Update versions and some other things

- Update version numbers for Doxygen
- Use vec3 instead of vec_3d

include/Particle.hpp

@@ -3,7 +3,7 @@
  *  @author Cory Alexander Balaton (coryab)
  *  @author Janita Ovidie Sandtrøen Willumsen (janitaws)
  *
- *  @version 0.1
+ *  @version 1.0
  *
  *  @brief A class that holds the properties of a particle.
  *
@@ -22,10 +22,10 @@
 class Particle
 {
 private:
-    vec_3d r_vec; ///< position
+    vec3 r_vec; ///< position
-    vec_3d v_vec; ///< velocity
+    vec3 v_vec; ///< velocity
-    double q;     ///< Charge
+    double q;   ///< Charge
-    double m;     ///< Mass
+    double m;   ///< Mass
 
 public:
     /** @brief Initialize the particle.
@@ -38,8 +38,7 @@ public:
      *  @param r_vec The initial position of the particle
      *  @param v_vec The initial velocity of the particle
      * */
-    Particle(vec_3d r_vec, vec_3d v_vec, double q = CA_CHARGE,
+    Particle(vec3 r_vec, vec3 v_vec, double q = CA_CHARGE, double m = CA_MASS);
-             double m = CA_MASS);
 
     /** @brief Make private attributes available for PenningTrap.
      * */

include/PenningTrap.hpp

@@ -3,7 +3,7 @@
  *  @author Cory Alexander Balaton (coryab)
  *  @author Janita Ovidie Sandtrøen Willumsen (janitaws)
  *
- *  @version 0.1
+ *  @version 1.0
  *
  *  @brief A class for simulating a Penning trap.
  *
@@ -20,7 +20,7 @@
 #include "typedefs.hpp"
 #include "utils.hpp"
 
-#pragma omp declare reduction(+ : vec_3d : omp_out += omp_in)                 \
+#pragma omp declare reduction(+ : vec3 : omp_out += omp_in)                    \
     initializer(omp_priv = omp_orig)
 
 /** @brief A class that simulates a Penning trap.
@@ -28,14 +28,15 @@
  *  This class simulates a Penning trap. It can take in a number of particles
  *  and simulate how they would behave inside a Penning trap.
  * */
-class PenningTrap {
+class PenningTrap
+{
 private:
-    double B_0;                        ///< Magnetic field strength
+    double B_0;                                 ///< Magnetic field strength
-    double V_0; ///< Applied potential
+    double V_0;                                 ///< Applied potential
     std::function<double(double)> perturbation; ///< Time-dependent perturbation
-    double d;                          ///< Characteristic dimension
+    double d;                                   ///< Characteristic dimension
-    double t;                          ///< Current time
+    double t;                                   ///< Current time
-    std::vector<Particle> particles;   ///< The particles in the Penning trap
+    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
     sim_arr k_r; ///< A 2D vector containing all \f$k_{i,j}\f$ where \f$j\f$ is
@@ -49,9 +50,9 @@ private:
      *  @param j Index j for \f$k_{v,i,j}\f$
      *  @param dt the step length (delta time)
      *
-     *  @return vec_3d
+     *  @return vec3
      * */
-    vec_3d v_func(uint i, uint j, double dt);
+    vec3 v_func(uint i, uint j, double dt);
 
