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        4
  26
  27 int hook(void *moldyn,void *hook_params) {
  28
  29         t_moldyn *md;
  30         t_3dvec r,v,dist;
  31         double d;
  32         unsigned char run;
  33         int i,j;
  34         t_atom *atom;
  35
  36         md=moldyn;
  37
  38         printf("\nschedule hook: ");
  39
  40         if(!(md->schedule.count%2)) {
  41                 /* add carbon at random place, and enable t scaling */
  42                 for(j=0;j<NR_ATOMS;j++) {
  43                 run=1;
  44                 while(run) {
  45                         r.x=rand_get_double(&(md->random))*md->dim.x;
  46                         r.y=rand_get_double(&(md->random))*md->dim.y;
  47                         r.z=rand_get_double(&(md->random))*md->dim.z;
  48                         for(i=0;i<md->count;i++) {
  49                                 atom=&(md->atom[i]);
  50                                 v3_sub(&dist,&(atom->r),&r);
  51                                 d=v3_absolute_square(&dist);
  52                                 if(d>TM_R_C)
  53                                         run=0;
  54                         }
  55                 }
  56                 v.x=0; v.y=0; v.z=0;
  57                 add_atom(md,C,M_C,1,
  58                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
  59                          &r,&v);
  60                 }
  61                 printf("adding atoms & enable t scaling\n");
  62                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  63         }
  64         else {
  65                 /* disable t scaling */
  66                 printf("disabling t scaling\n");
  67                 set_pt_scale(md,0,0,0,0);
  68         }
  69
  70         return 0;
  71 }
  72
  73 int main(int argc,char **argv) {
  74
  75         /* check argv */
  76         if(argc!=3) {
  77                 printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
  78                 return -1;
  79         }
  80
  81         /* main moldyn structure */
  82         t_moldyn md;
  83
  84         /* potential parameters */
  85         t_lj_params lj;
  86         t_ho_params ho;
  87         t_tersoff_mult_params tp;
  88         t_albe_mult_params ap;
  89
  90         /* atom injection counter */
  91         int inject;
  92
  93         /* testing location & velocity vector */
  94         t_3dvec r,v;
  95         memset(&r,0,sizeof(t_3dvec));
  96         memset(&v,0,sizeof(t_3dvec));
  97
  98         /* initialize moldyn */
  99         moldyn_init(&md,argc,argv);
 100
 101         /* choose integration algorithm */
 102         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 103
 104         /* choose potential */
 105         set_potential1b(&md,tersoff_mult_1bp);
 106 #ifdef TERSOFF_ORIG
 107         set_potential3b_j1(&md,tersoff_mult_2bp);
 108         set_potential3b_k1(&md,tersoff_mult_3bp);
 109         set_potential3b_j2(&md,tersoff_mult_post_2bp);
 110 #elif ALBE
 111         set_potential1b(&md,albe_mult_1bp);
 112         set_potential3b_j1(&md,albe_mult_3bp_j1);
 113         set_potential3b_k1(&md,albe_mult_3bp_k1);
 114         set_potential3b_j2(&md,albe_mult_3bp_j2);
 115         set_potential3b_k2(&md,albe_mult_3bp_k2);
 116 #else
 117         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 118         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 119         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 120         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 121 #endif
 122         //set_potential2b(&md,lennard_jones);
 123         //set_potential2b(&md,harmonic_oscillator);
 124
 125 #ifdef ALBE
 126         set_potential_params(&md,&ap);
 127 #else
 128         set_potential_params(&md,&tp);
 129 #endif
 130         //set_potential_params(&md,&lj);
 131         //set_potential_params(&md,&ho);
 132
