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"
18 #include "potentials/tersoff_orig.h"
20 #include "potentials/tersoff.h"
26 int hook(void *moldyn,void *hook_params) {
37 printf("\nschedule hook: ");
39 if(!(md->schedule.count%2)) {
40 /* add carbon at random place, and enable t scaling */
41 for(j=0;j<NR_ATOMS;j++) {
44 r.x=rand_get_double(&(md->random))*md->dim.x;
45 r.y=rand_get_double(&(md->random))*md->dim.y;
46 r.z=rand_get_double(&(md->random))*md->dim.z;
47 for(i=0;i<md->count;i++) {
49 v3_sub(&dist,&(atom->r),&r);
50 d=v3_absolute_square(&dist);
57 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
60 printf("adding atoms & enable t scaling\n");
61 set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
64 /* disable t scaling */
65 printf("disabling t scaling\n");
66 set_pt_scale(md,0,0,0,0);
72 int main(int argc,char **argv) {
76 printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
80 /* main moldyn structure */
83 /* potential parameters */
86 t_tersoff_mult_params tp;
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 */
103 set_potential1b(&md,tersoff_mult_1bp);
105 set_potential3b_j1(&md,tersoff_mult_2bp);
106 set_potential3b_k1(&md,tersoff_mult_3bp);
107 set_potential3b_j2(&md,tersoff_mult_post_2bp);
109 set_potential3b_j1(&md,tersoff_mult_3bp_j1);
110 set_potential3b_k1(&md,tersoff_mult_3bp_k1);
111 set_potential3b_j2(&md,tersoff_mult_3bp_j2);
112 set_potential3b_k2(&md,tersoff_mult_3bp_k2);
114 //set_potential2b(&md,lennard_jones);
115 //set_potential2b(&md,harmonic_oscillator);
116 set_potential_params(&md,&tp);
117 //set_potential_params(&md,&lj);
118 //set_potential_params(&md,&ho);
121 set_cutoff(&md,TM_S_SI);
122 //set_cutoff(&md,LC_SI*sqrt(3.0));
123 //set_cutoff(&md,2.0*LC_SI);
126 * potential parameters
130 lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA_SI;
131 lj.sigma6*=lj.sigma6;
132 lj.sigma12=lj.sigma6*lj.sigma6;
133 lj.epsilon4=4.0*LJ_EPSILON_SI;
134 lj.uc=lj.epsilon4*(lj.sigma12/pow(md.cutoff,12.0)-lj.sigma6/pow(md.cutoff,6));
136 /* harmonic oscillator */
137 ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
138 //ho.equilibrium_distance=LC_SI;
139 ho.spring_constant=LJ_EPSILON_SI;
142 * tersoff mult potential parameters for SiC
148 tp.lambda[0]=TM_LAMBDA_SI;
150 tp.beta[0]=TM_BETA_SI;
160 tp.lambda[1]=TM_LAMBDA_C;
162 tp.beta[1]=TM_BETA_C;
170 tersoff_mult_complete_params(&tp);
172 /* set (initial) dimensions of simulation volume */
173 //set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
174 set_dim(&md,6*TM_LC_3C_SIC,6*TM_LC_3C_SIC,6*TM_LC_3C_SIC,TRUE);
176 /* set periodic boundary conditions in all directions */
177 set_pbc(&md,TRUE,TRUE,TRUE);
179 /* create the lattice / place atoms */
180 //create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
181 //create_lattice(&md,FCC,LC_SI,SI,M_SI,
182 //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
183 //create_lattice(&md,DIAMOND,LC_C,C,M_C,
184 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
185 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
188 /* create centered zinc blende lattice */
189 r.x=0.5*0.25*TM_LC_3C_SIC; r.y=r.x; r.z=r.x;
190 create_lattice(&md,FCC,TM_LC_3C_SIC,SI,M_SI,
191 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
193 r.x+=0.25*TM_LC_3C_SIC; r.y=r.x; r.z=r.x;
194 create_lattice(&md,FCC,TM_LC_3C_SIC,C,M_C,
195 ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
197 moldyn_bc_check(&md);
199 /* testing configuration */
200 //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
201 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
204 //add_atom(&md,SI,M_SI,0,
205 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
206 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
208 //r.x=-r.x; v.x=-v.x;
211 //add_atom(&md,SI,M_SI,0,
212 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
213 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
215 //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
216 //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
219 //add_atom(&md,SI,M_SI,0,
220 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
221 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
223 //r.z=-r.z; v.z=-v.z;
226 //add_atom(&md,SI,M_SI,0,
227 // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
228 // ATOM_ATTR_2BP|ATOM_ATTR_HB,
231 /* set temperature & pressure */
232 set_temperature(&md,atof(argv[2])+273.0);
233 set_pressure(&md,BAR);
235 /* set p/t scaling */
236 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
237 // T_SCALE_BERENDSEN,100.0);
238 //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
239 //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
241 /* initial thermal fluctuations of particles (in equilibrium) */
242 thermal_init(&md,TRUE);
244 /* create the simulation schedule */
245 /* initial configuration */
246 moldyn_add_schedule(&md,1000,1.0);
248 //for(inject=0;inject<INJECT;inject++) {
249 // /* injecting atom and run with enabled t scaling */
250 // moldyn_add_schedule(&md,900,1.0);
251 // /* continue running with disabled t scaling */
252 // moldyn_add_schedule(&md,1100,1.0);
255 /* schedule hook function */
256 moldyn_set_schedule_hook(&md,&hook,NULL);
258 /* activate logging */
259 moldyn_set_log_dir(&md,argv[1]);
260 moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
261 moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
262 moldyn_set_log(&md,LOG_TEMPERATURE,1);
263 moldyn_set_log(&md,LOG_PRESSURE,1);
264 moldyn_set_log(&md,VISUAL_STEP,10);
265 moldyn_set_log(&md,SAVE_STEP,10);
266 moldyn_set_log(&md,CREATE_REPORT,0);
269 * let's do the actual md algorithm now
271 * integration of newtons equations
273 moldyn_integrate(&md);
279 moldyn_shutdown(&md);