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 #include "posic.h"
  12
  13 /* potential */
  14 #include "potentials/harmonic_oscillator.h"
  15 #include "potentials/lennard_jones.h"
  16 #include "potentials/albe.h"
  17
  18 #ifdef TERSOFF_ORIG
  19 #include "potentials/tersoff_orig.h"
  20 #else
  21 #include "potentials/tersoff.h"
  22 #endif
  23
  24 //#define INJECT                800
  25 #define INJECT          1
  26 #define NR_ATOMS        1
  27 #define R_C             1.5
  28 #define T_C             5.0
  29 //#define INJ_LENX      (1*ALBE_LC_SIC)
  30 //#define INJ_LENY      (1*ALBE_LC_SIC)
  31 //#define INJ_LENZ      (1*ALBE_LC_SIC)
  32 #define INJ_LENX        (1*ALBE_LC_SI)
  33 #define INJ_LENY        (1*ALBE_LC_SI)
  34 #define INJ_LENZ        (1*ALBE_LC_SI)
  35 #define INJ_TYPE_SILICON
  36 //#define INJ_TYPE_CARBON
  37 #define INJ_OFFSET      (ALBE_LC_SI/8.0)
  38 #define RELAX_S         20
  39
  40 #define LCNTX           5
  41 #define LCNTY           5
  42 #define LCNTZ           5
  43 #define PRERUN          10
  44 #define POSTRUN         2000
  45
  46 #define R_TITLE         "Silicon self-interstitial"
  47 #define LOG_E           10
  48 #define LOG_T           10
  49 #define LOG_P           10
  50 #define LOG_S           100
  51 #define LOG_V           20
  52
  53 typedef struct s_hp {
  54         int a_count;    /* atom count */
  55         u8 quit;        /* quit mark */
  56         int argc;       /* arg count */
  57         char **argv;    /* args */
  58 } t_hp;
  59
  60 int hook(void *moldyn,void *hook_params) {
  61
  62         t_moldyn *md;
  63         t_3dvec r,v,dist;
  64         double d;
  65         unsigned char run;
  66         int i,j;
  67         t_atom *atom;
  68         t_hp *hp;
  69
  70         md=moldyn;
  71         hp=hook_params;
  72
  73         /* quit */
  74         if(hp->quit)
  75                 return 0;
  76
  77         /* switch on t scaling */
  78         if(md->schedule.count==0)
  79                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  80
  81         /* last schedule add if there is enough carbon inside */
  82         if(hp->a_count==(INJECT*NR_ATOMS)) {
  83                 hp->quit=1;
  84                 moldyn_add_schedule(md,POSTRUN,1.0);
  85                 return 0;
  86         }
  87
  88         /* more relaxing time for too high temperatures */
  89         if(md->t-md->t_ref>T_C) {
  90                 moldyn_add_schedule(md,RELAX_S,1.0);
  91                 return 0;
  92         }
  93
  94         /* inject carbon atoms */
  95         printf("injecting another %d atoms ... (-> %d / %d)\n",
  96                NR_ATOMS,hp->a_count+NR_ATOMS,INJECT*NR_ATOMS);
  97         for(j=0;j<NR_ATOMS;j++) {
  98                 run=1;
  99                 while(run) {
 100                         r.x=(rand_get_double(&(md->random))-0.5)*INJ_LENX;
 101                         r.x+=INJ_OFFSET;
 102                         r.y=(rand_get_double(&(md->random))-0.5)*INJ_LENY;
 103                         r.y+=INJ_OFFSET;
 104                         r.z=(rand_get_double(&(md->random))-0.5)*INJ_LENZ;
 105                         r.z+=INJ_OFFSET;
 106                         /* assume valid coordinates */
 107                         run=0;
 108                         for(i=0;i<md->count;i++) {
 109                                 atom=&(md->atom[i]);
 110                                 v3_sub(&dist,&(atom->r),&r);
 111                                 d=v3_absolute_square(&dist);
 112                                 /* reject coordinates */
 113                                 if(d<R_C) {
 114                                         run=1;
 115                                         break;
 116                                 }
 117                         }
 118                 }
 119                 v.x=0; v.y=0; v.z=0;
 120 #ifdef INJ_TYPE_CARBON
 121                 add_atom(md,C,M_C,1,
 122 #else
 123                 add_atom(md,SI,M_SI,0,
 124 #endif
 125                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 126                          &r,&v);
 127         }
 128         hp->a_count+=NR_ATOMS;
 129
 130         /* add schedule for simulating injected atoms ;) */
 131         moldyn_add_schedule(md,RELAX_S,1.0);
 132
 133         return 0;
 134 }
 135
 136 int main(int argc,char **argv) {
 137
 138         /* check argv */
 139         //if(argc!=3) {
 140         //      printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
 141         //      return -1;
 142         //}
 143
 144         /* main moldyn structure */
 145         t_moldyn md;
 146
 147         /* hook parameter structure */
 148         t_hp hookparam;
 149
 150         /* potential parameters */
 151         t_tersoff_mult_params tp;
