Merge pull request #11 from FYS3150-G2-2023/coryab/code

Coryab/code

.gitignore

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

src/Makefile

@@ -8,7 +8,8 @@ CLASSOBJS=$(CLASSSRCS:.cpp=.o)
 
 INCLUDE=../include
 
-CFLAGS=-Wall -larmadillo -lblas -llapack -std=c++11 -O3 -fomit-frame-pointer
+CFLAGS=-Wall -larmadillo -std=c++11 -O3 -fomit-frame-pointer
+#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)
@@ -46,6 +47,10 @@ instrument:
 main: main.o $(LIBOBJS) $(CLASSOBJS)
 	$(CC) $^ -o $@ $(CFLAGS) $(DBGFLAG) $(PROFFLAG) -I$(INCLUDE) $(OPENMP)
 
+frequency_narrow_sweeps_long: frequency_narrow_sweeps_long.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/PenningTrap.cpp

@@ -158,7 +158,7 @@ void PenningTrap::reinitialize(double f, double omega_V, double t)
 
     for (size_t i = 0; i < this->particles.size(); i++) {
         p = &this->particles[i];
-        p->v_vec = vec3().randn() * .1 * this->d;
+        p->r_vec = vec3().randn() * .1 * this->d;
         p->v_vec = vec3().randn() * .1 * this->d;
     }
 }
@@ -172,6 +172,7 @@ void PenningTrap::evolve_RK4(double dt, bool particle_interaction)
 {
     Particle *p;
 
+    // Keep original particles
     std::vector<Particle> original_particles = this->particles;
     std::vector<Particle> tmp_particles = this->particles;
 

src/frequency_narrow_sweeps_long.cpp

@@ -0,0 +1,154 @@
+/** @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
+
+/** @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 = 1.1;
+    double freq_end = 1.7;
+    double freq_increment = .0005;
+    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)PARTICLES);
+#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_fine.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 = 1.1;
+    double freq_end = 1.7;
+    double freq_increment = .0005;
+    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)PARTICLES);
+#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_fine.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, end;
+
+    start = omp_get_wtime();
+
+    potential_resonance_narrow_sweep();
+
+    potential_resonance_narrow_sweep_interaction();
+
+    end = omp_get_wtime();
+
+    std::cout << "Time: " << end - start << " seconds" << std::endl;
+
+    return 0;
+}

src/job.script

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+#SBATCH --account=ec54
+#SBATCH --job-name=particle-sim
+#SBATCH --time=0-01:30:00
+#SBATCH --mem-per-cpu=2G
+#SBATCH --cpus-per-task=16
+
+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
+module load Armadillo/11.4.3-foss-2022b
+
+srun ./frequency_narrow_sweeps_long

src/main.cpp

@@ -42,6 +42,7 @@ vec3 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::cout << A_p << "," << A_n << std::endl;
     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));
@@ -211,7 +212,7 @@ void potential_resonance_narrow_sweep()
 
     double amplitudes[]{.1, .4, .7};
 
-    double freq_start = 1.;
+    double freq_start = 1.1;
     double freq_end = 1.7;
     double freq_increment = .002;
     size_t freq_iterations =
@@ -268,7 +269,7 @@ void potential_resonance_narrow_sweep_interaction()
 
     double amplitudes[]{.1, .4, .7};
 
-    double freq_start = 1.;
+    double freq_start = 1.1;
     double freq_end = 1.7;
     double freq_increment = .002;
     size_t freq_iterations =

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])
 

src/scripts/plot_particles_left.py

@@ -23,12 +23,16 @@ def main():
     files = [
         "output/time_dependent_potential/wide_sweep.txt",
         "output/time_dependent_potential/narrow_sweep.txt",
+        "output/time_dependent_potential/narrow_sweep_fine.txt",
         "output/time_dependent_potential/narrow_sweep_interactions.txt",
+        "output/time_dependent_potential/narrow_sweep_interactions_fine.txt",
     ]
     outputs = [
         "../latex/images/particles_left_wide_sweep.pdf",
         "../latex/images/particles_left_narrow_sweep.pdf",
+        "../latex/images/particles_left_narrow_sweep_fine.pdf",
         "../latex/images/particles_left_narrow_sweep_interactions.pdf",
+        "../latex/images/particles_left_narrow_sweep_interactions_fine.pdf",
     ]
     for file, output in zip(files, outputs):
         with open(file) as f: