void force_LJ(mdsys_t *sys)
{
double rsq,ffac;
double rx,ry,rz;
double b = 0.5*sys->box;
double s = sys->sigma*sys->sigma;
double p = s*s*s;
double csq = sys->rcut*sys->rcut;
int i,j;
int natoms=sys->natoms;
/* zero energy and forces */
sys->epot=0.0;
azzero(sys->fx,natoms);
azzero(sys->fy,natoms);
azzero(sys->fz,natoms);
for(i=0; i < natoms-1; ++i) {
for(j=i+1; j < natoms; ++j) {
/* particles have no interactions with themselves */
if (i==j) continue;
/* get distance between particle i and j */
rx=pbc(sys->rx[i] - sys->rx[j], b);
ry=pbc(sys->ry[i] - sys->ry[j], b);
rz=pbc(sys->rz[i] - sys->rz[j], b);
rsq = rx*rx + ry*ry + rz*rz;
/* compute force and energy if within cutoff */
if (rsq < csq) {
double rsqinv = 1/rsq;
double r6 = rsqinv*rsqinv*rsqinv;
double pr = p*r6;
double p6 = 4.0*sys->epsilon*pr;
double p12 = p6*pr;
ffac = rsqinv*(12*p12-6*p6);
sys->epot += 0.5*(p12-p6);
sys->fx[i] += rx*ffac;
sys->fy[i] += ry*ffac;
sys->fz[i] += rz*ffac;
sys->fx[j] -= rx*ffac;
sys->fy[j] -= ry*ffac;
sys->fz[j] -= rz*ffac;
}
}
}
}
void force_morse(mdsys_t *sys)
{
double rsq,ffac;
double rx,ry,rz;
double b = 0.5*sys->box;
double s = sys->sigma*sys->sigma;
double p = s*s*s;
double csq = sys->rcut*sys->rcut;
int i,j;
int natoms=sys->natoms;
/* zero energy and forces */
sys->epot=0.0;
azzero(sys->fx,natoms);
azzero(sys->fy,natoms);
azzero(sys->fz,natoms);
for(i=0; i < natoms-1; ++i) {
for(j=i+1; j < natoms; ++j) {
/* particles have no interactions with themselves */
if (i==j) continue;
/* get distance between particle i and j */
rx=pbc(sys->rx[i] - sys->rx[j], b);
ry=pbc(sys->ry[i] - sys->ry[j], b);
rz=pbc(sys->rz[i] - sys->rz[j], b);
rsq = rx*rx + ry*ry + rz*rz;
rs = sqrt(rsqi);
rsq = rx*rx + ry*ry + rz*rz;
/* compute force and energy if within cutoff */
if (rsq < csq) {
esp = exp((-1)*sys->a*(rs-sys->rzero));
espq = exp((-1)*sys->a*(rs-sys->rzero)*(rs-sys->rzero));
ffac = 2*sys->De * (1-esp)*sys->a*esp;
sys->epot += sys->De*(1-espq)
sys->fx[i] += rx*ffac;
sys->fy[i] += ry*ffac;
sys->fz[i] += rz*ffac;
sys->fx[j] -= rx*ffac;
sys->fy[j] -= ry*ffac;
sys->fz[j] -= rz*ffac;
}
}
}
}
void MyMD::readRestart() {
FILE *fp=fopen(restfile,"r");
if(fp) {
int natoms=atoms->GetNAtoms();
double index1, index2, index3;
index1=index2=index3=0;
for(int i=0; i<natoms; ++i) {
fscanf(fp,"%lf%lf%lf", &index1, &index2, &index3);
atoms->SetPosition(i, index1);
atoms->SetPosition(i+natoms, index2);
atoms->SetPosition(i+2*natoms, index3);
}
for(int i=0; i<natoms; ++i) {
fscanf(fp,"%lf%lf%lf", &index1, &index2, &index3);
atoms->SetVelocity(i, index1);
atoms->SetVelocity(i+natoms, index2);
atoms->SetVelocity(i+2*natoms, index3);
}
fclose(fp);
azzero(atoms->GetForce(), 3*nthreads*natoms);
} else {
perror("cannot read restart file");
exit(1);
}
}
/* compute forces */
void force(mdsys_t *sys)
{
double r,ffac;
double rx,ry,rz;
int i,j;
/* zero energy and forces */
sys->epot=0.0;
azzero(sys->fx,sys->natoms);
azzero(sys->fy,sys->natoms);