 152         t_albe_mult_params ap;
 153
 154         /* testing location & velocity vector */
 155         t_3dvec r,v;
 156         memset(&r,0,sizeof(t_3dvec));
 157         memset(&v,0,sizeof(t_3dvec));
 158
 159         /* initialize moldyn */
 160         moldyn_init(&md,argc,argv);
 161
 162         /* choose integration algorithm */
 163         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 164
 165         /* choose potential */
 166 #ifdef ALBE
 167         set_potential3b_j1(&md,albe_mult_3bp_j1);
 168         set_potential3b_k1(&md,albe_mult_3bp_k1);
 169         set_potential3b_j2(&md,albe_mult_3bp_j2);
 170         set_potential3b_k2(&md,albe_mult_3bp_k2);
 171 #else
 172         set_potential1b(&md,tersoff_mult_1bp);
 173         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 174         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 175         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 176         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 177 #endif
 178
 179 #ifdef ALBE
 180         set_potential_params(&md,&ap);
 181 #else
 182         set_potential_params(&md,&tp);
 183 #endif
 184
 185         /* cutoff radius */
 186 #ifdef ALBE
 187         set_cutoff(&md,ALBE_S_SI);
 188         //set_cutoff(&md,ALBE_S_C);
 189 #else
 190         set_cutoff(&md,TM_S_SI);
 191         //set_cutoff(&md,TM_S_C);
 192 #endif
 193
 194         /*
 195          * potential parameters
 196          */
 197
 198         /*
 199          * tersoff mult potential parameters for SiC
 200          */
 201         tp.S[0]=TM_S_SI;
 202         tp.R[0]=TM_R_SI;
 203         tp.A[0]=TM_A_SI;
 204         tp.B[0]=TM_B_SI;
 205         tp.lambda[0]=TM_LAMBDA_SI;
 206         tp.mu[0]=TM_MU_SI;
 207         tp.beta[0]=TM_BETA_SI;
 208         tp.n[0]=TM_N_SI;
 209         tp.c[0]=TM_C_SI;
 210         tp.d[0]=TM_D_SI;
 211         tp.h[0]=TM_H_SI;
 212
 213         tp.S[1]=TM_S_C;
 214         tp.R[1]=TM_R_C;
 215         tp.A[1]=TM_A_C;
 216         tp.B[1]=TM_B_C;
 217         tp.lambda[1]=TM_LAMBDA_C;
 218         tp.mu[1]=TM_MU_C;
 219         tp.beta[1]=TM_BETA_C;
 220         tp.n[1]=TM_N_C;
 221         tp.c[1]=TM_C_C;
 222         tp.d[1]=TM_D_C;
 223         tp.h[1]=TM_H_C;
 224
 225         tp.chi=TM_CHI_SIC;
 226
 227         tersoff_mult_complete_params(&tp);
 228
 229         /*
 230          * albe mult potential parameters for SiC
 231          */
 232         ap.S[0]=ALBE_S_SI;
 233         ap.R[0]=ALBE_R_SI;
 234         ap.A[0]=ALBE_A_SI;
 235         ap.B[0]=ALBE_B_SI;
 236         ap.r0[0]=ALBE_R0_SI;
 237         ap.lambda[0]=ALBE_LAMBDA_SI;
 238         ap.mu[0]=ALBE_MU_SI;
 239         ap.gamma[0]=ALBE_GAMMA_SI;
 240         ap.c[0]=ALBE_C_SI;
 241         ap.d[0]=ALBE_D_SI;
 242         ap.h[0]=ALBE_H_SI;
 243
 244         ap.S[1]=ALBE_S_C;
 245         ap.R[1]=ALBE_R_C;
 246         ap.A[1]=ALBE_A_C;
 247         ap.B[1]=ALBE_B_C;
 248         ap.r0[1]=ALBE_R0_C;
 249         ap.lambda[1]=ALBE_LAMBDA_C;
 250         ap.mu[1]=ALBE_MU_C;
 251         ap.gamma[1]=ALBE_GAMMA_C;
 252         ap.c[1]=ALBE_C_C;
 253         ap.d[1]=ALBE_D_C;
 254         ap.h[1]=ALBE_H_C;
 255
 256         ap.Smixed=ALBE_S_SIC;
 257         ap.Rmixed=ALBE_R_SIC;
 258         ap.Amixed=ALBE_A_SIC;
 259         ap.Bmixed=ALBE_B_SIC;
 260         ap.r0_mixed=ALBE_R0_SIC;
 261         ap.lambda_m=ALBE_LAMBDA_SIC;
 262         ap.mu_m=ALBE_MU_SIC;
 263         ap.gamma_m=ALBE_GAMMA_SIC;
 264         ap.c_mixed=ALBE_C_SIC;
 265         ap.d_mixed=ALBE_D_SIC;
 266         ap.h_mixed=ALBE_H_SIC;
 267
 268         albe_mult_complete_params(&ap);
 269
 270         /* set (initial) dimensions of simulation volume */
 271 #ifdef ALBE
 272         set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
 273         //set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
 274         //set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
 275 #else
 276         set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE);
 277         //set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
 278         //set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
 279 #endif
 280
 281         /* set periodic boundary conditions in all directions */
 282         set_pbc(&md,TRUE,TRUE,TRUE);
 283
 284         /* create the lattice / place atoms */
 285 #ifdef ALBE
 286         create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
 287         //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 288 #else
 289         create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 290 #endif
 291                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 292         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 293                        0,LCNTX,LCNTY,LCNTZ,NULL);
 294         //               1,LCNTX,LCNTY,LCNTZ,NULL);
