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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
12 /* potential */
13 #include "potentials/harmonic_oscillator.h"
14 #include "potentials/lennard_jones.h"
15 #include "potentials/albe.h"
16 #ifdef TERSOFF_ORIG
17 #include "potentials/tersoff_orig.h"
18 #else
19 #include "potentials/tersoff.h"
20 #endif
21
22 typedef struct s_hp {
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 */
29 } t_hp;
30
31 #define STATE_PRERUN    0x00
32 #define STATE_INSERT    0x01
33 #define STATE_POSTRUN   0x02
34
35 /* include the config file */
36 #include "config.h"
37
38 int insert_atoms(t_moldyn *moldyn) {
39
40         int i,j;
41         u8 run;
42         t_3dvec r,v,dist;
43         double d,dmin;
44
45         t_atom *atom;
46
47         atom=moldyn->atom;
48
49         v.x=0; v.y=0; v.z=0;
50
51         for(j=0;j<INS_ATOMS;j++) {
52                 run=1;
53                 while(run) {
54 #ifdef INS_TETRA
55                         // tetrahedral
56                         r.x=0.0;
57                         r.y=0.0;
58                         r.z=0.0;
59 #endif
60 #ifdef INS_HEXA
61                         // hexagonal
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;
65 #endif
66 #ifdef INS_110DB
67                         // 110 dumbbell
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;
73 #endif
74 #ifdef INS_RAND
75                         // random
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;
79 #endif
80                         // offset
81                         r.x+=INS_OFFSET;
82                         r.y+=INS_OFFSET;
83                         r.z+=INS_OFFSET;
84                         /* assume valid coordinates */
85                         run=0;
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 */
93                                 if(d<INS_R_C) {
94                                         //printf("atom %d - %f\n",i,d);
95                                         run=1;
96                                         break;
97                                 }
98                                 if(d<dmin)
99                                         dmin=d;
100                         }
101                 }
102                 add_atom(moldyn,INS_TYPE,INS_MASS,INS_BRAND,
103                          ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|\
104                          INS_ATTR,
105                          &r,&v);
106                 printf(" %02d: atom %d | %f %f %f | %f\n",
107                        j,moldyn->count-1,r.x,r.y,r.z,dmin);
108         }
109
110         return 0;
111 }
112
113 int sic_hook(void *moldyn,void *hook_params) {
114
115         t_hp *hp;
116         t_moldyn *md;
117         int steps;
118         double tau;
119         double dt;
120
121         hp=hook_params;
122         md=moldyn;
123
124         tau=1.0;
125         steps=0;
126
127         /* switch on t scaling */
128         if(md->schedule.count==0)
129                 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
130
131         /* my lousy state machine ! */
132
133         /* switch to insert state immediately */
134         if(hp->state==STATE_PRERUN)
135                 hp->state=STATE_INSERT;
136
137         /* act according to state */
138         switch(hp->state) {
139                 case STATE_INSERT:
140                         /* assigne values */
141                         steps=INS_RELAX;
142                         tau=INS_TAU;
143                         /* check temperature */
144                         dt=md->t_avg-md->t_ref;
145                         if(dt<0)
146                                 dt=-dt;
147                         if(dt>INS_DELTA_TC)
148                                 break;
149                         /* insert atoms */
150                         hp->insert_count+=1;
151                         printf("   ### insert atoms (%d/%d) ###\n",
152                                hp->insert_count*INS_ATOMS,INS_RUNS*INS_ATOMS);
153                         insert_atoms(md);
154                         /* change state after last insertion */
155                         if(hp->insert_count==INS_RUNS)
156                                 hp->state=STATE_POSTRUN;
157                         break;
158                 case STATE_POSTRUN:
159                         /* assigne values */
160                         steps=POST_RELAX;
161                         tau=POST_TAU;
162                         /* check temperature */
163                         dt=md->t_avg-md->t_ref;
164                         if(dt<0)
165                                 dt=-dt;
166                         if(dt>POST_DELTA_TC)
167                                 break;
168                         /* decrease temperature */
169                         hp->postrun_count+=1;
170                         printf(" ### postrun (%d/%d) ###\n",
171                                hp->postrun_count,POST_RUNS);
172                         set_temperature(md,md->t_ref-POST_DT);
173                         if(hp->postrun_count==POST_RUNS)
174                                 return 0;
175                         break;
176                 default:
