Fixed a bug. added cells

Samo Penic

2014-03-06 063289f4f872d642078d70757685c728e3fdfc81

 src/io.c

@@ -19,7 +19,6 @@

    /* save current state with wrong pointers. Will fix that later */
    ts_uint i,j,k;
    ts_ulong off;
    FILE *fh=fopen("dump.bin","wb");

    /* dump vesicle */
@@ -46,64 +45,45 @@
                    cell is ignored
        */
        for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
            off=(ts_ulong)(vesicle->vlist->vtx[i]->neigh[j]-vesicle->vlist->vtx[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh); 
            fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh); 
        }
        for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
            off=(ts_ulong)(vesicle->vlist->vtx[i]->bond[j]-vesicle->blist->bond[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh); 
            fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh); 
        }
        for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
            off=(ts_ulong)(vesicle->vlist->vtx[i]->tristar[j]-vesicle->tlist->tria[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh); 
            fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh); 
        }
//        off=(ts_ulong)(vesicle->vlist->vtx[i]->cell-vesicle->clist->cell[0]);
//        fwrite(&off,sizeof(ts_ulong),1,fh); 

    }

    /*dump bonds*/
    for(i=0;i<vesicle->blist->n;i++){
        fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
        /* dump pointer offsets for vtx1 and vtx2 */
        off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
        fwrite(&off,sizeof(ts_ulong),1,fh); 
        off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
        fwrite(&off,sizeof(ts_ulong),1,fh); 
        //off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
        fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh); 
        //off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
        fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh); 
    }

    /*dump triangles*/
    for(i=0;i<vesicle->tlist->n;i++){
        fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
        /* dump pointer offsets for vertex */
        off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[0]-vesicle->vlist->vtx[0]);
        fwrite(&off,sizeof(ts_ulong),1,fh); 
        off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[1]-vesicle->vlist->vtx[0]);
        fwrite(&off,sizeof(ts_ulong),1,fh); 
        off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[2]-vesicle->vlist->vtx[0]);
        fwrite(&off,sizeof(ts_ulong),1,fh); 
        fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh); 
        fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh); 
        fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh); 
        /* dump pointer offsets for neigh */
        for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
            off=(ts_ulong)(vesicle->tlist->tria[i]->neigh[j]-vesicle->tlist->tria[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh); 
            fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh); 
        }
    }
   
    /*dump cells and its contents is not dumped but recalculated on restore*/

/*    for(i=0;i<vesicle->clist->cellno;i++){
        fwrite(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
        for(j=0;j<vesicle->clist->cell[i]->nvertex;j++){
            off=(ts_ulong)(vesicle->clist->cell[i]->vertex[j]-vesicle->vlist->vtx[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh);
        }
    }
*/


    /*dump polymeres */
    for(i=0;i<vesicle->poly_list->n;i++){
        fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
        fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
        fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
    } 
     
    /* dump poly vertex(monomer) list*/
@@ -112,24 +92,26 @@
            fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
            /* dump offset for neigh and bond */
            for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
                off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
                fwrite(&off,sizeof(ts_ulong),1,fh); 
               // off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
                fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh); 
            }
            for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
                off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
                fwrite(&off,sizeof(ts_ulong),1,fh); 
                //off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
                fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh); 
            }
        }
   // grafted vtx on vesicle data dump
      fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
    }
    /* dump poly bonds between monomers list*/
    for(i=0;i<vesicle->poly_list->n;i++){
        for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
            fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
            /* dump vtx1 and vtx2 offsets */
            off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh); 
            off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
            fwrite(&off,sizeof(ts_ulong),1,fh); 
            //off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
            fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh); 
//            off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
            fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh); 
        }
    }

