From a33fe7f5d4d7e09b5b52f5f4dadd462cf868ec2f Mon Sep 17 00:00:00 2001
From: hackbard <hackbard>
Date: Thu, 30 Nov 2006 20:52:12 +0000
Subject: [PATCH] testing

---
 moldyn.c | 107 +++++++++++++++++++++++++++++++++++--------------------
 sic.c    |  10 +++---
 2 files changed, 75 insertions(+), 42 deletions(-)

diff --git a/moldyn.c b/moldyn.c
index 815fc87..26f298f 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -635,7 +635,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 	/* zero absolute time */
 	moldyn->time=0.0;
-
 	for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 
 		/* setting amount of runs and finite time step size */
@@ -759,15 +758,15 @@ int velocity_verlet(t_moldyn *moldyn) {
 int potential_force_calc(t_moldyn *moldyn) {
 
 	int i,j,k,count;
-	t_atom *atom,*btom,*ktom;
+	t_atom *itom,*jtom,*ktom;
 	t_linkcell *lc;
-	t_list neighbour[27],neighbourk[27];
-	t_list *this,*thisk;
-	u8 bc,bck;
+	t_list neighbour_i[27],neighbour_j[27];
+	t_list *this,*that;
+	u8 bc_ij,bc_ijk;
 	int countn,dnlc;
 
 	count=moldyn->count;
-	atom=moldyn->atom;
+	itom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	/* reset energy */
@@ -776,85 +775,117 @@ int potential_force_calc(t_moldyn *moldyn) {
 	for(i=0;i<count;i++) {
 
 		/* reset force */
-		v3_zero(&(atom[i].f));
+		v3_zero(&(itom[i].f));
 
 		/* single particle potential/force */
-		if(atom[i].attr&ATOM_ATTR_1BP)
-			moldyn->func1b(moldyn,&(atom[i]));
+		if(itom[i].attr&ATOM_ATTR_1BP)
+			moldyn->func1b(moldyn,&(itom[i]));
 
 		/* 2 body pair potential/force */
-		if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
+		if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 	
 			link_cell_neighbour_index(moldyn,
-				(atom[i].r.x+moldyn->dim.x/2)/lc->x,
-				(atom[i].r.y+moldyn->dim.y/2)/lc->y,
-				(atom[i].r.z+moldyn->dim.z/2)/lc->z,
-				neighbour);
+				(itom[i].r.x+moldyn->dim.x/2)/lc->x,
+				(itom[i].r.y+moldyn->dim.y/2)/lc->y,
+				(itom[i].r.z+moldyn->dim.z/2)/lc->z,
+				neighbour_i);
 
 			countn=lc->countn;
 			dnlc=lc->dnlc;
 
 			for(j=0;j<countn;j++) {
 
-				this=&(neighbour[j]);
+				this=&(neighbour_i[j]);
 				list_reset(this);
 
 				if(this->start==NULL)
 					continue;
 
-				bc=(j<dnlc)?0:1;
+				bc_ij=(j<dnlc)?0:1;
 
 				do {
-					btom=this->current->data;
+					jtom=this->current->data;
 
-					if(btom==&(atom[i]))
+					if(jtom==&(itom[i]))
 						continue;
 
-					if((btom->attr&ATOM_ATTR_2BP)&
-					   (atom[i].attr&ATOM_ATTR_2BP))
+					if((jtom->attr&ATOM_ATTR_2BP)&
+					   (itom[i].attr&ATOM_ATTR_2BP))
 						moldyn->func2b(moldyn,
-						               &(atom[i]),
-						               btom,
-						               bc);
+						               &(itom[i]),
+						               jtom,
+						               bc_ij);
 
