gcc flags changed
This commit is contained in:
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4c27b3c774
commit
763c84739f
3 changed files with 526 additions and 538 deletions
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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.DEFAULT_GOAL = MD
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MD: $(SRC)/MD.cpp
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MD: $(SRC)/MD.cpp
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$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -O2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
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$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -march=native -mavx -O2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
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MDorig: $(SRC)/MD-original.cpp
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MDorig: $(SRC)/MD-original.cpp
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$(CC) $(CFLAGS) $(SRC)MD-original.cpp -lm -O2 -pg -o ./out/MD-original
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$(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.
274
src/MD.cpp
274
src/MD.cpp
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@ -65,28 +65,27 @@ char atype[10];
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// Function prototypes
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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 positions on simple cubic lattice, also calls function to
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// initialize velocities
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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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// 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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// print particle coordinates to file for rendering via VMD or other animation
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// software return 'instantaneous pressure'
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// software return 'instantaneous pressure'
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double VelocityVerlet (double dt, int iter, double *PE, FILE *fp);
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double VelocityVerlet(double dt, int iter, double *PE, FILE *fp);
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// Compute Force using F = -dV/dr
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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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// 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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// 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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// Initialize velocities according to user-supplied initial Temperature
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// (Tinit)
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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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// 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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// 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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// 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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int main() {
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main () {
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// variable delcarations
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// variable delcarations
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int i;
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int i;
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@ -96,21 +95,21 @@ main () {
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char trash[10000], prefix[1000], tfn[1000], ofn[1000], afn[1000];
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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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FILE *infp, *tfp, *ofp, *afp;
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printf ("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf (" WELCOME TO WILLY P CHEM MD!\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");
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printf ("\n ENTER A TITLE FOR YOUR CALCULATION!\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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scanf("%s", prefix);
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strcpy (tfn, prefix);
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strcpy(tfn, prefix);
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strcat (tfn, "_traj.xyz");
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strcat(tfn, "_traj.xyz");
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strcpy (ofn, prefix);
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strcpy(ofn, prefix);
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strcat (ofn, "_output.txt");
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strcat(ofn, "_output.txt");
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strcpy (afn, prefix);
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strcpy(afn, prefix);
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strcat (afn, "_average.txt");
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strcat(afn, "_average.txt");
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printf ("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf (" TITLE ENTERED AS '%s'\n", prefix);
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printf(" TITLE ENTERED AS '%s'\n", prefix);
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printf (" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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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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/* 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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* These are derived from Lennard-Jones parameters from the article
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@ -131,42 +130,42 @@ main () {
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// Edit these factors to be computed in terms of basic properties in
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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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// natural units of the gas being simulated
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printf ("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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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(" 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("\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 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 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 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(" FOR XENON, TYPE 'Xe' THEN PRESS 'return' TO CONTINUE\n");
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printf (" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf(" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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scanf ("%s", atype);
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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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VolFac = 1.8399744000000005e-29;
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PressFac = 8152287.336171632;
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PressFac = 8152287.336171632;
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TempFac = 10.864459551225972;
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TempFac = 10.864459551225972;
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timefac = 1.7572698825166272e-12;
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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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VolFac = 2.0570823999999997e-29;
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PressFac = 27223022.27659913;
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PressFac = 27223022.27659913;
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TempFac = 40.560648991243625;
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TempFac = 40.560648991243625;
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timefac = 2.1192341945685407e-12;
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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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VolFac = 3.7949992920124995e-29;
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PressFac = 51695201.06691862;
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PressFac = 51695201.06691862;
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TempFac = 142.0950000000000;
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TempFac = 142.0950000000000;
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timefac = 2.09618e-12;
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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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} 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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VolFac = 4.5882712000000004e-29;
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PressFac = 59935428.40275003;
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PressFac = 59935428.40275003;
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TempFac = 199.1817584391428;
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TempFac = 199.1817584391428;
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timefac = 8.051563913585078e-13;
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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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VolFac = 5.4872e-29;
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PressFac = 70527773.72794868;
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PressFac = 70527773.72794868;
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@ -178,34 +177,34 @@ main () {
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PressFac = 51695201.06691862;
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PressFac = 51695201.06691862;
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TempFac = 142.0950000000000;
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TempFac = 142.0950000000000;
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timefac = 2.09618e-12;
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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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}
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printf ("\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 YOU ARE SIMULATING %s GAS! \n", atype);
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printf ("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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printf ("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
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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 YOU WILL NOW ENTER A FEW SIMULATION PARAMETERS\n");
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printf (" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\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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printf("\n\n ENTER THE INTIAL TEMPERATURE OF YOUR GAS IN KELVIN\n");
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scanf ("%lf", &Tinit);
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scanf("%lf", &Tinit);
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// Make sure temperature is a positive number!
