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 */
87 t_tersoff_mult_params tp;
88 t_albe_mult_params ap;
90 /* atom injection counter */
93 /* testing location & velocity vector */
95 memset(&r,0,sizeof(t_3dvec));
96 memset(&v,0,sizeof(t_3dvec));
98 /* initialize moldyn */
99 moldyn_init(&md,argc,argv);
101 /* choose integration algorithm */
102 set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
104 /* choose potential */
105 set_potential1b(&md,tersoff_mult_1bp);
107 set_potential3b_j1(&md,tersoff_mult_2bp);
108 set_potential3b_k1(&md,tersoff_mult_3bp);
109 set_potential3b_j2(&md,tersoff_mult_post_2bp);
111 set_potential1b(&md,albe_mult_1bp);
112 set_potential3b_j1(&md,albe_mult_3bp_j1);
113 set_potential3b_k1(&md,albe_mult_3bp_k1);
114 set_potential3b_j2(&md,albe_mult_3bp_j2);
115 set_potential3b_k2(&md,albe_mult_3bp_k2);
117 set_potential3b_j1(&md,tersoff_mult_3bp_j1);
118 set_potential3b_k1(&md,tersoff_mult_3bp_k1);
119 set_potential3b_j2(&md,tersoff_mult_3bp_j2);
120 set_potential3b_k2(&md,tersoff_mult_3bp_k2);
122 //set_potential2b(&md,lennard_jones);
123 //set_potential2b(&md,harmonic_oscillator);
126 set_potential_params(&md,&ap);
128 set_potential_params(&md,&tp);
130 //set_potential_params(&md,&lj);
131 //set_potential_params(&md,&ho);
134 set_cutoff(&md,ALBE_S_SI);
135 //set_cutoff(&md,TM_S_SI);
136 //set_cutoff(&md,LC_SI*sqrt(3.0));
137 //set_cutoff(&md,2.0*LC_SI);
140 * potential parameters
144 lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA_SI;
145 lj.sigma6*=lj.sigma6;
146 lj.sigma12=lj.sigma6*lj.sigma6;
147 lj.epsilon4=4.0*LJ_EPSILON_SI;
148 lj.uc=lj.epsilon4*(lj.sigma12/pow(md.cutoff,12.0)-lj.sigma6/pow(md.cutoff,6));
150 /* harmonic oscillator */
151 ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
152 //ho.equilibrium_distance=LC_SI;
153 ho.spring_constant=LJ_EPSILON_SI;
156 * tersoff mult potential parameters for SiC
162 tp.lambda[0]=TM_LAMBDA_SI;
164 tp.beta[0]=TM_BETA_SI;
174 tp.lambda[1]=TM_LAMBDA_C;
176 tp.beta[1]=TM_BETA_C;
184 tersoff_mult_complete_params(&tp);
187 * albe mult potential parameters for SiC
194 ap.lambda[0]=ALBE_LAMBDA_SI;
196 ap.gamma[0]=ALBE_GAMMA_SI;
206 ap.lambda[1]=ALBE_LAMBDA_C;
208 ap.gamma[1]=ALBE_GAMMA_C;
213 ap.Smixed=ALBE_S_SIC;
214 ap.Rmixed=ALBE_R_SIC;
215 ap.Amixed=ALBE_A_SIC;
216 ap.Bmixed=ALBE_B_SIC;
217 ap.r0_mixed=ALBE_R0_SIC;
218 ap.lambda_m=ALBE_LAMBDA_SIC;
221 albe_mult_complete_params(&ap);
223 /* set (initial) dimensions of simulation volume */
224 set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
225 //set_dim(&md,6*LC_C,6*LC_C,6*LC_C,TRUE);
226 //set_dim(&md,6*TM_LC_3C_SIC,6*TM_LC_3C_SIC,6*TM_LC_3C_SIC,TRUE);
228 /* set periodic boundary conditions in all directions */
229 set_pbc(&md,TRUE,TRUE,TRUE);
231 /* create the lattice / place atoms */
232 //create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
233 //create_lattice(&md,FCC,LC_SI,SI,M_SI,
234 create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
235 //create_lattice(&md,DIAMOND,LC_C,C,M_C,
236 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
237 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
241 /* create centered zinc blende lattice */
242 //r.x=0.5*0.25*TM_LC_3C_SIC; r.y=r.x; r.z=r.x;
243 //create_lattice(&md,FCC,TM_LC_3C_SIC,SI,M_SI,
244 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
246 //r.x+=0.25*TM_LC_3C_SIC; r.y=r.x; r.z=r.x;
247 //create_lattice(&md,FCC,TM_LC_3C_SIC,C,M_C,
248 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
251 moldyn_bc_check(&md);
253 /* testing configuration */
254 //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=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.x=-r.x; v.x=-v.x;
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,
269 //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
270 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
273 //add_atom(&md,SI,M_SI,0,
274 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
275 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
277 //r.z=-r.z; v.z=-v.z;
280 //add_atom(&md,SI,M_SI,0,
281 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
282 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
285 /* set temperature & pressure */
286 set_temperature(&md,atof(argv[2])+273.0);
287 set_pressure(&md,BAR);
289 /* set p/t scaling */
290 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
291 // T_SCALE_BERENDSEN,100.0);
292 //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
293 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
295 /* initial thermal fluctuations of particles (in equilibrium) */
296 thermal_init(&md,TRUE);
298 /* create the simulation schedule */
299 /* initial configuration */
300 moldyn_add_schedule(&md,100,1.0);
302 //for(inject=0;inject<INJECT;inject++) {
303 // /* injecting atom and run with enabled t scaling */
304 // moldyn_add_schedule(&md,900,1.0);
305 // /* continue running with disabled t scaling */
306 // moldyn_add_schedule(&md,1100,1.0);
309 /* schedule hook function */
310 moldyn_set_schedule_hook(&md,&hook,NULL);
312 /* activate logging */
313 moldyn_set_log_dir(&md,argv[1]);
314 moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
315 moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
316 moldyn_set_log(&md,LOG_TEMPERATURE,1);
317 moldyn_set_log(&md,LOG_PRESSURE,1);
318 moldyn_set_log(&md,VISUAL_STEP,1);
319 moldyn_set_log(&md,SAVE_STEP,1);
320 moldyn_set_log(&md,CREATE_REPORT,0);
323 * let's do the actual md algorithm now
325 * integration of newtons equations
327 moldyn_integrate(&md);
333 moldyn_shutdown(&md);