenningTrap.hpp:37
+
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:281
+
PenningTrap::B_0
double B_0
Magnetic field strength.
Definition: PenningTrap.hpp:33
+
PenningTrap::external_E_field
vec_3d external_E_field(vec_3d r)
Calculate E at point r.
Definition: PenningTrap.cpp:84
+
PenningTrap::total_force
vec_3d total_force(unsigned int i)
calculate the total force on a particle p_i.
Definition: PenningTrap.cpp:140
+
PenningTrap::k_r
sim_arr k_r
Definition: PenningTrap.hpp:40
+
PenningTrap::evolve_RK4
void evolve_RK4(double dt, bool particle_interaction=true)
Go forward one timestep using the RK4 method.
Definition: PenningTrap.cpp:148
+
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:61
+
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:123
+
PenningTrap::d
double d
Characteristic dimension.
Definition: PenningTrap.hpp:35
+
PenningTrap::add_particle
void add_particle(Particle particle)
Add a particle to the system.
Definition: PenningTrap.cpp:79
+
PenningTrap::t
double t
Current time.
Definition: PenningTrap.hpp:36
+
PenningTrap::force_on_particle
vec_3d force_on_particle(unsigned int i, unsigned int j)
Calculate the force between 2 particles.
Definition: PenningTrap.cpp:97
+
PenningTrap::V_0
std::function< double(double)> V_0
Applied potential.
Definition: PenningTrap.hpp:34
+
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:183
+
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:246
+
PenningTrap::external_B_field
vec_3d external_B_field(vec_3d r)
Calculate B at point r.
Definition: PenningTrap.cpp:92
+
PenningTrap::simulate
simulation_t 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:212
+
PenningTrap::total_force_external
vec_3d total_force_external(unsigned int i)
Calculate the total external force on a particle.
Definition: PenningTrap.cpp:108
+
PenningTrap::k_v
sim_arr k_v
Definition: PenningTrap.hpp:38
+
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:43
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
+
simulation
Typedef for PenningTrap::simulation return value.
Definition: typedefs.hpp:40
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
+
utils.hpp
Function prototypes and macros that are useful.
diff --git a/docs/animate__100__particles_8py_source.html b/docs/animate__100__particles_8py_source.html index af734ca..0475106 100644 --- a/docs/animate__100__particles_8py_source.html +++ b/docs/animate__100__particles_8py_source.html @@ -5,7 +5,7 @@ -Penning Trap Simulation: src/animate_100_particles.py Source File +Penning Trap Simulation: src/scripts/animate_100_particles.py Source File @@ -177,7 +177,7 @@ $(document).ready(function(){initNavTree('animate__100__particles_8py_source.htm diff --git a/docs/annotated.html b/docs/annotated.html index fdee9b2..323b2f9 100644 --- a/docs/annotated.html +++ b/docs/annotated.html @@ -105,7 +105,8 @@ $(document).ready(function(){initNavTree('annotated.html',''); initResizable();
- + +
 CParticleA class that holds attributes of a particle
 CPenningTrapA class that simulates a Penning trap
 CPenningTrapTest
 CPenningTrapTestTest class for the Penning trap
 CsimulationTypedef for PenningTrap::simulation return value
diff --git a/docs/annotated_dup.js b/docs/annotated_dup.js index 574cc6b..c52b935 100644 --- a/docs/annotated_dup.js +++ b/docs/annotated_dup.js @@ -2,5 +2,6 @@ var annotated_dup = [ [ "Particle", "classParticle.html", "classParticle" ], [ "PenningTrap", "classPenningTrap.html", "classPenningTrap" ], - [ "PenningTrapTest", "classPenningTrapTest.html", null ] + [ "PenningTrapTest", "classPenningTrapTest.html", null ], + [ "simulation", "structsimulation.html", null ] ]; \ No newline at end of file diff --git a/docs/classPenningTrap-members.html b/docs/classPenningTrap-members.html index 859c052..973ffb0 100644 --- a/docs/classPenningTrap-members.html +++ b/docs/classPenningTrap-members.html @@ -113,6 +113,8 @@ $(document).ready(function(){initNavTree('classPenningTrap.html',''); initResiza 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 + get_r(int i) (defined in PenningTrap)PenningTrap + get_t() (defined in PenningTrap)PenningTrap k_rPenningTrapprivate k_vPenningTrapprivate particlesPenningTrapprivate @@ -120,7 +122,7 @@ $(document).ready(function(){initNavTree('classPenningTrap.html',''); initResiza 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 + 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 diff --git a/docs/classPenningTrap.html b/docs/classPenningTrap.html index 9afb617..f5952a9 100644 --- a/docs/classPenningTrap.html +++ b/docs/classPenningTrap.html @@ -150,15 +150,19 @@ Public Member Functions 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.
-  +simulation_t 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.
  +vec_3d get_r (int i) +  +double get_t () +  @@ -195,7 +199,7 @@ Private Attributes

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 30 of file PenningTrap.hpp.

+

Definition at line 31 of file PenningTrap.hpp.

Constructor & Destructor Documentation

◆ PenningTrap() [1/3]

@@ -246,7 +250,7 @@ Private Attributes -

Definition at line 18 of file PenningTrap.cpp.

+

Definition at line 15 of file PenningTrap.cpp.

@@ -306,7 +310,7 @@ Private Attributes -

Definition at line 27 of file PenningTrap.cpp.

+

Definition at line 24 of file PenningTrap.cpp.

@@ -366,7 +370,7 @@ Private Attributes -

Definition at line 39 of file PenningTrap.cpp.

+

Definition at line 36 of file PenningTrap.cpp.

@@ -395,7 +399,7 @@ Private Attributes -

Definition at line 82 of file PenningTrap.cpp.

+

Definition at line 79 of file PenningTrap.cpp.

@@ -434,7 +438,7 @@ Private Attributes -

Definition at line 186 of file PenningTrap.cpp.

+

Definition at line 183 of file PenningTrap.cpp.

@@ -473,7 +477,7 @@ Private Attributes -

Definition at line 151 of file PenningTrap.cpp.

+

Definition at line 148 of file PenningTrap.cpp.

@@ -502,7 +506,7 @@ Private Attributes
Returns
vec_3d
-

Definition at line 95 of file PenningTrap.cpp.

+

Definition at line 92 of file PenningTrap.cpp.

@@ -531,7 +535,7 @@ Private Attributes
Returns
vec_3d
-

Definition at line 87 of file PenningTrap.cpp.

+

Definition at line 84 of file PenningTrap.cpp.

@@ -572,7 +576,7 @@ Private Attributes
Returns
vec_3d
-

Definition at line 100 of file PenningTrap.cpp.

+

Definition at line 97 of file PenningTrap.cpp.

@@ -626,7 +630,46 @@ Private Attributes
Returns
double
-

Definition at line 266 of file PenningTrap.cpp.

+

Definition at line 281 of file PenningTrap.cpp.

+ + + + +

◆ get_r()

+ +
+
+

Private Member Functions

+ + + + + + + +
vec_3d PenningTrap::get_r (int i)
+
+ +

Definition at line 299 of file PenningTrap.cpp.

+ +
+ + +

◆ get_t()

+ +
+
+ + + + + + + +
double PenningTrap::get_t ()
+
+ +

Definition at line 304 of file PenningTrap.cpp.

@@ -676,24 +719,24 @@ Private Attributes - +
iIndex i for \(k_{r,i,j}\)
jIndex j for \(k_{r,i,j}\)
dtthe step length (delta time)
dtThe step length (delta time)
Returns
vec_3d
-

Definition at line 64 of file PenningTrap.cpp.

+

Definition at line 61 of file PenningTrap.cpp.

- -

◆ simulate()

+ +

◆ simulate()

- + @@ -730,12 +773,13 @@ Private Attributes - +
sim_arr PenningTrap::simulate simulation_t PenningTrap::simulate ( double  time,
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
particle_interactionTurn particle interactions on/off
+
Returns
simulation_t
-

Definition at line 211 of file PenningTrap.cpp.

+

Definition at line 212 of file PenningTrap.cpp.

@@ -764,7 +808,7 @@ Private Attributes
Returns
vec_3d
-

Definition at line 146 of file PenningTrap.cpp.

+

Definition at line 140 of file PenningTrap.cpp.

@@ -794,7 +838,7 @@ Private Attributes
Returns
vec_3d
-

Definition at line 114 of file PenningTrap.cpp.

+

Definition at line 108 of file PenningTrap.cpp.

@@ -823,7 +867,7 @@ Private Attributes
Returns
vec_3d
-

Definition at line 129 of file PenningTrap.cpp.

+

Definition at line 123 of file PenningTrap.cpp.

@@ -879,7 +923,7 @@ Private Attributes
Returns
vec_3d
-

Definition at line 46 of file PenningTrap.cpp.

+

Definition at line 43 of file PenningTrap.cpp.

@@ -939,7 +983,7 @@ Private Attributes -

Definition at line 240 of file PenningTrap.cpp.

+

Definition at line 246 of file PenningTrap.cpp.

@@ -966,7 +1010,7 @@ Private Attributes

Magnetic field strength.

-

Definition at line 32 of file PenningTrap.hpp.

+

Definition at line 33 of file PenningTrap.hpp.

@@ -992,7 +1036,7 @@ Private Attributes

Characteristic dimension.

-

Definition at line 34 of file PenningTrap.hpp.

+

Definition at line 35 of file PenningTrap.hpp.

@@ -1017,7 +1061,7 @@ Private Attributes

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

-

Definition at line 39 of file PenningTrap.hpp.

+

Definition at line 40 of file PenningTrap.hpp.

@@ -1042,7 +1086,7 @@ Private Attributes

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

-

Definition at line 37 of file PenningTrap.hpp.

+

Definition at line 38 of file PenningTrap.hpp.

@@ -1068,7 +1112,7 @@ Private Attributes

The particles in the Penning trap.

-

Definition at line 36 of file PenningTrap.hpp.

+

Definition at line 37 of file PenningTrap.hpp.

@@ -1094,7 +1138,7 @@ Private Attributes

Current time.

-

Definition at line 35 of file PenningTrap.hpp.

+

Definition at line 36 of file PenningTrap.hpp.

@@ -1120,7 +1164,7 @@ Private Attributes

Applied potential.

-

Definition at line 33 of file PenningTrap.hpp.

+

Definition at line 34 of file PenningTrap.hpp.

diff --git a/docs/classPenningTrap.js b/docs/classPenningTrap.js index 0fd7f36..c3edebd 100644 --- a/docs/classPenningTrap.js +++ b/docs/classPenningTrap.js @@ -11,7 +11,7 @@ var classPenningTrap = [ "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 ], + [ "simulate", "classPenningTrap.html#ae09ef9cfa7e4ed1c108c8576405b3599", null ], [ "total_force", "classPenningTrap.html#a1f668c4433421136ad51741741aa1bc8", null ], [ "total_force_external", "classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56", null ], [ "total_force_particles", "classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b", null ], diff --git a/docs/classPenningTrapTest-members.html b/docs/classPenningTrapTest-members.html index 1b1f2e1..6a01a89 100644 --- a/docs/classPenningTrapTest-members.html +++ b/docs/classPenningTrapTest-members.html @@ -104,11 +104,11 @@ $(document).ready(function(){initNavTree('classPenningTrapTest.html',''); initRe

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

- - - - - + + + + +
test_external_B_field() (defined in PenningTrapTest)PenningTrapTestinlinestatic
test_external_E_field() (defined in PenningTrapTest)PenningTrapTestinlinestatic
test_force_on_particle() (defined in PenningTrapTest)PenningTrapTestinlinestatic
test_total_force_external() (defined in PenningTrapTest)PenningTrapTestinlinestatic
test_total_force_particles() (defined in PenningTrapTest)PenningTrapTestinlinestatic
test_external_B_field()PenningTrapTestinlinestatic
test_external_E_field()PenningTrapTestinlinestatic
test_force_on_particle()PenningTrapTestinlinestatic
test_total_force_external()PenningTrapTestinlinestatic
test_total_force_particles()PenningTrapTestinlinestatic
diff --git a/docs/classPenningTrapTest.html b/docs/classPenningTrapTest.html index 8eda947..b058407 100644 --- a/docs/classPenningTrapTest.html +++ b/docs/classPenningTrapTest.html @@ -104,23 +104,32 @@ $(document).ready(function(){initNavTree('classPenningTrapTest.html',''); initRe
PenningTrapTest Class Reference
+ +

Test class for the Penning trap. + More...

+ + + + +

Static Public Member Functions

static void test_external_E_field ()
 Test that the external E field gives correct values.
 
static void test_external_B_field ()
 Test that the external B field gives correct values.
 
static void test_force_on_particle ()
 Test that the force between particles gives expected results.
 
static void test_total_force_external ()
 Test that the total external force returns expected results.
 
static void test_total_force_particles ()
 Test that the total force of all particles on a single particle returns expected results.
 

Detailed Description

-
-

Definition at line 20 of file test_suite.cpp.

+

Test class for the Penning trap.

+ +

Definition at line 22 of file test_suite.cpp.

Member Function Documentation

◆ test_external_B_field()

@@ -145,7 +154,9 @@ Static Public Member Functions
-

Definition at line 59 of file test_suite.cpp.

+

Test that the external B field gives correct values.

+ +

Definition at line 65 of file test_suite.cpp.

@@ -172,7 +183,9 @@ Static Public Member Functions
-

Definition at line 22 of file test_suite.cpp.

+

Test that the external E field gives correct values.

+ +

Definition at line 26 of file test_suite.cpp.

@@ -199,7 +212,9 @@ Static Public Member Functions
-

Definition at line 70 of file test_suite.cpp.

+

Test that the force between particles gives expected results.

+ +

Definition at line 78 of file test_suite.cpp.

@@ -226,7 +241,9 @@ Static Public Member Functions
-

Definition at line 95 of file test_suite.cpp.

+

Test that the total external force returns expected results.

+ +

Definition at line 105 of file test_suite.cpp.

@@ -253,7 +270,9 @@ Static Public Member Functions
-

Definition at line 108 of file test_suite.cpp.

+

Test that the total force of all particles on a single particle returns expected results.

