#include "potentials/harmonic_oscillator.h"
#include "potentials/lennard_jones.h"
#include "potentials/albe.h"
-
#ifdef TERSOFF_ORIG
#include "potentials/tersoff_orig.h"
#else
#include "potentials/tersoff.h"
#endif
-//#define INJECT 800
-#define INJECT 1
-#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 10
-#define POSTRUN 4000
-
-#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 */
+ int prerun_count; /* prerun count */
+ int insert_count; /* insert count */
+ int postrun_count; /* post run count */
+ unsigned char state; /* current state */
+ int argc; /* arg count */
+ char **argv; /* args */
} t_hp;
-int hook_del_atom(void *moldyn,void *hook_params) {
-
- t_moldyn *md;
- t_hp *hp;
-
- md=moldyn;
- hp=hook_params;
+#define STATE_PRERUN 0x00
+#define STATE_INSERT 0x01
+#define STATE_POSTRUN 0x02
- set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
- del_atom(md,2);
-
- return 0;
-}
+/* include the config file */
+#include "config.h"
-int hook_add_atom(void *moldyn,void *hook_params) {
+int insert_atoms(t_moldyn *moldyn) {
- t_moldyn *md;
- t_3dvec r,v,dist;
- double d;
- unsigned char run;
int i,j;
- t_atom *atom;
- t_hp *hp;
-
- md=moldyn;
- hp=hook_params;
-
- /* quit */
- if(hp->quit)
- return 0;
+ u8 run;
+ t_3dvec r,v,dist;
+ double d,dmin;
- /* switch on t scaling */
- if(md->schedule.count==0)
- set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+ t_atom *atom;
- /* 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;
- }
+ atom=moldyn->atom;
- /* 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;
- }
+ v.x=0; v.y=0; v.z=0;
- /* 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++) {
+ for(j=0;j<INS_ATOMS;j++) {
run=1;
while(run) {
- r.x=1.0/8.0*ALBE_LC_SI;
+#ifdef INS_TETRA
+ // tetrahedral
+ r.x=0.0;
+ r.y=0.0;
+ r.z=0.0;
+#endif
+#ifdef INS_HEXA
+ // 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;
- //r.x=(rand_get_double(&(md->random))-0.5)*INJ_LENX;
- r.x+=INJ_OFFSET;
- //r.y=(rand_get_double(&(md->random))-0.5)*INJ_LENY;
- r.y+=INJ_OFFSET;
- //r.z=(rand_get_double(&(md->random))-0.5)*INJ_LENZ;
- r.z+=INJ_OFFSET;
+ r.z=1.0/8.0*ALBE_LC_SI;
+#endif
+#ifdef INS_110DB
+ // 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;
+ moldyn->atom[4372].r.x=(-0.5+0.125+0.125)*ALBE_LC_SI;
+ moldyn->atom[4372].r.y=(-0.5+0.125+0.125)*ALBE_LC_SI;
+#endif
+#ifdef INS_001DB
+ // 001 dumbbell
+ r.x=(-0.5+0.25)*ALBE_LC_SI;
+ r.y=(-0.5+0.25)*ALBE_LC_SI;
+ r.z=(-0.5+0.25+0.125)*ALBE_LC_SI;
+ moldyn->atom[4372].r.z=(-0.5+0.25-0.125)*ALBE_LC_SI;
+#endif
+#ifdef INS_USER
+ // 001 dumbbell
+ r.x=INS_UX*ALBE_LC_SI;
+ r.y=INS_UY*ALBE_LC_SI;
+ r.z=INS_UZ*ALBE_LC_SI;
+#endif
+#ifdef INS_RAND
+ // random
+ r.x=(rand_get_double(&(moldyn->random))-0.5)*INS_LENX;
+ r.y=(rand_get_double(&(moldyn->random))-0.5)*INS_LENY;
+ r.z=(rand_get_double(&(moldyn->random))-0.5)*INS_LENZ;
+#endif
+ // offset
+ r.x+=INS_OFFSET;
+ r.y+=INS_OFFSET;
+ r.z+=INS_OFFSET;
/* assume valid coordinates */
run=0;
- for(i=0;i<md->count;i++) {
- atom=&(md->atom[i]);
+ dmin=10000000000.0; // for sure too high!
