#include <math.h>
#include "moldyn.h"
-#include "posic.h"
/* potential */
#include "potentials/harmonic_oscillator.h"
#include "potentials/tersoff.h"
#endif
+//#define INJECT 800
#define INJECT 1
-#define NR_ATOMS 4
+#define NR_ATOMS 1
+#define R_C 1.5
+#define T_C 5.0
+//#define INJ_LENX (1*ALBE_LC_SIC)
+//#define INJ_LENY (1*ALBE_LC_SIC)
+//#define INJ_LENZ (1*ALBE_LC_SIC)
+#define INJ_LENX (1*ALBE_LC_SI)
+#define INJ_LENY (1*ALBE_LC_SI)
+#define INJ_LENZ (1*ALBE_LC_SI)
+#define INJ_TYPE_SILICON
+//#define INJ_TYPE_CARBON
+#define INJ_OFFSET (ALBE_LC_SI/8.0)
+#define RELAX_S 20
+
+#define LCNTX 9
+#define LCNTY 9
+#define LCNTZ 9
+#define PRERUN 40
+#define POSTRUN 3000
+
+#define R_TITLE "Silicon self-interstitial"
+#define LOG_E 10
+#define LOG_T 10
+#define LOG_P 10
+#define LOG_S 100
+#define LOG_V 20
+
+typedef struct s_hp {
+ int a_count; /* atom count */
+ u8 quit; /* quit mark */
+ int argc; /* arg count */
+ char **argv; /* args */
+} t_hp;
+
+int hook_del_atom(void *moldyn,void *hook_params) {
-int hook(void *moldyn,void *hook_params) {
+ t_moldyn *md;
+ t_hp *hp;
+
+ md=moldyn;
+ hp=hook_params;
+
+ set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+ del_atom(md,2);
+
+ return 0;
+}
+
+int hook_add_atom(void *moldyn,void *hook_params) {
t_moldyn *md;
t_3dvec r,v,dist;
unsigned char run;
int i,j;
t_atom *atom;
+ t_hp *hp;
md=moldyn;
+ hp=hook_params;
-// vortrag
-set_temperature(moldyn,(4-md->schedule.count)*1000.0);
-set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+ /* quit */
+ if(hp->quit)
+ return 0;
-return 0;
+ /* switch on t scaling */
+ if(md->schedule.count==0)
+ set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+
+ /* last schedule add if there is enough carbon inside */
+ if(hp->a_count==(INJECT*NR_ATOMS)) {
+ hp->quit=1;
+ moldyn_add_schedule(md,POSTRUN,1.0);
+ return 0;
+ }
- printf("\nschedule hook: ");
+ /* more relaxing time for too high temperatures */
+ if(md->t-md->t_ref>T_C) {
+ moldyn_add_schedule(md,RELAX_S,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 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;
+ // tetrahedral
+ /*
+ r.x=0.0;
+ r.y=0.0;
+ r.z=0.0;
+ */
+ // hexagonal
+ //
+ r.x=-1.0/8.0*ALBE_LC_SI;
+ r.y=-1.0/8.0*ALBE_LC_SI;
+ r.z=1.0/8.0*ALBE_LC_SI;
+ //
+ // 110 dumbbell
+ /*
+ r.x=(-0.5+0.25+0.125)*ALBE_LC_SI;
+ r.y=(-0.5+0.25+0.125)*ALBE_LC_SI;
+ r.z=(-0.5+0.25)*ALBE_LC_SI;
+ md->atom[4372].r.x=(-0.5+0.125+0.125)*ALBE_LC_SI;
+ md->atom[4372].r.y=(-0.5+0.125+0.125)*ALBE_LC_SI;
+ */
+ // random
+ /*
+ r.x=(rand_get_double(&(md->random))-0.5)*INJ_LENX;
+ r.y=(rand_get_double(&(md->random))-0.5)*INJ_LENY;
+ r.z=(rand_get_double(&(md->random))-0.5)*INJ_LENZ;
+ */
+ // offset
+ r.x+=INJ_OFFSET;
+ r.y+=INJ_OFFSET;
+ r.z+=INJ_OFFSET;
+ /* 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) {
+ //printf("atom %d - %f\n",i,d);
+ run=1;
+ break;
+ }
}
}
v.x=0; v.y=0; v.z=0;
+#ifdef INJ_TYPE_CARBON
add_atom(md,C,M_C,1,
- ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+#else
+ add_atom(md,SI,M_SI,0,
+#endif
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB|ATOM_ATTR_VB,
&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,RELAX_S,1.0);
return 0;
}
int main(int argc,char **argv) {
/* check argv */
- if(argc!=3) {
- printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
- return -1;
- }
+ //if(argc!=3) {
+ // printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
+ // return -1;
+ //}
/* main moldyn structure */
t_moldyn md;
+ /* hook parameter structure */
+ t_hp hookparam;
+
/* potential parameters */
t_tersoff_mult_params tp;
t_albe_mult_params ap;
- /* atom injection counter */
- int inject;
-
/* testing location & velocity vector */
t_3dvec r,v;
memset(&r,0,sizeof(t_3dvec));
set_potential_params(&md,&tp);
