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Coryab/code #10

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coryab merged 37 commits from coryab/code into develop 2023-10-24 10:45:33 +00:00
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4 changed files with 158 additions and 79 deletions
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26
include/PenningTrap.hpp
View File

@ -30,6 +30,9 @@
* */
class PenningTrap
{
/** @brief Make PenningTrapTest a friend of PenningTrap.
* */
friend class PenningTrapTest;
private:
double B_0; ///< Magnetic field strength
double V_0; ///< Applied potential
@ -37,10 +40,16 @@ private:
double d; ///< Characteristic dimension
double t; ///< Current time
std::vector<Particle> particles; ///< The particles in the Penning trap
sim_arr k_v; ///< A 2D vector containing all \f$k_{i,j}\f$ where \f$j\f$ is
///< the index of a particle
sim_arr k_r; ///< A 2D vector containing all \f$k_{i,j}\f$ where \f$j\f$ is
///< the index of a particle
/** @brief A 2D vector containing all \f$k_{v,i,j}\f$ where \f$j\f$ is the
* index of a particle
* */
sim_arr k_v;
/** @brief A 2D vector containing all \f$k_{r,i,j}\f$ where \f$j\f$ is the
* index of a particle
* */
sim_arr k_r;
/** @brief Helper for evolve_RK4 when calculating \f$k_{v,i,j}\f$ values
*
@ -122,6 +131,14 @@ private:
* */
vec3 total_force(uint i);
/** @brief calculate the total force on a particle p_i without interaction
*
* @param i The index of particle p_i
*
* @return vec3
* */
vec3 total_force_no_interaction(uint i);
public:
/** @brief Constructor for the PenningTrap class
*
@ -229,7 +246,6 @@ public:
std::string method = "rk4",
bool particle_interaction = true);
friend class PenningTrapTest;
};
#endif

4
src/Makefile
View File

@ -8,7 +8,7 @@ CLASSOBJS=$(CLASSSRCS:.cpp=.o)
INCLUDE=../include
CFLAGS=-Wall -larmadillo -lblas -llapack -std=c++11 -O3
CFLAGS=-Wall -larmadillo -lblas -llapack -std=c++11 -O3 -fomit-frame-pointer
OPENMP=-fopenmp
# Add a debug flag when compiling (For the DEBUG macro in utils.hpp)
@ -19,6 +19,7 @@ else
DBGFLAG=
endif
# Add profiling for serial code
PROFILE ?= 0
ifeq ($(PROFILE), 1)
PROFFLAG=-pg -fno-inline-functions
@ -30,6 +31,7 @@ endif
all: test_suite main
# Instrumentation using scorep for parallel analysis
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)

