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
  17 #ifdef TERSOFF_ORIG
  18 #include "potentials/tersoff_orig.h"
  19 #else
  20 #include "potentials/tersoff.h"
  21 #endif
  22
  23 //#define INJECT                800
  24 #define INJECT          1
  25 #define NR_ATOMS        1
  26 #define R_C             1.5
  27 #define T_C             5.0
  28 //#define INJ_LENX      (1*ALBE_LC_SIC)
  29 //#define INJ_LENY      (1*ALBE_LC_SIC)
  30 //#define INJ_LENZ      (1*ALBE_LC_SIC)
  31 #define INJ_LENX        (1*ALBE_LC_SI)
  32 #define INJ_LENY        (1*ALBE_LC_SI)
  33 #define INJ_LENZ        (1*ALBE_LC_SI)
  34 #define INJ_TYPE_SILICON
  35 //#define INJ_TYPE_CARBON
  36 #define INJ_OFFSET      (ALBE_LC_SI/8.0)
  37 #define RELAX_S         20
  38
  39 #define LCNTX           9
  40 #define LCNTY           9
  41 #define LCNTZ           9
  42 #define PRERUN          40
  43 #define POSTRUN         3000
  44
  45 #define R_TITLE         "Silicon self-interstitial"
  46 #define LOG_E           10
  47 #define LOG_T           10
  48 #define LOG_P           10
  49 #define LOG_S           100
  50 #define LOG_V           20
  51
  52 typedef struct s_hp {
  53         int a_count;    /* atom count */
  54         u8 quit;        /* quit mark */
  55         int argc;       /* arg count */
  56         char **argv;    /* args */
  57 } t_hp;
  58
  59 int hook_del_atom(void *moldyn,void *hook_params) {
  60
  61         t_moldyn *md;
  62         t_hp *hp;
  63
  64         md=moldyn;
  65         hp=hook_params;
  66
  67         set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  68         del_atom(md,2);
  69
  70         return 0;
  71 }
  72
  73 int hook_add_atom(void *moldyn,void *hook_params) {
  74
  75         t_moldyn *md;
  76         t_3dvec r,v,dist;
  77         double d;
  78         unsigned char run;
  79         int i,j;
  80         t_atom *atom;
  81         t_hp *hp;
  82
  83         md=moldyn;
  84         hp=hook_params;
  85
  86         /* quit */
  87         if(hp->quit)
  88                 return 0;
  89
  90         /* switch on t scaling */
  91         if(md->schedule.count==0)
  92                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  93
  94         /* last schedule add if there is enough carbon inside */
  95         if(hp->a_count==(INJECT*NR_ATOMS)) {
  96                 hp->quit=1;
  97                 moldyn_add_schedule(md,POSTRUN,1.0);
  98                 return 0;
  99         }
 100
 101         /* more relaxing time for too high temperatures */
 102         if(md->t-md->t_ref>T_C) {
 103                 moldyn_add_schedule(md,RELAX_S,1.0);
 104                 return 0;
 105         }
 106
 107         /* inject carbon atoms */
 108         printf("injecting another %d atoms ... (-> %d / %d)\n",
 109                NR_ATOMS,hp->a_count+NR_ATOMS,INJECT*NR_ATOMS);
 110         for(j=0;j<NR_ATOMS;j++) {
 111                 run=1;
 112                 while(run) {
 113                         // tetrahedral
 114                         /*
 115                         r.x=0.0;
 116                         r.y=0.0;
 117                         r.z=0.0;
 118                         */
 119                         // hexagonal
 120                         //
 121                         r.x=-1.0/8.0*ALBE_LC_SI;
 122                         r.y=-1.0/8.0*ALBE_LC_SI;
 123                         r.z=1.0/8.0*ALBE_LC_SI;
 124                         //
 125                         // 110 dumbbell
 126                         /*
 127                         r.x=(-0.5+0.25+0.125)*ALBE_LC_SI;
 128                         r.y=(-0.5+0.25+0.125)*ALBE_LC_SI;
 129                         r.z=(-0.5+0.25)*ALBE_LC_SI;
 130                         md->atom[4372].r.x=(-0.5+0.125+0.125)*ALBE_LC_SI;
 131                         md->atom[4372].r.y=(-0.5+0.125+0.125)*ALBE_LC_SI;
 132                         */
 133                         // random
 134                         /*
 135                         r.x=(rand_get_double(&(md->random))-0.5)*INJ_LENX;
 136                         r.y=(rand_get_double(&(md->random))-0.5)*INJ_LENY;
 137                         r.z=(rand_get_double(&(md->random))-0.5)*INJ_LENZ;
 138                         */
 139                         // offset
 140                         r.x+=INJ_OFFSET;
 141                         r.y+=INJ_OFFSET;
 142                         r.z+=INJ_OFFSET;
 143                         /* assume valid coordinates */
 144                         run=0;
 145                         for(i=0;i<md->count;i++) {
 146                                 atom=&(md->atom[i]);
 147                                 v3_sub(&dist,&(atom->r),&r);
 148                                 d=v3_absolute_square(&dist);
 149                                 /* reject coordinates */
 150                                 if(d<R_C) {
 151                                         //printf("atom %d - %f\n",i,d);
 152                                         run=1;
 153                                         break;
 154                                 }
 155                         }
 156                 }
 157                 v.x=0; v.y=0; v.z=0;
