Add documentation

src/main.cpp

@@ -26,9 +26,15 @@
 #define MASS 40.  // unit: amu
 
 // Particles used for testing
-Particle p1(CHARGE, MASS, vec_3d{20., 0., 20.}, vec_3d{0., 25., 0.});
+Particle p1(CHARGE, MASS, vec_3d{20., 0., 20.}, vec_3d{0., 25., 0.}); ///< Particle 1
-Particle p2(CHARGE, MASS, vec_3d{25., 25., 0.}, vec_3d{0., 40., 5.});
+Particle p2(CHARGE, MASS, vec_3d{25., 25., 0.}, vec_3d{0., 40., 5.}); ///< Particle 2
 
+/** @brief The analytical solution for particle p1
+ *
+ *  @param t Time
+ *
+ *  @return vec_3d
+ * */
 vec_3d analytical_solution_particle_1(double t)
 {
     double w_0 = T / MASS;
@@ -44,6 +50,8 @@ vec_3d analytical_solution_particle_1(double t)
     return res;
 }
 
+/** @brief Simulate a single particle over the period of 50 \f$ \mu s \f$.
+ * */
 void simulate_single_particle()
 {
     // Initialize trap with particle 1
@@ -56,6 +64,9 @@ void simulate_single_particle()
                                  "rk4", false);
 }
 
+/** @brief Simulate 2 particles over the period of 50 \f$ \mu s \f$ with and
+ *  without particle interactions.
+ * */
 void simulate_two_particles()
 {
     // Initialize traps with particles
@@ -71,6 +82,9 @@ void simulate_two_particles()
         "output/simulate_2_particles/with_interaction", time, N);
 }
 
+/** @brief Simulate a single particle over 50 \f$ \mu s \f$ using different
+ *  amount of steps and different methods.
+ * */
 void simulate_single_particle_with_different_steps()
 {
     double time = 50.; // microseconds
@@ -112,16 +126,23 @@ void simulate_single_particle_with_different_steps()
     }
 }
 
+/** @brief Simulate 100 particles over 50 \f$ \mu s \f$.
+ * */
 void simulate_100_particles()
 {
     PenningTrap trap((unsigned)100);
 
     double time = 50.; // microseconds
 
-    trap.write_simulation_to_dir("output/simulate_100_particles", time, N, "rk4", false);
+    trap.write_simulation_to_dir("output/simulate_100_particles", time, N);
 }
 
-// Wide sweep
+/** @brief Simulate 100 particles over 500 \f$ \mu s \f$ using a time 
+ *  dependent potential.
+ *
+ *  @details The simulation sweeps over different frequencies in [0.2, 2.5] MHz.
+ *
+ * */
 void simulate_100_particles_with_time_potential()
 {
     double time = 500.;

src/test_suite.cpp

@@ -17,32 +17,36 @@
 #include "PenningTrap.hpp"
 #include "utils.hpp"
 
+/** @brief Test class for the Penning trap.
+ * */
 class PenningTrapTest {
 public:
+    /** @brief Test that the external E field gives correct values.
+     * */
     static void test_external_E_field()
     {
         PenningTrap trap;
 
         // Vector containing inputs and expected results
-        std::vector<std::pair<arma::vec, arma::vec>> tests;
+        std::vector<std::pair<vec_3d, vec_3d>> tests;
 
         tests.push_back(
-            std::make_pair(arma::vec{0., 0., 0.}, arma::vec{0., 0., 0.}));
+            std::make_pair(vec_3d{0., 0., 0.}, vec_3d{0., 0., 0.}));
 
-        tests.push_back(std::make_pair(arma::vec{10., 0., 0.},
+        tests.push_back(std::make_pair(vec_3d{10., 0., 0.},
-                                       arma::vec{96.4852558, 0., 0.}));
+                                       vec_3d{96.4852558, 0., 0.}));
 
-        tests.push_back(std::make_pair(arma::vec{10., 0., 0.},
+        tests.push_back(std::make_pair(vec_3d{10., 0., 0.},
-                                       arma::vec{96.4852558, 0., 0.}));
+                                       vec_3d{96.4852558, 0., 0.}));
 
-        tests.push_back(std::make_pair(arma::vec{0., 10., 0.},
+        tests.push_back(std::make_pair(vec_3d{0., 10., 0.},
-                                       arma::vec{0., 96.4852558, 0.}));
+                                       vec_3d{0., 96.4852558, 0.}));
 
-        tests.push_back(std::make_pair(arma::vec{0., 0., 10.},
+        tests.push_back(std::make_pair(vec_3d{0., 0., 10.},
-                                       arma::vec{0., 0., -192.9705116}));
+                                       vec_3d{0., 0., -192.9705116}));
 