61
src/PenningTrap.cpp
View File

@ -10,13 +10,14 @@
* @bug No known bugs
* */
#include "PenningTrap.hpp"
#include "typedefs.hpp"
#include <algorithm>
#include <functional>
#include <sys/types.h>
#include <vector>
#include "PenningTrap.hpp"
#include "typedefs.hpp"
vec3 PenningTrap::v_func(uint i, uint j, double dt)
{
switch (i) {
@ -59,8 +60,8 @@ vec3 PenningTrap::external_E_field(vec3 r)
{
r(2) *= -2.;
return vec3((this->V_0 * this->perturbation(this->t) / (this->d * this->d))
* r);
return vec3(
((this->V_0 * this->perturbation(this->t)) / (this->d * this->d)) * r);
}
vec3 PenningTrap::external_B_field(vec3 r)
@ -83,10 +84,6 @@ vec3 PenningTrap::total_force_external(uint i)
{
Particle *p = &this->particles[i];
if (arma::norm(p->r_vec) > this->d) {
return vec3{0., 0., 0.};
}
return vec3(p->q
* (this->external_E_field(p->r_vec)
+ arma::cross(p->v_vec, this->external_B_field(p->r_vec))));
@ -112,6 +109,14 @@ vec3 PenningTrap::total_force(uint i)
return vec3(this->total_force_external(i) - this->total_force_particles(i));
}
vec3 PenningTrap::total_force_no_interaction(uint i)
{
if (arma::norm(this->particles[i].r_vec) > this->d) {
return vec3{0., 0., 0.};
}
return vec3(this->total_force_external(i));
}
PenningTrap::PenningTrap(double B_0, double V_0, double d, double t)
{
this->B_0 = B_0;
@ -149,9 +154,12 @@ void PenningTrap::reinitialize(double f, double omega_V, double t)
{
this->t = t;
this->set_pertubation(f, omega_V);
Particle *p;
for (size_t i = 0; i < this->particles.size(); i++) {
this->particles[i].r_vec = vec3().randn() * .1 * this->d;
p = &this->particles[i];
p->v_vec = vec3().randn() * .1 * this->d;
p->v_vec = vec3().randn() * .1 * this->d;
}
}
@ -162,13 +170,14 @@ void PenningTrap::add_particle(Particle particle)
void PenningTrap::evolve_RK4(double dt, bool particle_interaction)
{
Particle *p;
std::vector<Particle> original_particles = this->particles;
std::vector<Particle> tmp_particles = this->particles;
vec3 (PenningTrap::*force)(uint) = particle_interaction
? &PenningTrap::total_force
: &PenningTrap::total_force_external;
vec3 (PenningTrap::*force)(uint) =
particle_interaction ? &PenningTrap::total_force
: &PenningTrap::total_force_no_interaction;
size_t size = this->particles.size();
@ -182,15 +191,15 @@ void PenningTrap::evolve_RK4(double dt, bool particle_interaction)
// 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
#pragma omp parallel for private(p)
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;
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);
p = &tmp_particles[j];
p->v_vec = original_particles[j].v_vec + this->v_func(i, j, dt);
p->r_vec = original_particles[j].r_vec + this->r_func(i, j, dt);
}
this->particles = tmp_particles;
}
@ -202,10 +211,11 @@ void PenningTrap::evolve_forward_euler(double dt, bool particle_interaction)
{
size_t size = this->particles.size();
vec3 force_res[size];
Particle *p;
vec3 (PenningTrap::*force)(uint) = particle_interaction
? &PenningTrap::total_force
: &PenningTrap::total_force_external;
vec3 (PenningTrap::*force)(uint) =
particle_interaction ? &PenningTrap::total_force
: &PenningTrap::total_force_no_interaction;
// Calculating the force for each particle is independent and therefore
// a good candidate for parallel execution
@ -218,8 +228,9 @@ void PenningTrap::evolve_forward_euler(double dt, bool particle_interaction)
// this as well
#pragma omp parallel for
for (size_t i = 0; i < size; i++) {
this->particles[i].r_vec += dt * this->particles[i].v_vec;
this->particles[i].v_vec += dt * force_res[i] / this->particles[i].m;
p = &this->particles[i];
p->r_vec += dt * p->v_vec;
p->v_vec += dt * force_res[i] / p->m;
}
this->t += dt;
@ -228,6 +239,7 @@ void PenningTrap::evolve_forward_euler(double dt, bool particle_interaction)
simulation_t PenningTrap::simulate(double time, uint steps, std::string method,
bool particle_interaction)
{
Particle *p;
double dt = time / (double)steps;
uint size = this->particles.size();
@ -247,8 +259,9 @@ simulation_t PenningTrap::simulate(double time, uint steps, std::string method,
for (size_t j = 0; j < steps; j++) {
for (size_t i = 0; i < size; i++) {
res.r_vecs[i][j] = this->particles[i].r_vec;
res.v_vecs[i][j] = this->particles[i].v_vec;
p = &this->particles[i];
res.r_vecs[i][j] = p->r_vec;
res.v_vecs[i][j] = p->v_vec;
}
(this->*func)(dt, particle_interaction);
}

