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_moldyn md;
  18
  19         t_atom *si;
  20
  21         t_visual vis;
  22
  23         t_random random;
  24
  25         int a,b,c;
  26         double t,e,u;
  27         double help;
  28         t_3dvec p;
  29         int count;
  30
  31         t_lj_params lj;
  32
  33         char fb[32]="saves/fcc_test";
  34
  35         /* init */
  36
  37         rand_init(&random,NULL,1);
  38         random.status|=RAND_STAT_VERBOSE;
  39
  40         /* testing random numbers */
  41         //for(a=0;a<1000000;a++)
  42         //      printf("%f %f\n",rand_get_gauss(&random),
  43         //                       rand_get_gauss(&random));
  44
  45         visual_init(&vis,fb);
  46
  47         a=LEN_X;
  48         b=LEN_Y;
  49         c=LEN_Z;
  50
  51         t=TEMPERATURE;
  52
  53         printf("placing silicon atoms ... ");
  54         //count=create_lattice(DIAMOND,Si,M_SI,LC_SI,a,b,c,&si);
  55         //printf("(%d) ok!\n",count);
  56         count=2;
  57         si=malloc(2*sizeof(t_atom));
  58         si[0].r.x=2.0;
  59         si[0].r.y=0;
  60         si[0].r.z=0;
  61         si[0].element=Si;
  62         si[0].mass=14.0;
  63         si[1].r.x=-2.0;
  64         si[1].r.y=0;
  65         si[1].r.z=0;
  66         si[1].element=Si;
  67         si[1].mass=14.0;
  68
  69         printf("setting thermal fluctuations\n");
  70         //thermal_init(si,&random,count,t);
  71         v3_zero(&(si[0].v));
  72         v3_zero(&(si[1].v));
  73
  74         /* check kinetic energy */
  75
  76         e=get_e_kin(si,count);
  77         printf("kinetic energy: %f\n",e);
  78         printf("3/2 N k T = %f\n",1.5*count*K_BOLTZMANN*t);
  79
  80         /* check total momentum */
  81         p=get_total_p(si,count);
  82         printf("total momentum: %f\n",v3_norm(&p));
  83
  84         /* check potential energy */
  85         md.count=count;
  86         md.atom=si;
  87         md.potential=potential_lennard_jones;
  88         md.force=force_lennard_jones;
  89         //md.cutoff_square=((LC_SI/4.0)*(LC_SI/4.0));
  90         md.cutoff_square=36.0;
  91         md.pot_params=&lj;
  92         md.integrate=velocity_verlet;
  93         md.time_steps=RUNS;
  94         md.tau=TAU;
  95         md.status=0;
  96         md.visual=&vis;
  97
  98         lj.sigma6=3.0/16.0*LC_SI*LC_SI;
  99         help=lj.sigma6*lj.sigma6;
 100         lj.sigma6*=help;
 101         lj.sigma12=lj.sigma6*lj.sigma6;
 102         lj.epsilon=10000;
 103
 104         u=get_e_pot(&md);
 105
 106         printf("potential energy: %f\n",u);
 107         printf("total energy (1): %f\n",e+u);
 108         printf("total energy (2): %f\n",get_total_energy(&md));
 109
 110         md.dim.x=a*LC_SI;
 111         md.dim.y=b*LC_SI;
 112         md.dim.z=c*LC_SI;
 113
 114         /*
 115          * let's do the actual md algorithm now
 116          *
 117          * integration of newtons equations
 118          */
 119
 120         /* visualize */
 121         //visual_atoms(&vis,0.0,si,count);
 122
 123
 124         moldyn_integrate(&md);
 125
 126         printf("total energy (after integration): %f\n",get_total_energy(&md));
 127
 128         /* close */
 129
 130         visual_tini(&vis);
 131
 132         rand_close(&random);
 133
 134
 135         //printf("starting velocity verlet: ");
 136         //fflush(stdout);
 137
 138         //for(runs=0;runs<RUNS;runs++) {
 139
 140         /*
 141          * velocity verlet
 142          *
 143          * r(t+h) = r(t) + h * dr/dt|t + h^2/2m * F(t)
 144          * dr/dt|(t+h) = dr/dt|t + h/2m * (F(t) + F(t+h))
 145          *
 146          */
 147         //for(i=0;i<amount_si;i++) {
 148 //              /* calculation of new positions r(t+h) */
 149 //              si[i].x+=si[i].vx*tau;
 150 //              si[i].y+=si[i].vy*tau;
 151 //              si[i].z+=si[i].vz*tau;
 152 //              si[i].x+=(tau2*si[i].fx/m2);
 153 //              if(si[i].x>LX) si[i].x-=LEN_X;
 154 //              else if(si[i].x<-LX) si[i].x+=LEN_X;
 155 //              si[i].y+=(tau2*si[i].fy/m2);
 156 //              if(si[i].y>LY) si[i].y-=LEN_Y;
 157 //              else if(si[i].y<-LY) si[i].y+=LEN_Y;
 158 //              si[i].z+=(tau2*si[i].fz/m2);
 159 //              if(si[i].z>LZ) si[i].z-=LEN_Z;
 160 //              else if(si[i].z<-LZ) si[i].z+=LEN_Z;
