int count;
t_lj_params lj;
- t_ho_params ho;
char fb[32]="saves/lj_test";
b=LEN_Y;
c=LEN_Z;
- vis.dim.x=a*LC_SI;
- vis.dim.y=b*LC_SI;
- vis.dim.z=c*LC_SI;
+ /* set for 'bounding atoms' */
+ //vis.dim.x=a*LC_SI;
+ //vis.dim.y=b*LC_SI;
+ //vis.dim.z=c*LC_SI;
t=TEMPERATURE;
printf("placing silicon atoms ... ");
- //count=create_lattice(DIAMOND,Si,M_SI,LC_SI,a,b,c,&si);
- //printf("(%d) ok!\n",count);
+ count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&si);
+ printf("(%d) ok!\n",count);
+
+ /* testing purpose
count=2;
si=malloc(2*sizeof(t_atom));
si[0].r.x=0.16e-9;
si[1].r.z=0;
si[1].element=SI;
si[1].mass=M_SI;
+ */
printf("setting thermal fluctuations\n");
- //thermal_init(si,&random,count,t);
- v3_zero(&(si[0].v));
- v3_zero(&(si[1].v));
+ thermal_init(si,&random,count,t);
+ //v3_zero(&(si[0].v));
+ //v3_zero(&(si[1].v));
/* check kinetic energy */
md.count=count;
md.atom=si;
md.potential=potential_lennard_jones;
- //md.potential=potential_harmonic_oscillator;
md.force=force_lennard_jones;
- //md.force=force_harmonic_oscillator;
- //md.cutoff_square=((LC_SI/4.0)*(LC_SI/4.0));
- md.cutoff=(0.4e-9);
- md.cutoff_square=(0.6e-9*0.6e-9);
+ md.cutoff=R_CUTOFF;
+ md.cutoff_square=(R_CUTOFF*R_CUTOFF);
md.pot_params=&lj;
- //md.pot_params=&ho;
md.integrate=velocity_verlet;
md.time_steps=RUNS;
md.tau=TAU;
lj.sigma12=lj.sigma6*lj.sigma6;
lj.epsilon=LJ_EPSILON_SI;
- ho.equilibrium_distance=0.3e-9;
- ho.spring_constant=1.0e-9;
-
u=get_e_pot(&md);
printf("potential energy: %.40f [J]\n",u);
rand_close(&random);
-
- //printf("starting velocity verlet: ");
- //fflush(stdout);
-
- //for(runs=0;runs<RUNS;runs++) {
-
- /*
- * velocity verlet
- *
- * r(t+h) = r(t) + h * dr/dt|t + h^2/2m * F(t)
- * dr/dt|(t+h) = dr/dt|t + h/2m * (F(t) + F(t+h))
- *
- */
- //for(i=0;i<amount_si;i++) {
-// /* calculation of new positions r(t+h) */
-// si[i].x+=si[i].vx*tau;
-// si[i].y+=si[i].vy*tau;
-// si[i].z+=si[i].vz*tau;
-// si[i].x+=(tau2*si[i].fx/m2);
-// if(si[i].x>LX) si[i].x-=LEN_X;
-// else if(si[i].x<-LX) si[i].x+=LEN_X;
-// si[i].y+=(tau2*si[i].fy/m2);
-// if(si[i].y>LY) si[i].y-=LEN_Y;
-// else if(si[i].y<-LY) si[i].y+=LEN_Y;
-// si[i].z+=(tau2*si[i].fz/m2);
-// if(si[i].z>LZ) si[i].z-=LEN_Z;
-// else if(si[i].z<-LZ) si[i].z+=LEN_Z;
-// /* calculation of velocities v(t+h/2) */
-// si[i].vx+=(tau*si[i].fx/m2);
-// si[i].vy+=(tau*si[i].fy/m2);
-// si[i].vz+=(tau*si[i].fz/m2);
-// /* reset of forces */
-// si[i].fx=.0;
-// si[i].fy=.0;
-// si[i].fz=.0;
-// }
-// for(i=0;i<amount_si;i++) {