132
src/main.cpp
View File

@ -13,6 +13,7 @@
#include <cmath>
#include <complex>
#include <fstream>
#include <ncurses.h>
#include <omp.h>
#include <string>
#include <vector>
@ -135,8 +136,9 @@ void simulate_100_particles()
double time = 50.; // microseconds
trap.write_simulation_to_dir("output/simulate_100_particles", time, N,
"rk4", false);
// trap.write_simulation_to_dir("output/simulate_100_particles", time, N,
//"rk4", false);
trap.simulate(time, N, "rk4", true);
}
/** @brief Simulate 100 particles over 500 \f$ \mu s \f$ using a time
@ -212,7 +214,8 @@ void potential_resonance_narrow_sweep()
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);
size_t freq_iterations =
(size_t)((freq_end - freq_start) / freq_increment) + 1;
double res[4][freq_iterations];
@ -268,7 +271,8 @@ void potential_resonance_narrow_sweep_interaction()
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);
size_t freq_iterations =
(size_t)((freq_end - freq_start) / freq_increment) + 1;
double res[4][freq_iterations];
@ -308,60 +312,104 @@ void potential_resonance_narrow_sweep_interaction()
int main()
{
double start, end, t1, t2;
start = omp_get_wtime();
int option = 1;
bool chosen = false;
system("clear");
std::cout << "(1) All (default)\n"
<< "(2) Simulate single particle\n"
<< "(3) simulate 2 particles\n"
<< "(4) Simulate single particle with different time steps\n"
<< "(5) Simulate 100 particles\n"
<< "(6) Potential resonance wide sweep\n"
<< "(7) Potential resonance narrow sweep without particle "
"interactions\n"
<< "(8) Potential resonance narrow sweep with particle "
"interaction\n"
<< "Select what to run: ";
std::cin >> std::noskipws;
do {
if (!(std::cin >> option) || option < 1 || option > 8) {
std::cin.clear();
std::cin.ignore(std::numeric_limits<std::streamsize>::max(), '\n');
system("clear");
std::cout
<< "(1) All (default)\n"
<< "(2) Simulate single particle\n"
<< "(3) simulate 2 particles\n"
<< "(4) Simulate single particle with different time steps\n"
<< "(5) Simulate 100 particles\n"
<< "(6) Potential resonance wide sweep\n"
<< "(7) Potential resonance narrow sweep without particle "
"interactions\n"
<< "(8) Potential resonance narrow sweep with particle "
"interaction\n"
<< "Not a valid option, please enter a valid number: ";
} else {
chosen = true;
}
} while (!chosen);
double start, end;
system("clear");
start = omp_get_wtime();
switch (option) {
case 1:
std::cout << "Running simulate_single_particle\n";
simulate_single_particle();
std::cout << "Running simulate_two_particles\n";
simulate_two_particles();
std::cout << "Running simulate_single_particle_with_different_steps\n";
simulate_single_particle_with_different_steps();
t2 = omp_get_wtime();
std::cout << "Time single and double : " << (t2 - start)
<< " seconds" << std::endl;
t1 = omp_get_wtime();
std::cout << "Running simulate_100_particles\n";
simulate_100_particles();
t2 = omp_get_wtime();
std::cout << "Time 100 particles : " << (t2 - t1)
<< " seconds" << std::endl;
t1 = omp_get_wtime();
std::cout << "Running potential_resonance_wide_sweep\n";
potential_resonance_wide_sweep();
t2 = omp_get_wtime();
std::cout << "Time wide sweep : " << (t2 - t1)
<< " seconds" << std::endl;
t1 = omp_get_wtime();
std::cout << "Running potential_resonance_narrow_sweep\n";
potential_resonance_narrow_sweep();
t2 = omp_get_wtime();
std::cout << "Time narrow sweep no interaction : " << (t2 - t1)
<< " seconds" << std::endl;
t1 = omp_get_wtime();
std::cout << "Running potential_resonance_narrow_sweep_interaction\n";
potential_resonance_narrow_sweep_interaction();
t2 = omp_get_wtime();
std::cout << "Time narrow sweep with interaction: " << (t2 - t1)
<< " seconds" << std::endl;
break;
case 2:
std::cout << "Running simulate_single_particle\n";
simulate_single_particle();
break;
case 3:
std::cout << "Running simulate_two_particles\n";
simulate_two_particles();
break;
case 4:
std::cout << "Running simulate_single_particle_with_different_steps\n";
simulate_single_particle_with_different_steps();
break;
case 5:
std::cout << "Running simulate_100_particles\n";
simulate_100_particles();
break;
case 6:
std::cout << "Running potential_resonance_wide_sweep\n";
potential_resonance_wide_sweep();
break;
case 7:
std::cout << "Running potential_resonance_narrow_sweep\n";
potential_resonance_narrow_sweep();
break;
case 8:
std::cout << "Running potential_resonance_narrow_sweep_interaction\n";
potential_resonance_narrow_sweep_interaction();
break;
}
end = omp_get_wtime();
std::cout << "Time : " << (end - start)
<< " seconds" << std::endl;
std::cout << "Time: " << end - start << " seconds" << std::endl;
return 0;
}