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          160
  25 #define NR_ATOMS        10
  26
  27 typedef struct s_hp {
  28         int a_count;    /* atom count */
  29         u8 quit;        /* quit mark */
  30 } t_hp;
  31
  32 #define TC              50
  33
  34 int hook(void *moldyn,void *hook_params) {
  35
  36         t_moldyn *md;
  37         t_3dvec r,v,dist;
  38         double d;
  39         unsigned char run;
  40         int i,j;
  41         t_atom *atom;
  42         t_hp *hp;
  43
  44         md=moldyn;
  45         hp=hook_params;
  46
  47         /* quit */
  48         if(hp->quit)
  49                 return 0;
  50
  51         /* switch on t scaling */
  52         if(md->schedule.count==0)
  53                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  54
  55         /* last schedule add if there is enough carbon inside */
  56         if(hp->a_count==(INJECT*NR_ATOMS)) {
  57                 hp->quit=1;
  58                 moldyn_add_schedule(md,10000,1.0);
  59                 return 0;
  60         }
  61
  62         /* more relaxing time for too high temperatures */
  63         if(md->t-md->t_ref>TC) {
  64                 moldyn_add_schedule(md,100,1.0);
  65                 return 0;
  66         }
  67
  68         /* inject carbon atoms */
  69         printf("injecting another 10 carbon atoms ...\n");
  70         for(j=0;j<NR_ATOMS;j++) {
  71                 run=1;
  72                 while(run) {
  73                         r.x=rand_get_double(&(md->random))*md->dim.x*0.37;
  74                         r.y=rand_get_double(&(md->random))*md->dim.y*0.37;
  75                         r.z=rand_get_double(&(md->random))*md->dim.z*0.37;
  76                         for(i=0;i<md->count;i++) {
  77                                 atom=&(md->atom[i]);
  78                                 v3_sub(&dist,&(atom->r),&r);
  79                                 d=v3_absolute_square(&dist);
  80                                 if(d>1.0)
  81                                         run=0;
  82                         }
  83                 }
  84                 v.x=0; v.y=0; v.z=0;
  85                 add_atom(md,C,M_C,1,
  86                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
  87                          &r,&v);
  88         }
  89         hp->a_count+=NR_ATOMS;
  90
  91         /* add schedule for simulating injected atoms ;) */
  92         moldyn_add_schedule(md,100,1.0);
  93
  94         return 0;
  95 }
  96
  97 int main(int argc,char **argv) {
  98
  99         /* check argv */
 100         if(argc!=3) {
 101                 printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
 102                 return -1;
 103         }
 104
 105         /* main moldyn structure */
 106         t_moldyn md;
 107
 108         /* hook parameter structure */
 109         t_hp hookparam;
 110
 111         /* potential parameters */
 112         t_tersoff_mult_params tp;
 113         t_albe_mult_params ap;
 114
 115         /* atom injection counter */
 116         int inject;
 117
 118         /* testing location & velocity vector */
 119         t_3dvec r,v;
 120         memset(&r,0,sizeof(t_3dvec));
 121         memset(&v,0,sizeof(t_3dvec));
 122
 123         /* initialize moldyn */
 124         moldyn_init(&md,argc,argv);
 125
 126         /* choose integration algorithm */
 127         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 128
 129         /* choose potential */
 130 #ifdef ALBE
 131         set_potential3b_j1(&md,albe_mult_3bp_j1);
 132         set_potential3b_k1(&md,albe_mult_3bp_k1);
 133         set_potential3b_j2(&md,albe_mult_3bp_j2);
 134         set_potential3b_k2(&md,albe_mult_3bp_k2);
 135 #else
 136         set_potential1b(&md,tersoff_mult_1bp);
 137         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 138         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 139         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 140         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 141 #endif
 142
 143 #ifdef ALBE
 144         set_potential_params(&md,&ap);