azzero(sys->fz,sys->natoms);
for(i=0; i < (sys->natoms); ++i) {
for(j=0; j < (sys->natoms); ++j) {
/* particles have no interactions with themselves */
if (i==j) continue;
/* get distance between particle i and j */
rx=pbc(sys->rx[i] - sys->rx[j], 0.5*sys->box);
ry=pbc(sys->ry[i] - sys->ry[j], 0.5*sys->box);
rz=pbc(sys->rz[i] - sys->rz[j], 0.5*sys->box);
r = sqrt(rx*rx + ry*ry + rz*rz);
/* compute force and energy if within cutoff */
if (r < sys->rcut) {
ffac = -4.0*sys->epsilon*(-12.0*pow(sys->sigma/r,12.0)/r
+6*pow(sys->sigma/r,6.0)/r);
sys->epot += 0.5*4.0*sys->epsilon*(pow(sys->sigma/r,12.0)
-pow(sys->sigma/r,6.0));
sys->fx[i] += rx/r*ffac;
sys->fy[i] += ry/r*ffac;
sys->fz[i] += rz/r*ffac;
}
}
}
}
/* compute forces */
void force(mdsys_t *sys)
{
double r_c2 = sys->rcut * sys->rcut;
double c1, c2, c3, c4, sig6;
double epot;
int i;
/* zero energy and forces */
epot=0.0;
azzero(sys->fx,sys->natoms);
azzero(sys->fy,sys->natoms);
azzero(sys->fz,sys->natoms);
/* Precalculate some of the constants used in the potential */
sig6 = (sys->sigma)*(sys->sigma)*(sys->sigma) * (sys->sigma)*(sys->sigma)*(sys->sigma);
c1 = -24.0 * sys->epsilon * sig6;
c2 = 48.0 * sys->epsilon * sig6 * sig6;
c3 = -4.0 * sys->epsilon * sig6; // Leading 4.0 includes factor 2
c4 = 4.0 * sys->epsilon * sig6 * sig6; // for using Newton's 3rd law (Epot)
#ifdef _OPENMP
#pragma omp parallel for private(i) reduction(+:epot)
#endif
for(i=0; i < (sys->natoms); ++i) {
int j;
double r6;
double rxi, ryi, rzi;
double fx, fy, fz;
fx = fy = fz = 0.0;
rxi = sys->rx[i];
ryi = sys->ry[i];
rzi = sys->rz[i];
for(j=i+1; j < (sys->natoms); ++j) {
double rx, ry, rz;
double r2, ffac;
/* get distance between particle i and j */
rx = pbc(rxi - sys->rx[j], 0.5*sys->box);
ry = pbc(ryi - sys->ry[j], 0.5*sys->box);
rz = pbc(rzi - sys->rz[j], 0.5*sys->box);
r2 = rx*rx + ry*ry + rz*rz;
/* compute force and energy if within cutoff */
if (r2 < r_c2) {
r6 = r2*r2*r2;
ffac = (c2 + c1*r6) / (r6*r6*r2);
epot += (c4 + c3*r6) / (r6*r6);
/*
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fx[i] += rx*ffac;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fy[i] += ry*ffac;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fz[i] += rz*ffac;
*/
fx += rx*ffac;
fy += ry*ffac;
fz += rz*ffac;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fx[j] -= rx*ffac;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fy[j] -= ry*ffac;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fz[j] -= rz*ffac;
}
} /* end loop j */
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fx[i] += fx;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fy[i] += fy;
#ifdef _OPENMP
#pragma omp atomic
#endif
sys->fz[i] += fz;
} /* end loop i */
sys->epot = epot;
}
/* main */
int main(int argc, char **argv)
{
omp_set_num_threads(MY_NUM_THREADS);
clock_t start,end; //timing variables
double time_spent;
int nprint, i;
char restfile[BLEN], trajfile[BLEN], ergfile[BLEN], line[BLEN];
