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moved stuff into function to remove a for loop

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Afonso Franco 2023-10-17 11:49:54 +01:00
parent 763c84739f
commit 1b0a9ab380
Signed by: afonso
SSH key fingerprint: SHA256:JiuxZNdA5bRWXPMUJChI0AQ75yC+cXY4xM0IaVwEVys
5 changed files with 524 additions and 539 deletions
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1
.clang-format
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@ -4,3 +4,4 @@ TabWidth: 4
UseTab: Always
BreakBeforeBraces: Attach
ColumnLimit: 100
AlignReturnType: Always

2
Makefile
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@ -6,7 +6,7 @@ ts := $(shell /usr/bin/date "+%d-%m__%H_%M_%S")
.DEFAULT_GOAL = MD
MD: $(SRC)/MD.cpp
$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -march=native -mavx -O2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
$(CC) $(CFLAGS) $(SRC)MD.cpp -lm -march=native -O2 -ftree-vectorize -funroll-loops -pg -g -o ./out/MD
MDorig: $(SRC)/MD-original.cpp
$(CC) $(CFLAGS) $(SRC)MD-original.cpp -lm -O2 -pg -o ./out/MD-original

BIN
out/MD
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77
src/MD-original.cpp
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@ -83,8 +83,7 @@ double MeanSquaredVelocity ();
// Compute total kinetic energy from particle mass and velocities
double Kinetic();
int
main () {
int main() {
// variable delcarations
int i;
@ -94,11 +93,9 @@ main () {
char trash[10000], prefix[1000], tfn[1000], ofn[1000], afn[1000];
FILE *infp, *tfp, *ofp, *afp;
printf (
"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf(" WELCOME TO WILLY P CHEM MD!\n");
printf (
" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf(" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf("\n ENTER A TITLE FOR YOUR CALCULATION!\n");
scanf("%s", prefix);
strcpy(tfn, prefix);
@ -108,11 +105,9 @@ main () {
strcpy(afn, prefix);
strcat(afn, "_average.txt");
printf (
"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf(" TITLE ENTERED AS '%s'\n", prefix);
printf (
" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf(" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
/* Table of values for Argon relating natural units to SI units:
* These are derived from Lennard-Jones parameters from the article
@ -133,17 +128,14 @@ main () {
// Edit these factors to be computed in terms of basic properties in
// natural units of the gas being simulated
printf (
"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf (
" WHICH NOBLE GAS WOULD YOU LIKE TO SIMULATE? (DEFAULT IS ARGON)\n");
printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf(" WHICH NOBLE GAS WOULD YOU LIKE TO SIMULATE? (DEFAULT IS ARGON)\n");
printf("\n FOR HELIUM, TYPE 'He' THEN PRESS 'return' TO CONTINUE\n");
printf(" FOR NEON, TYPE 'Ne' THEN PRESS 'return' TO CONTINUE\n");
printf(" FOR ARGON, TYPE 'Ar' THEN PRESS 'return' TO CONTINUE\n");
printf(" FOR KRYPTON, TYPE 'Kr' THEN PRESS 'return' TO CONTINUE\n");
printf(" FOR XENON, TYPE 'Xe' THEN PRESS 'return' TO CONTINUE\n");
printf (
" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf(" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
scanf("%s", atype);
if (strcmp(atype, "He") == 0) {
@ -190,17 +182,13 @@ main () {
timefac = 2.09618e-12;
strcpy(atype, "Ar");
}
printf (
"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf("\n YOU ARE SIMULATING %s GAS! \n", atype);
printf (
"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf (
"\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf("\n !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf("\n YOU WILL NOW ENTER A FEW SIMULATION PARAMETERS\n");
printf (
" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf(" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
printf("\n\n ENTER THE INTIAL TEMPERATURE OF YOUR GAS IN KELVIN\n");
scanf("%lf", &Tinit);
// Make sure temperature is a positive number!
@ -297,8 +285,7 @@ main () {
Tavg = 0;
int tenp = floor(NumTime / 10);
fprintf (
ofp,
fprintf(ofp,
" time (s) T(t) (K) P(t) (Pa) "
"Kinetic En. (n.u.) Potential En. (n.u.) Total En. (n.u.)\n");
printf(" PERCENTAGE OF CALCULATION COMPLETE:\n [");
@ -368,11 +355,9 @@ main () {
Tavg /= NumTime;
Z = Pavg * (Vol * VolFac) / (N * kBSI * 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");
fprintf (
afp,
fprintf(afp,
" -------------- ----------- --------------- "
"-------------- --------------- ------------ -----------\n");
fprintf(afp,
@ -407,8 +392,7 @@ main () {
return 0;
}
void
initialize () {
void initialize() {
int n, p, i, j, k;
double pos;
@ -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;
@ -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
@ -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.;
@ -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;
@ -677,8 +655,7 @@ initializeVelocities () {
}
// Numerical recipes Gaussian distribution number generator
double
gaussdist () {
double gaussdist() {
static bool available = false;
static double gset;
double fac, rsq, v1, v2;

65
src/MD.cpp
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@ -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++) {