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