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// Make sure temperature is a positive number!
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if (Tinit < 0.) {
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if (Tinit < 0.) {
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printf ("\n !!!!! ABSOLUTE TEMPERATURE MUST BE A POSITIVE "
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printf("\n !!!!! ABSOLUTE TEMPERATURE MUST BE A POSITIVE "
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"NUMBER! PLEASE "
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"NUMBER! PLEASE "
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"TRY AGAIN WITH A POSITIVE TEMPERATURE!!!\n");
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"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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}
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// Convert initial temperature from kelvin to natural units
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// Convert initial temperature from kelvin to natural units
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Tinit /= TempFac;
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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("\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 40 "
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printf(" FOR REFERENCE, NUMBER DENSITY OF AN IDEAL GAS AT STP IS ABOUT 40 "
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"moles/m^3\n");
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"moles/m^3\n");
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printf (" NUMBER DENSITY OF LIQUID ARGON AT 1 ATM AND 87 K IS ABOUT 35000 "
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printf(" NUMBER DENSITY OF LIQUID ARGON AT 1 ATM AND 87 K IS ABOUT 35000 "
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"moles/m^3\n");
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"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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N = 10 * 216;
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Vol = N / (rho * NA);
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Vol = N / (rho * NA);
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// Limiting N to MAXPART for practical reasons
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// Limiting N to MAXPART for practical reasons
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if (N >= MAXPART) {
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if (N >= MAXPART) {
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printf ("\n\n\n MAXIMUM NUMBER OF PARTICLES IS %i\n\n PLEASE "
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printf("\n\n\n MAXIMUM NUMBER OF PARTICLES IS %i\n\n PLEASE "
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"ADJUST YOUR "
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"ADJUST YOUR "
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"INPUT FILE ACCORDINGLY \n\n",
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"INPUT FILE ACCORDINGLY \n\n",
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MAXPART);
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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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}
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// Check to see if the volume makes sense - is it too small?
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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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// Remember VDW radius of the particles is 1 natural unit of length
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// radius
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// radius
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if (Vol < N) {
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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("\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 "
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printf(" THE NUMBER OF PARTICLES IS %i AND THE AVAILABLE VOLUME "
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"IS %f "
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"IS %f "
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"NATURAL UNITS\n",
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"NATURAL UNITS\n",
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N, Vol);
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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 "
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"Natural "
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"Unit of Volume) MAY DIVERGE\n");
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"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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printf(" PLEASE ADJUST YOUR INPUT FILE ACCORDINGLY AND RETRY\n\n");
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exit (0);
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exit(0);
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}
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}
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// Vol = L*L*L;
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// Vol = L*L*L;
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// Length of the box in natural units:
