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Bunch of stuff

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- Add reinitialize to reuse PenningTrap instance and its particles
- Reformatting
- Refactor fraction_of_particles_left to not use simulate
This commit is contained in:
Cory Balaton 2023-10-22 03:47:23 +02:00
parent 19e35f25ec
commit eb2a985b3b
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GPG Key ID: 3E5FCEBFD80F432B
2 changed files with 92 additions and 56 deletions
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29
include/PenningTrap.hpp
View File

@ -74,8 +74,8 @@ public:
* */
PenningTrap(
double B_0 = T,
std::function<double(double)> V_0 =
[](double t) { return 25. * V / 1000.; },
std::function<double(double)> V_0
= [](double t) { return 25. * V / 1000.; },
double d = 500., double t = 0.);
/** @brief Constructor for the PenningTrap class
@ -88,8 +88,8 @@ public:
* */
PenningTrap(
unsigned int i, double B_0 = T,
std::function<double(double)> V_0 =
[](double t) { return 25. * V / 1000.; },
std::function<double(double)> V_0
= [](double t) { return 25. * V / 1000.; },
double d = 500., double t = 0.);
/** @brief Constructor for the PenningTrap class
@ -102,10 +102,21 @@ public:
* */
PenningTrap(
std::vector<Particle> particles, double B_0 = T,
std::function<double(double)> V_0 =
[](double t) { return 25. * V / 1000.; },
std::function<double(double)> 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<double(double)> 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
@ -151,7 +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
*
@ -204,7 +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

115
src/PenningTrap.cpp
View File

@ -11,7 +11,10 @@
* */
#include "PenningTrap.hpp"
#include "typedefs.hpp"
#include <algorithm>
#include <functional>
#include <vector>
PenningTrap::PenningTrap(double B_0, std::function<double(double)> V_0,
double d, double t)
@ -26,11 +29,9 @@ PenningTrap::PenningTrap(unsigned int i, double B_0,
std::function<double(double)> 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)));
}
}
@ -41,6 +42,16 @@ PenningTrap::PenningTrap(std::vector<Particle> particles, double B_0,
this->particles = particles;
}
void PenningTrap::reinitialize(std::function<double(double)> 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) {
@ -109,15 +120,16 @@ vec_3d PenningTrap::force_on_particle(unsigned int i, unsigned int j)
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.};
}
return vec_3d(p.q
* (this->external_E_field(p.r_vec)
+ arma::cross(p.v_vec, this->external_B_field(p.r_vec))));
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)
@ -134,9 +146,10 @@ vec_3d PenningTrap::total_force_particles(unsigned int i)
vec_3d PenningTrap::total_force(unsigned int i)
{
return arma::norm(this->particles[i].r_vec) > this->d
? vec_3d{0., 0., 0.}
: vec_3d(this->total_force_external(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));
}
@ -146,13 +159,9 @@ void PenningTrap::evolve_RK4(double dt, bool particle_interaction)
std::vector<Particle> original_particles = this->particles;
std::vector<Particle> 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();
@ -163,7 +172,9 @@ void PenningTrap::evolve_RK4(double dt, bool particle_interaction)
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 < size; j++) {
this->k_v[i][j] = (this->*force)(j) / this->particles[j].m;
@ -176,6 +187,7 @@ void PenningTrap::evolve_RK4(double dt, bool particle_interaction)
}
this->particles = tmp_particles;
}
this->t += dt;
}
@ -185,19 +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_external;
}
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];
@ -251,8 +263,8 @@ 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
@ -260,18 +272,22 @@ void PenningTrap::write_simulation_to_dir(std::string path, double time,
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();
}
@ -281,26 +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;
}