moved stuff into function to remove a for loop
This commit is contained in:
parent
763c84739f
commit
1b0a9ab380
SSH key fingerprint:
SHA256:JiuxZNdA5bRWXPMUJChI0AQ75yC+cXY4xM0IaVwEVys
5 changed files with 524 additions and 539 deletions
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@ -4,3 +4,4 @@ TabWidth: 4
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UseTab: Always
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BreakBeforeBraces: Attach
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ColumnLimit: 100
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AlignReturnType: Always
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2
Makefile
2
Makefile
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@ -6,7 +6,7 @@ ts := $(shell /usr/bin/date "+%d-%m__%H_%M_%S")
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.DEFAULT_GOAL = MD
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MD: $(SRC)/MD.cpp
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$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -march=native -mavx -O2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
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$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -march=native -O2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
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MDorig: $(SRC)/MD-original.cpp
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$(CC) $(CFLAGS) $(SRC)MD-original.cpp -lm -O2 -pg -o ./out/MD-original
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BIN
out/MD
BIN
out/MD
Binary file not shown.
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@ -63,28 +63,27 @@ char atype[10];
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// Function prototypes
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// initialize positions on simple cubic lattice, also calls function to
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// initialize velocities
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void initialize ();
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void initialize();
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// update positions and velocities using Velocity Verlet algorithm
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// print particle coordinates to file for rendering via VMD or other animation
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// software return 'instantaneous pressure'
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double VelocityVerlet (double dt, int iter, FILE *fp);
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double VelocityVerlet(double dt, int iter, FILE *fp);
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// Compute Force using F = -dV/dr
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// solve F = ma for use in Velocity Verlet
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void computeAccelerations ();
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void computeAccelerations();
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// Numerical Recipes function for generation gaussian distribution
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double gaussdist ();
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double gaussdist();
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// Initialize velocities according to user-supplied initial Temperature
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// (Tinit)
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void initializeVelocities ();
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void initializeVelocities();
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// Compute total potential energy from particle coordinates
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double Potential ();
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double Potential();
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// Compute mean squared velocity from particle velocities
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double MeanSquaredVelocity ();
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double MeanSquaredVelocity();
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// Compute total kinetic energy from particle mass and velocities
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double Kinetic ();
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double Kinetic();
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int
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main () {
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int main() {
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// variable delcarations
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int i;
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@ -94,25 +93,21 @@ main () {
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char trash[10000], prefix[1000], tfn[1000], ofn[1000], afn[1000];
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FILE *infp, *tfp, *ofp, *afp;
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printf (
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"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf (" WELCOME TO WILLY P CHEM MD!\n");
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printf (
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" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf ("\n ENTER A TITLE FOR YOUR CALCULATION!\n");
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scanf ("%s", prefix);
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strcpy (tfn, prefix);
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strcat (tfn, "_traj.xyz");
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strcpy (ofn, prefix);
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strcat (ofn, "_output.txt");
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strcpy (afn, prefix);
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strcat (afn, "_average.txt");
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printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf(" WELCOME TO WILLY P CHEM MD!\n");
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printf(" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf("\n ENTER A TITLE FOR YOUR CALCULATION!\n");
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scanf("%s", prefix);
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strcpy(tfn, prefix);
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strcat(tfn, "_traj.xyz");
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strcpy(ofn, prefix);
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strcat(ofn, "_output.txt");
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strcpy(afn, prefix);
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strcat(afn, "_average.txt");
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printf (
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"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf (" TITLE ENTERED AS '%s'\n", prefix);
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printf (
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" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf(" TITLE ENTERED AS '%s'\n", prefix);
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printf(" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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/* Table of values for Argon relating natural units to SI units:
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* These are derived from Lennard-Jones parameters from the article
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@ -133,34 +128,31 @@ main () {
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// Edit these factors to be computed in terms of basic properties in
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// natural units of the gas being simulated
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printf (
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"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf (
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" WHICH NOBLE GAS WOULD YOU LIKE TO SIMULATE? (DEFAULT IS ARGON)\n");
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printf ("\n FOR HELIUM, TYPE 'He' THEN PRESS 'return' TO CONTINUE\n");
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printf (" FOR NEON, TYPE 'Ne' THEN PRESS 'return' TO CONTINUE\n");
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printf (" FOR ARGON, TYPE 'Ar' THEN PRESS 'return' TO CONTINUE\n");
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printf (" FOR KRYPTON, TYPE 'Kr' THEN PRESS 'return' TO CONTINUE\n");
