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;
  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                         for(i=0;i<moldyn->count;i++) {
  87                                 atom=&(moldyn->atom[i]);
  88                                 v3_sub(&dist,&(atom->r),&r);
  89                                 check_per_bound(moldyn,&dist);
  90                                 d=v3_absolute_square(&dist);
  91                                 /* reject coordinates */
  92                                 if(d<INS_R_C) {
  93                                         //printf("atom %d - %f\n",i,d);
  94                                         run=1;
  95                                         break;
  96                                 }
  97                         }
  98                 }
  99                 add_atom(moldyn,INS_TYPE,INS_MASS,INS_BRAND,
 100                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|\
 101                          //ATOM_ATTR_HB|ATOM_ATTR_VB,
 102                          ATOM_ATTR_HB,
 103                          &r,&v);
 104         }
 105
 106         return 0;
 107 }
 108
 109 int sic_hook(void *moldyn,void *hook_params) {
 110
 111         t_hp *hp;
 112         t_moldyn *md;
 113         int steps;
 114         double tau;
 115
 116         hp=hook_params;
 117         md=moldyn;
 118
 119         /* switch on t scaling */
 120         if(md->schedule.count==0)
 121                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
 122
 123         /* my lousy state machine ! */
 124
 125         /* switch to insert state immediately */
 126         if(hp->state==STATE_PRERUN)
 127                 hp->state=STATE_INSERT;
 128
 129         /* act according to state */
 130         switch(hp->state) {
 131                 case STATE_INSERT:
 132                         /* check temperature */
 133                         if(md->t_avg-md->t_ref>INS_DELTA_TC) {
 134                                 steps=INS_RELAX;
 135                                 tau=INS_TAU;
 136                                 break;
 137                         }
 138                         /* insert atoms */
 139                         hp->insert_count+=1;
 140                         printf("   ### insert atoms (%d/%d) ###\n",
 141                                hp->insert_count*INS_ATOMS,INS_RUNS*INS_ATOMS);
 142                         insert_atoms(md);
 143                         /* change state after last insertion */
 144                         if(hp->insert_count==INS_RUNS)
 145                                 hp->state=STATE_POSTRUN;
 146                         break;
 147                 case STATE_POSTRUN:
 148                         /* settings */
 149                         if(md->t-md->t_ref>POST_DELTA_TC) {
 150                                 steps=POST_RELAX;
 151                                 tau=POST_TAU;
 152                         }
 153                         /* decrease temperature */
 154                         hp->postrun_count+=1;
 155                         printf(" ### postrun (%d/%d) ###\n",
 156                                hp->postrun_count,POST_RUNS);
 157                         set_temperature(md,md->t_ref-POST_DT);
 158                         if(hp->postrun_count==POST_RUNS)
 159                                 return 0;
 160                         break;
 161                 default:
 162                         printf("[hook] FATAL (default case!?!)\n");
 163                         break;
 164         }
 165
 166         /* add schedule */
 167         moldyn_add_schedule(md,steps,tau);
 168
 169         return 0;
 170 }
 171
 172 int main(int argc,char **argv) {
 173
 174         /* main moldyn structure */
 175         t_moldyn md;
 176
 177         /* hook parameter structure */
 178         t_hp hookparam;
 179
 180         /* potential parameters */
 181         t_tersoff_mult_params tp;
 182         t_albe_mult_params ap;
 183
 184         /* testing location & velocity vector */
 185         t_3dvec r,v;
 186         memset(&r,0,sizeof(t_3dvec));
 187         memset(&v,0,sizeof(t_3dvec));
 188
 189         /* initialize moldyn */
 190         moldyn_init(&md,argc,argv);
 191
 192         /* choose integration algorithm */
 193         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 194
 195         /* choose potential */
 196 #ifdef ALBE
