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            5
  29 #define PRERUN          200
  30 #define POSTRUN         500
  31
  32 typedef struct s_hp {
  33         int a_count;    /* atom count */
  34         u8 quit;        /* quit mark */
  35         int argc;       /* arg count */
  36         char **argv;    /* args */
  37 } t_hp;
  38
  39 int hook(void *moldyn,void *hook_params) {
  40
  41         t_moldyn *md;
  42         t_3dvec r,v,dist;
  43         double d;
  44         unsigned char run;
  45         int i,j;
  46         t_atom *atom;
  47         t_hp *hp;
  48
  49         md=moldyn;
  50         hp=hook_params;
  51
  52         /* quit */
  53         if(hp->quit)
  54                 return 0;
  55
  56         /* switch on t scaling */
  57         if(md->schedule.count==0)
  58                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  59
  60         /* last schedule add if there is enough carbon inside */
  61         if(hp->a_count==(INJECT*NR_ATOMS)) {
  62                 hp->quit=1;
  63                 moldyn_add_schedule(md,POSTRUN,1.0);
  64                 return 0;
  65         }
  66
  67         /* more relaxing time for too high temperatures */
  68         if(md->t-md->t_ref>T_C) {
  69                 moldyn_add_schedule(md,10,1.0);
  70                 return 0;
  71         }
  72
  73         /* inject carbon atoms */
  74         printf("injecting another %d carbon atoms ...(-> %d / %d)\n",
  75                NR_ATOMS,hp->a_count+NR_ATOMS,INJECT*NR_ATOMS);
  76         for(j=0;j<NR_ATOMS;j++) {
  77                 run=1;
  78                 while(run) {
  79                         /*
  80                         r.x=(rand_get_double(&(md->random))-0.5)*md->dim.x*0.37;
  81                         r.y=(rand_get_double(&(md->random))-0.5)*md->dim.y*0.37;
  82                         r.z=(rand_get_double(&(md->random))-0.5)*md->dim.z*0.37;
  83                         r.x=(1.0*atoi(hp->argv[3])-4.5)/9.0*ALBE_LC_SI;
  84                         r.y=(1.0*atoi(hp->argv[4])-4.5)/9.0*ALBE_LC_SI;
  85                         r.z=(1.0*atoi(hp->argv[5])-4.5)/9.0*ALBE_LC_SI;
  86                         */
  87                         r.x=(rand_get_double(&(md->random))-0.5)*LC_SI;
  88                         r.y=(rand_get_double(&(md->random))-0.5)*LC_SI;
  89                         r.z=(rand_get_double(&(md->random))-0.5)*LC_SI;
  90                         /* assume valid coordinates */
  91                         run=0;
  92                         for(i=0;i<md->count;i++) {
  93                                 atom=&(md->atom[i]);
  94                                 v3_sub(&dist,&(atom->r),&r);
  95                                 d=v3_absolute_square(&dist);
  96                                 /* reject coordinates */
  97                                 if(d<R_C) {
  98                                         run=1;
  99                                         break;
 100                                 }
 101                         }
 102                 }
 103                 v.x=0; v.y=0; v.z=0;
 104                 add_atom(md,C,M_C,1,
 105                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 106                          &r,&v);
 107         }
 108         hp->a_count+=NR_ATOMS;
 109
 110         /* add schedule for simulating injected atoms ;) */
 111         moldyn_add_schedule(md,10,1.0);
 112
 113         return 0;
 114 }
 115
 116 int main(int argc,char **argv) {
 117
 118         /* check argv */
 119         //if(argc!=3) {
 120         //      printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
 121         //      return -1;
 122         //}
 123
 124         /* main moldyn structure */
 125         t_moldyn md;
 126
 127         /* hook parameter structure */
 128         t_hp hookparam;
 129
 130         /* potential parameters */
 131         t_tersoff_mult_params tp;
 132         t_albe_mult_params ap;
 133
 134         /* testing location & velocity vector */
 135         t_3dvec r,v;
 136         memset(&r,0,sizeof(t_3dvec));
 137         memset(&v,0,sizeof(t_3dvec));
 138
 139         /* initialize moldyn */
 140         moldyn_init(&md,argc,argv);
 141
 142         /* choose integration algorithm */
 143         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 144
 145         /* choose potential */
 146 #ifdef ALBE
