moved stuff into function to remove a for loop

.clang-format

@@ -4,3 +4,4 @@ TabWidth: 4
 UseTab: Always
 BreakBeforeBraces: Attach
 ColumnLimit: 100
+AlignReturnType: Always

Makefile

@@ -6,7 +6,7 @@ ts := $(shell /usr/bin/date "+%d-%m__%H_%M_%S")
 .DEFAULT_GOAL = MD
 
 MD: $(SRC)/MD.cpp
-	$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -march=native -mavx -O2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
+	$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -march=native -O2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
 
 MDorig: $(SRC)/MD-original.cpp
 	$(CC) $(CFLAGS) $(SRC)MD-original.cpp -lm -O2 -pg -o ./out/MD-original

src/MD.cpp

@@ -25,6 +25,7 @@
 
 */
 
+#include <emmintrin.h>
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
@@ -475,22 +476,26 @@ double Kinetic() { // Write Function here!
   return kin;
 }
 
-// void
-// transposeMatrix (double mat[MAXPART][3], double matT[3][MAXPART]) {
-//	for (int i = 0; i < 3; i++) {
-//		for (int j = 0; j < MAXPART; j++) {
-//			matT[i][j] = mat[j][i];
-//		}
-//	}
-// }
+void transposeMatrix(double mat[MAXPART][3], double matT[3][MAXPART]) {
+  for (int i = 0; i < 3; i++) {
+    for (int j = 0; j < MAXPART; j++) {
+      matT[i][j] = mat[j][i];
+    }
+  }
+}
+void transposeMatrix2(double matT[MAXPART][3], double mat[3][MAXPART]) {
+  for (int i = 0; i < MAXPART; i++) {
+    for (int j = 0; j < 3; j++) {
+      matT[i][j] = mat[j][i];
+    }
+  }
+}
 
-double PotentialAndAcceleration() {
+double PotentialAndAcceleration(double dt) {
   memset(a, 0, sizeof(a));
   double Pot = 0.;
-  // double rT[3][MAXPART];
-  // transposeMatrix (r, rT);
 
-  for (int i = 0; i < N - 1; i++) {
+  for (int i = 0; i < N; i++) {
     for (int j = i + 1; j < N; j++) {
       double quot, rnorm, term1, term2;
       // CALCULATE POTENTIAL ENERGY
@@ -504,23 +509,24 @@ double PotentialAndAcceleration() {
         // ACCEL
         posItoJ[k] = distTmp;
       }
-
-      quot = sigma * sigma / dist;
-      term2 = quot * quot * quot;
-      Pot += epsilon_8 * term2 * (term2 - 1);
-
       //  From derivative of Lennard-Jones with sigma and epsilon
       //  set equal to 1 in natural units!
-      double distSqd = dist * dist;
-      double rSqd_inv4 = 1.0 / (distSqd * distSqd);
-      double rSqd_inv7 = rSqd_inv4 / (distSqd * dist);
-      double f = 48.0 * rSqd_inv7 - 24 * rSqd_inv4;
+      double distSqd = dist * dist * dist;
+      double rSqd_inv7 = distSqd * distSqd * dist;
+      double f = (48. - (24. * distSqd)) / rSqd_inv7;
       //  from F = ma, where m = 1 in natural units!
       for (int k = 0; k < 3; k++) {
         double tmp = posItoJ[k] * f;
         a[i][k] += tmp;
         a[j][k] -= tmp;
       }
+
+      quot = sigma * sigma / dist;
+      term2 = quot * quot * quot;
+      Pot += epsilon_8 * term2 * (term2 - 1.);
+    }
+    for (int j = 0; j < 3; j++) {
+      v[i][j] += 0.5 * a[i][j] * dt;
     }
   }
   return Pot;
@@ -603,21 +609,22 @@ double VelocityVerlet(double dt, int iter, double *PE, FILE *fp) {
   // printf("  Updated Positions!\n");
   for (i = 0; i < N; i++) {
     for (j = 0; j < 3; j++) {
-      r[i][j] += v[i][j] * dt + 0.5 * a[i][j] * dt * dt;
+      double tmp = 0.5 * a[i][j] * dt;
+      r[i][j] += v[i][j] * dt + tmp * dt;
 
-      v[i][j] += 0.5 * a[i][j] * dt;
+      v[i][j] += tmp;
     }
     // printf("  %i  %6.4e   %6.4e %6.4e\n",i,r[i][0],r[i][1],r[i][2]);
   }
   //  Update accellerations from updated positions
   // computeAccelerations ();
-  *PE = PotentialAndAcceleration();
+  *PE = PotentialAndAcceleration(dt);
   //  Update velocity with updated acceleration
-  for (i = 0; i < N; i++) {
-    for (j = 0; j < 3; j++) {
-      v[i][j] += 0.5 * a[i][j] * dt;
-    }
-  }
+  // for (i = 0; i < N; i++) {
+  //  for (j = 0; j < 3; j++) {
+  //    v[i][j] += 0.5 * a[i][j] * dt;
+  //  }
+  //}
 
   // Elastic walls
   for (i = 0; i < N; i++) {