2 * sic.c - investigation of the sic precipitation process of silicon carbide
4 * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
13 #include "potentials/harmonic_oscillator.h"
14 #include "potentials/lennard_jones.h"
15 #include "potentials/albe.h"
17 #include "potentials/tersoff_orig.h"
19 #include "potentials/tersoff.h"
23 int prerun_count; /* prerun count */
24 int insert_count; /* insert count */
25 int postrun_count; /* post run count */
26 unsigned char state; /* current state */
27 int argc; /* arg count */
28 char **argv; /* args */
31 #define STATE_PRERUN 0x00
32 #define STATE_INSERT 0x01
33 #define STATE_POSTRUN 0x02
35 /* include the config file */
38 int insert_atoms(t_moldyn *moldyn) {
51 for(j=0;j<INS_ATOMS;j++) {
62 r.x=-1.0/8.0*ALBE_LC_SI;
63 r.y=-1.0/8.0*ALBE_LC_SI;
64 r.z=1.0/8.0*ALBE_LC_SI;
68 r.x=(-0.5+0.25+0.125)*ALBE_LC_SI;
69 r.y=(-0.5+0.25+0.125)*ALBE_LC_SI;
70 r.z=(-0.5+0.25)*ALBE_LC_SI;
71 md->atom[4372].r.x=(-0.5+0.125+0.125)*ALBE_LC_SI;
72 md->atom[4372].r.y=(-0.5+0.125+0.125)*ALBE_LC_SI;
76 r.x=(rand_get_double(&(moldyn->random))-0.5)*INS_LENX;
77 r.y=(rand_get_double(&(moldyn->random))-0.5)*INS_LENY;
78 r.z=(rand_get_double(&(moldyn->random))-0.5)*INS_LENZ;
84 /* assume valid coordinates */
86 dmin=10000000000.0; // for sure too high!
87 for(i=0;i<moldyn->count;i++) {
88 atom=&(moldyn->atom[i]);
89 v3_sub(&dist,&(atom->r),&r);
90 check_per_bound(moldyn,&dist);
91 d=v3_absolute_square(&dist);
92 /* reject coordinates */
94 //printf("atom %d - %f\n",i,d);
102 add_atom(moldyn,INS_TYPE,INS_MASS,INS_BRAND,
103 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|\
104 //ATOM_ATTR_HB|ATOM_ATTR_VB,
107 printf(" %02d: atom %d | %f %f %f | %f\n",
108 j,moldyn->count-1,r.x,r.y,r.z,dmin);
114 int sic_hook(void *moldyn,void *hook_params) {
125 /* switch on t scaling */
126 if(md->schedule.count==0)
127 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
129 /* my lousy state machine ! */
131 /* switch to insert state immediately */
132 if(hp->state==STATE_PRERUN)
133 hp->state=STATE_INSERT;
135 /* act according to state */
141 /* check temperature */
142 dt=md->t_avg-md->t_ref;
149 printf(" ### insert atoms (%d/%d) ###\n",
150 hp->insert_count*INS_ATOMS,INS_RUNS*INS_ATOMS);
152 /* change state after last insertion */
153 if(hp->insert_count==INS_RUNS)
154 hp->state=STATE_POSTRUN;
160 /* check temperature */
161 dt=md->t_avg-md->t_ref;
166 /* decrease temperature */
167 hp->postrun_count+=1;
168 printf(" ### postrun (%d/%d) ###\n",
169 hp->postrun_count,POST_RUNS);
170 set_temperature(md,md->t_ref-POST_DT);
171 if(hp->postrun_count==POST_RUNS)
175 printf("[hook] FATAL (default case!?!)\n");
179 /* reset the average counters */
183 moldyn_add_schedule(md,steps,tau);
188 int main(int argc,char **argv) {
190 /* main moldyn structure */
193 /* hook parameter structure */
196 /* potential parameters */
197 t_tersoff_mult_params tp;
198 t_albe_mult_params ap;
200 /* testing location & velocity vector */
202 memset(&r,0,sizeof(t_3dvec));
203 memset(&v,0,sizeof(t_3dvec));
205 /* initialize moldyn */
206 moldyn_init(&md,argc,argv);
208 /* choose integration algorithm */
209 set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
211 /* choose potential */
213 set_potential3b_j1(&md,albe_mult_3bp_j1);
214 set_potential3b_k1(&md,albe_mult_3bp_k1);
215 set_potential3b_j2(&md,albe_mult_3bp_j2);
216 set_potential3b_k2(&md,albe_mult_3bp_k2);
218 set_potential1b(&md,tersoff_mult_1bp);
219 set_potential3b_j1(&md,tersoff_mult_3bp_j1);
220 set_potential3b_k1(&md,tersoff_mult_3bp_k1);
221 set_potential3b_j2(&md,tersoff_mult_3bp_j2);
222 set_potential3b_k2(&md,tersoff_mult_3bp_k2);
226 set_potential_params(&md,&ap);
228 set_potential_params(&md,&tp);
231 /* cutoff radius & bondlen */
233 set_cutoff(&md,ALBE_S_SI);
234 set_bondlen(&md,ALBE_S_SI,ALBE_S_C,ALBE_S_SIC);
235 //set_cutoff(&md,ALBE_S_C);
237 set_cutoff(&md,TM_S_SI);
238 set_bondlen(&md,TM_S_SI,TM_S_C,-1.0);
239 //set_cutoff(&md,TM_S_C);
243 * potential parameters
247 * tersoff mult potential parameters for SiC
253 tp.lambda[0]=TM_LAMBDA_SI;
255 tp.beta[0]=TM_BETA_SI;
265 tp.lambda[1]=TM_LAMBDA_C;
267 tp.beta[1]=TM_BETA_C;
275 tersoff_mult_complete_params(&tp);
278 * albe mult potential parameters for SiC
285 ap.lambda[0]=ALBE_LAMBDA_SI;
287 ap.gamma[0]=ALBE_GAMMA_SI;
297 ap.lambda[1]=ALBE_LAMBDA_C;
299 ap.gamma[1]=ALBE_GAMMA_C;
304 ap.Smixed=ALBE_S_SIC;
305 ap.Rmixed=ALBE_R_SIC;
306 ap.Amixed=ALBE_A_SIC;
307 ap.Bmixed=ALBE_B_SIC;