+ +

Definition at line 121 of file test_suite.cpp.

diff --git a/docs/classes.html b/docs/classes.html index 7b8f02e..11e3ca3 100644 --- a/docs/classes.html +++ b/docs/classes.html @@ -101,11 +101,14 @@ $(document).ready(function(){initNavTree('classes.html',''); initResizable(); })
Class Index
-
P
+
P | S
P
Particle
PenningTrap
PenningTrapTest
+
+
S
+
simulation
diff --git a/docs/dir_634e799a3947388232110823971192a8.html b/docs/dir_634e799a3947388232110823971192a8.html new file mode 100644 index 0000000..95b55e3 --- /dev/null +++ b/docs/dir_634e799a3947388232110823971192a8.html @@ -0,0 +1,132 @@ + + + + + + + +Penning Trap Simulation: src/scripts Directory Reference + + + + + + + + + + + + + + + + +
+
+ + + + + + +
+
Penning Trap Simulation +
+
Simulate particle behavior inside a Penning Trap
+
+
+ + + + + + + +
+
+ +
+
+
+ +
+ +
+
+ + +
+
+
+
+
+
Loading...
+
Searching...
+
No Matches
+
+
+
+
+ +
+
scripts Directory Reference
+
+
+ + + + + + + + + + + + + + + + +

+Files

file  animate_100_particles.py [code]
 
file  plot_2_particles.py [code]
 
file  plot_3d.py [code]
 
file  plot_particles_left.py [code]
 
file  plot_phase_space.py [code]
 
file  plot_relative_error.py [code]
 
file  plot_single_particle.py [code]
 
+
+
+ + + + diff --git a/docs/dir_634e799a3947388232110823971192a8.js b/docs/dir_634e799a3947388232110823971192a8.js new file mode 100644 index 0000000..f6030ae --- /dev/null +++ b/docs/dir_634e799a3947388232110823971192a8.js @@ -0,0 +1,10 @@ +var dir_634e799a3947388232110823971192a8 = +[ + [ "animate_100_particles.py", "animate__100__particles_8py_source.html", null ], + [ "plot_2_particles.py", "plot__2__particles_8py_source.html", null ], + [ "plot_3d.py", "plot__3d_8py_source.html", null ], + [ "plot_particles_left.py", "plot__particles__left_8py_source.html", null ], + [ "plot_phase_space.py", "plot__phase__space_8py_source.html", null ], + [ "plot_relative_error.py", "plot__relative__error_8py_source.html", null ], + [ "plot_single_particle.py", "plot__single__particle_8py_source.html", null ] +]; \ No newline at end of file diff --git a/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html b/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html index 4313bbd..a595b88 100644 --- a/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html +++ b/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.html @@ -102,10 +102,13 @@ $(document).ready(function(){initNavTree('dir_68267d1309a1af8e8297ef4c3efbcdba.h
+ + + +

+Directories

directory  scripts
 
- - @@ -115,8 +118,6 @@ Files - - diff --git a/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.js b/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.js index 64ce7a5..b85a8c3 100644 --- a/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.js +++ b/docs/dir_68267d1309a1af8e8297ef4c3efbcdba.js @@ -1,10 +1,9 @@ var dir_68267d1309a1af8e8297ef4c3efbcdba = [ - [ "animate_100_particles.py", "animate__100__particles_8py_source.html", null ], - [ "main.cpp", "main_8cpp.html", null ], + [ "scripts", "dir_634e799a3947388232110823971192a8.html", "dir_634e799a3947388232110823971192a8" ], + [ "main.cpp", "main_8cpp.html", "main_8cpp" ], [ "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/files.html b/docs/files.html index e842a47..0176ee4 100644 --- a/docs/files.html +++ b/docs/files.html @@ -102,7 +102,7 @@ $(document).ready(function(){initNavTree('files.html',''); initResizable(); });
Here is a list of all documented files with brief descriptions:
-
[detail level 12]

Files

file  animate_100_particles.py [code]
 
file  main.cpp [code]
 The main program for this project.
 
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.
 
+
[detail level 123]
@@ -110,13 +110,19 @@ $(document).ready(function(){initNavTree('files.html',''); initResizable(); }); - - - - - - - + + + + + + + + + + + + +
 ▼ include
 constants.hppLibrary of constants
 Particle.hppA class that holds the properties of a particle
 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
 ▼ scripts
 animate_100_particles.py
 plot_2_particles.py
 plot_3d.py
 plot_particles_left.py
 plot_phase_space.py
 plot_relative_error.py
 plot_single_particle.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
diff --git a/docs/functions.html b/docs/functions.html index a2f04ea..cc1a7e4 100644 --- a/docs/functions.html +++ b/docs/functions.html @@ -98,33 +98,92 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
-
Here is a list of all documented class members with links to the class documentation for each member:
diff --git a/docs/functions_func.html b/docs/functions_func.html index 1182b1d..5d4f949 100644 --- a/docs/functions_func.html +++ b/docs/functions_func.html @@ -109,7 +109,12 @@ $(document).ready(function(){initNavTree('functions_func.html',''); initResizabl
  • Particle() : Particle
  • PenningTrap() : PenningTrap
  • r_func() : PenningTrap
    • -
  • simulate() : PenningTrap
    • +
  • simulate() : PenningTrap
    • +
  • test_external_B_field() : PenningTrapTest
    • +
  • test_external_E_field() : PenningTrapTest
    • +
  • test_force_on_particle() : PenningTrapTest
    • +
  • test_total_force_external() : PenningTrapTest
    • +
  • test_total_force_particles() : PenningTrapTest
  • total_force() : PenningTrap
  • total_force_external() : PenningTrap
  • total_force_particles() : PenningTrap
    • diff --git a/docs/globals.html b/docs/globals.html index 19a9638..66911fb 100644 --- a/docs/globals.html +++ b/docs/globals.html @@ -100,16 +100,25 @@ $(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_type.html b/docs/globals_type.html index b7735cc..775a687 100644 --- a/docs/globals_type.html +++ b/docs/globals_type.html @@ -102,6 +102,7 @@ $(document).ready(function(){initNavTree('globals_type.html',''); initResizable(
  • sim_arr : typedefs.hpp
  • sim_cols : typedefs.hpp
  • sim_rows : typedefs.hpp
    • +
  • simulation_t : typedefs.hpp
  • vec_3d : typedefs.hpp
    • diff --git a/docs/globals_vars.html b/docs/globals_vars.html new file mode 100644 index 0000000..2c80e49 --- /dev/null +++ b/docs/globals_vars.html @@ -0,0 +1,114 @@ + + + + + + + +Penning Trap Simulation: File Members + + + + + + + + + + + + + + + + +
    +
    + + + + + + +
    +
    Penning Trap Simulation +
    +
    Simulate particle behavior inside a Penning Trap
    +
    +
    + + + + + + + +
    +
    + +
    +
    +
    + +
    + +
    +
    + + +
    +
    +
    +
    +
    +
    Loading...
    +
    Searching...
    +
    No Matches
    +
    +
    +
    +
    + +
    +  +
    +
    + + + + diff --git a/docs/index.html b/docs/index.html index 29ac7fb..b9d7673 100644 --- a/docs/index.html +++ b/docs/index.html @@ -104,7 +104,65 @@ $(document).ready(function(){initNavTree('index.html',''); initResizable(); });

    -

    +

    Repo

    +

    Documentation

    +

    +Requirements

    +

    +Operating systems

    +
      +
    • Linux
        +
      • Has been tested on Fedora 38
        • +
      • Will most likely work on other Linux distributions
        • +
      +
      • +
    • MacOS
        +
      • Might work, but hasn't been tested
        • +
      +
      • +
    • Windows
        +
      • Will most likely not work
        • +
      +
      • +
    +

    +Libraries

    + +

    +Compiling

    +

    Compiling is as easy as running this command while being inside the src directory:

    +
    make
    +

    +Running programs

    +

    +C++ binaries

    +

    To run main or test_suite, just run this command while being inside src:

    +
    ./<program-name>
    +

    +Python scripts

    +

    +Install libraries

    +

    Before running the scripts, make sure that all libraries are installed. Using pip, you can install all requirements like this:

    +
    pip install -r requirements.txt
    +

    This recursively install all the packages that are listed in requirements.txt.

    +

    +Running scripts

    +

    For the Python scripts, run them from the src directory like this:

    +
    python scripts/<script-name>
    +

    If you have any problems running the scripts, you might have to run this instead:

    +
    python3 scripts/<script-name>
    +

    Credits

    The Doxygen theme used here is doxygen-awesome-css.

    diff --git a/docs/main_8cpp.html b/docs/main_8cpp.html index b83f224..c7ad43a 100644 --- a/docs/main_8cpp.html +++ b/docs/main_8cpp.html @@ -109,10 +109,10 @@ $(document).ready(function(){initNavTree('main_8cpp.html',''); initResizable();

    The main program for this project. More...

    #include <cmath>
    +#include <complex>
    #include <fstream>
    #include <omp.h>
    #include <string>
    -#include <sys/stat.h>
    #include <vector>
    #include "PenningTrap.hpp"
    #include "utils.hpp"
    @@ -123,7 +123,7 @@ $(document).ready(function(){initNavTree('main_8cpp.html',''); initResizable(); Macros #define PARTICLES   100   -#define N   10000 +#define N   40000   #define CHARGE   1.   @@ -132,15 +132,23 @@ Macros + + + + + + + + @@ -149,9 +157,11 @@ Functions Variables + +

    Functions

    vec_3d analytical_solution_particle_1 (double t)
     The analytical solution for particle p1.
     
    void simulate_single_particle ()
     Simulate a single particle over the period of 50 \( \mu s \).
     
    void simulate_two_particles ()
     Simulate 2 particles over the period of 50 \( \mu s \) with and without particle interactions.
     
    void simulate_single_particle_with_different_steps ()
     Simulate a single particle over 50 \( \mu s \) using different amount of steps and different methods.
     
    void simulate_100_particles ()
     Simulate 100 particles over 50 \( \mu s \).
     
    void simulate_100_particles_with_time_potential ()
     Simulate 100 particles over 500 \( \mu s \) using a time dependent potential.
     
    int main ()
     
    Particle p1 (CHARGE, MASS, vec_3d{20., 0., 20.}, vec_3d{0., 25., 0.})
     Particle 1.
     
    Particle p2 (CHARGE, MASS, vec_3d{25., 25., 0.}, vec_3d{0., 40., 5.})
     Particle 2.
     

    Detailed Description

    @@ -203,7 +213,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    - +
    #define N   10000#define N   40000
    @@ -229,6 +239,35 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)

    Function Documentation

    + +

    ◆ analytical_solution_particle_1()

    + +
    +
    + + + + + + + + +
    vec_3d analytical_solution_particle_1 (double t)
    +
    + +

    The analytical solution for particle p1.

    +
    Parameters
    + + +
    tTime
    +
    +
    +
    Returns
    vec_3d
    + +

    Definition at line 38 of file main.cpp.

    + +
    +

    ◆ main()

    @@ -244,7 +283,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 124 of file main.cpp.

    +

    Definition at line 194 of file main.cpp.

    @@ -263,7 +302,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 77 of file main.cpp.

    +

    Simulate 100 particles over 50 \( \mu s \).

    + +

    Definition at line 131 of file main.cpp.

    @@ -282,7 +323,10 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 91 of file main.cpp.

    +

    Simulate 100 particles over 500 \( \mu s \) using a time dependent potential.

    +

    The simulation sweeps over different frequencies in [0.2, 2.5] MHz.

    + +

    Definition at line 146 of file main.cpp.

    @@ -301,7 +345,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 31 of file main.cpp.

    +

    Simulate a single particle over the period of 50 \( \mu s \).

    + +

    Definition at line 55 of file main.cpp.

    @@ -320,7 +366,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 55 of file main.cpp.

    +

    Simulate a single particle over 50 \( \mu s \) using different amount of steps and different methods.

    + +

    Definition at line 88 of file main.cpp.

    @@ -339,7 +387,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    -

    Definition at line 42 of file main.cpp.

    +

    Simulate 2 particles over the period of 50 \( \mu s \) with and without particle interactions.

    + +

    Definition at line 70 of file main.cpp.

