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/tersoff.h"
  17 //#include "potentials/tersoff_orig.h"
  18
  19 #define INJECT          1
  20 #define NR_ATOMS        4
  21
  22 int hook(void *moldyn,void *hook_params) {
  23
  24         t_moldyn *md;
  25         t_3dvec r,v,dist;
  26         double d;
  27         unsigned char run;
  28         int i,j;
  29         t_atom *atom;
  30
  31         md=moldyn;
  32
  33         printf("\nschedule hook: ");
  34
  35         if(!(md->schedule.count%2)) {
  36                 /* add carbon at random place, and enable t scaling */
  37                 for(j=0;j<NR_ATOMS;j++) {
  38                 run=1;
  39                 while(run) {
  40                         r.x=rand_get_double(&(md->random))*md->dim.x;
  41                         r.y=rand_get_double(&(md->random))*md->dim.y;
  42                         r.z=rand_get_double(&(md->random))*md->dim.z;
  43                         for(i=0;i<md->count;i++) {
  44                                 atom=&(md->atom[i]);
  45                                 v3_sub(&dist,&(atom->r),&r);
  46                                 d=v3_absolute_square(&dist);
  47                                 if(d>TM_R_C)
  48                                         run=0;
  49                         }
  50                 }
  51                 v.x=0; v.y=0; v.z=0;
  52                 add_atom(md,C,M_C,1,
  53                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
  54                          &r,&v);
  55                 }
  56                 printf("adding atoms & enable t scaling\n");
  57                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  58         }
  59         else {
  60                 /* disable t scaling */
  61                 printf("disabling t scaling\n");
  62                 set_pt_scale(md,0,0,0,0);
  63         }
  64
  65         return 0;
  66 }
  67
  68 int main(int argc,char **argv) {
  69
  70         /* check argv */
  71         if(argc!=3) {
  72                 printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
  73                 return -1;
  74         }
  75
  76         /* main moldyn structure */
  77         t_moldyn md;
  78
  79         /* potential parameters */
  80         t_lj_params lj;
  81         t_ho_params ho;
  82         t_tersoff_mult_params tp;
  83
  84         /* atom injection counter */
  85         int inject;
  86
  87         /* testing location & velocity vector */
  88         t_3dvec r,v;
  89         memset(&r,0,sizeof(t_3dvec));
  90         memset(&v,0,sizeof(t_3dvec));
  91
  92         /* initialize moldyn */
  93         moldyn_init(&md,argc,argv);
  94
  95         /* choose integration algorithm */
  96         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
  97
  98         /* choose potential */
  99         set_potential1b(&md,tersoff_mult_1bp);
 100         set_potential2b(&md,tersoff_mult_2bp);
 101         //set_potential3b_j1(&md,tersoff_mult_2bp);
 102         //set_potential3b_k1(&md,tersoff_mult_3bp);
 103         //set_potential3b_j3(&md,tersoff_mult_post_2bp);
 104         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
 105         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
 106         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
 107         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 108         //set_potential2b(&md,lennard_jones);
 109         //set_potential2b(&md,harmonic_oscillator);
 110         set_potential_params(&md,&tp);
 111         //set_potential_params(&md,&lj);
 112         //set_potential_params(&md,&ho);
 113
 114         /* cutoff radius */
 115         set_cutoff(&md,TM_S_SI);
 116         //set_cutoff(&md,LC_SI*sqrt(3.0));
 117         //set_cutoff(&md,2.0*LC_SI);
 118
 119         /*
 120          * potential parameters
 121          */
 122
 123         /* lennard jones */
 124         lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA_SI;
 125         lj.sigma6*=lj.sigma6;
 126         lj.sigma12=lj.sigma6*lj.sigma6;
 127         lj.epsilon4=4.0*LJ_EPSILON_SI;
 128         lj.uc=lj.epsilon4*(lj.sigma12/pow(md.cutoff,12.0)-lj.sigma6/pow(md.cutoff,6));
 129
 130         /* harmonic oscillator */
 131         ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
 132         //ho.equilibrium_distance=LC_SI;
 133         ho.spring_constant=LJ_EPSILON_SI;
 134
 135         /*
 136          * tersoff mult potential parameters for SiC
 137          */
 138         tp.S[0]=TM_S_SI;
 139         tp.R[0]=TM_R_SI;
 140         tp.A[0]=TM_A_SI;
 141         tp.B[0]=TM_B_SI;
 142         tp.lambda[0]=TM_LAMBDA_SI;
 143         tp.mu[0]=TM_MU_SI;
 144         tp.beta[0]=TM_BETA_SI;
