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/albe.h"
19 #include "potentials/tersoff_orig.h"
21 #include "potentials/tersoff.h"
31 int a_count; /* atom count */
32 u8 quit; /* quit mark */
35 int hook(void *moldyn,void *hook_params) {
52 /* switch on t scaling */
53 if(md->schedule.count==0)
54 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
56 /* last schedule add if there is enough carbon inside */
57 if(hp->a_count==(INJECT*NR_ATOMS)) {
59 moldyn_add_schedule(md,5000,1.0);
63 /* more relaxing time for too high temperatures */
64 if(md->t-md->t_ref>T_C) {
65 moldyn_add_schedule(md,10,1.0);
69 /* inject carbon atoms */
70 printf("injecting another %d carbon atoms ...(-> %d / %d)\n",
71 NR_ATOMS,hp->a_count+NR_ATOMS,INJECT*NR_ATOMS);
72 for(j=0;j<NR_ATOMS;j++) {
75 r.x=(rand_get_double(&(md->random))-0.5)*md->dim.x*0.37;
76 r.y=(rand_get_double(&(md->random))-0.5)*md->dim.y*0.37;
77 r.z=(rand_get_double(&(md->random))-0.5)*md->dim.z*0.37;
78 /* assume valid coordinates */
80 for(i=0;i<md->count;i++) {
82 v3_sub(&dist,&(atom->r),&r);
83 d=v3_absolute_square(&dist);
84 /* reject coordinates */
93 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
96 hp->a_count+=NR_ATOMS;
98 /* add schedule for simulating injected atoms ;) */
99 moldyn_add_schedule(md,10,1.0);
104 int main(int argc,char **argv) {
108 printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
112 /* main moldyn structure */
115 /* hook parameter structure */
118 /* potential parameters */
119 t_tersoff_mult_params tp;
120 t_albe_mult_params ap;
122 /* atom injection counter */
125 /* testing location & velocity vector */
127 memset(&r,0,sizeof(t_3dvec));
128 memset(&v,0,sizeof(t_3dvec));
130 /* initialize moldyn */
131 moldyn_init(&md,argc,argv);
133 /* choose integration algorithm */
134 set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
136 /* choose potential */
138 set_potential3b_j1(&md,albe_mult_3bp_j1);
139 set_potential3b_k1(&md,albe_mult_3bp_k1);
140 set_potential3b_j2(&md,albe_mult_3bp_j2);
141 set_potential3b_k2(&md,albe_mult_3bp_k2);
143 set_potential1b(&md,tersoff_mult_1bp);
144 set_potential3b_j1(&md,tersoff_mult_3bp_j1);
145 set_potential3b_k1(&md,tersoff_mult_3bp_k1);
146 set_potential3b_j2(&md,tersoff_mult_3bp_j2);
147 set_potential3b_k2(&md,tersoff_mult_3bp_k2);
151 set_potential_params(&md,&ap);
153 set_potential_params(&md,&tp);
158 set_cutoff(&md,ALBE_S_SI);
160 set_cutoff(&md,TM_S_SI);
164 * potential parameters
168 * tersoff mult potential parameters for SiC
174 tp.lambda[0]=TM_LAMBDA_SI;
176 tp.beta[0]=TM_BETA_SI;
186 tp.lambda[1]=TM_LAMBDA_C;
188 tp.beta[1]=TM_BETA_C;
196 tersoff_mult_complete_params(&tp);
199 * albe mult potential parameters for SiC
206 ap.lambda[0]=ALBE_LAMBDA_SI;
208 ap.gamma[0]=ALBE_GAMMA_SI;
218 ap.lambda[1]=ALBE_LAMBDA_C;
220 ap.gamma[1]=ALBE_GAMMA_C;
225 ap.Smixed=ALBE_S_SIC;
226 ap.Rmixed=ALBE_R_SIC;
227 ap.Amixed=ALBE_A_SIC;
228 ap.Bmixed=ALBE_B_SIC;
229 ap.r0_mixed=ALBE_R0_SIC;
230 ap.lambda_m=ALBE_LAMBDA_SIC;
232 ap.gamma_m=ALBE_GAMMA_SIC;
233 ap.c_mixed=ALBE_C_SIC;
234 ap.d_mixed=ALBE_D_SIC;
235 ap.h_mixed=ALBE_H_SIC;
237 albe_mult_complete_params(&ap);
239 /* set (initial) dimensions of simulation volume */
241 set_dim(&md,LCNT*ALBE_LC_SI,LCNT*ALBE_LC_SI,LCNT*ALBE_LC_SI,TRUE);
242 //set_dim(&md,LCNT*ALBE_LC_C,LCNT*ALBE_LC_C,LCNT*ALBE_LC_C,TRUE);
243 //set_dim(&md,LCNT*ALBE_LC_SIC,LCNT*ALBE_LC_SIC,LCNT*ALBE_LC_SIC,TRUE);
245 //set_dim(&md,LCNT*LC_SI,LCNT*LC_SI,LCNT*LC_SI,TRUE);
246 //set_dim(&md,LCNT*LC_C,LCNT*LC_C,LCNT*LC_C,TRUE);
247 set_dim(&md,LCNT*TM_LC_SIC,LCNT*TM_LC_SIC,LCNT*TM_LC_SIC,TRUE);
250 /* set periodic boundary conditions in all directions */
251 set_pbc(&md,TRUE,TRUE,TRUE);
253 /* create the lattice / place atoms */
255 create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