-        arma::vec result;
+        vec_3d result;
-        arma::vec v;
+        vec_3d v;
         std::stringstream msg;
         for (size_t i = 0; i < tests.size(); i++) {
             v = tests.at(i).first;
@@ -56,75 +60,84 @@ public:
         }
     }
 
+    /** @brief Test that the external B field gives correct values.
+     * */
     static void test_external_B_field()
     {
         // No point in testing at different points since it's not dependent
         // on position.
         PenningTrap trap;
-        arma::vec expected{0., 0., T};
+        vec_3d expected{0., 0., T};
-        arma::vec result = trap.external_B_field(arma::vec{0., 0., 0.});
+        vec_3d result = trap.external_B_field(vec_3d{0., 0., 0.});
         ASSERT(close_to(expected, result),
                "Testing the external B field at (0,0,0)");
     }
 
+    /** @brief Test that the force between particles gives expected results.
+     * */
     static void test_force_on_particle()
     {
         PenningTrap trap;
-        arma::vec v{0., 0., 0.};
+        vec_3d v{0., 0., 0.};
 
         // Add particles to test
-        trap.add_particle(Particle(1., 40., arma::vec{0., 0., 0.}, v));
+        trap.add_particle(Particle(1., 40., vec_3d{0., 0., 0.}, v));
-        trap.add_particle(Particle(1., 40., arma::vec{1., 0., 0.}, v));
+        trap.add_particle(Particle(1., 40., vec_3d{1., 0., 0.}, v));
-        trap.add_particle(Particle(1., 40., arma::vec{0., 3., 4.}, v));
+        trap.add_particle(Particle(1., 40., vec_3d{0., 3., 4.}, v));
 
         // Test p0 and p1
-        arma::vec expected{-1., 0., 0.};
+        vec_3d expected{-1., 0., 0.};
-        arma::vec result = trap.force_on_particle(0, 1);
+        vec_3d result = trap.force_on_particle(0, 1);
         ASSERT(close_to(expected, result),
                "Testing the force on a particle at (0,0,0) from a "
                "particle at (1,0,0).");
 
         // Test p0 and p2
-        expected = arma::vec{0, -.024, -.032};
+        expected = vec_3d{0, -.024, -.032};
         result = trap.force_on_particle(0, 2);
         ASSERT(close_to(expected, result),
                "Testing the force on a particle at (0,0,0) from a "
                "particle at (0,3,4).");
     }
 
+    /** @brief Test that the total external force returns expected results
+     * */
     static void test_total_force_external()
     {
         PenningTrap trap;
         trap.add_particle(
-            Particle(1., 40., arma::vec{1., 2., 3.}, arma::vec{3., 4., 5.}));
+            Particle(1., 40., vec_3d{1., 2., 3.}, vec_3d{3., 4., 5.}));
 
-        arma::vec expected{395.58954878, -270.15871624, -57.89115348};
+        vec_3d expected{395.58954878, -270.15871624, -57.89115348};
-        arma::vec result = trap.total_force_external(0);
+        vec_3d result = trap.total_force_external(0);
         ASSERT(close_to(expected, result),
                "Testing the total external force on a particle at "
                "(1,2,3) with velocity (3,4,5)");
     }
 
+    /** @brief Test that the total force of all particles on a single particle
+     *  returns expected results.
+     * */
     static void test_total_force_particles()
     {
         PenningTrap trap;
         trap.add_particle(
-            Particle(1., 40., arma::vec{0., 0., 0.}, arma::vec{0., 0., 0.}));
+            Particle(1., 40., vec_3d{0., 0., 0.}, vec_3d{0., 0., 0.}));
 
-        arma::vec expected{0., 0., 0.};
+        vec_3d expected{0., 0., 0.};
-        arma::vec result = trap.total_force_particles(0);
+        vec_3d result = trap.total_force_particles(0);
         ASSERT(close_to(expected, result),
                "Testing the total force of all particles on particle 0 "
                "with only a single particle");
 
         trap.add_particle(
-            Particle(1., 40., arma::vec{1., 0., 0.}, arma::vec{0., 0., 0.}));
+            Particle(1., 40., vec_3d{1., 0., 0.}, vec_3d{0., 0., 0.}));
         trap.add_particle(
-            Particle(1., 40., arma::vec{0., 1., 0.}, arma::vec{0., 0., 0.}));
+            Particle(1., 40., vec_3d{0., 1., 0.}, vec_3d{0., 0., 0.}));
         trap.add_particle(
-            Particle(1., 40., arma::vec{0., 0., 1.}, arma::vec{0., 0., 0.}));
+            Particle(1., 40., vec_3d{0., 0., 1.}, vec_3d{0., 0., 0.}));
 
-        expected = arma::vec(3, arma::fill::value(-3473.383325));
+        expected = vec_3d().fill(-3473.383325);
         result = trap.total_force_particles(0);
         ASSERT(close_to(expected, result),
                "Testing the total force of all particles on particle 0 "