 161 //              /* calculation of velocities v(t+h/2) */
 162 //              si[i].vx+=(tau*si[i].fx/m2);
 163 //              si[i].vy+=(tau*si[i].fy/m2);
 164 //              si[i].vz+=(tau*si[i].fz/m2);
 165 //              /* reset of forces */
 166 //              si[i].fx=.0;
 167 //              si[i].fy=.0;
 168 //              si[i].fz=.0;
 169 //      }
 170 //      for(i=0;i<amount_si;i++) {
 171 //              /* calculation of forces at new positions r(t+h) */
 172 //              for(j=0;j<i;j++) {
 173 //                      deltax=si[i].x-si[j].x;
 174 //                      if(deltax>LX) deltax-=LEN_X;
 175 //                      else if(-deltax>LX) deltax+=LEN_X;
 176 //                      deltax2=deltax*deltax;
 177 //                      deltay=si[i].y-si[j].y;
 178 //                      if(deltay>LY) deltay-=LEN_Y;
 179 //                      else if(-deltay>LY) deltay+=LEN_Y;
 180 //                      deltay2=deltay*deltay;
 181 //                      deltaz=si[i].z-si[j].z;
 182 //                      if(deltaz>LZ) deltaz-=LEN_Z;
 183 //                      else if(-deltaz>LZ) deltaz+=LEN_Z;
 184 //                      deltaz2=deltaz*deltaz;
 185 //                      distance=deltax2+deltay2+deltaz2;
 186 //                      if(distance<=R2_CUTOFF) {
 187 //                              tmp=1.0/distance; // 1/r^2
 188 //                              lj1=tmp; // 1/r^2
 189 //                              tmp*=tmp; // 1/r^4
 190 //                              lj1*=tmp; // 1/r^6
 191 //                              tmp*=tmp; // 1/r^8
 192 //                              lj2=tmp; // 1/r^8
 193 //                              lj1*=tmp; // 1/r^14
 194 //                              lj1*=LJ_SIGMA_12;
 195 //                              lj2*=LJ_SIGMA_06;
 196 //                              lj=-2*lj1+lj2;
 197 //                              si[i].fx-=lj*deltax;
 198 //                              si[i].fy-=lj*deltay;
 199 //                              si[i].fz-=lj*deltaz;
 200 //                              si[j].fx+=lj*deltax;
 201 //                              si[j].fy+=lj*deltay;
 202 //                              si[j].fz+=lj*deltaz;
 203 //                      }
 204 //              }
 205 //      }
 206 //      for(i=0;i<amount_si;i++) {
 207 //              /* calculation of new velocities v(t+h) */
 208 //              si[i].vx+=(tau*si[i].fx/m2);
 209 //              si[i].vy+=(tau*si[i].fy/m2);
 210 //              si[i].vz+=(tau*si[i].fz/m2);
 211 //      }
 212 //
 213 //      if(!(runs%150)) {
 214 //
 215 //      /* rasmol script & xyz file */
 216 //      sprintf(xyz,"./saves/si-%.15f.xyz",time);
 217 //      sprintf(ppm,"./video/si-%.15f.ppm",time);
 218 //      fd1=open(xyz,O_WRONLY|O_CREAT|O_TRUNC);
 219 //      if(fd1<0) {
 220 //              perror("rasmol xyz file open");
 221 //              return -1;
 222 //      }
 223 //      dprintf(fd2,"load xyz %s\n",xyz);
 224 //      dprintf(fd2,"spacefill 200\n");
 225 //      dprintf(fd2,"rotate x 11\n");
 226 //      dprintf(fd2,"rotate y 13\n");
 227 //      dprintf(fd2,"set ambient 20\n");
 228 //      dprintf(fd2,"set specular on\n");
 229 //      dprintf(fd2,"zoom 400\n");
 230 //      dprintf(fd2,"write ppm %s\n",ppm);
 231 //      dprintf(fd2,"zap\n");
 232 //      dprintf(fd1,"%d\nsilicon\n",amount_si+9);
 233 //      for(i=0;i<amount_si;i++)
 234 //              dprintf(fd1,"Si %f %f %f %f\n",
 235 //                      si[i].x,si[i].y,si[i].z,time);
 236 //      dprintf(fd1,"H 0.0 0.0 0.0 %f\n",time);
 237 //      dprintf(fd1,"He %f %f %f %f\n",LX,LY,LZ,time);
 238 //      dprintf(fd1,"He %f %f %f %f\n",-LX,LY,LZ,time);
 239 //      dprintf(fd1,"He %f %f %f %f\n",LX,-LY,LZ,time);
 240 //      dprintf(fd1,"He %f %f %f %f\n",LX,LY,-LZ,time);
 241 //      dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,LZ,time);
 242 //      dprintf(fd1,"He %f %f %f %f\n",-LX,LY,-LZ,time);
 243 //      dprintf(fd1,"He %f %f %f %f\n",LX,-LY,-LZ,time);
 244 //      dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,-LZ,time);
 245 //      close(fd1);
 246 //
 247 //      }
 248 //
 249 //      /* increase time */
 250 //      time+=tau;
 251 //      printf(".");
 252 //      fflush(stdout);
 253 //
 254 //      }
 255 //
 256 //      printf(" done\n");
 257 //      close(fd2);
 258 //      free(si);
 259 //
 260
 261         return 0;
 262 }
 263