Refactor
- Change PenningTrap so that perturbation is its own field - Add Calcium mass and charge to constants
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@ -31,7 +31,8 @@
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class PenningTrap {
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private:
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double B_0; ///< Magnetic field strength
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std::function<double(double)> V_0; ///< Applied potential
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double V_0; ///< Applied potential
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std::function<double(double)> perturbation; ///< Time-dependent perturbation
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double d; ///< Characteristic dimension
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double t; ///< Current time
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std::vector<Particle> particles; ///< The particles in the Penning trap
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@ -50,7 +51,7 @@ private:
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*
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* @return vec_3d
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* */
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vec_3d v_func(unsigned int i, unsigned int j, double dt);
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vec_3d v_func(uint i, uint j, double dt);
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/** @brief Helper for evolve_RK4 when calculating \f$k_{r,i,j}\f$ values
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*
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@ -62,7 +63,7 @@ private:
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*
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* @return vec_3d
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* */
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vec_3d r_func(unsigned int i, unsigned int j, double dt);
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vec_3d r_func(uint i, uint j, double dt);
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public:
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/** @brief Constructor for the PenningTrap class
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@ -74,8 +75,7 @@ public:
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* */
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PenningTrap(
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double B_0 = T,
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std::function<double(double)> V_0
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= [](double t) { return (25. * V) / 1000.; },
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double V_0 = (25. * V) / 1000.,
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double d = 500., double t = 0.);
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/** @brief Constructor for the PenningTrap class
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@ -87,9 +87,8 @@ public:
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* @param t The starting time
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* */
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PenningTrap(
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unsigned int i, double B_0 = T,
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std::function<double(double)> V_0
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= [](double t) { return 25. * V / 1000.; },
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uint i, double B_0 = T,
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double V_0 = (25. * V) / 1000.,
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double d = 500., double t = 0.);
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/** @brief Constructor for the PenningTrap class
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@ -102,10 +101,11 @@ public:
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* */
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PenningTrap(
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std::vector<Particle> particles, double B_0 = T,
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std::function<double(double)> V_0
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= [](double t) { return 25. * V / 1000.; },
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double V_0 = (25. * V) / 1000.,
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double d = 500., double t = 0.);
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void set_pertubation(double f, double omega_V);
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/** @brief Give all particles new positions and velocities, and change t
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* and V_0.
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*
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@ -113,8 +113,7 @@ public:
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* @param t The starting time
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* */
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void reinitialize(
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std::function<double(double)> V_0
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= [](double t) { return 25. * V / 1000.; },
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double f, double omega_V,
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double t = 0.);
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/** @brief Add a particle to the system
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@ -149,7 +148,7 @@ public:
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*
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* @return vec_3d
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* */
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vec_3d force_on_particle(unsigned int i, unsigned int j);
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vec_3d force_on_particle(uint i, uint j);
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/** @brief Calculate the total external force on a particle.
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*
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@ -160,7 +159,7 @@ public:
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*
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* @return vec_3d
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* */
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vec_3d total_force_external(unsigned int i);
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vec_3d total_force_external(uint i);
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/** @brief Calculate the total force on a particle p_i from other
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* particles.
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@ -169,7 +168,7 @@ public:
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*
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* @return vec_3d
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* */
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vec_3d total_force_particles(unsigned int i);
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vec_3d total_force_particles(uint i);
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/** @brief calculate the total force on a particle p_i.