FILE *fp,*traj,*erg;
mdsys_t sys;
/* read input file */
if(get_a_line(stdin,line)) return 1;
sys.natoms=atoi(line);
if(get_a_line(stdin,line)) return 1;
sys.mass=atof(line);
if(get_a_line(stdin,line)) return 1;
sys.epsilon=atof(line);
if(get_a_line(stdin,line)) return 1;
sys.sigma=atof(line);
if(get_a_line(stdin,line)) return 1;
sys.rcut=atof(line);
if(get_a_line(stdin,line)) return 1;
sys.box=atof(line);
if(get_a_line(stdin,restfile)) return 1;
if(get_a_line(stdin,trajfile)) return 1;
if(get_a_line(stdin,ergfile)) return 1;
if(get_a_line(stdin,line)) return 1;
sys.nsteps=atoi(line);
if(get_a_line(stdin,line)) return 1;
sys.dt=atof(line);
if(get_a_line(stdin,line)) return 1;
nprint=atoi(line);
/* allocate memory */
sys.rx=(double *)malloc(sys.natoms*sizeof(double));
sys.ry=(double *)malloc(sys.natoms*sizeof(double));
sys.rz=(double *)malloc(sys.natoms*sizeof(double));
sys.vx=(double *)malloc(sys.natoms*sizeof(double));
sys.vy=(double *)malloc(sys.natoms*sizeof(double));
sys.vz=(double *)malloc(sys.natoms*sizeof(double));
sys.fx=(double *)malloc(sys.natoms*sizeof(double));
sys.fy=(double *)malloc(sys.natoms*sizeof(double));
sys.fz=(double *)malloc(sys.natoms*sizeof(double));
/* read restart */
fp=fopen(restfile,"r");
if(fp) {
for (i=0; i<sys.natoms; ++i) {
fscanf(fp,"%lf%lf%lf",sys.rx+i, sys.ry+i, sys.rz+i);
}
for (i=0; i<sys.natoms; ++i) {
fscanf(fp,"%lf%lf%lf",sys.vx+i, sys.vy+i, sys.vz+i);
}
fclose(fp);
azzero(sys.fx, sys.natoms);
azzero(sys.fy, sys.natoms);
azzero(sys.fz, sys.natoms);
} else {
perror("cannot read restart file");
return 3;
}
/* initialize forces and energies.*/
sys.nfi=0;
force(&sys);
ekin(&sys);
erg=fopen(ergfile,"w");
traj=fopen(trajfile,"w");
printf("Starting simulation with %d atoms for %d steps.\n",sys.natoms, sys.nsteps);
printf(" NFI TEMP EKIN EPOT ETOT\n");
output(&sys, erg, traj);
//Start timing
start = clock();
/**************************************************/
/* main MD loop */
for(sys.nfi=1; sys.nfi <= sys.nsteps; ++sys.nfi) {
/* write output, if requested */
if ((sys.nfi % nprint) == 0)
output(&sys, erg, traj);
/* propagate system and recompute energies */
velverlet1(&sys); //Velocity verlet Part 1
/* compute forces and potential energy */
force(&sys);
velverlet2(&sys); //Velocity verlet Part 2
ekin(&sys);
}
/**************************************************/
end = clock();
//end timing
time_spent = (double) (end - start) / CLOCKS_PER_SEC;
/* clean up: close files, free memory */
printf("Simulation Done.\n");
printf("Timing: %f Seconds.\n", time_spent);
fclose(erg);
fclose(traj);
free(sys.rx);
free(sys.ry);
free(sys.rz);
free(sys.vx);
free(sys.vy);
free(sys.vz);
free(sys.fx);
free(sys.fy);
free(sys.fz);
return 0;
}
/* compute LJ forces */
void force_LJ(mdsys_t *sys)
{
double pot;
double b = 0.5*sys->box;
double s = sys->sigma*sys->sigma;
double p = s*s*s;
double csq = sys->rcut*sys->rcut;
int i;
int natoms=sys->natoms;