 145         tp.n[0]=TM_N_SI;
 146         tp.c[0]=TM_C_SI;
 147         tp.d[0]=TM_D_SI;
 148         tp.h[0]=TM_H_SI;
 149
 150         tp.S[1]=TM_S_C;
 151         tp.R[1]=TM_R_C;
 152         tp.A[1]=TM_A_C;
 153         tp.B[1]=TM_B_C;
 154         tp.lambda[1]=TM_LAMBDA_C;
 155         tp.mu[1]=TM_MU_C;
 156         tp.beta[1]=TM_BETA_C;
 157         tp.n[1]=TM_N_C;
 158         tp.c[1]=TM_C_C;
 159         tp.d[1]=TM_D_C;
 160         tp.h[1]=TM_H_C;
 161
 162         tp.chi=TM_CHI_SIC;
 163
 164         tersoff_mult_complete_params(&tp);
 165
 166         /* set (initial) dimensions of simulation volume */
 167         set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
 168
 169         /* set periodic boundary conditions in all directions */
 170         set_pbc(&md,TRUE,TRUE,TRUE);
 171
 172         /* create the lattice / place atoms */
 173         //create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
 174         //create_lattice(&md,FCC,LC_SI,SI,M_SI,
 175         create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 176                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 177         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 178                        0,6,6,6);
 179         moldyn_bc_check(&md);
 180
 181         /* testing configuration */
 182         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 183         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 184         //r.y=0;                v.y=0;
 185         //r.z=0;                v.z=0;
 186         //add_atom(&md,SI,M_SI,0,
 187         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 188         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 189         //           &r,&v);
 190         //r.x=-r.x;     v.x=-v.x;
 191         //r.y=0;                v.y=0;
 192         //r.z=0;                v.z=0;
 193         //add_atom(&md,SI,M_SI,0,
 194         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 195         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 196         //           &r,&v);
 197         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
 198         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 199         //r.y=0;                v.y=0;
 200         //r.x=0;                v.x=0;
 201         //add_atom(&md,SI,M_SI,0,
 202         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 203         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 204         //           &r,&v);
 205         //r.z=-r.z;     v.z=-v.z;
 206         //r.y=0;                v.y=0;
 207         //r.x=0;                v.x=0;
 208         //add_atom(&md,SI,M_SI,0,
 209         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 210         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 211         //           &r,&v);
 212
 213         /* set temperature & pressure */
 214         set_temperature(&md,atof(argv[2])+273.0);
 215         set_pressure(&md,BAR);
 216
 217         /* set p/t scaling */
 218         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 219         //                 T_SCALE_BERENDSEN,100.0);
 220         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 221         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 222
 223         /* initial thermal fluctuations of particles (in equilibrium) */
 224         thermal_init(&md,TRUE);
 225
 226         /* create the simulation schedule */
 227         /* initial configuration */
 228         moldyn_add_schedule(&md,10000,1.0);
 229         /* adding atoms */
 230         //for(inject=0;inject<INJECT;inject++) {
 231         //      /* injecting atom and run with enabled t scaling */
 232         //      moldyn_add_schedule(&md,900,1.0);
 233         //      /* continue running with disabled t scaling */
 234         //      moldyn_add_schedule(&md,1100,1.0);
 235         //}
 236
 237         /* schedule hook function */
 238         moldyn_set_schedule_hook(&md,&hook,NULL);
 239
 240         /* activate logging */
 241         moldyn_set_log_dir(&md,argv[1]);
 242         moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
 243         moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
 244         moldyn_set_log(&md,LOG_TEMPERATURE,1);
 245         moldyn_set_log(&md,LOG_PRESSURE,1);
 246         moldyn_set_log(&md,VISUAL_STEP,100);
 247         moldyn_set_log(&md,SAVE_STEP,100);
 248         moldyn_set_log(&md,CREATE_REPORT,0);
 249
 250         /*
 251          * let's do the actual md algorithm now
 252          *
 253          * integration of newtons equations
 254          */
 255         moldyn_integrate(&md);
 256
 257         /* close */
 258         moldyn_shutdown(&md);
 259
 260         return 0;
 261 }
 262