X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=sic.c;h=a78f3a0a9396318d91ddf5d3662eaeb2215e7ea9;hb=0b96eb313c9bfec6272b1f8de0d99c4ce26d1686;hp=167735f2fa75f7ebdcc32d12b5d4f9f66c61dc05;hpb=e25ff194682ff5fac86c60701343103e74973bed;p=physik%2Fposic.git

diff --git a/sic.c b/sic.c
index 167735f..a78f3a0 100644
--- a/sic.c
+++ b/sic.c
@@ -14,21 +14,53 @@
 #include "potentials/harmonic_oscillator.h"
 #include "potentials/lennard_jones.h"
 #include "potentials/tersoff.h"
+//#include "potentials/tersoff_orig.h"
+
+#define INJECT		1
+#define NR_ATOMS	4
 
 int hook(void *moldyn,void *hook_params) {
 
 	t_moldyn *md;
+	t_3dvec r,v,dist;
+	double d;
+	unsigned char run;
+	int i,j;
+	t_atom *atom;
 
 	md=moldyn;
 
- 	/* switch to direct scaling in first hook */	
-	if(md->schedule.count==0)
+	printf("\nschedule hook: ");
+
+	if(!(md->schedule.count%2)) {
+		/* add carbon at random place, and enable t scaling */
+		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;
+			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;
+			}
+		}
+		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);
-	/* switch off temp scaling in second hook */
-	if(md->schedule.count==1)
+	}
+	else {
+		/* disable t scaling */
+		printf("disabling t scaling\n");
 		set_pt_scale(md,0,0,0,0);
-		
-	//set_temperature(md,md->t_ref-100.0);
+	}
 
 	return 0;
 }
@@ -49,6 +81,9 @@ int main(int argc,char **argv) {
 	t_ho_params ho;
 	t_tersoff_mult_params tp;
 
+	/* atom injection counter */
+	int inject;
+
 	/* testing location & velocity vector */
 	t_3dvec r,v;
 	memset(&r,0,sizeof(t_3dvec));
@@ -63,8 +98,13 @@ int main(int argc,char **argv) {
 	/* choose potential */
 	set_potential1b(&md,tersoff_mult_1bp);
 	set_potential2b(&md,tersoff_mult_2bp);
-	set_potential2b_post(&md,tersoff_mult_post_2bp);
-	set_potential3b(&md,tersoff_mult_3bp);
+	//set_potential3b_j1(&md,tersoff_mult_2bp);
+	//set_potential3b_k1(&md,tersoff_mult_3bp);
+	//set_potential3b_j3(&md,tersoff_mult_post_2bp);
+	set_potential3b_j1(&md,tersoff_mult_3bp_j1);
+	set_potential3b_k1(&md,tersoff_mult_3bp_k1);
+	set_potential3b_j2(&md,tersoff_mult_3bp_j2);
+	set_potential3b_k2(&md,tersoff_mult_3bp_k2);
 	//set_potential2b(&md,lennard_jones);
 	//set_potential2b(&md,harmonic_oscillator);
 	set_potential_params(&md,&tp);
@@ -164,7 +204,7 @@ int main(int argc,char **argv) {
 
 	/* set temperature & pressure */
 	set_temperature(&md,atof(argv[2])+273.0);
-	set_pressure(&md,ATM);
+	set_pressure(&md,BAR);
 
 	/* set p/t scaling */
 	//set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
@@ -176,18 +216,27 @@ int main(int argc,char **argv) {
 	thermal_init(&md,TRUE);
 
 	/* create the simulation schedule */
-	moldyn_add_schedule(&md,10001,1.0);
-	//moldyn_add_schedule(&md,501,1.0);
-	//moldyn_add_schedule(&md,501,1.0);
+	/* initial configuration */
+	moldyn_add_schedule(&md,10000,1.0);
+	/* 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);
+	//}
 
 	/* schedule hook function */
-	//moldyn_set_schedule_hook(&md,&hook,NULL);
+	moldyn_set_schedule_hook(&md,&hook,NULL);
 
 	/* 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_log(&md,CREATE_REPORT,0);
 
 	/*