#endif
- /* cutoff radius */
+ /* cutoff radius & bondlen */
#ifdef ALBE
set_cutoff(&md,ALBE_S_SI);
+ set_bondlen(&md,ALBE_S_SI,ALBE_S_C,ALBE_S_SIC);
+ //set_cutoff(&md,ALBE_S_C);
#else
set_cutoff(&md,TM_S_SI);
+ set_bondlen(&md,TM_S_SI,TM_S_C,-1.0);
+ //set_cutoff(&md,TM_S_C);
#endif
/*
albe_mult_complete_params(&ap);
/* set (initial) dimensions of simulation volume */
-#ifdef ALBLE
- set_dim(&md,6*LC_SI_ALBE,6*LC_SI_ALBE,6*LC_SI_ALBE,TRUE);
- //set_dim(&md,6*LC_C_ALBE,6*LC_C_ALBE,6*LC_C_ALBE,TRUE);
- //set_dim(&md,6*LC_SIC_ALBE,6*LC_SIC_ALBE,6*LC_SIC_ALBE,TRUE);
+#ifdef ALBE
+ set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
+ //set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
+ //set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
#else
- set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
- //set_dim(&md,6*LC_C,6*LC_C,6*LC_C,TRUE);
+ set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE);
+ //set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
+ //set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
#endif
/* set periodic boundary conditions in all directions */
set_pbc(&md,TRUE,TRUE,TRUE);
/* create the lattice / place atoms */
-#ifdef ALBLE
- create_lattice(&md,DIAMOND,LC_SI_ALBE,SI,M_SI,
+ //
+#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,
#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,LCNTX,LCNTY,LCNTZ,NULL);
+ // 1,LCNTX,LCNTY,LCNTZ,NULL);
+ //
- /* create centered zinc blende lattice */
+ /* create zinkblende structure */
/*
- 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,
+#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,
- 0,6,6,6,&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,
+ 0,LCNTX,LCNTY,LCNTZ,&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,
- 1,6,6,6,&r);
+ 1,LCNTX,LCNTY,LCNTZ,&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,LCNTX,LCNTY,LCNTZ,&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,LCNTX,LCNTY,LCNTZ,&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,(8.0/10.0*PRERUN));
+
/* set p/t scaling */
//set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
//set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
thermal_init(&md,TRUE);
/* create the simulation schedule */
- /* initial configuration */
- moldyn_add_schedule(&md,3000,1.0);
- //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);
- //}
-
+ moldyn_add_schedule(&md,PRERUN,1.0);
/* schedule hook function */
- moldyn_set_schedule_hook(&md,&hook,NULL);
+ memset(&hookparam,0,sizeof(t_hp));
+ hookparam.argc=argc;
+ hookparam.argv=argv;
+ moldyn_set_schedule_hook(&md,&hook_add_atom,&hookparam);
+ //moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam);
+ //moldyn_add_schedule(&md,POSTRUN,1.0);
/* activate logging */
moldyn_set_log_dir(&md,argv[1]);
- moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
- moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
- moldyn_set_log(&md,LOG_TEMPERATURE,1);
- moldyn_set_log(&md,LOG_PRESSURE,1);
- moldyn_set_log(&md,VISUAL_STEP,100);
- moldyn_set_log(&md,SAVE_STEP,100);
+ moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
+ moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
+ moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
+ moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
+ moldyn_set_log(&md,VISUAL_STEP,LOG_V);
+ moldyn_set_log(&md,SAVE_STEP,LOG_S);
moldyn_set_log(&md,CREATE_REPORT,0);
/*
* integration of newtons equations
*/
moldyn_integrate(&md);
-#ifdef DEBUG
+#ifdef dEBUG
return 0;
#endif
* post processing the data
*/
- /* response functions expressed by energy fluctuations */
- calc_fluctuations(1000.0,2999.0,&md);
- get_heat_capacity(&md);
-
/* close */
moldyn_shutdown(&md);
projects / physik / posic.git / blobdiff