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          10
  43 #define POSTRUN         4000
  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                         r.x=1.0/8.0*ALBE_LC_SI;
 114                         r.y=-1.0/8.0*ALBE_LC_SI;
 115                         r.z=-1.0/8.0*ALBE_LC_SI;
 116                         //r.x=(rand_get_double(&(md->random))-0.5)*INJ_LENX;
 117                         r.x+=INJ_OFFSET;
 118                         //r.y=(rand_get_double(&(md->random))-0.5)*INJ_LENY;
 119                         r.y+=INJ_OFFSET;
 120                         //r.z=(rand_get_double(&(md->random))-0.5)*INJ_LENZ;
 121                         r.z+=INJ_OFFSET;
 122                         /* assume valid coordinates */
 123                         run=0;
 124                         for(i=0;i<md->count;i++) {
 125                                 atom=&(md->atom[i]);
 126                                 v3_sub(&dist,&(atom->r),&r);
 127                                 d=v3_absolute_square(&dist);
 128                                 /* reject coordinates */
 129                                 if(d<R_C) {
 130                                         run=1;
 131                                         break;
 132                                 }
 133                         }
 134                 }
 135                 v.x=0; v.y=0; v.z=0;
 136 #ifdef INJ_TYPE_CARBON
 137                 add_atom(md,C,M_C,1,
 138 #else
 139                 add_atom(md,SI,M_SI,0,
 140 #endif
 141                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB|ATOM_ATTR_VB,
 142                          &r,&v);
 143         }
 144         hp->a_count+=NR_ATOMS;
 145
 146         /* add schedule for simulating injected atoms ;) */
 147         moldyn_add_schedule(md,RELAX_S,1.0);
 148
 149         return 0;
 150 }
 151
 152 int main(int argc,char **argv) {
 153
 154         /* check argv */
 155         //if(argc!=3) {
 156         //      printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
 157         //      return -1;
 158         //}
 159
 160         /* main moldyn structure */
 161         t_moldyn md;
 162
 163         /* hook parameter structure */
 164         t_hp hookparam;
 165
 166         /* potential parameters */
 167         t_tersoff_mult_params tp;
 168         t_albe_mult_params ap;
 169
 170         /* testing location & velocity vector */
 171         t_3dvec r,v;
 172         memset(&r,0,sizeof(t_3dvec));
 173         memset(&v,0,sizeof(t_3dvec));
 174
 175         /* initialize moldyn */
 176         moldyn_init(&md,argc,argv);
 177
 178         /* choose integration algorithm */
 179         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 180
 181         /* choose potential */
 182 #ifdef ALBE
 183         set_potential3b_j1(&md,albe_mult_3bp_j1);
 184         set_potential3b_k1(&md,albe_mult_3bp_k1);
 185         set_potential3b_j2(&md,albe_mult_3bp_j2);
 186         set_potential3b_k2(&md,albe_mult_3bp_k2);
 187 #else
 188         set_potential1b(&md,tersoff_mult_1bp);
 189         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 190         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 191         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 192         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 193 #endif
 194
 195 #ifdef ALBE
 196         set_potential_params(&md,&ap);
 197 #else
 198         set_potential_params(&md,&tp);
 199 #endif
 200
 201         /* cutoff radius & bondlen */
 202 #ifdef ALBE
 203         set_cutoff(&md,ALBE_S_SI);
 204         set_bondlen(&md,ALBE_S_SI,ALBE_S_C,ALBE_S_SIC);
 205         //set_cutoff(&md,ALBE_S_C);
 206 #else
 207         set_cutoff(&md,TM_S_SI);
 208         set_bondlen(&md,TM_S_SI,TM_S_C,-1.0);
 209         //set_cutoff(&md,TM_S_C);
 210 #endif
 211
 212         /*
 213          * potential parameters
 214          */
 215
 216         /*
 217          * tersoff mult potential parameters for SiC
 218          */
 219         tp.S[0]=TM_S_SI;
 220         tp.R[0]=TM_R_SI;
 221         tp.A[0]=TM_A_SI;
 222         tp.B[0]=TM_B_SI;
 223         tp.lambda[0]=TM_LAMBDA_SI;
 224         tp.mu[0]=TM_MU_SI;
 225         tp.beta[0]=TM_BETA_SI;
 226         tp.n[0]=TM_N_SI;
 227         tp.c[0]=TM_C_SI;
 228         tp.d[0]=TM_D_SI;
 229         tp.h[0]=TM_H_SI;
 230
 231         tp.S[1]=TM_S_C;
 232         tp.R[1]=TM_R_C;
 233         tp.A[1]=TM_A_C;
 234         tp.B[1]=TM_B_C;
 235         tp.lambda[1]=TM_LAMBDA_C;
 236         tp.mu[1]=TM_MU_C;
 237         tp.beta[1]=TM_BETA_C;
 238         tp.n[1]=TM_N_C;
 239         tp.c[1]=TM_C_C;
 240         tp.d[1]=TM_D_C;
 241         tp.h[1]=TM_H_C;
 242
 243         tp.chi=TM_CHI_SIC;
 244
 245         tersoff_mult_complete_params(&tp);
 246
 247         /*
 248          * albe mult potential parameters for SiC
 249          */
 250         ap.S[0]=ALBE_S_SI;
 251         ap.R[0]=ALBE_R_SI;
 252         ap.A[0]=ALBE_A_SI;
 253         ap.B[0]=ALBE_B_SI;
 254         ap.r0[0]=ALBE_R0_SI;
 255         ap.lambda[0]=ALBE_LAMBDA_SI;
 256         ap.mu[0]=ALBE_MU_SI;
 257         ap.gamma[0]=ALBE_GAMMA_SI;
 258         ap.c[0]=ALBE_C_SI;
 259         ap.d[0]=ALBE_D_SI;
 260         ap.h[0]=ALBE_H_SI;
 261
 262         ap.S[1]=ALBE_S_C;
 263         ap.R[1]=ALBE_R_C;
 264         ap.A[1]=ALBE_A_C;
 265         ap.B[1]=ALBE_B_C;
 266         ap.r0[1]=ALBE_R0_C;
 267         ap.lambda[1]=ALBE_LAMBDA_C;
 268         ap.mu[1]=ALBE_MU_C;
 269         ap.gamma[1]=ALBE_GAMMA_C;
 270         ap.c[1]=ALBE_C_C;
 271         ap.d[1]=ALBE_D_C;
 272         ap.h[1]=ALBE_H_C;
 273
 274         ap.Smixed=ALBE_S_SIC;
 275         ap.Rmixed=ALBE_R_SIC;
 276         ap.Amixed=ALBE_A_SIC;
 277         ap.Bmixed=ALBE_B_SIC;
 278         ap.r0_mixed=ALBE_R0_SIC;
 279         ap.lambda_m=ALBE_LAMBDA_SIC;
 280         ap.mu_m=ALBE_MU_SIC;
 281         ap.gamma_m=ALBE_GAMMA_SIC;
 282         ap.c_mixed=ALBE_C_SIC;
 283         ap.d_mixed=ALBE_D_SIC;
 284         ap.h_mixed=ALBE_H_SIC;
 285
 286         albe_mult_complete_params(&ap);
 287
 288         /* set (initial) dimensions of simulation volume */
