From 22a224e0f41f996954049c69bcc6fbb3cf62325f Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Tue, 9 Sep 2008 23:04:05 +0200
Subject: [PATCH] introduced process_neighbours function

---
 moldyn.c | 82 ++++++++++++++++++++++++++++++++++++++++++++++++++++++--
 moldyn.h |  4 +++
 2 files changed, 84 insertions(+), 2 deletions(-)

diff --git a/moldyn.c b/moldyn.c
index 6da2b95..3ac0a2d 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -1772,7 +1772,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 
 		/* display progress */
-		//if(!(moldyn->total_steps%10)) {
+		if(!(moldyn->total_steps%10)) {
 			/* get current time */
 			gettimeofday(&t2,NULL);
 
@@ -1788,7 +1788,7 @@ printf("\rsched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)",
 
 			/* copy over time */
 			t1=t2;
-		//}
+		}
 
 		/* increase absolute time */
 		moldyn->time+=moldyn->tau;
@@ -2515,6 +2515,84 @@ int process_2b_bonds(t_moldyn *moldyn,void *data,
 
 }
 
+/*
+ * function to find neighboured atoms
+ */
+
+int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
+                       int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
+		                      void *data,u8 bc)) {
+
+	t_linkcell *lc;
+#ifdef STATIC_LISTS
+	int *neighbour[27];
+	int p;
+#elif LOWMEM_LISTS
+	int neighbour[27];
+	int p;
+#else
+	t_list neighbour[27];
+	t_list *this;
+#endif
+	u8 bc;
+	t_atom *natom;
+	int j;
+
+	lc=&(moldyn->lc);
+	
+	/* neighbour indexing */
+	link_cell_neighbour_index(moldyn,
+	                          (atom->r.x+moldyn->dim.x/2)/lc->x,
+	                          (atom->r.y+moldyn->dim.y/2)/lc->x,
+	                          (atom->r.z+moldyn->dim.z/2)/lc->x,
+	                          neighbour);
+
+	for(j=0;j<27;j++) {
+
+		bc=(j<lc->dnlc)?0:1;
+
+#ifdef STATIC_LISTS
+		p=0;
+
+		while(neighbour[j][p]!=-1) {
+
+			natom=&(moldyn->atom[neighbour[j][p]]);
+			p++;
+#elif LOWMEM_LISTS
+		p=neighbour[j];
+
+		while(p!=-1) {
+
+			natom=&(moldyn->atom[p]);
+			p=lc->subcell->list[p];
+#else
+		this=&(neighbour[j]);
+		list_reset_f(this);
+
+		if(this->start==NULL)
+			continue;
+
+		do {
+
+			natom=this->current->data;
+#endif
+
+			/* process bond */
+			process(moldyn,atom,natom,data,bc);
+
+#ifdef STATIC_LISTS
+		}
+#elif LOWMEM_LISTS
+		}
+#else
+		} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+	}
+
+	return 0;
+
+}
+
 /*
  * post processing functions
  */
diff --git a/moldyn.h b/moldyn.h
index da951b5..87c8948 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -463,6 +463,10 @@ int moldyn_load(t_moldyn *moldyn);
 int process_2b_bonds(t_moldyn *moldyn,void *data,
                      int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
                                     void *data,u8 bc));
+int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
+                       int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
+                                      void *data,u8 bc));
+
 int get_line(int fd,char *line,int max);
 
 int pair_correlation_init(t_moldyn *moldyn,double dr);
-- 
2.20.1