    diff --git a/docs/main_8cpp.js b/docs/main_8cpp.js new file mode 100644 index 0000000..8b2b87e --- /dev/null +++ b/docs/main_8cpp.js @@ -0,0 +1,11 @@ +var main_8cpp = +[ + [ "analytical_solution_particle_1", "main_8cpp.html#a6451833d72816ef393087956c766125b", null ], + [ "simulate_100_particles", "main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513", null ], + [ "simulate_100_particles_with_time_potential", "main_8cpp.html#a330668384dc073980ba11116309bacc5", null ], + [ "simulate_single_particle", "main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6", null ], + [ "simulate_single_particle_with_different_steps", "main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2", null ], + [ "simulate_two_particles", "main_8cpp.html#a783789519f97c6430081171cacb0ffb1", null ], + [ "p1", "main_8cpp.html#a87da4ef9f2cd753579484824310467b8", null ], + [ "p2", "main_8cpp.html#a90f661586eb3c318fdca6f95ebc4fc46", null ] +]; \ No newline at end of file diff --git a/docs/main_8cpp_source.html b/docs/main_8cpp_source.html index d437689..276eed1 100644 --- a/docs/main_8cpp_source.html +++ b/docs/main_8cpp_source.html @@ -103,148 +103,205 @@ $(document).ready(function(){initNavTree('main_8cpp_source.html',''); initResiza
    Go to the documentation of this file.
    1
    13#include <cmath>
    -
    14#include <fstream>
    -
    15#include <omp.h>
    -
    16#include <string>
    -
    17#include <sys/stat.h>
    +
    14#include <complex>
    +
    15#include <fstream>
    +
    16#include <omp.h>
    +
    17#include <string>
    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
    +
    24#define N 40000
    +
    25#define CHARGE 1. // unit: e
    +
    26#define MASS 40. // unit: amu
    27
    -
    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
    -
    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
    -
    55void simulate_single_particle_with_different_steps()
    +
    28// Particles used for testing
    +
    29Particle p1(CHARGE, MASS, vec_3d{20., 0., 20.}, vec_3d{0., 25., 0.});
    +
    30Particle p2(CHARGE, MASS, vec_3d{25., 25., 0.}, vec_3d{0., 40., 5.});
    +
    31
    +
    38vec_3d analytical_solution_particle_1(double t)
    +
    39{
    +
    40 double w_0 = T / MASS;
    +
    41 double w_z2 = (50. * V / 1000.) / (MASS * 500. * 500.);
    +
    42 double w_p = (w_0 + std::sqrt(w_0 * w_0 - 2. * w_z2)) / 2.;
    +
    43 double w_n = (w_0 - std::sqrt(w_0 * w_0 - 2. * w_z2)) / 2.;
    +
    44 double A_p = (25. + w_n * 20.) / (w_n - w_p);
    +
    45 double A_n = -(25. + w_p * 20.) / (w_n - w_p);
    +
    46 std::complex<double> f =
    +
    47 A_p * std::exp(std::complex<double>(0., -w_p * t)) +
    +
    48 A_n * std::exp(std::complex<double>(0., -w_n * t));
    +
    49 vec_3d res{std::real(f), std::imag(f), 20. * std::cos(std::sqrt(w_z2) * t)};
    +
    50 return res;
    +
    51}
    +
    52
    +
    55void simulate_single_particle()
    56{
    -
    57
    -
    58 double time = 50; // microseconds
    +
    57 // Initialize trap with particle 1
    +
    58 PenningTrap trap(std::vector<Particle>{p1});
    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
    -
    77void simulate_100_particles()
    -
    78{
    -
    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();
    +
    60 double time = 50.; // microseconds
    +
    61
    +
    62 // Simulate and write results to file
    +
    63 trap.write_simulation_to_dir("output/simulate_single_particle", time, N,
    +
    64 "rk4", false);
    +
    65}
    +
    66
    +
    70void simulate_two_particles()
    +
    71{
    +
    72 // Initialize traps with particles
    +
    73 PenningTrap trap_no_interaction(std::vector<Particle>{p1, p2});
    +
    74 PenningTrap trap_with_interaction(std::vector<Particle>{p1, p2});
    +
    75
    +
    76 double time = 50.; // microseconds
    +
    77
    +
    78 // Simulate and write results to files
    +
    79 trap_no_interaction.write_simulation_to_dir(
    +
    80 "output/simulate_2_particles/no_interaction", time, N, "rk4", false);
    +
    81 trap_with_interaction.write_simulation_to_dir(
    +
    82 "output/simulate_2_particles/with_interaction", time, N);
    +
    83}
    +
    84
    +
    88void simulate_single_particle_with_different_steps()
    +
    89{
    +
    90 double time = 50.; // microseconds
    +
    91
    +
    92 std::ofstream ofile;
    +
    93
    +
    94 // Calculate relative error for RK4
    +
    95 std::string path = "output/relative_error/RK4/";
    +
    96 mkpath(path);
    +
    97 for (int i = 0; i < 4; i++) {
    +
    98 int steps = 4000 * std::pow(2, i);
    +
    99 double dt = time / (double)steps;
    +
    100 ofile.open(path + std::to_string(steps) + "_steps.txt");
    +
    101 PenningTrap trap(std::vector<Particle>{p1});
    +
    102 simulation_t res = trap.simulate(time, steps, "rk4", false);
    +
    103 for (int i = 0; i < steps; i++) {
    +
    104 ofile << arma::norm(res.r_vecs[0][i] -
    +
    105 analytical_solution_particle_1(dt*i))
    +
    106 << "\n";
    +
    107 }
    +
    108 ofile.close();
    +
    109 }
    +
    110
    +
    111 // Calculate relative error for forward Euler
    +
    112 path = "output/relative_error/euler/";
    +
    113 mkpath(path);
    +
    114 for (int i = 0; i < 4; i++) {
    +
    115 int steps = 4000 * std::pow(2, i);
    +
    116 double dt = time / (double)steps;
    +
    117 ofile.open(path + std::to_string(steps) + "_steps.txt");
    +
    118 PenningTrap trap(std::vector<Particle>{p1});
    +
    119 simulation_t res = trap.simulate(time, steps, "euler", false);
    +
    120 for (int i = 0; i < steps; i++) {
    +
    121 ofile << arma::norm(res.r_vecs[0][i] -
    +
    122 analytical_solution_particle_1(dt*i))
    +
    123 << "\n";
    +
    124 }
    +
    125 ofile.close();
    +
    126 }
    +
    127}
    128
    -
    129 simulate_two_particles();
    -
    130
    -
    131 simulate_single_particle_with_different_steps();
    -
    132
    -
    133 double start = omp_get_wtime();
    +
    131void simulate_100_particles()
    +
    132{
    +
    133 PenningTrap trap((unsigned)100);
    134
    -
    135 //simulate_100_particles();
    +
    135 double time = 50.; // microseconds
    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}
    +
    137 trap.write_simulation_to_dir("output/simulate_100_particles", time, N);
    +
    138}
    +
    139
    +
    146void simulate_100_particles_with_time_potential()
    +
    147{
    +
    148 double time = 500.;
    +
    149
    +
    150 double amplitudes[]{.1, .4, .7};
    +
    151
    +
    152 double freq_start = .2;
    +
    153 double freq_end = 2.5;
    +
    154 double freq_increment = .02;
    +
    155 size_t freq_iterations = (size_t)((freq_end - freq_start) / freq_increment);
    +
    156
    +
    157 double res[4][freq_iterations];
    +
    158
    +
    159 std::string path = "output/time_dependent_potential/";
    +
    160 mkpath(path);
    +
    161
    +
    162 std::ofstream ofile;
    +
    163
    +
    164 double freq = freq_start;
    +
    165 for (size_t i = 0; i < freq_iterations; i++) {
    +
    166 res[0][i] = freq;
    +
    167 freq += freq_increment;
    +
    168 }
    +
    169
    +
    170#pragma omp parallel for collapse(2) num_threads(4)
    +
    171 for (size_t i = 0; i < 3; i++) {
    +
    172 for (size_t j = 0; j < freq_iterations; j++) {
    +
    173 PenningTrap trap(
    +
    174 (unsigned)100, T,
    +
    175 std::bind(
    +
    176 [](double f, double r, double t) {
    +
    177 return (25. * V / 1000.) * (1. + f * std::cos(r * t));
    +
    178 },
    +
    179 amplitudes[i], res[0][j], std::placeholders::_1),
    +
    180 500., 0.);
    +
    181 res[i + 1][j] =
    +
    182 trap.fraction_of_particles_left(time, N, "rk4", false);
    +
    183 }
    +
    184 }
    +
    185
    +
    186 ofile.open(path + "res.txt");
    +
    187 for (size_t i = 0; i < freq_iterations; i++) {
    +
    188 ofile << res[0][i] << "," << res[1][i] << "," << res[2][i] << ","
    +
    189 << res[3][i] << "\n";
    +
    190 }
    +
    191 ofile.close();
    +
    192}
    +
    193
    +
    194int main()
    +
    195{
    +
    196 double t0 = omp_get_wtime();
    +
    197
    +
    198 // simulate_single_particle();
    +
    199
    +
    200 // simulate_two_particles();
    +
    201
    +
    202 simulate_single_particle_with_different_steps();
    +
    203
    +
    204 double t1 = omp_get_wtime();
    +
    205
    +
    206 simulate_100_particles();
    +
    207
    +
    208 //simulate_100_particles_with_time_potential();
    +
    209
    +
    210 double end = omp_get_wtime();
    +
    211
    +
    212 std::cout << "Time: " << (end - t1) << " seconds" << std::endl;
    +
    213
    +
    214 return 0;
    +
    215}
    PenningTrap.hpp
    A class for simulating a Penning trap.
    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
    +
    PenningTrap
    A class that simulates a Penning trap.
    Definition: PenningTrap.hpp:31
    +
    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:281
    +
    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:246
    T
    #define T
    1 Tesla. unit:
    Definition: constants.hpp:17
    V
    #define V
    1 Volt. unit:
    Definition: constants.hpp:19
    +
    simulate_100_particles
    void simulate_100_particles()
    Simulate 100 particles over 50 .
    Definition: main.cpp:131
    +
    simulate_100_particles_with_time_potential
    void simulate_100_particles_with_time_potential()
    Simulate 100 particles over 500 using a time dependent potential.
    Definition: main.cpp:146
    +
    analytical_solution_particle_1
    vec_3d analytical_solution_particle_1(double t)
    The analytical solution for particle p1.
    Definition: main.cpp:38
    +
    simulate_two_particles
    void simulate_two_particles()
    Simulate 2 particles over the period of 50 with and without particle interactions.
    Definition: main.cpp:70
    +
    p1
    Particle p1(CHARGE, MASS, vec_3d{20., 0., 20.}, vec_3d{0., 25., 0.})
    Particle 1.
    +
    simulate_single_particle
    void simulate_single_particle()
    Simulate a single particle over the period of 50 .
    Definition: main.cpp:55
    +
    p2
    Particle p2(CHARGE, MASS, vec_3d{25., 25., 0.}, vec_3d{0., 40., 5.})
    Particle 2.
    +
    simulate_single_particle_with_different_steps
    void simulate_single_particle_with_different_steps()
    Simulate a single particle over 50 using different amount of steps and different methods.
    Definition: main.cpp:88
    +
    simulation
    Typedef for PenningTrap::simulation return value.
    Definition: typedefs.hpp:40
    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
    +
    mkpath
    bool mkpath(std::string path, int mode=0777)
    Make path given.
    Definition: utils.cpp:74
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+"typedefs_8hpp.html#a9f33f4962c8fb62cc5ccd0e4e039a8df":[6,0,0,3,5], +"typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af":[6,0,0,3,1], +"typedefs_8hpp_source.html":[6,0,0,3], +"utils_8cpp.html":[6,0,1,5], +"utils_8cpp.html#a58565270b643b24e3132f38c653e0199":[6,0,1,5,3], +"utils_8cpp.html#a6be6f938bcbb235ebb6a2ed9d08411b2":[6,0,1,5,0], +"utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746":[6,0,1,5,4], +"utils_8cpp.html#acf13f4e492199cb7231bfa646dbd08de":[6,0,1,5,2], +"utils_8cpp.html#aff5e07c3c1d321709b0cc38e999f427b":[6,0,1,5,1], +"utils_8cpp_source.html":[6,0,1,5], +"utils_8hpp.html":[6,0,0,4], +"utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38":[6,0,0,4,4], +"utils_8hpp.html#a60dca3177fb9cb5256609adc7af55168":[6,0,0,4,0], +"utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa":[6,0,0,4,5], +"utils_8hpp.html#a73d4f21ad937dbc50a0c0538c78fd4f9":[6,0,0,4,1], +"utils_8hpp.html#ab3e0cf669bddc59bd53998490ffb68b9":[6,0,0,4,3], +"utils_8hpp.html#ad54b96a1074f9df4dc892a41d115b72d":[6,0,0,4,6], +"utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384":[6,0,0,4,7], +"utils_8hpp.html#aecc1f7a8a2493b9e021e5bff76a00a5b":[6,0,0,4,2], +"utils_8hpp_source.html":[6,0,0,4] }; diff --git a/docs/plot__2__particles_8py_source.html b/docs/plot__2__particles_8py_source.html new file mode 100644 index 0000000..648387a --- /dev/null +++ b/docs/plot__2__particles_8py_source.html @@ -0,0 +1,153 @@ + + + + + + + +Penning Trap Simulation: src/scripts/plot_2_particles.py Source File + + + + + + + + + + + + + + + + +
    +
    + + + + + + +
    +
    Penning Trap Simulation +
    +
    Simulate particle behavior inside a Penning Trap
    +
    +
    + + + + + + + +
    +
    + +
    +
    +
    + +
    + +
    +
    + + +
    +
    +
    +
    +
    +
    Loading...
    +
    Searching...
    +
    No Matches
    +
    +
    +
    +
    + +
    +
    plot_2_particles.py
    +
    +
    +
    1import matplotlib.pyplot as plt
    +
    2import numpy as np
    +
    3
    +
    4def main():
    +
    5 files = [
    +
    6 "output/simulate_2_particles/no_interaction/particle_0_r.txt",
    +
    7 "output/simulate_2_particles/no_interaction/particle_1_r.txt",
    +
    8 "output/simulate_2_particles/with_interaction/particle_0_r.txt",
    +
    9 "output/simulate_2_particles/with_interaction/particle_1_r.txt"
    +
    10 ]
    +
    11 labels = [
    +
    12 "particle 1 no interaction",
    +
    13 "particle 2 no interaction",
    +
    14 "particle 1 with interaction",
    +
    15 "particle 2 with interaction",
    +
    16 ]
    +
    17 colors = [
    +
    18 "lightskyblue",
    +
    19 "lightskyblue",
    +
    20 "salmon",
    +
    21 "salmon"
    +
    22 ]
    +
    23 for label, color, file in zip(labels, colors, files):
    +
    24 with open(file) as f:
    +
    25 lines = f.readlines()
    +
    26 t = np.linspace(0, 50, len(lines))
    +
    27 r = np.array([list(map(float, line.strip().split(","))) for line in lines])
    +
    28 plt.plot(r[:,0], r[:,1], label=label, color=color)
    +
    29
    +
    30 plt.xlabel(r"x $(\mu m)$")
    +
    31 plt.ylabel(r"y $(\mu m)$")
    +
    32 plt.title(r"2 particles with and without interactions.")
    +
    33 # plt.legend()
    +
    34 # plt.show()
    +
    35 plt.savefig("../latex/images/plot_2_particles_xy.pdf")
    +
    36
    +
    37
    +
    38if __name__ == "__main__":
    +
    39 main()
    +
    +
    + + + + diff --git a/docs/plot__3d_8py_source.html b/docs/plot__3d_8py_source.html new file mode 100644 index 0000000..d297968 --- /dev/null +++ b/docs/plot__3d_8py_source.html @@ -0,0 +1,154 @@ + + + + + + + +Penning Trap Simulation: src/scripts/plot_3d.py Source File + + + + + + + + + + + + + + + + +
    +
    + + + + + + +
    +
    Penning Trap Simulation +
    +
    Simulate particle behavior inside a Penning Trap
    +
    +
    + + + + + + + +
    +
    + +
    +
    +
    + +
    + +
    +
    + + +
    +
    +
    +
    +
    +
    Loading...
    +
    Searching...
    +
    No Matches
    +
    +
    +
    +
    + +
    +
    plot_3d.py
    +
    +
    +
    1import matplotlib.pyplot as plt
    +
    2import numpy as np
    +
    3
    +
    4def main():
    +
    5 files = [
    +
    6 "output/simulate_2_particles/no_interaction/particle_0_r.txt",
    +
    7 "output/simulate_2_particles/no_interaction/particle_1_r.txt",
    +
    8 "output/simulate_2_particles/with_interaction/particle_0_r.txt",
    +
    9 "output/simulate_2_particles/with_interaction/particle_1_r.txt"
    +
    10 ]
    +
    11 labels = [
    +
    12 "particle 1 no interaction",
    +
    13 "particle 2 no interaction",
    +
    14 "particle 1 with interaction",
    +
    15 "particle 2 with interaction",
    +
    16 ]
    +
    17 colors = [
    +
    18 "lightskyblue",
    +
    19 "deepskyblue",
    +
    20 "salmon",
    +
    21 "darkred"
    +
    22 ]
    +
    23 ax = plt.figure().add_subplot(projection="3d")
    +
    24 for label, color, file in zip(labels, colors, files):
    +
    25 with open(file) as f:
    +
    26 lines = f.readlines()
    +
    27 t = np.linspace(0, 50, len(lines))
    +
    28 r = np.array([list(map(float, line.strip().split(","))) for line in lines])
    +
    29 ax.plot(r[:,0], r[:,1], r[:,2], label=label, color=color)
    +
    30
    +
    31 ax.set_xlabel(r"x $(\mu m)$")
    +
    32 ax.set_ylabel(r"y $(\mu m)$")
    +
    33 ax.set_zlabel(r"z $(\mu m)$")
