Make some changes

include/PenningTrap.hpp

@@ -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
+    /** @brief A 2D vector containing all \f$k_{v,i,j}\f$ where \f$j\f$ is the
-    sim_arr k_r; ///< A 2D vector containing all \f$k_{i,j}\f$ where \f$j\f$ is
+     *  index of a particle
-                 ///< 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

src/Makefile

@@ -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)

src/PenningTrap.cpp

@@ -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))
+    return vec3(
-                * r);
+        ((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
+    vec3 (PenningTrap::*force)(uint) =
-                                           ? &PenningTrap::total_force
+        particle_interaction ? &PenningTrap::total_force
-                                           : &PenningTrap::total_force_external;
+                             : &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 =
+            p = &tmp_particles[j];
-                original_particles[j].v_vec + this->v_func(i, j, dt);
+
-            tmp_particles[j].r_vec =
+            p->v_vec = original_particles[j].v_vec + this->v_func(i, j, dt);
-                original_particles[j].r_vec + this->r_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
+    vec3 (PenningTrap::*force)(uint) =
-                                           ? &PenningTrap::total_force
+        particle_interaction ? &PenningTrap::total_force
-                                           : &PenningTrap::total_force_external;
+                             : &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;
+        p = &this->particles[i];
-        this->particles[i].v_vec += dt * force_res[i] / this->particles[i].m;
+        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;
+            p = &this->particles[i];
-            res.v_vecs[i][j] = this->particles[i].v_vec;
+            res.r_vecs[i][j] = p->r_vec;
+            res.v_vecs[i][j] = p->v_vec;
         }
         (this->*func)(dt, particle_interaction);
     }

src/main.cpp

@@ -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,
+    // trap.write_simulation_to_dir("output/simulate_100_particles", time, N,
-                                 "rk4", false);
+    //"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;
+    int option = 1;
-    start = omp_get_wtime();
+    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 << "Running simulate_100_particles\n";
-
-    std::cout << "Time single and double            : " << (t2 - start)
-              << " seconds" << std::endl;
-
-    t1 = omp_get_wtime();
-
         simulate_100_particles();
 
-    t2 = omp_get_wtime();
+        std::cout << "Running potential_resonance_wide_sweep\n";
-
-    std::cout << "Time 100 particles                : " << (t2 - t1)
-              << " seconds" << std::endl;
-
-    t1 = omp_get_wtime();
-
         potential_resonance_wide_sweep();
 
-    t2 = omp_get_wtime();
+        std::cout << "Running potential_resonance_narrow_sweep\n";
-
-    std::cout << "Time wide sweep                   : " << (t2 - t1)
-              << " seconds" << std::endl;
-
-    t1 = omp_get_wtime();
-
         potential_resonance_narrow_sweep();
 
-    t2 = omp_get_wtime();
+        std::cout << "Running potential_resonance_narrow_sweep_interaction\n";
-
-    std::cout << "Time narrow sweep no interaction  : " << (t2 - t1)
-              << " seconds" << std::endl;
-
-    t1 = omp_get_wtime();
-
         potential_resonance_narrow_sweep_interaction();
-
+        break;
-    t2 = omp_get_wtime();
+    case 2:
-
+        std::cout << "Running simulate_single_particle\n";
-    std::cout << "Time narrow sweep with interaction: " << (t2 - t1)
+        simulate_single_particle();
-              << " seconds" << std::endl;
+        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)
+    std::cout << "Time: " << end - start << " seconds" << std::endl;
-              << " seconds" << std::endl;
 
     return 0;
 }