177                         printf("[hook] FATAL (default case!?!)\n");
178                         break;
179         }
180
181         /* reset the average counters */
182         average_reset(md);
183
184         /* add schedule */
185         moldyn_add_schedule(md,steps,tau);
186
187         return 0;
188 }
189
190 int main(int argc,char **argv) {
191
192         /* main moldyn structure */
193         t_moldyn md;
194
195         /* hook parameter structure */
196         t_hp hookparam;
197
198         /* potential parameters */
199         t_tersoff_mult_params tp;
200         t_albe_mult_params ap;
201
202         /* testing location & velocity vector */
203         t_3dvec r,v;
204         memset(&r,0,sizeof(t_3dvec));
205         memset(&v,0,sizeof(t_3dvec));
206
207         /* initialize moldyn */
208         moldyn_init(&md,argc,argv);
209
210         /* choose integration algorithm */
211         set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
212
213         /* choose potential */
214 #ifdef ALBE
215         set_potential3b_j1(&md,albe_mult_3bp_j1);
216         set_potential3b_k1(&md,albe_mult_3bp_k1);
217         set_potential3b_j2(&md,albe_mult_3bp_j2);
218         set_potential3b_k2(&md,albe_mult_3bp_k2);
219 #else
220         set_potential1b(&md,tersoff_mult_1bp);
221         set_potential3b_j1(&md,tersoff_mult_3bp_j1);
222         set_potential3b_k1(&md,tersoff_mult_3bp_k1);
223         set_potential3b_j2(&md,tersoff_mult_3bp_j2);
224         set_potential3b_k2(&md,tersoff_mult_3bp_k2);
225 #endif
226
227 #ifdef ALBE
228         set_potential_params(&md,&ap);
229 #else
230         set_potential_params(&md,&tp);
231 #endif
232
233         /* cutoff radius & bondlen */
234 #ifdef ALBE
235         set_cutoff(&md,ALBE_S_SI);
236         set_bondlen(&md,ALBE_S_SI,ALBE_S_C,ALBE_S_SIC);
237         //set_cutoff(&md,ALBE_S_C);
238 #else
239         set_cutoff(&md,TM_S_SI);
240         set_bondlen(&md,TM_S_SI,TM_S_C,-1.0);
241         //set_cutoff(&md,TM_S_C);
242 #endif
243
244         /*
245          * potential parameters
246          */
247
248         /*
249          * tersoff mult potential parameters for SiC
250          */
251         tp.S[0]=TM_S_SI;
252         tp.R[0]=TM_R_SI;
253         tp.A[0]=TM_A_SI;
254         tp.B[0]=TM_B_SI;
255         tp.lambda[0]=TM_LAMBDA_SI;
256         tp.mu[0]=TM_MU_SI;
257         tp.beta[0]=TM_BETA_SI;
258         tp.n[0]=TM_N_SI;
259         tp.c[0]=TM_C_SI;
260         tp.d[0]=TM_D_SI;
261         tp.h[0]=TM_H_SI;
262
263         tp.S[1]=TM_S_C;
264         tp.R[1]=TM_R_C;
265         tp.A[1]=TM_A_C;
266         tp.B[1]=TM_B_C;
267         tp.lambda[1]=TM_LAMBDA_C;
268         tp.mu[1]=TM_MU_C;
269         tp.beta[1]=TM_BETA_C;
270         tp.n[1]=TM_N_C;
271         tp.c[1]=TM_C_C;
272         tp.d[1]=TM_D_C;
273         tp.h[1]=TM_H_C;
274
275         tp.chi=TM_CHI_SIC;
276
277         tersoff_mult_complete_params(&tp);
278
279         /*
280          * albe mult potential parameters for SiC
281          */
282         ap.S[0]=ALBE_S_SI;
283         ap.R[0]=ALBE_R_SI;
284         ap.A[0]=ALBE_A_SI;
285         ap.B[0]=ALBE_B_SI;
286         ap.r0[0]=ALBE_R0_SI;
287         ap.lambda[0]=ALBE_LAMBDA_SI;
288         ap.mu[0]=ALBE_MU_SI;
289         ap.gamma[0]=ALBE_GAMMA_SI;
290         ap.c[0]=ALBE_C_SI;
291         ap.d[0]=ALBE_D_SI;
292         ap.h[0]=ALBE_H_SI;
293
294         ap.S[1]=ALBE_S_C;
295         ap.R[1]=ALBE_R_C;
296         ap.A[1]=ALBE_A_C;
297         ap.B[1]=ALBE_B_C;
298         ap.r0[1]=ALBE_R0_C;
299         ap.lambda[1]=ALBE_LAMBDA_C;
300         ap.mu[1]=ALBE_MU_C;
301         ap.gamma[1]=ALBE_GAMMA_C;
302         ap.c[1]=ALBE_C_C;
303         ap.d[1]=ALBE_D_C;
304         ap.h[1]=ALBE_H_C;
305
306         ap.Smixed=ALBE_S_SIC;
307         ap.Rmixed=ALBE_R_SIC;
308         ap.Amixed=ALBE_A_SIC;
309         ap.Bmixed=ALBE_B_SIC;
310         ap.r0_mixed=ALBE_R0_SIC;
311         ap.lambda_m=ALBE_LAMBDA_SIC;
312         ap.mu_m=ALBE_MU_SIC;
313         ap.gamma_m=ALBE_GAMMA_SIC;
314         ap.c_mixed=ALBE_C_SIC;
315         ap.d_mixed=ALBE_D_SIC;
316         ap.h_mixed=ALBE_H_SIC;
317
318         albe_mult_complete_params(&ap);
319
320         /* set (initial) dimensions of simulation volume */
321 #ifdef ALBE
322         set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
323         //set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
324         //set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
325 #else
326         set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE);
327         //set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
328         //set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
329 #endif
330
331         /* set periodic boundary conditions in all directions */
332         set_pbc(&md,TRUE,TRUE,TRUE);
333
334         /* create the lattice / place atoms */
335         //
336 #ifdef ALBE
337         create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
338         //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
339 #else
340         create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
341 #endif
342                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