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*
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@ -177,7 +176,7 @@ public:
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*
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* @return vec_3d
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* */
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vec_3d total_force(unsigned int i);
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vec_3d total_force(uint i);
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/** @brief Go forward one timestep using the RK4 method
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*
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@ -203,7 +202,7 @@ public:
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*
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* @return simulation_t
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* */
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simulation_t simulate(double time, unsigned int steps,
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simulation_t simulate(double time, uint steps,
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std::string method = "rk4",
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bool particle_interaction = true);
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@ -216,7 +215,7 @@ public:
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* @param particle_interaction Turn particle interactions on/off
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* */
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void write_simulation_to_dir(std::string path, double time,
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unsigned int steps,
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uint steps,
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std::string method = "rk4",
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bool particle_interaction = true);
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@ -230,12 +229,9 @@ public:
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*
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* @return double
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* */
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double fraction_of_particles_left(double time, unsigned int steps,
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double fraction_of_particles_left(double time, uint steps,
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std::string method = "rk4",
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bool particle_interaction = true);
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vec_3d get_r(int i);
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double get_t();
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};
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#endif
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@ -18,4 +18,8 @@
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#define V 9.64852558*1e7 ///< 1 Volt. unit: \f$ \frac{u (\mu m)^2}{(\mu s)^2 e} \f$
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#define CA_MASS 40.078 ///< Mass of a single calcium ion. unit: amu
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#define CA_CHARGE 1. ///< Charge of a singly charged calcium ion. unit: e
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#endif
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@ -14,45 +14,52 @@
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#include "typedefs.hpp"
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#include <algorithm>
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#include <functional>
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#include <sys/types.h>
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#include <vector>
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PenningTrap::PenningTrap(double B_0, std::function<double(double)> V_0,
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double d, double t)
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PenningTrap::PenningTrap(double B_0, double V_0, double d, double t)
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{
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this->B_0 = B_0;
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this->V_0 = V_0;
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this->d = d;
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this->t = t;
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this->perturbation = [](double t) { return 1.; };
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}
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PenningTrap::PenningTrap(unsigned int i, double B_0,
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std::function<double(double)> V_0, double d, double t)
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PenningTrap::PenningTrap(uint i, double B_0, double V_0, double d, double t)
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: PenningTrap::PenningTrap(B_0, V_0, d)
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{
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for (size_t j = 0; j < i; j++) {
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this->particles.push_back(Particle(1., 40., vec_3d(vec_3d().randn() * .1 * this->d),
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this->particles.push_back(
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Particle(1., 40., vec_3d(vec_3d().randn() * .1 * this->d),
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vec_3d(vec_3d().randn() * .1 * this->d)));
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}
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}
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PenningTrap::PenningTrap(std::vector<Particle> particles, double B_0,
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std::function<double(double)> V_0, double d, double t)
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double V_0, double d, double t)
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: PenningTrap::PenningTrap(B_0, V_0, d)
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{
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this->particles = particles;
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}
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void PenningTrap::reinitialize(std::function<double(double)> V_0, double t)
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void PenningTrap::set_pertubation(double f, double omega_V)
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{
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this->perturbation
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= [f, omega_V](double t) { return f * std::cos(omega_V * t); };
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}
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void PenningTrap::reinitialize(double f, double omega_V, double t)
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{
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this->V_0 = V_0;
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this->t = t;
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this->set_pertubation(f, omega_V);
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for (size_t i = 0; i < this->particles.size(); i++) {
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this->particles[i].r_vec = vec_3d().randn() * .1 * this->d;
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}
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}
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vec_3d PenningTrap::v_func(unsigned int i, unsigned int j, double dt)
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vec_3d PenningTrap::v_func(uint i, uint j, double dt)
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{
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switch (i) {
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case 0:
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@ -71,7 +78,7 @@ vec_3d PenningTrap::v_func(unsigned int i, unsigned int j, double dt)
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}
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}
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vec_3d PenningTrap::r_func(unsigned int i, unsigned int j, double dt)
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vec_3d PenningTrap::r_func(uint i, uint j, double dt)
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{
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switch (i) {
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case 0:
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@ -99,7 +106,8 @@ vec_3d PenningTrap::external_E_field(vec_3d r)
