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 // vortrag
  39 set_temperature(moldyn,(4-md->schedule.count)*1000.0);
  40 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  41
  42 return 0;
  43
  44         printf("\nschedule hook: ");
  45
  46         if(!(md->schedule.count%2)) {
  47                 /* add carbon at random place, and enable t scaling */
  48                 for(j=0;j<NR_ATOMS;j++) {
  49                 run=1;
  50                 while(run) {
  51                         r.x=rand_get_double(&(md->random))*md->dim.x;
  52                         r.y=rand_get_double(&(md->random))*md->dim.y;
  53                         r.z=rand_get_double(&(md->random))*md->dim.z;
  54                         for(i=0;i<md->count;i++) {
  55                                 atom=&(md->atom[i]);
  56                                 v3_sub(&dist,&(atom->r),&r);
  57                                 d=v3_absolute_square(&dist);
  58                                 if(d>TM_R_C)
  59                                         run=0;
  60                         }
  61                 }
  62                 v.x=0; v.y=0; v.z=0;
  63                 add_atom(md,C,M_C,1,
  64                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
  65                          &r,&v);
  66                 }
  67                 printf("adding atoms & enable t scaling\n");
  68                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  69         }
  70         else {
  71                 /* disable t scaling */
  72                 printf("disabling t scaling\n");
  73                 set_pt_scale(md,0,0,0,0);
  74         }
  75
  76         return 0;
  77 }
  78
  79 int main(int argc,char **argv) {
  80
  81         /* check argv */
  82         if(argc!=3) {
  83                 printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
  84                 return -1;
  85         }
  86
  87         /* main moldyn structure */
  88         t_moldyn md;
  89
  90         /* potential parameters */
  91         t_tersoff_mult_params tp;
  92         t_albe_mult_params ap;
  93
  94         /* atom injection counter */
  95         int inject;
  96
  97         /* testing location & velocity vector */
  98         t_3dvec r,v;
  99         memset(&r,0,sizeof(t_3dvec));
 100         memset(&v,0,sizeof(t_3dvec));
 101
 102         /* initialize moldyn */
 103         moldyn_init(&md,argc,argv);
 104
 105         /* choose integration algorithm */
 106         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 107
 108         /* choose potential */
 109 #ifdef ALBE
 110         set_potential3b_j1(&md,albe_mult_3bp_j1);
 111         set_potential3b_k1(&md,albe_mult_3bp_k1);
 112         set_potential3b_j2(&md,albe_mult_3bp_j2);
 113         set_potential3b_k2(&md,albe_mult_3bp_k2);
 114 #else
 115         set_potential1b(&md,tersoff_mult_1bp);
 116         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 117         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 118         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 119         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 120 #endif
 121
 122 #ifdef ALBE
 123         set_potential_params(&md,&ap);
 124 #else
 125         set_potential_params(&md,&tp);
 126 #endif
 127
 128         /* cutoff radius */
 129 #ifdef ALBE
 130         set_cutoff(&md,ALBE_S_SI);
 131 #else
 132         set_cutoff(&md,TM_S_SI);
 133 #endif
 134
 135         /*
 136          * potential parameters
 137          */
 138
 139         /*
 140          * tersoff mult potential parameters for SiC
 141          */
 142         tp.S[0]=TM_S_SI;
 143         tp.R[0]=TM_R_SI;
 144         tp.A[0]=TM_A_SI;
 145         tp.B[0]=TM_B_SI;
 146         tp.lambda[0]=TM_LAMBDA_SI;
