X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=sic.c;h=05de728c9e9cdd4be50bf73a1e1a51fd6956d195;hb=b5b47daaa3718c4dec2056fe5147668023575b8e;hp=7855cc2e38eb81ab935c2bbd38c1746b10e2e52a;hpb=0d2926a23ea7bbf7654da88770c827ad041357a5;p=physik%2Fposic.git

diff --git a/sic.c b/sic.c
index 7855cc2..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"
@@ -37,11 +36,11 @@
 #define INJ_OFFSET	(ALBE_LC_SI/8.0)
 #define RELAX_S		20
 
-#define LCNTX		5
-#define LCNTY		5
-#define LCNTZ		5
-#define PRERUN		10
-#define POSTRUN		2000
+#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
@@ -57,7 +56,21 @@ typedef struct s_hp {
 	char **argv;	/* args */
 } t_hp;
 
-int hook(void *moldyn,void *hook_params) {
+int hook_del_atom(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;
@@ -97,11 +110,35 @@ int hook(void *moldyn,void *hook_params) {
 	for(j=0;j<NR_ATOMS;j++) {
 		run=1;
 		while(run) {
+			// 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.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;
+			*/
+			// offset
+			r.x+=INJ_OFFSET;
+			r.y+=INJ_OFFSET;
 			r.z+=INJ_OFFSET;
 			/* assume valid coordinates */
 			run=0;
@@ -111,6 +148,7 @@ int hook(void *moldyn,void *hook_params) {
 				d=v3_absolute_square(&dist);
 				/* reject coordinates */
 				if(d<R_C) {
+					//printf("atom %d - %f\n",i,d);
 					run=1;
 					break;
 				}
@@ -122,7 +160,7 @@ int hook(void *moldyn,void *hook_params) {
 #else
 		add_atom(md,SI,M_SI,0,
 #endif
-		         ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+		         ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB|ATOM_ATTR_VB,
 		         &r,&v);
 	}
 	hp->a_count+=NR_ATOMS;
@@ -182,12 +220,14 @@ 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
 
@@ -282,6 +322,7 @@ int main(int argc,char **argv) {
 	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,
@@ -292,6 +333,7 @@ int main(int argc,char **argv) {
 	//               ATOM_ATTR_2BP|ATOM_ATTR_HB,
 	               0,LCNTX,LCNTY,LCNTZ,NULL);
 	//               1,LCNTX,LCNTY,LCNTZ,NULL);
+	//
 
 	/* create zinkblende structure */
 	/*
@@ -375,7 +417,9 @@ int main(int argc,char **argv) {
 	memset(&hookparam,0,sizeof(t_hp));
 	hookparam.argc=argc;
 	hookparam.argv=argv;
-	moldyn_set_schedule_hook(&md,&hook,&hookparam);
+	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]);