It seems that bondlip is debugged. Still, recommend testing

Samo Penic

2014-03-08 7efbb1dbd7c2c1368c429858a32fbeb9467420a8

 src/poly.c

@@ -4,7 +4,17 @@
#include"vertex.h"
#include"bond.h"
#include<math.h>
#include"energy.h"

ts_bool poly_assign_spring_const(ts_vesicle *vesicle){
   ts_uint i;

   for(i=0;i<vesicle->poly_list->n;i++){
    vesicle->poly_list->poly[i]->k = vesicle->spring_constant;
       }
	
   return TS_SUCCESS;
}

ts_poly   *init_poly(ts_uint n, ts_vertex *grafted_vtx){
   ts_poly   *poly=(ts_poly *)calloc(1,sizeof(ts_poly));
@@ -19,6 +29,11 @@
      vtx_add_neighbour(poly->vlist->vtx[i+1], poly->vlist->vtx[i]);
   }

   for(i=0;i<poly->blist->n;i++){
   poly->blist->bond[i]->bond_length=sqrt(vtx_distance_sq(poly->blist->bond[i]->vtx1,poly->blist->bond[i]->vtx2));
   bond_energy(poly->blist->bond[i],poly);
   }

   return poly;
}

@@ -26,7 +41,7 @@
ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist){
   ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
   poly_list->poly   = (ts_poly **)calloc(n_poly,sizeof(ts_poly *));
   ts_uint i=0,j=0;
   ts_uint i=0,j=0, idx;
   ts_uint gvtxi;
   ts_double xnorm,ynorm,znorm,normlength;

@@ -49,9 +64,9 @@
      ynorm=0.0;
      znorm=0.0;
      for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){
         xnorm+=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
         ynorm+=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
         znorm+=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;	
         xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
         ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
         znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;	
      }
      normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
      xnorm=xnorm/normlength;
@@ -65,6 +80,17 @@
      }
   }

      //index correction for polymeres. Important, since each vtx has to have unique id
   idx=vlist->n;
   for(i=0;i<n_poly;i++){
      for(j=0;j<n_mono;j++,idx++){

         poly_list->poly[i]->vlist->vtx[j]->idx=idx;

      }
   }


   return poly_list;
}