-// /* calculation of forces at new positions r(t+h) */
-// for(j=0;j<i;j++) {
-// deltax=si[i].x-si[j].x;
-// if(deltax>LX) deltax-=LEN_X;
-// else if(-deltax>LX) deltax+=LEN_X;
-// deltax2=deltax*deltax;
-// deltay=si[i].y-si[j].y;
-// if(deltay>LY) deltay-=LEN_Y;
-// else if(-deltay>LY) deltay+=LEN_Y;
-// deltay2=deltay*deltay;
-// deltaz=si[i].z-si[j].z;
-// if(deltaz>LZ) deltaz-=LEN_Z;
-// else if(-deltaz>LZ) deltaz+=LEN_Z;
-// deltaz2=deltaz*deltaz;
-// distance=deltax2+deltay2+deltaz2;
-// if(distance<=R2_CUTOFF) {
-// tmp=1.0/distance; // 1/r^2
-// lj1=tmp; // 1/r^2
-// tmp*=tmp; // 1/r^4
-// lj1*=tmp; // 1/r^6
-// tmp*=tmp; // 1/r^8
-// lj2=tmp; // 1/r^8
-// lj1*=tmp; // 1/r^14
-// lj1*=LJ_SIGMA_12;
-// lj2*=LJ_SIGMA_06;
-// lj=-2*lj1+lj2;
-// si[i].fx-=lj*deltax;
-// si[i].fy-=lj*deltay;
-// si[i].fz-=lj*deltaz;
-// si[j].fx+=lj*deltax;
-// si[j].fy+=lj*deltay;
-// si[j].fz+=lj*deltaz;
-// }
-// }
-// }
-// for(i=0;i<amount_si;i++) {
-// /* calculation of new velocities v(t+h) */
-// si[i].vx+=(tau*si[i].fx/m2);
-// si[i].vy+=(tau*si[i].fy/m2);
-// si[i].vz+=(tau*si[i].fz/m2);
-// }
-//
-// if(!(runs%150)) {
-//
-// /* rasmol script & xyz file */
-// sprintf(xyz,"./saves/si-%.15f.xyz",time);
-// sprintf(ppm,"./video/si-%.15f.ppm",time);
-// fd1=open(xyz,O_WRONLY|O_CREAT|O_TRUNC);
-// if(fd1<0) {
-// perror("rasmol xyz file open");
-// return -1;
-// }
-// dprintf(fd2,"load xyz %s\n",xyz);
-// dprintf(fd2,"spacefill 200\n");
-// dprintf(fd2,"rotate x 11\n");
-// dprintf(fd2,"rotate y 13\n");
-// dprintf(fd2,"set ambient 20\n");
-// dprintf(fd2,"set specular on\n");
-// dprintf(fd2,"zoom 400\n");
-// dprintf(fd2,"write ppm %s\n",ppm);
-// dprintf(fd2,"zap\n");
-// dprintf(fd1,"%d\nsilicon\n",amount_si+9);
-// for(i=0;i<amount_si;i++)
-// dprintf(fd1,"Si %f %f %f %f\n",
-// si[i].x,si[i].y,si[i].z,time);
-// dprintf(fd1,"H 0.0 0.0 0.0 %f\n",time);
-// dprintf(fd1,"He %f %f %f %f\n",LX,LY,LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",-LX,LY,LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",LX,-LY,LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",LX,LY,-LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",-LX,LY,-LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",LX,-LY,-LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,-LZ,time);
-// close(fd1);
-//
-// }
-//
-// /* increase time */
-// time+=tau;
-// printf(".");
-// fflush(stdout);
-//
-// }
-//
-// printf(" done\n");
-// close(fd2);
-// free(si);
-//
-
return 0;
}
projects / physik / posic.git / blobdiff