/* zero energy and forces */
pot=0.0;
azzero(sys->fx,natoms);
azzero(sys->fy,natoms);
azzero(sys->fz,natoms);
#pragma omp parallel for default(shared) private(i) reduction(+:pot)
for(i = 0; i < (natoms - 1); ++i) {
/* private versions of sys->rx[i] */
int j;
double rxi,ryi,rzi;
rxi = sys->rx[i];
ryi = sys->ry[i];
rzi = sys->rz[i];
for(j = (1 + i); j < natoms; ++j) {
double rx,ry,rz,rsq;
/* particles have no interactions with themselves */
if (i==j) continue;
/* get distance between particle i and j */
rx=pbc(rxi - sys->rx[j], b);
ry=pbc(ryi - sys->ry[j], b);
rz=pbc(rzi - sys->rz[j], b);
rsq = rx*rx + ry*ry + rz*rz;
/* compute force and energy if within cutoff */
if (rsq < csq) {
double rsqinv = 1/rsq;
double r6 = rsqinv*rsqinv*rsqinv;
double pr = p*r6;
double p6 = 4.0*sys->epsilon*pr;
double p12 = p6*pr;
double ffac;
ffac = rsqinv*(12*p12-6*p6);
pot += 0.5*(p12-p6);
#pragma omp atomic
sys->fx[i] += rx*ffac;
#pragma omp atomic
sys->fy[i] += ry*ffac;
#pragma omp atomic
sys->fz[i] += rz*ffac;
#pragma omp atomic
sys->fx[j] -= rx*ffac;
#pragma omp atomic
sys->fy[j] -= ry*ffac;
#pragma omp atomic
sys->fz[j] -= rz*ffac;
}
}
}
sys->epot = pot;
}
/* compute MORSE forces */
void force_morse(mdsys_t *sys)
{
double pot;
double b = 0.5*sys->box;
double s = sys->sigma*sys->sigma;
double p = s*s*s;
double csq = sys->rcut*sys->rcut;
int i;
int natoms=sys->natoms;
/* zero energy and forces */
pot=0.0;
azzero(sys->fx,natoms);
azzero(sys->fy,natoms);
azzero(sys->fz,natoms);
#pragma omp parallel for default(shared) private(i) reduction(+:pot)
for(i = 0; i < (natoms - 1); ++i) {
/* private versions of sys->rx[i] */
int j;
double rxi,ryi,rzi;
rxi = sys->rx[i];
ryi = sys->ry[i];
rzi = sys->rz[i];
for(j = (1 + i); j < natoms; ++j) {
double rx,ry,rz,rsq;
/* particles have no interactions with themselves */
if (i==j) continue;
/* get distance between particle i and j */
rx=pbc(rxi - sys->rx[j], b);
ry=pbc(ryi - sys->ry[j], b);
rz=pbc(rzi - sys->rz[j], b);
rs = sqrt(rsqi);
rsq = rx*rx + ry*ry + rz*rz;
/* compute force and energy if within cutoff */
if (rsq < csq) {
esp = exp((-1)*sys->a*(rs-sys->rzero));
espq = exp((-1)*sys->a*(rs-sys->rzero)*(rs-sys->rzero));
ffac = 2*sys->De * (1-esp)*sys->a*esp;
pot += sys->De*(1-espq)
sys->fx[i] += rx*ffac;
#pragma omp atomic
sys->fy[i] += ry*ffac;
#pragma omp atomic
sys->fz[i] += rz*ffac;
#pragma omp atomic
sys->fx[j] -= rx*ffac;
#pragma omp atomic
sys->fy[j] -= ry*ffac;
#pragma omp atomic
sys->fz[j] -= rz*ffac;
}
}
}
sys->epot = pot;
}
/* main */
int main(int argc, char **argv)
{
int nprint, i;
char restfile[BLEN], trajfile[BLEN], ergfile[BLEN], line[BLEN];
FILE *fp,*traj,*erg;
mdsys_t sys;
/* read input file */
if(get_me_a_line(stdin,line)) return 1;
sys.natoms=atoi(line);
if(get_me_a_line(stdin,line)) return 1;
sys.mass=atof(line);
if(get_me_a_line(stdin,line)) return 1;
sys.epsilon=atof(line);
if(get_me_a_line(stdin,line)) return 1;
sys.sigma=atof(line);