 133         /* cutoff radius */
 134         set_cutoff(&md,ALBE_S_SI);
 135         //set_cutoff(&md,TM_S_SI);
 136         //set_cutoff(&md,LC_SI*sqrt(3.0));
 137         //set_cutoff(&md,2.0*LC_SI);
 138
 139         /*
 140          * potential parameters
 141          */
 142
 143         /* lennard jones */
 144         lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA_SI;
 145         lj.sigma6*=lj.sigma6;
 146         lj.sigma12=lj.sigma6*lj.sigma6;
 147         lj.epsilon4=4.0*LJ_EPSILON_SI;
 148         lj.uc=lj.epsilon4*(lj.sigma12/pow(md.cutoff,12.0)-lj.sigma6/pow(md.cutoff,6));
 149
 150         /* harmonic oscillator */
 151         ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
 152         //ho.equilibrium_distance=LC_SI;
 153         ho.spring_constant=LJ_EPSILON_SI;
 154
 155         /*
 156          * tersoff mult potential parameters for SiC
 157          */
 158         tp.S[0]=TM_S_SI;
 159         tp.R[0]=TM_R_SI;
 160         tp.A[0]=TM_A_SI;
 161         tp.B[0]=TM_B_SI;
 162         tp.lambda[0]=TM_LAMBDA_SI;
 163         tp.mu[0]=TM_MU_SI;
 164         tp.beta[0]=TM_BETA_SI;
 165         tp.n[0]=TM_N_SI;
 166         tp.c[0]=TM_C_SI;
 167         tp.d[0]=TM_D_SI;
 168         tp.h[0]=TM_H_SI;
 169
 170         tp.S[1]=TM_S_C;
 171         tp.R[1]=TM_R_C;
 172         tp.A[1]=TM_A_C;
 173         tp.B[1]=TM_B_C;
 174         tp.lambda[1]=TM_LAMBDA_C;
 175         tp.mu[1]=TM_MU_C;
 176         tp.beta[1]=TM_BETA_C;
 177         tp.n[1]=TM_N_C;
 178         tp.c[1]=TM_C_C;
 179         tp.d[1]=TM_D_C;
 180         tp.h[1]=TM_H_C;
 181
 182         tp.chi=TM_CHI_SIC;
 183
 184         tersoff_mult_complete_params(&tp);
 185
 186         /*
 187          * albe mult potential parameters for SiC
 188          */
 189         ap.S[0]=ALBE_S_SI;
 190         ap.R[0]=ALBE_R_SI;
 191         ap.A[0]=ALBE_A_SI;
 192         ap.B[0]=ALBE_B_SI;
 193         ap.r0[0]=ALBE_R0_SI;
 194         ap.lambda[0]=ALBE_LAMBDA_SI;
 195         ap.mu[0]=ALBE_MU_SI;
 196         ap.gamma[0]=ALBE_GAMMA_SI;
 197         ap.c[0]=ALBE_C_SI;
 198         ap.d[0]=ALBE_D_SI;
 199         ap.h[0]=ALBE_H_SI;
 200
 201         ap.S[1]=ALBE_S_C;
 202         ap.R[1]=ALBE_R_C;
 203         ap.A[1]=ALBE_A_C;
 204         ap.B[1]=ALBE_B_C;
 205         ap.r0[1]=ALBE_R0_C;
 206         ap.lambda[1]=ALBE_LAMBDA_C;
 207         ap.mu[1]=ALBE_MU_C;
 208         ap.gamma[1]=ALBE_GAMMA_C;
 209         ap.c[1]=ALBE_C_C;
 210         ap.d[1]=ALBE_D_C;
 211         ap.h[1]=ALBE_H_C;
 212
 213         ap.Smixed=ALBE_S_SIC;
 214         ap.Rmixed=ALBE_R_SIC;
 215         ap.Amixed=ALBE_A_SIC;
 216         ap.Bmixed=ALBE_B_SIC;
 217         ap.r0_mixed=ALBE_R0_SIC;
 218         ap.lambda_m=ALBE_LAMBDA_SIC;
 219         ap.mu_m=ALBE_MU_SIC;
 220
 221         albe_mult_complete_params(&ap);
 222
 223         /* set (initial) dimensions of simulation volume */
 224         set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
 225         //set_dim(&md,6*LC_C,6*LC_C,6*LC_C,TRUE);
 226         //set_dim(&md,6*TM_LC_3C_SIC,6*TM_LC_3C_SIC,6*TM_LC_3C_SIC,TRUE);
 227
 228         /* set periodic boundary conditions in all directions */
 229         set_pbc(&md,TRUE,TRUE,TRUE);
 230
 231         /* create the lattice / place atoms */
 232         //create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
 233         //create_lattice(&md,FCC,LC_SI,SI,M_SI,
 234         create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 235         //create_lattice(&md,DIAMOND,LC_C,C,M_C,
 236                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 237         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 238                        0,6,6,6,NULL);
 239         //               1,6,6,6,NULL);
 240
 241         /* create centered zinc blende lattice */
 242         //r.x=0.5*0.25*TM_LC_3C_SIC; r.y=r.x; r.z=r.x;
 243         //create_lattice(&md,FCC,TM_LC_3C_SIC,SI,M_SI,