    +
    34 plt.title(r"2 particles with and without interactions.")
    +
    35 plt.legend()
    +
    36 plt.savefig("../latex/images/3d_plot.pdf")
    +
    37
    +
    38
    +
    39if __name__ == "__main__":
    +
    40 main()
    +
    +
    + + + + diff --git a/docs/plot__particles__left_8py_source.html b/docs/plot__particles__left_8py_source.html index c9ab258..33e15f0 100644 --- a/docs/plot__particles__left_8py_source.html +++ b/docs/plot__particles__left_8py_source.html @@ -5,7 +5,7 @@ -Penning Trap Simulation: src/plot_particles_left.py Source File +Penning Trap Simulation: src/scripts/plot_particles_left.py Source File @@ -104,42 +104,39 @@ $(document).ready(function(){initNavTree('plot__particles__left_8py_source.html'
    1import matplotlib.pyplot as plt
    2
    3def main():
    -
    4 files = [
    -
    5 "output/time_dependent_potential/f_0.100000.txt",
    -
    6 "output/time_dependent_potential/f_0.400000.txt",
    -
    7 "output/time_dependent_potential/f_0.700000.txt",
    -
    8 ]
    -
    9 vals = [
    -
    10 .1,
    -
    11 .4,
    -
    12 .7
    -
    13 ]
    -
    14 for i in range(3):
    -
    15 with open(files[i]) as f:
    -
    16 lines = f.readlines()
    -
    17 x = []
    -
    18 y = []
    -
    19 for line in lines:
    -
    20 a,b = line.strip().split(",")
    -
    21 x.append(float(a))
    -
    22 y.append(float(b))
    -
    23 plt.plot(x,y,label=f"amplitude: {vals[i]}")
    -
    24
    -
    25 plt.xlabel(r"$\omega_V$")
    -
    26 plt.ylabel(r"Fraction of particles left")
    -
    27 plt.title(r"The fraction of particles left in the Penning trap "
    -
    28 "after 500 microseconds for different amplitudes and frequencies")
    -
    29 plt.legend()
    -
    30 plt.show()
    -
    31
    -
    32if __name__ == "__main__":
    -
    33 main()
    +
    4 with open("output/time_dependent_potential/res.txt") as f:
    +
    5 lines = f.readlines()
    +
    6 x = []
    +
    7 y1 = []
    +
    8 y2 = []
    +
    9 y3 = []
    +
    10 for line in lines:
    +
    11 l = line.strip().split(",")
    +
    12 x.append(float(l[0]))
    +
    13 y1.append(float(l[1]))
    +
    14 y2.append(float(l[2]))
    +
    15 y3.append(float(l[3]))
    +
    16
    +
    17 plt.plot(x,y1,label=f"amplitude: 0.1")
    +
    18 plt.plot(x,y2,label=f"amplitude: 0.4")
    +
    19 plt.plot(x,y3,label=f"amplitude: 0.7")
    +
    20
    +
    21 plt.xlabel(r"$\omega_V$ (MHz)")
    +
    22 plt.ylabel(r"Fraction of particles left")
    +
    23 plt.title(r"The fraction of particles left in the Penning trap "
    +
    24 "after 500 microseconds for different amplitudes and frequencies")
    +
    25 plt.legend()
    +
    26 # plt.show()
    +
    27 plt.savefig("../latex/images/particles_left.pdf")
    +
    28
    +
    29if __name__ == "__main__":
    +
    30 main()
    diff --git a/docs/plot__phase__space_8py_source.html b/docs/plot__phase__space_8py_source.html new file mode 100644 index 0000000..c746ef7 --- /dev/null +++ b/docs/plot__phase__space_8py_source.html @@ -0,0 +1,167 @@ + + + + + + + +Penning Trap Simulation: src/scripts/plot_phase_space.py Source File + + + + + + + + + + + + + + + + +
    +
    + + + + + + +
    +
    Penning Trap Simulation +
    +
    Simulate particle behavior inside a Penning Trap
    +
    +
    + + + + + + + +
    +
    + +
    +
    +
    + +
    + +
    +
    + + +
    +
    +
    +
    +
    +
    Loading...
    +
    Searching...
    +
    No Matches
    +
    +
    +
    +
    + +
    +
    plot_phase_space.py
    +
    +
    +
    1import matplotlib.pyplot as plt
    +
    2import numpy as np
    +
    3
    +
    4def main():
    +
    5 directories = {
    +
    6 "output/simulate_2_particles/no_interaction/",
    +
    7 "output/simulate_2_particles/with_interaction/",
    +
    8 }
    +
    9 titles = {
    +
    10 "particles without interaction",
    +
    11 "particles with interaction"
    +
    12 }
    +
    13 files = [
    +
    14 "particle_0_r.txt",
    +
    15 "particle_0_v.txt",
    +
    16 "particle_1_r.txt",
    +
    17 "particle_1_v.txt",
    +
    18 ]
    +
    19 labels = [
    +
    20 r"particle 1 r",
    +
    21 r"particle 1 v",
    +
    22 r"particle 2 r",
    +
    23 r"particle 2 v",
    +
    24 ]
    +
    25 colors = [
    +
    26 "lightskyblue",
    +
    27 "deepskyblue",
    +
    28 "salmon",
    +
    29 "tomato",
    +
    30 ]
    +
    31 fig1, axs1 = plt.subplots(2,1)
    +
    32 fig2, axs2 = plt.subplots(2,1)
    +
    33 for i, (dir, title) in enumerate(zip(directories, titles)):
    +
    34 for label, color, file in zip(labels, colors, files):
    +
    35 with open(dir+file) as f:
    +
    36 lines = f.readlines()
    +
    37 t = np.linspace(0, 50, len(lines))
    +
    38 r = np.array([list(map(float, line.strip().split(","))) for line in lines])
    +
    39 axs1[i].plot(t, r[:,0], label=label, color=color)
    +
    40 axs2[i].plot(t, r[:,2], label=label, color=color)
    +
    41
    +
    42 axs1[i].set(xlabel=r"t $(\mu s)$", ylabel = r"z $(\mu m)$")
    +
    43
    +
    44 axs1[i].legend()
    +
    45 axs1[i].set_title(title)
    +
    46
    +
    47 # plt.show()
    +
    48 fig1.savefig("../latex/images/phase_space_2_particles_x.pdf")
    +
    49 fig2.savefig("../latex/images/phase_space_2_particles_z.pdf")
    +
    50
    +
    51
    +
    52if __name__ == "__main__":
    +
    53 main()
    +
    +
    + + + + diff --git a/docs/plot__relative__error_8py_source.html b/docs/plot__relative__error_8py_source.html new file mode 100644 index 0000000..8628d31 --- /dev/null +++ b/docs/plot__relative__error_8py_source.html @@ -0,0 +1,165 @@ + + + + + + + +Penning Trap Simulation: src/scripts/plot_relative_error.py Source File + + + + + + + + + + + + + + + + +
    +
    + + + + + + +
    +
    Penning Trap Simulation +
    +
    Simulate particle behavior inside a Penning Trap
    +
    +
    + + + + + + + +
    +
    + +
    +
    +
    + +
    + +
    +
    + + +
    +
    +
    +
    +
    +
    Loading...
    +
    Searching...
    +
    No Matches
    +
    +
    +
    +
    + +
    +
    plot_relative_error.py
    +
    +
    +
    1import matplotlib.pyplot as plt
    +
    2import numpy as np
    +
    3
    +
    4def main():
    +
    5 directories = [
    +
    6 "output/relative_error/RK4/",
    +
    7 "output/relative_error/euler/",
    +
    8 ]
    +
    9 files = [
    +
    10 "4000_steps.txt",
    +
    11 "8000_steps.txt",
    +
    12 "16000_steps.txt",
    +
    13 "32000_steps.txt",
    +
    14 ]
    +
    15 labels = [
    +
    16 r"4000 steps",
    +
    17 r"8000 steps",
    +
    18 r"16000 steps",
    +
    19 r"32000 steps",
    +
    20 ]
    +
    21 titles = [
    +
    22 "Relative error for the RK4 method",
    +
    23 "Relative error for the forward Euler method"
    +
    24 ]
    +
    25 methods = [
    +
    26 "rk4",
    +
    27 "euler"
    +
    28 ]
    +
    29 fig1, axs1 = plt.subplots(2,1)
    +
    30 for i, (dir, title) in enumerate(list(zip(directories, titles))):
    +
    31 max_err = []
    +
    32 for label, file in zip(labels, files):
    +
    33 with open(dir+file) as f:
    +
    34 lines = f.readlines()
    +
    35 t = np.linspace(0, 50, len(lines))
    +
    36 r = np.array([float(line.strip()) for line in lines])
    +
    37 max_err.append(max(r))
    +
    38 axs1[i].plot(t, r, label=label)
    +
    39
    +
    40 axs1[i].set(xlabel=r"t $(\mu s)$", ylabel = r"relative_error $(\mu m)$")
    +
    41 axs1[i].legend()
    +
    42 axs1[i].set_title(title)
    +
    43
    +
    44 conv_rate = 1/3 * sum([np.log2(max_err[i+1]/max_err[i])/np.log2(.5) for i in range(3)])
    +
    45 print(f"{methods[i]}: {conv_rate}")
    +
    46
    +
    47 fig1.savefig("../latex/images/phase_space_2_particles_x.pdf")
    +
    48
    +
    49
    +
    50if __name__ == "__main__":
    +
    51 main()
    +
    +
    + + + + diff --git a/docs/plot__single__particle_8py_source.html b/docs/plot__single__particle_8py_source.html new file mode 100644 index 0000000..d5eff34 --- /dev/null +++ b/docs/plot__single__particle_8py_source.html @@ -0,0 +1,144 @@ + + + + + + + +Penning Trap Simulation: src/scripts/plot_single_particle.py Source File + + + + + + + + + + + + + + + + +
    +
    + + + + + + +
    +
    Penning Trap Simulation +
    +
    Simulate particle behavior inside a Penning Trap
    +
    +
    + + + + + + + +
    +
    + +
    +
    +
    + +
    + +
    +
    + + +
    +
    +
    +
    +
    +
    Loading...
    +
    Searching...
    +
    No Matches
    +
    +
    +
    +
    + +
    +
    plot_single_particle.py
    +
    +
    +
    1import matplotlib.pyplot as plt
    +
    2import numpy as np
    +
    3
    +
    4def z(t):
    +
    5 V_0 = 25.*9.64852558 * 10**4
    +
    6 m = 40.
    +
    7 d = 500.
    +
    8 w_z = np.sqrt((2.*V_0)/(m*d*d))
    +
    9 return 20.*np.cos(w_z*t)
    +
    10
    +
    11def main():
    +
    12 filename = "output/simulate_single_particle/particle_0_r.txt"
    +
    13 r = t = []
    +
    14 with open(filename) as f:
    +
    15 lines = f.readlines()
    +
    16 t = np.linspace(0, 50, len(lines))
    +
    17 r = np.array([list(map(float, line.strip().split(","))) for line in lines])
    +
    18
    +
    19 plt.plot(t, r[:, 2], label="approximation")
    +
    20 plt.plot(t, z(t), label="analytical")
    +
    21 plt.xlabel(r"time $(\mu s)$")
    +
    22 plt.ylabel(r"z $(\mu m)$")
    +
    23 plt.title(r"Movement of a single particle in the x direction")
    +
    24 plt.legend()
    +
    25 # plt.savefig("../latex/images/single_particle.pdf")
    +
    26 plt.show()
    +
    27
    +
    28
    +
    29if __name__ == "__main__":
    +
    30 main()
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diff --git a/docs/search/functions_7.js b/docs/search/functions_7.js index 73e1881..d253bda 100644 --- a/docs/search/functions_7.js +++ b/docs/search/functions_7.js @@ -1,6 +1,10 @@ var searchData= [ - ['total_5fforce_0',['total_force',['../classPenningTrap.html#a1f668c4433421136ad51741741aa1bc8',1,'PenningTrap']]], - ['total_5fforce_5fexternal_1',['total_force_external',['../classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56',1,'PenningTrap']]], - ['total_5fforce_5fparticles_2',['total_force_particles',['../classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b',1,'PenningTrap']]] + ['scientific_5fformat_0',['scientific_format',['../utils_8hpp.html#adfb618b2fdff47ef30a4a2b62c04f384',1,'scientific_format(double d, int width=20, int prec=10): utils.cpp'],['../utils_8hpp.html#ad54b96a1074f9df4dc892a41d115b72d',1,'scientific_format(const std::vector< double > &v, int width=20, int prec=10): utils.cpp'],['../utils_8cpp.html#acd2a9c7a7d5a7fe9163be8c4cc110746',1,'scientific_format(double d, int width, int prec): utils.cpp'],['../utils_8cpp.html#a58565270b643b24e3132f38c653e0199',1,'scientific_format(const std::vector< double > &v, int width, int prec): utils.cpp']]], + ['simulate_1',['simulate',['../classPenningTrap.html#ae09ef9cfa7e4ed1c108c8576405b3599',1,'PenningTrap']]], + ['simulate_5f100_5fparticles_2',['simulate_100_particles',['../main_8cpp.html#a213713d6ecc02a32b588ffd179dc7513',1,'main.cpp']]], + ['simulate_5f100_5fparticles_5fwith_5ftime_5fpotential_3',['simulate_100_particles_with_time_potential',['../main_8cpp.html#a330668384dc073980ba11116309bacc5',1,'main.cpp']]], + ['simulate_5fsingle_5fparticle_4',['simulate_single_particle',['../main_8cpp.html#a8fdbe2d5a872e50ef5ec1263243589d6',1,'main.cpp']]], + ['simulate_5fsingle_5fparticle_5fwith_5fdifferent_5fsteps_5',['simulate_single_particle_with_different_steps',['../main_8cpp.html#ac67e0d59227856c4d42e7d01c75e0ad2',1,'main.cpp']]], + ['simulate_5ftwo_5fparticles_6',['simulate_two_particles',['../main_8cpp.html#a783789519f97c6430081171cacb0ffb1',1,'main.cpp']]] ]; diff --git a/docs/search/functions_8.js b/docs/search/functions_8.js index 8d7b6ff..d230e8d 100644 --- a/docs/search/functions_8.js +++ b/docs/search/functions_8.js @@ -1,4 +1,11 @@ var searchData= [ - ['v_5ffunc_0',['v_func',['../classPenningTrap.html#af98a720da60b0e1a62aefa5f5cb37c1e',1,'PenningTrap']]] + ['test_5fexternal_5fb_5ffield_0',['test_external_B_field',['../classPenningTrapTest.html#acb806e49a688424588e0c501bc57a230',1,'PenningTrapTest']]], + ['test_5fexternal_5fe_5ffield_1',['test_external_E_field',['../classPenningTrapTest.html#a542996d72c713636b95e0aa9118f7901',1,'PenningTrapTest']]], + ['test_5fforce_5fon_5fparticle_2',['test_force_on_particle',['../classPenningTrapTest.html#addf81fa5692d8146cce5571ccdc5999b',1,'PenningTrapTest']]], + ['test_5ftotal_5fforce_5fexternal_3',['test_total_force_external',['../classPenningTrapTest.html#ae104e04dcd21ac63281c908132fdf255',1,'PenningTrapTest']]], + ['test_5ftotal_5fforce_5fparticles_4',['test_total_force_particles',['../classPenningTrapTest.html#a0ee2bbf5e26c115164208b89c5a29e3d',1,'PenningTrapTest']]], + ['total_5fforce_5',['total_force',['../classPenningTrap.html#a1f668c4433421136ad51741741aa1bc8',1,'PenningTrap']]], + ['total_5fforce_5fexternal_6',['total_force_external',['../classPenningTrap.html#ae72d203b0bfa1b9e72bea28cb2863c56',1,'PenningTrap']]], + ['total_5fforce_5fparticles_7',['total_force_particles',['../classPenningTrap.html#a46a954a0946def199e30fb300ba1c47b',1,'PenningTrap']]] ]; diff --git a/docs/search/functions_9.js b/docs/search/functions_9.js index 1b9fc74..8d7b6ff 100644 --- a/docs/search/functions_9.js +++ b/docs/search/functions_9.js @@ -1,4 +1,4 @@ var searchData= [ - ['write_5fsimulation_5fto_5fdir_0',['write_simulation_to_dir',['../classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57',1,'PenningTrap']]] + ['v_5ffunc_0',['v_func',['../classPenningTrap.html#af98a720da60b0e1a62aefa5f5cb37c1e',1,'PenningTrap']]] ]; diff --git a/docs/search/functions_a.js b/docs/search/functions_a.js new file mode 100644 index 0000000..1b9fc74 --- /dev/null +++ b/docs/search/functions_a.js @@ -0,0 +1,4 @@ +var searchData= +[ + ['write_5fsimulation_5fto_5fdir_0',['write_simulation_to_dir',['../classPenningTrap.html#abbb832a85139b1a56ebde57d7b8f9a57',1,'PenningTrap']]] +]; diff --git a/docs/search/searchdata.js b/docs/search/searchdata.js index 4d47bbf..a67f3d1 100644 --- a/docs/search/searchdata.js +++ b/docs/search/searchdata.js @@ -1,9 +1,9 @@ var indexSectionsWithContent = { 0: "_abcdefkmpqrstuvw", - 1: "p", + 1: "ps", 2: "cmptu", - 3: "aefmprstvw", + 3: "acefmprstvw", 4: "bdkmpqrtv", 5: "sv", 6: "p", diff --git a/docs/search/typedefs_0.js b/docs/search/typedefs_0.js index e79ff95..75b98c8 100644 --- a/docs/search/typedefs_0.js +++ b/docs/search/typedefs_0.js @@ -2,5 +2,6 @@ var searchData= [ ['sim_5farr_0',['sim_arr',['../typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af',1,'typedefs.hpp']]], ['sim_5fcols_1',['sim_cols',['../typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23',1,'typedefs.hpp']]], - ['sim_5frows_2',['sim_rows',['../typedefs_8hpp.html#a8502989b1b361725834fc185bd575f66',1,'typedefs.hpp']]] + ['sim_5frows_2',['sim_rows',['../typedefs_8hpp.html#a8502989b1b361725834fc185bd575f66',1,'typedefs.hpp']]], + ['simulation_5ft_3',['simulation_t',['../typedefs_8hpp.html#a784799c37b5e4fb8bf4f6368e004dec6',1,'typedefs.hpp']]] ]; diff --git a/docs/search/variables_4.js b/docs/search/variables_4.js index c9f603d..89df031 100644 --- a/docs/search/variables_4.js +++ b/docs/search/variables_4.js @@ -1,4 +1,6 @@ var searchData= [ - ['particles_0',['particles',['../classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f',1,'PenningTrap']]] + ['p1_0',['p1',['../main_8cpp.html#a87da4ef9f2cd753579484824310467b8',1,'main.cpp']]], + ['p2_1',['p2',['../main_8cpp.html#a90f661586eb3c318fdca6f95ebc4fc46',1,'main.cpp']]], + ['particles_2',['particles',['../classPenningTrap.html#a0112525d9e79a472e761f8ef402a339f',1,'PenningTrap']]] ]; diff --git a/docs/structsimulation-members.html b/docs/structsimulation-members.html new file mode 100644 index 0000000..e81bad3 --- /dev/null +++ b/docs/structsimulation-members.html @@ -0,0 +1,118 @@ + + + + + + + +Penning Trap Simulation: Member List + + + + + + + + + + + + + + + + +
    +
    + + + + + + +
    +
    Penning Trap Simulation +
    +
    Simulate particle behavior inside a Penning Trap
    +
    +
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    simulation Member List
    +
    +
    + +