 158 #ifdef INJ_TYPE_CARBON
 159                 add_atom(md,C,M_C,1,
 160 #else
 161                 add_atom(md,SI,M_SI,0,
 162 #endif
 163                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB|ATOM_ATTR_VB,
 164                          &r,&v);
 165         }
 166         hp->a_count+=NR_ATOMS;
 167
 168         /* add schedule for simulating injected atoms ;) */
 169         moldyn_add_schedule(md,RELAX_S,1.0);
 170
 171         return 0;
 172 }
 173
 174 int main(int argc,char **argv) {
 175
 176         /* check argv */
 177         //if(argc!=3) {
 178         //      printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
 179         //      return -1;
 180         //}
 181
 182         /* main moldyn structure */
 183         t_moldyn md;
 184
 185         /* hook parameter structure */
 186         t_hp hookparam;
 187
 188         /* potential parameters */
 189         t_tersoff_mult_params tp;
 190         t_albe_mult_params ap;
 191
 192         /* testing location & velocity vector */
 193         t_3dvec r,v;
 194         memset(&r,0,sizeof(t_3dvec));
 195         memset(&v,0,sizeof(t_3dvec));
 196
 197         /* initialize moldyn */
 198         moldyn_init(&md,argc,argv);
 199
 200         /* choose integration algorithm */
 201         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 202
 203         /* choose potential */
 204 #ifdef ALBE
 205         set_potential3b_j1(&md,albe_mult_3bp_j1);
 206         set_potential3b_k1(&md,albe_mult_3bp_k1);
 207         set_potential3b_j2(&md,albe_mult_3bp_j2);
 208         set_potential3b_k2(&md,albe_mult_3bp_k2);
 209 #else
 210         set_potential1b(&md,tersoff_mult_1bp);
 211         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 212         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 213         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 214         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 215 #endif
 216
 217 #ifdef ALBE
 218         set_potential_params(&md,&ap);
 219 #else
 220         set_potential_params(&md,&tp);
 221 #endif
 222
 223         /* cutoff radius & bondlen */
 224 #ifdef ALBE
 225         set_cutoff(&md,ALBE_S_SI);
 226         set_bondlen(&md,ALBE_S_SI,ALBE_S_C,ALBE_S_SIC);
 227         //set_cutoff(&md,ALBE_S_C);
 228 #else
 229         set_cutoff(&md,TM_S_SI);
 230         set_bondlen(&md,TM_S_SI,TM_S_C,-1.0);
 231         //set_cutoff(&md,TM_S_C);
 232 #endif
 233
 234         /*
 235          * potential parameters
 236          */
 237
 238         /*
 239          * tersoff mult potential parameters for SiC
 240          */
 241         tp.S[0]=TM_S_SI;
 242         tp.R[0]=TM_R_SI;
 243         tp.A[0]=TM_A_SI;
 244         tp.B[0]=TM_B_SI;
 245         tp.lambda[0]=TM_LAMBDA_SI;
 246         tp.mu[0]=TM_MU_SI;
 247         tp.beta[0]=TM_BETA_SI;
 248         tp.n[0]=TM_N_SI;
 249         tp.c[0]=TM_C_SI;
 250         tp.d[0]=TM_D_SI;
 251         tp.h[0]=TM_H_SI;
 252
 253         tp.S[1]=TM_S_C;
 254         tp.R[1]=TM_R_C;
 255         tp.A[1]=TM_A_C;
 256         tp.B[1]=TM_B_C;
 257         tp.lambda[1]=TM_LAMBDA_C;
 258         tp.mu[1]=TM_MU_C;
 259         tp.beta[1]=TM_BETA_C;
 260         tp.n[1]=TM_N_C;
 261         tp.c[1]=TM_C_C;
 262         tp.d[1]=TM_D_C;
 263         tp.h[1]=TM_H_C;
 264
 265         tp.chi=TM_CHI_SIC;
 266
 267         tersoff_mult_complete_params(&tp);
 268
 269         /*
 270          * albe mult potential parameters for SiC
 271          */
 272         ap.S[0]=ALBE_S_SI;
 273         ap.R[0]=ALBE_R_SI;
 274         ap.A[0]=ALBE_A_SI;
 275         ap.B[0]=ALBE_B_SI;
 276         ap.r0[0]=ALBE_R0_SI;
 277         ap.lambda[0]=ALBE_LAMBDA_SI;
 278         ap.mu[0]=ALBE_MU_SI;
 279         ap.gamma[0]=ALBE_GAMMA_SI;
 280         ap.c[0]=ALBE_C_SI;
 281         ap.d[0]=ALBE_D_SI;
 282         ap.h[0]=ALBE_H_SI;
 283
 284         ap.S[1]=ALBE_S_C;
 285         ap.R[1]=ALBE_R_C;
 286         ap.A[1]=ALBE_A_C;
 287         ap.B[1]=ALBE_B_C;
 288         ap.r0[1]=ALBE_R0_C;
 289         ap.lambda[1]=ALBE_LAMBDA_C;
 290         ap.mu[1]=ALBE_MU_C;
 291         ap.gamma[1]=ALBE_GAMMA_C;
 292         ap.c[1]=ALBE_C_C;
 293         ap.d[1]=ALBE_D_C;
 294         ap.h[1]=ALBE_H_C;
 295
 296         ap.Smixed=ALBE_S_SIC;
 297         ap.Rmixed=ALBE_R_SIC;
 298         ap.Amixed=ALBE_A_SIC;
 299         ap.Bmixed=ALBE_B_SIC;
 300         ap.r0_mixed=ALBE_R0_SIC;
 301         ap.lambda_m=ALBE_LAMBDA_SIC;
 302         ap.mu_m=ALBE_MU_SIC;
 303         ap.gamma_m=ALBE_GAMMA_SIC;
 304         ap.c_mixed=ALBE_C_SIC;
 305         ap.d_mixed=ALBE_D_SIC;
 306         ap.h_mixed=ALBE_H_SIC;
 307
 308         albe_mult_complete_params(&ap);
 309
 310         /* set (initial) dimensions of simulation volume */
 311 #ifdef ALBE
 312         set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
 313         //set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
 314         //set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
 315 #else
 316         set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE);
 317         //set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
 318         //set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