 244         //               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 245         //               0,6,6,6,&r);
 246         //r.x+=0.25*TM_LC_3C_SIC; r.y=r.x; r.z=r.x;
 247         //create_lattice(&md,FCC,TM_LC_3C_SIC,C,M_C,
 248         //               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 249         //               1,6,6,6,&r);
 250
 251         moldyn_bc_check(&md);
 252
 253         /* testing configuration */
 254         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 255         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 256         //r.y=0;                v.y=0;
 257         //r.z=0;                v.z=0;
 258         //add_atom(&md,SI,M_SI,0,
 259         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 260         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 261         //           &r,&v);
 262         //r.x=-r.x;     v.x=-v.x;
 263         //r.y=0;                v.y=0;
 264         //r.z=0;                v.z=0;
 265         //add_atom(&md,SI,M_SI,0,
 266         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 267         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 268         //           &r,&v);
 269         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 270         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 271         //r.y=0;                v.y=0;
 272         //r.x=0;                v.x=0;
 273         //add_atom(&md,SI,M_SI,0,
 274         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 275         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 276         //           &r,&v);
 277         //r.z=-r.z;     v.z=-v.z;
 278         //r.y=0;                v.y=0;
 279         //r.x=0;                v.x=0;
 280         //add_atom(&md,SI,M_SI,0,
 281         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 282         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 283         //           &r,&v);
 284
 285         /* set temperature & pressure */
 286         set_temperature(&md,atof(argv[2])+273.0);
 287         set_pressure(&md,BAR);
 288
 289         /* set p/t scaling */
 290         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 291         //                 T_SCALE_BERENDSEN,100.0);
 292         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 293         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 294
 295         /* initial thermal fluctuations of particles (in equilibrium) */
 296         thermal_init(&md,TRUE);
 297
 298         /* create the simulation schedule */
 299         /* initial configuration */
 300         moldyn_add_schedule(&md,100,1.0);
 301         /* adding atoms */
 302         //for(inject=0;inject<INJECT;inject++) {
 303         //      /* injecting atom and run with enabled t scaling */
 304         //      moldyn_add_schedule(&md,900,1.0);
 305         //      /* continue running with disabled t scaling */
 306         //      moldyn_add_schedule(&md,1100,1.0);
 307         //}
 308
 309         /* schedule hook function */
 310         moldyn_set_schedule_hook(&md,&hook,NULL);
 311
 312         /* activate logging */
 313         moldyn_set_log_dir(&md,argv[1]);
 314         moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
 315         moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
 316         moldyn_set_log(&md,LOG_TEMPERATURE,1);
 317         moldyn_set_log(&md,LOG_PRESSURE,1);
 318         moldyn_set_log(&md,VISUAL_STEP,1);
 319         moldyn_set_log(&md,SAVE_STEP,1);
 320         moldyn_set_log(&md,CREATE_REPORT,0);
 321
 322         /*
 323          * let's do the actual md algorithm now
 324          *
 325          * integration of newtons equations
 326          */
 327         moldyn_integrate(&md);
 328 #ifdef DEBUG
 329 return 0;
 330 #endif
 331
 332         /* close */
 333         moldyn_shutdown(&md);
 334
 335         return 0;
 336 }
 337