First of all we sincerely thank you.

How to fix ghost atoms and boundary conditions for the functionalized ZGNR structure which is already given in as image file in attachment???

We want to compute the workfunction of functionalized ZGNR.

We have tutorial only for Silver work function.

Do we need to include ghost atoms or can we consider the chemical potential as work function???

That are two completely different things. Work function is in the energy required to remove an electron from the Fermi level and move it far from the surface to the vacuum level. If the vacuum level energy coincides with zero energy (which can be checked by computing the effective potential or Hartree difference potential), then work function is absolute value of the chemical potential. Otherwise, you have to measure the energy between the Fermi energy (chemical potential) and the vacuum level energy as given by the effective or Hartree difference potential.

Using ghost atoms might be required for more accurate description of wave function tails in the vacuum region, i.e., relatively-far from the surface, when using an LCAO basis set, because of the localized nature of the numerical atomic orbitals.

As per this reply we calculated the Hartree Difference potential and effective potential of ZGNR and functionalized ZGNR and obtained + 0.14 eV and -0.71 eV respectively.Whereas the effective potential came as -52 eV and -53 eV respectively.But we calculated without inclusion of ghost atoms.We took difference between this Hartree difference potential and Chemical potential which is the work function and obtained 5.24 eV for ZGNR.But the maximum reported value in litreature for graphene is 4.9 eV.

How and where to include the ghost atoms???

What should be the maximum vacuum padding to be fixed???

What boundary conditions to be employed for this kind of structure???