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,6*LC_SI_ALBE,6*LC_SI_ALBE,6*LC_SI_ALBE,TRUE);
214 //set_dim(&md,6*LC_C_ALBE,6*LC_C_ALBE,6*LC_C_ALBE,TRUE);
215 //set_dim(&md,6*LC_SIC_ALBE,6*LC_SIC_ALBE,6*LC_SIC_ALBE,TRUE);
217 set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
218 //set_dim(&md,6*LC_C,6*LC_C,6*LC_C,TRUE);
221 /* set periodic boundary conditions in all directions */
222 set_pbc(&md,TRUE,TRUE,TRUE);
224 /* create the lattice / place atoms */
226 create_lattice(&md,DIAMOND,LC_SI_ALBE,SI,M_SI,
228 create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
229 //create_lattice(&md,DIAMOND,LC_C_ALBE,C,M_C,
231 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
232 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
236 /* create centered zinc blende lattice */
238 r.x=0.5*0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
239 create_lattice(&md,FCC,LC_SIC_ALBE,SI,M_SI,
240 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
242 r.x+=0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
243 create_lattice(&md,FCC,LC_SIC_ALBE,C,M_C,
244 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
248 moldyn_bc_check(&md);
250 /* testing configuration */
251 //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
252 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
255 //add_atom(&md,SI,M_SI,0,
256 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
257 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
259 //r.x=-r.x; v.x=-v.x;
262 //add_atom(&md,SI,M_SI,0,
263 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
264 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
266 //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
267 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
270 //add_atom(&md,SI,M_SI,0,
271 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
272 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
274 //r.z=-r.z; v.z=-v.z;
277 //add_atom(&md,SI,M_SI,0,
278 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
279 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
282 /* set temperature & pressure */
283 set_temperature(&md,atof(argv[2])+273.0);
284 set_pressure(&md,BAR);
286 /* set p/t scaling */
287 //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
288 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
289 // T_SCALE_BERENDSEN,100.0);
290 //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
291 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
293 /* initial thermal fluctuations of particles (in equilibrium) */
294 thermal_init(&md,TRUE);
296 /* create the simulation schedule */
297 /* initial configuration */
298 moldyn_add_schedule(&md,3000,1.0);
299 //moldyn_add_schedule(&md,1000,1.0);
300 //moldyn_add_schedule(&md,1000,1.0);
301 //moldyn_add_schedule(&md,1000,1.0);
302 //moldyn_add_schedule(&md,1000,1.0);
303 //moldyn_add_schedule(&md,1000,1.0);
305 //for(inject=0;inject<INJECT;inject++) {
306 // /* injecting atom and run with enabled t scaling */
307 // moldyn_add_schedule(&md,900,1.0);
308 // /* continue running with disabled t scaling */
309 // moldyn_add_schedule(&md,1100,1.0);
313 /* schedule hook function */
314 moldyn_set_schedule_hook(&md,&hook,NULL);
316 /* activate logging */
317 moldyn_set_log_dir(&md,argv[1]);
318 moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
319 moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
320 moldyn_set_log(&md,LOG_TEMPERATURE,1);
321 moldyn_set_log(&md,LOG_PRESSURE,1);
322 moldyn_set_log(&md,VISUAL_STEP,100);
323 moldyn_set_log(&md,SAVE_STEP,100);
324 moldyn_set_log(&md,CREATE_REPORT,0);
327 * let's do the actual md algorithm now
329 * integration of newtons equations
331 moldyn_integrate(&md);
337 * post processing the data
340 /* response functions expressed by energy fluctuations */
341 calc_fluctuations(1000.0,2999.0,&md);
342 get_heat_capacity(&md);
345 moldyn_shutdown(&md);