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printf (" FOR XENON, TYPE 'Xe' THEN PRESS 'return' TO CONTINUE\n");
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printf (
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" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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scanf ("%s", atype);
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printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf(" WHICH NOBLE GAS WOULD YOU LIKE TO SIMULATE? (DEFAULT IS ARGON)\n");
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printf("\n FOR HELIUM, TYPE 'He' THEN PRESS 'return' TO CONTINUE\n");
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printf(" FOR NEON, TYPE 'Ne' THEN PRESS 'return' TO CONTINUE\n");
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printf(" FOR ARGON, TYPE 'Ar' THEN PRESS 'return' TO CONTINUE\n");
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printf(" FOR KRYPTON, TYPE 'Kr' THEN PRESS 'return' TO CONTINUE\n");
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printf(" FOR XENON, TYPE 'Xe' THEN PRESS 'return' TO CONTINUE\n");
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printf(" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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scanf("%s", atype);
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if (strcmp (atype, "He") == 0) {
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if (strcmp(atype, "He") == 0) {
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VolFac = 1.8399744000000005e-29;
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PressFac = 8152287.336171632;
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TempFac = 10.864459551225972;
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timefac = 1.7572698825166272e-12;
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} else if (strcmp (atype, "Ne") == 0) {
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} else if (strcmp(atype, "Ne") == 0) {
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VolFac = 2.0570823999999997e-29;
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PressFac = 27223022.27659913;
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TempFac = 40.560648991243625;
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timefac = 2.1192341945685407e-12;
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} else if (strcmp (atype, "Ar") == 0) {
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} else if (strcmp(atype, "Ar") == 0) {
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VolFac = 3.7949992920124995e-29;
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PressFac = 51695201.06691862;
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@ -168,14 +160,14 @@ main () {
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timefac = 2.09618e-12;
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// strcpy(atype,"Ar");
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} else if (strcmp (atype, "Kr") == 0) {
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} else if (strcmp(atype, "Kr") == 0) {
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VolFac = 4.5882712000000004e-29;
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PressFac = 59935428.40275003;
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TempFac = 199.1817584391428;
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timefac = 8.051563913585078e-13;
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} else if (strcmp (atype, "Xe") == 0) {
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} else if (strcmp(atype, "Xe") == 0) {
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VolFac = 5.4872e-29;
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PressFac = 70527773.72794868;
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@ -188,37 +180,33 @@ main () {
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PressFac = 51695201.06691862;
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TempFac = 142.0950000000000;
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timefac = 2.09618e-12;
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strcpy (atype, "Ar");
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strcpy(atype, "Ar");
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}
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printf (
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"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf ("\n YOU ARE SIMULATING %s GAS! \n", atype);
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printf (
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"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf("\n YOU ARE SIMULATING %s GAS! \n", atype);
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printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf (
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"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf ("\n YOU WILL NOW ENTER A FEW SIMULATION PARAMETERS\n");
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printf (
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" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf ("\n\n ENTER THE INTIAL TEMPERATURE OF YOUR GAS IN KELVIN\n");
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scanf ("%lf", &Tinit);
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printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf("\n YOU WILL NOW ENTER A FEW SIMULATION PARAMETERS\n");
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printf(" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf("\n\n ENTER THE INTIAL TEMPERATURE OF YOUR GAS IN KELVIN\n");
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scanf("%lf", &Tinit);
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// Make sure temperature is a positive number!
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if (Tinit < 0.) {
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printf ("\n !!!!! ABSOLUTE TEMPERATURE MUST BE A POSITIVE NUMBER! "
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printf("\n !!!!! ABSOLUTE TEMPERATURE MUST BE A POSITIVE NUMBER! "
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"PLEASE TRY AGAIN WITH A POSITIVE TEMPERATURE!!!\n");
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exit (0);
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exit(0);
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}
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// Convert initial temperature from kelvin to natural units
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Tinit /= TempFac;
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printf ("\n\n ENTER THE NUMBER DENSITY IN moles/m^3\n");
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printf (" FOR REFERENCE, NUMBER DENSITY OF AN IDEAL GAS AT STP IS ABOUT "
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printf("\n\n ENTER THE NUMBER DENSITY IN moles/m^3\n");
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printf(" FOR REFERENCE, NUMBER DENSITY OF AN IDEAL GAS AT STP IS ABOUT "
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"40 moles/m^3\n");
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printf (" NUMBER DENSITY OF LIQUID ARGON AT 1 ATM AND 87 K IS ABOUT "
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printf(" NUMBER DENSITY OF LIQUID ARGON AT 1 ATM AND 87 K IS ABOUT "
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"35000 moles/m^3\n");
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scanf ("%lf", &rho);
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scanf("%lf", &rho);
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N = 10 * 216;
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Vol = N / (rho * NA);
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@ -228,10 +216,10 @@ main () {
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// Limiting N to MAXPART for practical reasons
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if (N >= MAXPART) {
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printf ("\n\n\n MAXIMUM NUMBER OF PARTICLES IS %i\n\n PLEASE ADJUST "
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printf("\n\n\n MAXIMUM NUMBER OF PARTICLES IS %i\n\n PLEASE ADJUST "
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"YOUR INPUT FILE ACCORDINGLY \n\n",
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MAXPART);
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exit (0);
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exit(0);
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}
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// Check to see if the volume makes sense - is it too small?
