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
  18 #define INJECT          20
  19 #define NR_ATOMS        20
  20
  21 int hook(void *moldyn,void *hook_params) {
  22
  23         t_moldyn *md;
  24         t_3dvec r,v,dist;
  25         double d;
  26         unsigned char run;
  27         int i,j;
  28         t_atom *atom;
  29
  30         md=moldyn;
  31
  32         printf("\nschedule hook: ");
  33
  34         if(!(md->schedule.count%2)) {
  35                 /* add carbon at random place, and enable t scaling */
  36                 for(j=0;j<NR_ATOMS;j++) {
  37                 run=1;
  38                 while(run) {
  39                         r.x=rand_get_double(&(md->random))*md->dim.x;
  40                         r.y=rand_get_double(&(md->random))*md->dim.y;
  41                         r.z=rand_get_double(&(md->random))*md->dim.z;
  42                         for(i=0;i<md->count;i++) {
  43                                 atom=&(md->atom[i]);
  44                                 v3_sub(&dist,&(atom->r),&r);
  45                                 d=v3_absolute_square(&dist);
  46                                 if(d>TM_R_C)
  47                                         run=0;
  48                         }
  49                 }
  50                 v.x=0; v.y=0; v.z=0;
  51                 add_atom(md,C,M_C,1,
  52                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
  53                          &r,&v);
  54                 }
  55                 printf("adding atoms & enable t scaling\n");
  56                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
  57         }
  58         else {
  59                 /* disable t scaling */
  60                 printf("disabling t scaling\n");
  61                 set_pt_scale(md,0,0,0,0);
  62         }
  63
  64         return 0;
  65 }
  66
  67 int main(int argc,char **argv) {
  68
  69         /* check argv */
  70         if(argc!=3) {
  71                 printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
  72                 return -1;
  73         }
  74
  75         /* main moldyn structure */
  76         t_moldyn md;
  77
  78         /* potential parameters */
  79         t_lj_params lj;
  80         t_ho_params ho;
  81         t_tersoff_mult_params tp;
  82
  83         /* atom injection counter */
  84         int inject;
  85
  86         /* testing location & velocity vector */
  87         t_3dvec r,v;
  88         memset(&r,0,sizeof(t_3dvec));
  89         memset(&v,0,sizeof(t_3dvec));
  90
  91         /* initialize moldyn */
  92         moldyn_init(&md,argc,argv);
  93
  94         /* choose integration algorithm */
  95         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
  96
  97         /* choose potential */
  98         set_potential1b(&md,tersoff_mult_1bp);
  99         set_potential2b(&md,tersoff_mult_2bp);
 100         set_potential2b_post(&md,tersoff_mult_post_2bp);
 101         set_potential3b(&md,tersoff_mult_3bp);
 102         //set_potential2b(&md,lennard_jones);
 103         //set_potential2b(&md,harmonic_oscillator);
 104         set_potential_params(&md,&tp);
 105         //set_potential_params(&md,&lj);
 106         //set_potential_params(&md,&ho);
 107
 108         /* cutoff radius */
 109         set_cutoff(&md,TM_S_SI);
 110         //set_cutoff(&md,LC_SI*sqrt(3.0));
 111         //set_cutoff(&md,2.0*LC_SI);
 112
 113         /*
 114          * potential parameters
 115          */
 116
 117         /* lennard jones */
 118         lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA_SI;
 119         lj.sigma6*=lj.sigma6;
 120         lj.sigma12=lj.sigma6*lj.sigma6;
 121         lj.epsilon4=4.0*LJ_EPSILON_SI;
 122         lj.uc=lj.epsilon4*(lj.sigma12/pow(md.cutoff,12.0)-lj.sigma6/pow(md.cutoff,6));
 123
 124         /* harmonic oscillator */
 125         ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
 126         //ho.equilibrium_distance=LC_SI;
 127         ho.spring_constant=LJ_EPSILON_SI;
 128
 129         /*
 130          * tersoff mult potential parameters for SiC
 131          */
 132         tp.S[0]=TM_S_SI;
 133         tp.R[0]=TM_R_SI;
 134         tp.A[0]=TM_A_SI;
 135         tp.B[0]=TM_B_SI;
 136         tp.lambda[0]=TM_LAMBDA_SI;
 137         tp.mu[0]=TM_MU_SI;
 138         tp.beta[0]=TM_BETA_SI;
