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         printf("simulating %d silicon atoms\n",amount_si);
  31         si=malloc(amount_si*sizeof(t_atom));
  32         if(!si) {
  33                 perror("silicon malloc");
  34                 return -1;
  35         }
  36         memset(si,0,amount_si*sizeof(t_atom));
  37         m=SI_M; m2=2.0*m;
  38
  39         /* init */
  40         printf("placing silicon atoms\n");
  41         for(i=0;i<amount_si;i++) {
  42                 si[i].x=RAND(LEN_X);
  43                 si[i].y=RAND(LEN_Y);
  44                 si[i].z=RAND(LEN_Z);
  45                 si[i].vx=.0;
  46                 si[i].vy=.0;
  47                 si[i].vz=.0;
  48                 si[i].fx=.0;
  49                 si[i].fy=.0;
  50                 si[i].fz=.0;
  51         }
  52
  53         /* time */
  54         time=.0;
  55         tau=TAU;
  56         tau2=tau*tau;
  57
  58
  59         printf("starting velocity verlet: ");
  60         fflush(stdout);
  61
  62         for(runs=0;runs<RUNS;runs++) {
  63
  64         /*
  65          * velocity verlet
  66          *
  67          * r(t+h) = r(t) + h * dr/dt|t + h^2/2m * F(t)
  68          * dr/dt|(t+h) = dr/dt|t + h/2m * (F(t) + F(t+h))
  69          *
  70          */
  71         for(i=0;i<amount_si;i++) {
  72                 /* calculation of new positions r(t+h) */
  73                 si[i].x+=si[i].vx*tau;
  74                 si[i].y+=si[i].vy*tau;
  75                 si[i].z+=si[i].vz*tau;
  76                 si[i].x+=(tau2*si[i].fx/m2);
  77                 if(si[i].x>LX) si[i].x-=LEN_X;
  78                 else if(si[i].x<-LX) si[i].x+=LEN_X;
  79                 si[i].y+=(tau2*si[i].fy/m2);
  80                 if(si[i].y>LY) si[i].y-=LEN_Y;
  81                 else if(si[i].y<-LY) si[i].y+=LEN_Y;
  82                 si[i].z+=(tau2*si[i].fz/m2);
  83                 if(si[i].z>LZ) si[i].z-=LEN_Z;
  84                 else if(si[i].z<-LZ) si[i].z+=LEN_Z;
  85                 /* calculation of velocities v(t+h/2) */
  86                 si[i].vx+=(tau*si[i].fx/m2);
  87                 si[i].vy+=(tau*si[i].fy/m2);
  88                 si[i].vz+=(tau*si[i].fz/m2);
  89         }
  90         for(i=0;i<amount_si;i++) {
  91                 /* calculation of forces at new positions r(t+h) */
  92                 for(j=0;j<i;j++) {
  93                         deltax=si[i].x-si[j].x;
  94                         if(deltax>LX) deltax-=LEN_X;
  95                         else if(-deltax>LX) deltax+=LEN_X;
  96                         deltax2=deltax*deltax;
  97                         deltay=si[i].y-si[j].y;
  98                         if(deltay>LY) deltay-=LEN_Y;
  99                         else if(-deltay>LY) deltay+=LEN_Y;
 100                         deltay2=deltay*deltay;
 101                         deltaz=si[i].z-si[j].z;
 102                         if(deltaz>LZ) deltaz-=LEN_Z;
 103                         else if(-deltaz>LZ) deltaz+=LEN_Z;
 104                         deltaz2=deltaz*deltaz;
 105                         distance=deltax2+deltay2+deltaz2;
 106                         if(distance<=R2_CUTOFF) {
 107                                 tmp=1.0/distance; // 1/r^2
 108                                 lj1=tmp; // 1/r^2
 109                                 tmp*=tmp; // 1/r^4
 110                                 lj1*=tmp; // 1/r^6
 111                                 tmp*=tmp; // 1/r^8
 112                                 lj2=tmp; // 1/r^8
 113                                 lj1*=tmp; // 1/r^14
 114                                 lj1*=LJ_SIGMA_12;
 115                                 lj2*=LJ_SIGMA_06;
 116                                 lj=-2*lj1+lj2;
 117                                 si[i].fx=lj*deltax;
 118                                 si[i].fy=lj*deltay;
 119                                 si[i].fz=lj*deltaz;
 120                                 si[i].fx=-lj*deltax;
 121                                 si[i].fy=-lj*deltay;
 122                                 si[i].fz=-lj*deltaz;
 123                         }
 124                 }
 125                 /* calculation of new velocities v(t+h) */
 126                 si[i].vx+=(tau*si[i].fx/m2);
 127                 si[i].vy+=(tau*si[i].fy/m2);
 128                 si[i].vz+=(tau*si[i].fz/m2);
 129         }
 130
 131         if(!(runs%10)) {
 132
 133         /* rasmol script & xyz file */
 134         sprintf(xyz,"./saves/si-%.15f.xyz",time);
 135         sprintf(scr,"./saves/si-%.15f.scr",time);
 136         sprintf(ppm,"./video/si-%.15f.ppm",time);
 137         fd1=open(xyz,O_WRONLY|O_CREAT|O_TRUNC);
 138         fd2=open(scr,O_WRONLY|O_CREAT|O_TRUNC);
 139         if((fd1<0)||(fd2<0)) {
 140                 perror("rasmol file open");
 141                 return -1;
 142         }
 143         dprintf(fd2,"load xyz %s\n",xyz);
 144         dprintf(fd2,"spacefill 200\n");
 145         dprintf(fd2,"rotate x 11\n");
 146         dprintf(fd2,"rotate y 13\n");
 147         dprintf(fd2,"set ambient 20\n");
 148         dprintf(fd2,"set specular on\n");
 149         dprintf(fd2,"set write on\n");
 150         dprintf(fd2,"write ppm %s\n",ppm);
 151         dprintf(fd1,"%d\nsilicon\n",amount_si);
 152         for(i=0;i<amount_si;i++)
 153                 dprintf(fd1,"Si %f %f %f %f\n",
 154                         si[i].x,si[i].y,si[i].z,time);
 155         close(fd1);
 156         close(fd2);
 157
 158         }
 159
 160         /* increase time */
 161         time+=tau;
 162         printf(".");
 163         fflush(stdout);
 164
 165         }
 166
 167         printf(" done\n");
 168         free(si);
 169
 170         return 0;
 171 }
 172