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 "moldyn.h"
   9 #include "math/math.h"
  10 #include "init/init.h"
  11 #include "visual/visual.h"
  12
  13 #include "posic.h"
  14
  15 int main(int argc,char **argv) {
  16
  17         t_atom *si;
  18
  19         t_visual vis;
  20
  21         t_random random;
  22
  23         int a,b,c;
  24         double t,e;
  25         int count;
  26
  27         char fb[32]="saves/fcc_test";
  28
  29         /* init */
  30
  31         rand_init(&random,NULL,1);
  32         random.status|=RAND_STAT_VERBOSE;
  33
  34         visual_init(&vis,fb);
  35
  36         a=LEN_X;
  37         b=LEN_Y;
  38         c=LEN_Z;
  39
  40         t=TEMPERATURE;
  41
  42         printf("placing silicon atoms\n");
  43         count=create_lattice(DIAMOND,Si,M_SI,LC_SI,a,b,c,&si);
  44
  45         printf("setting thermal fluctuations\n");
  46         thermal_init(si,&random,count,t);
  47
  48
  49         /* visualize */
  50
  51         visual_atoms(&vis,0.0,si,count);
  52
  53         /* check kinetic energy */
  54
  55         e=get_e_kin(si,count);
  56         printf("kinetic energy: %f\n",e);
  57         printf("3/2 N k T = %f\n",1.5*count*K_BOLTZMANN*t);
  58
  59         /* close */
  60
  61         visual_tini(&vis);
  62
  63         rand_close(&random);
  64
  65
  66         //printf("starting velocity verlet: ");
  67         //fflush(stdout);
  68
  69         //for(runs=0;runs<RUNS;runs++) {
  70
  71         /*
  72          * velocity verlet
  73          *
  74          * r(t+h) = r(t) + h * dr/dt|t + h^2/2m * F(t)
  75          * dr/dt|(t+h) = dr/dt|t + h/2m * (F(t) + F(t+h))
  76          *
  77          */
  78         //for(i=0;i<amount_si;i++) {
  79 //              /* calculation of new positions r(t+h) */
  80 //              si[i].x+=si[i].vx*tau;
  81 //              si[i].y+=si[i].vy*tau;
  82 //              si[i].z+=si[i].vz*tau;
  83 //              si[i].x+=(tau2*si[i].fx/m2);
  84 //              if(si[i].x>LX) si[i].x-=LEN_X;
  85 //              else if(si[i].x<-LX) si[i].x+=LEN_X;
  86 //              si[i].y+=(tau2*si[i].fy/m2);
  87 //              if(si[i].y>LY) si[i].y-=LEN_Y;
  88 //              else if(si[i].y<-LY) si[i].y+=LEN_Y;
  89 //              si[i].z+=(tau2*si[i].fz/m2);
  90 //              if(si[i].z>LZ) si[i].z-=LEN_Z;
  91 //              else if(si[i].z<-LZ) si[i].z+=LEN_Z;
  92 //              /* calculation of velocities v(t+h/2) */
  93 //              si[i].vx+=(tau*si[i].fx/m2);
  94 //              si[i].vy+=(tau*si[i].fy/m2);
  95 //              si[i].vz+=(tau*si[i].fz/m2);
  96 //              /* reset of forces */
  97 //              si[i].fx=.0;
  98 //              si[i].fy=.0;
  99 //              si[i].fz=.0;
 100 //      }
 101 //      for(i=0;i<amount_si;i++) {
 102 //              /* calculation of forces at new positions r(t+h) */
 103 //              for(j=0;j<i;j++) {
 104 //                      deltax=si[i].x-si[j].x;
 105 //                      if(deltax>LX) deltax-=LEN_X;
 106 //                      else if(-deltax>LX) deltax+=LEN_X;
 107 //                      deltax2=deltax*deltax;
 108 //                      deltay=si[i].y-si[j].y;
 109 //                      if(deltay>LY) deltay-=LEN_Y;
 110 //                      else if(-deltay>LY) deltay+=LEN_Y;
 111 //                      deltay2=deltay*deltay;
 112 //                      deltaz=si[i].z-si[j].z;
