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 fd;
  19
  20         double tau,tau2,m,m2;
  21         double deltax,deltay,deltaz,distance;
  22         double deltax2,deltay2,deltaz2,tmp;
  23         double lj1,lj2,lj;
  24
  25         /* silicon */
  26         amount_si=AMOUNT_SI;
  27         printf("simulating %d silicon atoms\n",amount_si);
  28         si=malloc(amount_si*sizeof(t_atom));
  29         if(!si) {
  30                 perror("silicon malloc");
  31                 return -1;
  32         }
  33         memset(si,0,amount_si*sizeof(t_atom));
  34         m=SI_M; m2=2.0*m;
  35
  36         /* init */
  37         printf("placing silicon atoms\n");
  38         for(i=0;i<amount_si;i++) {
  39                 si[i].x=RAND(LEN_X);
  40                 si[i].y=RAND(LEN_Y);
  41                 si[i].z=RAND(LEN_Z);
  42                 si[i].vx=.0;
  43                 si[i].vy=.0;
  44                 si[i].vz=.0;
  45                 si[i].fx=.0;
  46                 si[i].fy=.0;
  47                 si[i].fz=.0;
  48         }
  49
  50         /* time */
  51         time=.0;
  52         tau=TAU;
  53         tau2=tau*tau;
  54
  55         /* rasmol */
  56         printf("opening the rasmol file\n");
  57         fd=open("rasmol.xyz",O_WRONLY);
  58         if(fd<0) {
  59                 perror("rasmol file open");
  60                 return -1;
  61         }
  62
  63         printf("starting velocity verlet: ");
  64         fflush(stdout);
  65
  66         for(runs=0;runs<RUNS;runs++) {
  67
  68         /*
  69          * velocity verlet
  70          *
  71          * r(t+h) = r(t) + h * dr/dt|t + h^2/2m * F(t)
  72          * dr/dt|(t+h) = dr/dt|t + h/2m * (F(t) + F(t+h))
  73          *
  74          */
  75         for(i=0;i<amount_si;i++) {
  76                 /* calculation of new positions r(t+h) */
  77                 si[i].x+=si[i].vx*tau;
  78                 si[i].y+=si[i].vy*tau;
  79                 si[i].z+=si[i].vz*tau;
  80                 si[i].x+=(tau2*si[i].fx/m2);
  81                 if(si[i].x>LX) si[i].x-=LEN_X;
  82                 else if(si[i].x<-LX) si[i].x+=LEN_X;
  83                 si[i].y+=(tau2*si[i].fy/m2);
  84                 if(si[i].y>LY) si[i].y-=LEN_Y;
  85                 else if(si[i].y<-LY) si[i].y+=LEN_Y;
  86                 si[i].z+=(tau2*si[i].fz/m2);
  87                 if(si[i].z>LZ) si[i].z-=LEN_Z;
  88                 else if(si[i].z<-LZ) si[i].z+=LEN_Z;
  89                 /* calculation of velocities v(t+h/2) */
  90                 si[i].vx+=(tau*si[i].fx/m2);
  91                 si[i].vy+=(tau*si[i].fy/m2);
  92                 si[i].vz+=(tau*si[i].fz/m2);
  93         }
  94         for(i=0;i<amount_si;i++) {
  95                 /* calculation of forces at new positions r(t+h) */
  96                 for(j=0;j<i;j++) {
  97                         deltax=si[i].x-si[j].x;
  98                         if(deltax>LX) deltax-=LEN_X;
  99                         else if(-deltax>LX) deltax+=LEN_X;
 100                         deltax2=deltax*deltax;
 101                         deltay=si[i].y-si[j].y;
 102                         if(deltay>LY) deltay-=LEN_Y;
 103                         else if(-deltay>LY) deltay+=LEN_Y;
 104                         deltay2=deltay*deltay;
 105                         deltaz=si[i].z-si[j].z;
 106                         if(deltaz>LZ) deltaz-=LEN_Z;
 107                         else if(-deltaz>LZ) deltaz+=LEN_Z;
 108                         deltaz2=deltaz*deltaz;
 109                         distance=deltax2+deltay2+deltaz2;
 110                         if(distance<=R2_CUTOFF) {
 111                                 tmp=1.0/distance; // 1/r^2
 112                                 lj1=tmp; // 1/r^2
 113                                 tmp*=tmp; // 1/r^4
 114                                 lj1*=tmp; // 1/r^6
 115                                 tmp*=tmp; // 1/r^8
 116                                 lj2=tmp; // 1/r^8
 117                                 lj1*=tmp; // 1/r^14
 118                                 lj1*=LJ_SIGMA_12;
 119                                 lj2*=LJ_SIGMA_06;
 120                                 lj=-2*lj1+lj2;
 121                                 si[i].fx=lj*deltax;
 122                                 si[i].fy=lj*deltay;
 123                                 si[i].fz=lj*deltaz;
 124                                 si[i].fx=-lj*deltax;
 125                                 si[i].fy=-lj*deltay;
 126                                 si[i].fz=-lj*deltaz;
 127                         }
 128                 }
 129                 /* calculation of new velocities v(t+h) */
 130                 si[i].vx+=(tau*si[i].fx/m2);
 131                 si[i].vy+=(tau*si[i].fy/m2);
 132                 si[i].vz+=(tau*si[i].fz/m2);
 133         }
 134
 135         time+=tau;
 136
 137         /* print out positions in rasmol format */
 138         dprintf(fd,"%d\nTime %f\n",amount_si,time);
 139         for(i=0;i<amount_si;i++)
 140                 dprintf(fd,"Si %f %f %f %f\n",
 141                         si[i].x,si[i].y,si[i].z,time);
 142         printf(".");
 143         fflush(stdout);
 144         dprintf(fd,"\n");
 145
 146         }
 147
 148         printf("done\n");
 149         close(fd);
 150         free(si);
 151
 152         return 0;
 153 }
 154