 319 #endif
 320
 321         /* set periodic boundary conditions in all directions */
 322         set_pbc(&md,TRUE,TRUE,TRUE);
 323
 324         /* create the lattice / place atoms */
 325         //
 326 #ifdef ALBE
 327         create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
 328         //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 329 #else
 330         create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 331 #endif
 332                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 333         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 334                        0,LCNTX,LCNTY,LCNTZ,NULL);
 335         //               1,LCNTX,LCNTY,LCNTZ,NULL);
 336         //
 337
 338         /* create zinkblende structure */
 339         /*
 340 #ifdef ALBE
 341         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 342         create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
 343                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 344                        0,LCNTX,LCNTY,LCNTZ,&r);
 345         r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 346         create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
 347                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 348                        1,LCNTX,LCNTY,LCNTZ,&r);
 349 #else
 350         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 351         create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
 352                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 353                        0,LCNTX,LCNTY,LCNTZ,&r);
 354         r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 355         create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
 356                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 357                        1,LCNTX,LCNTY,LCNTZ,&r);
 358 #endif
 359         */
 360
 361         /* check for right atom placing */
 362         moldyn_bc_check(&md);
 363
 364         /* testing configuration */
 365         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 366         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 367         //r.y=0;                v.y=0;
 368         //r.z=0;                v.z=0;
 369         //add_atom(&md,SI,M_SI,0,
 370         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 371         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 372         //           &r,&v);
 373         //r.x=-r.x;     v.x=-v.x;
 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.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 381         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 382         //r.y=0;                v.y=0;
 383         //r.x=0;                v.x=0;
 384         //add_atom(&md,SI,M_SI,0,
 385         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 386         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 387         //           &r,&v);
 388         //r.z=-r.z;     v.z=-v.z;
 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
 396         /* set temperature & pressure */
 397         set_temperature(&md,atof(argv[2])+273.0);
 398         set_pressure(&md,BAR);
 399
 400         /* set amount of steps to skip before average calc */
 401         set_avg_skip(&md,(8.0/10.0*PRERUN));
 402
 403         /* set p/t scaling */
 404         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
 405         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 406         //                 T_SCALE_BERENDSEN,100.0);
 407         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 408         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 409
 410         /* initial thermal fluctuations of particles (in equilibrium) */
 411         thermal_init(&md,TRUE);
 412
 413         /* create the simulation schedule */
 414         moldyn_add_schedule(&md,PRERUN,1.0);
 415
 416         /* schedule hook function */
 417         memset(&hookparam,0,sizeof(t_hp));
 418         hookparam.argc=argc;
 419         hookparam.argv=argv;
 420         moldyn_set_schedule_hook(&md,&hook_add_atom,&hookparam);
 421         //moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam);
 422         //moldyn_add_schedule(&md,POSTRUN,1.0);
 423
 424         /* activate logging */
 425         moldyn_set_log_dir(&md,argv[1]);
 426         moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
 427         moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
 428         moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
 429         moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
 430         moldyn_set_log(&md,VISUAL_STEP,LOG_V);
 431         moldyn_set_log(&md,SAVE_STEP,LOG_S);
 432         moldyn_set_log(&md,CREATE_REPORT,0);
 433
 434         /*
 435          * let's do the actual md algorithm now
 436          *
 437          * integration of newtons equations
 438          */
 439         moldyn_integrate(&md);
 440 #ifdef dEBUG
 441 return 0;
 442 #endif
 443
 444         /*
 445          * post processing the data
 446          */
 447
 448         /* close */
 449         moldyn_shutdown(&md);
 450
 451         return 0;
 452 }
 453