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         /* switch on t scaling */
 126         if(md->schedule.count==0)
 127                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
 128
 129         /* my lousy state machine ! */
 130
 131         /* switch to insert state immediately */
 132         if(hp->state==STATE_PRERUN)
 133                 hp->state=STATE_INSERT;
 134
 135         /* act according to state */
 136         switch(hp->state) {
 137                 case STATE_INSERT:
 138                         /* assigne values */
 139                         steps=INS_RELAX;
 140                         tau=INS_TAU;
 141                         /* check temperature */
 142                         dt=md->t_avg-md->t_ref;
 143                         if(dt<0)
 144                                 dt=-dt;
 145                         if(dt>INS_DELTA_TC)
 146                                 break;
 147                         /* insert atoms */
 148                         hp->insert_count+=1;
 149                         printf("   ### insert atoms (%d/%d) ###\n",
 150                                hp->insert_count*INS_ATOMS,INS_RUNS*INS_ATOMS);
 151                         insert_atoms(md);
 152                         /* change state after last insertion */
 153                         if(hp->insert_count==INS_RUNS)
 154                                 hp->state=STATE_POSTRUN;
 155                         break;
 156                 case STATE_POSTRUN:
 157                         /* assigne values */
 158                         steps=POST_RELAX;
 159                         tau=POST_TAU;
 160                         /* check temperature */
 161                         dt=md->t_avg-md->t_ref;
 162                         if(dt<0)
 163                                 dt=-dt;
 164                         if(dt>INS_DELTA_TC)
 165                                 break;
 166                         /* decrease temperature */
 167                         hp->postrun_count+=1;
 168                         printf(" ### postrun (%d/%d) ###\n",
 169                                hp->postrun_count,POST_RUNS);
 170                         set_temperature(md,md->t_ref-POST_DT);
 171                         if(hp->postrun_count==POST_RUNS)
 172                                 return 0;
 173                         break;
 174                 default:
 175                         printf("[hook] FATAL (default case!?!)\n");
 176                         break;
 177         }
 178
 179         /* reset the average counters */
 180         average_reset(md);
 181
 182         /* add schedule */
 183         moldyn_add_schedule(md,steps,tau);
 184
 185         return 0;
 186 }
 187
 188 int main(int argc,char **argv) {
 189
 190         /* main moldyn structure */
 191         t_moldyn md;
 192
 193         /* hook parameter structure */
 194         t_hp hookparam;
 195
 196         /* potential parameters */
 197         t_tersoff_mult_params tp;
 198         t_albe_mult_params ap;
 199
 200         /* testing location & velocity vector */
 201         t_3dvec r,v;
 202         memset(&r,0,sizeof(t_3dvec));
 203         memset(&v,0,sizeof(t_3dvec));
 204
 205         /* initialize moldyn */
 206         moldyn_init(&md,argc,argv);
 207
 208         /* choose integration algorithm */
 209         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 210
 211         /* choose potential */
 212 #ifdef ALBE
 213         set_potential3b_j1(&md,albe_mult_3bp_j1);
 214         set_potential3b_k1(&md,albe_mult_3bp_k1);
 215         set_potential3b_j2(&md,albe_mult_3bp_j2);
 216         set_potential3b_k2(&md,albe_mult_3bp_k2);
 217 #else
 218         set_potential1b(&md,tersoff_mult_1bp);
 219         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 220         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 221         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 222         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 223 #endif
 224
 225 #ifdef ALBE
 226         set_potential_params(&md,&ap);
 227 #else
 228         set_potential_params(&md,&tp);
 229 #endif
 230
 231         /* cutoff radius & bondlen */
 232 #ifdef ALBE
 233         set_cutoff(&md,ALBE_S_SI);
 234         set_bondlen(&md,ALBE_S_SI,ALBE_S_C,ALBE_S_SIC);
