It seems bondflip is fixed. Before 'for' loops I had to set j=0 in vertex.c...

Samo Penic

2012-07-10 e19e790e95f14ca69a7ce9c5e45d815fe21df36e

 src/vertex.c

@@ -72,25 +72,25 @@
ts_bool vtx_remove_neighbour(ts_vertex *vtx, ts_vertex *nvtx){
/* find a neighbour */
/* remove it from the list while shifting remaining neighbours up */
    ts_int i,j=-1;
    ts_uint i,j=0;
    for(i=0;i<vtx->neigh_no;i++){
//      fprintf(stderr,"neigh_addr=%ld\n", (long)vtx->neigh[i]);
        if(vtx->neigh[i]!=nvtx){
            vtx->neigh[j]=vtx->neigh[i];
            j++;
        }
    }
    if(j==0) { 
        fatal("vtx_remove_neighbour: Error, vertices are not neighbours", 100);
    }
//   fprintf(stderr,"remove_neighbour: vtx1_addr=%ld, vtx2_addr=%ld\n",(long)vtx,(long)nvtx);
/* resize memory. potentionally time consuming */
    vtx->neigh_no--;
    vtx->neigh=(ts_vertex **)realloc(vtx->neigh,vtx->neigh_no*sizeof(ts_vertex *));
    if(vtx->neigh == NULL && vtx->neigh_no!=0)
        fatal("Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
fprintf(stderr,"first alloc");
        fatal("(1) Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
//fprintf(stderr,"first alloc");
/* repeat for the neighbour */
/* find a neighbour */
/* remove it from the list while shifting remaining neighbours up */
   j=0;
    for(i=0;i<nvtx->neigh_no;i++){
        if(nvtx->neigh[i]!=vtx){
            nvtx->neigh[j]=nvtx->neigh[i];
@@ -98,10 +98,12 @@
        }
    }
/* resize memory. potentionally time consuming. */
//   fprintf(stderr,"Neigbours=%d\n",nvtx->neigh_no);
    nvtx->neigh_no--;
    nvtx->neigh=(ts_vertex **)realloc(nvtx->neigh,nvtx->neigh_no*sizeof(ts_vertex *));
//   fprintf(stderr,"Neigbours=%d\n",nvtx->neigh_no);
    if(nvtx->neigh == NULL && nvtx->neigh_no!=0)
        fatal("Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
        fatal("(2) Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);

    return TS_SUCCESS;
}
@@ -128,6 +130,7 @@
ts_bool vtx_add_cneighbour(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex *vtx2){
    ts_bool retval;
    retval=vtx_add_neighbour(vtx1,vtx2);
  //  retval=vtx_add_neighbour(vtx2,vtx1);
    if(retval==TS_SUCCESS)
    retval=vtx_add_bond(blist,vtx1,vtx2); 
    return retval;