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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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// 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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// particle at each timestep
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ofp = fopen (ofn,
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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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"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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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
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// dt in natural units of time s.t. in SI it is 5 f.s. for all
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// other gasses
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// other gasses
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// Put all the atoms in simple crystal lattice and give them random
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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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// velocities that corresponds to the initial temperature we have
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// specified
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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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// 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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// 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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// their mass, and this will allow us to update their positions via
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// Newton's law
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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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// 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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// 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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// simulation The variables need to be set to zero initially
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Pavg = 0;
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Pavg = 0;
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Tavg = 0;
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Tavg = 0;
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int tenp = floor (NumTime / 10);
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int tenp = floor(NumTime / 10);
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fprintf (ofp, " time (s) T(t) (K) P(t) (Pa) "
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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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"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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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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// This just prints updates on progress of the calculation for the
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// users convenience
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// users convenience
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if (i == tenp)
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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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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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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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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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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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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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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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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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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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else if (i == 10 * tenp)
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printf (" 100 ]\n");
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printf(" 100 ]\n");
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fflush (stdout);
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fflush(stdout);
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// This updates the positions and velocities using Newton's Laws
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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
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// Also computes the Pressure as the sum of momentum changes from
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// wall collisions / timestep which is a Kinetic Theory of gasses
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// wall collisions / timestep which is a Kinetic Theory of gasses
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// concept of Pressure
|
// concept of Pressure
|
||||||
Press = VelocityVerlet (dt, i + 1, &PE, tfp);
|
Press = VelocityVerlet(dt, i + 1, &PE, tfp);
|
||||||
Press *= PressFac;
