Refactor

- Change PenningTrap so that perturbation is its own field
- Add Calcium mass and charge to constants

include/PenningTrap.hpp

@@ -31,7 +31,8 @@
 class PenningTrap {
 private:
     double B_0;                        ///< Magnetic field strength
-    std::function<double(double)> V_0; ///< Applied potential
+    double V_0; ///< Applied potential
+    std::function<double(double)> perturbation; ///< Time-dependent perturbation
     double d;                          ///< Characteristic dimension
     double t;                          ///< Current time
     std::vector<Particle> particles;   ///< The particles in the Penning trap
@@ -50,7 +51,7 @@ private:
      *
      *  @return vec_3d
      * */
-    vec_3d v_func(unsigned int i, unsigned int j, double dt);
+    vec_3d v_func(uint i, uint j, double dt);
 
     /** @brief Helper for evolve_RK4 when calculating \f$k_{r,i,j}\f$ values
      *
@@ -62,7 +63,7 @@ private:
      *
      *  @return vec_3d
      * */
-    vec_3d r_func(unsigned int i, unsigned int j, double dt);
+    vec_3d r_func(uint i, uint j, double dt);
 
 public:
     /** @brief Constructor for the PenningTrap class
@@ -74,8 +75,7 @@ public:
      * */
     PenningTrap(
         double B_0 = T,
-        std::function<double(double)> V_0
-        = [](double t) { return (25. * V) / 1000.; },
+        double V_0 = (25. * V) / 1000.,
         double d = 500., double t = 0.);
 
     /** @brief Constructor for the PenningTrap class
@@ -87,9 +87,8 @@ public:
      *  @param t The starting time
      * */
     PenningTrap(
-        unsigned int i, double B_0 = T,
-        std::function<double(double)> V_0
-        = [](double t) { return 25. * V / 1000.; },
+        uint i, double B_0 = T,
+        double V_0 = (25. * V) / 1000.,
         double d = 500., double t = 0.);
 
     /** @brief Constructor for the PenningTrap class
@@ -102,10 +101,11 @@ public:
      * */
     PenningTrap(
         std::vector<Particle> particles, double B_0 = T,
-        std::function<double(double)> V_0
-        = [](double t) { return 25. * V / 1000.; },
+        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.
      *
@@ -113,8 +113,7 @@ public:
      *  @param t The starting time
      * */
     void reinitialize(
-        std::function<double(double)> V_0
-        = [](double t) { return 25. * V / 1000.; },
+        double f, double omega_V,
         double t = 0.);
 
     /** @brief Add a particle to the system
@@ -149,7 +148,7 @@ public:
      *
      *  @return vec_3d
      * */
-    vec_3d force_on_particle(unsigned int i, unsigned int j);
+    vec_3d force_on_particle(uint i, uint j);
 
     /** @brief Calculate the total external force on a particle.
      *
@@ -160,7 +159,7 @@ public:
      *
      *  @return vec_3d
      * */
-    vec_3d total_force_external(unsigned int i);
+    vec_3d total_force_external(uint i);
 
     /** @brief Calculate the total force on a particle p_i from other
      * particles.
@@ -169,7 +168,7 @@ public:
      *
      *  @return vec_3d
      * */
-    vec_3d total_force_particles(unsigned int i);
+    vec_3d total_force_particles(uint i);
 
     /** @brief calculate the total force on a particle p_i.
      *
@@ -177,7 +176,7 @@ public:
      *
      *  @return vec_3d
      * */
-    vec_3d total_force(unsigned int i);
+    vec_3d total_force(uint i);
 
     /** @brief Go forward one timestep using the RK4 method
      *
@@ -203,7 +202,7 @@ public:
      *
      *  @return simulation_t
      * */
-    simulation_t simulate(double time, unsigned int steps,
+    simulation_t simulate(double time, uint steps,
                           std::string method = "rk4",
                           bool particle_interaction = true);
 
@@ -216,7 +215,7 @@ public:
      *  @param particle_interaction Turn particle interactions on/off
      * */
     void write_simulation_to_dir(std::string path, double time,
-                                 unsigned int steps,
+                                 uint steps,
                                  std::string method = "rk4",
                                  bool particle_interaction = true);
 
@@ -230,12 +229,9 @@ public:
      *
      *  @return double
      * */
-    double fraction_of_particles_left(double time, unsigned int steps,
+    double fraction_of_particles_left(double time, uint steps,
                                       std::string method = "rk4",
                                       bool particle_interaction = true);
-
-    vec_3d get_r(int i);
-    double get_t();
 };
 
 #endif

include/constants.hpp

@@ -18,4 +18,8 @@
 
 #define V 9.64852558*1e7 ///< 1 Volt. unit: \f$ \frac{u (\mu m)^2}{(\mu s)^2 e} \f$
 
+#define CA_MASS 40.078 ///< Mass of a single calcium ion. unit: amu
+
+#define CA_CHARGE 1. ///< Charge of a singly charged calcium ion. unit: e
+
 #endif