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         t_3dvec p;
  26         int count;
  27
  28         char fb[32]="saves/fcc_test";
  29
  30         /* init */
  31
  32         rand_init(&random,NULL,1);
  33         random.status|=RAND_STAT_VERBOSE;
  34
  35         /* testing random numbers */
  36         //for(a=0;a<1000000;a++)
  37         //      printf("%f %f\n",rand_get_gauss(&random),
  38         //                       rand_get_gauss(&random));
  39
  40         visual_init(&vis,fb);
  41
  42         a=LEN_X;
  43         b=LEN_Y;
  44         c=LEN_Z;
  45
  46         t=TEMPERATURE;
  47
  48         printf("placing silicon atoms ... ");
  49         count=create_lattice(DIAMOND,Si,M_SI,LC_SI,a,b,c,&si);
  50         printf("(%d) ok!\n",count);
  51
  52         printf("setting thermal fluctuations\n");
  53         thermal_init(si,&random,count,t);
  54
  55         /* visualize */
  56
  57         visual_atoms(&vis,0.0,si,count);
  58
  59         /* check kinetic energy */
  60
  61         e=get_e_kin(si,count);
  62         printf("kinetic energy: %f\n",e);
  63         printf("3/2 N k T = %f\n",1.5*count*K_BOLTZMANN*t);
  64
  65         /* check total momentum */
  66         p=get_total_p(si,count);
  67         printf("total momentum: %f\n",v3_norm(&p));
  68
  69         /*
  70          * let's do the actual md algorithm now
  71          *
  72          * integration of newtons equations
  73          */
  74
  75         /* close */
  76
  77         visual_tini(&vis);
  78
  79         rand_close(&random);
  80
  81
  82         //printf("starting velocity verlet: ");
  83         //fflush(stdout);
  84
  85         //for(runs=0;runs<RUNS;runs++) {
  86
  87         /*
  88          * velocity verlet
  89          *
  90          * r(t+h) = r(t) + h * dr/dt|t + h^2/2m * F(t)
  91          * dr/dt|(t+h) = dr/dt|t + h/2m * (F(t) + F(t+h))
  92          *
  93          */
  94         //for(i=0;i<amount_si;i++) {
  95 //              /* calculation of new positions r(t+h) */
  96 //              si[i].x+=si[i].vx*tau;
  97 //              si[i].y+=si[i].vy*tau;
  98 //              si[i].z+=si[i].vz*tau;
  99 //              si[i].x+=(tau2*si[i].fx/m2);
 100 //              if(si[i].x>LX) si[i].x-=LEN_X;
 101 //              else if(si[i].x<-LX) si[i].x+=LEN_X;
 102 //              si[i].y+=(tau2*si[i].fy/m2);
 103 //              if(si[i].y>LY) si[i].y-=LEN_Y;
 104 //              else if(si[i].y<-LY) si[i].y+=LEN_Y;
 105 //              si[i].z+=(tau2*si[i].fz/m2);
 106 //              if(si[i].z>LZ) si[i].z-=LEN_Z;
 107 //              else if(si[i].z<-LZ) si[i].z+=LEN_Z;
 108 //              /* calculation of velocities v(t+h/2) */
 109 //              si[i].vx+=(tau*si[i].fx/m2);
 110 //              si[i].vy+=(tau*si[i].fy/m2);
 111 //              si[i].vz+=(tau*si[i].fz/m2);
 112 //              /* reset of forces */
 113 //              si[i].fx=.0;
 114 //              si[i].fy=.0;
 115 //              si[i].fz=.0;
 116 //      }
 117 //      for(i=0;i<amount_si;i++) {
 118 //              /* calculation of forces at new positions r(t+h) */
 119 //              for(j=0;j<i;j++) {
 120 //                      deltax=si[i].x-si[j].x;
 121 //                      if(deltax>LX) deltax-=LEN_X;
 122 //                      else if(-deltax>LX) deltax+=LEN_X;
 123 //                      deltax2=deltax*deltax;
 124 //                      deltay=si[i].y-si[j].y;
 125 //                      if(deltay>LY) deltay-=LEN_Y;