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

    + + + +
    r_vecs (defined in simulation)simulation
    v_vecs (defined in simulation)simulation
    +
    + + + + diff --git a/docs/structsimulation.html b/docs/structsimulation.html new file mode 100644 index 0000000..ea17361 --- /dev/null +++ b/docs/structsimulation.html @@ -0,0 +1,170 @@ + + + + + + + +Penning Trap Simulation: simulation Struct Reference + + + + + + + + + + + + + + + + +
    +
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    +
    Penning Trap Simulation +
    +
    Simulate particle behavior inside a Penning Trap
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    +Public Attributes | +List of all members
    +
    simulation Struct Reference
    +
    +
    + +

    Typedef for PenningTrap::simulation return value. + More...

    + +

    #include <typedefs.hpp>

    + + + + + + +

    +Public Attributes

    sim_arr r_vecs
     
    sim_arr v_vecs
     
    +

    Detailed Description

    +

    Typedef for PenningTrap::simulation return value.

    + +

    Definition at line 40 of file typedefs.hpp.

    +

    Member Data Documentation

    + +

    ◆ r_vecs

    + +
    +
    + + + + +
    sim_arr simulation::r_vecs
    +
    + +

    Definition at line 41 of file typedefs.hpp.

    + +
    +
    + +

    ◆ v_vecs

    + +
    +
    + + + + +
    sim_arr simulation::v_vecs
    +
    + +

    Definition at line 42 of file typedefs.hpp.

    + +
    +
    +
    The documentation for this struct was generated from the following file: +
    +
    + + + + diff --git a/docs/test__suite_8cpp.html b/docs/test__suite_8cpp.html index 7c69921..ccc234d 100644 --- a/docs/test__suite_8cpp.html +++ b/docs/test__suite_8cpp.html @@ -107,17 +107,18 @@ $(document).ready(function(){initNavTree('test__suite_8cpp.html',''); initResiza

    The test suite for the project. More...

    -
    #include "PenningTrap.hpp"
    -#include "utils.hpp"
    -#include <iomanip>
    +
    #include <iomanip>
    #include <sstream>
    #include <string>
    +#include "PenningTrap.hpp"
    +#include "utils.hpp"

    Go to the source code of this file.

    +

    Classes

    class  PenningTrapTest
     Test class for the Penning trap. More...
     

    @@ -150,7 +151,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)

    -

    Definition at line 135 of file test_suite.cpp.

    +

    Definition at line 148 of file test_suite.cpp.

    diff --git a/docs/test__suite_8cpp_source.html b/docs/test__suite_8cpp_source.html index b317c82..5341d26 100644 --- a/docs/test__suite_8cpp_source.html +++ b/docs/test__suite_8cpp_source.html @@ -102,151 +102,157 @@ $(document).ready(function(){initNavTree('test__suite_8cpp_source.html',''); ini
    Go to the documentation of this file.
    1
    -
    13#include "PenningTrap.hpp"
    -
    14#include "utils.hpp"
    -
    15
    -
    16#include <iomanip>
    -
    17#include <sstream>
    -
    18#include <string>
    +
    13#include <iomanip>
    +
    14#include <sstream>
    +
    15#include <string>
    +
    16
    +
    17#include "PenningTrap.hpp"
    +
    18#include "utils.hpp"
    19
    -
    20class PenningTrapTest {
    -
    21public:
    -
    22 static void test_external_E_field()
    -
    23 {
    -
    24 PenningTrap trap;
    -
    25
    -
    26 // Vector containing inputs and expected results
    -
    27 std::vector<std::pair<arma::vec, arma::vec>> tests;
    -
    28
    -
    29 tests.push_back(
    -
    30 std::make_pair(arma::vec{0., 0., 0.}, arma::vec{0., 0., 0.}));
    -
    31
    -
    32 tests.push_back(std::make_pair(arma::vec{10., 0., 0.},
    -
    33 arma::vec{96.4852558, 0., 0.}));
    -
    34
    -
    35 tests.push_back(std::make_pair(arma::vec{10., 0., 0.},
    -
    36 arma::vec{96.4852558, 0., 0.}));
    -
    37
    -
    38 tests.push_back(std::make_pair(arma::vec{0., 10., 0.},
    -
    39 arma::vec{0., 96.4852558, 0.}));
    -
    40
    -
    41 tests.push_back(std::make_pair(arma::vec{0., 0., 10.},
    -
    42 arma::vec{0., 0., -192.9705116}));
    -
    43
    -
    44 arma::vec result;
    -
    45 arma::vec v;
    -
    46 std::stringstream msg;
    -
    47 for (size_t i = 0; i < tests.size(); i++) {
    -
    48 v = tests.at(i).first;
    -
    49 result = trap.external_E_field(v);
    -
    50
    -
    51 msg.str("");
    -
    52 msg << "Testing the external E field at (" << std::setprecision(2)
    -
    53 << v(0) << "," << v(1) << "," << v(2) << ").";
    +
    22class PenningTrapTest {
    +
    23public:
    +
    26 static void test_external_E_field()
    +
    27 {
    +
    28 PenningTrap trap;
    +
    29
    +
    30 // Vector containing inputs and expected results
    +
    31 std::vector<std::pair<vec_3d, vec_3d>> tests;
    +
    32
    +
    33 tests.push_back(
    +
    34 std::make_pair(vec_3d{0., 0., 0.}, vec_3d{0., 0., 0.}));
    +
    35
    +
    36 tests.push_back(std::make_pair(vec_3d{10., 0., 0.},
    +
    37 vec_3d{96.4852558, 0., 0.}));
    +
    38
    +
    39 tests.push_back(std::make_pair(vec_3d{10., 0., 0.},
    +
    40 vec_3d{96.4852558, 0., 0.}));
    +
    41
    +
    42 tests.push_back(std::make_pair(vec_3d{0., 10., 0.},
    +
    43 vec_3d{0., 96.4852558, 0.}));
    +
    44
    +
    45 tests.push_back(std::make_pair(vec_3d{0., 0., 10.},
    +
    46 vec_3d{0., 0., -192.9705116}));
    +
    47
    +
    48 vec_3d result;
    +
    49 vec_3d v;
    +
    50 std::stringstream msg;
    +
    51 for (size_t i = 0; i < tests.size(); i++) {
    +
    52 v = tests.at(i).first;
    +
    53 result = trap.external_E_field(v);
    54
    -
    55 ASSERT(arma_vector_close_to(result, tests.at(i).second), msg.str());
    -
    56 }
    -
    57 }
    +
    55 msg.str("");
    +
    56 msg << "Testing the external E field at (" << std::setprecision(2)
    +
    57 << v(0) << "," << v(1) << "," << v(2) << ").";
    58
    -
    59 static void test_external_B_field()
    -
    60 {
    -
    61 // No point in testing at different points since it's not dependent
    -
    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.});
    -
    66 ASSERT(arma_vector_close_to(expected, result),
    -
    67 "Testing the external B field at (0,0,0)");
    -
    68 }
    -
    69
    -
    70 static void test_force_on_particle()
    -
    71 {
    -
    72 PenningTrap trap;
    -
    73 arma::vec v{0., 0., 0.};
    -
    74
    -
    75 // Add particles to test
    -
    76 trap.add_particle(Particle(1., 40., arma::vec{0., 0., 0.}, v));
    -
    77 trap.add_particle(Particle(1., 40., arma::vec{1., 0., 0.}, v));
    -
    78 trap.add_particle(Particle(1., 40., arma::vec{0., 3., 4.}, v));
    -
    79
    -
    80 // Test p0 and p1
    -
    81 arma::vec expected{-1., 0., 0.};
    -
    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);
    -
    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).");
    -
    93 }
    +
    59 ASSERT(close_to(result, tests.at(i).second), msg.str());
    +
    60 }
    +
    61 }
    +
    62
    +
    65 static void test_external_B_field()
    +
    66 {
    +
    67 // No point in testing at different points since it's not dependent
    +
    68 // on position.
    +
    69 PenningTrap trap;
    +
    70 vec_3d expected{0., 0., T};
    +
    71 vec_3d result = trap.external_B_field(vec_3d{0., 0., 0.});
    +
    72 ASSERT(close_to(expected, result),
    +
    73 "Testing the external B field at (0,0,0)");
    +
    74 }
    +
    75
    +
    78 static void test_force_on_particle()
    +
    79 {
    +
    80 PenningTrap trap;
    +
    81 vec_3d v{0., 0., 0.};
    +
    82
    +
    83 // Add particles to test
    +
    84 trap.add_particle(Particle(1., 40., vec_3d{0., 0., 0.}, v));
    +
    85 trap.add_particle(Particle(1., 40., vec_3d{1., 0., 0.}, v));
    +
    86 trap.add_particle(Particle(1., 40., vec_3d{0., 3., 4.}, v));
    +
    87
    +
    88 // Test p0 and p1
    +
    89 vec_3d expected{-1., 0., 0.};
    +
    90 vec_3d result = trap.force_on_particle(0, 1);
    +
    91 ASSERT(close_to(expected, result),
    +
    92 "Testing the force on a particle at (0,0,0) from a "
    +
    93 "particle at (1,0,0).");
    94
    -
    95 static void test_total_force_external()
    -
    96 {
    -
    97 PenningTrap trap;
    -
    98 trap.add_particle(
    -
    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);
    -
    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)");
    -
    106 }
    -
    107
    -
    108 static void test_total_force_particles()
    -
    109 {
    -
    110 PenningTrap trap;
    -
    111 trap.add_particle(
    -
    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);
    -
    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");
    -
    119
    -
    120 trap.add_particle(
    -
    121 Particle(1., 40., arma::vec{1., 0., 0.}, arma::vec{0., 0., 0.}));
    -
    122 trap.add_particle(
    -
    123 Particle(1., 40., arma::vec{0., 1., 0.}, arma::vec{0., 0., 0.}));
    +
    95 // Test p0 and p2
    +
    96 expected = vec_3d{0, -.024, -.032};
    +
    97 result = trap.force_on_particle(0, 2);
    +
    98 ASSERT(close_to(expected, result),
    +
    99 "Testing the force on a particle at (0,0,0) from a "
    +
    100 "particle at (0,3,4).");
    +
    101 }
    +
    102
    +
    105 static void test_total_force_external()
    +
    106 {
    +
    107 PenningTrap trap;
    +
    108 trap.add_particle(
    +
    109 Particle(1., 40., vec_3d{1., 2., 3.}, vec_3d{3., 4., 5.}));
    +
    110
    +
    111 vec_3d expected{395.58954878, -270.15871624, -57.89115348};
    +
    112 vec_3d result = trap.total_force_external(0);
    +
    113 ASSERT(close_to(expected, result),
    +
    114 "Testing the total external force on a particle at "
    +
    115 "(1,2,3) with velocity (3,4,5)");
    +
    116 }
    +
    117
    +
    121 static void test_total_force_particles()
    +
    122 {
    +
    123 PenningTrap trap;
    124 trap.add_particle(
    -
    125 Particle(1., 40., arma::vec{0., 0., 1.}, arma::vec{0., 0., 0.}));
    +
    125 Particle(1., 40., vec_3d{0., 0., 0.}, vec_3d{0., 0., 0.}));
    126
    -
    127 expected = arma::vec(3, arma::fill::value(-3473.383325));
    -
    128 result = trap.total_force_particles(0);
    -
    129 ASSERT(arma_vector_close_to(expected, result),
    +
    127 vec_3d expected{0., 0., 0.};
    +
    128 vec_3d result = trap.total_force_particles(0);
    +
    129 ASSERT(close_to(expected, result),
    130 "Testing the total force of all particles on particle 0 "
    -
    131 "with 3 other particles.");
    -
    132 }
    -
    133};
    -
    134
    -
    135int main()
    -
    136{
    -
    137 PenningTrapTest::test_external_E_field();
    -
    138 PenningTrapTest::test_external_B_field();
    -
    139 PenningTrapTest::test_force_on_particle();
    -
    140 PenningTrapTest::test_total_force_external();
    -
    141 PenningTrapTest::test_total_force_particles();
    -
    142 return 0;
    -
    143}
    +
    131 "with only a single particle");
    +
    132
    +
    133 trap.add_particle(
    +
    134 Particle(1., 40., vec_3d{1., 0., 0.}, vec_3d{0., 0., 0.}));
    +
    135 trap.add_particle(
    +
    136 Particle(1., 40., vec_3d{0., 1., 0.}, vec_3d{0., 0., 0.}));
    +
    137 trap.add_particle(
    +
    138 Particle(1., 40., vec_3d{0., 0., 1.}, vec_3d{0., 0., 0.}));
    +
    139
    +
    140 expected = vec_3d().fill(-3473.383325);
    +
    141 result = trap.total_force_particles(0);
    +
    142 ASSERT(close_to(expected, result),
    +
    143 "Testing the total force of all particles on particle 0 "
    +
    144 "with 3 other particles.");
    +
    145 }
    +
    146};
    +
    147
    +
    148int main()
    +
    149{
    +
    150 PenningTrapTest::test_external_E_field();
    +
    151 PenningTrapTest::test_external_B_field();
    +
    152 PenningTrapTest::test_force_on_particle();
    +
    153 PenningTrapTest::test_total_force_external();
    +
    154 PenningTrapTest::test_total_force_particles();
    +
    155 return 0;
    +
    156}
    PenningTrap.hpp
    A class for simulating a Penning trap.
    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::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
    +
    PenningTrapTest
    Test class for the Penning trap.
    Definition: test_suite.cpp:22
    +
    PenningTrapTest::test_total_force_particles
    static void test_total_force_particles()
    Test that the total force of all particles on a single particle returns expected results.
    Definition: test_suite.cpp:121
    +
    PenningTrapTest::test_external_E_field
    static void test_external_E_field()
    Test that the external E field gives correct values.
    Definition: test_suite.cpp:26
    +
    PenningTrapTest::test_external_B_field
    static void test_external_B_field()
    Test that the external B field gives correct values.
    Definition: test_suite.cpp:65
    +
    PenningTrapTest::test_force_on_particle
    static void test_force_on_particle()
    Test that the force between particles gives expected results.
    Definition: test_suite.cpp:78
    +
    PenningTrapTest::test_total_force_external
    static void test_total_force_external()
    Test that the total external force returns expected results.
    Definition: test_suite.cpp:105
    +
    PenningTrap
    A class that simulates a Penning trap.
    Definition: PenningTrap.hpp:31
    +
    PenningTrap::external_E_field
    vec_3d external_E_field(vec_3d r)
    Calculate E at point r.
    Definition: PenningTrap.cpp:84
    +
    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:123
    +
    PenningTrap::add_particle
    void add_particle(Particle particle)
    Add a particle to the system.
    Definition: PenningTrap.cpp:79
    +
    PenningTrap::force_on_particle
    vec_3d force_on_particle(unsigned int i, unsigned int j)
    Calculate the force between 2 particles.
    Definition: PenningTrap.cpp:97
    +
    PenningTrap::external_B_field
    vec_3d external_B_field(vec_3d r)
    Calculate B at point r.
    Definition: PenningTrap.cpp:92
    +
    PenningTrap::total_force_external
    vec_3d total_force_external(unsigned int i)
    Calculate the total external force on a particle.
    Definition: PenningTrap.cpp:108
    T
    #define T
    1 Tesla. unit:
    Definition: constants.hpp:17
    +
    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.
    -
    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
    +
    ASSERT
    #define ASSERT(expr, msg)
    A prettier assertion function.
    Definition: utils.hpp:46
    +
    close_to
    bool 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:60
    diff --git a/docs/typedefs_8hpp.html b/docs/typedefs_8hpp.html index 1f2eedb..1225a91 100644 --- a/docs/typedefs_8hpp.html +++ b/docs/typedefs_8hpp.html @@ -99,6 +99,7 @@ $(document).ready(function(){initNavTree('typedefs_8hpp.html',''); initResizable
    +Classes | Typedefs
    typedefs.hpp File Reference
    @@ -106,11 +107,17 @@ $(document).ready(function(){initNavTree('typedefs_8hpp.html',''); initResizable

    Useful typedefs for cleaner code. More...