343         //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
344                        0,LCNTX,LCNTY,LCNTZ,NULL);
345         //               1,LCNTX,LCNTY,LCNTZ,NULL);
346
347         /* create zinkblende structure */
348         /*
349 #ifdef ALBE
350         r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
351         create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
352                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
353                        0,LCNTX,LCNTY,LCNTZ,&r);
354         r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
355         create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
356                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
357                        1,LCNTX,LCNTY,LCNTZ,&r);
358 #else
359         r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
360         create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
361                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
362                        0,LCNTX,LCNTY,LCNTZ,&r);
363         r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
364         create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
365                        ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
366                        1,LCNTX,LCNTY,LCNTZ,&r);
367 #endif
368         */
369
370         /* check for right atom placing */
371         moldyn_bc_check(&md);
372
373         /* testing configuration */
374         //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
375         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
376         //r.y=0;                v.y=0;
377         //r.z=0;                v.z=0;
378         //add_atom(&md,SI,M_SI,0,
379         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
380         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
381         //           &r,&v);
382         //r.x=-r.x;     v.x=-v.x;
383         //r.y=0;                v.y=0;
384         //r.z=0;                v.z=0;
385         //add_atom(&md,SI,M_SI,0,
386         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
387         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
388         //           &r,&v);
389         //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
390         //r.x=(TM_S_SI+TM_R_SI)/4.0;    v.x=0;
391         //r.y=0;                v.y=0;
392         //r.x=0;                v.x=0;
393         //add_atom(&md,SI,M_SI,0,
394         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
395         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
396         //           &r,&v);
397         //r.z=-r.z;     v.z=-v.z;
398         //r.y=0;                v.y=0;
399         //r.x=0;                v.x=0;
400         //add_atom(&md,SI,M_SI,0,
401         //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
402         //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
403         //           &r,&v);
404
405         /* set temperature & pressure */
406         set_temperature(&md,atof(argv[2])+273.0);
407         set_pressure(&md,BAR);
408
409         /* set amount of steps to skip before average calc */
410         set_avg_skip(&md,AVG_SKIP);
411
412         /* set p/t scaling */
413         //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
414         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
415         //                 T_SCALE_BERENDSEN,100.0);
416         //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
417         //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
418         
419         /* initial thermal fluctuations of particles (in equilibrium) */
420         thermal_init(&md,TRUE);
421
422         /* create the simulation schedule */
423         moldyn_add_schedule(&md,PRERUN,PRE_TAU);
424
425         /* schedule hook function */
426         memset(&hookparam,0,sizeof(t_hp));
427         hookparam.argc=argc;
428         hookparam.argv=argv;
429         moldyn_set_schedule_hook(&md,&sic_hook,&hookparam);
430         //moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam);
431         //moldyn_add_schedule(&md,POSTRUN,1.0);
432
433         /* activate logging */
434         moldyn_set_log_dir(&md,argv[1]);
435         moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
436         moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
437         moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
438         moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
439         moldyn_set_log(&md,VISUAL_STEP,LOG_V);
440         moldyn_set_log(&md,SAVE_STEP,LOG_S);
441         moldyn_set_log(&md,CREATE_REPORT,0);
442
443         /* next neighbour distance for critical checking */
444         set_nn_dist(&md,0.25*ALBE_LC_SI*sqrt(3.0));
445
446         /*
447          * let's do the actual md algorithm now
448          *
449          * integration of newtons equations
450          */
451         moldyn_integrate(&md);
452 #ifdef dEBUG
453 return 0;
454 #endif
455
456         /*
457          * post processing the data
458          */
459
460         /* close */
461         moldyn_shutdown(&md);
462         
463         return 0;
464 }
465