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 #ifdef INS_TETRA
  55                         // tetrahedral
  56                         r.x=0.0;
  57                         r.y=0.0;
  58                         r.z=0.0;
  59 #endif
  60 #ifdef INS_HEXA
  61                         // hexagonal
  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 #endif
  66 #ifdef INS_110DB
  67                         // 110 dumbbell
  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                         moldyn->atom[4372].r.x=(-0.5+0.125+0.125)*ALBE_LC_SI;
  72                         moldyn->atom[4372].r.y=(-0.5+0.125+0.125)*ALBE_LC_SI;
  73 #endif
  74 #ifdef INS_001DB
  75                         // 001 dumbbell
  76                         r.x=(-0.5+0.25)*ALBE_LC_SI;
  77                         r.y=(-0.5+0.25)*ALBE_LC_SI;
  78                         r.z=(-0.1)*ALBE_LC_SI;
  79                         moldyn->atom[4372].r.z=(-0.4)*ALBE_LC_SI;
  80 #endif
  81 #ifdef INS_USER
  82                         // 001 dumbbell
  83                         r.x=INS_UX*ALBE_LC_SI;
  84                         r.y=INS_UY*ALBE_LC_SI;
  85                         r.z=INS_UZ*ALBE_LC_SI;
  86 #endif
  87 #ifdef INS_RAND
  88                         // random
  89 #ifdef INS_DYNAMIC_LEN
  90                         r.x=(rand_get_double(&(moldyn->random))-0.5)*\
  91                             moldyn->dim.x;
  92                         r.y=(rand_get_double(&(moldyn->random))-0.5)*\
  93                             moldyn->dim.y;
  94                         r.z=(rand_get_double(&(moldyn->random))-0.5)*\
  95                             moldyn->dim.z;
  96 #else
  97                         r.x=(rand_get_double(&(moldyn->random))-0.5)*INS_LENX;
  98                         r.y=(rand_get_double(&(moldyn->random))-0.5)*INS_LENY;
  99                         r.z=(rand_get_double(&(moldyn->random))-0.5)*INS_LENZ;
 100 #endif
 101 #endif
 102                         // offset
 103                         r.x+=INS_OFFSET;
 104                         r.y+=INS_OFFSET;
 105                         r.z+=INS_OFFSET;
 106                         /* assume valid coordinates */
 107                         run=0;
 108                         dmin=10000000000.0;             // for sure too high!
 109                         for(i=0;i<moldyn->count;i++) {
 110                                 atom=&(moldyn->atom[i]);
 111                                 v3_sub(&dist,&(atom->r),&r);
 112                                 check_per_bound(moldyn,&dist);
 113                                 d=v3_absolute_square(&dist);
 114                                 /* reject coordinates */
 115                                 if(d<INS_R_C) {
 116                                         //printf("atom %d - %f\n",i,d);
 117                                         run=1;
 118                                         break;
 119                                 }
 120                                 if(d<dmin)
 121                                         dmin=d;
 122                         }
 123                 }
 124                 add_atom(moldyn,INS_TYPE,INS_MASS,INS_BRAND,
 125                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|\
 126                          INS_ATTR,
 127                          &r,&v);
 128                 printf(" %02d: atom %d | %f %f %f | %f\n",
 129                        j,moldyn->count-1,r.x,r.y,r.z,dmin);
 130         }
 131
 132         return 0;
 133 }
 134
 135 int sic_hook(void *moldyn,void *hook_params) {
 136
 137         t_hp *hp;
 138         t_moldyn *md;
 139         int steps;
 140         double tau;
 141         double dt;
 142         double dp;
 143
 144         hp=hook_params;
 145         md=moldyn;
 146
 147         tau=1.0;
 148         steps=0;
 149
 150         /* switch on t scaling */
 151         if(md->schedule.count==0)
 152                 set_pt_scale(md,P_SCALE_BERENDSEN,P_SCALE_TAU,
 153                                 T_SCALE_BERENDSEN,T_SCALE_TAU);
 154
 155         /* my lousy state machine ! */
 156
 157         /* switch to insert state immediately */
 158         if(hp->state==STATE_PRERUN)
 159                 hp->state=STATE_INSERT;
 160
 161         switch(hp->state) {
 162                 case STATE_INSERT:
 163                         goto insert;
 164                         break;
 165                 case STATE_POSTRUN:
