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          1
  25 #define NR_ATOMS        1
  26 #define R_C             1.0
  27 #define T_C             10.0
  28 #define LCNT            3
  29
  30 typedef struct s_hp {
  31         int a_count;    /* atom count */
  32         u8 quit;        /* quit mark */
  33         int argc;       /* arg count */
  34         char **argv;    /* args */
  35 } t_hp;
  36
  37 int hook(void *moldyn,void *hook_params) {
  38
  39         t_moldyn *md;
  40         t_3dvec r,v,dist;
  41         double d;
  42         unsigned char run;
  43         int i,j;
  44         t_atom *atom;
  45         t_hp *hp;
  46
  47         md=moldyn;
  48         hp=hook_params;
  49
  50         /* quit */
  51         if(hp->quit)
  52                 return 0;
  53
  54         /* switch on t scaling */
  55         if(md->schedule.count==0)
  56                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  57
  58         /* last schedule add if there is enough carbon inside */
  59         if(hp->a_count==(INJECT*NR_ATOMS)) {
  60                 hp->quit=1;
  61                 moldyn_add_schedule(md,5000,1.0);
  62                 return 0;
  63         }
  64
  65         /* more relaxing time for too high temperatures */
  66         if(md->t-md->t_ref>T_C) {
  67                 moldyn_add_schedule(md,10,1.0);
  68                 return 0;
  69         }
  70
  71         /* inject carbon atoms */
  72         printf("injecting another %d carbon atoms ...(-> %d / %d)\n",
  73                NR_ATOMS,hp->a_count+NR_ATOMS,INJECT*NR_ATOMS);
  74         for(j=0;j<NR_ATOMS;j++) {
  75                 run=1;
  76                 while(run) {
  77                         r.x=(rand_get_double(&(md->random))-0.5)*md->dim.x*0.37;
  78                         r.y=(rand_get_double(&(md->random))-0.5)*md->dim.y*0.37;
  79                         r.z=(rand_get_double(&(md->random))-0.5)*md->dim.z*0.37;
  80                         //r.x=(1.0*atoi(hp->argv[3])-4.5)/9.0*ALBE_LC_SI;
  81                         //r.y=(1.0*atoi(hp->argv[4])-4.5)/9.0*ALBE_LC_SI;
  82                         //r.z=(1.0*atoi(hp->argv[5])-4.5)/9.0*ALBE_LC_SI;
  83                         /* assume valid coordinates */
  84                         run=0;
  85                         for(i=0;i<md->count;i++) {
  86                                 atom=&(md->atom[i]);
  87                                 v3_sub(&dist,&(atom->r),&r);
  88                                 d=v3_absolute_square(&dist);
  89                                 /* reject coordinates */
  90                                 if(d<R_C) {
  91                                         run=1;
  92                                         break;
  93                                 }
  94                         }
  95                 }
  96                 v.x=0; v.y=0; v.z=0;
  97                 add_atom(md,C,M_C,1,
  98                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
  99                          &r,&v);
 100         }
 101         hp->a_count+=NR_ATOMS;
 102
 103         /* add schedule for simulating injected atoms ;) */
 104         moldyn_add_schedule(md,10,1.0);
 105
 106         return 0;
 107 }
 108
 109 int main(int argc,char **argv) {
 110
 111         /* check argv */
 112         //if(argc!=3) {
 113         //      printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
 114         //      return -1;
 115         //}
 116
 117         /* main moldyn structure */
 118         t_moldyn md;
 119
 120         /* hook parameter structure */
 121         t_hp hookparam;
 122
 123         /* potential parameters */
 124         t_tersoff_mult_params tp;
 125         t_albe_mult_params ap;
 126
 127         /* atom injection counter */
 128         int inject;
 129
 130         /* testing location & velocity vector */
 131         t_3dvec r,v;
 132         memset(&r,0,sizeof(t_3dvec));
 133         memset(&v,0,sizeof(t_3dvec));
 134
 135         /* initialize moldyn */
 136         moldyn_init(&md,argc,argv);
 137
 138         /* choose integration algorithm */
 139         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 140
 141         /* choose potential */
 142 #ifdef ALBE
 143         set_potential3b_j1(&md,albe_mult_3bp_j1);
 144         set_potential3b_k1(&md,albe_mult_3bp_k1);
 145         set_potential3b_j2(&md,albe_mult_3bp_j2);
 146         set_potential3b_k2(&md,albe_mult_3bp_k2);
 147 #else
 148         set_potential1b(&md,tersoff_mult_1bp);
