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         if(!(md->schedule.count%2)) {
  39                 /* add carbon at random place, and enable t scaling */
  40                 for(j=0;j<NR_ATOMS;j++) {
  41                 run=1;
  42                 while(run) {
  43                         r.x=rand_get_double(&(md->random))*md->dim.x;
  44                         r.y=rand_get_double(&(md->random))*md->dim.y;
  45                         r.z=rand_get_double(&(md->random))*md->dim.z;
  46                         for(i=0;i<md->count;i++) {
  47                                 atom=&(md->atom[i]);
  48                                 v3_sub(&dist,&(atom->r),&r);
  49                                 d=v3_absolute_square(&dist);
  50                                 if(d>TM_R_C)
  51                                         run=0;
  52                         }
  53                 }
  54                 v.x=0; v.y=0; v.z=0;
  55                 add_atom(md,C,M_C,1,
  56                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
  57                          &r,&v);
  58                 }
  59                 printf("adding atoms & enable t scaling\n");
  60                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  61         }
  62         else {
  63                 /* disable t scaling */
  64                 printf("disabling t scaling\n");
  65                 set_pt_scale(md,0,0,0,0);
  66         }
  67
  68         return 0;
  69 }
  70
  71 int main(int argc,char **argv) {
  72
  73         /* check argv */
  74         if(argc!=3) {
  75                 printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
  76                 return -1;
  77         }
  78
  79         /* main moldyn structure */
  80         t_moldyn md;
  81
  82         /* potential parameters */
  83         t_tersoff_mult_params tp;
  84         t_albe_mult_params ap;
  85
  86         /* atom injection counter */
  87         int inject;
  88
  89         /* testing location & velocity vector */
  90         t_3dvec r,v;
  91         memset(&r,0,sizeof(t_3dvec));
  92         memset(&v,0,sizeof(t_3dvec));
  93
  94         /* initialize moldyn */
  95         moldyn_init(&md,argc,argv);
  96
  97         /* choose integration algorithm */
  98         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
  99
 100         /* choose potential */
 101 #ifdef ALBE
 102         set_potential3b_j1(&md,albe_mult_3bp_j1);
 103         set_potential3b_k1(&md,albe_mult_3bp_k1);
 104         set_potential3b_j2(&md,albe_mult_3bp_j2);
 105         set_potential3b_k2(&md,albe_mult_3bp_k2);
 106 #else
 107         set_potential1b(&md,tersoff_mult_1bp);
 108         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 109         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 110         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 111         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 112 #endif
 113
 114 #ifdef ALBE
 115         set_potential_params(&md,&ap);
 116 #else
 117         set_potential_params(&md,&tp);
 118 #endif
 119
 120         /* cutoff radius */
 121 #ifdef ALBE
 122         set_cutoff(&md,ALBE_S_SI);
 123 #else
 124         set_cutoff(&md,TM_S_SI);
 125 #endif
 126
 127         /*
 128          * potential parameters
 129          */
 130
 131         /*
 132          * tersoff mult potential parameters for SiC
 133          */
 134         tp.S[0]=TM_S_SI;
 135         tp.R[0]=TM_R_SI;
 136         tp.A[0]=TM_A_SI;
 137         tp.B[0]=TM_B_SI;
 138         tp.lambda[0]=TM_LAMBDA_SI;
 139         tp.mu[0]=TM_MU_SI;
 140         tp.beta[0]=TM_BETA_SI;
 141         tp.n[0]=TM_N_SI;
 142         tp.c[0]=TM_C_SI;
 143         tp.d[0]=TM_D_SI;
 144         tp.h[0]=TM_H_SI;
 145
 146         tp.S[1]=TM_S_C;
 147         tp.R[1]=TM_R_C;
 148         tp.A[1]=TM_A_C;
 149         tp.B[1]=TM_B_C;
 150         tp.lambda[1]=TM_LAMBDA_C;
 151         tp.mu[1]=TM_MU_C;
