sic.c

   1 /*
   2  * sic.c - investigation of the sic precipitation process of silicon carbide
   3  *
   4  * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
   5  *
   6  */
   7
   8 #include <math.h>
   9
  10 #include "moldyn.h"
  11
  12 /* potential */
  13 #include "potentials/harmonic_oscillator.h"
  14 #include "potentials/lennard_jones.h"
  15 #include "potentials/albe.h"
  16 #ifdef TERSOFF_ORIG
  17 #include "potentials/tersoff_orig.h"
  18 #else
  19 #include "potentials/tersoff.h"
  20 #endif
  21
  22 typedef struct s_hp {
  23         int prerun_count;       /* prerun count */
  24         int insert_count;       /* insert count */
  25         int postrun_count;      /* post run count */
  26         unsigned char state;    /* current state */
  27         int argc;               /* arg count */
  28         char **argv;            /* args */
  29 } t_hp;
  30
  31 #define STATE_PRERUN    0x00
  32 #define STATE_INSERT    0x01
  33 #define STATE_POSTRUN   0x02
  34
  35 /* include the config file */
  36 #include "config.h"
  37
  38 int insert_atoms(t_moldyn *moldyn) {
  39
  40         int i,j;
  41         u8 run;
  42         t_3dvec r,v,dist;
  43         double d,dmin;
  44
  45         t_atom *atom;
  46
  47         atom=moldyn->atom;
  48
  49         v.x=0; v.y=0; v.z=0;
  50
  51         for(j=0;j<INS_ATOMS;j++) {
  52                 run=1;
  53                 while(run) {
  54                         // tetrahedral
  55                         /*
  56                         r.x=0.0;
  57                         r.y=0.0;
  58                         r.z=0.0;
  59                         */
  60                         // hexagonal
  61                         /*
  62                         r.x=-1.0/8.0*ALBE_LC_SI;
  63                         r.y=-1.0/8.0*ALBE_LC_SI;
  64                         r.z=1.0/8.0*ALBE_LC_SI;
  65                         */
  66                         // 110 dumbbell
  67                         /*
  68                         r.x=(-0.5+0.25+0.125)*ALBE_LC_SI;
  69                         r.y=(-0.5+0.25+0.125)*ALBE_LC_SI;
  70                         r.z=(-0.5+0.25)*ALBE_LC_SI;
  71                         md->atom[4372].r.x=(-0.5+0.125+0.125)*ALBE_LC_SI;
  72                         md->atom[4372].r.y=(-0.5+0.125+0.125)*ALBE_LC_SI;
  73                         */
  74                         // random
  75                         //
  76                         r.x=(rand_get_double(&(moldyn->random))-0.5)*INS_LENX;
  77                         r.y=(rand_get_double(&(moldyn->random))-0.5)*INS_LENY;
  78                         r.z=(rand_get_double(&(moldyn->random))-0.5)*INS_LENZ;
  79                         //
  80                         // offset
  81                         r.x+=INS_OFFSET;
  82                         r.y+=INS_OFFSET;
  83                         r.z+=INS_OFFSET;
  84                         /* assume valid coordinates */
  85                         run=0;
  86                         dmin=10000000000.0;             // for sure too high!