     /** @brief Helper for evolve_RK4 when calculating \f$k_{r,i,j}\f$ values
      *
@@ -61,82 +62,25 @@ private:
      *  @param j Index j for \f$k_{r,i,j}\f$
      *  @param dt The step length (delta time)
      *
-     *  @return vec_3d
+     *  @return vec3
      * */
-    vec_3d r_func(uint i, uint j, double dt);
+    vec3 r_func(uint i, uint j, double dt);
-
-public:
-    /** @brief Constructor for the PenningTrap class
-     *
-     *  @param B_0 The magnetic field strength
-     *  @param V_0 The time dependent applied potential
-     *  @param d The characteristic dimension
-     *  @param t The starting time
-     * */
-    PenningTrap(
-        double B_0 = T,
-        double V_0 = (25. * V) / 1000.,
-        double d = 500., double t = 0.);
-
-    /** @brief Constructor for the PenningTrap class
-     *
-     *  @param i The number of particles to generate
-     *  @param B_0 The magnetic field strength
-     *  @param V_0 The time dependent applied potential
-     *  @param d The characteristic dimension
-     *  @param t The starting time
-     * */
-    PenningTrap(
-        uint i, double B_0 = T,
-        double V_0 = (25. * V) / 1000.,
-        double d = 500., double t = 0.);
-
-    /** @brief Constructor for the PenningTrap class
-     *
-     *  @param particles The starting particles
-     *  @param B_0 The magnetic field strength
-     *  @param V_0 The time dependent applied potential
-     *  @param d The characteristic dimension
-     *  @param t The starting time
-     * */
-    PenningTrap(
-        std::vector<Particle> particles, double B_0 = T,
-        double V_0 = (25. * V) / 1000.,
-        double d = 500., double t = 0.);
-
-    void set_pertubation(double f, double omega_V);
-
-    /** @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(
-        double f, double omega_V,
-        double t = 0.);
-
-    /** @brief Add a particle to the system
-     *
-     *  @param particle The particle to add to the Penning trap
-     * */
-    void add_particle(Particle particle);
 
     /** @brief Calculate E at point r
      *
      *  @param r The position where we want to calculate the E field
      *
-     *  @return vec_3d
+     *  @return vec3
      * */
-    vec_3d external_E_field(vec_3d r);
+    vec3 external_E_field(vec3 r);
 
     /** @brief Calculate B at point r
      *
      *  @param r The position where we want to calculate the B field
      *
-     *  @return vec_3d
+     *  @return vec3
      * */
-    vec_3d external_B_field(vec_3d r);
+    vec3 external_B_field(vec3 r);
 
     /** @brief Calculate the force between 2 particles.
      *
@@ -146,9 +90,9 @@ public:
      *  @param i The index of particle p_i
      *  @param j The index of particle p_j
      *
-     *  @return vec_3d
+     *  @return vec3
      * */
-    vec_3d force_on_particle(uint i, uint j);
+    vec3 force_on_particle(uint i, uint j);
 
     /** @brief Calculate the total external force on a particle.
      *
@@ -157,26 +101,80 @@ public:
      *
      *  @param i The index of particle p_i
      *
-     *  @return vec_3d
+     *  @return vec3
      * */
-    vec_3d total_force_external(uint i);
+    vec3 total_force_external(uint i);
 
     /** @brief Calculate the total force on a particle p_i from other
      * particles.
      *
      *  @param i The index of particle p_i
      *
-     *  @return vec_3d
+     *  @return vec3
      * */
-    vec_3d total_force_particles(uint i);
+    vec3 total_force_particles(uint i);
 
     /** @brief calculate the total force on a particle p_i.
      *
      *  @param i The index of particle p_i
      *
-     *  @return vec_3d
+     *  @return vec3
      * */
-    vec_3d total_force(uint i);
+    vec3 total_force(uint i);
+
+public:
+    /** @brief Constructor for the PenningTrap class
+     *
+     *  @param B_0 The magnetic field strength
+     *  @param V_0 The time dependent applied potential
+     *  @param d The characteristic dimension
+     *  @param t The starting time
+     * */
+    PenningTrap(double B_0 = T, double V_0 = (25. * V) / 1000., double d = 500.,
+                double t = 0.);
+
+    /** @brief Constructor for the PenningTrap class
+     *
+     *  @param i The number of particles to generate
+     *  @param B_0 The magnetic field strength
+     *  @param V_0 The time dependent applied potential
+     *  @param d The characteristic dimension
+     *  @param t The starting time
+     * */
+    PenningTrap(uint i, double B_0 = T, double V_0 = (25. * V) / 1000.,
+                double d = 500., double t = 0.);
+
+    /** @brief Constructor for the PenningTrap class
+     *
+     *  @param particles The starting particles
+     *  @param B_0 The magnetic field strength
+     *  @param V_0 The time dependent applied potential
+     *  @param d The characteristic dimension
+     *  @param t The starting time
+     * */
+    PenningTrap(std::vector<Particle> particles, double B_0 = T,
+                double V_0 = (25. * V) / 1000., double d = 500., double t = 0.);
+
+    /** @brief Time dependent perturbation to V_0
+     *
+     *  @param f The amplitude of the perturbation
+     *  @parma omega_V the angular frequency of the perturbation
+     * */
+    void set_pertubation(double f, double omega_V);
+
+    /** @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(double f, double omega_V, double t = 0.);
+
+    /** @brief Add a particle to the system
+     *
+     *  @param particle The particle to add to the Penning trap
+     * */
+    void add_particle(Particle particle);
 