 113 //                      if(deltaz>LZ) deltaz-=LEN_Z;
 114 //                      else if(-deltaz>LZ) deltaz+=LEN_Z;
 115 //                      deltaz2=deltaz*deltaz;
 116 //                      distance=deltax2+deltay2+deltaz2;
 117 //                      if(distance<=R2_CUTOFF) {
 118 //                              tmp=1.0/distance; // 1/r^2
 119 //                              lj1=tmp; // 1/r^2
 120 //                              tmp*=tmp; // 1/r^4
 121 //                              lj1*=tmp; // 1/r^6
 122 //                              tmp*=tmp; // 1/r^8
 123 //                              lj2=tmp; // 1/r^8
 124 //                              lj1*=tmp; // 1/r^14
 125 //                              lj1*=LJ_SIGMA_12;
 126 //                              lj2*=LJ_SIGMA_06;
 127 //                              lj=-2*lj1+lj2;
 128 //                              si[i].fx-=lj*deltax;
 129 //                              si[i].fy-=lj*deltay;
 130 //                              si[i].fz-=lj*deltaz;
 131 //                              si[j].fx+=lj*deltax;
 132 //                              si[j].fy+=lj*deltay;
 133 //                              si[j].fz+=lj*deltaz;
 134 //                      }
 135 //              }
 136 //      }
 137 //      for(i=0;i<amount_si;i++) {
 138 //              /* calculation of new velocities v(t+h) */
 139 //              si[i].vx+=(tau*si[i].fx/m2);
 140 //              si[i].vy+=(tau*si[i].fy/m2);
 141 //              si[i].vz+=(tau*si[i].fz/m2);
 142 //      }
 143 //
 144 //      if(!(runs%150)) {
 145 //
 146 //      /* rasmol script & xyz file */
 147 //      sprintf(xyz,"./saves/si-%.15f.xyz",time);
 148 //      sprintf(ppm,"./video/si-%.15f.ppm",time);
 149 //      fd1=open(xyz,O_WRONLY|O_CREAT|O_TRUNC);
 150 //      if(fd1<0) {
 151 //              perror("rasmol xyz file open");
 152 //              return -1;
 153 //      }
 154 //      dprintf(fd2,"load xyz %s\n",xyz);
 155 //      dprintf(fd2,"spacefill 200\n");
 156 //      dprintf(fd2,"rotate x 11\n");
 157 //      dprintf(fd2,"rotate y 13\n");
 158 //      dprintf(fd2,"set ambient 20\n");
 159 //      dprintf(fd2,"set specular on\n");
 160 //      dprintf(fd2,"zoom 400\n");
 161 //      dprintf(fd2,"write ppm %s\n",ppm);
 162 //      dprintf(fd2,"zap\n");
 163 //      dprintf(fd1,"%d\nsilicon\n",amount_si+9);
 164 //      for(i=0;i<amount_si;i++)
 165 //              dprintf(fd1,"Si %f %f %f %f\n",
 166 //                      si[i].x,si[i].y,si[i].z,time);
 167 //      dprintf(fd1,"H 0.0 0.0 0.0 %f\n",time);
 168 //      dprintf(fd1,"He %f %f %f %f\n",LX,LY,LZ,time);
 169 //      dprintf(fd1,"He %f %f %f %f\n",-LX,LY,LZ,time);
 170 //      dprintf(fd1,"He %f %f %f %f\n",LX,-LY,LZ,time);
 171 //      dprintf(fd1,"He %f %f %f %f\n",LX,LY,-LZ,time);
 172 //      dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,LZ,time);
 173 //      dprintf(fd1,"He %f %f %f %f\n",-LX,LY,-LZ,time);
 174 //      dprintf(fd1,"He %f %f %f %f\n",LX,-LY,-LZ,time);
 175 //      dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,-LZ,time);
 176 //      close(fd1);
 177 //
 178 //      }
 179 //
 180 //      /* increase time */
 181 //      time+=tau;
 182 //      printf(".");
 183 //      fflush(stdout);
 184 //
 185 //      }
 186 //
 187 //      printf(" done\n");
 188 //      close(fd2);
 189 //      free(si);
 190 //
 191
 192         return 0;
 193 }
 194