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_tersoff_mult_params tp;
  86         t_albe_mult_params ap;
  87
  88         /* atom injection counter */
  89         int inject;
  90
  91         /* testing location & velocity vector */
  92         t_3dvec r,v;
  93         memset(&r,0,sizeof(t_3dvec));
  94         memset(&v,0,sizeof(t_3dvec));
  95
  96         /* initialize moldyn */
  97         moldyn_init(&md,argc,argv);
  98
  99         /* choose integration algorithm */
 100         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 101
 102         /* choose potential */
 103 #ifdef ALBE
 104         set_potential3b_j1(&md,albe_mult_3bp_j1);
 105         set_potential3b_k1(&md,albe_mult_3bp_k1);
 106         set_potential3b_j2(&md,albe_mult_3bp_j2);
 107         set_potential3b_k2(&md,albe_mult_3bp_k2);
 108 #else
 109         set_potential1b(&md,tersoff_mult_1bp);
 110         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 111         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 112         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 113         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 114 #endif
 115
 116 #ifdef ALBE
 117         set_potential_params(&md,&ap);
 118 #else
 119         set_potential_params(&md,&tp);
 120 #endif
 121
 122         /* cutoff radius */
 123 #ifdef ALBE
 124         set_cutoff(&md,ALBE_S_SI);
 125 #else
 126         set_cutoff(&md,TM_S_SI);
 127 #endif
 128
 129         /*
 130          * potential parameters
 131          */
 132
 133         /*
 134          * tersoff mult potential parameters for SiC
 135          */
 136         tp.S[0]=TM_S_SI;
 137         tp.R[0]=TM_R_SI;
 138         tp.A[0]=TM_A_SI;
 139         tp.B[0]=TM_B_SI;
 140         tp.lambda[0]=TM_LAMBDA_SI;
 141         tp.mu[0]=TM_MU_SI;
 142         tp.beta[0]=TM_BETA_SI;
 143         tp.n[0]=TM_N_SI;
 144         tp.c[0]=TM_C_SI;
 145         tp.d[0]=TM_D_SI;
 146         tp.h[0]=TM_H_SI;
 147
 148         tp.S[1]=TM_S_C;
 149         tp.R[1]=TM_R_C;
 150         tp.A[1]=TM_A_C;
 151         tp.B[1]=TM_B_C;
 152         tp.lambda[1]=TM_LAMBDA_C;
 153         tp.mu[1]=TM_MU_C;
 154         tp.beta[1]=TM_BETA_C;
 155         tp.n[1]=TM_N_C;
 156         tp.c[1]=TM_C_C;
 157         tp.d[1]=TM_D_C;
 158         tp.h[1]=TM_H_C;
 159
 160         tp.chi=TM_CHI_SIC;
 161
 162         tersoff_mult_complete_params(&tp);
 163
 164         /*
 165          * albe mult potential parameters for SiC
 166          */
 167         ap.S[0]=ALBE_S_SI;
 168         ap.R[0]=ALBE_R_SI;
 169         ap.A[0]=ALBE_A_SI;
 170         ap.B[0]=ALBE_B_SI;
 171         ap.r0[0]=ALBE_R0_SI;
 172         ap.lambda[0]=ALBE_LAMBDA_SI;
 173         ap.mu[0]=ALBE_MU_SI;
 174         ap.gamma[0]=ALBE_GAMMA_SI;
 175         ap.c[0]=ALBE_C_SI;
 176         ap.d[0]=ALBE_D_SI;
 177         ap.h[0]=ALBE_H_SI;
 178
 179         ap.S[1]=ALBE_S_C;
 180         ap.R[1]=ALBE_R_C;
 181         ap.A[1]=ALBE_A_C;
 182         ap.B[1]=ALBE_B_C;
 183         ap.r0[1]=ALBE_R0_C;
 184         ap.lambda[1]=ALBE_LAMBDA_C;
 185         ap.mu[1]=ALBE_MU_C;
 186         ap.gamma[1]=ALBE_GAMMA_C;
 187         ap.c[1]=ALBE_C_C;
 188         ap.d[1]=ALBE_D_C;
 189         ap.h[1]=ALBE_H_C;
 190
 191         ap.Smixed=ALBE_S_SIC;
 192         ap.Rmixed=ALBE_R_SIC;
 193         ap.Amixed=ALBE_A_SIC;
 194         ap.Bmixed=ALBE_B_SIC;
 195         ap.r0_mixed=ALBE_R0_SIC;
 196         ap.lambda_m=ALBE_LAMBDA_SIC;
 197         ap.mu_m=ALBE_MU_SIC;
 198         ap.gamma_m=ALBE_GAMMA_SIC;
 199         ap.c_mixed=ALBE_C_SIC;
 200         ap.d_mixed=ALBE_D_SIC;
 201         ap.h_mixed=ALBE_H_SIC;
 202
 203         albe_mult_complete_params(&ap);
 204
 205         /* set (initial) dimensions of simulation volume */
 206         //set_dim(&md,6*LC_SI_ALBE,6*LC_SI_ALBE,6*LC_SI_ALBE,TRUE);
 207         //set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
 208         //set_dim(&md,6*LC_C_ALBE,6*LC_C_ALBE,6*LC_C_ALBE,TRUE);
 209         //set_dim(&md,6*LC_C,6*LC_C,6*LC_C,TRUE);
 210         set_dim(&md,6*LC_SIC_ALBE,6*LC_SIC_ALBE,6*LC_SIC_ALBE,TRUE);
 211
 212         /* set periodic boundary conditions in all directions */
 213         set_pbc(&md,TRUE,TRUE,TRUE);
 214
 215         /* create the lattice / place atoms */
