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) {
38 printf("\nschedule hook: ");
40 if(!(md->schedule.count%2)) {
41 /* add carbon at random place, and enable t scaling */
42 for(j=0;j<NR_ATOMS;j++) {
45 r.x=rand_get_double(&(md->random))*md->dim.x;
46 r.y=rand_get_double(&(md->random))*md->dim.y;
47 r.z=rand_get_double(&(md->random))*md->dim.z;
48 for(i=0;i<md->count;i++) {
50 v3_sub(&dist,&(atom->r),&r);
51 d=v3_absolute_square(&dist);
58 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
61 printf("adding atoms & enable t scaling\n");
62 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
65 /* disable t scaling */
66 printf("disabling t scaling\n");
67 set_pt_scale(md,0,0,0,0);
73 int main(int argc,char **argv) {
77 printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
81 /* main moldyn structure */
84 /* potential parameters */
85 t_tersoff_mult_params tp;
86 t_albe_mult_params ap;
88 /* atom injection counter */
91 /* testing location & velocity vector */
93 memset(&r,0,sizeof(t_3dvec));
94 memset(&v,0,sizeof(t_3dvec));
96 /* initialize moldyn */
97 moldyn_init(&md,argc,argv);
99 /* choose integration algorithm */
100 set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
102 /* choose potential */
104 set_potential3b_j1(&md,albe_mult_3bp_j1);
105 set_potential3b_k1(&md,albe_mult_3bp_k1);
106 set_potential3b_j2(&md,albe_mult_3bp_j2);
107 set_potential3b_k2(&md,albe_mult_3bp_k2);
109 set_potential1b(&md,tersoff_mult_1bp);
110 set_potential3b_j1(&md,tersoff_mult_3bp_j1);
111 set_potential3b_k1(&md,tersoff_mult_3bp_k1);
112 set_potential3b_j2(&md,tersoff_mult_3bp_j2);
113 set_potential3b_k2(&md,tersoff_mult_3bp_k2);
117 set_potential_params(&md,&ap);
119 set_potential_params(&md,&tp);
124 set_cutoff(&md,ALBE_S_SI);
126 set_cutoff(&md,TM_S_SI);
130 * potential parameters
134 * tersoff mult potential parameters for SiC
140 tp.lambda[0]=TM_LAMBDA_SI;
142 tp.beta[0]=TM_BETA_SI;
152 tp.lambda[1]=TM_LAMBDA_C;
154 tp.beta[1]=TM_BETA_C;
162 tersoff_mult_complete_params(&tp);
165 * albe mult potential parameters for SiC
172 ap.lambda[0]=ALBE_LAMBDA_SI;
174 ap.gamma[0]=ALBE_GAMMA_SI;
184 ap.lambda[1]=ALBE_LAMBDA_C;
186 ap.gamma[1]=ALBE_GAMMA_C;
191 ap.Smixed=ALBE_S_SIC;
192 ap.Rmixed=ALBE_R_SIC;
193 ap.Amixed=ALBE_A_SIC;
194 ap.Bmixed=ALBE_B_SIC;
195 ap.r0_mixed=ALBE_R0_SIC;
196 ap.lambda_m=ALBE_LAMBDA_SIC;
198 ap.gamma_m=ALBE_GAMMA_SIC;
199 ap.c_mixed=ALBE_C_SIC;
200 ap.d_mixed=ALBE_D_SIC;
201 ap.h_mixed=ALBE_H_SIC;
203 albe_mult_complete_params(&ap);
205 /* set (initial) dimensions of simulation volume */
206 //set_dim(&md,6*LC_SI_ALBE,6*LC_SI_ALBE,6*LC_SI_ALBE,TRUE);
207 //set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
208 //set_dim(&md,6*LC_C_ALBE,6*LC_C_ALBE,6*LC_C_ALBE,TRUE);
209 //set_dim(&md,6*LC_C,6*LC_C,6*LC_C,TRUE);
210 set_dim(&md,6*LC_SIC_ALBE,6*LC_SIC_ALBE,6*LC_SIC_ALBE,TRUE);
212 /* set periodic boundary conditions in all directions */
213 set_pbc(&md,TRUE,TRUE,TRUE);
215 /* create the lattice / place atoms */
216 //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
217 //create_lattice(&md,DIAMOND,LC_C_ALBE,C,M_C,
218 //create_lattice(&md,DIAMOND,LC_SI_ALBE,SI,M_SI,
219 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
220 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
224 /* create centered zinc blende lattice */
226 r.x=0.5*0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
227 create_lattice(&md,FCC,LC_SIC_ALBE,SI,M_SI,
228 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
230 r.x+=0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
231 create_lattice(&md,FCC,LC_SIC_ALBE,C,M_C,
232 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
236 moldyn_bc_check(&md);
238 /* testing configuration */
239 //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
240 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
243 //add_atom(&md,SI,M_SI,0,
244 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
245 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
247 //r.x=-r.x; v.x=-v.x;
250 //add_atom(&md,SI,M_SI,0,
251 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
252 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
254 //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
255 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
258 //add_atom(&md,SI,M_SI,0,
259 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
260 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
262 //r.z=-r.z; v.z=-v.z;
265 //add_atom(&md,SI,M_SI,0,
266 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
267 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
270 /* set temperature & pressure */
271 set_temperature(&md,atof(argv[2])+273.0);
272 set_pressure(&md,BAR);
274 /* set p/t scaling */
275 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
276 // T_SCALE_BERENDSEN,100.0);
277 //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
278 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
280 /* initial thermal fluctuations of particles (in equilibrium) */
281 thermal_init(&md,TRUE);
283 /* create the simulation schedule */
284 /* initial configuration */
285 moldyn_add_schedule(&md,10000,1.0);
287 //for(inject=0;inject<INJECT;inject++) {
288 // /* injecting atom and run with enabled t scaling */
289 // moldyn_add_schedule(&md,900,1.0);
290 // /* continue running with disabled t scaling */
291 // moldyn_add_schedule(&md,1100,1.0);
294 /* schedule hook function */
295 moldyn_set_schedule_hook(&md,&hook,NULL);
297 /* activate logging */
298 moldyn_set_log_dir(&md,argv[1]);
299 moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
300 moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
301 moldyn_set_log(&md,LOG_TEMPERATURE,1);
302 moldyn_set_log(&md,LOG_PRESSURE,1);
303 moldyn_set_log(&md,VISUAL_STEP,100);
304 moldyn_set_log(&md,SAVE_STEP,100);
305 moldyn_set_log(&md,CREATE_REPORT,0);
308 * let's do the actual md algorithm now
310 * integration of newtons equations
312 moldyn_integrate(&md);
318 moldyn_shutdown(&md);