 					/* 3 body potential/force */
 
-					if(!(atom[i].attr&ATOM_ATTR_3BP)||
-					   !(btom->attr&ATOM_ATTR_3BP))
+					if(!(itom[i].attr&ATOM_ATTR_3BP)||
+					   !(jtom->attr&ATOM_ATTR_3BP))
 						continue;
 
 					link_cell_neighbour_index(moldyn,
-					   (btom->r.x+moldyn->dim.x/2)/lc->x,
-					   (btom->r.y+moldyn->dim.y/2)/lc->y,
-					   (btom->r.z+moldyn->dim.z/2)/lc->z,
-					   neighbourk);
+					   (jtom->r.x+moldyn->dim.x/2)/lc->x,
+					   (jtom->r.y+moldyn->dim.y/2)/lc->y,
+					   (jtom->r.z+moldyn->dim.z/2)/lc->z,
+					   neighbour_j);
 
+					/* neighbours of j */
 					for(k=0;k<lc->countn;k++) {
 
-						thisk=&(neighbourk[k]);
-						list_reset(thisk);
+						that=&(neighbour_j[k]);
+						list_reset(that);
+					
+						if(that->start==NULL)
+							continue;
+
+						bc_ijk=(k<lc->dnlc)?0:1;
+
+						do {
+
+			ktom=that->current->data;
+
+			if(!(ktom->attr&ATOM_ATTR_3BP))
+				continue;
+
+			if(ktom==jtom)
+				continue;
+
+			if(ktom==&(itom[i]))
+				continue;
+
+			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
+
+						} while(list_next(that)!=\
+						        L_NO_NEXT_ELEMENT);
+
+					}
+					
+					/* neighbours of i */
+					for(k=0;k<countn;k++) {
+
+						that=&(neighbour_i[k]);
+						list_reset(that);
 					
-						if(thisk->start==NULL)
+						if(that->start==NULL)
 							continue;
 
-						bck=(k<lc->dnlc)?0:1;
+						bc_ijk=(k<dnlc)?0:1;
 
 						do {
 
-			ktom=thisk->current->data;
+			ktom=that->current->data;
 
 			if(!(ktom->attr&ATOM_ATTR_3BP))
 				continue;
 
-			if(ktom==btom)
+			if(ktom==jtom)
 				continue;
 
-			if(ktom==&(atom[i]))
+			if(ktom==&(itom[i]))
 				continue;
 
-			moldyn->func3b(moldyn,&(atom[i]),btom,ktom,bck);
+			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
 
-						} while(list_next(thisk)!=\
+						} while(list_next(that)!=\
 						        L_NO_NEXT_ELEMENT);
 
 					}
diff --git a/sic.c b/sic.c
index 2cd32eb..82b3710 100644
--- a/sic.c
+++ b/sic.c
@@ -86,6 +86,7 @@ printf("%d\n",sizeof(t_atom));
 	/* cutoff radius */
 	printf("[sic] setting cutoff radius\n");
 	set_cutoff(&md,TM_S_SI);
+	//set_cutoff(&md,1.0*LC_SI);
 
 	/* set (initial) dimensions of simulation volume */
 	printf("[sic] setting dimensions\n");
@@ -99,6 +100,7 @@ printf("%d\n",sizeof(t_atom));
 	printf("[sic] creating atoms\n");
 	create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 	               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,
+	               //ATOM_ATTR_2BP,
 	               0,4,4,4);
 
 	/* setting a nearest neighbour distance for the moldyn checks */
@@ -106,7 +108,7 @@ printf("%d\n",sizeof(t_atom));
 
 	/* set temperature */
 	printf("[sic] setting temperature\n");
-	set_temperature(&md,273.0+450.0);
+	set_temperature(&md,10.0);
 	
 	/* initial thermal fluctuations of particles */
 	printf("[sic] thermal init\n");
@@ -114,12 +116,12 @@ printf("%d\n",sizeof(t_atom));
 
 	/* create the simulation schedule */
 	printf("[sic] adding schedule\n");
-	moldyn_add_schedule(&md,10000,1.0e-15);
+	moldyn_add_schedule(&md,1000,1.0e-15);
 
 	/* activate logging */
 	printf("[sic] activate logging\n");
-	moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",100);
-	moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",100);
+	moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",10);
+	moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",10);
 
 	/*
 	 * let's do the actual md algorithm now
-- 
2.20.1