if(get_me_a_line(stdin,line)) return 1;
sys.rcut=atof(line);
if(get_me_a_line(stdin,line)) return 1;
sys.box=atof(line);
if(get_me_a_line(stdin,restfile)) return 1;
if(get_me_a_line(stdin,trajfile)) return 1;
if(get_me_a_line(stdin,ergfile)) return 1;
if(get_me_a_line(stdin,line)) return 1;
sys.nsteps=atoi(line);
if(get_me_a_line(stdin,line)) return 1;
sys.dt=atof(line);
if(get_me_a_line(stdin,line)) return 1;
nprint=atoi(line);
/* allocate memory */
sys.rx=(double *)malloc(sys.natoms*sizeof(double));
sys.ry=(double *)malloc(sys.natoms*sizeof(double));
sys.rz=(double *)malloc(sys.natoms*sizeof(double));
sys.vx=(double *)malloc(sys.natoms*sizeof(double));
sys.vy=(double *)malloc(sys.natoms*sizeof(double));
sys.vz=(double *)malloc(sys.natoms*sizeof(double));
sys.fx=(double *)malloc(sys.natoms*sizeof(double));
sys.fy=(double *)malloc(sys.natoms*sizeof(double));
sys.fz=(double *)malloc(sys.natoms*sizeof(double));
/* read restart */
fp=fopen(restfile,"r");
if(fp) {
for (i=0; i<sys.natoms; ++i) {
fscanf(fp,"%lf%lf%lf",sys.rx+i, sys.ry+i, sys.rz+i);
}
for (i=0; i<sys.natoms; ++i) {
fscanf(fp,"%lf%lf%lf",sys.vx+i, sys.vy+i, sys.vz+i);
}
fclose(fp);
azzero(sys.fx, sys.natoms);
azzero(sys.fy, sys.natoms);
azzero(sys.fz, sys.natoms);
} else {
perror("cannot read restart file");
return 3;
}
/* initialize forces and energies.*/
sys.nfi=0;
force(&sys);
ekin(&sys);
erg=fopen(ergfile,"w");
traj=fopen(trajfile,"w");
printf("Starting simulation with %d atoms for %d steps.\n",sys.natoms, sys.nsteps);
printf(" NFI TEMP EKIN EPOT ETOT\n");
output(&sys, erg, traj);
/**************************************************/
/* main MD loop */
for(sys.nfi=1; sys.nfi <= sys.nsteps; ++sys.nfi) {
/* write output, if requested */
if ((sys.nfi % nprint) == 0)
output(&sys, erg, traj);
/* propagate system and recompute energies */
velverlet(&sys);
ekin(&sys);
}
/**************************************************/
/* clean up: close files, free memory */
printf("Simulation Done.\n");
fclose(erg);
fclose(traj);
free(sys.rx);
free(sys.ry);
free(sys.rz);
free(sys.vx);
free(sys.vy);
free(sys.vz);
free(sys.fx);
free(sys.fy);
free(sys.fz);
return 0;
}
/* main */
int main(int argc, char **argv)
{
int nprint, i;
char restfile[BLEN], trajfile[BLEN], ergfile[BLEN], line[BLEN];
FILE *fp,*traj,*erg;
mdsys_t sys;
#if defined(_OPENMP)
#pragma omp parallel
{
if(0 == omp_get_thread_num()) {
sys.nthreads=omp_get_num_threads();
printf("Running OpenMP version using %d threads\n", sys.nthreads);
}
}
#else
sys.nthreads=1;
#endif
/* read input file */
if(get_a_line(stdin,line)) return 1;
sys.natoms=atoi(line);
if(get_a_line(stdin,line)) return 1;
sys.mass=atof(line);
if(get_a_line(stdin,line)) return 1;
sys.epsilon=atof(line);
if(get_a_line(stdin,line)) return 1;
sys.sigma=atof(line);
if(get_a_line(stdin,line)) return 1;
sys.rcut=atof(line);
if(get_a_line(stdin,line)) return 1;
sys.box=atof(line);
if(get_a_line(stdin,restfile)) return 1;
