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 NR_ATOMS        10
  26 #define R_C             1.5
  27 #define T_C             10.0
  28 #define INJ_LENX        (10*ALBE_LC_SIC)
  29 #define INJ_LENY        (10*ALBE_LC_SIC)
  30 #define INJ_LENZ        (10*ALBE_LC_SIC)
  31 #define INJ_OFFSET      (ALBE_LC_SI/8.0)
  32
  33 #define LCNTX           50
  34 #define LCNTY           50
  35 #define LCNTZ           50
  36 #define PRERUN          1000
  37 #define POSTRUN         10000
  38
  39 #define R_TITLE         "Insertion of 8000 carbon atoms in silicon"
  40 #define LOG_E           10
  41 #define LOG_T           10
  42 #define LOG_P           10
  43 #define LOG_S           100
  44 #define LOG_V           100
  45
  46 typedef struct s_hp {
  47         int a_count;    /* atom count */
  48         u8 quit;        /* quit mark */
  49         int argc;       /* arg count */
  50         char **argv;    /* args */
  51 } t_hp;
  52
  53 int hook(void *moldyn,void *hook_params) {
  54
  55         t_moldyn *md;
  56         t_3dvec r,v,dist;
  57         double d;
  58         unsigned char run;
  59         int i,j;
  60         t_atom *atom;
  61         t_hp *hp;
  62
  63         md=moldyn;
  64         hp=hook_params;
  65
  66         /* quit */
  67         if(hp->quit)
  68                 return 0;
  69
  70         /* switch on t scaling */
  71         if(md->schedule.count==0)
  72                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  73
  74         /* last schedule add if there is enough carbon inside */
  75         if(hp->a_count==(INJECT*NR_ATOMS)) {
  76                 hp->quit=1;
  77                 moldyn_add_schedule(md,POSTRUN,1.0);
  78                 return 0;
  79         }
  80
  81         /* more relaxing time for too high temperatures */
  82         if(md->t-md->t_ref>T_C) {
  83                 moldyn_add_schedule(md,10,1.0);
  84                 return 0;
  85         }
  86
  87         /* inject carbon atoms */
  88         printf("injecting another %d carbon atoms ...(-> %d / %d)\n",
  89                NR_ATOMS,hp->a_count+NR_ATOMS,INJECT*NR_ATOMS);
  90         for(j=0;j<NR_ATOMS;j++) {
  91                 run=1;
  92                 while(run) {
  93                         r.x=(rand_get_double(&(md->random))-0.5)*INJ_LENX;
  94                         r.x+=INJ_OFFSET;
  95                         r.y=(rand_get_double(&(md->random))-0.5)*INJ_LENY;
  96                         r.y+=INJ_OFFSET;
  97                         r.z=(rand_get_double(&(md->random))-0.5)*INJ_LENZ;
  98                         r.z+=INJ_OFFSET;
  99                         /* assume valid coordinates */
 100                         run=0;
 101                         for(i=0;i<md->count;i++) {
 102                                 atom=&(md->atom[i]);
 103                                 v3_sub(&dist,&(atom->r),&r);
 104                                 d=v3_absolute_square(&dist);
 105                                 /* reject coordinates */
 106                                 if(d<R_C) {
 107                                         run=1;
 108                                         break;
 109                                 }
 110                         }
 111                 }
 112                 v.x=0; v.y=0; v.z=0;
 113                 //add_atom(md,C,M_C,1,
 114                 add_atom(md,SI,M_SI,1,
 115                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 116                          &r,&v);
 117         }
 118         hp->a_count+=NR_ATOMS;
 119
 120         /* add schedule for simulating injected atoms ;) */
 121         moldyn_add_schedule(md,10,1.0);
 122
 123         return 0;
 124 }
 125
 126 int main(int argc,char **argv) {
 127
 128         /* check argv */
 129         //if(argc!=3) {
 130         //      printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
 131         //      return -1;
 132         //}
 133
 134         /* main moldyn structure */
 135         t_moldyn md;
 136
 137         /* hook parameter structure */
 138         t_hp hookparam;
 139
 140         /* potential parameters */
 141         t_tersoff_mult_params tp;
 142         t_albe_mult_params ap;
 143
 144         /* testing location & velocity vector */
 145         t_3dvec r,v;
 146         memset(&r,0,sizeof(t_3dvec));
 147         memset(&v,0,sizeof(t_3dvec));
 148
 149         /* initialize moldyn */
 150         moldyn_init(&md,argc,argv);
 151
 152         /* choose integration algorithm */
 153         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 154
 155         /* choose potential */