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// Remember VDW radius of the particles is 1 natural unit of length
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@ -240,29 +228,29 @@ main () {
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// radius
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if (Vol < N) {
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printf ("\n\n\n YOUR DENSITY IS VERY HIGH!\n\n");
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printf (" THE NUMBER OF PARTICLES IS %i AND THE AVAILABLE VOLUME IS "
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printf("\n\n\n YOUR DENSITY IS VERY HIGH!\n\n");
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printf(" THE NUMBER OF PARTICLES IS %i AND THE AVAILABLE VOLUME IS "
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"%f NATURAL UNITS\n",
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N, Vol);
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printf (" SIMULATIONS WITH DENSITY GREATER THAN 1 PARTCICLE/(1 "
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printf(" SIMULATIONS WITH DENSITY GREATER THAN 1 PARTCICLE/(1 "
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"Natural Unit of Volume) MAY DIVERGE\n");
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printf (" PLEASE ADJUST YOUR INPUT FILE ACCORDINGLY AND RETRY\n\n");
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exit (0);
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printf(" PLEASE ADJUST YOUR INPUT FILE ACCORDINGLY AND RETRY\n\n");
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exit(0);
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}
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// Vol = L*L*L;
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// Length of the box in natural units:
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L = pow (Vol, (1. / 3));
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L = pow(Vol, (1. / 3));
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// Files that we can write different quantities to
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tfp = fopen (tfn, "w"); // The MD trajectory, coordinates of every
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tfp = fopen(tfn, "w"); // The MD trajectory, coordinates of every
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// particle at each timestep
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ofp = fopen (
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ofp = fopen(
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ofn,
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"w"); // Output of other quantities (T, P, gc, etc) at every timestep
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afp = fopen (afn, "w"); // Average T, P, gc, etc from the simulation
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afp = fopen(afn, "w"); // Average T, P, gc, etc from the simulation
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int NumTime;
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if (strcmp (atype, "He") == 0) {
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if (strcmp(atype, "He") == 0) {
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// dt in natural units of time s.t. in SI it is 5 f.s. for all other
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// gasses
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@ -280,59 +268,58 @@ main () {
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// Put all the atoms in simple crystal lattice and give them random
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// velocities that corresponds to the initial temperature we have
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// specified
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initialize ();
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initialize();
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// Based on their positions, calculate the ininial intermolecular forces
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// The accellerations of each particle will be defined from the forces and
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// their mass, and this will allow us to update their positions via
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// Newton's law
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computeAccelerations ();
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computeAccelerations();
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// Print number of particles to the trajectory file
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fprintf (tfp, "%i\n", N);
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fprintf(tfp, "%i\n", N);
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// We want to calculate the average Temperature and Pressure for the
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// simulation The variables need to be set to zero initially
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Pavg = 0;
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Tavg = 0;
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int tenp = floor (NumTime / 10);
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fprintf (
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ofp,
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int tenp = floor(NumTime / 10);
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fprintf(ofp,
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" time (s) T(t) (K) P(t) (Pa) "
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"Kinetic En. (n.u.) Potential En. (n.u.) Total En. (n.u.)\n");
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printf (" PERCENTAGE OF CALCULATION COMPLETE:\n [");