  87                         for(i=0;i<moldyn->count;i++) {
  88                                 atom=&(moldyn->atom[i]);
  89                                 v3_sub(&dist,&(atom->r),&r);
  90                                 check_per_bound(moldyn,&dist);
  91                                 d=v3_absolute_square(&dist);
  92                                 /* reject coordinates */
  93                                 if(d<INS_R_C) {
  94                                         //printf("atom %d - %f\n",i,d);
  95                                         run=1;
  96                                         break;
  97                                 }
  98                                 if(d<dmin)
  99                                         dmin=d;
 100                         }
 101                 }
 102                 add_atom(moldyn,INS_TYPE,INS_MASS,INS_BRAND,
 103                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|\
 104                          //ATOM_ATTR_HB|ATOM_ATTR_VB,
 105                          ATOM_ATTR_HB,
 106                          &r,&v);
 107                 printf(" %02d: atom %d | %f %f %f | %f\n",
 108                        j,moldyn->count-1,r.x,r.y,r.z,dmin);
 109         }
 110
 111         return 0;
 112 }
 113
 114 int sic_hook(void *moldyn,void *hook_params) {
 115
 116         t_hp *hp;
 117         t_moldyn *md;
 118         int steps;
 119         double tau;
 120         double dt;
 121
 122         hp=hook_params;
 123         md=moldyn;
 124
 125         tau=1.0;
 126         steps=0;
 127
 128         /* switch on t scaling */
 129         if(md->schedule.count==0)
 130                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
 131
 132         /* my lousy state machine ! */
 133
 134         /* switch to insert state immediately */
 135         if(hp->state==STATE_PRERUN)
 136                 hp->state=STATE_INSERT;
 137
 138         /* act according to state */
 139         switch(hp->state) {
 140                 case STATE_INSERT:
 141                         /* assigne values */
 142                         steps=INS_RELAX;
 143                         tau=INS_TAU;
 144                         /* check temperature */
 145                         dt=md->t_avg-md->t_ref;
 146                         if(dt<0)
 147                                 dt=-dt;
 148                         if(dt>INS_DELTA_TC)
 149                                 break;
 150                         /* insert atoms */
 151                         hp->insert_count+=1;
 152                         printf("   ### insert atoms (%d/%d) ###\n",
 153                                hp->insert_count*INS_ATOMS,INS_RUNS*INS_ATOMS);
 154                         insert_atoms(md);
 155                         /* change state after last insertion */
 156                         if(hp->insert_count==INS_RUNS)
 157                                 hp->state=STATE_POSTRUN;
 158                         break;
 159                 case STATE_POSTRUN:
 160                         /* assigne values */
 161                         steps=POST_RELAX;
 162                         tau=POST_TAU;
 163                         /* check temperature */
 164                         dt=md->t_avg-md->t_ref;
 165                         if(dt<0)
 166                                 dt=-dt;
 167                         if(dt>INS_DELTA_TC)
 168                                 break;
 169                         /* decrease temperature */
 170                         hp->postrun_count+=1;
 171                         printf(" ### postrun (%d/%d) ###\n",
 172                                hp->postrun_count,POST_RUNS);
 173                         set_temperature(md,md->t_ref-POST_DT);
 174                         if(hp->postrun_count==POST_RUNS)
 175                                 return 0;
 176                         break;
 177                 default:
 178                         printf("[hook] FATAL (default case!?!)\n");
 179                         break;
 180         }
 181
 182         /* reset the average counters */
 183         average_reset(md);
 184
 185         /* add schedule */
 186         moldyn_add_schedule(md,steps,tau);
 187
 188         return 0;
 189 }
 190
 191 int main(int argc,char **argv) {
 192
 193         /* main moldyn structure */
 194         t_moldyn md;
 195
 196         /* hook parameter structure */
 197         t_hp hookparam;
 198
 199         /* potential parameters */
 200         t_tersoff_mult_params tp;
 201         t_albe_mult_params ap;
 202
 203         /* testing location & velocity vector */
 204         t_3dvec r,v;
 205         memset(&r,0,sizeof(t_3dvec));
 206         memset(&v,0,sizeof(t_3dvec));
 207
 208         /* initialize moldyn */
 209         moldyn_init(&md,argc,argv);
 210
 211         /* choose integration algorithm */