@@ -145,15 +127,8 @@
        poly_list->poly->bond
*/

    fwrite(vesicle->vlist->vtx, sizeof(ts_vertex *),1,fh);
    fwrite(vesicle->blist->bond, sizeof(ts_bond *),1,fh);
    fwrite(vesicle->tlist->tria, sizeof(ts_triangle *),1,fh);
    fwrite(vesicle->clist->cell, sizeof(ts_cell *),1,fh);
    fwrite(vesicle->poly_list->poly, sizeof(ts_poly *),1,fh);
    for(i=0;i<vesicle->poly_list->n;i++){
        fwrite(vesicle->poly_list->poly[i]->vlist->vtx, sizeof(ts_vertex *),1,fh);
        fwrite(vesicle->poly_list->poly[i]->blist->bond, sizeof(ts_bond *),1,fh);
    }
   fwrite(vesicle->clist, sizeof(ts_cell_list),1,  fh);

    fclose(fh);
    return TS_SUCCESS;
}
@@ -164,7 +139,7 @@
    ts_uint i,j,k;
    FILE *fh=fopen("dump.bin","rb");
    ts_uint retval;
    ts_ulong off;
   ts_uint idx;

/* we restore all the data from the dump */
    /* restore vesicle */
@@ -187,6 +162,17 @@
    retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
    /* level 1 complete */

/* prerequisity. Bonds must be malloced before vertexes are recreated */
  vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *));
    for(i=0;i<vesicle->blist->n;i++){
        vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
   }
/* prerequisity. Triangles must be malloced before vertexes are recreated */
  vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *));
    for(i=0;i<vesicle->tlist->n;i++){
        vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
}

  /*restore vertices*/
    vesicle->vlist->vtx=(ts_vertex **)calloc(vesicle->vlist->n,sizeof(ts_vertex *));
    for(i=0;i<vesicle->vlist->n;i++){
@@ -195,51 +181,54 @@
        /*restore neigh, bond, tristar. Ignoring cell */
        vesicle->vlist->vtx[i]->neigh=(ts_vertex **)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex *));
        for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
            retval=fread(&off,sizeof(ts_ulong),1,fh);
            vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[0]+off;
            retval=fread(&idx,sizeof(ts_uint),1,fh);
            vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
        }
        vesicle->vlist->vtx[i]->bond=(ts_bond **)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond *));
        for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
            retval=fread(&off,sizeof(ts_ulong),1,fh);
            vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[0]+off;    
            retval=fread(&idx,sizeof(ts_uint),1,fh);
/* pointer can be assigned only when list of bonds is fully initialized in memory. Thus bondlist popularization must be done before vertex can reference to it */
            vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];    
        }

        vesicle->vlist->vtx[i]->tristar=(ts_triangle **)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle *));
        for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
            retval=fread(&off,sizeof(ts_ulong),1,fh);
            vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[0]+off;
            retval=fread(&idx,sizeof(ts_uint),1,fh);
/* same comment as above */
            vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
        }

    }

    /*restore bonds*/
    vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *));
   // vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *)); // done before.
    for(i=0;i<vesicle->blist->n;i++){
        vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
     //   vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
        retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
        /* restore vtx1 and vtx2 */
        retval=fread(&off,sizeof(ts_ulong),1,fh);
        vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[0]+off;
        retval=fread(&off,sizeof(ts_ulong),1,fh);
        vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[0]+off;
        retval=fread(&idx,sizeof(ts_uint),1,fh);
        vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
        retval=fread(&idx,sizeof(ts_uint),1,fh);
        vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
    }

    /*restore triangles*/
    vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *));
//    vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *)); // done before
    for(i=0;i<vesicle->tlist->n;i++){
        vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
 //       vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
        retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
        /* restore pointers for vertices */
        retval=fread(&off,sizeof(ts_ulong),1,fh);
        vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[0]+off;
        retval=fread(&off,sizeof(ts_ulong),1,fh);
        vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[0]+off;
        retval=fread(&off,sizeof(ts_ulong),1,fh);
        vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[0]+off;
        retval=fread(&idx,sizeof(ts_uint),1,fh);
        vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
        retval=fread(&idx,sizeof(ts_uint),1,fh);
        vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
        retval=fread(&idx,sizeof(ts_uint),1,fh);
        vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
        /* restore pointers for neigh */
    vesicle->tlist->tria[i]->neigh=(ts_triangle **)malloc(vesicle->tlist->tria[i]->neigh_no*sizeof(ts_triangle *));
        for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
            retval=fread(&off,sizeof(ts_ulong),1,fh);
            vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[0]+off;
            retval=fread(&idx,sizeof(ts_uint),1,fh);
            vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
        }