|
Press *= PressFac;
|
||||||
|
|
||||||
// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||||
|
@ -328,8 +329,8 @@ main () {
|
||||||
// Potential, and Kinetic Energy
|
// Potential, and Kinetic Energy
|
||||||
// We would also like to use the IGL to try to see if we can
|
// We would also like to use the IGL to try to see if we can
|
||||||
// extract the gas constant
|
// extract the gas constant
|
||||||
mvs = MeanSquaredVelocity ();
|
mvs = MeanSquaredVelocity();
|
||||||
KE = Kinetic ();
|
KE = Kinetic();
|
||||||
|
|
||||||
// Temperature from Kinetic Theory
|
// Temperature from Kinetic Theory
|
||||||
Temp = m * mvs / (3 * kB) * TempFac;
|
Temp = m * mvs / (3 * kB) * TempFac;
|
||||||
|
@ -344,8 +345,8 @@ main () {
|
||||||
Tavg += Temp;
|
Tavg += Temp;
|
||||||
Pavg += Press;
|
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,
|
// Because we have calculated the instantaneous temperature and pressure,
|
||||||
|
@ -354,48 +355,49 @@ main () {
|
||||||
Tavg /= NumTime;
|
Tavg /= NumTime;
|
||||||
Z = Pavg * (Vol * VolFac) / (N * kBSI * Tavg);
|
Z = Pavg * (Vol * VolFac) / (N * kBSI * Tavg);
|
||||||
gc = NA * Pavg * (Vol * VolFac) / (N * Tavg);
|
gc = NA * Pavg * (Vol * VolFac) / (N * Tavg);
|
||||||
fprintf (afp, " Total Time (s) T (K) P (Pa) PV/nT "
|
fprintf(afp, " Total Time (s) T (K) P (Pa) PV/nT "
|
||||||
"(J/(mol K)) Z V (m^3) N\n");
|
"(J/(mol K)) Z V (m^3) N\n");
|
||||||
fprintf (afp, " -------------- ----------- --------------- "
|
fprintf(afp,
|
||||||
|
" -------------- ----------- --------------- "
|
||||||
"-------------- --------------- ------------ -----------\n");
|
"-------------- --------------- ------------ -----------\n");
|
||||||
fprintf (afp,
|
fprintf(afp,
|
||||||
" %8.4e %15.5f %15.5f %10.5f %10.5f %10.5e "
|
" %8.4e %15.5f %15.5f %10.5f %10.5f %10.5e "
|
||||||
" %i\n",
|
" %i\n",
|
||||||
i * dt * timefac, Tavg, Pavg, gc, Z, Vol * VolFac, N);
|
i * dt * timefac, Tavg, Pavg, gc, Z, Vol * VolFac, N);
|
||||||
|
|
||||||
printf ("\n TO ANIMATE YOUR SIMULATION, OPEN THE FILE \n '%s' WITH VMD "
|
printf("\n TO ANIMATE YOUR SIMULATION, OPEN THE FILE \n '%s' WITH VMD "
|
||||||
"AFTER THE SIMULATION COMPLETES\n",
|
"AFTER THE SIMULATION COMPLETES\n",
|
||||||
tfn);
|
tfn);
|
||||||
printf ("\n TO ANALYZE INSTANTANEOUS DATA ABOUT YOUR MOLECULE, OPEN THE FILE "
|
printf("\n TO ANALYZE INSTANTANEOUS DATA ABOUT YOUR MOLECULE, OPEN THE FILE "
|
||||||
"\n "
|
"\n "
|
||||||
" '%s' WITH YOUR FAVORITE TEXT EDITOR OR IMPORT THE DATA INTO EXCEL\n",
|
" '%s' WITH YOUR FAVORITE TEXT EDITOR OR IMPORT THE DATA INTO EXCEL\n",
|
||||||
ofn);
|
ofn);
|
||||||
printf ("\n THE FOLLOWING THERMODYNAMIC AVERAGES WILL BE COMPUTED AND "
|
printf("\n THE FOLLOWING THERMODYNAMIC AVERAGES WILL BE COMPUTED AND "
|
||||||
"WRITTEN TO THE FILE \n '%s':\n",
|
"WRITTEN TO THE FILE \n '%s':\n",
|
||||||
afn);
|
afn);
|
||||||
printf ("\n AVERAGE TEMPERATURE (K): %15.5f\n", Tavg);
|
printf("\n AVERAGE TEMPERATURE (K): %15.5f\n", Tavg);
|
||||||
printf ("\n AVERAGE PRESSURE (Pa): %15.5f\n", Pavg);
|
printf("\n AVERAGE PRESSURE (Pa): %15.5f\n", Pavg);
|
||||||
printf ("\n PV/nT (J * mol^-1 K^-1): %15.5f\n", gc);
|
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",
|
printf("\n PERCENT ERROR of pV/nT AND GAS CONSTANT: %15.5f\n",
|
||||||
100 * fabs (gc - 8.3144598) / 8.3144598);
|
100 * fabs(gc - 8.3144598) / 8.3144598);
|
||||||
printf ("\n THE COMPRESSIBILITY (unitless): %15.5f \n", Z);
|
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",
|
||||||
printf ("\n NUMBER OF PARTICLES (unitless): %i \n", N);
|
Vol * VolFac);
|
||||||
|
printf("\n NUMBER OF PARTICLES (unitless): %i \n", N);
|
||||||
|
|
||||||
fclose (tfp);
|
fclose(tfp);
|
||||||
fclose (ofp);
|
fclose(ofp);
|
||||||
fclose (afp);
|
fclose(afp);
|
||||||
|
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
void
|
void initialize() {
|
||||||
initialize () {
|
|
||||||
int n, p, i, j, k;
|
int n, p, i, j, k;
|
||||||
double pos;
|
double pos;
|
||||||
|
|
||||||
// Number of atoms in each direction
|
// 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
|
// spacing between atoms along a given direction
|
||||||
pos = L / n;
|
pos = L / n;
|
||||||
|
@ -418,7 +420,7 @@ initialize () {
|
||||||
}
|
}
|
||||||
|
|
||||||
// Call function to initialize velocities
|
// Call function to initialize velocities
|
||||||
initializeVelocities ();
|
initializeVelocities();
|
||||||
|
|
||||||
/***********************************************
|
/***********************************************
|
||||||
* Uncomment if you want to see what the initial positions and velocities
|
* Uncomment if you want to see what the initial positions and velocities
|
||||||
|
@ -434,8 +436,7 @@ initialize () {
|
||||||
}
|
}
|
||||||
|
|
||||||
// Function to calculate the averaged velocity squared
|
// Function to calculate the averaged velocity squared
|
||||||
double
|
double MeanSquaredVelocity() {
|
||||||
MeanSquaredVelocity () {
|
|
||||||
|
|
||||||
double vx2 = 0;
|
double vx2 = 0;
|
||||||
double vy2 = 0;
|
double vy2 = 0;
|
||||||
|
@ -455,8 +456,7 @@ MeanSquaredVelocity () {
|
||||||
}
|
}
|
||||||
|
|
||||||
// Function to calculate the kinetic energy of the system
|
// Function to calculate the kinetic energy of the system
|
||||||
double
|
double Kinetic() { // Write Function here!
|
||||||
Kinetic () { // Write Function here!
|
|
||||||
|
|
||||||
double v2, kin;
|
double v2, kin;
|
||||||
|
|
||||||
|
@ -475,12 +475,6 @@ Kinetic () { // Write Function here!
