From 944c52d22fa28b95b02afe6ab61b47913d68f281 Mon Sep 17 00:00:00 2001
From: Cory <cory@balaton.dev>
Date: Sun, 22 Oct 2023 14:11:15 +0200
Subject: [PATCH] Add commments

---
 src/main.cpp | 22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/src/main.cpp b/src/main.cpp
index bdc967f..08fd84e 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -170,16 +170,20 @@ void potential_resonance_wide_sweep()
     std::ofstream ofile;
 
 #pragma omp parallel for
+    // Insert frequencies
     for (size_t i = 0; i < freq_iterations; i++) {
         res[0][i] = freq_start + freq_increment * i;
     }
 
 #pragma omp parallel
     {
+        // Each thread creates a PenningTrap instance and reuses it throughout
+        // the sweep.
         PenningTrap trap((unsigned int)100);
 #pragma omp for collapse(2)
         for (size_t i = 0; i < 3; i++) {
             for (size_t j = 0; j < freq_iterations; j++) {
+                // Reset particles and give new time dependent potential.
                 trap.reinitialize(std::bind(
                     [](double f, double r, double t) {
                         return (25. * V / 1000.) * (1. + f * std::cos(r * t));
@@ -191,6 +195,7 @@ void potential_resonance_wide_sweep()
         }
     }
 
+    // Write results to file
     ofile.open(path + "wide_sweep.txt");
     for (size_t i = 0; i < freq_iterations; i++) {
         ofile << res[0][i] << ',' << res[1][i] << ',' << res[2][i] << ','
@@ -225,17 +230,15 @@ void potential_resonance_no_interaction_narrow_sweep()
 
     std::ofstream ofile;
 
-#pragma omp parallel for
-    for (size_t i = 0; i < freq_iterations; i++) {
-        res[0][i] = freq_start + freq_increment * i;
-    }
-
 #pragma omp parallel
     {
+        // Each thread creates a PenningTrap instance and reuses it throughout
+        // the sweep.
         PenningTrap trap((unsigned int)100);
 #pragma omp for collapse(2)
         for (size_t i = 0; i < 3; i++) {
             for (size_t j = 0; j < freq_iterations; j++) {
+                // Reset particles and give new time dependent potential.
                 trap.reinitialize(std::bind(
                     [](double f, double r, double t) {
                         return (25. * V / 1000.) * (1. + f * std::cos(r * t));
@@ -247,6 +250,7 @@ void potential_resonance_no_interaction_narrow_sweep()
         }
     }
 
+    // Write results to file
     ofile.open(path + "narrow_sweep.txt");
     for (size_t i = 0; i < freq_iterations; i++) {
         ofile << res[0][i] << ',' << res[1][i] << ',' << res[2][i] << ','
@@ -288,10 +292,13 @@ void potential_resonance_with_interaction_narrow_sweep()
 
 #pragma omp parallel
     {
+        // Each thread creates a PenningTrap instance and reuses it throughout
+        // the sweep.
         PenningTrap trap((unsigned int)100);
 #pragma omp for collapse(2)
         for (size_t i = 0; i < 3; i++) {
             for (size_t j = 0; j < freq_iterations; j++) {
+                // Reset particles and give new time dependent potential.
                 trap.reinitialize(std::bind(
                     [](double f, double r, double t) {
                         return (25. * V / 1000.) * (1. + f * std::cos(r * t));
@@ -302,6 +309,7 @@ void potential_resonance_with_interaction_narrow_sweep()
         }
     }
 
+    // Write results to file
     ofile.open(path + "narrow_sweep_interactions.txt");
     for (size_t i = 0; i < freq_iterations; i++) {
         ofile << res[0][i] << ',' << res[1][i] << ',' << res[2][i] << ','
@@ -312,7 +320,7 @@ void potential_resonance_with_interaction_narrow_sweep()
 
 int main()
 {
-    double start,end,t1,t2;
+    double start, end, t1, t2;
     start = omp_get_wtime();
 
     simulate_single_particle();
@@ -361,7 +369,7 @@ int main()
 
     std::cout << "Time narrow sweep with interaction: " << (t2 - t1)
               << " seconds" << std::endl;
-    
+
     end = omp_get_wtime();
 
     std::cout << "Time                              : " << (end - start)