 166                         goto postrun;
 167                         break;
 168                 default:
 169                         printf("[sic hook] unknown state\n");
 170                         return -1;
 171         }
 172
 173         /* act according to state */
 174
 175 insert:
 176
 177         /* assigne values */
 178         steps=INS_RELAX;
 179         tau=INS_TAU;
 180
 181         /* check temperature */
 182         dt=md->t_avg-md->t_ref;
 183         dp=md->p_avg-md->p_ref;
 184         if(dt<0)
 185                 dt=-dt;
 186         if(dp<0)
 187                 dp=-dp;
 188         if((dt>INS_DELTA_TC)|(dp>INS_DELTA_PC))
 189                 goto addsched;
 190
 191         /* immediately go on if no job is to be done */
 192         if(hp->insert_count==INS_RUNS) {
 193                 printf("    --- leaving insert state ---\n");
 194                 hp->state=STATE_POSTRUN;
 195                 goto postrun;
 196         }
 197
 198         /* else -> insert atoms */
 199         hp->insert_count+=1;
 200         printf("   ### insert atoms (%d/%d) ###\n",
 201                hp->insert_count*INS_ATOMS,INS_RUNS*INS_ATOMS);
 202         insert_atoms(md);
 203         goto addsched;
 204
 205 postrun:
 206
 207         /* assigne values */
 208         steps=POST_RELAX;
 209         tau=POST_TAU;
 210
 211         /* check temperature */
 212         dt=md->t_avg-md->t_ref;
 213         dp=md->p_avg-md->p_ref;
 214         if(dt<0)
 215                 dt=-dt;
 216         if(dp<0)
 217                 dp=-dp;
 218         if((dt>POST_DELTA_TC)|(dp>POST_DELTA_PC))
 219                 goto addsched;
 220
 221         /* immediately return if no job is to be done */
 222         if(hp->postrun_count==POST_RUNS) {
 223                 printf("    --- leaving post run state ---\n");
 224                 return 0;
 225         }
 226
 227         /* postrun action */
 228         hp->postrun_count+=1;
 229         printf(" ### postrun (%d/%d) ###\n",
 230                hp->postrun_count,POST_RUNS);
 231         set_temperature(md,md->t_ref-POST_DT);
 232
 233 addsched:
 234
 235         /* reset the average counters */
 236         average_reset(md);
 237
 238         /* add schedule */
 239         moldyn_add_schedule(md,steps,tau);
 240
 241         return 0;
 242 }
 243
 244 int main(int argc,char **argv) {
 245
 246         /* main moldyn structure */
 247         t_moldyn md;
 248
 249         /* hook parameter structure */
 250         t_hp hookparam;
 251
 252         /* potential parameters */
 253         t_tersoff_mult_params tp;
 254         t_albe_mult_params ap;
 255
 256         /* testing location & velocity vector */
 257         t_3dvec r,v;
 258         memset(&r,0,sizeof(t_3dvec));
 259         memset(&v,0,sizeof(t_3dvec));
 260
 261         /* initialize moldyn */
 262         moldyn_init(&md,argc,argv);
 263
 264         /* choose integration algorithm */
 265         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 266
 267         /* choose potential */
 268 #ifdef ALBE
 269         set_potential3b_j1(&md,albe_mult_3bp_j1);
 270         set_potential3b_k1(&md,albe_mult_3bp_k1);
 271         set_potential3b_j2(&md,albe_mult_3bp_j2);
 272         set_potential3b_k2(&md,albe_mult_3bp_k2);
 273 #else
 274         set_potential1b(&md,tersoff_mult_1bp);
 275         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 276         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 277         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 278         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 279 #endif
 280
 281 #ifdef ALBE
 282         set_potential_params(&md,&ap);
 283 #else
 284         set_potential_params(&md,&tp);
 285 #endif
 286
 287         /* cutoff radius & bondlen */
 288 #ifdef ALBE
 289         set_cutoff(&md,ALBE_S_SI);
 290         set_bondlen(&md,ALBE_S_SI,ALBE_S_C,ALBE_S_SIC);
 291         //set_cutoff(&md,ALBE_S_C);
 292 #else
 293         set_cutoff(&md,TM_S_SI);
 294         set_bondlen(&md,TM_S_SI,TM_S_C,-1.0);
 295         //set_cutoff(&md,TM_S_C);
 296 #endif
 297
 298         /*
 299          * potential parameters
 300          */
 301
 302         /*
 303          * tersoff mult potential parameters for SiC
 304          */
 305         tp.S[0]=TM_S_SI;
 306         tp.R[0]=TM_R_SI;
 307         tp.A[0]=TM_A_SI;
 308         tp.B[0]=TM_B_SI;
 309         tp.lambda[0]=TM_LAMBDA_SI;
 310         tp.mu[0]=TM_MU_SI;