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

    Go to the source code of this file.

    + + + + +

    +Classes

    struct  simulation
     Typedef for PenningTrap::simulation return value. More...
     
    @@ -125,6 +132,10 @@ Typedefs + + +

    Typedefs

    typedef std::vector< arma::vec::fixed< 3 > > sim_cols
    typedef arma::vec::fixed< 3 > vec_3d
     Typedef for a fixed 3d arma vector.
     
    +typedef struct simulation simulation_t
     Typedef for PenningTrap::simulation return value.
     

    Detailed Description

    Useful typedefs for cleaner code.

    diff --git a/docs/typedefs_8hpp.js b/docs/typedefs_8hpp.js index d014844..ddf845a 100644 --- a/docs/typedefs_8hpp.js +++ b/docs/typedefs_8hpp.js @@ -1,7 +1,9 @@ var typedefs_8hpp = [ + [ "simulation", "structsimulation.html", null ], [ "sim_arr", "typedefs_8hpp.html#aec69d34220fff45de238b9e01f2686af", null ], [ "sim_cols", "typedefs_8hpp.html#a7c2dfa854274262c4e00e4ef0ab2ce23", null ], [ "sim_rows", "typedefs_8hpp.html#a8502989b1b361725834fc185bd575f66", null ], + [ "simulation_t", "typedefs_8hpp.html#a784799c37b5e4fb8bf4f6368e004dec6", 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 index 475ff07..b7cf904 100644 --- a/docs/typedefs_8hpp_source.html +++ b/docs/typedefs_8hpp_source.html @@ -105,8 +105,8 @@ $(document).ready(function(){initNavTree('typedefs_8hpp_source.html',''); initRe
    15#ifndef __TYPEDEFS__
    16#define __TYPEDEFS__
    17
    -
    18#include <vector>
    -
    19#include <armadillo>
    +
    18#include <armadillo>
    +
    19#include <vector>
    20
    24typedef std::vector<arma::vec::fixed<3>> sim_cols;
    25
    @@ -116,7 +116,14 @@ $(document).ready(function(){initNavTree('typedefs_8hpp_source.html',''); initRe
    33
    36typedef arma::vec::fixed<3> vec_3d;
    37
    -
    38#endif
    +
    40typedef struct simulation {
    +
    41 sim_arr r_vecs;
    +
    42 sim_arr v_vecs;
    +
    43} simulation_t;
    +
    44
    +
    45#endif
    +
    simulation
    Typedef for PenningTrap::simulation return value.
    Definition: typedefs.hpp:40
    +
    simulation_t
    struct simulation simulation_t
    Typedef for PenningTrap::simulation return value.
    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
    diff --git a/docs/utils_8cpp.html b/docs/utils_8cpp.html index 9401b51..f76d7e7 100644 --- a/docs/utils_8cpp.html +++ b/docs/utils_8cpp.html @@ -106,8 +106,7 @@ $(document).ready(function(){initNavTree('utils_8cpp.html',''); initResizable();

    Implementation of the utils. More...

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

    Go to the source code of this file.

    @@ -122,9 +121,9 @@ Functions - - - + + + @@ -139,14 +138,14 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)

    Definition in file utils.cpp.

    Function Documentation

    - -

    ◆ arma_vector_close_to()

    + +

    ◆ close_to()

    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.
     
    bool arma_vector_close_to (arma::vec &a, arma::vec &b, double tol)
     Test if two armadillo vectors are close to each other.
     
    bool 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.
     
    - + @@ -183,7 +182,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    Returns
    bool
    -

    Definition at line 62 of file utils.cpp.

    +

    Definition at line 60 of file utils.cpp.

    @@ -251,7 +250,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws) -

    Definition at line 43 of file utils.cpp.

    +

    Definition at line 41 of file utils.cpp.

    @@ -290,9 +289,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    bool arma_vector_close_to bool close_to ( arma::vec &  a,
    -
    Returns
    bool
    +
    Returns
    bool Success/Fail
    -

    Definition at line 76 of file utils.cpp.

    +

    Definition at line 74 of file utils.cpp.

    @@ -340,7 +339,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    Returns
    std::string
    -

    Definition at line 24 of file utils.cpp.

    +

    Definition at line 22 of file utils.cpp.

    @@ -388,7 +387,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    Returns
    std::string
    -

    Definition at line 17 of file utils.cpp.

    +

    Definition at line 15 of file utils.cpp.

    diff --git a/docs/utils_8cpp.js b/docs/utils_8cpp.js index 362b36a..a2d8610 100644 --- a/docs/utils_8cpp.js +++ b/docs/utils_8cpp.js @@ -1,6 +1,6 @@ var utils_8cpp = [ - [ "arma_vector_close_to", "utils_8cpp.html#a5d2e1e032fd19614f2fbb58149a7b02a", null ], + [ "close_to", "utils_8cpp.html#a6be6f938bcbb235ebb6a2ed9d08411b2", null ], [ "m_assert", "utils_8cpp.html#aff5e07c3c1d321709b0cc38e999f427b", null ], [ "mkpath", "utils_8cpp.html#acf13f4e492199cb7231bfa646dbd08de", null ], [ "scientific_format", "utils_8cpp.html#a58565270b643b24e3132f38c653e0199", null ], diff --git a/docs/utils_8cpp_source.html b/docs/utils_8cpp_source.html index 5ed9571..24a0002 100644 --- a/docs/utils_8cpp_source.html +++ b/docs/utils_8cpp_source.html @@ -102,97 +102,95 @@ $(document).ready(function(){initNavTree('utils_8cpp_source.html',''); initResiz
    Go to the documentation of this file.
    1
    -
    13#include <sys/stat.h>
    +
    13#include "utils.hpp"
    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 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
    +
    15std::string scientific_format(double d, int width, int prec)
    +
    16{
    +
    17 std::stringstream ss;
    +
    18 ss << std::setw(width) << std::setprecision(prec) << std::scientific << d;
    +
    19 return ss.str();
    +
    20}
    +
    21
    +
    22std::string scientific_format(const std::vector<double> &v, int width, int prec)
    +
    23{
    +
    24 std::stringstream ss;
    +
    25 for (double elem : v) {
    +
    26 ss << scientific_format(elem, width, prec);
    +
    27 }
    +
    28 return ss.str();
    +
    29}
    +
    30
    +
    31static void print_message(std::string msg)
    +
    32{
    +
    33 if (msg.size() > 0) {
    +
    34 std::cout << "message: " << msg << "\n\n";
    +
    35 }
    +
    36 else {
    +
    37 std::cout << "\n";
    +
    38 }
    +
    39}
    +
    40
    +
    41void m_assert(bool expr, std::string expr_str, std::string f, std::string file,
    +
    42 int line, std::string msg)
    +
    43{
    +
    44 std::string new_assert(f.size() + (expr ? 4 : 6), '-');
    +
    45 std::cout << "\x1B[36m" << new_assert << "\033[0m\n";
    +
    46 std::cout << f << ": ";
    +
    47 if (expr) {
    +
    48 std::cout << "\x1B[32mOK\033[0m\n";
    +
    49 print_message(msg);
    +
    50 }
    +
    51 else {
    +
    52 std::cout << "\x1B[31mFAIL\033[0m\n";
    +
    53 print_message(msg);
    +
    54 std::cout << file << " " << line << ": Assertion \"" << expr_str
    +
    55 << "\" Failed\n\n";
    +
    56 abort();
    +
    57 }
    +
    58}
    +
    59
    +
    60bool close_to(arma::vec &a, arma::vec &b, double tol)
    +
    61{
    +
    62 if (a.n_elem != b.n_elem) {
    +
    63 return false;
    +
    64 }
    +
    65
    +
    66 for (size_t i = 0; i < a.n_elem; i++) {
    +
    67 if (std::abs(a(i) - b(i)) >= tol) {
    +
    68 return false;
    +
    69 }
    +
    70 }
    +
    71 return true;
    +
    72}
    +
    73
    +
    74bool mkpath(std::string path, int mode)
    +
    75{
    +
    76 std::string cur_dir;
    +
    77 std::string::size_type pos = -1;
    +
    78 struct stat buf;
    +
    79
    +
    80 if (path.back() != '/') {
    +
    81 path += '/';
    +
    82 }
    +
    83 while (true) {
    +
    84 pos++;
    +
    85 pos = path.find('/', pos);
    +
    86 if (pos != std::string::npos) {
    +
    87 cur_dir = path.substr(0, pos);
    +
    88 if (mkdir(cur_dir.c_str(), mode) != 0 && stat(cur_dir.c_str(), &buf) != 0) {
    +
    89 return -1;
    +
    90 }
    +
    91 }
    +
    92 else {
    +
    93 break;
    +
    94 }
    +
    95 }
    +
    96 return 0;
    +
    97}
    +
    close_to
    bool close_to(arma::vec &a, arma::vec &b, double tol)
    Test if two armadillo vectors are close to each other.
    Definition: utils.cpp:60
    +
    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:15
    +
    mkpath
    bool mkpath(std::string path, int mode)
    Make path given.
    Definition: utils.cpp:74
    +
    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:41
    utils.hpp
    Function prototypes and macros that are useful.
    diff --git a/docs/utils_8hpp.html b/docs/utils_8hpp.html index 2866ae0..129e846 100644 --- a/docs/utils_8hpp.html +++ b/docs/utils_8hpp.html @@ -111,6 +111,7 @@ $(document).ready(function(){initNavTree('utils_8hpp.html',''); initResizable(); #include <iomanip>
    #include <sstream>
    #include <string>
    +#include <sys/stat.h>
    #include <vector>

    Go to the source code of this file.

    @@ -124,7 +125,7 @@ Macros  A prettier assertion function.
      #define __METHOD_NAME__   methodName(__PRETTY_FUNCTION__) - Get the name of the current method/function.
    + Get the name of the current method/function without the return type.
      - - - + + + @@ -168,9 +169,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)

    @@ -138,9 +139,9 @@ Functions

    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.
     
    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 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.
     
    -

    Get the name of the current method/function.

    +

    Get the name of the current method/function without the return type.

    -

    Definition at line 51 of file utils.hpp.

    +

    Definition at line 52 of file utils.hpp.

    @@ -201,13 +202,13 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    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:43
    -
    __METHOD_NAME__
    #define __METHOD_NAME__
    Get the name of the current method/function.
    Definition: utils.hpp:51
    +
    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:41
    +
    __METHOD_NAME__
    #define __METHOD_NAME__
    Get the name of the current method/function without the return type.
    Definition: utils.hpp:52

    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.

    -

    Definition at line 45 of file utils.hpp.

    +

    Definition at line 46 of file utils.hpp.

    @@ -230,19 +231,19 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)

    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.

    -

    Definition at line 36 of file utils.hpp.

    +

    Definition at line 37 of file utils.hpp.

    Function Documentation

    - -

    ◆ arma_vector_close_to()

    + +

    ◆ close_to()

    - + @@ -279,7 +280,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    Returns
    bool
    -

    Definition at line 62 of file utils.cpp.

    +

    Definition at line 60 of file utils.cpp.

    @@ -347,7 +348,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws) -

    Definition at line 43 of file utils.cpp.

    +

    Definition at line 41 of file utils.cpp.

    @@ -386,9 +387,9 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    bool arma_vector_close_to bool close_to ( arma::vec &  a,
    -
    Returns
    bool
    +
    Returns
    bool Success/Fail
    -

    Definition at line 76 of file utils.cpp.

    +

    Definition at line 74 of file utils.cpp.

    @@ -436,7 +437,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    Returns
    std::string
    -

    Definition at line 24 of file utils.cpp.

    +

    Definition at line 22 of file utils.cpp.

    @@ -484,7 +485,7 @@ Janita Ovidie Sandtrøen Willumsen (janitaws)
    Returns
    std::string
    -

    Definition at line 17 of file utils.cpp.

    +

    Definition at line 15 of file utils.cpp.