 126 //                      else if(-deltay>LY) deltay+=LEN_Y;
 127 //                      deltay2=deltay*deltay;
 128 //                      deltaz=si[i].z-si[j].z;
 129 //                      if(deltaz>LZ) deltaz-=LEN_Z;
 130 //                      else if(-deltaz>LZ) deltaz+=LEN_Z;
 131 //                      deltaz2=deltaz*deltaz;
 132 //                      distance=deltax2+deltay2+deltaz2;
 133 //                      if(distance<=R2_CUTOFF) {
 134 //                              tmp=1.0/distance; // 1/r^2
 135 //                              lj1=tmp; // 1/r^2
 136 //                              tmp*=tmp; // 1/r^4
 137 //                              lj1*=tmp; // 1/r^6
 138 //                              tmp*=tmp; // 1/r^8
 139 //                              lj2=tmp; // 1/r^8
 140 //                              lj1*=tmp; // 1/r^14
 141 //                              lj1*=LJ_SIGMA_12;
 142 //                              lj2*=LJ_SIGMA_06;
 143 //                              lj=-2*lj1+lj2;
 144 //                              si[i].fx-=lj*deltax;
 145 //                              si[i].fy-=lj*deltay;
 146 //                              si[i].fz-=lj*deltaz;
 147 //                              si[j].fx+=lj*deltax;
 148 //                              si[j].fy+=lj*deltay;
 149 //                              si[j].fz+=lj*deltaz;
 150 //                      }
 151 //              }
 152 //      }
 153 //      for(i=0;i<amount_si;i++) {
 154 //              /* calculation of new velocities v(t+h) */
 155 //              si[i].vx+=(tau*si[i].fx/m2);
 156 //              si[i].vy+=(tau*si[i].fy/m2);
 157 //              si[i].vz+=(tau*si[i].fz/m2);
 158 //      }
 159 //
 160 //      if(!(runs%150)) {
 161 //
 162 //      /* rasmol script & xyz file */
 163 //      sprintf(xyz,"./saves/si-%.15f.xyz",time);
 164 //      sprintf(ppm,"./video/si-%.15f.ppm",time);
 165 //      fd1=open(xyz,O_WRONLY|O_CREAT|O_TRUNC);
 166 //      if(fd1<0) {
 167 //              perror("rasmol xyz file open");
 168 //              return -1;
 169 //      }
 170 //      dprintf(fd2,"load xyz %s\n",xyz);
 171 //      dprintf(fd2,"spacefill 200\n");
 172 //      dprintf(fd2,"rotate x 11\n");
 173 //      dprintf(fd2,"rotate y 13\n");
 174 //      dprintf(fd2,"set ambient 20\n");
 175 //      dprintf(fd2,"set specular on\n");
 176 //      dprintf(fd2,"zoom 400\n");
 177 //      dprintf(fd2,"write ppm %s\n",ppm);
 178 //      dprintf(fd2,"zap\n");
 179 //      dprintf(fd1,"%d\nsilicon\n",amount_si+9);
 180 //      for(i=0;i<amount_si;i++)
 181 //              dprintf(fd1,"Si %f %f %f %f\n",
 182 //                      si[i].x,si[i].y,si[i].z,time);
 183 //      dprintf(fd1,"H 0.0 0.0 0.0 %f\n",time);
 184 //      dprintf(fd1,"He %f %f %f %f\n",LX,LY,LZ,time);
 185 //      dprintf(fd1,"He %f %f %f %f\n",-LX,LY,LZ,time);
 186 //      dprintf(fd1,"He %f %f %f %f\n",LX,-LY,LZ,time);
 187 //      dprintf(fd1,"He %f %f %f %f\n",LX,LY,-LZ,time);
 188 //      dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,LZ,time);
 189 //      dprintf(fd1,"He %f %f %f %f\n",-LX,LY,-LZ,time);
 190 //      dprintf(fd1,"He %f %f %f %f\n",LX,-LY,-LZ,time);
 191 //      dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,-LZ,time);
 192 //      close(fd1);
 193 //
 194 //      }
 195 //
 196 //      /* increase time */
 197 //      time+=tau;
 198 //      printf(".");
 199 //      fflush(stdout);
 200 //
 201 //      }
 202 //
 203 //      printf(" done\n");
 204 //      close(fd2);
 205 //      free(si);
 206 //
 207
 208         return 0;
 209 }
 210