|
||||||
return kin;
|
return kin;
|
||||||
}
|
}
|
||||||
|
|
||||||
double
|
|
||||||
getF (double dist) {}
|
|
||||||
|
|
||||||
double
|
|
||||||
getLocalPot (double dist) {}
|
|
||||||
|
|
||||||
// void
|
// void
|
||||||
// transposeMatrix (double mat[MAXPART][3], double matT[3][MAXPART]) {
|
// transposeMatrix (double mat[MAXPART][3], double matT[3][MAXPART]) {
|
||||||
// for (int i = 0; i < 3; i++) {
|
// for (int i = 0; i < 3; i++) {
|
||||||
|
@ -490,9 +484,8 @@ getLocalPot (double dist) {}
|
||||||
// }
|
// }
|
||||||
// }
|
// }
|
||||||
|
|
||||||
double
|
double PotentialAndAcceleration() {
|
||||||
PotentialAndAcceleration () {
|
memset(a, 0, sizeof(a));
|
||||||
memset (a, 0, sizeof (a));
|
|
||||||
double Pot = 0.;
|
double Pot = 0.;
|
||||||
// double rT[3][MAXPART];
|
// double rT[3][MAXPART];
|
||||||
// transposeMatrix (r, rT);
|
// transposeMatrix (r, rT);
|
||||||
|
@ -521,7 +514,7 @@ PotentialAndAcceleration () {
|
||||||
double distSqd = dist * dist;
|
double distSqd = dist * dist;
|
||||||
double rSqd_inv4 = 1.0 / (distSqd * distSqd);
|
double rSqd_inv4 = 1.0 / (distSqd * distSqd);
|
||||||
double rSqd_inv7 = rSqd_inv4 / (distSqd * dist);
|
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!
|
// from F = ma, where m = 1 in natural units!
|
||||||
for (int k = 0; k < 3; k++) {
|
for (int k = 0; k < 3; k++) {
|
||||||
double tmp = posItoJ[k] * f;
|
double tmp = posItoJ[k] * f;
|
||||||
|
@ -534,8 +527,7 @@ PotentialAndAcceleration () {
|
||||||
}
|
}
|
||||||
|
|
||||||
// Function to calculate the potential energy of the system
|
// Function to calculate the potential energy of the system
|
||||||
double
|
double Potential() {
|
||||||
Potential () {
|
|
||||||
double quot, r2, rnorm, term1, term2, Pot;
|
double quot, r2, rnorm, term1, term2, Pot;
|
||||||
int i, j;
|
int i, j;
|
||||||
|
|
||||||
|
@ -550,7 +542,7 @@ Potential () {
|
||||||
r2 += tmp * tmp;
|
r2 += tmp * tmp;
|
||||||
}
|
}
|
||||||
|
|
||||||
quot = sigma / sqrt (r2);
|
quot = sigma / sqrt(r2);
|
||||||
term2 = quot * quot;
|
term2 = quot * quot;
|
||||||
term2 = term2 * term2 * term2;
|
term2 = term2 * term2 * term2;
|
||||||
term1 = term2 * term2;
|
term1 = term2 * term2;
|
||||||
|
@ -564,13 +556,12 @@ Potential () {
|
||||||
// Uses the derivative of the Lennard-Jones potential to calculate
|
// Uses the derivative of the Lennard-Jones potential to calculate
|
||||||
// the forces on each atom. Then uses a = F/m to calculate the
|
// the forces on each atom. Then uses a = F/m to calculate the
|
||||||
// accelleration of each atom.
|
// accelleration of each atom.
|
||||||
void
|
void computeAccelerations() {
|
||||||
computeAccelerations () {
|
|
||||||
int i, j, k;
|
int i, j, k;
|
||||||
double f, rSqd, tmp = 0.;
|
double f, rSqd, tmp = 0.;
|
||||||
double rij[3]; // position of i relative to j
|
double rij[3]; // position of i relative to j
|
||||||
|
|
||||||
memset (a, 0, sizeof (a));
|
memset(a, 0, sizeof(a));
|
||||||
for (i = 0; i < N - 1; i++) { // loop over all distinct pairs i,j
|
for (i = 0; i < N - 1; i++) { // loop over all distinct pairs i,j
|
||||||
for (j = i + 1; j < N; j++) {
|
for (j = i + 1; j < N; j++) {
|
||||||
// initialize r^2 to zero
|
// initialize r^2 to zero
|
||||||
|
@ -600,8 +591,7 @@ computeAccelerations () {
|
||||||
}
|
}
|
||||||
|
|
||||||
// returns sum of dv/dt*m/A (aka Pressure) from elastic collisions with walls
|
// 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;
|
int i, j, k;
|
||||||
|
|
||||||
double psum = 0.;
|
double psum = 0.;
|
||||||
|