 147         tp.mu[0]=TM_MU_SI;
 148         tp.beta[0]=TM_BETA_SI;
 149         tp.n[0]=TM_N_SI;
 150         tp.c[0]=TM_C_SI;
 151         tp.d[0]=TM_D_SI;
 152         tp.h[0]=TM_H_SI;
 153
 154         tp.S[1]=TM_S_C;
 155         tp.R[1]=TM_R_C;
 156         tp.A[1]=TM_A_C;
 157         tp.B[1]=TM_B_C;
 158         tp.lambda[1]=TM_LAMBDA_C;
 159         tp.mu[1]=TM_MU_C;
 160         tp.beta[1]=TM_BETA_C;
 161         tp.n[1]=TM_N_C;
 162         tp.c[1]=TM_C_C;
 163         tp.d[1]=TM_D_C;
 164         tp.h[1]=TM_H_C;
 165
 166         tp.chi=TM_CHI_SIC;
 167
 168         tersoff_mult_complete_params(&tp);
 169
 170         /*
 171          * albe mult potential parameters for SiC
 172          */
 173         ap.S[0]=ALBE_S_SI;
 174         ap.R[0]=ALBE_R_SI;
 175         ap.A[0]=ALBE_A_SI;
 176         ap.B[0]=ALBE_B_SI;
 177         ap.r0[0]=ALBE_R0_SI;
 178         ap.lambda[0]=ALBE_LAMBDA_SI;
 179         ap.mu[0]=ALBE_MU_SI;
 180         ap.gamma[0]=ALBE_GAMMA_SI;
 181         ap.c[0]=ALBE_C_SI;
 182         ap.d[0]=ALBE_D_SI;
 183         ap.h[0]=ALBE_H_SI;
 184
 185         ap.S[1]=ALBE_S_C;
 186         ap.R[1]=ALBE_R_C;
 187         ap.A[1]=ALBE_A_C;
 188         ap.B[1]=ALBE_B_C;
 189         ap.r0[1]=ALBE_R0_C;
 190         ap.lambda[1]=ALBE_LAMBDA_C;
 191         ap.mu[1]=ALBE_MU_C;
 192         ap.gamma[1]=ALBE_GAMMA_C;
 193         ap.c[1]=ALBE_C_C;
 194         ap.d[1]=ALBE_D_C;
 195         ap.h[1]=ALBE_H_C;
 196
 197         ap.Smixed=ALBE_S_SIC;
 198         ap.Rmixed=ALBE_R_SIC;
 199         ap.Amixed=ALBE_A_SIC;
 200         ap.Bmixed=ALBE_B_SIC;
 201         ap.r0_mixed=ALBE_R0_SIC;
 202         ap.lambda_m=ALBE_LAMBDA_SIC;
 203         ap.mu_m=ALBE_MU_SIC;
 204         ap.gamma_m=ALBE_GAMMA_SIC;
 205         ap.c_mixed=ALBE_C_SIC;
 206         ap.d_mixed=ALBE_D_SIC;
 207         ap.h_mixed=ALBE_H_SIC;
 208
 209         albe_mult_complete_params(&ap);
 210
 211         /* set (initial) dimensions of simulation volume */
 212         set_dim(&md,6*LC_SI_ALBE,6*LC_SI_ALBE,6*LC_SI_ALBE,TRUE);
 213         //set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
 214         //set_dim(&md,6*LC_C_ALBE,6*LC_C_ALBE,6*LC_C_ALBE,TRUE);
 215         //set_dim(&md,6*LC_C,6*LC_C,6*LC_C,TRUE);
 216         //set_dim(&md,6*LC_SIC_ALBE,6*LC_SIC_ALBE,6*LC_SIC_ALBE,TRUE);
 217
 218         /* set periodic boundary conditions in all directions */
 219         set_pbc(&md,TRUE,TRUE,TRUE);
 220
 221         /* create the lattice / place atoms */
 222         //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 223         //create_lattice(&md,DIAMOND,LC_C_ALBE,C,M_C,
 224         create_lattice(&md,DIAMOND,LC_SI_ALBE,SI,M_SI,
 225                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 226         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 227                        0,6,6,6,NULL);
 228         //               1,6,6,6,NULL);
 229
 230         /* create centered zinc blende lattice */
 231         /*
 232         r.x=0.5*0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
 233         create_lattice(&md,FCC,LC_SIC_ALBE,SI,M_SI,
 234                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 235                        0,6,6,6,&r);
 236         r.x+=0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
 237         create_lattice(&md,FCC,LC_SIC_ALBE,C,M_C,
 238                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 239                        1,6,6,6,&r);
 240         */
 241
 242         moldyn_bc_check(&md);
 243
 244         /* testing configuration */
 245         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 246         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 247         //r.y=0;                v.y=0;
