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