    }
@@ -257,74 +246,68 @@
    for(i=0;i<vesicle->poly_list->n;i++){
        vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
        retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
        vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
        retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
        vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
        retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
   /* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
        vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex *));
        vesicle->poly_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond *));
    for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
            vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
   }
   for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
            vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
   }

    } 

     
    /* restore poly vertex(monomer) list*/
    for(i=0;i<vesicle->poly_list->n;i++){
        vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex *));
        for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
            vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
            retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
            
           	 
            /* restore neigh and bonds */
            vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
            for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
                retval=fread(&off,sizeof(ts_ulong),1,fh);
                vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
            }
            vesicle->poly_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
            for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
                retval=fread(&off,sizeof(ts_ulong),1,fh);
                vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[0]+off;
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
            }

        }
   /* restore grafted vtx on vesicle and grafted_poly */
                retval=fread(&idx,sizeof(ts_uint),1,fh);
      vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
      vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];	
    }

    /* restore poly bonds between monomers list*/
    for(i=0;i<vesicle->poly_list->n;i++){
        vesicle->poly_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond *));
        for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
            vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
       //     vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
            retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
            /* restore vtx1 and vtx2 */
                retval=fread(&off,sizeof(ts_ulong),1,fh);
                vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
                retval=fread(&off,sizeof(ts_ulong),1,fh);
                vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
                retval=fread(&idx,sizeof(ts_uint),1,fh);
                vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
        }
    }


    /* recalculate pointers using saved information on pointer addresses */
    /* following pointers need to be recalculated:
        all vtx->neigh
        all vtx->tristar
        all vtx->bond
        vtx->cell
        vtx->grafted_poly
        bond->vtx1
        bond->vtx2
        tria->vertex[*]
        tria->neigh
        cell->vertex
        poly->grafted_vtx
        poly->vlist->vtx->neigh
        poly->vlist->vtx->bond
        poly->vlist->vtx->cell
    */

    /* read pointers from disk */
/*    fwrite(vesicle->vlist->vtx, sizeof(ts_vertex *),1,fh);
    fwrite(vesicle->blist->bond, sizeof(ts_bond *),1,fh);
    fwrite(vesicle->tlist->tria, sizeof(ts_triangle *),1,fh);
    fwrite(vesicle->clist->cell, sizeof(ts_cell *),1,fh);
    fwrite(vesicle->poly_list->poly, sizeof(ts_poly *),1,fh);
    for(i=0;i<vesicle->poly_list->n;i++){
        fwrite(vesicle->poly_list->poly[i]->vlist->vtx, sizeof(ts_vertex *),1,fh);
        fwrite(vesicle->poly_list->poly[i]->blist->bond, sizeof(ts_bond *),1,fh);
    }
*/

// recreating space for cells // 
   vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
   retval=fread(vesicle->clist, sizeof(ts_cell_list), 1,fh); 
   vesicle->clist->cell=(ts_cell **)malloc(sizeof(ts_cell *)*vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2]);
   for(i=0;i<vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2];i++){
           vesicle->clist->cell[i]=(ts_cell *)calloc(1,sizeof(ts_cell));
           vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
       }

    if(retval); 
    fclose(fh);
@@ -542,7 +525,7 @@
   /* Here comes header of the file */

   //find number of extra vtxs and bonds of polymeres
   ts_uint monono=0, polyno=0;
   ts_uint monono=0, polyno=0, poly_idx=0;
   ts_bool poly=0;
   if(vesicle->poly_list!=NULL){
      if(vesicle->poly_list->poly[0]!=NULL){
@@ -559,9 +542,10 @@
    }
   //polymeres
   if(poly){
      poly_idx=vlist->n;
      for(i=0;i<vesicle->poly_list->n;i++){
         for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
            fprintf(fh,"%u ", vesicle->poly_list->poly[i]->vlist->vtx[j]->idx);
         for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
            fprintf(fh,"%u ", poly_idx);
         }
      }
   }
@@ -585,12 +569,14 @@
   }
   //polymeres
   if(poly){
      poly_idx=vlist->n;
      for(i=0;i<vesicle->poly_list->n;i++){
         for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
            fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx);
//            fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx);
            fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+i*monono,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+i*monono);
         }
   //grafted bonds
      fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx);
      fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx+vlist->n+i*monono);
      }

   }