 152         tp.beta[1]=TM_BETA_C;
 153         tp.n[1]=TM_N_C;
 154         tp.c[1]=TM_C_C;
 155         tp.d[1]=TM_D_C;
 156         tp.h[1]=TM_H_C;
 157
 158         tp.chi=TM_CHI_SIC;
 159
 160         tersoff_mult_complete_params(&tp);
 161
 162         /*
 163          * albe mult potential parameters for SiC
 164          */
 165         ap.S[0]=ALBE_S_SI;
 166         ap.R[0]=ALBE_R_SI;
 167         ap.A[0]=ALBE_A_SI;
 168         ap.B[0]=ALBE_B_SI;
 169         ap.r0[0]=ALBE_R0_SI;
 170         ap.lambda[0]=ALBE_LAMBDA_SI;
 171         ap.mu[0]=ALBE_MU_SI;
 172         ap.gamma[0]=ALBE_GAMMA_SI;
 173         ap.c[0]=ALBE_C_SI;
 174         ap.d[0]=ALBE_D_SI;
 175         ap.h[0]=ALBE_H_SI;
 176
 177         ap.S[1]=ALBE_S_C;
 178         ap.R[1]=ALBE_R_C;
 179         ap.A[1]=ALBE_A_C;
 180         ap.B[1]=ALBE_B_C;
 181         ap.r0[1]=ALBE_R0_C;
 182         ap.lambda[1]=ALBE_LAMBDA_C;
 183         ap.mu[1]=ALBE_MU_C;
 184         ap.gamma[1]=ALBE_GAMMA_C;
 185         ap.c[1]=ALBE_C_C;
 186         ap.d[1]=ALBE_D_C;
 187         ap.h[1]=ALBE_H_C;
 188
 189         ap.Smixed=ALBE_S_SIC;
 190         ap.Rmixed=ALBE_R_SIC;
 191         ap.Amixed=ALBE_A_SIC;
 192         ap.Bmixed=ALBE_B_SIC;
 193         ap.r0_mixed=ALBE_R0_SIC;
 194         ap.lambda_m=ALBE_LAMBDA_SIC;
 195         ap.mu_m=ALBE_MU_SIC;
 196         ap.gamma_m=ALBE_GAMMA_SIC;
 197         ap.c_mixed=ALBE_C_SIC;
 198         ap.d_mixed=ALBE_D_SIC;
 199         ap.h_mixed=ALBE_H_SIC;
 200
 201         albe_mult_complete_params(&ap);
 202
 203         /* set (initial) dimensions of simulation volume */
 204 #ifdef ALBE
 205         //set_dim(&md,8*ALBE_LC_SI,8*ALBE_LC_SI,8*ALBE_LC_SI,TRUE);
 206         //set_dim(&md,8*ALBE_LC_C,8*ALBE_LC_C,8*ALBE_LC_C,TRUE);
 207         set_dim(&md,8*ALBE_LC_SIC,8*ALBE_LC_SIC,8*ALBE_LC_SIC,TRUE);
 208 #else
 209         //set_dim(&md,8*LC_SI,8*LC_SI,8*LC_SI,TRUE);
 210         //set_dim(&md,8*LC_C,8*LC_C,8*LC_C,TRUE);
 211         set_dim(&md,8*TM_LC_SIC,8*TM_LC_SIC,8*TM_LC_SIC,TRUE);
 212 #endif
 213
 214         /* set periodic boundary conditions in all directions */
 215         set_pbc(&md,TRUE,TRUE,TRUE);
 216
 217         /* create the lattice / place atoms */
 218 #ifdef ALBE
 219         //create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
 220         //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
 221 #else
 222         //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 223 #endif
 224         //               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 225         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 226         //               0,8,8,8,NULL);
 227         //               1,8,8,8,NULL);
 228
 229         /* create zinkblende structure */
 230         /**/
 231 #ifdef ALBE
 232         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 233         create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
 234                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 235                        0,8,8,8,&r);
 236         r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
 237         create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
 238                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 239                        1,8,8,8,&r);
 240 #else
 241         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 242         create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
 243                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 244                        0,8,8,8,&r);
 245         r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
 246         create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
 247                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 248                        1,8,8,8,&r);
 249 #endif
 250         /**/
 251
 252         /* check for right atom placing */
 253         moldyn_bc_check(&md);
 254
 255         /* testing configuration */
