Many changes to the code to allow internal pegs

Samo Penic

2016-07-13 90882f51387b945bc0f660d8b12200b2f48e80fa

 src/main.c

@@ -126,7 +126,8 @@
      }
   }
         //printf("nucleus coords: %.17e %.17e %.17e\n",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);

//   write_vertex_xml_file(vesicle,0);
//   exit(1);
   run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration);
   write_master_xml_file(command_line_args.output_fullfilename);
   write_dout_fcompat_file(vesicle,"dout");