X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=sic.c;h=05de728c9e9cdd4be50bf73a1e1a51fd6956d195;hb=b5b47daaa3718c4dec2056fe5147668023575b8e;hp=751cb066d10ea97e3b19334875ba1a9f031edb35;hpb=a34e2dc3f17670f3b91d9b63a1d3a44832e4fc85;p=physik%2Fposic.git

diff --git a/sic.c b/sic.c
index 751cb06..05de728 100644
--- a/sic.c
+++ b/sic.c
@@ -8,7 +8,6 @@
 #include <math.h>
  
 #include "moldyn.h"
-#include "posic.h"
 
 /* potential */
 #include "potentials/harmonic_oscillator.h"
@@ -21,17 +20,57 @@
 #include "potentials/tersoff.h"
 #endif
 
-#define INJECT		160
-#define NR_ATOMS	10
+//#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		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;
 
-#define TC		50
+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;
@@ -55,41 +94,79 @@ int hook(void *moldyn,void *hook_params) {
 	/* last schedule add if there is enough carbon inside */
 	if(hp->a_count==(INJECT*NR_ATOMS)) {
 		hp->quit=1;
-		moldyn_add_schedule(md,10000,1.0);
+		moldyn_add_schedule(md,POSTRUN,1.0);
 		return 0;
 	}
 
 	/* more relaxing time for too high temperatures */
-	if(md->t-md->t_ref>TC) {
-		moldyn_add_schedule(md,100,1.0);
+	if(md->t-md->t_ref>T_C) {
+		moldyn_add_schedule(md,RELAX_S,1.0);
 		return 0;
 	}
 
 	/* inject carbon atoms */
-	printf("injecting another 10 carbon atoms ...\n");
+	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*0.37;
-			r.y=rand_get_double(&(md->random))*md->dim.y*0.37;
-			r.z=rand_get_double(&(md->random))*md->dim.z*0.37;
+			// 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>1.0)
-					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);
 	}
 	hp->a_count+=NR_ATOMS;
 
 	/* add schedule for simulating injected atoms ;) */
-	moldyn_add_schedule(md,100,1.0);
+	moldyn_add_schedule(md,RELAX_S,1.0);
 
 	return 0;
 }
@@ -97,10 +174,10 @@ int hook(void *moldyn,void *hook_params) {
 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;
@@ -112,9 +189,6 @@ int main(int argc,char **argv) {
 	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));
@@ -146,11 +220,15 @@ int main(int argc,char **argv) {
 	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
 
 	/*
@@ -231,29 +309,31 @@ int main(int argc,char **argv) {
 
 	/* set (initial) dimensions of simulation volume */
 #ifdef ALBE
-	set_dim(&md,20*ALBE_LC_SI,20*ALBE_LC_SI,20*ALBE_LC_SI,TRUE);
-	//set_dim(&md,8*ALBE_LC_C,8*ALBE_LC_C,8*ALBE_LC_C,TRUE);
-	//set_dim(&md,8*ALBE_LC_SIC,8*ALBE_LC_SIC,8*ALBE_LC_SIC,TRUE);
+	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,8*LC_SI,8*LC_SI,8*LC_SI,TRUE);
-	//set_dim(&md,8*LC_C,8*LC_C,8*LC_C,TRUE);
-	set_dim(&md,8*TM_LC_SIC,8*TM_LC_SIC,8*TM_LC_SIC,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 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_SI,SI,M_SI,
 #endif
 	               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 	//               ATOM_ATTR_2BP|ATOM_ATTR_HB,
-	               0,20,20,20,NULL);
-	//               1,8,8,8,NULL);
+	               0,LCNTX,LCNTY,LCNTZ,NULL);
+	//               1,LCNTX,LCNTY,LCNTZ,NULL);
+	//
 
 	/* create zinkblende structure */
 	/*
@@ -261,20 +341,20 @@ int main(int argc,char **argv) {
 	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,
-	               0,8,8,8,&r);
+	               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,
-	               1,8,8,8,&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,
-	               0,8,8,8,&r);
+	               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,
-	               1,8,8,8,&r);
+	               1,LCNTX,LCNTY,LCNTZ,&r);
 #endif
 	*/
 
@@ -318,7 +398,7 @@ int main(int argc,char **argv) {
 	set_pressure(&md,BAR);
 
 	/* set amount of steps to skip before average calc */
-	set_avg_skip(&md,500);
+	set_avg_skip(&md,(8.0/10.0*PRERUN));
 
 	/* set p/t scaling */
 	//set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
@@ -331,30 +411,24 @@ int main(int argc,char **argv) {
 	thermal_init(&md,TRUE);
 
 	/* create the simulation schedule */
-	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 atoms */
-	//	moldyn_add_schedule(&md,10,1.0);
-	//}
+	moldyn_add_schedule(&md,PRERUN,1.0);
 
 	/* schedule hook function */
 	memset(&hookparam,0,sizeof(t_hp));
-	moldyn_set_schedule_hook(&md,&hook,&hookparam);
+	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);
 
 	/*