 248         //r.z=0;                v.z=0;
 249         //add_atom(&md,SI,M_SI,0,
 250         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 251         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 252         //           &r,&v);
 253         //r.x=-r.x;     v.x=-v.x;
 254         //r.y=0;                v.y=0;
 255         //r.z=0;                v.z=0;
 256         //add_atom(&md,SI,M_SI,0,
 257         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 258         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 259         //           &r,&v);
 260         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 261         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 262         //r.y=0;                v.y=0;
 263         //r.x=0;                v.x=0;
 264         //add_atom(&md,SI,M_SI,0,
 265         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 266         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 267         //           &r,&v);
 268         //r.z=-r.z;     v.z=-v.z;
 269         //r.y=0;                v.y=0;
 270         //r.x=0;                v.x=0;
 271         //add_atom(&md,SI,M_SI,0,
 272         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 273         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 274         //           &r,&v);
 275
 276         /* set temperature & pressure */
 277         set_temperature(&md,atof(argv[2])+273.0);
 278         set_pressure(&md,BAR);
 279
 280         /* set p/t scaling */
 281         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 282         //                 T_SCALE_BERENDSEN,100.0);
 283         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 284         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 285
 286         /* initial thermal fluctuations of particles (in equilibrium) */
 287         thermal_init(&md,TRUE);
 288
 289         /* create the simulation schedule */
 290         /* initial configuration */
 291         moldyn_add_schedule(&md,10000,1.0);
 292         //moldyn_add_schedule(&md,1000,1.0);
 293         //moldyn_add_schedule(&md,1000,1.0);
 294         //moldyn_add_schedule(&md,1000,1.0);
 295         //moldyn_add_schedule(&md,1000,1.0);
 296         //moldyn_add_schedule(&md,1000,1.0);
 297         /* adding atoms */
 298         //for(inject=0;inject<INJECT;inject++) {
 299         //      /* injecting atom and run with enabled t scaling */
 300         //      moldyn_add_schedule(&md,900,1.0);
 301         //      /* continue running with disabled t scaling */
 302         //      moldyn_add_schedule(&md,1100,1.0);
 303         //}
 304
 305
 306         /* schedule hook function */
 307         moldyn_set_schedule_hook(&md,&hook,NULL);
 308
 309         /* activate logging */
 310         moldyn_set_log_dir(&md,argv[1]);
 311         moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
 312         moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
 313         moldyn_set_log(&md,LOG_TEMPERATURE,1);
 314         moldyn_set_log(&md,LOG_PRESSURE,1);
 315         moldyn_set_log(&md,VISUAL_STEP,100);
 316         moldyn_set_log(&md,SAVE_STEP,100);
 317         moldyn_set_log(&md,CREATE_REPORT,0);
 318
 319         /*
 320          * let's do the actual md algorithm now
 321          *
 322          * integration of newtons equations
 323          */
 324         moldyn_integrate(&md);
 325 #ifdef DEBUG
 326 return 0;
 327 #endif
 328
 329         /*
 330          * post processing the data
 331          */
 332
 333         /* response functions expressed by energy fluctuations */
 334         calc_fluctuations(1000.0,9999.0,&md);
 335         get_heat_capacity(&md);
 336
 337         /* close */
 338         moldyn_shutdown(&md);
 339
 340         return 0;
 341 }
 342