308 ap.r0_mixed=ALBE_R0_SIC;
309 ap.lambda_m=ALBE_LAMBDA_SIC;
311 ap.gamma_m=ALBE_GAMMA_SIC;
312 ap.c_mixed=ALBE_C_SIC;
313 ap.d_mixed=ALBE_D_SIC;
314 ap.h_mixed=ALBE_H_SIC;
316 albe_mult_complete_params(&ap);
318 /* set (initial) dimensions of simulation volume */
320 set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
321 //set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
322 //set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
324 set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE);
325 //set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
326 //set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
329 /* set periodic boundary conditions in all directions */
330 set_pbc(&md,TRUE,TRUE,TRUE);
332 /* create the lattice / place atoms */
335 create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
336 //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
338 create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
340 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
341 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
342 0,LCNTX,LCNTY,LCNTZ,NULL);
343 // 1,LCNTX,LCNTY,LCNTZ,NULL);
345 /* create zinkblende structure */
348 r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
349 create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
350 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
351 0,LCNTX,LCNTY,LCNTZ,&r);
352 r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
353 create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
354 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
355 1,LCNTX,LCNTY,LCNTZ,&r);
357 r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
358 create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
359 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
360 0,LCNTX,LCNTY,LCNTZ,&r);
361 r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
362 create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
363 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
364 1,LCNTX,LCNTY,LCNTZ,&r);
368 /* check for right atom placing */
369 moldyn_bc_check(&md);
371 /* testing configuration */
372 //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
373 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
376 //add_atom(&md,SI,M_SI,0,
377 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
378 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
380 //r.x=-r.x; v.x=-v.x;
383 //add_atom(&md,SI,M_SI,0,
384 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
385 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
387 //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
388 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
391 //add_atom(&md,SI,M_SI,0,
392 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
393 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
395 //r.z=-r.z; v.z=-v.z;
398 //add_atom(&md,SI,M_SI,0,
399 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
400 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
403 /* set temperature & pressure */
404 set_temperature(&md,atof(argv[2])+273.0);
405 set_pressure(&md,BAR);
407 /* set amount of steps to skip before average calc */
408 set_avg_skip(&md,AVG_SKIP);
410 /* set p/t scaling */
411 //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
412 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
413 // T_SCALE_BERENDSEN,100.0);
414 //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
415 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
417 /* initial thermal fluctuations of particles (in equilibrium) */
418 thermal_init(&md,TRUE);
420 /* create the simulation schedule */
421 moldyn_add_schedule(&md,PRERUN,PRE_TAU);
423 /* schedule hook function */
424 memset(&hookparam,0,sizeof(t_hp));
427 moldyn_set_schedule_hook(&md,&sic_hook,&hookparam);
428 //moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam);
429 //moldyn_add_schedule(&md,POSTRUN,1.0);
431 /* activate logging */
432 moldyn_set_log_dir(&md,argv[1]);
433 moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
434 moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
435 moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
436 moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
437 moldyn_set_log(&md,VISUAL_STEP,LOG_V);
438 moldyn_set_log(&md,SAVE_STEP,LOG_S);
439 moldyn_set_log(&md,CREATE_REPORT,0);
442 * let's do the actual md algorithm now
444 * integration of newtons equations
446 moldyn_integrate(&md);
452 * post processing the data
456 moldyn_shutdown(&md);