    diff --git a/docs/utils_8hpp.js b/docs/utils_8hpp.js index 68951df..35bac4e 100644 --- a/docs/utils_8hpp.js +++ b/docs/utils_8hpp.js @@ -3,7 +3,7 @@ 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 ], + [ "close_to", "utils_8hpp.html#ab3e0cf669bddc59bd53998490ffb68b9", null ], [ "m_assert", "utils_8hpp.html#a2cc3a2cdb635bac3c8b02e89d4d6af38", null ], [ "mkpath", "utils_8hpp.html#a6fdd7217b750aff5b6295ece7cbdeffa", null ], [ "scientific_format", "utils_8hpp.html#ad54b96a1074f9df4dc892a41d115b72d", null ], diff --git a/docs/utils_8hpp_source.html b/docs/utils_8hpp_source.html index 1c7052d..23a5d44 100644 --- a/docs/utils_8hpp_source.html +++ b/docs/utils_8hpp_source.html @@ -109,57 +109,58 @@ $(document).ready(function(){initNavTree('utils_8hpp_source.html',''); initResiz
    19#include <iomanip>
    20#include <sstream>
    21#include <string>
    -
    22#include <vector>
    -
    23
    -
    32#ifdef DBG
    -
    33 #define DEBUG(msg) std::cout << __FILE__ << " " << __LINE__ << ": " \
    -
    34 << msg << std::endl
    -
    35#else
    -
    36 #define DEBUG(msg)
    -
    37#endif
    -
    38
    -
    45#define ASSERT(expr, msg) m_assert(expr, #expr, __METHOD_NAME__, __FILE__, \
    -
    46 __LINE__, msg)
    -
    47
    -
    51#define __METHOD_NAME__ methodName(__PRETTY_FUNCTION__)
    -
    52
    +
    22#include <sys/stat.h>
    +
    23#include <vector>
    +
    24
    +
    33#ifdef DBG
    +
    34 #define DEBUG(msg) std::cout << __FILE__ << " " << __LINE__ << ": " \
    +
    35 << msg << std::endl
    +
    36#else
    +
    37 #define DEBUG(msg)
    +
    38#endif
    +
    39
    +
    46#define ASSERT(expr, msg) m_assert(expr, #expr, __METHOD_NAME__, __FILE__, \
    +
    47 __LINE__, msg)
    +
    48
    +
    52#define __METHOD_NAME__ methodName(__PRETTY_FUNCTION__)
    53
    -
    64std::string scientific_format(double d, int width=20, int prec=10);
    -
    65
    +
    54
    +
    65std::string scientific_format(double d, int width=20, int prec=10);
    66
    -
    77std::string scientific_format(const std::vector<double>& v,
    -
    78 int width=20,
    -
    79 int prec=10);
    -
    80
    +
    67
    +
    78std::string scientific_format(const std::vector<double>& v,
    +
    79 int width=20,
    +
    80 int prec=10);
    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
    +
    82
    +
    95void m_assert(bool expr,
    +
    96 std::string expr_str,
    +
    97 std::string func,
    +
    98 std::string file,
    +
    99 int line,
    +
    100 std::string msg);
    101
    -
    113bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8);
    -
    114
    +
    102
    +
    114bool close_to(arma::vec &a, arma::vec &b, double tol=1e-8);
    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
    +
    116
    +
    127static inline std::string methodName(const std::string& pretty_function)
    +
    128{
    +
    129 size_t colons = pretty_function.find("::");
    +
    130 size_t begin = pretty_function.substr(0,colons).rfind(" ") + 1;
    +
    131 size_t end = pretty_function.rfind("(") - begin;
    +
    132
    +
    133 return pretty_function.substr(begin,end) + "()";
    +
    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
    +
    136
    +
    147bool mkpath(std::string path, int mode = 0777);
    +
    148
    +
    149#endif
    +
    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:41
    +
    mkpath
    bool mkpath(std::string path, int mode=0777)
    Make path given.
    Definition: utils.cpp:74
    +
    close_to
    bool 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:60
    +
    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:15
    diff --git a/include/PenningTrap.hpp b/include/PenningTrap.hpp index 9a78784..411b3cc 100644 --- a/include/PenningTrap.hpp +++ b/include/PenningTrap.hpp @@ -18,15 +18,11 @@ #include "Particle.hpp" #include "constants.hpp" #include "typedefs.hpp" +#include "utils.hpp" -#pragma omp declare reduction(+ : vec_3d : omp_out += omp_in) \ +#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. * * This class simulates a Penning trap. It can take in a number of particles @@ -62,7 +58,7 @@ private: * * @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) + * @param dt The step length (delta time) * * @return vec_3d * */ @@ -78,8 +74,8 @@ public: * */ PenningTrap( double B_0 = T, - std::function V_0 = - [](double t) { return 25. * V / 1000.; }, + std::function V_0 + = [](double t) { return (25. * V) / 1000.; }, double d = 500., double t = 0.); /** @brief Constructor for the PenningTrap class @@ -92,8 +88,8 @@ public: * */ PenningTrap( unsigned int i, double B_0 = T, - std::function V_0 = - [](double t) { return 25. * V / 1000.; }, + std::function V_0 + = [](double t) { return 25. * V / 1000.; }, double d = 500., double t = 0.); /** @brief Constructor for the PenningTrap class @@ -106,10 +102,21 @@ public: * */ PenningTrap( std::vector particles, double B_0 = T, - std::function V_0 = - [](double t) { return 25. * V / 1000.; }, + std::function V_0 + = [](double t) { return 25. * V / 1000.; }, double d = 500., double t = 0.); + /** @brief Give all particles new positions and velocities, and change t + * and V_0. + * + * @param V_0 The tiome dependent applied potential + * @param t The starting time + * */ + void reinitialize( + std::function V_0 + = [](double t) { return 25. * V / 1000.; }, + double t = 0.); + /** @brief Add a particle to the system * * @param particle The particle to add to the Penning trap @@ -155,7 +162,8 @@ public: * */ vec_3d total_force_external(unsigned int i); - /** @brief Calculate the total force on a particle p_i from other particles. + /** @brief Calculate the total force on a particle p_i from other + * particles. * * @param i The index of particle p_i * @@ -192,6 +200,8 @@ public: * @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 simulation_t * */ simulation_t simulate(double time, unsigned int steps, std::string method = "rk4", @@ -206,7 +216,8 @@ public: * @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", + unsigned int steps, + std::string method = "rk4", bool particle_interaction = true); /** @brief Simulate and calculate what fraction of particles are still diff --git a/include/constants.hpp b/include/constants.hpp index 592b48a..06942ee 100644 --- a/include/constants.hpp +++ b/include/constants.hpp @@ -12,10 +12,10 @@ #ifndef __CONST__ #define __CONST__ -#define K_E 138935.333 ///< Coulomb constant. unit: \f$\frac{u(\mu m)^3}{(\mu s)^2 e^2}\f$ +#define K_E 1.38935333*1e5 ///< Coulomb constant. unit: \f$\frac{u(\mu m)^3}{(\mu s)^2 e^2}\f$ -#define T 96.4852558 ///< 1 Tesla. unit: \f$ \frac{u}{(\mu s) e} \f$ +#define T 9.64852558*1e1 ///< 1 Tesla. unit: \f$ \frac{u}{(\mu s) e} \f$ -#define V 96485255.8 ///< 1 Volt. unit: \f$ \frac{u (\mu m)^2}{(\mu s)^2 e} \f$ +#define V 9.64852558*1e7 ///< 1 Volt. unit: \f$ \frac{u (\mu m)^2}{(\mu s)^2 e} \f$ #endif diff --git a/include/typedefs.hpp b/include/typedefs.hpp index f0ceca2..a5154b8 100644 --- a/include/typedefs.hpp +++ b/include/typedefs.hpp @@ -15,8 +15,8 @@ #ifndef __TYPEDEFS__ #define __TYPEDEFS__ -#include #include +#include /** @brief Typedef for the column of the result vector from simulating * particles. @@ -35,4 +35,11 @@ typedef std::vector sim_arr; * */ typedef arma::vec::fixed<3> vec_3d; +/** @brief Typedef for PenningTrap::simulation return value. + * */ +typedef struct simulation { + sim_arr r_vecs; + sim_arr v_vecs; +} simulation_t; + #endif diff --git a/include/utils.hpp b/include/utils.hpp index c9c9485..c8469c9 100644 --- a/include/utils.hpp +++ b/include/utils.hpp @@ -19,6 +19,7 @@ #include #include #include +#include #include /** @def DEBUG(msg) @@ -46,7 +47,7 @@ __LINE__, msg) /** @def __METHOD_NAME__ - * @brief Get the name of the current method/function. + * @brief Get the name of the current method/function without the return type. * */ #define __METHOD_NAME__ methodName(__PRETTY_FUNCTION__) @@ -110,7 +111,7 @@ void m_assert(bool expr, * * @return bool * */ -bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol=1e-8); +bool close_to(arma::vec &a, arma::vec &b, double tol=1e-8); /** @brief Takes in the __PRETTY_FUNCTION__ string and removes the return type. @@ -141,7 +142,7 @@ static inline std::string methodName(const std::string& pretty_function) * @param path The path to be created * @param mode The mode/permissions for all the new directories * - * @return bool + * @return bool Success/Fail * */ bool mkpath(std::string path, int mode = 0777); diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..db5d81e --- /dev/null +++ b/requirements.txt @@ -0,0 +1,2 @@ +matplotlib +numpy diff --git a/src/Makefile b/src/Makefile index f678e43..3718e50 100644 --- a/src/Makefile +++ b/src/Makefile @@ -21,7 +21,7 @@ endif PROFILE ?= 0 ifeq ($(PROFILE), 1) - PROFFLAG=-pg + PROFFLAG=-pg -fno-inline-functions else PROFFLAG= endif @@ -30,6 +30,16 @@ endif all: test_suite main +instrument: + scorep $(CC) -c PenningTrap.cpp -o PenningTrap.o $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP) + scorep $(CC) -c Particle.cpp -o Particle.o $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP) + scorep $(CC) -c utils.cpp -o utils.o $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP) + scorep $(CC) -c main.cpp -o main.o $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP) + scorep $(CC) $(LIBOBJS) $(CLASSOBJS) main.o -o main $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP) + + + + # Rules for executables main: main.o $(LIBOBJS) $(CLASSOBJS) $(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP) diff --git a/src/Particle.cpp b/src/Particle.cpp index 2caad68..374812f 100644 --- a/src/Particle.cpp +++ b/src/Particle.cpp @@ -13,8 +13,8 @@ #include "Particle.hpp" Particle::Particle(double q, double m, - arma::vec::fixed<3> r_vec, - arma::vec::fixed<3> v_vec) + vec_3d r_vec, + vec_3d v_vec) { // Giving the particle its properties this->q = q; diff --git a/src/PenningTrap.cpp b/src/PenningTrap.cpp index d5a3b16..af4b19e 100644 --- a/src/PenningTrap.cpp +++ b/src/PenningTrap.cpp @@ -11,9 +11,10 @@ * */ #include "PenningTrap.hpp" -#include "constants.hpp" #include "typedefs.hpp" -#include "utils.hpp" +#include +#include +#include PenningTrap::PenningTrap(double B_0, std::function V_0, double d, double t) @@ -28,11 +29,9 @@ 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)); + this->particles.push_back(Particle(1., 40., vec_3d(vec_3d().randn() * .1 * this->d), + vec_3d(vec_3d().randn() * .1 * this->d))); } } @@ -43,6 +42,16 @@ PenningTrap::PenningTrap(std::vector particles, double B_0, this->particles = particles; } +void PenningTrap::reinitialize(std::function V_0, double t) +{ + this->V_0 = V_0; + this->t = t; + + for (size_t i = 0; i < this->particles.size(); i++) { + this->particles[i].r_vec = vec_3d().randn() * .1 * this->d; + } +} + vec_3d PenningTrap::v_func(unsigned int i, unsigned int j, double dt) { switch (i) { @@ -53,8 +62,9 @@ vec_3d PenningTrap::v_func(unsigned int i, unsigned int j, double dt) 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]); + return vec_3d((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(); @@ -71,8 +81,9 @@ vec_3d PenningTrap::r_func(unsigned int i, unsigned int j, double dt) 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]); + return vec_3d((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(); @@ -87,9 +98,8 @@ void PenningTrap::add_particle(Particle particle) vec_3d PenningTrap::external_E_field(vec_3d r) { r(2) *= -2.; - double f = this->V_0(this->t) / (this->d * this->d); - return f * r; + return vec_3d((this->V_0(this->t) / (this->d * this->d)) * r); } vec_3d PenningTrap::external_B_field(vec_3d r) @@ -99,51 +109,48 @@ vec_3d PenningTrap::external_B_field(vec_3d r) 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 - vec_3d res = this->particles[i].r_vec - p_j.r_vec; + vec_3d res = this->particles[i].r_vec - this->particles[j].r_vec; // Get the distance between the particles double norm = arma::norm(res, 2); - return vec_3d(res * p_j.q / (norm * norm * norm)); + return vec_3d((this->particles[j].q / (norm * norm * norm)) * res); } vec_3d PenningTrap::total_force_external(unsigned int i) { - Particle p = this->particles[i]; + Particle *p = &this->particles[i]; - if (arma::norm(p.r_vec) > this->d) { + if (arma::norm(p->r_vec) > this->d) { return vec_3d{0., 0., 0.}; } - 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; + return vec_3d( + p->q + * (this->external_E_field(p->r_vec) + + arma::cross(p->v_vec, this->external_B_field(p->r_vec)))); } vec_3d PenningTrap::total_force_particles(unsigned int i) { - Particle p = this->particles[i]; - vec_3d res; for (size_t j = 0; j < this->particles.size(); j++) { - if (i == j) { - continue; - } - - res += this->force_on_particle(i, j); + if (i != j) + res += this->force_on_particle(i, j); } - return vec_3d(res * K_E * (p.q / p.m)); + return vec_3d(res * K_E * (this->particles[i].q)); } vec_3d PenningTrap::total_force(unsigned int i) { - return this->total_force_external(i) - this->total_force_particles(i); + if (arma::norm(this->particles[i].r_vec) > this->d) { + return vec_3d{0., 0., 0.}; + } + return vec_3d(this->total_force_external(i) + - this->total_force_particles(i)); } void PenningTrap::evolve_RK4(double dt, bool particle_interaction) @@ -152,32 +159,35 @@ void PenningTrap::evolve_RK4(double dt, bool particle_interaction) std::vector original_particles = this->particles; std::vector tmp_particles = this->particles; - vec_3d (PenningTrap::*force)(unsigned int); - if (particle_interaction) { - force = &PenningTrap::total_force; - } - else { - force = &PenningTrap::total_force_external; - } + vec_3d (PenningTrap::*force)(unsigned int) + = particle_interaction ? &PenningTrap::total_force + : &PenningTrap::total_force_external; size_t size = this->particles.size(); - this->k_v = sim_arr(4, sim_cols(size)); - this->k_r = sim_arr(4, sim_cols(size)); + // Allocating takes a long time, so reuse sim_arr if possible + if (this->k_v.size() != 4 || this->k_r.size() != 4 + || this->k_v[0].size() != size || this->k_r[0].size() != size) { + this->k_v = sim_arr(4, sim_cols(size)); + this->k_r = sim_arr(4, sim_cols(size)); + } + // Each k_{i+1} is dependent on k_i, so outer loop is not parallelizable for (size_t i = 0; i < 4; i++) { + // Inner loop is able to be parallelized #pragma omp parallel for - for (size_t j = 0; j < this->particles.size(); j++) { + for (size_t j = 0; j < 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); + tmp_particles[j].v_vec + = original_particles[j].v_vec + this->v_func(i, j, dt); + tmp_particles[j].r_vec + = original_particles[j].r_vec + this->r_func(i, j, dt); } - this->particles.swap(tmp_particles); + this->particles = tmp_particles; } + this->t += dt; } @@ -187,19 +197,19 @@ void PenningTrap::evolve_forward_euler(double dt, bool particle_interaction) vec_3d force_res[size]; Particle *p; - vec_3d (PenningTrap::*force)(unsigned int); - if (particle_interaction) { - force = &PenningTrap::total_force; - } - else { - force = &PenningTrap::total_force_external; - } + vec_3d (PenningTrap::*force)(unsigned int) + = particle_interaction ? &PenningTrap::total_force + : &PenningTrap::total_force_external; + // Calculating the force for each particle is independent and therefore + // a good candidate for parallel execution #pragma omp parallel for for (size_t i = 0; i < size; i++) { force_res[i] = (this->*force)(i); } + // Updating the particles is also independent, so we can parallelize + // this as well #pragma omp parallel for private(p) for (size_t i = 0; i < size; i++) { p = &this->particles[i]; @@ -217,7 +227,7 @@ simulation_t PenningTrap::simulate(double time, unsigned int steps, 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))}; @@ -253,27 +263,31 @@ void PenningTrap::write_simulation_to_dir(std::string path, double time, path += '/'; } if (mkpath(path, 0777) != 0) { - std::cout << "Hello" << std::endl; - return; + std::cout << "Failed to make path" << std::endl; + abort(); } - simulation_t res = - this->simulate(time, steps, method, particle_interaction); + simulation_t res + = this->simulate(time, steps, method, particle_interaction); std::ofstream ofile; + // Writing each particle to its own file is independent and can be run in + // parallel. #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 << scientific_format(vec(0), 10, 8) << ',' + << scientific_format(vec(1), 10, 8) << ',' + << scientific_format(vec(2), 10, 8) << '\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 << scientific_format(vec(0), 10, 8) << ',' + << scientific_format(vec(1), 10, 8) << ',' + << scientific_format(vec(2), 10, 8) << '\n'; } ofile.close(); } @@ -283,26 +297,33 @@ 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); + double dt = time / (double)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++) { + (this->*func)(dt, particle_interaction); + } int particles_left = 0; - for (Particle p : this->particles) { - if (arma::norm(p.r_vec) < this->d) { + // A reduction is perfect here + #pragma omp parallel for reduction(+:particles_left) + for (size_t i=0; i < this->particles.size(); i++) { + if (arma::norm(this->particles[i].