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{
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r(2) *= -2.;
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return vec_3d((this->V_0(this->t) / (this->d * this->d)) * r);
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return vec_3d(
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(this->V_0 * this->perturbation(this->t) / (this->d * this->d)) * r);
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}
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vec_3d PenningTrap::external_B_field(vec_3d r)
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@ -107,7 +115,7 @@ vec_3d PenningTrap::external_B_field(vec_3d r)
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return vec_3d{0., 0., this->B_0};
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}
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vec_3d PenningTrap::force_on_particle(unsigned int i, unsigned int j)
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vec_3d PenningTrap::force_on_particle(uint i, uint j)
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{
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// Calculate the difference between the particles' position
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vec_3d res = this->particles[i].r_vec - this->particles[j].r_vec;
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@ -118,7 +126,7 @@ vec_3d PenningTrap::force_on_particle(unsigned int i, unsigned int j)
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return vec_3d((this->particles[j].q / (norm * norm * norm)) * res);
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}
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vec_3d PenningTrap::total_force_external(unsigned int i)
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vec_3d PenningTrap::total_force_external(uint i)
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{
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Particle *p = &this->particles[i];
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@ -132,7 +140,7 @@ vec_3d PenningTrap::total_force_external(unsigned int i)
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+ arma::cross(p->v_vec, this->external_B_field(p->r_vec))));
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}
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vec_3d PenningTrap::total_force_particles(unsigned int i)
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vec_3d PenningTrap::total_force_particles(uint i)
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{
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vec_3d res;
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@ -141,10 +149,10 @@ vec_3d PenningTrap::total_force_particles(unsigned int i)
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res += this->force_on_particle(i, j);
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}
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return vec_3d(res * K_E * (this->particles[i].q));
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return vec_3d(res * (K_E * this->particles[i].q));
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}
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vec_3d PenningTrap::total_force(unsigned int i)
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vec_3d PenningTrap::total_force(uint i)
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{
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if (arma::norm(this->particles[i].r_vec) > this->d) {
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return vec_3d{0., 0., 0.};
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@ -159,7 +167,7 @@ void PenningTrap::evolve_RK4(double dt, bool particle_interaction)
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std::vector<Particle> original_particles = this->particles;
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std::vector<Particle> tmp_particles = this->particles;
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vec_3d (PenningTrap::*force)(unsigned int)
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vec_3d (PenningTrap::*force)(uint)
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= particle_interaction ? &PenningTrap::total_force
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: &PenningTrap::total_force_external;
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@ -197,7 +205,7 @@ void PenningTrap::evolve_forward_euler(double dt, bool particle_interaction)
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vec_3d force_res[size];
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Particle *p;
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vec_3d (PenningTrap::*force)(unsigned int)
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vec_3d (PenningTrap::*force)(uint)
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= particle_interaction ? &PenningTrap::total_force
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: &PenningTrap::total_force_external;
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@ -220,13 +228,12 @@ void PenningTrap::evolve_forward_euler(double dt, bool particle_interaction)
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this->t += dt;
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}
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simulation_t PenningTrap::simulate(double time, unsigned int steps,
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std::string method,
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simulation_t PenningTrap::simulate(double time, uint steps, std::string method,
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bool particle_interaction)
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{
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double dt = time / (double)steps;
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unsigned int size = this->particles.size();
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uint size = this->particles.size();
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simulation_t res{sim_arr(size, sim_cols(steps)),
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sim_arr(size, sim_cols(steps))};
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@ -255,8 +262,7 @@ simulation_t PenningTrap::simulate(double time, unsigned int steps,
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}
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void PenningTrap::write_simulation_to_dir(std::string path, double time,
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unsigned int steps,
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std::string method,
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uint steps, std::string method,
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bool particle_interaction)
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{
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if (path.back() != '/') {
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@ -293,7 +299,7 @@ void PenningTrap::write_simulation_to_dir(std::string path, double time,
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}
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}
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double PenningTrap::fraction_of_particles_left(double time, unsigned int steps,
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double PenningTrap::fraction_of_particles_left(double time, uint steps,
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std::string method,
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bool particle_interaction)
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{
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@ -317,9 +323,9 @@ double PenningTrap::fraction_of_particles_left(double time, unsigned int steps,
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int particles_left = 0;
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// A reduction is perfect here
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#pragma omp parallel for reduction(+:particles_left)
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for (size_t i=0; i < this->particles.size(); i++) {
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// A reduction is perfect here
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#pragma omp parallel for reduction(+ : particles_left)
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for (size_t i = 0; i < this->particles.size(); i++) {
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if (arma::norm(this->particles[i].r_vec) < this->d) {
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particles_left++;
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}
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