 212         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 213
 214         /* choose potential */
 215 #ifdef ALBE
 216         set_potential3b_j1(&md,albe_mult_3bp_j1);
 217         set_potential3b_k1(&md,albe_mult_3bp_k1);
 218         set_potential3b_j2(&md,albe_mult_3bp_j2);
 219         set_potential3b_k2(&md,albe_mult_3bp_k2);
 220 #else
 221         set_potential1b(&md,tersoff_mult_1bp);
 222         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 223         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 224         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 225         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 226 #endif
 227
 228 #ifdef ALBE
 229         set_potential_params(&md,&ap);
 230 #else
 231         set_potential_params(&md,&tp);
 232 #endif
 233
 234         /* cutoff radius & bondlen */
 235 #ifdef ALBE
 236         set_cutoff(&md,ALBE_S_SI);
 237         set_bondlen(&md,ALBE_S_SI,ALBE_S_C,ALBE_S_SIC);
 238         //set_cutoff(&md,ALBE_S_C);
 239 #else
 240         set_cutoff(&md,TM_S_SI);
 241         set_bondlen(&md,TM_S_SI,TM_S_C,-1.0);
 242         //set_cutoff(&md,TM_S_C);
 243 #endif
 244
 245         /*
 246          * potential parameters
 247          */
 248
 249         /*
 250          * tersoff mult potential parameters for SiC
 251          */
 252         tp.S[0]=TM_S_SI;
 253         tp.R[0]=TM_R_SI;
 254         tp.A[0]=TM_A_SI;
 255         tp.B[0]=TM_B_SI;
 256         tp.lambda[0]=TM_LAMBDA_SI;
 257         tp.mu[0]=TM_MU_SI;
 258         tp.beta[0]=TM_BETA_SI;
 259         tp.n[0]=TM_N_SI;
 260         tp.c[0]=TM_C_SI;
 261         tp.d[0]=TM_D_SI;
 262         tp.h[0]=TM_H_SI;
 263
 264         tp.S[1]=TM_S_C;
 265         tp.R[1]=TM_R_C;
 266         tp.A[1]=TM_A_C;
 267         tp.B[1]=TM_B_C;
 268         tp.lambda[1]=TM_LAMBDA_C;
 269         tp.mu[1]=TM_MU_C;
 270         tp.beta[1]=TM_BETA_C;
 271         tp.n[1]=TM_N_C;
 272         tp.c[1]=TM_C_C;
 273         tp.d[1]=TM_D_C;
 274         tp.h[1]=TM_H_C;
 275
 276         tp.chi=TM_CHI_SIC;
 277
 278         tersoff_mult_complete_params(&tp);
 279
 280         /*
 281          * albe mult potential parameters for SiC
 282          */
 283         ap.S[0]=ALBE_S_SI;
 284         ap.R[0]=ALBE_R_SI;
 285         ap.A[0]=ALBE_A_SI;
 286         ap.B[0]=ALBE_B_SI;
 287         ap.r0[0]=ALBE_R0_SI;
 288         ap.lambda[0]=ALBE_LAMBDA_SI;
 289         ap.mu[0]=ALBE_MU_SI;
 290         ap.gamma[0]=ALBE_GAMMA_SI;
 291         ap.c[0]=ALBE_C_SI;
 292         ap.d[0]=ALBE_D_SI;
 293         ap.h[0]=ALBE_H_SI;
 294
 295         ap.S[1]=ALBE_S_C;
 296         ap.R[1]=ALBE_R_C;
 297         ap.A[1]=ALBE_A_C;
 298         ap.B[1]=ALBE_B_C;
 299         ap.r0[1]=ALBE_R0_C;
 300         ap.lambda[1]=ALBE_LAMBDA_C;
 301         ap.mu[1]=ALBE_MU_C;
 302         ap.gamma[1]=ALBE_GAMMA_C;
 303         ap.c[1]=ALBE_C_C;
 304         ap.d[1]=ALBE_D_C;
 305         ap.h[1]=ALBE_H_C;
 306
 307         ap.Smixed=ALBE_S_SIC;
 308         ap.Rmixed=ALBE_R_SIC;
 309         ap.Amixed=ALBE_A_SIC;
 310         ap.Bmixed=ALBE_B_SIC;
 311         ap.r0_mixed=ALBE_R0_SIC;
 312         ap.lambda_m=ALBE_LAMBDA_SIC;
 313         ap.mu_m=ALBE_MU_SIC;
 314         ap.gamma_m=ALBE_GAMMA_SIC;
 315         ap.c_mixed=ALBE_C_SIC;
 316         ap.d_mixed=ALBE_D_SIC;
 317         ap.h_mixed=ALBE_H_SIC;
 318
 319         albe_mult_complete_params(&ap);
 320
 321         /* set (initial) dimensions of simulation volume */
 322 #ifdef ALBE
 323         set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
 324         //set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
 325         //set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
 326 #else
 327         set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE);
 328         //set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
 329         //set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
 330 #endif
 331
 332         /* set periodic boundary conditions in all directions */
 333         set_pbc(&md,TRUE,TRUE,TRUE);
 334
 335         /* create the lattice / place atoms */
 336         //
 337 #ifdef ALBE
 338         create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
 339         //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 340 #else
 341         create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 342 #endif
 343                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 344         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 345                        0,LCNTX,LCNTY,LCNTZ,NULL);
 346         //               1,LCNTX,LCNTY,LCNTZ,NULL);
 347
 348         /* create zinkblende structure */
 349         /*
 350 #ifdef ALBE
 351         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 352         create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