 156 #ifdef ALBE
 157         set_potential3b_j1(&md,albe_mult_3bp_j1);
 158         set_potential3b_k1(&md,albe_mult_3bp_k1);
 159         set_potential3b_j2(&md,albe_mult_3bp_j2);
 160         set_potential3b_k2(&md,albe_mult_3bp_k2);
 161 #else
 162         set_potential1b(&md,tersoff_mult_1bp);
 163         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 164         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 165         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 166         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 167 #endif
 168
 169 #ifdef ALBE
 170         set_potential_params(&md,&ap);
 171 #else
 172         set_potential_params(&md,&tp);
 173 #endif
 174
 175         /* cutoff radius */
 176 #ifdef ALBE
 177         set_cutoff(&md,ALBE_S_SI);
 178         //set_cutoff(&md,ALBE_S_C);
 179 #else
 180         set_cutoff(&md,TM_S_SI);
 181         //set_cutoff(&md,TM_S_C);
 182 #endif
 183
 184         /*
 185          * potential parameters
 186          */
 187
 188         /*
 189          * tersoff mult potential parameters for SiC
 190          */
 191         tp.S[0]=TM_S_SI;
 192         tp.R[0]=TM_R_SI;
 193         tp.A[0]=TM_A_SI;
 194         tp.B[0]=TM_B_SI;
 195         tp.lambda[0]=TM_LAMBDA_SI;
 196         tp.mu[0]=TM_MU_SI;
 197         tp.beta[0]=TM_BETA_SI;
 198         tp.n[0]=TM_N_SI;
 199         tp.c[0]=TM_C_SI;
 200         tp.d[0]=TM_D_SI;
 201         tp.h[0]=TM_H_SI;
 202
 203         tp.S[1]=TM_S_C;
 204         tp.R[1]=TM_R_C;
 205         tp.A[1]=TM_A_C;
 206         tp.B[1]=TM_B_C;
 207         tp.lambda[1]=TM_LAMBDA_C;
 208         tp.mu[1]=TM_MU_C;
 209         tp.beta[1]=TM_BETA_C;
 210         tp.n[1]=TM_N_C;
 211         tp.c[1]=TM_C_C;
 212         tp.d[1]=TM_D_C;
 213         tp.h[1]=TM_H_C;
 214
 215         tp.chi=TM_CHI_SIC;
 216
 217         tersoff_mult_complete_params(&tp);
 218
 219         /*
 220          * albe mult potential parameters for SiC
 221          */
 222         ap.S[0]=ALBE_S_SI;
 223         ap.R[0]=ALBE_R_SI;
 224         ap.A[0]=ALBE_A_SI;
 225         ap.B[0]=ALBE_B_SI;
 226         ap.r0[0]=ALBE_R0_SI;
 227         ap.lambda[0]=ALBE_LAMBDA_SI;
 228         ap.mu[0]=ALBE_MU_SI;
 229         ap.gamma[0]=ALBE_GAMMA_SI;
 230         ap.c[0]=ALBE_C_SI;
 231         ap.d[0]=ALBE_D_SI;
 232         ap.h[0]=ALBE_H_SI;
 233
 234         ap.S[1]=ALBE_S_C;
 235         ap.R[1]=ALBE_R_C;
 236         ap.A[1]=ALBE_A_C;
 237         ap.B[1]=ALBE_B_C;
 238         ap.r0[1]=ALBE_R0_C;
 239         ap.lambda[1]=ALBE_LAMBDA_C;
 240         ap.mu[1]=ALBE_MU_C;
 241         ap.gamma[1]=ALBE_GAMMA_C;
 242         ap.c[1]=ALBE_C_C;
 243         ap.d[1]=ALBE_D_C;
 244         ap.h[1]=ALBE_H_C;
 245
 246         ap.Smixed=ALBE_S_SIC;
 247         ap.Rmixed=ALBE_R_SIC;
 248         ap.Amixed=ALBE_A_SIC;
 249         ap.Bmixed=ALBE_B_SIC;
 250         ap.r0_mixed=ALBE_R0_SIC;
 251         ap.lambda_m=ALBE_LAMBDA_SIC;
 252         ap.mu_m=ALBE_MU_SIC;
 253         ap.gamma_m=ALBE_GAMMA_SIC;
 254         ap.c_mixed=ALBE_C_SIC;
 255         ap.d_mixed=ALBE_D_SIC;
 256         ap.h_mixed=ALBE_H_SIC;
 257
 258         albe_mult_complete_params(&ap);
 259
 260         /* set (initial) dimensions of simulation volume */
 261 #ifdef ALBE
 262         set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
 263         //set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
 264         //set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
 265 #else
 266         set_dim(&md,LCNTX*LC_SI,LCNT*LC_SI,LCNT*LC_SI,TRUE);
 267         //set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
 268         //set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
 269 #endif
 270
 271         /* set periodic boundary conditions in all directions */
 272         set_pbc(&md,TRUE,TRUE,TRUE);
 273
 274         /* create the lattice / place atoms */
 275 #ifdef ALBE
 276         create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
 277         //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 278 #else
 279         //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 280 #endif
 281                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 282         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 283                        0,LCNTX,LCNTY,LCNTZ,NULL);
 284         //               1,LCNTX,LCNTY,LCNTZ,NULL);
 285
 286         /* create zinkblende structure */
 287         /*
 288 #ifdef ALBE
 289         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 290         create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
