Bunch of stuff

- Add reinitialize to reuse PenningTrap instance and its particles
- Reformatting
- Refactor fraction_of_particles_left to not use simulate

include/PenningTrap.hpp

@@ -20,7 +20,7 @@
 #include "typedefs.hpp"
 #include "utils.hpp"
 
-#pragma omp declare reduction(+ : vec_3d : omp_out += omp_in)                  \
+#pragma omp declare reduction(+ : vec_3d : omp_out += omp_in)                 \
     initializer(omp_priv = omp_orig)
 
 /** @brief A class that simulates a Penning trap.
@@ -74,8 +74,8 @@ public:
      * */
     PenningTrap(
         double B_0 = T,
-        std::function<double(double)> V_0 =
-            [](double t) { return 25. * V / 1000.; },
+        std::function<double(double)> V_0
+        = [](double t) { return 25. * V / 1000.; },
         double d = 500., double t = 0.);
 
     /** @brief Constructor for the PenningTrap class
@@ -88,8 +88,8 @@ public:
      * */
     PenningTrap(
         unsigned int i, double B_0 = T,
-        std::function<double(double)> V_0 =
-            [](double t) { return 25. * V / 1000.; },
+        std::function<double(double)> V_0
+        = [](double t) { return 25. * V / 1000.; },
         double d = 500., double t = 0.);
 
     /** @brief Constructor for the PenningTrap class
@@ -102,10 +102,21 @@ public:
      * */
     PenningTrap(
         std::vector<Particle> particles, double B_0 = T,
-        std::function<double(double)> V_0 =
-            [](double t) { return 25. * V / 1000.; },
+        std::function<double(double)> V_0
+        = [](double t) { return 25. * V / 1000.; },
         double d = 500., double t = 0.);
 
+    /** @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(
+        std::function<double(double)> V_0
+        = [](double t) { return 25. * V / 1000.; },
+        double t = 0.);
+
     /** @brief Add a particle to the system
      *
      *  @param particle The particle to add to the Penning trap
@@ -151,7 +162,8 @@ public:
      * */
     vec_3d total_force_external(unsigned int i);
 
-    /** @brief Calculate the total force on a particle p_i from other particles.
+    /** @brief Calculate the total force on a particle p_i from other
+     * particles.
      *
      *  @param i The index of particle p_i
      *
@@ -204,7 +216,8 @@ public:
      *  @param particle_interaction Turn particle interactions on/off
      * */
     void write_simulation_to_dir(std::string path, double time,
-                                 unsigned int steps, std::string method = "rk4",
+                                 unsigned int steps,
+                                 std::string method = "rk4",
                                  bool particle_interaction = true);
 
     /** @brief Simulate and calculate what fraction of particles are still