 311         tp.beta[0]=TM_BETA_SI;
 312         tp.n[0]=TM_N_SI;
 313         tp.c[0]=TM_C_SI;
 314         tp.d[0]=TM_D_SI;
 315         tp.h[0]=TM_H_SI;
 316
 317         tp.S[1]=TM_S_C;
 318         tp.R[1]=TM_R_C;
 319         tp.A[1]=TM_A_C;
 320         tp.B[1]=TM_B_C;
 321         tp.lambda[1]=TM_LAMBDA_C;
 322         tp.mu[1]=TM_MU_C;
 323         tp.beta[1]=TM_BETA_C;
 324         tp.n[1]=TM_N_C;
 325         tp.c[1]=TM_C_C;
 326         tp.d[1]=TM_D_C;
 327         tp.h[1]=TM_H_C;
 328
 329         tp.chi=TM_CHI_SIC;
 330
 331         tersoff_mult_complete_params(&tp);
 332
 333         /*
 334          * albe mult potential parameters for SiC
 335          */
 336         ap.S[0]=ALBE_S_SI;
 337         ap.R[0]=ALBE_R_SI;
 338         ap.A[0]=ALBE_A_SI;
 339         ap.B[0]=ALBE_B_SI;
 340         ap.r0[0]=ALBE_R0_SI;
 341         ap.lambda[0]=ALBE_LAMBDA_SI;
 342         ap.mu[0]=ALBE_MU_SI;
 343         ap.gamma[0]=ALBE_GAMMA_SI;
 344         ap.c[0]=ALBE_C_SI;
 345         ap.d[0]=ALBE_D_SI;
 346         ap.h[0]=ALBE_H_SI;
 347
 348         ap.S[1]=ALBE_S_C;
 349         ap.R[1]=ALBE_R_C;
 350         ap.A[1]=ALBE_A_C;
 351         ap.B[1]=ALBE_B_C;
 352         ap.r0[1]=ALBE_R0_C;
 353         ap.lambda[1]=ALBE_LAMBDA_C;
 354         ap.mu[1]=ALBE_MU_C;
 355         ap.gamma[1]=ALBE_GAMMA_C;
 356         ap.c[1]=ALBE_C_C;
 357         ap.d[1]=ALBE_D_C;
 358         ap.h[1]=ALBE_H_C;
 359
 360         ap.Smixed=ALBE_S_SIC;
 361         ap.Rmixed=ALBE_R_SIC;
 362         ap.Amixed=ALBE_A_SIC;
 363         ap.Bmixed=ALBE_B_SIC;
 364         ap.r0_mixed=ALBE_R0_SIC;
 365         ap.lambda_m=ALBE_LAMBDA_SIC;
 366         ap.mu_m=ALBE_MU_SIC;
 367         ap.gamma_m=ALBE_GAMMA_SIC;
 368         ap.c_mixed=ALBE_C_SIC;
 369         ap.d_mixed=ALBE_D_SIC;
 370         ap.h_mixed=ALBE_H_SIC;
 371
 372         albe_mult_complete_params(&ap);
 373
 374         /* set (initial) dimensions of simulation volume */
 375 #ifdef ALBE
 376  #ifdef INIT_SI
 377         set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
 378  #endif
 379  #ifdef INIT_C
 380         set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
 381  #endif
 382  #ifdef INIT_3CSIC
 383         set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
 384  #endif
 385 #else
 386  #ifdef INIT_SI
 387         set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE);
 388  #endif
 389  #ifdef INIT_C
 390         set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
 391  #endif
 392  #ifdef INIT_3CSIC
 393         set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
 394  #endif
 395 #endif
 396
 397         /* set periodic boundary conditions in all directions */
 398         set_pbc(&md,TRUE,TRUE,TRUE);
 399
 400         /* create the lattice / place atoms */
 401
 402         // diamond
 403 #ifdef ALBE
 404  #ifdef INIT_SI
 405         create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
 406                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 407                        0,LCNTX,LCNTY,LCNTZ,NULL);
 408  #endif
 409  #ifdef INIT_C
 410         create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 411                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 412                        1,LCNTX,LCNTY,LCNTZ,NULL);
 413  #endif
 414 #else
 415  #ifdef INIT_SI
 416         create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 417                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 418                        0,LCNTX,LCNTY,LCNTZ,NULL);
 419  #endif
 420  #ifdef INIT_C
 421         create_lattice(&md,DIAMOND,LC_C,SI,M_SI,
 422                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 423                        1,LCNTX,LCNTY,LCNTZ,NULL);
 424  #endif
 425 #endif
 426
 427         // zinkblende
 428 #ifdef INIT_3CSIC
 429  #ifdef ALBE
 430         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 431         create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
 432                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 433                        0,LCNTX,LCNTY,LCNTZ,&r);
 434         r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 435         create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
 436                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB|ATOM_ATTR_VB,
 437                        1,LCNTX,LCNTY,LCNTZ,&r);
 438  #else