 235         //set_cutoff(&md,ALBE_S_C);
 236 #else
 237         set_cutoff(&md,TM_S_SI);
 238         set_bondlen(&md,TM_S_SI,TM_S_C,-1.0);
 239         //set_cutoff(&md,TM_S_C);
 240 #endif
 241
 242         /*
 243          * potential parameters
 244          */
 245
 246         /*
 247          * tersoff mult potential parameters for SiC
 248          */
 249         tp.S[0]=TM_S_SI;
 250         tp.R[0]=TM_R_SI;
 251         tp.A[0]=TM_A_SI;
 252         tp.B[0]=TM_B_SI;
 253         tp.lambda[0]=TM_LAMBDA_SI;
 254         tp.mu[0]=TM_MU_SI;
 255         tp.beta[0]=TM_BETA_SI;
 256         tp.n[0]=TM_N_SI;
 257         tp.c[0]=TM_C_SI;
 258         tp.d[0]=TM_D_SI;
 259         tp.h[0]=TM_H_SI;
 260
 261         tp.S[1]=TM_S_C;
 262         tp.R[1]=TM_R_C;
 263         tp.A[1]=TM_A_C;
 264         tp.B[1]=TM_B_C;
 265         tp.lambda[1]=TM_LAMBDA_C;
 266         tp.mu[1]=TM_MU_C;
 267         tp.beta[1]=TM_BETA_C;
 268         tp.n[1]=TM_N_C;
 269         tp.c[1]=TM_C_C;
 270         tp.d[1]=TM_D_C;
 271         tp.h[1]=TM_H_C;
 272
 273         tp.chi=TM_CHI_SIC;
 274
 275         tersoff_mult_complete_params(&tp);
 276
 277         /*
 278          * albe mult potential parameters for SiC
 279          */
 280         ap.S[0]=ALBE_S_SI;
 281         ap.R[0]=ALBE_R_SI;
 282         ap.A[0]=ALBE_A_SI;
 283         ap.B[0]=ALBE_B_SI;
 284         ap.r0[0]=ALBE_R0_SI;
 285         ap.lambda[0]=ALBE_LAMBDA_SI;
 286         ap.mu[0]=ALBE_MU_SI;
 287         ap.gamma[0]=ALBE_GAMMA_SI;
 288         ap.c[0]=ALBE_C_SI;
 289         ap.d[0]=ALBE_D_SI;
 290         ap.h[0]=ALBE_H_SI;
 291
 292         ap.S[1]=ALBE_S_C;
 293         ap.R[1]=ALBE_R_C;
 294         ap.A[1]=ALBE_A_C;
 295         ap.B[1]=ALBE_B_C;
 296         ap.r0[1]=ALBE_R0_C;
 297         ap.lambda[1]=ALBE_LAMBDA_C;
 298         ap.mu[1]=ALBE_MU_C;
 299         ap.gamma[1]=ALBE_GAMMA_C;
 300         ap.c[1]=ALBE_C_C;
 301         ap.d[1]=ALBE_D_C;
 302         ap.h[1]=ALBE_H_C;
 303
 304         ap.Smixed=ALBE_S_SIC;
 305         ap.Rmixed=ALBE_R_SIC;
 306         ap.Amixed=ALBE_A_SIC;
 307         ap.Bmixed=ALBE_B_SIC;
 308         ap.r0_mixed=ALBE_R0_SIC;
 309         ap.lambda_m=ALBE_LAMBDA_SIC;
 310         ap.mu_m=ALBE_MU_SIC;
 311         ap.gamma_m=ALBE_GAMMA_SIC;
 312         ap.c_mixed=ALBE_C_SIC;
 313         ap.d_mixed=ALBE_D_SIC;
 314         ap.h_mixed=ALBE_H_SIC;
 315
 316         albe_mult_complete_params(&ap);
 317
 318         /* set (initial) dimensions of simulation volume */
 319 #ifdef ALBE
 320         set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
 321         //set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
 322         //set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
 323 #else
 324         set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE);
 325         //set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
 326         //set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
 327 #endif
 328
 329         /* set periodic boundary conditions in all directions */
 330         set_pbc(&md,TRUE,TRUE,TRUE);
 331
 332         /* create the lattice / place atoms */
 333         //
 334 #ifdef ALBE
 335         create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
 336         //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 337 #else
 338         create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 339 #endif
 340                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 341         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 342                        0,LCNTX,LCNTY,LCNTZ,NULL);
 343         //               1,LCNTX,LCNTY,LCNTZ,NULL);
 344
 345         /* create zinkblende structure */
 346         /*
 347 #ifdef ALBE
 348         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 349         create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
 350                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 351                        0,LCNTX,LCNTY,LCNTZ,&r);
 352         r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 353         create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
 354                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 355                        1,LCNTX,LCNTY,LCNTZ,&r);
 356 #else
