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
  17 #ifdef TERSOFF_ORIG
  18 #include "potentials/tersoff_orig.h"
  19 #else
  20 #include "potentials/tersoff.h"
  21 #endif
  22
  23 #define INJECT          1
  24 #define NR_ATOMS        4
  25
  26 int hook(void *moldyn,void *hook_params) {
  27
  28         t_moldyn *md;
  29         t_3dvec r,v,dist;
  30         double d;
  31         unsigned char run;
  32         int i,j;
  33         t_atom *atom;
  34
  35         md=moldyn;
  36
  37         printf("\nschedule hook: ");
  38
  39         if(!(md->schedule.count%2)) {
  40                 /* add carbon at random place, and enable t scaling */
  41                 for(j=0;j<NR_ATOMS;j++) {
  42                 run=1;
  43                 while(run) {
  44                         r.x=rand_get_double(&(md->random))*md->dim.x;
  45                         r.y=rand_get_double(&(md->random))*md->dim.y;
  46                         r.z=rand_get_double(&(md->random))*md->dim.z;
  47                         for(i=0;i<md->count;i++) {
  48                                 atom=&(md->atom[i]);
  49                                 v3_sub(&dist,&(atom->r),&r);
  50                                 d=v3_absolute_square(&dist);
  51                                 if(d>TM_R_C)
  52                                         run=0;
  53                         }
  54                 }
  55                 v.x=0; v.y=0; v.z=0;
  56                 add_atom(md,C,M_C,1,
  57                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
  58                          &r,&v);
  59                 }
  60                 printf("adding atoms & enable t scaling\n");
  61                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  62         }
  63         else {
  64                 /* disable t scaling */
  65                 printf("disabling t scaling\n");
  66                 set_pt_scale(md,0,0,0,0);
  67         }
  68
  69         return 0;
  70 }
  71
  72 int main(int argc,char **argv) {
  73
  74         /* check argv */
  75         if(argc!=3) {
  76                 printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
  77                 return -1;
  78         }
  79
  80         /* main moldyn structure */
  81         t_moldyn md;
  82
  83         /* potential parameters */
  84         t_lj_params lj;
  85         t_ho_params ho;
  86         t_tersoff_mult_params tp;
  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         set_potential1b(&md,tersoff_mult_1bp);
 104 #ifdef TERSOFF_ORIG
 105         set_potential3b_j1(&md,tersoff_mult_2bp);
 106         set_potential3b_k1(&md,tersoff_mult_3bp);
 107         set_potential3b_j2(&md,tersoff_mult_post_2bp);
 108 #else
 109         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 110         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 111         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 112         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 113 #endif
 114         //set_potential2b(&md,lennard_jones);
 115         //set_potential2b(&md,harmonic_oscillator);
 116         set_potential_params(&md,&tp);
 117         //set_potential_params(&md,&lj);
 118         //set_potential_params(&md,&ho);
 119
 120         /* cutoff radius */
 121         set_cutoff(&md,TM_S_SI);
 122         //set_cutoff(&md,LC_SI*sqrt(3.0));
 123         //set_cutoff(&md,2.0*LC_SI);
 124
 125         /*
 126          * potential parameters
 127          */
 128
 129         /* lennard jones */
 130         lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA_SI;
 131         lj.sigma6*=lj.sigma6;
 132         lj.sigma12=lj.sigma6*lj.sigma6;
 133         lj.epsilon4=4.0*LJ_EPSILON_SI;
 134         lj.uc=lj.epsilon4*(lj.sigma12/pow(md.cutoff,12.0)-lj.sigma6/pow(md.cutoff,6));
 135
 136         /* harmonic oscillator */
 137         ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
 138         //ho.equilibrium_distance=LC_SI;
 139         ho.spring_constant=LJ_EPSILON_SI;
 140
 141         /*
 142          * tersoff mult potential parameters for SiC
 143          */
 144         tp.S[0]=TM_S_SI;
 145         tp.R[0]=TM_R_SI;
 146         tp.A[0]=TM_A_SI;
 147         tp.B[0]=TM_B_SI;
 148         tp.lambda[0]=TM_LAMBDA_SI;
 149         tp.mu[0]=TM_MU_SI;
 150         tp.beta[0]=TM_BETA_SI;
 151         tp.n[0]=TM_N_SI;
 152         tp.c[0]=TM_C_SI;
 153         tp.d[0]=TM_D_SI;
 154         tp.h[0]=TM_H_SI;
 155
 156         tp.S[1]=TM_S_C;
 157         tp.R[1]=TM_R_C;
 158         tp.A[1]=TM_A_C;
 159         tp.B[1]=TM_B_C;
 160         tp.lambda[1]=TM_LAMBDA_C;
 161         tp.mu[1]=TM_MU_C;
 162         tp.beta[1]=TM_BETA_C;
 163         tp.n[1]=TM_N_C;
 164         tp.c[1]=TM_C_C;
 165         tp.d[1]=TM_D_C;
 166         tp.h[1]=TM_H_C;
 167
 168         tp.chi=TM_CHI_SIC;
 169
 170         tersoff_mult_complete_params(&tp);
