posic.c

   1 /*
   2  * posic.c - precipitation process of silicon carbide in silicon
   3  *
   4  * author: Frank Zirkelbach <hackbard@hackdaworld.org>
   5  *
   6  */
   7
   8 #include "posic.h"
   9
  10 #define RAND(max) (max*(0.5-(1.0*rand()/RAND_MAX+1)));
  11
  12 int main(int argc,char **argv) {
  13
  14         t_atom *si;
  15         //t_si *c;
  16         int i,j,runs,amount_si;
  17         double time;
  18         int fd1,fd2;
  19         unsigned char xyz[128];
  20         unsigned char scr[128];
  21         unsigned char ppm[128];
  22
  23         double tau,tau2,m,m2;
  24         double deltax,deltay,deltaz,distance;
  25         double deltax2,deltay2,deltaz2,tmp;
  26         double lj1,lj2,lj;
  27
  28         /* silicon */
  29         //amount_si=AMOUNT_SI;
  30         amount_si=2;
  31         printf("simulating %d silicon atoms\n",amount_si);
  32         si=malloc(amount_si*sizeof(t_atom));
  33         if(!si) {
  34                 perror("silicon malloc");
  35                 return -1;
  36         }
  37         memset(si,0,amount_si*sizeof(t_atom));
  38         m=SI_M; m2=2.0*m;
  39
  40         /* init */
  41         printf("placing silicon atoms\n");
  42         /*
  43         for(i=0;i<amount_si;i++) {
  44                 si[i].x=RAND(LEN_X);
  45                 si[i].y=RAND(LEN_Y);
  46                 si[i].z=RAND(LEN_Z);
  47                 si[i].vx=.0;
  48                 si[i].vy=.0;
  49                 si[i].vz=.0;
  50                 si[i].fx=.0;
  51                 si[i].fy=.0;
  52                 si[i].fz=.0;
  53         }
  54         */
  55         si[0].x=-2.0;
  56         si[1].x=+2.0;
  57         si[0].y=0;
  58         si[0].z=0;
  59         si[1].y=0;
  60         si[1].z=0;
  61
  62         /* time */
  63         time=.0;
  64         tau=TAU;
  65         tau2=tau*tau;
  66
  67         /* rasmol script file */
  68         sprintf(scr,"./saves/si.scr");
  69         fd2=open(scr,O_WRONLY|O_CREAT|O_TRUNC);
  70         if(fd2<0) {
  71                 perror("rasmol script file open");
  72                 return -1;
  73         }
  74
  75         printf("starting velocity verlet: ");
  76         fflush(stdout);
  77
  78         for(runs=0;runs<RUNS;runs++) {
  79
  80         /*
  81          * velocity verlet
  82          *
  83          * r(t+h) = r(t) + h * dr/dt|t + h^2/2m * F(t)
  84          * dr/dt|(t+h) = dr/dt|t + h/2m * (F(t) + F(t+h))
  85          *
  86          */
  87         for(i=0;i<amount_si;i++) {
  88                 /* calculation of new positions r(t+h) */
  89                 si[i].x+=si[i].vx*tau;
  90                 si[i].y+=si[i].vy*tau;
  91                 si[i].z+=si[i].vz*tau;
  92                 si[i].x+=(tau2*si[i].fx/m2);
  93                 if(si[i].x>LX) si[i].x-=LEN_X;
  94                 else if(si[i].x<-LX) si[i].x+=LEN_X;
  95                 si[i].y+=(tau2*si[i].fy/m2);
  96                 if(si[i].y>LY) si[i].y-=LEN_Y;
  97                 else if(si[i].y<-LY) si[i].y+=LEN_Y;
  98                 si[i].z+=(tau2*si[i].fz/m2);
  99                 if(si[i].z>LZ) si[i].z-=LEN_Z;
 100                 else if(si[i].z<-LZ) si[i].z+=LEN_Z;
 101                 /* calculation of velocities v(t+h/2) */
 102                 si[i].vx+=(tau*si[i].fx/m2);
 103                 si[i].vy+=(tau*si[i].fy/m2);
 104                 si[i].vz+=(tau*si[i].fz/m2);
 105                 /* reset of forces */
 106                 si[i].fx=.0;
 107                 si[i].fy=.0;
 108                 si[i].fz=.0;
 109         }
 110         for(i=0;i<amount_si;i++) {
 111                 /* calculation of forces at new positions r(t+h) */
 112                 for(j=0;j<i;j++) {
 113                         deltax=si[i].x-si[j].x;
