gcc flags changed

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 -O2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
+	$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -march=native -mavx -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

@@ -85,8 +85,7 @@ double MeanSquaredVelocity ();
 //  Compute total kinetic energy from particle mass and velocities
 double Kinetic();
 
-int
+int main() {
-main () {
 
   //  variable delcarations
   int i;
@@ -246,7 +245,8 @@ main () {
   //  Files that we can write different quantities to
   tfp = fopen(tfn, "w"); //  The MD trajectory, coordinates of every
                          //  particle at each timestep
-	ofp = fopen (ofn,
+  ofp = fopen(
+      ofn,
       "w"); //  Output of other quantities (T, P, gc, etc) at every timestep
   afp = fopen(afn, "w"); //  Average T, P, gc, etc from the simulation
 
@@ -286,7 +286,8 @@ main () {
   Tavg = 0;
 
   int tenp = floor(NumTime / 10);
-	fprintf (ofp, "  time (s)              T(t) (K)              P(t) (Pa)           "
+  fprintf(ofp,
+          "  time (s)              T(t) (K)              P(t) (Pa)           "
           "Kinetic En. (n.u.)     Potential En. (n.u.) Total En. (n.u.)\n");
   printf("  PERCENTAGE OF CALCULATION COMPLETE:\n  [");
   for (i = 0; i < NumTime + 1; i++) {
@@ -344,8 +345,8 @@ main () {
     Tavg += Temp;
     Pavg += Press;
 
-		fprintf (ofp, "  %8.4e  %20.12f  %20.12f %20.12f  %20.12f  %20.12f \n", i * dt * timefac,
+    fprintf(ofp, "  %8.4e  %20.12f  %20.12f %20.12f  %20.12f  %20.12f \n",
-				 Temp, Press, KE, PE, KE + PE);
+            i * dt * timefac, Temp, Press, KE, PE, KE + PE);
   }
 
   // Because we have calculated the instantaneous temperature and pressure,
@@ -356,7 +357,8 @@ main () {
   gc = NA * Pavg * (Vol * VolFac) / (N * Tavg);
   fprintf(afp, "  Total Time (s)      T (K)               P (Pa)      PV/nT "
                "(J/(mol K))         Z           V (m^3)              N\n");
-	fprintf (afp, " --------------   -----------        ---------------   "
+  fprintf(afp,
+          " --------------   -----------        ---------------   "
           "--------------   ---------------   ------------   -----------\n");
   fprintf(afp,
           "  %8.4e  %15.5f       %15.5f     %10.5f       %10.5f        %10.5e  "
@@ -379,7 +381,8 @@ main () {
   printf("\n  PERCENT ERROR of pV/nT AND GAS CONSTANT: %15.5f\n",
          100 * fabs(gc - 8.3144598) / 8.3144598);
   printf("\n  THE COMPRESSIBILITY (unitless):          %15.5f \n", Z);
-	printf ("\n  TOTAL VOLUME (m^3):                      %10.5e \n", Vol * VolFac);
+  printf("\n  TOTAL VOLUME (m^3):                      %10.5e \n",
+         Vol * VolFac);
   printf("\n  NUMBER OF PARTICLES (unitless):          %i \n", N);
 
   fclose(tfp);
@@ -389,8 +392,7 @@ main () {
   return 0;
 }
 
-void
+void initialize() {
-initialize () {
   int n, p, i, j, k;
   double pos;
 
@@ -434,8 +436,7 @@ initialize () {
 }
 
 //  Function to calculate the averaged velocity squared
-double
+double MeanSquaredVelocity() {
-MeanSquaredVelocity () {
 
   double vx2 = 0;
   double vy2 = 0;
@@ -455,8 +456,7 @@ MeanSquaredVelocity () {
 }
 
 //  Function to calculate the kinetic energy of the system
-double
+double Kinetic() { // Write Function here!
-Kinetic () { // Write Function here!
 
   double v2, kin;
 
@@ -475,12 +475,6 @@ Kinetic () { // Write Function here!
   return kin;
 }
 
-double
-getF (double dist) {}
-
-double
-getLocalPot (double dist) {}
-
 // void
 // transposeMatrix (double mat[MAXPART][3], double matT[3][MAXPART]) {
 //	for (int i = 0; i < 3; i++) {
@@ -490,8 +484,7 @@ getLocalPot (double dist) {}
 //	}
 // }
 
-double
+double PotentialAndAcceleration() {
-PotentialAndAcceleration () {
   memset(a, 0, sizeof(a));
   double Pot = 0.;
   // double rT[3][MAXPART];
@@ -521,7 +514,7 @@ PotentialAndAcceleration () {
       double distSqd = dist * dist;
       double rSqd_inv4 = 1.0 / (distSqd * distSqd);
       double rSqd_inv7 = rSqd_inv4 / (distSqd * dist);
-			double f = 24.0 * (2.0 * rSqd_inv7 - rSqd_inv4);
+      double f = 48.0 * rSqd_inv7 - 24 * rSqd_inv4;
       //  from F = ma, where m = 1 in natural units!
       for (int k = 0; k < 3; k++) {
         double tmp = posItoJ[k] * f;
@@ -534,8 +527,7 @@ PotentialAndAcceleration () {
 }
 
 // Function to calculate the potential energy of the system
-double
+double Potential() {
-Potential () {
   double quot, r2, rnorm, term1, term2, Pot;
   int i, j;
 
@@ -564,8 +556,7 @@ Potential () {
 //   Uses the derivative of the Lennard-Jones potential to calculate
 //   the forces on each atom.  Then uses a = F/m to calculate the
 //   accelleration of each atom.
-void
+void computeAccelerations() {
-computeAccelerations () {
   int i, j, k;
   double f, rSqd, tmp = 0.;
   double rij[3]; // position of i relative to j
@@ -600,8 +591,7 @@ computeAccelerations () {
 }
 
 // returns sum of dv/dt*m/A (aka Pressure) from elastic collisions with walls
-double
+double VelocityVerlet(double dt, int iter, double *PE, FILE *fp) {
-VelocityVerlet (double dt, int iter, double *PE, FILE *fp) {
   int i, j, k;
 
   double psum = 0.;
@@ -658,8 +648,7 @@ VelocityVerlet (double dt, int iter, double *PE, FILE *fp) {
   return psum / (6 * L * L);
 }
 
-void
+void initializeVelocities() {
-initializeVelocities () {
 
   int i, j;
 
@@ -718,8 +707,7 @@ initializeVelocities () {
 }
 
 //  Numerical recipes Gaussian distribution number generator
-double
+double gaussdist() {
-gaussdist () {
   static bool available = false;
   static double gset;
   double fac, rsq, v1, v2;