 256         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 257         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 258         //r.y=0;                v.y=0;
 259         //r.z=0;                v.z=0;
 260         //add_atom(&md,SI,M_SI,0,
 261         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 262         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 263         //           &r,&v);
 264         //r.x=-r.x;     v.x=-v.x;
 265         //r.y=0;                v.y=0;
 266         //r.z=0;                v.z=0;
 267         //add_atom(&md,SI,M_SI,0,
 268         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 269         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 270         //           &r,&v);
 271         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 272         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 273         //r.y=0;                v.y=0;
 274         //r.x=0;                v.x=0;
 275         //add_atom(&md,SI,M_SI,0,
 276         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 277         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 278         //           &r,&v);
 279         //r.z=-r.z;     v.z=-v.z;
 280         //r.y=0;                v.y=0;
 281         //r.x=0;                v.x=0;
 282         //add_atom(&md,SI,M_SI,0,
 283         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 284         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 285         //           &r,&v);
 286
 287         /* set temperature & pressure */
 288         set_temperature(&md,atof(argv[2])+273.0);
 289         set_pressure(&md,BAR);
 290
 291         /* set amount of steps to skip before average calc */
 292         set_avg_skip(&md,1000);
 293
 294         /* set p/t scaling */
 295         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
 296         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 297         //                 T_SCALE_BERENDSEN,100.0);
 298         //set_pt_scale(&md,0,0,T_SCALE_dIRECT,1.0);
 299         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 300
 301         /* initial thermal fluctuations of particles (in equilibrium) */
 302         thermal_init(&md,TRUE);
 303
 304         /* create the simulation schedule */
 305         /* initial configuration */
 306         moldyn_add_schedule(&md,10000,1.0);
 307         //moldyn_add_schedule(&md,1000,1.0);
 308         //moldyn_add_schedule(&md,1000,1.0);
 309         //moldyn_add_schedule(&md,1000,1.0);
 310         //moldyn_add_schedule(&md,1000,1.0);
 311         //moldyn_add_schedule(&md,1000,1.0);
 312         /* adding atoms */
 313         //for(inject=0;inject<INJECT;inject++) {
 314         //      /* injecting atom and run with enabled t scaling */
 315         //      moldyn_add_schedule(&md,900,1.0);
 316         //      /* continue running with disabled t scaling */
 317         //      moldyn_add_schedule(&md,1100,1.0);
 318         //}
 319
 320
 321         /* schedule hook function */
 322         moldyn_set_schedule_hook(&md,&hook,NULL);
 323
 324         /* activate logging */
 325         moldyn_set_log_dir(&md,argv[1]);
 326         moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
 327         moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
 328         moldyn_set_log(&md,LOG_TEMPERATURE,1);
 329         moldyn_set_log(&md,LOG_PRESSURE,1);
 330         moldyn_set_log(&md,VISUAL_STEP,100);
 331         moldyn_set_log(&md,SAVE_STEP,100);
 332         moldyn_set_log(&md,CREATE_REPORT,0);
 333
 334         /*
 335          * let's do the actual md algorithm now
 336          *
 337          * integration of newtons equations
 338          */
 339         moldyn_integrate(&md);
 340 #ifdef dEBUG
 341 return 0;
 342 #endif
 343
 344         /*
 345          * post processing the data
 346          */
 347
 348         /* close */
 349         moldyn_shutdown(&md);
 350
 351         return 0;
 352 }
 353