@ -621,7 +611,7 @@ VelocityVerlet (double dt, int iter, double *PE, FILE *fp) {
|
||||||
}
|
}
|
||||||
// Update accellerations from updated positions
|
// Update accellerations from updated positions
|
||||||
// computeAccelerations ();
|
// computeAccelerations ();
|
||||||
*PE = PotentialAndAcceleration ();
|
*PE = PotentialAndAcceleration();
|
||||||
// Update velocity with updated acceleration
|
// Update velocity with updated acceleration
|
||||||
for (i = 0; i < N; i++) {
|
for (i = 0; i < N; i++) {
|
||||||
for (j = 0; j < 3; j++) {
|
for (j = 0; j < 3; j++) {
|
||||||
|
@ -634,12 +624,12 @@ VelocityVerlet (double dt, int iter, double *PE, FILE *fp) {
|
||||||
for (j = 0; j < 3; j++) {
|
for (j = 0; j < 3; j++) {
|
||||||
if (r[i][j] < 0.) {
|
if (r[i][j] < 0.) {
|
||||||
v[i][j] *= -1.; //- elastic walls
|
v[i][j] *= -1.; //- elastic walls
|
||||||
psum += 2 * m * fabs (v[i][j]) / dt; // contribution to pressure
|
psum += 2 * m * fabs(v[i][j]) / dt; // contribution to pressure
|
||||||
// from "left" walls
|
// from "left" walls
|
||||||
}
|
}
|
||||||
if (r[i][j] >= L) {
|
if (r[i][j] >= L) {
|
||||||
v[i][j] *= -1.; //- elastic walls
|
v[i][j] *= -1.; //- elastic walls
|
||||||
psum += 2 * m * fabs (v[i][j]) / dt; // contribution to pressure
|
psum += 2 * m * fabs(v[i][j]) / dt; // contribution to pressure
|
||||||
// from "right" walls
|
// from "right" walls
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
@ -658,8 +648,7 @@ VelocityVerlet (double dt, int iter, double *PE, FILE *fp) {
|
||||||
return psum / (6 * L * L);
|
return psum / (6 * L * L);
|
||||||
}
|
}
|
||||||
|
|
||||||
void
|
void initializeVelocities() {
|
||||||
initializeVelocities () {
|
|
||||||
|
|
||||||
int i, j;
|
int i, j;
|
||||||
|
|
||||||
|
@ -667,13 +656,13 @@ initializeVelocities () {
|
||||||
|
|
||||||
for (j = 0; j < 3; j++) {
|
for (j = 0; j < 3; j++) {
|
||||||
// Pull a number from a Gaussian Distribution
|
// 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
|
// Vcm = sum_i^N m*v_i/ sum_i^N M
|
||||||
// Compute center-of-mas velocity according to the formula above
|
// 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 (i = 0; i < N; i++) {
|
||||||
for (j = 0; j < 3; j++) {
|
for (j = 0; j < 3; j++) {
|
||||||
|
@ -707,7 +696,7 @@ initializeVelocities () {
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
lambda = sqrt (3 * (N - 1) * Tinit / vSqdSum);
|
lambda = sqrt(3 * (N - 1) * Tinit / vSqdSum);
|
||||||
|
|
||||||
for (i = 0; i < N; i++) {
|
for (i = 0; i < N; i++) {
|
||||||
for (j = 0; j < 3; j++) {
|
for (j = 0; j < 3; j++) {
|
||||||
|
@ -718,19 +707,18 @@ initializeVelocities () {
|
||||||
}
|
}
|
||||||
|
|
||||||
// Numerical recipes Gaussian distribution number generator
|
// Numerical recipes Gaussian distribution number generator
|
||||||
double
|
double gaussdist() {
|
||||||
gaussdist () {
|
|
||||||
static bool available = false;
|
static bool available = false;
|
||||||
static double gset;
|
static double gset;
|
||||||
double fac, rsq, v1, v2;
|
double fac, rsq, v1, v2;
|
||||||
if (!available) {
|
if (!available) {
|
||||||
do {
|
do {
|
||||||
v1 = 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;
|
v2 = 2.0 * rand() / double(RAND_MAX) - 1.0;
|
||||||
rsq = v1 * v1 + v2 * v2;
|
rsq = v1 * v1 + v2 * v2;
|
||||||
} while (rsq >= 1.0 || rsq == 0.0);
|
} while (rsq >= 1.0 || rsq == 0.0);
|
||||||
|
|
||||||
fac = sqrt (-2.0 * log (rsq) / rsq);
|
fac = sqrt(-2.0 * log(rsq) / rsq);
|
||||||
gset = v1 * fac;
|
gset = v1 * fac;
|
||||||
available = true;
|
available = true;
|
||||||
|
|
||||||
|
|
Loading…
Reference in a new issue