 197         set_potential3b_j1(&md,albe_mult_3bp_j1);
 198         set_potential3b_k1(&md,albe_mult_3bp_k1);
 199         set_potential3b_j2(&md,albe_mult_3bp_j2);
 200         set_potential3b_k2(&md,albe_mult_3bp_k2);
 201 #else
 202         set_potential1b(&md,tersoff_mult_1bp);
 203         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 204         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 205         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 206         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 207 #endif
 208
 209 #ifdef ALBE
 210         set_potential_params(&md,&ap);
 211 #else
 212         set_potential_params(&md,&tp);
 213 #endif
 214
 215         /* cutoff radius & bondlen */
 216 #ifdef ALBE
 217         set_cutoff(&md,ALBE_S_SI);
 218         set_bondlen(&md,ALBE_S_SI,ALBE_S_C,ALBE_S_SIC);
 219         //set_cutoff(&md,ALBE_S_C);
 220 #else
 221         set_cutoff(&md,TM_S_SI);
 222         set_bondlen(&md,TM_S_SI,TM_S_C,-1.0);
 223         //set_cutoff(&md,TM_S_C);
 224 #endif
 225
 226         /*
 227          * potential parameters
 228          */
 229
 230         /*
 231          * tersoff mult potential parameters for SiC
 232          */
 233         tp.S[0]=TM_S_SI;
 234         tp.R[0]=TM_R_SI;
 235         tp.A[0]=TM_A_SI;
 236         tp.B[0]=TM_B_SI;
 237         tp.lambda[0]=TM_LAMBDA_SI;
 238         tp.mu[0]=TM_MU_SI;
 239         tp.beta[0]=TM_BETA_SI;
 240         tp.n[0]=TM_N_SI;
 241         tp.c[0]=TM_C_SI;
 242         tp.d[0]=TM_D_SI;
 243         tp.h[0]=TM_H_SI;
 244
 245         tp.S[1]=TM_S_C;
 246         tp.R[1]=TM_R_C;
 247         tp.A[1]=TM_A_C;
 248         tp.B[1]=TM_B_C;
 249         tp.lambda[1]=TM_LAMBDA_C;
 250         tp.mu[1]=TM_MU_C;
 251         tp.beta[1]=TM_BETA_C;
 252         tp.n[1]=TM_N_C;
 253         tp.c[1]=TM_C_C;
 254         tp.d[1]=TM_D_C;
 255         tp.h[1]=TM_H_C;
 256
 257         tp.chi=TM_CHI_SIC;
 258
 259         tersoff_mult_complete_params(&tp);
 260
 261         /*
 262          * albe mult potential parameters for SiC
 263          */
 264         ap.S[0]=ALBE_S_SI;
 265         ap.R[0]=ALBE_R_SI;
 266         ap.A[0]=ALBE_A_SI;
 267         ap.B[0]=ALBE_B_SI;
 268         ap.r0[0]=ALBE_R0_SI;
 269         ap.lambda[0]=ALBE_LAMBDA_SI;
 270         ap.mu[0]=ALBE_MU_SI;
 271         ap.gamma[0]=ALBE_GAMMA_SI;
 272         ap.c[0]=ALBE_C_SI;
 273         ap.d[0]=ALBE_D_SI;
 274         ap.h[0]=ALBE_H_SI;
 275
 276         ap.S[1]=ALBE_S_C;
 277         ap.R[1]=ALBE_R_C;
 278         ap.A[1]=ALBE_A_C;
 279         ap.B[1]=ALBE_B_C;
 280         ap.r0[1]=ALBE_R0_C;
 281         ap.lambda[1]=ALBE_LAMBDA_C;
 282         ap.mu[1]=ALBE_MU_C;
 283         ap.gamma[1]=ALBE_GAMMA_C;
 284         ap.c[1]=ALBE_C_C;
 285         ap.d[1]=ALBE_D_C;
 286         ap.h[1]=ALBE_H_C;
 287
 288         ap.Smixed=ALBE_S_SIC;
 289         ap.Rmixed=ALBE_R_SIC;
 290         ap.Amixed=ALBE_A_SIC;
 291         ap.Bmixed=ALBE_B_SIC;
 292         ap.r0_mixed=ALBE_R0_SIC;
 293         ap.lambda_m=ALBE_LAMBDA_SIC;
 294         ap.mu_m=ALBE_MU_SIC;
 295         ap.gamma_m=ALBE_GAMMA_SIC;
 296         ap.c_mixed=ALBE_C_SIC;
 297         ap.d_mixed=ALBE_D_SIC;
 298         ap.h_mixed=ALBE_H_SIC;
 299
 300         albe_mult_complete_params(&ap);
 301
 302         /* set (initial) dimensions of simulation volume */
 303 #ifdef ALBE
 304         set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
 305         //set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
 306         //set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
 307 #else
 308         set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE);
 309         //set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
 310         //set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
 311 #endif
 312
 313         /* set periodic boundary conditions in all directions */
 314         set_pbc(&md,TRUE,TRUE,TRUE);
 315
 316         /* create the lattice / place atoms */
 317         //
 318 #ifdef ALBE
 319         create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
 320         //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 321 #else
 322         create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 323 #endif
 324                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 325         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 326                        0,LCNTX,LCNTY,LCNTZ,NULL);