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 19ef8fd..641c66a 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -13,10 +13,8 @@ #include #include #include -#include #include #include -#include #include #include "PenningTrap.hpp" @@ -24,12 +22,21 @@ #define PARTICLES 100 #define N 40000 -#define CHARGE 1. -#define MASS 40. // unit: amu +#define CHARGE 1. // unit: e +#define MASS 40.078 // unit: amu -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.}); +// Particles used for testing +Particle p1(CHARGE, MASS, vec_3d{20., 0., 20.}, + vec_3d{0., 25., 0.}); ///< Particle 1 +Particle p2(CHARGE, MASS, vec_3d{25., 25., 0.}, + vec_3d{0., 40., 5.}); ///< Particle 2 +/** @brief The analytical solution for particle p1 + * + * @param t Time + * + * @return vec_3d + * */ vec_3d analytical_solution_particle_1(double t) { double w_0 = T / MASS; @@ -38,98 +45,122 @@ vec_3d analytical_solution_particle_1(double t) 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)}; + 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; } +/** @brief Simulate a single particle over the period of 50 \f$ \mu s \f$. + * */ void simulate_single_particle() { - DEBUG("Inside single particle sim"); + // Initialize trap with particle 1 PenningTrap trap(std::vector{p1}); double time = 50.; // microseconds - DEBUG("Write to dir"); + // Simulate and write results to file trap.write_simulation_to_dir("output/simulate_single_particle", time, N, "rk4", false); } +/** @brief Simulate 2 particles over the period of 50 \f$ \mu s \f$ with and + * without particle interactions. + * */ void simulate_two_particles() { + // Initialize traps with particles PenningTrap trap_no_interaction(std::vector{p1, p2}); PenningTrap trap_with_interaction(std::vector{p1, p2}); double time = 50.; // microseconds + // Simulate and write results to files 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); } +/** @brief Simulate a single particle over 50 \f$ \mu s \f$ using different + * amount of steps and different methods. + * */ void simulate_single_particle_with_different_steps() { - double time = 50.; // microseconds std::ofstream ofile; + // Calculate relative error for RK4 + std::string path = "output/relative_error/RK4/"; + mkpath(path); +#pragma omp parallel for 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}); + simulation_t res = trap.simulate(time, steps, "rk4", false); 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 << arma::norm(res.r_vecs[0][i] + - analytical_solution_particle_1(dt * i)) + << '\n'; } ofile.close(); } + // Calculate relative error for forward Euler + path = "output/relative_error/euler/"; + mkpath(path); +#pragma omp parallel for 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}); + simulation_t res = trap.simulate(time, steps, "euler", false); 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 << arma::norm(res.r_vecs[0][i] + - analytical_solution_particle_1(dt * i)) + << '\n'; } ofile.close(); } } +/** @brief Simulate 100 particles over 50 \f$ \mu s \f$. + * */ void simulate_100_particles() { - PenningTrap trap((unsigned)100, T, - [](double t) { - return 25. * V / 1000. * (1. + .4 * std::cos(1.5 * t)); - }, - 500., 0); + PenningTrap trap((unsigned)100); - double time = 500.; // microseconds + double time = 50.; // microseconds - trap.write_simulation_to_dir("output/simulate_100_particles", time, N * 4); + trap.write_simulation_to_dir("output/simulate_100_particles", time, N, + "rk4", false); } -void simulate_100_particles_with_time_potential() +/** @brief Simulate 100 particles over 500 \f$ \mu s \f$ using a time + * dependent potential. + * + * @details The simulation sweeps over different frequencies in [0.2, 2.5] + * MHz. + * + * */ +void potential_resonance_wide_sweep() { + double time = 500.; + 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); + size_t freq_iterations + = (size_t)((freq_end - freq_start) / freq_increment) + 1; double res[4][freq_iterations]; @@ -138,53 +169,211 @@ void simulate_100_particles_with_time_potential() std::ofstream ofile; - double freq = freq_start; +#pragma omp parallel for + // Insert frequencies for (size_t i = 0; i < freq_iterations; i++) { - res[0][i] = freq; - freq += freq_increment; + res[0][i] = freq_start + freq_increment * i; } -#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( +#pragma omp parallel + { + // Each thread creates a PenningTrap instance and reuses it throughout + // the sweep. + PenningTrap trap((unsigned int)100); +#pragma omp for collapse(2) + for (size_t i = 0; i < 3; i++) { + for (size_t j = 0; j < freq_iterations; j++) { + // Reset particles and give new time dependent potential. + trap.reinitialize(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); + amplitudes[i], res[0][j], std::placeholders::_1)); + res[i + 1][j] + = trap.fraction_of_particles_left(time, N, "rk4", false); + } } } - ofile.open(path + "res.txt"); + // Write results to file + ofile.open(path + "wide_sweep.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 << res[0][i] << ',' << res[1][i] << ',' << res[2][i] << ',' + << res[3][i] << '\n'; + } + ofile.close(); +} + +/** @brief Simulate 100 particles over 500 \f$ \mu s \f$ using a time + * dependent potential. + * + * @details The simulation sweeps over different frequencies in [1., 1.7] + * MHz. + * + * */ +void potential_resonance_no_interaction_narrow_sweep() +{ + double time = 500.; + + double amplitudes[]{.1, .4, .7}; + + double freq_start = 1.; + double freq_end = 1.7; + double freq_increment = .002; + 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; + +#pragma omp parallel + { + // Each thread creates a PenningTrap instance and reuses it throughout + // the sweep. + PenningTrap trap((unsigned int)100); +#pragma omp for collapse(2) + for (size_t i = 0; i < 3; i++) { + for (size_t j = 0; j < freq_iterations; j++) { + // Reset particles and give new time dependent potential. + trap.reinitialize(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)); + res[i + 1][j] + = trap.fraction_of_particles_left(time, N, "rk4", false); + } + } + } + + // Write results to file + ofile.open(path + "narrow_sweep.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(); +} + +/** @brief Simulate 100 particles over 500 \f$ \mu s \f$ using a time + * dependent potential. + * + * @details The simulation sweeps over different frequencies in [1., 1.7] + * MHz. + * + * */ +void potential_resonance_with_interaction_narrow_sweep() +{ + double time = 500.; + + double amplitudes[]{.1, .4, .7}; + + double freq_start = 1.; + double freq_end = 1.7; + double freq_increment = .002; + 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; + +#pragma omp parallel for + for (size_t i = 0; i < freq_iterations; i++) { + res[0][i] = freq_start + freq_increment * i; + } + +#pragma omp parallel + { + // Each thread creates a PenningTrap instance and reuses it throughout + // the sweep. + PenningTrap trap((unsigned int)100); +#pragma omp for collapse(2) + for (size_t i = 0; i < 3; i++) { + for (size_t j = 0; j < freq_iterations; j++) { + // Reset particles and give new time dependent potential. + trap.reinitialize(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)); + res[i + 1][j] = trap.fraction_of_particles_left(time, N); + } + } + } + + // Write results to file + ofile.open(path + "narrow_sweep_interactions.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(); + double start, end, t1, t2; + start = omp_get_wtime(); simulate_single_particle(); simulate_two_particles(); - simulate_single_particle_with_different_steps(); + simulate_single_particle_with_different_steps(); - // simulate_100_particles(); + t2 = omp_get_wtime(); - // simulate_100_particles_with_time_potential(); + std::cout << "Time single and double : " << (t2 - start) + << " seconds" << std::endl; - double end = omp_get_wtime(); + t1 = omp_get_wtime(); - std::cout << "Time: " << (end - start) << " seconds" << std::endl; + simulate_100_particles(); + + t2 = omp_get_wtime(); + + std::cout << "Time 100 particles : " << (t2 - t1) + << " seconds" << std::endl; + + t1 = omp_get_wtime(); + + potential_resonance_wide_sweep(); + + t2 = omp_get_wtime(); + + std::cout << "Time wide sweep : " << (t2 - t1) + << " seconds" << std::endl; + + t1 = omp_get_wtime(); + + potential_resonance_no_interaction_narrow_sweep(); + + t2 = omp_get_wtime(); + + std::cout << "Time narrow sweep no interaction : " << (t2 - t1) + << " seconds" << std::endl; + + t1 = omp_get_wtime(); + + potential_resonance_with_interaction_narrow_sweep(); + + t2 = omp_get_wtime(); + + std::cout << "Time narrow sweep with interaction: " << (t2 - t1) + << " seconds" << std::endl; + + end = omp_get_wtime(); + + std::cout << "Time : " << (end - start) + << " seconds" << std::endl; return 0; } diff --git a/src/scripts/plot_relative_error.py b/src/scripts/plot_relative_error.py index 54214c8..de8b692 100644 --- a/src/scripts/plot_relative_error.py +++ b/src/scripts/plot_relative_error.py @@ -2,10 +2,10 @@ import matplotlib.pyplot as plt import numpy as np def main(): - directories = { + directories = [ "output/relative_error/RK4/", "output/relative_error/euler/", - } + ] files = [ "4000_steps.txt", "8000_steps.txt", @@ -22,8 +22,12 @@ def main(): "Relative error for the RK4 method", "Relative error for the forward Euler method" ] + methods = [ + "rk4", + "euler" + ] fig1, axs1 = plt.subplots(2,1) - for i, (dir, title) in enumerate(zip(directories, titles)): + for i, (dir, title) in enumerate(list(zip(directories, titles))): max_err = [] for label, file in zip(labels, files): with open(dir+file) as f: @@ -33,17 +37,14 @@ def main(): 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].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) + conv_rate = 1/3 * sum([np.log2(max_err[i+1]/max_err[i])/np.log2(.5) for i in range(3)]) + print(f"{methods[i]}: {conv_rate}") - plt.show() - # fig1.savefig("../latex/images/phase_space_2_particles_x.pdf") + fig1.savefig("../latex/images/phase_space_2_particles_x.pdf") if __name__ == "__main__": diff --git a/src/test_suite.cpp b/src/test_suite.cpp index cd422c5..a2a0639 100644 --- a/src/test_suite.cpp +++ b/src/test_suite.cpp @@ -10,39 +10,43 @@ * @bug No known bugs * */ -#include "PenningTrap.hpp" -#include "utils.hpp" - #include #include #include +#include "PenningTrap.hpp" +#include "utils.hpp" + +/** @brief Test class for the Penning trap. + * */ class PenningTrapTest { public: + /** @brief Test that the external E field gives correct values. + * */ static void test_external_E_field() { PenningTrap trap; // Vector containing inputs and expected results - std::vector> tests; + std::vector> tests; tests.push_back( - std::make_pair(arma::vec{0., 0., 0.}, arma::vec{0., 0., 0.})); + std::make_pair(vec_3d{0., 0., 0.}, vec_3d{0., 0., 0.})); - tests.push_back(std::make_pair(arma::vec{10., 0., 0.}, - arma::vec{96.4852558, 0., 0.})); + tests.push_back(std::make_pair(vec_3d{10., 0., 0.}, + vec_3d{96.4852558, 0., 0.})); - tests.push_back(std::make_pair(arma::vec{10., 0., 0.}, - arma::vec{96.4852558, 0., 0.})); + tests.push_back(std::make_pair(vec_3d{10., 0., 0.}, + vec_3d{96.4852558, 0., 0.})); - tests.push_back(std::make_pair(arma::vec{0., 10., 0.}, - arma::vec{0., 96.4852558, 0.})); + tests.push_back(std::make_pair(vec_3d{0., 10., 0.}, + vec_3d{0., 96.4852558, 0.})); - tests.push_back(std::make_pair(arma::vec{0., 0., 10.}, - arma::vec{0., 0., -192.9705116})); + tests.push_back(std::make_pair(vec_3d{0., 0., 10.}, + vec_3d{0., 0., -192.9705116})); - arma::vec result; - arma::vec v; + vec_3d result; + vec_3d v; std::stringstream msg; for (size_t i = 0; i < tests.size(); i++) { v = tests.at(i).first; @@ -52,81 +56,90 @@ public: msg << "Testing the external E field at (" << std::setprecision(2) << v(0) << "," << v(1) << "," << v(2) << ")."; - ASSERT(arma_vector_close_to(result, tests.at(i).second), msg.str()); + ASSERT(close_to(result, tests.at(i).second), msg.str()); } } + /** @brief Test that the external B field gives correct values. + * */ static void test_external_B_field() { // No point in testing at different points since it's not dependent // on position. PenningTrap trap; - arma::vec expected{0., 0., T}; - arma::vec result = trap.external_B_field(arma::vec{0., 0., 0.}); - ASSERT(arma_vector_close_to(expected, result), + vec_3d expected{0., 0., T}; + vec_3d result = trap.external_B_field(vec_3d{0., 0., 0.}); + ASSERT(close_to(expected, result), "Testing the external B field at (0,0,0)"); } + /** @brief Test that the force between particles gives expected results. + * */ static void test_force_on_particle() { PenningTrap trap; - arma::vec v{0., 0., 0.}; + vec_3d v{0., 0., 0.}; // Add particles to test - trap.add_particle(Particle(1., 40., arma::vec{0., 0., 0.}, v)); - trap.add_particle(Particle(1., 40., arma::vec{1., 0., 0.}, v)); - trap.add_particle(Particle(1., 40., arma::vec{0., 3., 4.}, v)); + trap.add_particle(Particle(1., 40., vec_3d{0., 0., 0.}, v)); + trap.add_particle(Particle(1., 40., vec_3d{1., 0., 0.}, v)); + trap.add_particle(Particle(1., 40., vec_3d{0., 3., 4.}, v)); // Test p0 and p1 - arma::vec expected{-1., 0., 0.}; - arma::vec result = trap.force_on_particle(0, 1); - ASSERT(arma_vector_close_to(expected, result), + vec_3d expected{-1., 0., 0.}; + vec_3d result = trap.force_on_particle(0, 1); + ASSERT(close_to(expected, result), "Testing the force on a particle at (0,0,0) from a " "particle at (1,0,0)."); // Test p0 and p2 - expected = arma::vec{0, -.024, -.032}; + expected = vec_3d{0, -.024, -.032}; result = trap.force_on_particle(0, 2); - ASSERT(arma_vector_close_to(expected, result), + ASSERT(close_to(expected, result), "Testing the force on a particle at (0,0,0) from a " "particle at (0,3,4)."); } + /** @brief Test that the total external force returns expected results + * */ static void test_total_force_external() { PenningTrap trap; trap.add_particle( - Particle(1., 40., arma::vec{1., 2., 3.}, arma::vec{3., 4., 5.})); + Particle(1., 40., vec_3d{1., 2., 3.}, vec_3d{3., 4., 5.})); - arma::vec expected{395.58954878, -270.15871624, -57.89115348}; - arma::vec result = trap.total_force_external(0); - ASSERT(arma_vector_close_to(expected, result), + vec_3d expected{395.58954878, -270.15871624, -57.89115348}; + vec_3d result = trap.total_force_external(0); + ASSERT(close_to(expected, result), "Testing the total external force on a particle at " "(1,2,3) with velocity (3,4,5)"); } + /** @brief Test that the total force of all particles on a single particle + * returns expected results. + * */ static void test_total_force_particles() { PenningTrap trap; trap.add_particle( - Particle(1., 40., arma::vec{0., 0., 0.}, arma::vec{0., 0., 0.})); + Particle(1., 40., vec_3d{0., 0., 0.}, vec_3d{0., 0., 0.})); - arma::vec expected{0., 0., 0.}; - arma::vec result = trap.total_force_particles(0); - ASSERT(arma_vector_close_to(expected, result), + vec_3d expected{0., 0., 0.}; + vec_3d result = trap.total_force_particles(0); + ASSERT(close_to(expected, result), "Testing the total force of all particles on particle 0 " "with only a single particle"); trap.add_particle( - Particle(1., 40., arma::vec{1., 0., 0.}, arma::vec{0., 0., 0.})); + Particle(1., 40., vec_3d{1., 0., 0.}, vec_3d{0., 0., 0.})); trap.add_particle( - Particle(1., 40., arma::vec{0., 1., 0.}, arma::vec{0., 0., 0.})); + Particle(1., 40., vec_3d{0., 1., 0.}, vec_3d{0., 0., 0.})); trap.add_particle( - Particle(1., 40., arma::vec{0., 0., 1.}, arma::vec{0., 0., 0.})); + Particle(1., 40., vec_3d{0., 0., 1.}, vec_3d{0., 0., 0.})); - expected = arma::vec(3, arma::fill::value(-3473.383325)); + expected = vec_3d().fill(-3473.383325); result = trap.total_force_particles(0); - ASSERT(arma_vector_close_to(expected, result), + ASSERT(close_to(expected, result), "Testing the total force of all particles on particle 0 " "with 3 other particles."); } diff --git a/src/utils.cpp b/src/utils.cpp index 14670f0..83e67a8 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -10,8 +10,6 @@ * @bug No known bugs * */ -#include - #include "utils.hpp" std::string scientific_format(double d, int width, int prec) @@ -59,7 +57,7 @@ void m_assert(bool expr, std::string expr_str, std::string f, std::string file, } } -bool arma_vector_close_to(arma::vec &a, arma::vec &b, double tol) +bool close_to(arma::vec &a, arma::vec &b, double tol) { if (a.n_elem != b.n_elem) { return false;