#endif
#define INJECT 1
-#define NR_ATOMS 4
+#define NR_ATOMS 1
+#define R_C 2.0
+#define T_C 10.0
+#define LCNT 2
+
+typedef struct s_hp {
+ int a_count; /* atom count */
+ u8 quit; /* quit mark */
+} t_hp;
int hook(void *moldyn,void *hook_params) {
unsigned char run;
int i,j;
t_atom *atom;
+ t_hp *hp;
md=moldyn;
+ hp=hook_params;
+
+ /* quit */
+ if(hp->quit)
+ return 0;
+
+ /* switch on t scaling */
+ if(md->schedule.count==0)
+ set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
- printf("\nschedule hook: ");
+ /* last schedule add if there is enough carbon inside */
+ if(hp->a_count==(INJECT*NR_ATOMS)) {
+ hp->quit=1;
+ moldyn_add_schedule(md,5000,1.0);
+ return 0;
+ }
+
+ /* more relaxing time for too high temperatures */
+ if(md->t-md->t_ref>T_C) {
+ moldyn_add_schedule(md,10,1.0);
+ return 0;
+ }
- if(!(md->schedule.count%2)) {
- /* add carbon at random place, and enable t scaling */
- for(j=0;j<NR_ATOMS;j++) {
+ /* inject carbon atoms */
+ printf("injecting another %d carbon atoms ...(-> %d / %d)\n",
+ NR_ATOMS,hp->a_count+NR_ATOMS,INJECT*NR_ATOMS);
+ for(j=0;j<NR_ATOMS;j++) {
run=1;
while(run) {
- r.x=rand_get_double(&(md->random))*md->dim.x;
- r.y=rand_get_double(&(md->random))*md->dim.y;
- r.z=rand_get_double(&(md->random))*md->dim.z;
+ r.x=(rand_get_double(&(md->random))-0.5)*md->dim.x*0.37;
+ r.y=(rand_get_double(&(md->random))-0.5)*md->dim.y*0.37;
+ r.z=(rand_get_double(&(md->random))-0.5)*md->dim.z*0.37;
+ /* assume valid coordinates */
+ run=0;
for(i=0;i<md->count;i++) {
atom=&(md->atom[i]);
v3_sub(&dist,&(atom->r),&r);
d=v3_absolute_square(&dist);
- if(d>TM_R_C)
- run=0;
+ /* reject coordinates */
+ if(d<R_C) {
+ run=1;
+ break;
+ }
}
}
v.x=0; v.y=0; v.z=0;
add_atom(md,C,M_C,1,
ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
&r,&v);
- }
- printf("adding atoms & enable t scaling\n");
- set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
- }
- else {
- /* disable t scaling */
- printf("disabling t scaling\n");
- set_pt_scale(md,0,0,0,0);
}
+ hp->a_count+=NR_ATOMS;
+
+ /* add schedule for simulating injected atoms ;) */
+ moldyn_add_schedule(md,10,1.0);
return 0;
}
/* main moldyn structure */
t_moldyn md;
+ /* hook parameter structure */
+ t_hp hookparam;
+
/* potential parameters */
t_tersoff_mult_params tp;
t_albe_mult_params ap;
albe_mult_complete_params(&ap);
/* set (initial) dimensions of simulation volume */
- //set_dim(&md,6*LC_SI_ALBE,6*LC_SI_ALBE,6*LC_SI_ALBE,TRUE);
- //set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
- //set_dim(&md,6*LC_C_ALBE,6*LC_C_ALBE,6*LC_C_ALBE,TRUE);
- //set_dim(&md,6*LC_C,6*LC_C,6*LC_C,TRUE);
- set_dim(&md,6*LC_SIC_ALBE,6*LC_SIC_ALBE,6*LC_SIC_ALBE,TRUE);
+#ifdef ALBE
+ set_dim(&md,LCNT*ALBE_LC_SI,LCNT*ALBE_LC_SI,LCNT*ALBE_LC_SI,TRUE);
+ //set_dim(&md,LCNT*ALBE_LC_C,LCNT*ALBE_LC_C,LCNT*ALBE_LC_C,TRUE);
+ //set_dim(&md,LCNT*ALBE_LC_SIC,LCNT*ALBE_LC_SIC,LCNT*ALBE_LC_SIC,TRUE);
+#else
+ //set_dim(&md,LCNT*LC_SI,LCNT*LC_SI,LCNT*LC_SI,TRUE);
+ //set_dim(&md,LCNT*LC_C,LCNT*LC_C,LCNT*LC_C,TRUE);
+ set_dim(&md,LCNT*TM_LC_SIC,LCNT*TM_LC_SIC,LCNT*TM_LC_SIC,TRUE);
+#endif
/* set periodic boundary conditions in all directions */
set_pbc(&md,TRUE,TRUE,TRUE);
/* create the lattice / place atoms */
+#ifdef ALBE
+ create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
+ //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
+#else
//create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
- //create_lattice(&md,DIAMOND,LC_C_ALBE,C,M_C,
- //create_lattice(&md,DIAMOND,LC_SI_ALBE,SI,M_SI,
- // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+#endif
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
// ATOM_ATTR_2BP|ATOM_ATTR_HB,
- // 0,6,6,6,NULL);
- // 1,6,6,6,NULL);
+ 0,LCNT,LCNT,LCNT,NULL);
+ // 1,LCNT,LCNT,LCNT,NULL);
- /* create centered zinc blende lattice */
- /**/
- r.x=0.5*0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
- create_lattice(&md,FCC,LC_SIC_ALBE,SI,M_SI,
+ /* create zinkblende structure */
+ /*
+#ifdef ALBE
+ r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
+ create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 0,LCNT,LCNT,LCNT,&r);
+ r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
+ create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
- 0,6,6,6,&r);
- r.x+=0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
- create_lattice(&md,FCC,LC_SIC_ALBE,C,M_C,
+ 1,LCNT,LCNT,LCNT,&r);
+#else
+ r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
+ create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 0,LCNT,LCNT,LCNT,&r);
+ r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
+ create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
- 1,6,6,6,&r);
- /**/
+ 1,LCNT,LCNT,LCNT,&r);
+#endif
+ */
+ /* check for right atom placing */
moldyn_bc_check(&md);
/* testing configuration */
set_temperature(&md,atof(argv[2])+273.0);
set_pressure(&md,BAR);
+ /* set amount of steps to skip before average calc */
+ set_avg_skip(&md,1000);
+
/* set p/t scaling */
+ //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
//set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
// T_SCALE_BERENDSEN,100.0);
//set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
thermal_init(&md,TRUE);
/* create the simulation schedule */
- /* initial configuration */
- moldyn_add_schedule(&md,10000,1.0);
+ moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
/* adding atoms */
//for(inject=0;inject<INJECT;inject++) {
- // /* injecting atom and run with enabled t scaling */
- // moldyn_add_schedule(&md,900,1.0);
- // /* continue running with disabled t scaling */
- // moldyn_add_schedule(&md,1100,1.0);
+ // /* injecting atoms */
+ // moldyn_add_schedule(&md,10,1.0);
//}
/* schedule hook function */
- moldyn_set_schedule_hook(&md,&hook,NULL);
+ memset(&hookparam,0,sizeof(t_hp));
+ moldyn_set_schedule_hook(&md,&hook,&hookparam);
/* activate logging */
moldyn_set_log_dir(&md,argv[1]);
* integration of newtons equations
*/
moldyn_integrate(&md);
-#ifdef DEBUG
+#ifdef dEBUG
return 0;
#endif
+ /*
+ * post processing the data
+ */
+
/* close */
moldyn_shutdown(&md);