Sambit,

your minimal example fails, because you are calling 
  GridTools::collect_periodic_faces(triangulation, /*b_id1*/ 2*i+1, 
/*b_id2*/ 2*i+2,/*direction*/ i, periodicity_vector);
after 
  triangulation.refine_global(2);
again. As explained in the documentation 
<https://www.dealii.org/8.5.1/doxygen/deal.II/namespaceGridTools.html#aaeadfc0053429f542fbfd48d192b94f0>
 
this is not unexpected.

Does your issue pertain after making sure to call
  GridTools::collect_periodic_faces(triangulation, /*b_id1*/ 2*i+1, 
/*b_id2*/ 2*i+2,/*direction*/ i, periodicity_vector);
only before mesh refinement?

Best,
Daniel

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