 145 #else
 146         set_potential_params(&md,&tp);
 147 #endif
 148
 149         /* cutoff radius */
 150 #ifdef ALBE
 151         set_cutoff(&md,ALBE_S_SI);
 152 #else
 153         set_cutoff(&md,TM_S_SI);
 154 #endif
 155
 156         /*
 157          * potential parameters
 158          */
 159
 160         /*
 161          * tersoff mult potential parameters for SiC
 162          */
 163         tp.S[0]=TM_S_SI;
 164         tp.R[0]=TM_R_SI;
 165         tp.A[0]=TM_A_SI;
 166         tp.B[0]=TM_B_SI;
 167         tp.lambda[0]=TM_LAMBDA_SI;
 168         tp.mu[0]=TM_MU_SI;
 169         tp.beta[0]=TM_BETA_SI;
 170         tp.n[0]=TM_N_SI;
 171         tp.c[0]=TM_C_SI;
 172         tp.d[0]=TM_D_SI;
 173         tp.h[0]=TM_H_SI;
 174
 175         tp.S[1]=TM_S_C;
 176         tp.R[1]=TM_R_C;
 177         tp.A[1]=TM_A_C;
 178         tp.B[1]=TM_B_C;
 179         tp.lambda[1]=TM_LAMBDA_C;
 180         tp.mu[1]=TM_MU_C;
 181         tp.beta[1]=TM_BETA_C;
 182         tp.n[1]=TM_N_C;
 183         tp.c[1]=TM_C_C;
 184         tp.d[1]=TM_D_C;
 185         tp.h[1]=TM_H_C;
 186
 187         tp.chi=TM_CHI_SIC;
 188
 189         tersoff_mult_complete_params(&tp);
 190
 191         /*
 192          * albe mult potential parameters for SiC
 193          */
 194         ap.S[0]=ALBE_S_SI;
 195         ap.R[0]=ALBE_R_SI;
 196         ap.A[0]=ALBE_A_SI;
 197         ap.B[0]=ALBE_B_SI;
 198         ap.r0[0]=ALBE_R0_SI;
 199         ap.lambda[0]=ALBE_LAMBDA_SI;
 200         ap.mu[0]=ALBE_MU_SI;
 201         ap.gamma[0]=ALBE_GAMMA_SI;
 202         ap.c[0]=ALBE_C_SI;
 203         ap.d[0]=ALBE_D_SI;
 204         ap.h[0]=ALBE_H_SI;
 205
 206         ap.S[1]=ALBE_S_C;
 207         ap.R[1]=ALBE_R_C;
 208         ap.A[1]=ALBE_A_C;
 209         ap.B[1]=ALBE_B_C;
 210         ap.r0[1]=ALBE_R0_C;
 211         ap.lambda[1]=ALBE_LAMBDA_C;
 212         ap.mu[1]=ALBE_MU_C;
 213         ap.gamma[1]=ALBE_GAMMA_C;
 214         ap.c[1]=ALBE_C_C;
 215         ap.d[1]=ALBE_D_C;
 216         ap.h[1]=ALBE_H_C;
 217
 218         ap.Smixed=ALBE_S_SIC;
 219         ap.Rmixed=ALBE_R_SIC;
 220         ap.Amixed=ALBE_A_SIC;
 221         ap.Bmixed=ALBE_B_SIC;
 222         ap.r0_mixed=ALBE_R0_SIC;
 223         ap.lambda_m=ALBE_LAMBDA_SIC;
 224         ap.mu_m=ALBE_MU_SIC;
 225         ap.gamma_m=ALBE_GAMMA_SIC;
 226         ap.c_mixed=ALBE_C_SIC;
 227         ap.d_mixed=ALBE_D_SIC;
 228         ap.h_mixed=ALBE_H_SIC;
 229
 230         albe_mult_complete_params(&ap);
 231
 232         /* set (initial) dimensions of simulation volume */
 233 #ifdef ALBE
 234         set_dim(&md,20*ALBE_LC_SI,20*ALBE_LC_SI,20*ALBE_LC_SI,TRUE);
 235         //set_dim(&md,8*ALBE_LC_C,8*ALBE_LC_C,8*ALBE_LC_C,TRUE);
 236         //set_dim(&md,8*ALBE_LC_SIC,8*ALBE_LC_SIC,8*ALBE_LC_SIC,TRUE);
 237 #else
 238         //set_dim(&md,8*LC_SI,8*LC_SI,8*LC_SI,TRUE);
 239         //set_dim(&md,8*LC_C,8*LC_C,8*LC_C,TRUE);
 240         set_dim(&md,8*TM_LC_SIC,8*TM_LC_SIC,8*TM_LC_SIC,TRUE);
 241 #endif
 242
 243         /* set periodic boundary conditions in all directions */
 244         set_pbc(&md,TRUE,TRUE,TRUE);
 245
 246         /* create the lattice / place atoms */
 247 #ifdef ALBE
 248         create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
 249         //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 250 #else
 251         //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 252 #endif
 253                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 254         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 255                        0,20,20,20,NULL);
 256         //               1,8,8,8,NULL);
 257
 258         /* create zinkblende structure */
 259         /*
 260 #ifdef ALBE
 261         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 262         create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
 263                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 264                        0,8,8,8,&r);
 265         r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 266         create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