 295
 296         /* create zinkblende structure */
 297         /*
 298 #ifdef ALBE
 299         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 300         create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
 301                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 302                        0,LCNTX,LCNTY,LCNTZ,&r);
 303         r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 304         create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
 305                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 306                        1,LCNTX,LCNTY,LCNTZ,&r);
 307 #else
 308         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 309         create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
 310                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 311                        0,LCNTX,LCNTY,LCNTZ,&r);
 312         r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 313         create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
 314                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 315                        1,LCNTX,LCNTY,LCNTZ,&r);
 316 #endif
 317         */
 318
 319         /* check for right atom placing */
 320         moldyn_bc_check(&md);
 321
 322         /* testing configuration */
 323         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 324         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 325         //r.y=0;                v.y=0;
 326         //r.z=0;                v.z=0;
 327         //add_atom(&md,SI,M_SI,0,
 328         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 329         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 330         //           &r,&v);
 331         //r.x=-r.x;     v.x=-v.x;
 332         //r.y=0;                v.y=0;
 333         //r.z=0;                v.z=0;
 334         //add_atom(&md,SI,M_SI,0,
 335         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 336         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 337         //           &r,&v);
 338         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 339         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 340         //r.y=0;                v.y=0;
 341         //r.x=0;                v.x=0;
 342         //add_atom(&md,SI,M_SI,0,
 343         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 344         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 345         //           &r,&v);
 346         //r.z=-r.z;     v.z=-v.z;
 347         //r.y=0;                v.y=0;
 348         //r.x=0;                v.x=0;
 349         //add_atom(&md,SI,M_SI,0,
 350         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 351         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 352         //           &r,&v);
 353
 354         /* set temperature & pressure */
 355         set_temperature(&md,atof(argv[2])+273.0);
 356         set_pressure(&md,BAR);
 357
 358         /* set amount of steps to skip before average calc */
 359         set_avg_skip(&md,(8.0/10.0*PRERUN));
 360
 361         /* set p/t scaling */
 362         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
 363         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 364         //                 T_SCALE_BERENDSEN,100.0);
 365         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 366         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 367
 368         /* initial thermal fluctuations of particles (in equilibrium) */
 369         thermal_init(&md,TRUE);
 370
 371         /* create the simulation schedule */
 372         moldyn_add_schedule(&md,PRERUN,1.0);
 373
 374         /* schedule hook function */
 375         memset(&hookparam,0,sizeof(t_hp));
 376         hookparam.argc=argc;
 377         hookparam.argv=argv;
 378         moldyn_set_schedule_hook(&md,&hook,&hookparam);
 379
 380         /* activate logging */
 381         moldyn_set_log_dir(&md,argv[1]);
 382         moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
 383         moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
 384         moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
 385         moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
 386         moldyn_set_log(&md,VISUAL_STEP,LOG_V);
 387         moldyn_set_log(&md,SAVE_STEP,LOG_S);
 388         moldyn_set_log(&md,CREATE_REPORT,0);
 389
 390         /*
 391          * let's do the actual md algorithm now
 392          *
 393          * integration of newtons equations
 394          */
 395         moldyn_integrate(&md);
 396 #ifdef dEBUG
 397 return 0;
 398 #endif
 399
 400         /*
 401          * post processing the data
 402          */
 403
 404         /* close */
 405         moldyn_shutdown(&md);
 406
 407         return 0;
 408 }
 409