From 20ae8328e6eb4b99c8e9c306ab6e09ac4922f395 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 30 Nov 2013 10:50:54 +0000
Subject: [PATCH] step in rewritting

---
 src/bondflip.c |   41 ++++++++++++++++++++++-------------------
 1 files changed, 22 insertions(+), 19 deletions(-)

diff --git a/src/bondflip.c b/src/bondflip.c
index 478027d..17a1977 100644
--- a/src/bondflip.c
+++ b/src/bondflip.c
@@ -34,27 +34,27 @@
 
     ts_vertex *kp,*km;
 
-    if(it->neigh_no< 3) return TS_FAIL;
-    if(k->neigh_no< 3) return TS_FAIL;
+    if(it->neigh->n< 3) return TS_FAIL;
+    if(k->neigh->n< 3) return TS_FAIL;
     if(k==NULL || it==NULL){
         fatal("In bondflip, number of neighbours of k or it is less than 3!",999);
     }
 
     nei=0;
-    for(i=0;i<it->neigh_no;i++){ // Finds the nn of it, that is k 
-        if(it->neigh[i]==k){
+    for(i=0;i<it->neigh->n;i++){ // Finds the nn of it, that is k 
+        if(it->neigh->vtx[i]==k){
             nei=i;
             break;
         }
     }
     neip=nei+1;  // I don't like it.. Smells like I must have it in correct order
     neim=nei-1;
-    if(neip>=it->neigh_no) neip=0;
-    if((ts_int)neim<0) neim=it->neigh_no-1; /* casting is essential... If not
+    if(neip>=it->neigh->n) neip=0;
+    if((ts_int)neim<0) neim=it->neigh->n-1; /* casting is essential... If not
 there the neim is never <0 !!! */
   //  fprintf(stderr,"The numbers are: %u %u\n",neip, neim);
-    km=it->neigh[neim];  // We located km and kp
-    kp=it->neigh[neip];
+    km=it->neigh->vtx[neim];  // We located km and kp
+    kp=it->neigh->vtx[neip];
 
     if(km==NULL || kp==NULL){
         fatal("In bondflip, cannot determine km and kp!",999);
@@ -64,8 +64,8 @@
 
 /* test if the membrane is wrapped too much, so that kp is nearest neighbour of
  * km. If it is true, then don't flip! */
-    for(i=0;i<km->neigh_no;i++){
-        if(km->neigh[i] == kp) return TS_FAIL;
+    for(i=0;i<km->neigh->n;i++){
+        if(km->neigh->vtx[i] == kp) return TS_FAIL;
     }
  //   fprintf(stderr,"Membrane didn't wrap too much.. Continue.\n");
 /* if bond would be too long, return... */
@@ -107,10 +107,10 @@
 
 /* Calculating the new energy */
   delta_energy=0;
-  for(i=0;i<k->neigh_no;i++) energy_vertex(k->neigh[i]);
-  for(i=0;i<kp->neigh_no;i++) energy_vertex(kp->neigh[i]);
-  for(i=0;i<km->neigh_no;i++) energy_vertex(km->neigh[i]);
-  for(i=0;i<it->neigh_no;i++) energy_vertex(it->neigh[i]);
+  for(i=0;i<k->neigh->n;i++) energy_vertex(k->neigh->vtx[i]);
+  for(i=0;i<kp->neigh->n;i++) energy_vertex(kp->neigh->vtx[i]);
+  for(i=0;i<km->neigh->n;i++) energy_vertex(km->neigh->vtx[i]);
+  for(i=0;i<it->neigh->n;i++) energy_vertex(it->neigh->vtx[i]);
   delta_energy+=k->xk* k->energy;
   delta_energy+=kp->xk* kp->energy;
   delta_energy+=km->xk* km->energy;
@@ -279,15 +279,18 @@
 // 3. step. Correct neighbours in vertex_list
 
 
-            vtx_remove_neighbour(k,it);
+            vertex_list_remove_vtx(k->neigh, it);
+            vertex_list_remove_vtx(it->neigh, k);
+	//vtx_remove_neighbour(k,it);
 //            vtx_remove_neighbour(it,k);
 //fprintf(stderr,"3. step (PROGRESS): removed k and it neighbours\n");
     
             //Tukaj pa nastopi tezava... Kam dodati soseda?
-            vtx_insert_neighbour(km,kp,k);
-            vtx_insert_neighbour(kp,km,it);
-//            vertex_add_neighbour(km,kp); //pazi na vrstni red.
-//            vertex_add_neighbour(kp,km);
+		
+//            vtx_insert_neighbour(km,kp,k);
+//            vtx_insert_neighbour(kp,km,it);
+            vtx_add_neighbour(km,kp); //pazi na vrstni red.
+            vtx_add_neighbour(kp,km);
 //fprintf(stderr,"3. step: vertex neighbours corrected\n");
 
 // 3a. step. If any changes to ts_vertex, do it here!

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