 267                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 268                        1,8,8,8,&r);
 269 #else
 270         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 271         create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
 272                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 273                        0,8,8,8,&r);
 274         r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 275         create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
 276                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 277                        1,8,8,8,&r);
 278 #endif
 279         */
 280
 281         /* check for right atom placing */
 282         moldyn_bc_check(&md);
 283
 284         /* testing configuration */
 285         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 286         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 287         //r.y=0;                v.y=0;
 288         //r.z=0;                v.z=0;
 289         //add_atom(&md,SI,M_SI,0,
 290         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 291         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 292         //           &r,&v);
 293         //r.x=-r.x;     v.x=-v.x;
 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.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 301         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 302         //r.y=0;                v.y=0;
 303         //r.x=0;                v.x=0;
 304         //add_atom(&md,SI,M_SI,0,
 305         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 306         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 307         //           &r,&v);
 308         //r.z=-r.z;     v.z=-v.z;
 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
 316         /* set temperature & pressure */
 317         set_temperature(&md,atof(argv[2])+273.0);
 318         set_pressure(&md,BAR);
 319
 320         /* set amount of steps to skip before average calc */
 321         set_avg_skip(&md,500);
 322
 323         /* set p/t scaling */
 324         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
 325         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 326         //                 T_SCALE_BERENDSEN,100.0);
 327         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 328         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 329
 330         /* initial thermal fluctuations of particles (in equilibrium) */
 331         thermal_init(&md,TRUE);
 332
 333         /* create the simulation schedule */
 334         moldyn_add_schedule(&md,1000,1.0);
 335         //moldyn_add_schedule(&md,1000,1.0);
 336         //moldyn_add_schedule(&md,1000,1.0);
 337         //moldyn_add_schedule(&md,1000,1.0);
 338         //moldyn_add_schedule(&md,1000,1.0);
 339         //moldyn_add_schedule(&md,1000,1.0);
 340         /* adding atoms */
 341         //for(inject=0;inject<INJECT;inject++) {
 342         //      /* injecting atoms */
 343         //      moldyn_add_schedule(&md,10,1.0);
 344         //}
 345
 346         /* schedule hook function */
 347         memset(&hookparam,0,sizeof(t_hp));
 348         moldyn_set_schedule_hook(&md,&hook,&hookparam);
 349
 350         /* activate logging */
 351         moldyn_set_log_dir(&md,argv[1]);
 352         moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
 353         moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
 354         moldyn_set_log(&md,LOG_TEMPERATURE,1);
 355         moldyn_set_log(&md,LOG_PRESSURE,1);
 356         moldyn_set_log(&md,VISUAL_STEP,100);
 357         moldyn_set_log(&md,SAVE_STEP,100);
 358         moldyn_set_log(&md,CREATE_REPORT,0);
 359
 360         /*
 361          * let's do the actual md algorithm now
 362          *
 363          * integration of newtons equations
 364          */
 365         moldyn_integrate(&md);
 366 #ifdef dEBUG
 367 return 0;
 368 #endif
 369
 370         /*
 371          * post processing the data
 372          */
 373
 374         /* close */
 375         moldyn_shutdown(&md);
 376
 377         return 0;
 378 }
 379