2 * sic.c - investigation of the sic precipitation process of silicon carbide
4 * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
14 #include "potentials/harmonic_oscillator.h"
15 #include "potentials/lennard_jones.h"
16 #include "potentials/tersoff.h"
17 //#include "potentials/tersoff_orig.h"
22 int hook(void *moldyn,void *hook_params) {
33 printf("\nschedule hook: ");
35 if(!(md->schedule.count%2)) {
36 /* add carbon at random place, and enable t scaling */
37 for(j=0;j<NR_ATOMS;j++) {
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++) {
45 v3_sub(&dist,&(atom->r),&r);
46 d=v3_absolute_square(&dist);
53 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
56 printf("adding atoms & enable t scaling\n");
57 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
60 /* disable t scaling */
61 printf("disabling t scaling\n");
62 set_pt_scale(md,0,0,0,0);
68 int main(int argc,char **argv) {
72 printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
76 /* main moldyn structure */
79 /* potential parameters */
82 t_tersoff_mult_params tp;
84 /* atom injection counter */
87 /* testing location & velocity vector */
89 memset(&r,0,sizeof(t_3dvec));
90 memset(&v,0,sizeof(t_3dvec));
92 /* initialize moldyn */
93 moldyn_init(&md,argc,argv);
95 /* choose integration algorithm */
96 set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
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);
115 set_cutoff(&md,TM_S_SI);
116 //set_cutoff(&md,LC_SI*sqrt(3.0));
117 //set_cutoff(&md,2.0*LC_SI);
120 * potential parameters
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));
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;
136 * tersoff mult potential parameters for SiC
142 tp.lambda[0]=TM_LAMBDA_SI;
144 tp.beta[0]=TM_BETA_SI;
154 tp.lambda[1]=TM_LAMBDA_C;
156 tp.beta[1]=TM_BETA_C;
164 tersoff_mult_complete_params(&tp);
166 /* set (initial) dimensions of simulation volume */
167 set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
169 /* set periodic boundary conditions in all directions */
170 set_pbc(&md,TRUE,TRUE,TRUE);
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,
179 moldyn_bc_check(&md);
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;
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,
190 //r.x=-r.x; v.x=-v.x;
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,
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;
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,
205 //r.z=-r.z; v.z=-v.z;
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,
213 /* set temperature & pressure */
214 set_temperature(&md,atof(argv[2])+273.0);
215 set_pressure(&md,BAR);
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);
223 /* initial thermal fluctuations of particles (in equilibrium) */
224 thermal_init(&md,TRUE);
226 /* create the simulation schedule */
227 /* initial configuration */
228 moldyn_add_schedule(&md,10000,1.0);
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);
237 /* schedule hook function */
238 moldyn_set_schedule_hook(&md,&hook,NULL);
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);
251 * let's do the actual md algorithm now
253 * integration of newtons equations
255 moldyn_integrate(&md);
258 moldyn_shutdown(&md);