 289 #ifdef ALBE
 290         set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
 291         //set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
 292         //set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
 293 #else
 294         set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE);
 295         //set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
 296         //set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
 297 #endif
 298
 299         /* set periodic boundary conditions in all directions */
 300         set_pbc(&md,TRUE,TRUE,TRUE);
 301
 302         /* create the lattice / place atoms */
 303 #ifdef ALBE
 304         create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
 305         //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 306 #else
 307         create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 308 #endif
 309                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 310         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 311                        0,LCNTX,LCNTY,LCNTZ,NULL);
 312         //               1,LCNTX,LCNTY,LCNTZ,NULL);
 313
 314         /* create zinkblende structure */
 315         /*
 316 #ifdef ALBE
 317         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 318         create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
 319                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 320                        0,LCNTX,LCNTY,LCNTZ,&r);
 321         r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 322         create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
 323                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 324                        1,LCNTX,LCNTY,LCNTZ,&r);
 325 #else
 326         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 327         create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
 328                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 329                        0,LCNTX,LCNTY,LCNTZ,&r);
 330         r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 331         create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
 332                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 333                        1,LCNTX,LCNTY,LCNTZ,&r);
 334 #endif
 335         */
 336
 337         /* check for right atom placing */
 338         moldyn_bc_check(&md);
 339
 340         /* testing configuration */
 341         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 342         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 343         //r.y=0;                v.y=0;
 344         //r.z=0;                v.z=0;
 345         //add_atom(&md,SI,M_SI,0,
 346         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 347         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 348         //           &r,&v);
 349         //r.x=-r.x;     v.x=-v.x;
 350         //r.y=0;                v.y=0;
 351         //r.z=0;                v.z=0;
 352         //add_atom(&md,SI,M_SI,0,
 353         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 354         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 355         //           &r,&v);
 356         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 357         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 358         //r.y=0;                v.y=0;
 359         //r.x=0;                v.x=0;
 360         //add_atom(&md,SI,M_SI,0,
 361         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 362         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 363         //           &r,&v);
 364         //r.z=-r.z;     v.z=-v.z;
 365         //r.y=0;                v.y=0;
 366         //r.x=0;                v.x=0;
 367         //add_atom(&md,SI,M_SI,0,
 368         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 369         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 370         //           &r,&v);
 371
 372         /* set temperature & pressure */
 373         set_temperature(&md,atof(argv[2])+273.0);
 374         set_pressure(&md,BAR);
 375
 376         /* set amount of steps to skip before average calc */
 377         set_avg_skip(&md,(8.0/10.0*PRERUN));
 378
 379         /* set p/t scaling */
 380         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
 381         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 382         //                 T_SCALE_BERENDSEN,100.0);
 383         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 384         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 385
 386         /* initial thermal fluctuations of particles (in equilibrium) */
 387         thermal_init(&md,TRUE);
 388
 389         /* create the simulation schedule */
 390         moldyn_add_schedule(&md,PRERUN,1.0);
 391
 392         /* schedule hook function */
 393         memset(&hookparam,0,sizeof(t_hp));
 394         hookparam.argc=argc;
 395         hookparam.argv=argv;
 396         moldyn_set_schedule_hook(&md,&hook_add_atom,&hookparam);
 397         //moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam);
 398         //moldyn_add_schedule(&md,POSTRUN,1.0);
 399
 400         /* activate logging */
 401         moldyn_set_log_dir(&md,argv[1]);
 402         moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
 403         moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
 404         moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
 405         moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
 406         moldyn_set_log(&md,VISUAL_STEP,LOG_V);
 407         moldyn_set_log(&md,SAVE_STEP,LOG_S);
 408         moldyn_set_log(&md,CREATE_REPORT,0);
 409
 410         /*
 411          * let's do the actual md algorithm now
 412          *
 413          * integration of newtons equations
 414          */
 415         moldyn_integrate(&md);
 416 #ifdef dEBUG
 417 return 0;
 418 #endif
 419
 420         /*
 421          * post processing the data
 422          */
 423
 424         /* close */
 425         moldyn_shutdown(&md);
 426
 427         return 0;
 428 }
 429