 147         set_potential3b_j1(&md,albe_mult_3bp_j1);
 148         set_potential3b_k1(&md,albe_mult_3bp_k1);
 149         set_potential3b_j2(&md,albe_mult_3bp_j2);
 150         set_potential3b_k2(&md,albe_mult_3bp_k2);
 151 #else
 152         set_potential1b(&md,tersoff_mult_1bp);
 153         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 154         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 155         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 156         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 157 #endif
 158
 159 #ifdef ALBE
 160         set_potential_params(&md,&ap);
 161 #else
 162         set_potential_params(&md,&tp);
 163 #endif
 164
 165         /* cutoff radius */
 166 #ifdef ALBE
 167         set_cutoff(&md,ALBE_S_SI);
 168 #else
 169         set_cutoff(&md,TM_S_SI);
 170 #endif
 171
 172         /*
 173          * potential parameters
 174          */
 175
 176         /*
 177          * tersoff mult potential parameters for SiC
 178          */
 179         tp.S[0]=TM_S_SI;
 180         tp.R[0]=TM_R_SI;
 181         tp.A[0]=TM_A_SI;
 182         tp.B[0]=TM_B_SI;
 183         tp.lambda[0]=TM_LAMBDA_SI;
 184         tp.mu[0]=TM_MU_SI;
 185         tp.beta[0]=TM_BETA_SI;
 186         tp.n[0]=TM_N_SI;
 187         tp.c[0]=TM_C_SI;
 188         tp.d[0]=TM_D_SI;
 189         tp.h[0]=TM_H_SI;
 190
 191         tp.S[1]=TM_S_C;
 192         tp.R[1]=TM_R_C;
 193         tp.A[1]=TM_A_C;
 194         tp.B[1]=TM_B_C;
 195         tp.lambda[1]=TM_LAMBDA_C;
 196         tp.mu[1]=TM_MU_C;
 197         tp.beta[1]=TM_BETA_C;
 198         tp.n[1]=TM_N_C;
 199         tp.c[1]=TM_C_C;
 200         tp.d[1]=TM_D_C;
 201         tp.h[1]=TM_H_C;
 202
 203         tp.chi=TM_CHI_SIC;
 204
 205         tersoff_mult_complete_params(&tp);
 206
 207         /*
 208          * albe mult potential parameters for SiC
 209          */
 210         ap.S[0]=ALBE_S_SI;
 211         ap.R[0]=ALBE_R_SI;
 212         ap.A[0]=ALBE_A_SI;
 213         ap.B[0]=ALBE_B_SI;
 214         ap.r0[0]=ALBE_R0_SI;
 215         ap.lambda[0]=ALBE_LAMBDA_SI;
 216         ap.mu[0]=ALBE_MU_SI;
 217         ap.gamma[0]=ALBE_GAMMA_SI;
 218         ap.c[0]=ALBE_C_SI;
 219         ap.d[0]=ALBE_D_SI;
 220         ap.h[0]=ALBE_H_SI;
 221
 222         ap.S[1]=ALBE_S_C;
 223         ap.R[1]=ALBE_R_C;
 224         ap.A[1]=ALBE_A_C;
 225         ap.B[1]=ALBE_B_C;
 226         ap.r0[1]=ALBE_R0_C;
 227         ap.lambda[1]=ALBE_LAMBDA_C;
 228         ap.mu[1]=ALBE_MU_C;
 229         ap.gamma[1]=ALBE_GAMMA_C;
 230         ap.c[1]=ALBE_C_C;
 231         ap.d[1]=ALBE_D_C;
 232         ap.h[1]=ALBE_H_C;
 233
 234         ap.Smixed=ALBE_S_SIC;
 235         ap.Rmixed=ALBE_R_SIC;
 236         ap.Amixed=ALBE_A_SIC;
 237         ap.Bmixed=ALBE_B_SIC;
 238         ap.r0_mixed=ALBE_R0_SIC;
 239         ap.lambda_m=ALBE_LAMBDA_SIC;
 240         ap.mu_m=ALBE_MU_SIC;
 241         ap.gamma_m=ALBE_GAMMA_SIC;
 242         ap.c_mixed=ALBE_C_SIC;
 243         ap.d_mixed=ALBE_D_SIC;
 244         ap.h_mixed=ALBE_H_SIC;
 245
 246         albe_mult_complete_params(&ap);
 247
 248         /* set (initial) dimensions of simulation volume */
 249 #ifdef ALBE
 250         set_dim(&md,LCNT*ALBE_LC_SI,LCNT*ALBE_LC_SI,LCNT*ALBE_LC_SI,TRUE);
 251         //set_dim(&md,LCNT*ALBE_LC_C,LCNT*ALBE_LC_C,LCNT*ALBE_LC_C,TRUE);
 252         //set_dim(&md,LCNT*ALBE_LC_SIC,LCNT*ALBE_LC_SIC,LCNT*ALBE_LC_SIC,TRUE);
 253 #else
 254         //set_dim(&md,LCNT*LC_SI,LCNT*LC_SI,LCNT*LC_SI,TRUE);
 255         //set_dim(&md,LCNT*LC_C,LCNT*LC_C,LCNT*LC_C,TRUE);
 256         set_dim(&md,LCNT*TM_LC_SIC,LCNT*TM_LC_SIC,LCNT*TM_LC_SIC,TRUE);
 257 #endif
 258
 259         /* set periodic boundary conditions in all directions */
 260         set_pbc(&md,TRUE,TRUE,TRUE);
 261
 262         /* create the lattice / place atoms */
 263 #ifdef ALBE
 264         create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
 265         //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 266 #else
 267         //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 268 #endif
 269                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 270         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 271                        0,LCNT,LCNT,LCNT,NULL);
 272         //               1,LCNT,LCNT,LCNT,NULL);
 273
 274         /* create zinkblende structure */
 275         /*
 276 #ifdef ALBE
