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 moldyn->atom[4372].r.x=(-0.5+0.125+0.125)*ALBE_LC_SI;
72 moldyn->atom[4372].r.y=(-0.5+0.125+0.125)*ALBE_LC_SI;
76 r.x=(-0.5+0.25)*ALBE_LC_SI;
77 r.y=(-0.5+0.25)*ALBE_LC_SI;
78 r.z=(-0.1)*ALBE_LC_SI;
79 moldyn->atom[4372].r.z=(-0.4)*ALBE_LC_SI;
83 r.x=INS_UX*ALBE_LC_SI;
84 r.y=INS_UY*ALBE_LC_SI;
85 r.z=INS_UZ*ALBE_LC_SI;
89 #ifdef INS_DYNAMIC_LEN
90 r.x=(rand_get_double(&(moldyn->random))-0.5)*\
92 r.y=(rand_get_double(&(moldyn->random))-0.5)*\
94 r.z=(rand_get_double(&(moldyn->random))-0.5)*\
97 r.x=(rand_get_double(&(moldyn->random))-0.5)*INS_LENX;
98 r.y=(rand_get_double(&(moldyn->random))-0.5)*INS_LENY;
99 r.z=(rand_get_double(&(moldyn->random))-0.5)*INS_LENZ;
106 /* assume valid coordinates */
108 dmin=10000000000.0; // for sure too high!
109 for(i=0;i<moldyn->count;i++) {
110 atom=&(moldyn->atom[i]);
111 v3_sub(&dist,&(atom->r),&r);
112 check_per_bound(moldyn,&dist);
113 d=v3_absolute_square(&dist);
114 /* reject coordinates */
116 //printf("atom %d - %f\n",i,d);
124 add_atom(moldyn,INS_TYPE,INS_BRAND,
125 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|\
128 printf(" %02d: atom %d | %f %f %f | %f\n",
129 j,moldyn->count-1,r.x,r.y,r.z,dmin);
135 int sic_hook(void *moldyn,void *hook_params) {
150 /* switch on t scaling */
151 if(md->schedule.count==0)
152 set_pt_scale(md,P_SCALE_BERENDSEN,P_SCALE_TAU,
153 T_SCALE_BERENDSEN,T_SCALE_TAU);
155 /* my lousy state machine ! */
157 /* switch to insert state immediately */
158 if(hp->state==STATE_PRERUN)
159 hp->state=STATE_INSERT;
169 printf("[sic hook] unknown state\n");
173 /* act according to state */
181 /* check temperature */
182 dt=md->t_avg-md->t_ref;
183 dp=md->p_avg-md->p_ref;
188 if((dt>INS_DELTA_TC)|(dp>INS_DELTA_PC))
191 /* immediately go on if no job is to be done */
192 if(hp->insert_count==INS_RUNS) {
193 printf(" --- leaving insert state ---\n");
194 hp->state=STATE_POSTRUN;
198 /* else -> insert atoms */
200 printf(" ### insert atoms (%d/%d) ###\n",
201 hp->insert_count*INS_ATOMS,INS_RUNS*INS_ATOMS);
211 /* check temperature */
212 dt=md->t_avg-md->t_ref;
213 dp=md->p_avg-md->p_ref;
218 if((dt>POST_DELTA_TC)|(dp>POST_DELTA_PC))
221 /* immediately return if no job is to be done */
222 if(hp->postrun_count==POST_RUNS) {
223 printf(" --- leaving post run state ---\n");
228 hp->postrun_count+=1;
229 printf(" ### postrun (%d/%d) ###\n",
230 hp->postrun_count,POST_RUNS);
231 set_temperature(md,md->t_ref-POST_DT);
235 /* reset the average counters */
239 moldyn_add_schedule(md,steps,tau);
244 int main(int argc,char **argv) {
246 /* main moldyn structure */
249 /* hook parameter structure */
252 /* testing location & velocity vector */
254 memset(&r,0,sizeof(t_3dvec));
255 memset(&v,0,sizeof(t_3dvec));
257 /* initialize moldyn */
258 moldyn_init(&md,argc,argv);
260 /* choose integration algorithm */
261 set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
263 /* choose potential */
265 if(set_potential(&md,MOLDYN_POTENTIAL_AM)<0)
268 if(set_potential(&md,MOLDYN_POTENTIAL_TM)<0)
272 /* cutoff radius & bondlen */
274 set_cutoff(&md,ALBE_S_SI);
275 //set_cutoff(&md,ALBE_S_C);
277 set_cutoff(&md,TM_S_SI);
278 //set_cutoff(&md,TM_S_C);
282 * potential parameters
287 * tersoff mult potential parameters for SiC
289 tersoff_mult_set_params(&md,SI,C);
292 * albe mult potential parameters for SiC
294 albe_mult_set_params(&md,SI,C);
297 /* set (initial) dimensions of simulation volume */
300 set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
303 set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
306 set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
310 set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE);
313 set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
316 set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
320 /* set periodic boundary conditions in all directions */
321 set_pbc(&md,TRUE,TRUE,TRUE);
323 /* create the lattice / place atoms */