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printf(" PERCENTAGE OF CALCULATION COMPLETE:\n [");
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for (i = 0; i < NumTime + 1; i++) {
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// This just prints updates on progress of the calculation for the
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// users convenience
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if (i == tenp)
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printf (" 10 |");
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printf(" 10 |");
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else if (i == 2 * tenp)
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printf (" 20 |");
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printf(" 20 |");
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else if (i == 3 * tenp)
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printf (" 30 |");
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printf(" 30 |");
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else if (i == 4 * tenp)
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printf (" 40 |");
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printf(" 40 |");
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else if (i == 5 * tenp)
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printf (" 50 |");
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printf(" 50 |");
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else if (i == 6 * tenp)
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printf (" 60 |");
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printf(" 60 |");
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else if (i == 7 * tenp)
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printf (" 70 |");
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printf(" 70 |");
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else if (i == 8 * tenp)
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printf (" 80 |");
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printf(" 80 |");
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else if (i == 9 * tenp)
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printf (" 90 |");
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printf(" 90 |");
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else if (i == 10 * tenp)
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printf (" 100 ]\n");
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fflush (stdout);
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printf(" 100 ]\n");
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fflush(stdout);
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// This updates the positions and velocities using Newton's Laws
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// Also computes the Pressure as the sum of momentum changes from wall
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// collisions / timestep which is a Kinetic Theory of gasses concept of
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// Pressure
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Press = VelocityVerlet (dt, i + 1, tfp);
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Press = VelocityVerlet(dt, i + 1, tfp);
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Press *= PressFac;
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// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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@ -341,9 +328,9 @@ main () {
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// Potential, and Kinetic Energy
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// We would also like to use the IGL to try to see if we can extract
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// the gas constant
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mvs = MeanSquaredVelocity ();
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KE = Kinetic ();
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PE = Potential ();
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mvs = MeanSquaredVelocity();
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KE = Kinetic();
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PE = Potential();
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// Temperature from Kinetic Theory
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Temp = m * mvs / (3 * kB) * TempFac;
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@ -358,7 +345,7 @@ main () {
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Tavg += Temp;
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Pavg += Press;
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fprintf (ofp, " %8.4e %20.12f %20.12f %20.12f %20.12f %20.12f \n",
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fprintf(ofp, " %8.4e %20.12f %20.12f %20.12f %20.12f %20.12f \n",
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i * dt * timefac, Temp, Press, KE, PE, KE + PE);
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}
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@ -368,52 +355,49 @@ main () {
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Tavg /= NumTime;
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Z = Pavg * (Vol * VolFac) / (N * kBSI * Tavg);
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gc = NA * Pavg * (Vol * VolFac) / (N * Tavg);
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fprintf (afp,
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" Total Time (s) T (K) P (Pa) PV/nT "
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fprintf(afp, " Total Time (s) T (K) P (Pa) PV/nT "
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"(J/(mol K)) Z V (m^3) N\n");
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fprintf (
