/* 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;
}