 277         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 278         create_lattice(&md,FCC,ALBE_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*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 282         create_lattice(&md,FCC,ALBE_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 #else
 286         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 287         create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
 288                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 289                        0,LCNT,LCNT,LCNT,&r);
 290         r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 291         create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
 292                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 293                        1,LCNT,LCNT,LCNT,&r);
 294 #endif
 295         */
 296
 297         /* check for right atom placing */
 298         moldyn_bc_check(&md);
 299
 300         /* testing configuration */
 301         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 302         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 303         //r.y=0;                v.y=0;
 304         //r.z=0;                v.z=0;
 305         //add_atom(&md,SI,M_SI,0,
 306         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 307         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 308         //           &r,&v);
 309         //r.x=-r.x;     v.x=-v.x;
 310         //r.y=0;                v.y=0;
 311         //r.z=0;                v.z=0;
 312         //add_atom(&md,SI,M_SI,0,
 313         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 314         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 315         //           &r,&v);
 316         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 317         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 318         //r.y=0;                v.y=0;
 319         //r.x=0;                v.x=0;
 320         //add_atom(&md,SI,M_SI,0,
 321         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 322         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 323         //           &r,&v);
 324         //r.z=-r.z;     v.z=-v.z;
 325         //r.y=0;                v.y=0;
 326         //r.x=0;                v.x=0;
 327         //add_atom(&md,SI,M_SI,0,
 328         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 329         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 330         //           &r,&v);
 331
 332         /* set temperature & pressure */
 333         set_temperature(&md,atof(argv[2])+273.0);
 334         set_pressure(&md,BAR);
 335
 336         /* set amount of steps to skip before average calc */
 337         set_avg_skip(&md,PRERUN);
 338
 339         /* set p/t scaling */
 340         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
 341         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 342         //                 T_SCALE_BERENDSEN,100.0);
 343         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 344         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 345
 346         /* initial thermal fluctuations of particles (in equilibrium) */
 347         thermal_init(&md,TRUE);
 348
 349         /* create the simulation schedule */
 350         moldyn_add_schedule(&md,PRERUN,1.0);
 351
 352         /* schedule hook function */
 353         memset(&hookparam,0,sizeof(t_hp));
 354         hookparam.argc=argc;
 355         hookparam.argv=argv;
 356         moldyn_set_schedule_hook(&md,&hook,&hookparam);
 357
 358         /* activate logging */
 359         moldyn_set_log_dir(&md,argv[1]);
 360         moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
 361         moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
 362         moldyn_set_log(&md,LOG_TEMPERATURE,1);
 363         moldyn_set_log(&md,LOG_PRESSURE,1);
 364         moldyn_set_log(&md,VISUAL_STEP,100);
 365         moldyn_set_log(&md,SAVE_STEP,100);
 366         moldyn_set_log(&md,CREATE_REPORT,0);
 367
 368         /*
 369          * let's do the actual md algorithm now
 370          *
 371          * integration of newtons equations
 372          */
 373         moldyn_integrate(&md);
 374 #ifdef dEBUG
 375 return 0;
 376 #endif
 377
 378         /*
 379          * post processing the data
 380          */
 381
 382         /* close */
 383         moldyn_shutdown(&md);
 384
 385         return 0;
 386 }
 387