 353                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 354                        0,LCNTX,LCNTY,LCNTZ,&r);
 355         r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 356         create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
 357                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 358                        1,LCNTX,LCNTY,LCNTZ,&r);
 359 #else
 360         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 361         create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
 362                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 363                        0,LCNTX,LCNTY,LCNTZ,&r);
 364         r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 365         create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
 366                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 367                        1,LCNTX,LCNTY,LCNTZ,&r);
 368 #endif
 369         */
 370
 371         /* check for right atom placing */
 372         moldyn_bc_check(&md);
 373
 374         /* testing configuration */
 375         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 376         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 377         //r.y=0;                v.y=0;
 378         //r.z=0;                v.z=0;
 379         //add_atom(&md,SI,M_SI,0,
 380         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 381         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 382         //           &r,&v);
 383         //r.x=-r.x;     v.x=-v.x;
 384         //r.y=0;                v.y=0;
 385         //r.z=0;                v.z=0;
 386         //add_atom(&md,SI,M_SI,0,
 387         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 388         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 389         //           &r,&v);
 390         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 391         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 392         //r.y=0;                v.y=0;
 393         //r.x=0;                v.x=0;
 394         //add_atom(&md,SI,M_SI,0,
 395         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 396         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 397         //           &r,&v);
 398         //r.z=-r.z;     v.z=-v.z;
 399         //r.y=0;                v.y=0;
 400         //r.x=0;                v.x=0;
 401         //add_atom(&md,SI,M_SI,0,
 402         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 403         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 404         //           &r,&v);
 405
 406         /* set temperature & pressure */
 407         set_temperature(&md,atof(argv[2])+273.0);
 408         set_pressure(&md,BAR);
 409
 410         /* set amount of steps to skip before average calc */
 411         set_avg_skip(&md,AVG_SKIP);
 412
 413         /* set p/t scaling */
 414         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
 415         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 416         //                 T_SCALE_BERENDSEN,100.0);
 417         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 418         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 419
 420         /* initial thermal fluctuations of particles (in equilibrium) */
 421         thermal_init(&md,TRUE);
 422
 423         /* create the simulation schedule */
 424         moldyn_add_schedule(&md,PRERUN,PRE_TAU);
 425
 426         /* schedule hook function */
 427         memset(&hookparam,0,sizeof(t_hp));
 428         hookparam.argc=argc;
 429         hookparam.argv=argv;
 430         moldyn_set_schedule_hook(&md,&sic_hook,&hookparam);
 431         //moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam);
 432         //moldyn_add_schedule(&md,POSTRUN,1.0);
 433
 434         /* activate logging */
 435         moldyn_set_log_dir(&md,argv[1]);
 436         moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
 437         moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
 438         moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
 439         moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
 440         moldyn_set_log(&md,VISUAL_STEP,LOG_V);
 441         moldyn_set_log(&md,SAVE_STEP,LOG_S);
 442         moldyn_set_log(&md,CREATE_REPORT,0);
 443
 444         /* next neighbour distance for critical checking */
 445         set_nn_dist(&md,0.25*ALBE_LC_SI*sqrt(3.0));
 446
 447         /*
 448          * let's do the actual md algorithm now
 449          *
 450          * integration of newtons equations
 451          */
 452         moldyn_integrate(&md);
 453 #ifdef dEBUG
 454 return 0;
 455 #endif
 456
 457         /*
 458          * post processing the data
 459          */
 460
 461         /* close */
 462         moldyn_shutdown(&md);
 463
 464         return 0;
 465 }
 466