Added dmin_interspecies.

mihaf

2014-03-24 ea1cce4c80ddb68c0b46a6873ef3b64cc4a958a1

 src/initial_distribution.c

@@ -37,13 +37,49 @@

ts_vesicle *create_vesicle_from_tape(ts_tape *tape){
   ts_vesicle *vesicle;
   ts_vertex *vtx;

   vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
   vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist);
   // Nucleus:
   vesicle->R_nucleus=tape->R_nucleus;

   //Initialize grafted polymers (brush):
   vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
   vesicle->spring_constant=tape->kspring;
   poly_assign_spring_const(vesicle);

   //Initialize filaments (polymers inside the vesicle):
   vesicle->filament_list=init_poly_list(tape->nfil,tape->nfono, NULL, vesicle);
   poly_assign_filament_xi(vesicle,tape);

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

   for(i=0;i<vesicle->filament_list->n;i++){
      for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
         vtx = vesicle->filament_list->poly[i]->vlist->vtx[j];
         if(vtx->bond_no == 2){
         vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
         }
      }
   }

   for(i=0;i<vesicle->filament_list->n;i++){
      vertex_list_assign_id(vesicle->filament_list->poly[i]->vlist,TS_ID_FILAMENT);
   }

//   vesicle->spring_constant=tape->kspring;
//   poly_assign_spring_const(vesicle);

   
   vesicle->nshell=tape->nshell;
   vesicle->dmax=tape->dmax*tape->dmax; /* dmax^2 in the vesicle dmax variable */
   vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
   vesicle->bending_rigidity=tape->xk0;
   vtx_set_global_values(vesicle); /* make xk0 default value for every vertex */ 
   ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);