if(get_a_line(stdin,trajfile)) return 1;
if(get_a_line(stdin,ergfile)) return 1;
if(get_a_line(stdin,line)) return 1;
sys.nsteps=atoi(line);
if(get_a_line(stdin,line)) return 1;
sys.dt=atof(line);
if(get_a_line(stdin,line)) return 1;
nprint=atoi(line);
/* allocate memory */
sys.pos=(double *)malloc(3*sys.natoms*sizeof(double));
sys.vel=(double *)malloc(3*sys.natoms*sizeof(double));
sys.frc=(double *)malloc(sys.nthreads*3*sys.natoms*sizeof(double));
/* read restart */
fp=fopen(restfile,"r");
if(fp) {
int natoms;
natoms=sys.natoms;
for (i=0; i<natoms; ++i) {
fscanf(fp,"%lf%lf%lf",sys.pos+i, sys.pos+natoms+i, sys.pos+2*natoms+i);
}
for (i=0; i<natoms; ++i) {
fscanf(fp,"%lf%lf%lf",sys.vel+i, sys.vel+natoms+i, sys.vel+2*natoms+i);
}
fclose(fp);
azzero(sys.frc, 3*sys.nthreads*sys.natoms);
} else {
perror("cannot read restart file");
return 3;
}
/* initialize forces and energies.*/
sys.nfi=0;
sys.clist=NULL;
sys.plist=NULL;
updcells(&sys);
force(&sys);
ekin(&sys);
erg=fopen(ergfile,"w");
traj=fopen(trajfile,"w");
printf("Starting simulation with %d atoms for %d steps.\n",sys.natoms, sys.nsteps);
printf(" NFI TEMP EKIN EPOT ETOT\n");
output(&sys, erg, traj);
/**************************************************/
/* main MD loop */
for(sys.nfi=1; sys.nfi <= sys.nsteps; ++sys.nfi) {
/* write output, if requested */
if ((sys.nfi % nprint) == 0)
output(&sys, erg, traj);
/* propagate system and recompute energies */
velverlet(&sys);
ekin(&sys);
/* update cell list */
if ((sys.nfi % cellfreq) == 0)
updcells(&sys);
}
/**************************************************/
/* clean up: close files, free memory */
printf("Simulation Done.\n");
fclose(erg);
fclose(traj);
free(sys.pos);
free(sys.vel);
free(sys.frc);
free_cell_list(&sys);
return 0;
}
/* compute forces */
static void force(mdsys_t *sys)
{
double epot;
epot = 0.0;
#if defined(_OPENMP)
#pragma omp parallel reduction(+:epot)
#endif
{
double c12,c6,boxby2,rcsq;
double *fx, *fy, *fz;
const double *rx, *ry, *rz;
int i, tid, fromidx, toidx, natoms;
/* precompute some constants */
c12 = 4.0*sys->epsilon*pow(sys->sigma,12.0);
c6 = 4.0*sys->epsilon*pow(sys->sigma, 6.0);
rcsq= sys->rcut * sys->rcut;
boxby2 = 0.5*sys->box;
natoms = sys->natoms;
epot = 0.0;
/* let each thread operate on a different
part of the enlarged force array */
#if defined(_OPENMP)
tid=omp_get_thread_num();
#else
tid=0;
#endif
fx=sys->frc + (3*tid*natoms);
azzero(fx,3*natoms);
fy=sys->frc + ((3*tid+1)*natoms);
fz=sys->frc + ((3*tid+2)*natoms);
rx=sys->pos;
ry=sys->pos + natoms;
rz=sys->pos + 2*natoms;
/* self interaction of atoms in cell */
for(i=0; i < sys->ncell; i += sys->nthreads) {
int j;
const cell_t *c1;
j = i + tid;
if (j >= (sys->ncell)) break;
c1=sys->clist + j;
for (j=0; j < c1->natoms-1; ++j) {
int ii,k;
double rx1, ry1, rz1;
ii=c1->idxlist[j];
rx1=rx[ii];
ry1=ry[ii];
rz1=rz[ii];
for(k=j+1; k < c1->natoms; ++k) {
int jj;
double rx2,ry2,rz2,rsq;
jj=c1->idxlist[k];