 327         //               1,LCNTX,LCNTY,LCNTZ,NULL);
 328
 329         /* create zinkblende structure */
 330         /*
 331 #ifdef ALBE
 332         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 333         create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
 334                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 335                        0,LCNTX,LCNTY,LCNTZ,&r);
 336         r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 337         create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
 338                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 339                        1,LCNTX,LCNTY,LCNTZ,&r);
 340 #else
 341         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 342         create_lattice(&md,FCC,TM_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*TM_LC_SIC; r.y=r.x; r.z=r.x;
 346         create_lattice(&md,FCC,TM_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 #endif
 350         */
 351
 352         /* check for right atom placing */
 353         moldyn_bc_check(&md);
 354
 355         /* testing configuration */
 356         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 357         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 358         //r.y=0;                v.y=0;
 359         //r.z=0;                v.z=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.x=-r.x;     v.x=-v.x;
 365         //r.y=0;                v.y=0;
 366         //r.z=0;                v.z=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         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 372         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 373         //r.y=0;                v.y=0;
 374         //r.x=0;                v.x=0;
 375         //add_atom(&md,SI,M_SI,0,
 376         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 377         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 378         //           &r,&v);
 379         //r.z=-r.z;     v.z=-v.z;
 380         //r.y=0;                v.y=0;
 381         //r.x=0;                v.x=0;
 382         //add_atom(&md,SI,M_SI,0,
 383         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 384         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 385         //           &r,&v);
 386
 387         /* set temperature & pressure */
 388         set_temperature(&md,atof(argv[2])+273.0);
 389         set_pressure(&md,BAR);
 390
 391         /* set amount of steps to skip before average calc */
 392         set_avg_skip(&md,AVG_SKIP);
 393
 394         /* set p/t scaling */
 395         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
 396         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 397         //                 T_SCALE_BERENDSEN,100.0);
 398         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 399         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 400
 401         /* initial thermal fluctuations of particles (in equilibrium) */
 402         thermal_init(&md,TRUE);
 403
 404         /* create the simulation schedule */
 405         moldyn_add_schedule(&md,PRERUN,PRE_TAU);
 406
 407         /* schedule hook function */
 408         memset(&hookparam,0,sizeof(t_hp));
 409         hookparam.argc=argc;
 410         hookparam.argv=argv;
 411         moldyn_set_schedule_hook(&md,&sic_hook,&hookparam);
 412         //moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam);
 413         //moldyn_add_schedule(&md,POSTRUN,1.0);
 414
 415         /* activate logging */
 416         moldyn_set_log_dir(&md,argv[1]);
 417         moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
 418         moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
 419         moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
 420         moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
 421         moldyn_set_log(&md,VISUAL_STEP,LOG_V);
 422         moldyn_set_log(&md,SAVE_STEP,LOG_S);
 423         moldyn_set_log(&md,CREATE_REPORT,0);
 424
 425         /*
 426          * let's do the actual md algorithm now
 427          *
 428          * integration of newtons equations
 429          */
 430         moldyn_integrate(&md);
 431 #ifdef dEBUG
 432 return 0;
 433 #endif
 434
 435         /*
 436          * post processing the data
 437          */
 438
 439         /* close */
 440         moldyn_shutdown(&md);
 441
 442         return 0;
 443 }
 444