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"
27 int hook(void *moldyn,void *hook_params) {
39 set_temperature(moldyn,(4-md->schedule.count)*1000.0);
40 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
44 printf("\nschedule hook: ");
46 if(!(md->schedule.count%2)) {
47 /* add carbon at random place, and enable t scaling */
48 for(j=0;j<NR_ATOMS;j++) {
51 r.x=rand_get_double(&(md->random))*md->dim.x;
52 r.y=rand_get_double(&(md->random))*md->dim.y;
53 r.z=rand_get_double(&(md->random))*md->dim.z;
54 for(i=0;i<md->count;i++) {
56 v3_sub(&dist,&(atom->r),&r);
57 d=v3_absolute_square(&dist);
64 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
67 printf("adding atoms & enable t scaling\n");
68 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
71 /* disable t scaling */
72 printf("disabling t scaling\n");
73 set_pt_scale(md,0,0,0,0);
79 int main(int argc,char **argv) {
83 printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
87 /* main moldyn structure */
90 /* potential parameters */
91 t_tersoff_mult_params tp;
92 t_albe_mult_params ap;
94 /* atom injection counter */
97 /* testing location & velocity vector */
99 memset(&r,0,sizeof(t_3dvec));
100 memset(&v,0,sizeof(t_3dvec));
102 /* initialize moldyn */
103 moldyn_init(&md,argc,argv);
105 /* choose integration algorithm */
106 set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
108 /* choose potential */
110 set_potential3b_j1(&md,albe_mult_3bp_j1);
111 set_potential3b_k1(&md,albe_mult_3bp_k1);
112 set_potential3b_j2(&md,albe_mult_3bp_j2);
113 set_potential3b_k2(&md,albe_mult_3bp_k2);
115 set_potential1b(&md,tersoff_mult_1bp);
116 set_potential3b_j1(&md,tersoff_mult_3bp_j1);
117 set_potential3b_k1(&md,tersoff_mult_3bp_k1);
118 set_potential3b_j2(&md,tersoff_mult_3bp_j2);
119 set_potential3b_k2(&md,tersoff_mult_3bp_k2);
123 set_potential_params(&md,&ap);
125 set_potential_params(&md,&tp);
130 set_cutoff(&md,ALBE_S_SI);
132 set_cutoff(&md,TM_S_SI);
136 * potential parameters
140 * tersoff mult potential parameters for SiC
146 tp.lambda[0]=TM_LAMBDA_SI;
148 tp.beta[0]=TM_BETA_SI;
158 tp.lambda[1]=TM_LAMBDA_C;
160 tp.beta[1]=TM_BETA_C;
168 tersoff_mult_complete_params(&tp);
171 * albe mult potential parameters for SiC
178 ap.lambda[0]=ALBE_LAMBDA_SI;
180 ap.gamma[0]=ALBE_GAMMA_SI;
190 ap.lambda[1]=ALBE_LAMBDA_C;
192 ap.gamma[1]=ALBE_GAMMA_C;
197 ap.Smixed=ALBE_S_SIC;
198 ap.Rmixed=ALBE_R_SIC;
199 ap.Amixed=ALBE_A_SIC;
200 ap.Bmixed=ALBE_B_SIC;
201 ap.r0_mixed=ALBE_R0_SIC;
202 ap.lambda_m=ALBE_LAMBDA_SIC;
204 ap.gamma_m=ALBE_GAMMA_SIC;
205 ap.c_mixed=ALBE_C_SIC;
206 ap.d_mixed=ALBE_D_SIC;
207 ap.h_mixed=ALBE_H_SIC;
209 albe_mult_complete_params(&ap);
211 /* set (initial) dimensions of simulation volume */
213 //set_dim(&md,8*ALBE_LC_SI,8*ALBE_LC_SI,8*ALBE_LC_SI,TRUE);
214 //set_dim(&md,8*ALBE_LC_C,8*ALBE_LC_C,8*ALBE_LC_C,TRUE);
215 set_dim(&md,8*ALBE_LC_SIC,8*ALBE_LC_SIC,8*ALBE_LC_SIC,TRUE);
217 //set_dim(&md,8*LC_SI,8*LC_SI,8*LC_SI,TRUE);
218 //set_dim(&md,8*LC_C,8*LC_C,8*LC_C,TRUE);
219 set_dim(&md,8*TM_LC_SIC,8*TM_LC_SIC,8*TM_LC_SIC,TRUE);
222 /* set periodic boundary conditions in all directions */
223 set_pbc(&md,TRUE,TRUE,TRUE);
225 /* create the lattice / place atoms */
227 //create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
228 //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
230 //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
232 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
233 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
237 /* create zinkblende structure */
240 r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
241 create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
242 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
244 r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
245 create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
246 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
249 r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
250 create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
251 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
253 r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
254 create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
255 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
260 /* check for right atom placing */
261 moldyn_bc_check(&md);
263 /* testing configuration */
264 //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
265 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
268 //add_atom(&md,SI,M_SI,0,
269 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
270 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
272 //r.x=-r.x; v.x=-v.x;
275 //add_atom(&md,SI,M_SI,0,
276 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
277 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
279 //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
280 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
283 //add_atom(&md,SI,M_SI,0,
284 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
285 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
287 //r.z=-r.z; v.z=-v.z;
290 //add_atom(&md,SI,M_SI,0,
291 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
292 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
295 /* set temperature & pressure */
296 set_temperature(&md,atof(argv[2])+273.0);
297 set_pressure(&md,BAR);
299 /* set amount of steps to skip before average calc */
300 set_mean_skip(&md,500);
302 /* set p/t scaling */
303 //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
304 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
305 // T_SCALE_BERENDSEN,100.0);
306 //set_pt_scale(&md,0,0,T_SCALE_dIRECT,1.0);
307 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
309 /* initial thermal fluctuations of particles (in equilibrium) */
310 thermal_init(&md,TRUE);
312 /* create the simulation schedule */
313 /* initial configuration */
314 moldyn_add_schedule(&md,10000,1.0);
315 //moldyn_add_schedule(&md,1000,1.0);
316 //moldyn_add_schedule(&md,1000,1.0);
317 //moldyn_add_schedule(&md,1000,1.0);
318 //moldyn_add_schedule(&md,1000,1.0);
319 //moldyn_add_schedule(&md,1000,1.0);
321 //for(inject=0;inject<INJECT;inject++) {
322 // /* injecting atom and run with enabled t scaling */
323 // moldyn_add_schedule(&md,900,1.0);
324 // /* continue running with disabled t scaling */
325 // moldyn_add_schedule(&md,1100,1.0);
329 /* schedule hook function */
330 moldyn_set_schedule_hook(&md,&hook,NULL);
332 /* activate logging */
333 moldyn_set_log_dir(&md,argv[1]);
334 moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
335 moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
336 moldyn_set_log(&md,LOG_TEMPERATURE,1);
337 moldyn_set_log(&md,LOG_PRESSURE,1);
338 moldyn_set_log(&md,VISUAL_STEP,100);
339 moldyn_set_log(&md,SAVE_STEP,100);
340 moldyn_set_log(&md,CREATE_REPORT,0);
343 * let's do the actual md algorithm now
345 * integration of newtons equations
347 moldyn_integrate(&md);
353 * post processing the data
357 moldyn_shutdown(&md);