 149         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 150         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 151         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 152         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 153 #endif
 154
 155 #ifdef ALBE
 156         set_potential_params(&md,&ap);
 157 #else
 158         set_potential_params(&md,&tp);
 159 #endif
 160
 161         /* cutoff radius */
 162 #ifdef ALBE
 163         set_cutoff(&md,ALBE_S_SI);
 164 #else
 165         set_cutoff(&md,TM_S_SI);
 166 #endif
 167
 168         /*
 169          * potential parameters
 170          */
 171
 172         /*
 173          * tersoff mult potential parameters for SiC
 174          */
 175         tp.S[0]=TM_S_SI;
 176         tp.R[0]=TM_R_SI;
 177         tp.A[0]=TM_A_SI;
 178         tp.B[0]=TM_B_SI;
 179         tp.lambda[0]=TM_LAMBDA_SI;
 180         tp.mu[0]=TM_MU_SI;
 181         tp.beta[0]=TM_BETA_SI;
 182         tp.n[0]=TM_N_SI;
 183         tp.c[0]=TM_C_SI;
 184         tp.d[0]=TM_D_SI;
 185         tp.h[0]=TM_H_SI;
 186
 187         tp.S[1]=TM_S_C;
 188         tp.R[1]=TM_R_C;
 189         tp.A[1]=TM_A_C;
 190         tp.B[1]=TM_B_C;
 191         tp.lambda[1]=TM_LAMBDA_C;
 192         tp.mu[1]=TM_MU_C;
 193         tp.beta[1]=TM_BETA_C;
 194         tp.n[1]=TM_N_C;
 195         tp.c[1]=TM_C_C;
 196         tp.d[1]=TM_D_C;
 197         tp.h[1]=TM_H_C;
 198
 199         tp.chi=TM_CHI_SIC;
 200
 201         tersoff_mult_complete_params(&tp);
 202
 203         /*
 204          * albe mult potential parameters for SiC
 205          */
 206         ap.S[0]=ALBE_S_SI;
 207         ap.R[0]=ALBE_R_SI;
 208         ap.A[0]=ALBE_A_SI;
 209         ap.B[0]=ALBE_B_SI;
 210         ap.r0[0]=ALBE_R0_SI;
 211         ap.lambda[0]=ALBE_LAMBDA_SI;
 212         ap.mu[0]=ALBE_MU_SI;
 213         ap.gamma[0]=ALBE_GAMMA_SI;
 214         ap.c[0]=ALBE_C_SI;
 215         ap.d[0]=ALBE_D_SI;
 216         ap.h[0]=ALBE_H_SI;
 217
 218         ap.S[1]=ALBE_S_C;
 219         ap.R[1]=ALBE_R_C;
 220         ap.A[1]=ALBE_A_C;
 221         ap.B[1]=ALBE_B_C;
 222         ap.r0[1]=ALBE_R0_C;
 223         ap.lambda[1]=ALBE_LAMBDA_C;
 224         ap.mu[1]=ALBE_MU_C;
 225         ap.gamma[1]=ALBE_GAMMA_C;
 226         ap.c[1]=ALBE_C_C;
 227         ap.d[1]=ALBE_D_C;
 228         ap.h[1]=ALBE_H_C;
 229
 230         ap.Smixed=ALBE_S_SIC;
 231         ap.Rmixed=ALBE_R_SIC;
 232         ap.Amixed=ALBE_A_SIC;
 233         ap.Bmixed=ALBE_B_SIC;
 234         ap.r0_mixed=ALBE_R0_SIC;
 235         ap.lambda_m=ALBE_LAMBDA_SIC;
 236         ap.mu_m=ALBE_MU_SIC;
 237         ap.gamma_m=ALBE_GAMMA_SIC;
 238         ap.c_mixed=ALBE_C_SIC;
 239         ap.d_mixed=ALBE_D_SIC;
 240         ap.h_mixed=ALBE_H_SIC;
 241
 242         albe_mult_complete_params(&ap);
 243
 244         /* set (initial) dimensions of simulation volume */
 245 #ifdef ALBE
 246         set_dim(&md,LCNT*ALBE_LC_SI,LCNT*ALBE_LC_SI,LCNT*ALBE_LC_SI,TRUE);
 247         //set_dim(&md,LCNT*ALBE_LC_C,LCNT*ALBE_LC_C,LCNT*ALBE_LC_C,TRUE);
 248         //set_dim(&md,LCNT*ALBE_LC_SIC,LCNT*ALBE_LC_SIC,LCNT*ALBE_LC_SIC,TRUE);
 249 #else
 250         //set_dim(&md,LCNT*LC_SI,LCNT*LC_SI,LCNT*LC_SI,TRUE);
 251         //set_dim(&md,LCNT*LC_C,LCNT*LC_C,LCNT*LC_C,TRUE);
 252         set_dim(&md,LCNT*TM_LC_SIC,LCNT*TM_LC_SIC,LCNT*TM_LC_SIC,TRUE);
 253 #endif
 254
 255         /* set periodic boundary conditions in all directions */
 256         set_pbc(&md,TRUE,TRUE,TRUE);
 257
 258         /* create the lattice / place atoms */
 259 #ifdef ALBE
 260         create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
 261         //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 262 #else
 263         //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 264 #endif
 265                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 266         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 267                        0,LCNT,LCNT,LCNT,NULL);
 268         //               1,LCNT,LCNT,LCNT,NULL);
 269
 270         /* create zinkblende structure */
 271         /*
 272 #ifdef ALBE
 273         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 274         create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
 275                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 276                        0,LCNT,LCNT,LCNT,&r);
 277         r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 278         create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
 279                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 280                        1,LCNT,LCNT,LCNT,&r);
 281 #else