     /** @brief Go forward one timestep using the RK4 method
      *
@@ -202,8 +200,7 @@ public:
      *
      *  @return simulation_t
      * */
-    simulation_t simulate(double time, uint steps,
+    simulation_t simulate(double time, uint steps, std::string method = "rk4",
-                          std::string method = "rk4",
                           bool particle_interaction = true);
 
     /** @brief Simulate and write the displacement of all particles to files.
@@ -214,8 +211,7 @@ public:
      *  @param method The method to use when moving forward a timestep
      *  @param particle_interaction Turn particle interactions on/off
      * */
-    void write_simulation_to_dir(std::string path, double time,
+    void write_simulation_to_dir(std::string path, double time, uint steps,
-                                 uint steps,
                                  std::string method = "rk4",
                                  bool particle_interaction = true);
 
@@ -232,6 +228,8 @@ public:
     double fraction_of_particles_left(double time, uint steps,
                                       std::string method = "rk4",
                                       bool particle_interaction = true);
+
+    friend class PenningTrapTest;
 };
 
 #endif

include/constants.hpp

@@ -3,7 +3,7 @@
  *  @author Cory Alexander Balaton (coryab)
  *  @author Janita Ovidie Sandtrøen Willumsen (janitaws)
  *
- *  @version 0.1
+ *  @version 1.0
  *
  *  @brief Library of constants
  *

include/typedefs.hpp

@@ -18,23 +18,23 @@
 #include <armadillo>
 #include <vector>
 
+/** @brief Typedef for a fixed 3d arma vector.
+ * */
+typedef arma::vec::fixed<3> vec3;
+
 /** @brief Typedef for the column of the result vector from simulating
  *  particles.
  * */
-typedef std::vector<arma::vec::fixed<3>> sim_cols;
+typedef std::vector<vec3> sim_cols;
 
 /** @brief Typedef for the row of the result vector from simulating particles.
  * */
-typedef std::vector<arma::vec::fixed<3>> sim_rows;
+typedef std::vector<vec3> sim_rows;
 
 /** @brief Typedef for the result of the simulate method.
  * */
 typedef std::vector<sim_cols> sim_arr;
 
-/** @brief Typedef for a fixed 3d arma vector.
- * */
-typedef arma::vec::fixed<3> vec_3d;
-
 /** @brief Typedef for PenningTrap::simulation return value.
  * */
 typedef struct simulation {

include/utils.hpp

@@ -31,7 +31,7 @@
  *  messages by adding the -DDBG flag when compiling.
  * */
 #ifdef DBG
-#define DEBUG(msg)                                                            \
+#define DEBUG(msg)                                                             \
     std::cout << __FILE__ << " " << __LINE__ << ": " << msg << std::endl
 #else
 #define DEBUG(msg)
@@ -43,7 +43,7 @@
  *  This macro calls the m_assert function which is a more informative
  *  assertion function than the regular assert function from cassert.
  * */
-#define ASSERT(expr, msg)                                                     \
+#define ASSERT(expr, msg)                                                      \
     m_assert(expr, #expr, __METHOD_NAME__, __FILE__, __LINE__, msg)
 
 /** @def __METHOD_NAME__