 439         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 440         create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
 441                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 442                        0,LCNTX,LCNTY,LCNTZ,&r);
 443         r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 444         create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
 445                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 446                        1,LCNTX,LCNTY,LCNTZ,&r);
 447  #endif
 448 #endif
 449
 450         /* check for right atom placing */
 451         moldyn_bc_check(&md);
 452
 453         /* testing configuration */
 454         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 455         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 456         //r.y=0;                v.y=0;
 457         //r.z=0;                v.z=0;
 458         //add_atom(&md,SI,M_SI,0,
 459         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 460         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 461         //           &r,&v);
 462         //r.x=-r.x;     v.x=-v.x;
 463         //r.y=0;                v.y=0;
 464         //r.z=0;                v.z=0;
 465         //add_atom(&md,SI,M_SI,0,
 466         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 467         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 468         //           &r,&v);
 469         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 470         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 471         //r.y=0;                v.y=0;
 472         //r.x=0;                v.x=0;
 473         //add_atom(&md,SI,M_SI,0,
 474         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 475         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 476         //           &r,&v);
 477         //r.z=-r.z;     v.z=-v.z;
 478         //r.y=0;                v.y=0;
 479         //r.x=0;                v.x=0;
 480         //add_atom(&md,SI,M_SI,0,
 481         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 482         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 483         //           &r,&v);
 484
 485         /* set temperature & pressure */
 486         set_temperature(&md,atof(argv[2])+273.0);
 487         set_pressure(&md,0.0);
 488
 489         /* set amount of steps to skip before average calc */
 490         set_avg_skip(&md,AVG_SKIP);
 491
 492         /* set p/t scaling */
 493         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
 494         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.01/(100*GPA),
 495         //                 T_SCALE_BERENDSEN,100.0);
 496         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 497         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 498
 499         /* initial thermal fluctuations of particles (in equilibrium) */
 500         thermal_init(&md,TRUE);
 501
 502         /* create the simulation schedule */
 503         moldyn_add_schedule(&md,PRERUN,PRE_TAU);
 504
 505         /* schedule hook function */
 506         memset(&hookparam,0,sizeof(t_hp));
 507         hookparam.argc=argc;
 508         hookparam.argv=argv;
 509         moldyn_set_schedule_hook(&md,&sic_hook,&hookparam);
 510         //moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam);
 511         //moldyn_add_schedule(&md,POSTRUN,1.0);
 512
 513         /* activate logging */
 514         moldyn_set_log_dir(&md,argv[1]);
 515         moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
 516         moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
 517         moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
 518         moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
 519         moldyn_set_log(&md,LOG_VOLUME,LOG_V);
 520         moldyn_set_log(&md,VISUAL_STEP,LOG_A);
 521         moldyn_set_log(&md,SAVE_STEP,LOG_S);
 522         moldyn_set_log(&md,CREATE_REPORT,0);
 523
 524         /* next neighbour distance for critical checking */
 525         set_nn_dist(&md,0.25*ALBE_LC_SI*sqrt(3.0));
 526
 527         /*
 528          * let's do the actual md algorithm now
 529          *
 530          * integration of newtons equations
 531          */
 532         moldyn_integrate(&md);
 533 #ifdef dEBUG
 534 return 0;
 535 #endif
 536
 537         /*
 538          * post processing the data
 539          */
 540
 541         /* close */
 542         moldyn_shutdown(&md);
 543
 544         return 0;
 545 }
 546