 357         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 358         create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
 359                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 360                        0,LCNTX,LCNTY,LCNTZ,&r);
 361         r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 362         create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
 363                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 364                        1,LCNTX,LCNTY,LCNTZ,&r);
 365 #endif
 366         */
 367
 368         /* check for right atom placing */
 369         moldyn_bc_check(&md);
 370
 371         /* testing configuration */
 372         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 373         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 374         //r.y=0;                v.y=0;
 375         //r.z=0;                v.z=0;
 376         //add_atom(&md,SI,M_SI,0,
 377         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 378         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 379         //           &r,&v);
 380         //r.x=-r.x;     v.x=-v.x;
 381         //r.y=0;                v.y=0;
 382         //r.z=0;                v.z=0;
 383         //add_atom(&md,SI,M_SI,0,
 384         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 385         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 386         //           &r,&v);
 387         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 388         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 389         //r.y=0;                v.y=0;
 390         //r.x=0;                v.x=0;
 391         //add_atom(&md,SI,M_SI,0,
 392         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 393         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 394         //           &r,&v);
 395         //r.z=-r.z;     v.z=-v.z;
 396         //r.y=0;                v.y=0;
 397         //r.x=0;                v.x=0;
 398         //add_atom(&md,SI,M_SI,0,
 399         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 400         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 401         //           &r,&v);
 402
 403         /* set temperature & pressure */
 404         set_temperature(&md,atof(argv[2])+273.0);
 405         set_pressure(&md,BAR);
 406
 407         /* set amount of steps to skip before average calc */
 408         set_avg_skip(&md,AVG_SKIP);
 409
 410         /* set p/t scaling */
 411         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
 412         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 413         //                 T_SCALE_BERENDSEN,100.0);
 414         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 415         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 416
 417         /* initial thermal fluctuations of particles (in equilibrium) */
 418         thermal_init(&md,TRUE);
 419
 420         /* create the simulation schedule */
 421         moldyn_add_schedule(&md,PRERUN,PRE_TAU);
 422
 423         /* schedule hook function */
 424         memset(&hookparam,0,sizeof(t_hp));
 425         hookparam.argc=argc;
 426         hookparam.argv=argv;
 427         moldyn_set_schedule_hook(&md,&sic_hook,&hookparam);
 428         //moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam);
 429         //moldyn_add_schedule(&md,POSTRUN,1.0);
 430
 431         /* activate logging */
 432         moldyn_set_log_dir(&md,argv[1]);
 433         moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
 434         moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
 435         moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
 436         moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
 437         moldyn_set_log(&md,VISUAL_STEP,LOG_V);
 438         moldyn_set_log(&md,SAVE_STEP,LOG_S);
 439         moldyn_set_log(&md,CREATE_REPORT,0);
 440
 441         /*
 442          * let's do the actual md algorithm now
 443          *
 444          * integration of newtons equations
 445          */
 446         moldyn_integrate(&md);
 447 #ifdef dEBUG
 448 return 0;
 449 #endif
 450
 451         /*
 452          * post processing the data
 453          */
 454
 455         /* close */
 456         moldyn_shutdown(&md);
 457
 458         return 0;
 459 }
 460