 282         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 283         create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
 284                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 285                        0,LCNT,LCNT,LCNT,&r);
 286         r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 287         create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
 288                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 289                        1,LCNT,LCNT,LCNT,&r);
 290 #endif
 291         */
 292
 293         /* check for right atom placing */
 294         moldyn_bc_check(&md);
 295
 296         /* testing configuration */
 297         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 298         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 299         //r.y=0;                v.y=0;
 300         //r.z=0;                v.z=0;
 301         //add_atom(&md,SI,M_SI,0,
 302         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 303         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 304         //           &r,&v);
 305         //r.x=-r.x;     v.x=-v.x;
 306         //r.y=0;                v.y=0;
 307         //r.z=0;                v.z=0;
 308         //add_atom(&md,SI,M_SI,0,
 309         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 310         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 311         //           &r,&v);
 312         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 313         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 314         //r.y=0;                v.y=0;
 315         //r.x=0;                v.x=0;
 316         //add_atom(&md,SI,M_SI,0,
 317         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 318         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 319         //           &r,&v);
 320         //r.z=-r.z;     v.z=-v.z;
 321         //r.y=0;                v.y=0;
 322         //r.x=0;                v.x=0;
 323         //add_atom(&md,SI,M_SI,0,
 324         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 325         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 326         //           &r,&v);
 327
 328         /* set temperature & pressure */
 329         set_temperature(&md,atof(argv[2])+273.0);
 330         set_pressure(&md,BAR);
 331
 332         /* set amount of steps to skip before average calc */
 333         set_avg_skip(&md,1000);
 334
 335         /* set p/t scaling */
 336         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
 337         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 338         //                 T_SCALE_BERENDSEN,100.0);
 339         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 340         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 341
 342         /* initial thermal fluctuations of particles (in equilibrium) */
 343         thermal_init(&md,TRUE);
 344
 345         /* create the simulation schedule */
 346         moldyn_add_schedule(&md,1000,1.0);
 347         //moldyn_add_schedule(&md,1000,1.0);
 348         //moldyn_add_schedule(&md,1000,1.0);
 349         //moldyn_add_schedule(&md,1000,1.0);
 350         //moldyn_add_schedule(&md,1000,1.0);
 351         //moldyn_add_schedule(&md,1000,1.0);
 352         /* adding atoms */
 353         //for(inject=0;inject<INJECT;inject++) {
 354         //      /* injecting atoms */
 355         //      moldyn_add_schedule(&md,10,1.0);
 356         //}
 357
 358         /* schedule hook function */
 359         memset(&hookparam,0,sizeof(t_hp));
 360         hookparam.argc=argc;
 361         hookparam.argv=argv;
 362         moldyn_set_schedule_hook(&md,&hook,&hookparam);
 363
 364         /* activate logging */
 365         moldyn_set_log_dir(&md,argv[1]);
 366         moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
 367         moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
 368         moldyn_set_log(&md,LOG_TEMPERATURE,1);
 369         moldyn_set_log(&md,LOG_PRESSURE,1);
 370         moldyn_set_log(&md,VISUAL_STEP,100);
 371         moldyn_set_log(&md,SAVE_STEP,100);
 372         moldyn_set_log(&md,CREATE_REPORT,0);
 373
 374         /*
 375          * let's do the actual md algorithm now
 376          *
 377          * integration of newtons equations
 378          */
 379         moldyn_integrate(&md);
 380 #ifdef dEBUG
 381 return 0;
 382 #endif
 383
 384         /*
 385          * post processing the data
 386          */
 387
 388         /* close */
 389         moldyn_shutdown(&md);
 390
 391         return 0;
 392 }
 393