256 //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
258 //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
260 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
261 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
262 0,LCNT,LCNT,LCNT,NULL);
263 // 1,LCNT,LCNT,LCNT,NULL);
265 /* create zinkblende structure */
268 r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
269 create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
270 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
271 0,LCNT,LCNT,LCNT,&r);
272 r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
273 create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
274 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
275 1,LCNT,LCNT,LCNT,&r);
277 r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
278 create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
279 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
280 0,LCNT,LCNT,LCNT,&r);
281 r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
282 create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
283 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
284 1,LCNT,LCNT,LCNT,&r);
288 /* check for right atom placing */
289 moldyn_bc_check(&md);
291 /* testing configuration */
292 //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
293 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
296 //add_atom(&md,SI,M_SI,0,
297 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
298 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
300 //r.x=-r.x; v.x=-v.x;
303 //add_atom(&md,SI,M_SI,0,
304 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
305 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
307 //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
308 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
311 //add_atom(&md,SI,M_SI,0,
312 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
313 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
315 //r.z=-r.z; v.z=-v.z;
318 //add_atom(&md,SI,M_SI,0,
319 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
320 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
323 /* set temperature & pressure */
324 set_temperature(&md,atof(argv[2])+273.0);
325 set_pressure(&md,BAR);
327 /* set amount of steps to skip before average calc */
328 set_avg_skip(&md,1000);
330 /* set p/t scaling */
331 //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
332 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
333 // T_SCALE_BERENDSEN,100.0);
334 //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
335 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
337 /* initial thermal fluctuations of particles (in equilibrium) */
338 thermal_init(&md,TRUE);
340 /* create the simulation schedule */
341 moldyn_add_schedule(&md,1000,1.0);
342 //moldyn_add_schedule(&md,1000,1.0);
343 //moldyn_add_schedule(&md,1000,1.0);
344 //moldyn_add_schedule(&md,1000,1.0);
345 //moldyn_add_schedule(&md,1000,1.0);
346 //moldyn_add_schedule(&md,1000,1.0);
348 //for(inject=0;inject<INJECT;inject++) {
349 // /* injecting atoms */
350 // moldyn_add_schedule(&md,10,1.0);
353 /* schedule hook function */
354 memset(&hookparam,0,sizeof(t_hp));
355 moldyn_set_schedule_hook(&md,&hook,&hookparam);
357 /* activate logging */
358 moldyn_set_log_dir(&md,argv[1]);
359 moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
360 moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
361 moldyn_set_log(&md,LOG_TEMPERATURE,1);
362 moldyn_set_log(&md,LOG_PRESSURE,1);
363 moldyn_set_log(&md,VISUAL_STEP,100);
364 moldyn_set_log(&md,SAVE_STEP,100);
365 moldyn_set_log(&md,CREATE_REPORT,0);
368 * let's do the actual md algorithm now
370 * integration of newtons equations
372 moldyn_integrate(&md);
378 * post processing the data
382 moldyn_shutdown(&md);