 216         //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 217         //create_lattice(&md,DIAMOND,LC_C_ALBE,C,M_C,
 218         //create_lattice(&md,DIAMOND,LC_SI_ALBE,SI,M_SI,
 219         //               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 220         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 221         //               0,6,6,6,NULL);
 222         //               1,6,6,6,NULL);
 223
 224         /* create centered zinc blende lattice */
 225         /**/
 226         r.x=0.5*0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
 227         create_lattice(&md,FCC,LC_SIC_ALBE,SI,M_SI,
 228                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 229                        0,6,6,6,&r);
 230         r.x+=0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
 231         create_lattice(&md,FCC,LC_SIC_ALBE,C,M_C,
 232                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 233                        1,6,6,6,&r);
 234         /**/
 235
 236         moldyn_bc_check(&md);
 237
 238         /* testing configuration */
 239         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 240         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 241         //r.y=0;                v.y=0;
 242         //r.z=0;                v.z=0;
 243         //add_atom(&md,SI,M_SI,0,
 244         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 245         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 246         //           &r,&v);
 247         //r.x=-r.x;     v.x=-v.x;
 248         //r.y=0;                v.y=0;
 249         //r.z=0;                v.z=0;
 250         //add_atom(&md,SI,M_SI,0,
 251         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 252         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 253         //           &r,&v);
 254         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 255         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 256         //r.y=0;                v.y=0;
 257         //r.x=0;                v.x=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.z=-r.z;     v.z=-v.z;
 263         //r.y=0;                v.y=0;
 264         //r.x=0;                v.x=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
 270         /* set temperature & pressure */
 271         set_temperature(&md,atof(argv[2])+273.0);
 272         set_pressure(&md,BAR);
 273
 274         /* set p/t scaling */
 275         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 276         //                 T_SCALE_BERENDSEN,100.0);
 277         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 278         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 279
 280         /* initial thermal fluctuations of particles (in equilibrium) */
 281         thermal_init(&md,TRUE);
 282
 283         /* create the simulation schedule */
 284         /* initial configuration */
 285         moldyn_add_schedule(&md,10000,1.0);
 286         /* adding atoms */
 287         //for(inject=0;inject<INJECT;inject++) {
 288         //      /* injecting atom and run with enabled t scaling */
 289         //      moldyn_add_schedule(&md,900,1.0);
 290         //      /* continue running with disabled t scaling */
 291         //      moldyn_add_schedule(&md,1100,1.0);
 292         //}
 293
 294         /* schedule hook function */
 295         moldyn_set_schedule_hook(&md,&hook,NULL);
 296
 297         /* activate logging */
 298         moldyn_set_log_dir(&md,argv[1]);
 299         moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
 300         moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
 301         moldyn_set_log(&md,LOG_TEMPERATURE,1);
 302         moldyn_set_log(&md,LOG_PRESSURE,1);
 303         moldyn_set_log(&md,VISUAL_STEP,100);
 304         moldyn_set_log(&md,SAVE_STEP,100);
 305         moldyn_set_log(&md,CREATE_REPORT,0);
 306
 307         /*
 308          * let's do the actual md algorithm now
 309          *
 310          * integration of newtons equations
 311          */
 312         moldyn_integrate(&md);
 313 #ifdef DEBUG
 314 return 0;
 315 #endif
 316
 317         /* close */
 318         moldyn_shutdown(&md);
 319
 320         return 0;
 321 }
 322