.gitignore

@@ -48,3 +48,6 @@ src/*
 !src/*.py
 !src/Doxyfile
 !src/scripts
+
+# Job
+!src/job.script

src/Makefile

@@ -46,6 +46,10 @@ instrument:
 main: main.o $(LIBOBJS) $(CLASSOBJS)
 	$(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP)
 
+main_no_interface: main_no_interface.o $(LIBOBJS) $(CLASSOBJS)
+	$(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP)
+
+
 test_suite: test_suite.o $(LIBOBJS) $(CLASSOBJS)
 	$(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP)
 

src/job.script

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+#SBATCH --account=ec54
+#SBATCH --job-name=simple
+#SBATCH --time=0-00:05:00
+#SBATCH --mem-per-cpu=4G
+#SBATCH --cpus-per-task=8
+
+set -o errexit # Exit the script on any error
+set -o nounset # Treat any unset variables as an error
+module --quiet purge # Reset the modules to the system default
+
+srun ./main_no_interface

src/main_no_interface.cpp

@@ -0,0 +1,334 @@
+/** @file main.cpp
+ *
+ *  @author Cory Alexander Balaton (coryab)
+ *  @author Janita Ovidie Sandtrøen Willumsen (janitaws)
+ *
+ *  @version 1.0
+ *
+ *  @brief The main program for this project
+ *
+ *  @bug No known bugs
+ * */
+
+#include <cmath>
+#include <complex>
+#include <fstream>
+#include <omp.h>
+#include <string>
+#include <vector>
+
+#include "PenningTrap.hpp"
+#include "constants.hpp"
+#include "utils.hpp"
+
+#define PARTICLES 100
+#define N 40000
+
+// Particles used for testing
+Particle p1(vec3{20., 0., 20.}, vec3{0., 25., 0.}); ///< Particle 1
+Particle p2(vec3{25., 25., 0.}, vec3{0., 40., 5.}); ///< Particle 2
+
+/** @brief The analytical solution for particle p1
+ *
+ *  @param t Time
+ *
+ *  @return vec3
+ * */
+vec3 analytical_solution_particle_1(double t)
+{
+    double w_0 = T / CA_MASS;
+    double w_z2 = (50. * V / 1000.) / (CA_MASS * 500. * 500.);
+    double w_p = (w_0 + std::sqrt(w_0 * w_0 - 2. * w_z2)) / 2.;
+    double w_n = (w_0 - std::sqrt(w_0 * w_0 - 2. * w_z2)) / 2.;
+    double A_p = (25. + w_n * 20.) / (w_n - w_p);
+    double A_n = -(25. + w_p * 20.) / (w_n - w_p);
+    std::complex<double> f =
+        A_p * std::exp(std::complex<double>(0., -w_p * t))
+        + A_n * std::exp(std::complex<double>(0., -w_n * t));
+    vec3 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$.
+ * */
+void simulate_single_particle()
+{
+    // Initialize trap with particle 1
+    PenningTrap trap(std::vector<Particle>{p1});
+
+    double time = 50.; // microseconds
+
+    // Simulate and write results to file
+    trap.write_simulation_to_dir("output/simulate_single_particle", time, N,
+                                 "rk4", false);
+}
+
+/** @brief Simulate 2 particles over the period of 50 \f$ \mu s \f$ with and
+ *  without particle interactions.
+ * */
+void simulate_two_particles()
+{
+    // Initialize traps with particles
+    PenningTrap trap_no_interaction(std::vector<Particle>{p1, p2});
+    PenningTrap trap_with_interaction(std::vector<Particle>{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 private(ofile)
+    for (int i = 0; i < 4; i++) {
+        int steps = 4000 * std::pow(2, i);
+        std::cout << steps << std::endl;
+        double dt = time / (double)steps;
+        ofile.open(path + std::to_string(steps) + "_steps.txt");
+        PenningTrap trap(std::vector<Particle>{p1});
+        simulation_t res = trap.simulate(time, steps, "rk4", false);
+        for (int i = 0; i < steps; i++) {
+            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 private(ofile)
+    for (int i = 0; i < 4; i++) {
+        int steps = 4000 * std::pow(2, i);
+        double dt = time / (double)steps;
+        ofile.open(path + std::to_string(steps) + "_steps.txt");
+        PenningTrap trap(std::vector<Particle>{p1});
+        simulation_t res = trap.simulate(time, steps, "euler", false);
+        for (int i = 0; i < steps; i++) {
+            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$.
+ * */
+void simulate_100_particles()
+{
+    PenningTrap trap((unsigned)100);
+
+    double time = 50.; // microseconds
+
+    // trap.write_simulation_to_dir("output/simulate_100_particles", time, N,
+    //"rk4", false);
+    trap.simulate(time, N, "rk4", true);
+}
+
+/** @brief Simulate 100 particles over 500 \f$ \mu s \f$ using a time
+ *  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) + 1;
+
+    double res[4][freq_iterations];
+
+    std::string path = "output/time_dependent_potential/";
+    mkpath(path);
+
+    std::ofstream ofile;
+
+#pragma omp parallel for
+    // Insert frequencies
+    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((uint)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(amplitudes[i], res[0][j]);
+                res[i + 1][j] =
+                    trap.fraction_of_particles_left(time, N, "rk4", false);
+            }
+        }
+    }
+
+    // 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.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_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) + 1;
+
+    double res[4][freq_iterations];
+
+    std::string path = "output/time_dependent_potential/";
+    mkpath(path);
+
+    std::ofstream ofile;
+
+#pragma omp parallel for
+    // Insert frequencies
+    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((uint)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(amplitudes[i], res[0][j]);
+                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_narrow_sweep_interaction()
+{
+    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) + 1;
+
+    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((uint)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(amplitudes[i], res[0][j]);
+                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()
+{
+    int option = 1;
+    bool chosen = false;
+
+    double start, end;
+
+    start = omp_get_wtime();
+
+    simulate_100_particles();
+
+    potential_resonance_wide_sweep();
+
+    // potential_resonance_narrow_sweep();
+
+    // potential_resonance_narrow_sweep_interaction();
+    end = omp_get_wtime();
+
+    std::cout << "Time: " << end - start << " seconds" << std::endl;
+
+    return 0;
+}

src/scripts/animate_100_particles.py

@@ -34,7 +34,7 @@ def animate():
 
     arr = get_data([f"output/simulate_100_particles/particle_{i}_r.txt" for i in range(100)])
 
-    arr = arr[:, :, ::10]
+    arr = arr[:, :, ::40]
 
     N = len(arr[0][0])