From 6c3bb91fea92c5013507bdf4f5ac49e889e213ff Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 06 Oct 2015 12:07:39 +0000
Subject: [PATCH] Unkonown merge difference between different directories are merged together.

---
 src/bond.c |   53 +++++++++++++++++++++++++++++++++++++++++++----------
 1 files changed, 43 insertions(+), 10 deletions(-)

diff --git a/src/bond.c b/src/bond.c
index 492ad24..ce255ca 100644
--- a/src/bond.c
+++ b/src/bond.c
@@ -1,24 +1,57 @@
 #include<stdlib.h>
 #include "general.h"
-#include<stdio.h>
+#include "vertex.h"
 
-ts_bool init_bond_list(ts_bond_list *blist){
+ts_bond_list *init_bond_list(){
+    ts_bond_list *blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
 	blist->n=0;
 	blist->bond=NULL;
-	return TS_SUCCESS;
+	return blist;
 }
 
-ts_bool bond_add(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex *vtx2){
+ts_bond  *bond_add(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex *vtx2){
+    ts_uint i;
+    /* no vertices must be null! */
+    if(vtx1==NULL || vtx2==NULL) return NULL;
+    /* Verify if the bond already exists... Don't do multiple bonds */
+    for(i=0;i<blist->n;i++){
+       if((blist->bond[i]->vtx1==vtx1 || blist->bond[i]->vtx1==vtx2)
+        &&(blist->bond[i]->vtx2==vtx1 || blist->bond[i]->vtx2==vtx2))
+        return blist->bond[i];
+    }
 	blist->n++;
-	blist->bond=realloc(blist->bond,blist->n*sizeof(ts_bond));
-	if(blist->bond==NULL) fatal("Cannot reallocate memory for additional *ts_bond.",5);
-	//NOW insert vertices!	
-	blist->bond[blist->n - 1].vtx1=vtx1;	
-	blist->bond[blist->n - 1].vtx2=vtx2;	
-	return TS_SUCCESS;
+	blist->bond=(ts_bond **)realloc(blist->bond,blist->n*sizeof(ts_bond *));
+	if(blist->bond==NULL) fatal("Cannot reallocate memory for additional **ts_bond.",100);
+    blist->bond[blist->n-1]=(ts_bond *)malloc(sizeof(ts_bond));
+    if(blist->bond[blist->n-1]==NULL) fatal("Cannot allocate memory for additional *ts_bond.",100);
+    
+	//NOW insert vertices into data!	
+	blist->bond[blist->n - 1]->vtx1=vtx1;	
+	blist->bond[blist->n - 1]->vtx2=vtx2;
+	blist->bond[blist->n - 1]->tainted=0;
+	blist->bond[blist->n - 1]->idx=blist->n-1;
+    //Should we calculate bond length NOW?
+	
+	return blist->bond[blist->n-1];
 }
+
+
+ts_bool bond_vector(ts_bond *bond){
+	
+	bond->x = bond->vtx1->x - bond->vtx2->x;
+	bond->y = bond->vtx1->y - bond->vtx2->y;
+	bond->z = bond->vtx1->z - bond->vtx2->z;
+
+	return TS_SUCCESS;	
+}
+
 
 ts_bool bond_list_free(ts_bond_list *blist){
+    ts_uint i;
+    for(i=0;i<blist->n;i++){
+    free(blist->bond[i]);
+    }
     free(blist->bond);
+    free(blist);
     return TS_SUCCESS;
 }

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