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afp,
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fprintf(afp,
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" -------------- ----------- --------------- "
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"-------------- --------------- ------------ -----------\n");
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fprintf (afp,
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fprintf(afp,
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" %8.4e %15.5f %15.5f %10.5f %10.5f "
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"%10.5e %i\n",
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i * dt * timefac, Tavg, Pavg, gc, Z, Vol * VolFac, N);
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printf ("\n TO ANIMATE YOUR SIMULATION, OPEN THE FILE \n '%s' WITH VMD "
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printf("\n TO ANIMATE YOUR SIMULATION, OPEN THE FILE \n '%s' WITH VMD "
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"AFTER THE SIMULATION COMPLETES\n",
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tfn);
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printf ("\n TO ANALYZE INSTANTANEOUS DATA ABOUT YOUR MOLECULE, OPEN THE "
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printf("\n TO ANALYZE INSTANTANEOUS DATA ABOUT YOUR MOLECULE, OPEN THE "
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"FILE \n '%s' WITH YOUR FAVORITE TEXT EDITOR OR IMPORT THE DATA "
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"INTO EXCEL\n",
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ofn);
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printf ("\n THE FOLLOWING THERMODYNAMIC AVERAGES WILL BE COMPUTED AND "
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printf("\n THE FOLLOWING THERMODYNAMIC AVERAGES WILL BE COMPUTED AND "
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"WRITTEN TO THE FILE \n '%s':\n",
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afn);
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printf ("\n AVERAGE TEMPERATURE (K): %15.5f\n", Tavg);
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printf ("\n AVERAGE PRESSURE (Pa): %15.5f\n", Pavg);
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printf ("\n PV/nT (J * mol^-1 K^-1): %15.5f\n", gc);
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printf ("\n PERCENT ERROR of pV/nT AND GAS CONSTANT: %15.5f\n",
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100 * fabs (gc - 8.3144598) / 8.3144598);
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printf ("\n THE COMPRESSIBILITY (unitless): %15.5f \n", Z);
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||||
printf ("\n TOTAL VOLUME (m^3): %10.5e \n",
|
||||
printf("\n AVERAGE TEMPERATURE (K): %15.5f\n", Tavg);
|
||||
printf("\n AVERAGE PRESSURE (Pa): %15.5f\n", Pavg);
|
||||
printf("\n PV/nT (J * mol^-1 K^-1): %15.5f\n", gc);
|
||||
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 NUMBER OF PARTICLES (unitless): %i \n", N);
|
||||
printf("\n NUMBER OF PARTICLES (unitless): %i \n", N);
|
||||
|
||||
fclose (tfp);
|
||||
fclose (ofp);
|
||||
fclose (afp);
|
||||
fclose(tfp);
|
||||
fclose(ofp);
|
||||
fclose(afp);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
void
|
||||
initialize () {
|
||||
void initialize() {
|
||||
int n, p, i, j, k;
|
||||
double pos;
|
||||
|
||||
// Number of atoms in each direction
|
||||
n = int (ceil (pow (N, 1.0 / 3)));
|
||||
n = int(ceil(pow(N, 1.0 / 3)));
|
||||
|
||||
// spacing between atoms along a given direction
|
||||
pos = L / n;
|
||||
|
|
@ -436,7 +420,7 @@ initialize () {
|
|||
}
|
||||
|
||||
// Call function to initialize velocities
|
||||
initializeVelocities ();
|
||||
initializeVelocities();
|
||||
|
||||
/***********************************************
|
||||
* Uncomment if you want to see what the initial positions and velocities
|
||||
|
|
@ -452,8 +436,7 @@ initialize () {
|
|||
}
|
||||
|
||||
// Function to calculate the averaged velocity squared
|
||||
double
|
||||
MeanSquaredVelocity () {
|
||||
double MeanSquaredVelocity() {
|
||||
|
||||
double vx2 = 0;
|
||||
double vy2 = 0;
|
||||
|
|
@ -473,8 +456,7 @@ MeanSquaredVelocity () {
|
|||
}
|
||||
|
||||
// Function to calculate the kinetic energy of the system
|
||||
double
|
||||
Kinetic () { // Write Function here!
|
||||
double Kinetic() { // Write Function here!
|
||||
|
||||
double v2, kin;
|
||||
|
||||
|
|
@ -494,8 +476,7 @@ Kinetic () { // Write Function here!
|
|||
}
|
||||
|
||||
// Function to calculate the potential energy of the system
|
||||
double
|
||||
Potential () {
|
||||
double Potential() {
|
||||
double quot, r2, rnorm, term1, term2, Pot;
|
||||
int i, j, k;
|
||||
|
||||
|
|
@ -508,10 +489,10 @@ Potential () {
|
|||
for (k = 0; k < 3; k++) {
|
||||
r2 += (r[i][k] - r[j][k]) * (r[i][k] - r[j][k]);
|
||||
}
|
||||
rnorm = sqrt (r2);
|
||||
rnorm = sqrt(r2);
|
||||
quot = sigma / rnorm;
|
||||
term1 = pow (quot, 12.);
|
||||
term2 = pow (quot, 6.);
|
||||
term1 = pow(quot, 12.);
|
||||
term2 = pow(quot, 6.);
|
||||
|
||||
Pot += 4 * epsilon * (term1 - term2);
|
||||
}
|
||||
|
|
@ -524,8 +505,7 @@ 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
|
||||
computeAccelerations () {
|
||||
void computeAccelerations() {
|
||||
int i, j, k;
|
||||
double f, rSqd;
|
||||
double rij[3]; // position of i relative to j
|
||||
|
|
@ -549,7 +529,7 @@ computeAccelerations () {
|
|||
|
||||
// From derivative of Lennard-Jones with sigma and epsilon set
|
||||
// equal to 1 in natural units!
|
||||
f = 24 * (2 * pow (rSqd, -7) - pow (rSqd, -4));
|
||||
f = 24 * (2 * pow(rSqd, -7) - pow(rSqd, -4));
|
||||
for (k = 0; k < 3; k++) {
|
||||
// from F = ma, where m = 1 in natural units!