 291                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 292                        0,LCNTX,LCNTY,LCNTZ,&r);
 293         r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 294         create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
 295                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 296                        1,LCNTX,LCNTY,LCNTZ,&r);
 297 #else
 298         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 299         create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
 300                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 301                        0,LCNTX,LCNTY,LCNTZ,&r);
 302         r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 303         create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
 304                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 305                        1,LCNTX,LCNTY,LCNTZ,&r);
 306 #endif
 307         */
 308
 309         /* check for right atom placing */
 310         moldyn_bc_check(&md);
 311
 312         /* testing configuration */
 313         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 314         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 315         //r.y=0;                v.y=0;
 316         //r.z=0;                v.z=0;
 317         //add_atom(&md,SI,M_SI,0,
 318         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 319         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 320         //           &r,&v);
 321         //r.x=-r.x;     v.x=-v.x;
 322         //r.y=0;                v.y=0;
 323         //r.z=0;                v.z=0;
 324         //add_atom(&md,SI,M_SI,0,
 325         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 326         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 327         //           &r,&v);
 328         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 329         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 330         //r.y=0;                v.y=0;
 331         //r.x=0;                v.x=0;
 332         //add_atom(&md,SI,M_SI,0,
 333         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 334         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 335         //           &r,&v);
 336         //r.z=-r.z;     v.z=-v.z;
 337         //r.y=0;                v.y=0;
 338         //r.x=0;                v.x=0;
 339         //add_atom(&md,SI,M_SI,0,
 340         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 341         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 342         //           &r,&v);
 343
 344         /* set temperature & pressure */
 345         set_temperature(&md,atof(argv[2])+273.0);
 346         set_pressure(&md,BAR);
 347
 348         /* set amount of steps to skip before average calc */
 349         set_avg_skip(&md,(8.0/10.0*PRERUN));
 350
 351         /* set p/t scaling */
 352         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
 353         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 354         //                 T_SCALE_BERENDSEN,100.0);
 355         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 356         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 357
 358         /* initial thermal fluctuations of particles (in equilibrium) */
 359         thermal_init(&md,TRUE);
 360
 361         /* create the simulation schedule */
 362         moldyn_add_schedule(&md,PRERUN,1.0);
 363
 364         /* schedule hook function */
 365         memset(&hookparam,0,sizeof(t_hp));
 366         hookparam.argc=argc;
 367         hookparam.argv=argv;
 368         moldyn_set_schedule_hook(&md,&hook,&hookparam);
 369
 370         /* activate logging */
 371         moldyn_set_log_dir(&md,argv[1]);
 372         moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
 373         moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
 374         moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
 375         moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
 376         moldyn_set_log(&md,VISUAL_STEP,LOG_V);
 377         moldyn_set_log(&md,SAVE_STEP,LOG_S);
 378         moldyn_set_log(&md,CREATE_REPORT,0);
 379
 380         /*
 381          * let's do the actual md algorithm now
 382          *
 383          * integration of newtons equations
 384          */
 385         moldyn_integrate(&md);
 386 #ifdef dEBUG
 387 return 0;
 388 #endif
 389
 390         /*
 391          * post processing the data
 392          */
 393
 394         /* close */
 395         moldyn_shutdown(&md);
 396
 397         return 0;
 398 }
 399