/* get distance between particle i and j */
rx2=pbc(rx1 - rx[jj], boxby2, sys->box);
ry2=pbc(ry1 - ry[jj], boxby2, sys->box);
rz2=pbc(rz1 - rz[jj], boxby2, sys->box);
rsq = rx2*rx2 + ry2*ry2 + rz2*rz2;
/* compute force and energy if within cutoff */
if (rsq < rcsq) {
double r6,rinv,ffac;
rinv=1.0/rsq;
r6=rinv*rinv*rinv;
ffac = (12.0*c12*r6 - 6.0*c6)*r6*rinv;
epot += r6*(c12*r6 - c6);
fx[ii] += rx2*ffac;
fy[ii] += ry2*ffac;
fz[ii] += rz2*ffac;
fx[jj] -= rx2*ffac;
fy[jj] -= ry2*ffac;
fz[jj] -= rz2*ffac;
}
}
}
}
/* interaction of atoms in different cells */
for(i=0; i < sys->npair; i += sys->nthreads) {
int j;
const cell_t *c1, *c2;
j = i + tid;
if (j >= (sys->npair)) break;
c1=sys->clist + sys->plist[2*j];
c2=sys->clist + sys->plist[2*j+1];
for (j=0; j < c1->natoms; ++j) {
int ii, k;
double rx1, ry1, rz1;
ii=c1->idxlist[j];
rx1=rx[ii];
ry1=ry[ii];
rz1=rz[ii];
for(k=0; k < c2->natoms; ++k) {
int jj;
double rx2,ry2,rz2,rsq;
jj=c2->idxlist[k];
/* get distance between particle i and j */
rx2=pbc(rx1 - rx[jj], boxby2, sys->box);
ry2=pbc(ry1 - ry[jj], boxby2, sys->box);
rz2=pbc(rz1 - rz[jj], boxby2, sys->box);
rsq = rx2*rx2 + ry2*ry2 + rz2*rz2;
/* compute force and energy if within cutoff */
if (rsq < rcsq) {
double r6,rinv,ffac;
rinv=1.0/rsq;
r6=rinv*rinv*rinv;
ffac = (12.0*c12*r6 - 6.0*c6)*r6*rinv;
epot += r6*(c12*r6 - c6);
fx[ii] += rx2*ffac;
fy[ii] += ry2*ffac;
fz[ii] += rz2*ffac;
fx[jj] -= rx2*ffac;
fy[jj] -= ry2*ffac;
fz[jj] -= rz2*ffac;
}
}
}
}
/* before reducing the forces, we have to make sure
that all threads are done adding to them. */
#if defined (_OPENMP)
#pragma omp barrier
#endif
/* set equal chunks of index ranges */
i = 1 + (3*natoms / sys->nthreads);
fromidx = tid * i;
toidx = fromidx + i;
if (toidx > 3*natoms) toidx = 3*natoms;
/* reduce forces from threads with tid != 0 into
the storage of the first thread. since we have
threads already spawned, we do this in parallel. */
for (i=1; i < sys->nthreads; ++i) {
int offs, j;
offs = 3*i*natoms;
for (j=fromidx; j < toidx; ++j) {
sys->frc[j] += sys->frc[offs+j];
}
}
}
sys->epot = epot;
}
void Pair_LJ::ComputeForce(Atoms *atom)
{
double epot;
#if defined(_OPENMP)
#pragma omp parallel reduction(+:epot)
#endif
{
double c12,c6,boxby2,rcsq;
double *fx, *fy, *fz;
double *rx, *ry, *rz;
int i, tid, fromidx, toidx, natoms, nthreads;
/* precompute some constants */
c12 = 4.0*epsilon*pow(sigma,12.0);
c6 = 4.0*epsilon*pow(sigma, 6.0);
rcsq= atom->GetRadCut() * atom->GetRadCut();
boxby2 = 0.5*atom->GetBoxSize();
natoms = atom->GetNAtoms();
epot = 0.0;
/* let each thread operate on a different
part of the enlarged force array */
#if defined(_OPENMP)
nthreads=omp_get_num_threads();
tid=omp_get_thread_num();
#else
nthreads=1;
tid=0;
#endif
fx=atom->GetForce() + (3*tid*natoms);
azzero(fx,3*natoms);
fy=atom->GetForce() + ((3*tid+1)*natoms);
fz=atom->GetForce() + ((3*tid+2)*natoms);
rx=atom->GetPosition();
ry=atom->GetPosition() + natoms;