 171
 172         /* set (initial) dimensions of simulation volume */
 173         //set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
 174         set_dim(&md,6*TM_LC_3C_SIC,6*TM_LC_3C_SIC,6*TM_LC_3C_SIC,TRUE);
 175
 176         /* set periodic boundary conditions in all directions */
 177         set_pbc(&md,TRUE,TRUE,TRUE);
 178
 179         /* create the lattice / place atoms */
 180         //create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
 181         //create_lattice(&md,FCC,LC_SI,SI,M_SI,
 182         //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 183         //create_lattice(&md,DIAMOND,LC_C,C,M_C,
 184         //               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 185         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 186         //               1,6,6,6,NULL);
 187
 188         /* create centered zinc blende lattice */
 189         r.x=0.5*0.25*TM_LC_3C_SIC; r.y=r.x; r.z=r.x;
 190         create_lattice(&md,FCC,TM_LC_3C_SIC,SI,M_SI,
 191                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 192                        0,6,6,6,&r);
 193         r.x+=0.25*TM_LC_3C_SIC; r.y=r.x; r.z=r.x;
 194         create_lattice(&md,FCC,TM_LC_3C_SIC,C,M_C,
 195                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 196                        1,6,6,6,&r);
 197         moldyn_bc_check(&md);
 198
 199         /* testing configuration */
 200         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 201         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 202         //r.y=0;                v.y=0;
 203         //r.z=0;                v.z=0;
 204         //add_atom(&md,SI,M_SI,0,
 205         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 206         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 207         //           &r,&v);
 208         //r.x=-r.x;     v.x=-v.x;
 209         //r.y=0;                v.y=0;
 210         //r.z=0;                v.z=0;
 211         //add_atom(&md,SI,M_SI,0,
 212         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 213         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 214         //           &r,&v);
 215         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 216         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 217         //r.y=0;                v.y=0;
 218         //r.x=0;                v.x=0;
 219         //add_atom(&md,SI,M_SI,0,
 220         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 221         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 222         //           &r,&v);
 223         //r.z=-r.z;     v.z=-v.z;
 224         //r.y=0;                v.y=0;
 225         //r.x=0;                v.x=0;
 226         //add_atom(&md,SI,M_SI,0,
 227         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 228         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 229         //           &r,&v);
 230
 231         /* set temperature & pressure */
 232         set_temperature(&md,atof(argv[2])+273.0);
 233         set_pressure(&md,BAR);
 234
 235         /* set p/t scaling */
 236         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 237         //                 T_SCALE_BERENDSEN,100.0);
 238         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 239         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 240
 241         /* initial thermal fluctuations of particles (in equilibrium) */
 242         thermal_init(&md,TRUE);
 243
 244         /* create the simulation schedule */
 245         /* initial configuration */
 246         moldyn_add_schedule(&md,1000,1.0);
 247         /* adding atoms */
 248         //for(inject=0;inject<INJECT;inject++) {
 249         //      /* injecting atom and run with enabled t scaling */
 250         //      moldyn_add_schedule(&md,900,1.0);
 251         //      /* continue running with disabled t scaling */
 252         //      moldyn_add_schedule(&md,1100,1.0);
 253         //}
 254
 255         /* schedule hook function */
 256         moldyn_set_schedule_hook(&md,&hook,NULL);
 257
 258         /* activate logging */
 259         moldyn_set_log_dir(&md,argv[1]);
 260         moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
 261         moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
 262         moldyn_set_log(&md,LOG_TEMPERATURE,1);
 263         moldyn_set_log(&md,LOG_PRESSURE,1);
 264         moldyn_set_log(&md,VISUAL_STEP,10);
 265         moldyn_set_log(&md,SAVE_STEP,10);
 266         moldyn_set_log(&md,CREATE_REPORT,0);
 267
 268         /*
 269          * let's do the actual md algorithm now
 270          *
 271          * integration of newtons equations
 272          */
 273         moldyn_integrate(&md);
 274 #ifdef DEBUG
 275 return 0;
 276 #endif
 277
 278         /* close */
 279         moldyn_shutdown(&md);
 280
 281         return 0;
 282 }
 283