 114                         if(deltax>LX) deltax-=LEN_X;
 115                         else if(-deltax>LX) deltax+=LEN_X;
 116                         deltax2=deltax*deltax;
 117                         deltay=si[i].y-si[j].y;
 118                         if(deltay>LY) deltay-=LEN_Y;
 119                         else if(-deltay>LY) deltay+=LEN_Y;
 120                         deltay2=deltay*deltay;
 121                         deltaz=si[i].z-si[j].z;
 122                         if(deltaz>LZ) deltaz-=LEN_Z;
 123                         else if(-deltaz>LZ) deltaz+=LEN_Z;
 124                         deltaz2=deltaz*deltaz;
 125                         distance=deltax2+deltay2+deltaz2;
 126                         if(distance<=R2_CUTOFF) {
 127                                 tmp=1.0/distance; // 1/r^2
 128                                 lj1=tmp; // 1/r^2
 129                                 tmp*=tmp; // 1/r^4
 130                                 lj1*=tmp; // 1/r^6
 131                                 tmp*=tmp; // 1/r^8
 132                                 lj2=tmp; // 1/r^8
 133                                 lj1*=tmp; // 1/r^14
 134                                 lj1*=LJ_SIGMA_12;
 135                                 lj2*=LJ_SIGMA_06;
 136                                 lj=-2*lj1+lj2;
 137                                 si[i].fx-=lj*deltax;
 138                                 si[i].fy-=lj*deltay;
 139                                 si[i].fz-=lj*deltaz;
 140                                 si[j].fx+=lj*deltax;
 141                                 si[j].fy+=lj*deltay;
 142                                 si[j].fz+=lj*deltaz;
 143                         }
 144                 }
 145         }
 146         for(i=0;i<amount_si;i++) {
 147                 /* calculation of new velocities v(t+h) */
 148                 si[i].vx+=(tau*si[i].fx/m2);
 149                 si[i].vy+=(tau*si[i].fy/m2);
 150                 si[i].vz+=(tau*si[i].fz/m2);
 151         }
 152
 153         if(!(runs%100)) {
 154
 155         /* rasmol script & xyz file */
 156         sprintf(xyz,"./saves/si-%.15f.xyz",time);
 157         sprintf(ppm,"./video/si-%.15f.ppm",time);
 158         fd1=open(xyz,O_WRONLY|O_CREAT|O_TRUNC);
 159         if(fd1<0) {
 160                 perror("rasmol xyz file open");
 161                 return -1;
 162         }
 163         dprintf(fd2,"load xyz %s\n",xyz);
 164         //dprintf(fd2,"spacefill 200\n");
 165         dprintf(fd2,"spacefill\n");
 166         dprintf(fd2,"rotate x 11\n");
 167         dprintf(fd2,"rotate y 13\n");
 168         dprintf(fd2,"set ambient 20\n");
 169         dprintf(fd2,"set specular on\n");
 170         dprintf(fd2,"write ppm %s\n",ppm);
 171         dprintf(fd2,"zap\n");
 172         dprintf(fd1,"%d\nsilicon\n",amount_si+9);
 173         for(i=0;i<amount_si;i++)
 174                 dprintf(fd1,"Si %f %f %f %f\n",
 175                         si[i].x,si[i].y,si[i].z,time);
 176         dprintf(fd1,"H 0.0 0.0 0.0 %f\n",time);
 177         dprintf(fd1,"He %f %f %f %f\n",LX,LY,LZ,time);
 178         dprintf(fd1,"He %f %f %f %f\n",-LX,LY,LZ,time);
 179         dprintf(fd1,"He %f %f %f %f\n",LX,-LY,LZ,time);
 180         dprintf(fd1,"He %f %f %f %f\n",LX,LY,-LZ,time);
 181         dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,LZ,time);
 182         dprintf(fd1,"He %f %f %f %f\n",-LX,LY,-LZ,time);
 183         dprintf(fd1,"He %f %f %f %f\n",LX,-LY,-LZ,time);
 184         dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,-LZ,time);
 185         close(fd1);
 186
 187         }
 188
 189         /* increase time */
 190         time+=tau;
 191         printf(".");
 192         fflush(stdout);
 193
 194         }
 195
 196         printf(" done\n");
 197         close(fd2);
 198         free(si);
 199
 200         return 0;
 201 }
 202