+ for(i=0;i<moldyn->count;i++) {
+ atom=&(moldyn->atom[i]);
v3_sub(&dist,&(atom->r),&r);
+ check_per_bound(moldyn,&dist);
d=v3_absolute_square(&dist);
/* reject coordinates */
- if(d<R_C) {
+ if(d<INS_R_C) {
+ //printf("atom %d - %f\n",i,d);
run=1;
break;
}
+ if(d<dmin)
+ dmin=d;
}
}
- v.x=0; v.y=0; v.z=0;
-#ifdef INJ_TYPE_CARBON
- add_atom(md,C,M_C,1,
-#else
- add_atom(md,SI,M_SI,0,
-#endif
- ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ add_atom(moldyn,INS_TYPE,INS_MASS,INS_BRAND,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|\
+ INS_ATTR,
&r,&v);
+ printf(" %02d: atom %d | %f %f %f | %f\n",
+ j,moldyn->count-1,r.x,r.y,r.z,dmin);
}
- hp->a_count+=NR_ATOMS;
- /* add schedule for simulating injected atoms ;) */
- moldyn_add_schedule(md,RELAX_S,1.0);
+ return 0;
+}
+
+int sic_hook(void *moldyn,void *hook_params) {
+
+ t_hp *hp;
+ t_moldyn *md;
+ int steps;
+ double tau;
+ double dt;
+
+ hp=hook_params;
+ md=moldyn;
+
+ tau=1.0;
+ steps=0;
+
+ /* switch on t scaling */
+ if(md->schedule.count==0)
+ set_pt_scale(md,0,0,T_SCALE_BERENDSEN,T_SCALE_TAU);
+
+ /* my lousy state machine ! */
+
+ /* switch to insert state immediately */
+ if(hp->state==STATE_PRERUN)
+ hp->state=STATE_INSERT;
+
+ switch(hp->state) {
+ case STATE_INSERT:
+ goto insert;
+ break;
+ case STATE_POSTRUN:
+ goto postrun;
+ break;
+ default:
+ printf("[sic hook] unknown state\n");
+ return -1;
+ }
+
+ /* act according to state */
+
+insert:
+
+ /* immediately go on if no job is to be done */
+ if(hp->insert_count==INS_RUNS) {
+ printf(" --- insert run return ---\n");
+ hp->state=STATE_POSTRUN;
+ goto postrun;
+ }
+
+ /* assigne values */
+ steps=INS_RELAX;
+ tau=INS_TAU;
+
+ /* check temperature */
+ dt=md->t_avg-md->t_ref;
+ if(dt<0)
+ dt=-dt;
+ if(dt>INS_DELTA_TC)
+ goto addsched;
+
+ /* else -> insert atoms */
+ hp->insert_count+=1;
+ printf(" ### insert atoms (%d/%d) ###\n",
+ hp->insert_count*INS_ATOMS,INS_RUNS*INS_ATOMS);
+ insert_atoms(md);
+ goto addsched;
+
+postrun:
+
+ /* immediately return if no job is to be done */
+ if(hp->postrun_count==POST_RUNS) {
+ printf(" --- post run return ---\n");
+ return 0;
+ }
+
+ /* assigne values */
+ steps=POST_RELAX;
+ tau=POST_TAU;
+
+ /* check temperature */
+ dt=md->t_avg-md->t_ref;
+ if(dt<0)
+ dt=-dt;
+ if(dt>POST_DELTA_TC)
+ goto addsched;
+
+ /* postrun action */
+ hp->postrun_count+=1;
+ printf(" ### postrun (%d/%d) ###\n",
+ hp->postrun_count,POST_RUNS);
+ set_temperature(md,md->t_ref-POST_DT);
+
+addsched:
+
+ /* reset the average counters */
+ average_reset(md);
+
+ /* add schedule */
+ moldyn_add_schedule(md,steps,tau);
return 0;
}
int main(int argc,char **argv) {
- /* check argv */
- //if(argc!=3) {
- // printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
- // return -1;
- //}
-
/* main moldyn structure */
t_moldyn md;
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
/* set (initial) dimensions of simulation volume */
#ifdef ALBE
+ #ifdef INIT_SI
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);
+ #endif
+ #ifdef INIT_C
+ set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
+ #endif
+ #ifdef INIT_3CSIC
+ set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
+ #endif
#else
+ #ifdef INIT_SI
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
+ #ifdef INIT_C
+ set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
+ #endif
+ #ifdef INIT_3CSIC
+ set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
+ #endif
#endif
/* set periodic boundary conditions in all directions */
set_pbc(&md,TRUE,TRUE,TRUE);
/* create the lattice / place atoms */
+
+ // diamond
#ifdef ALBE
+ #ifdef INIT_SI
create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
- //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 0,LCNTX,LCNTY,LCNTZ,NULL);
+ #endif
+ #ifdef INIT_C
+ create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 1,LCNTX,LCNTY,LCNTZ,NULL);
+ #endif
#else
+ #ifdef INIT_SI
create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
-#endif
ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
- // ATOM_ATTR_2BP|ATOM_ATTR_HB,
- 0,LCNTX,LCNTY,LCNTZ,NULL);
- // 1,LCNTX,LCNTY,LCNTZ,NULL);
+ 0,LCNTX,LCNTY,LCNTZ,NULL);
+ #endif
+ #ifdef INIT_C
+ create_lattice(&md,DIAMOND,LC_C,SI,M_SI,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 1,LCNTX,LCNTY,LCNTZ,NULL);
+ #endif
+#endif
- /* create zinkblende structure */
- /*
-#ifdef ALBE
+ // zinkblende
+#ifdef INIT_3CSIC
+ #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,
create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
1,LCNTX,LCNTY,LCNTZ,&r);
-#else
+ #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,
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
#endif
- */
/* check for right atom placing */
moldyn_bc_check(&md);
set_pressure(&md,BAR);
/* set amount of steps to skip before average calc */
- set_avg_skip(&md,(8.0/10.0*PRERUN));
+ set_avg_skip(&md,AVG_SKIP);
/* set p/t scaling */
//set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
thermal_init(&md,TRUE);
/* create the simulation schedule */
- moldyn_add_schedule(&md,PRERUN,1.0);
+ moldyn_add_schedule(&md,PRERUN,PRE_TAU);
/* schedule hook function */
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,&sic_hook,&hookparam);
//moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam);
//moldyn_add_schedule(&md,POSTRUN,1.0);
moldyn_set_log(&md,SAVE_STEP,LOG_S);
moldyn_set_log(&md,CREATE_REPORT,0);
+ /* next neighbour distance for critical checking */
+ set_nn_dist(&md,0.25*ALBE_LC_SI*sqrt(3.0));
+
/*
* let's do the actual md algorithm now
*
projects / physik / posic.git / blobdiff