rz=atom->GetPosition() + 2*natoms;
int x;
/* self interaction of atoms in cell */
for(i=0; i < atom->GetNCells(); i += nthreads) {
int j;
// cell_t *c1;
j = x = i + tid;
if (j >= (atom->GetNCells())) break;
// c1=atom->clist + j;
// afc=getlist(j)
for (j=0; j < atom->GetCellNAtoms(x)-1; ++j) {
// for (j=0; j < GetCellData()-1; ++j) {
int ii,k;
double rx1, ry1, rz1;
// ii=c1->idxlist[j];
ii=atom->GetCellIndex(x,j);
rx1=rx[ii];
ry1=ry[ii];
rz1=rz[ii];
for(k=j+1; k < atom->GetCellNAtoms(x); ++k) {
int jj;
double rx2,ry2,rz2,rsq;
jj=atom->GetCellIndex(x,k);
/* get distance between particle i and j */
rx2=pbc(rx1 - rx[jj], boxby2, atom->GetBoxSize());
ry2=pbc(ry1 - ry[jj], boxby2, atom->GetBoxSize());
rz2=pbc(rz1 - rz[jj], boxby2, atom->GetBoxSize());
rsq = rx2*rx2 + ry2*ry2 + rz2*rz2;
/* compute force and energy if within cutoff */
if (rsq < rcsq) {
double r6,rinv,ffac;
rinv=1.0/rsq;
r6=rinv*rinv*rinv;
ffac = (12.0*c12*r6 - 6.0*c6)*r6*rinv;
epot += r6*(c12*r6 - c6);
fx[ii] += rx2*ffac;
fy[ii] += ry2*ffac;
fz[ii] += rz2*ffac;
fx[jj] -= rx2*ffac;
fy[jj] -= ry2*ffac;
fz[jj] -= rz2*ffac;
}
}
}
}
/* interaction of atoms in different cells */
for(i=0; i < atom->GetNPairs(); i += nthreads) {
int j;
// const cell_t *c1, *c2;
j = x = i + tid;
if (x >= (atom->GetNPairs())) break;
// c1=atom->clist + atom->plist[2*x];
// c2=atom->clist + atom->plist[2*x+1];
for (j=0; j < atom->GetCellNAtoms(atom->GetPairItem(2*x)); ++j) {
int ii, k;
double rx1, ry1, rz1;
ii=atom->GetCellIndex(atom->GetPairItem(2*x),j);
rx1=rx[ii];
ry1=ry[ii];
rz1=rz[ii];
for(k=0; k < atom->GetCellNAtoms(atom->GetPairItem(2*x+1)); ++k) {
int jj;
double rx2,ry2,rz2,rsq;
// jj=c2->idxlist[k];
jj = atom->GetCellIndex(atom->GetPairItem(2*x+1),k);
/* get distance between particle i and j */
rx2=pbc(rx1 - rx[jj], boxby2, atom->GetBoxSize());
ry2=pbc(ry1 - ry[jj], boxby2, atom->GetBoxSize());
rz2=pbc(rz1 - rz[jj], boxby2, atom->GetBoxSize());
rsq = rx2*rx2 + ry2*ry2 + rz2*rz2;
/* compute force and energy if within cutoff */
if (rsq < rcsq) {
double r6,rinv,ffac;
rinv=1.0/rsq;
r6=rinv*rinv*rinv;
ffac = (12.0*c12*r6 - 6.0*c6)*r6*rinv;
epot += r6*(c12*r6 - c6);
fx[ii] += rx2*ffac;
fy[ii] += ry2*ffac;
fz[ii] += rz2*ffac;
fx[jj] -= rx2*ffac;
fy[jj] -= ry2*ffac;
fz[jj] -= rz2*ffac;
}
}
}
}
/* before reducing the forces, we have to make sure
that all threads are done adding to them. */
#if defined (_OPENMP)
#pragma omp barrier
#endif
/* set equal chunks of index ranges */
i = 1 + (3*natoms / nthreads);
fromidx = tid * i;
toidx = fromidx + i;
if (toidx > 3*natoms) toidx = 3*natoms;
/* reduce forces from threads with tid != 0 into
the storage of the first thread. since we have
threads already spawned, we do this in parallel. */
for (i=1; i < nthreads; ++i) {
int offs, j;
offs = 3*i*natoms;
for (j=fromidx; j < toidx; ++j) {
// atom->frc[j] += atom->frc[offs+j];
atom->SetForce(j,atom->GetForce(j)+atom->GetForce(offs+j));
}
}
}
atom->SetPotEnergy(epot);
}