# Binding energy calculation for Zn atom on armchair graphene slab?

I am trying to repeat the result of this paper for Zn absorbed on the armchair graphene slab.

The relaxed top and side structures are the following:

The relaxed structure is almost the same as the cited paper. Then the energy calculation based on this relaxed structure is listed below:

• E(slab+Zn)=-759.31696 (eV)
• E(slab)=-759.30724 (eV)

The energy of Zn is obtained from its bulk calculation:

• E(Zn)=-1.1078938 (eV)

Then the binding energy is estimated as:

• $$\Delta E$$=E(slab+Zn)-E(slab)-E(Zn)=1.0981738 (eV)

However, the result of the cited paper is -0.2 eV:

What am I missing?

For completeness, I will give my input cards for relaxation and static calculations as follows:

 System=2D
ISTART=0        !startjob: 0-new 1-cont 2-samecut
ICHARG=2        !charge: 1-file 2-atom 10-const
ENCUT=500       !energy cutoff in eV
EDIFF=1E-6      !stopping-criterion for electronic upd.
NELM=300        !nr. of electronic steps
ISMEAR=0        !part. occupancies
SIGMA=0.05      !broadening in eV -4-tet -1-fermi 0-gaus
IALGO=38
LREAL=Auto
IVDW=11

#------------------
#ISPIN=2        !spin polarized calculation (2-yes 1-no)
#MAGMOM=128*0   !initial mag moment / atom
#LSORBIT=.TRUE. !if .TRUE. switches on spin-orbit coupling
#SAXIS= 0 0 1   !quantisation axis for spin
#ISYM=0         !symmetry: 0-nonsym 1-usesym

Dynamic:
ISIF=2
IBRION=2
NSW=300
EDIFFG=-0.005

Parallelization:
NPAR=8
#KPAR=4

Output:
LCHARG=.FALSE.
LWAVE=.FALSE.


=========================================

 System=2D
ISTART=0        !startjob: 0-new 1-cont 2-samecut
ICHARG=2        !charge: 1-file 2-atom 10-const
ENCUT=500       !energy cutoff in eV
EDIFF=1E-6      !stopping-criterion for electronic upd.
NELM=300        !nr. of electronic steps
ISMEAR=0        !part. occupancies
SIGMA=0.05      !broadening in eV -4-tet -1-fermi 0-gaus
IALGO=38
LREAL=Auto
IVDW=11

#------------------
#ISPIN=2        !spin polarized calculation (2-yes 1-no)
#MAGMOM=128*0   !initial mag moment / atom
#LSORBIT=.TRUE. !if .TRUE. switches on spin-orbit coupling
#SAXIS= 0 0 1   !quantisation axis for spin
#ISYM=0         !symmetry: 0-nonsym 1-usesym

Dynamic:
#ISIF=2
#IBRION=2
#NSW=300
#EDIFFG=-0.005

#Parallelization:
NPAR=8
#KPAR=4

Output:
#LCHARG=.FALSE.
#LWAVE=.FALSE.


For convenience, the computational details for the cited paper are put below:

• Can you share your INCAR? Are you reproducing their exact theory? Oct 13, 2020 at 16:03
• The energy of Zn was obtained from bulk but is not the bulk energy right?
– Camps
Oct 13, 2020 at 18:03
• @Camps I calculated from bulk because from this information: [The energy of the Zn atom was calculated using the metallic Zn configuration]. Am I wrong? How can estimate the energy of the single Zn atom?
– Jack
Oct 13, 2020 at 21:16
• Yes, you should use the energy of a single atom, as it is a single atom interacting with your slab.
– Camps
Oct 14, 2020 at 12:26
• Using the energy of a single atom can mean many things. It should be a single atom in its standard state (Zn metal) not a single atom in gas phase. Technically you could use a single atom in gas phase as the reference if you wanted to calculate a true "binding" energy but this sort of binding is unreasonable to look at. Using the metallic state you would get a formation energy. Maybe this is the confusion. Oct 14, 2020 at 15:06