 139         tp.n[0]=TM_N_SI;
 140         tp.c[0]=TM_C_SI;
 141         tp.d[0]=TM_D_SI;
 142         tp.h[0]=TM_H_SI;
 143
 144         tp.S[1]=TM_S_C;
 145         tp.R[1]=TM_R_C;
 146         tp.A[1]=TM_A_C;
 147         tp.B[1]=TM_B_C;
 148         tp.lambda[1]=TM_LAMBDA_C;
 149         tp.mu[1]=TM_MU_C;
 150         tp.beta[1]=TM_BETA_C;
 151         tp.n[1]=TM_N_C;
 152         tp.c[1]=TM_C_C;
 153         tp.d[1]=TM_D_C;
 154         tp.h[1]=TM_H_C;
 155
 156         tp.chi=TM_CHI_SIC;
 157
 158         tersoff_mult_complete_params(&tp);
 159
 160         /* set (initial) dimensions of simulation volume */
 161         set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
 162
 163         /* set periodic boundary conditions in all directions */
 164         set_pbc(&md,TRUE,TRUE,TRUE);
 165
 166         /* create the lattice / place atoms */
 167         //create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
 168         //create_lattice(&md,FCC,LC_SI,SI,M_SI,
 169         create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 170                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 171         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 172                        0,6,6,6);
 173         moldyn_bc_check(&md);
 174
 175         /* testing configuration */
 176         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
 177         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
 178         //r.y=0;                v.y=0;
 179         //r.z=0;                v.z=0;
 180         //add_atom(&md,SI,M_SI,0,
 181         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 182         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 183         //           &r,&v);
 184         //r.x=-r.x;     v.x=-v.x;
 185         //r.y=0;                v.y=0;
 186         //r.z=0;                v.z=0;
 187         //add_atom(&md,SI,M_SI,0,
 188         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 189         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 190         //           &r,&v);
 191         //r.x=0;                v.x=0;
 192         //r.y=0;        v.y=0;
 193         //r.z=sin(M_PI*60.0/180.0)*(TM_S_SI+TM_R_SI)/4.0;       v.z=0;
 194         //add_atom(&md,SI,M_SI,0,
 195         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 196         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 197         //           &r,&v);
 198
 199         /* set temperature & pressure */
 200         set_temperature(&md,atof(argv[2])+273.0);
 201         set_pressure(&md,ATM);
 202
 203         /* set p/t scaling */
 204         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
 205         //                 T_SCALE_BERENDSEN,100.0);
 206         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
 207         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 208
 209         /* initial thermal fluctuations of particles (in equilibrium) */
 210         thermal_init(&md,TRUE);
 211
 212         /* create the simulation schedule */
 213         /* initial configuration */
 214         moldyn_add_schedule(&md,500,1.0);
 215         /* adding atoms */
 216         for(inject=0;inject<INJECT;inject++) {
 217                 /* injecting atom and run with enabled t scaling */
 218                 moldyn_add_schedule(&md,400,1.0);
 219                 /* continue running with disabled t scaling */
 220                 moldyn_add_schedule(&md,100,1.0);
 221         }
 222
 223         /* schedule hook function */
 224         moldyn_set_schedule_hook(&md,&hook,NULL);
 225
 226         /* activate logging */
 227         moldyn_set_log_dir(&md,argv[1]);
 228         moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
 229         moldyn_set_log(&md,LOG_TOTAL_ENERGY,10);
 230         moldyn_set_log(&md,LOG_TEMPERATURE,10);
 231         moldyn_set_log(&md,LOG_PRESSURE,10);
 232         moldyn_set_log(&md,VISUAL_STEP,100);
 233         moldyn_set_log(&md,SAVE_STEP,100);
 234         moldyn_set_log(&md,CREATE_REPORT,0);
 235
 236         /*
 237          * let's do the actual md algorithm now
 238          *
 239          * integration of newtons equations
 240          */
 241         moldyn_integrate(&md);
 242
 243         /* close */
 244         moldyn_shutdown(&md);
 245
 246         return 0;
 247 }
 248