328 create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,
329 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
330 0,LCNTX,LCNTY,LCNTZ,NULL,0,NULL);
333 create_lattice(&md,DIAMOND,ALBE_LC_C,C,
334 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
335 1,LCNTX,LCNTY,LCNTZ,NULL,0,NULL);
339 create_lattice(&md,DIAMOND,LC_SI,SI,
340 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
341 0,LCNTX,LCNTY,LCNTZ,NULL,0,NULL);
344 create_lattice(&md,DIAMOND,LC_C,SI,
345 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
346 1,LCNTX,LCNTY,LCNTZ,NULL,0,NULL);
353 r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
354 create_lattice(&md,FCC,ALBE_LC_SIC,SI,
355 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
356 0,LCNTX,LCNTY,LCNTZ,&r,0,NULL);
357 r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
358 create_lattice(&md,FCC,ALBE_LC_SIC,C,
359 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB|ATOM_ATTR_VB,
360 1,LCNTX,LCNTY,LCNTZ,&r,0,NULL);
362 r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
363 create_lattice(&md,FCC,TM_LC_SIC,SI,
364 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
365 0,LCNTX,LCNTY,LCNTZ,&r,0,NULL);
366 r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
367 create_lattice(&md,FCC,TM_LC_SIC,C,
368 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
369 1,LCNTX,LCNTY,LCNTZ,&r,0,NULL);
373 /* check for right atom placing */
374 moldyn_bc_check(&md);
376 /* testing configuration */
377 //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
378 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
381 //add_atom(&md,SI,M_SI,0,
382 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
383 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
385 //r.x=-r.x; v.x=-v.x;
388 //add_atom(&md,SI,M_SI,0,
389 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
390 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
392 //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
393 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
396 //add_atom(&md,SI,M_SI,0,
397 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
398 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
400 //r.z=-r.z; v.z=-v.z;
403 //add_atom(&md,SI,M_SI,0,
404 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
405 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
408 /* set temperature & pressure */
409 set_temperature(&md,atof(argv[2])+273.0);
410 set_pressure(&md,0.0);
412 /* set amount of steps to skip before average calc */
413 set_avg_skip(&md,AVG_SKIP);
415 /* set p/t scaling */
416 //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
417 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.01/(100*GPA),
418 // T_SCALE_BERENDSEN,100.0);
419 //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
420 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
422 /* initial thermal fluctuations of particles (in equilibrium) */
423 thermal_init(&md,TRUE);
425 /* create the simulation schedule */
426 moldyn_add_schedule(&md,PRERUN,PRE_TAU);
428 /* schedule hook function */
429 memset(&hookparam,0,sizeof(t_hp));
432 moldyn_set_schedule_hook(&md,&sic_hook,&hookparam);
433 //moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam);
434 //moldyn_add_schedule(&md,POSTRUN,1.0);
436 /* activate logging */
437 moldyn_set_log_dir(&md,argv[1]);
438 moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
439 moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
440 moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
441 moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
442 moldyn_set_log(&md,LOG_VOLUME,LOG_V);
443 moldyn_set_log(&md,VISUAL_STEP,LOG_A);
444 moldyn_set_log(&md,SAVE_STEP,LOG_S);
445 moldyn_set_log(&md,CREATE_REPORT,0);
447 /* next neighbour distance for critical checking */
448 set_nn_dist(&md,0.25*ALBE_LC_SI*sqrt(3.0));
451 * let's do the actual md algorithm now
453 * integration of newtons equations
455 moldyn_integrate(&md);
461 * post processing the data
465 moldyn_shutdown(&md);