|
||||
a[i][k] += rij[k] * f;
|
||||
|
|
@ -560,8 +540,7 @@ computeAccelerations () {
|
|||
}
|
||||
|
||||
// returns sum of dv/dt*m/A (aka Pressure) from elastic collisions with walls
|
||||
double
|
||||
VelocityVerlet (double dt, int iter, double *PE, FILE *fp) {
|
||||
double VelocityVerlet(double dt, int iter, double *PE, FILE *fp) {
|
||||
int i, j, k;
|
||||
|
||||
double psum = 0.;
|
||||
|
|
@ -580,7 +559,7 @@ VelocityVerlet (double dt, int iter, double *PE, FILE *fp) {
|
|||
// 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 ();
|
||||
computeAccelerations();
|
||||
// Update velocity with updated acceleration
|
||||
for (i = 0; i < N; i++) {
|
||||
for (j = 0; j < 3; j++) {
|
||||
|
|
@ -593,13 +572,13 @@ VelocityVerlet (double dt, int iter, double *PE, FILE *fp) {
|
|||
for (j = 0; j < 3; j++) {
|
||||
if (r[i][j] < 0.) {
|
||||
v[i][j] *= -1.; //- elastic walls
|
||||
psum += 2 * m * fabs (v[i][j])
|
||||
/ dt; // contribution to pressure from "left" walls
|
||||
psum += 2 * m * fabs(v[i][j]) /
|
||||
dt; // contribution to pressure from "left" walls
|
||||
}
|
||||
if (r[i][j] >= L) {
|
||||
v[i][j] *= -1.; //- elastic walls
|
||||
psum += 2 * m * fabs (v[i][j])
|
||||
/ dt; // contribution to pressure from "right" walls
|
||||
psum += 2 * m * fabs(v[i][j]) /
|
||||
dt; // contribution to pressure from "right" walls
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -617,8 +596,7 @@ VelocityVerlet (double dt, int iter, double *PE, FILE *fp) {
|
|||
return psum / (6 * L * L);
|
||||
}
|
||||
|
||||
void
|
||||
initializeVelocities () {
|
||||
void initializeVelocities() {
|
||||
|
||||
int i, j;
|
||||
|
||||
|
|
@ -626,13 +604,13 @@ initializeVelocities () {
|
|||
|
||||
for (j = 0; j < 3; j++) {
|
||||
// Pull a number from a Gaussian Distribution
|
||||
v[i][j] = gaussdist ();
|
||||
v[i][j] = gaussdist();
|
||||
}
|
||||
}
|
||||
|
||||
// Vcm = sum_i^N m*v_i/ sum_i^N M
|
||||
// Compute center-of-mas velocity according to the formula above
|
||||
double vCM[3] = { 0, 0, 0 };
|
||||
double vCM[3] = {0, 0, 0};
|
||||
|
||||
for (i = 0; i < N; i++) {
|
||||
for (j = 0; j < 3; j++) {
|
||||
|
|
@ -666,7 +644,7 @@ initializeVelocities () {
|
|||
}
|
||||
}
|
||||
|
||||
lambda = sqrt (3 * (N - 1) * Tinit / vSqdSum);
|
||||
lambda = sqrt(3 * (N - 1) * Tinit / vSqdSum);
|
||||
|
||||
for (i = 0; i < N; i++) {
|
||||
for (j = 0; j < 3; j++) {
|
||||
|
|
@ -677,19 +655,18 @@ initializeVelocities () {
|
|||
}
|
||||
|
||||
// Numerical recipes Gaussian distribution number generator
|
||||
double
|
||||
gaussdist () {
|
||||
double gaussdist() {
|
||||
static bool available = false;
|
||||
static double gset;
|
||||
double fac, rsq, v1, v2;
|
||||
if (!available) {
|
||||
do {
|
||||
v1 = 2.0 * rand () / double (RAND_MAX) - 1.0;
|
||||
v2 = 2.0 * rand () / double (RAND_MAX) - 1.0;
|
||||
v1 = 2.0 * rand() / double(RAND_MAX) - 1.0;
|
||||
v2 = 2.0 * rand() / double(RAND_MAX) - 1.0;
|
||||
rsq = v1 * v1 + v2 * v2;
|
||||
} while (rsq >= 1.0 || rsq == 0.0);
|
||||
|
||||
fac = sqrt (-2.0 * log (rsq) / rsq);
|
||||
fac = sqrt(-2.0 * log(rsq) / rsq);
|
||||
gset = v1 * fac;
|
||||
available = true;
|
||||
|
||||
|
|
|
|||
65
src/MD.cpp
65
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++) {
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue