Now we are going to draw our attention towards surfaces and the effect of defects on them.

Use the following input file as a starting point for this exercise, noting that you will have to make some modifications to it:

grapehene.inp

&GLOBAL
  PROJECT graphene
  RUN_TYPE ENERGY 
  PRINT_LEVEL MEDIUM
&END GLOBAL
 
&FORCE_EVAL
  METHOD Quickstep
  &DFT
    BASIS_SET_FILE_NAME  BASIS_MOLOPT
    POTENTIAL_FILE_NAME  POTENTIAL
 
    &POISSON
      PERIODIC XYZ
    &END POISSON
    &SCF
      SCF_GUESS ATOMIC
      EPS_SCF 1.0E-6
      MAX_SCF 300
 
      # The following settings help with convergence:
      ADDED_MOS 100
      CHOLESKY INVERSE
      &SMEAR ON
        METHOD FERMI_DIRAC
        ELECTRONIC_TEMPERATURE [K] 300
      &END SMEAR
      &DIAGONALIZATION
        ALGORITHM STANDARD
        EPS_ADAPT 0.01
      &END DIAGONALIZATION
      &MIXING
        METHOD BROYDEN_MIXING
        ALPHA 0.2
        BETA 1.5
        NBROYDEN 8
      &END MIXING
    &END SCF
    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC
    &PRINT
      &PDOS
        # print all projected DOS available:
        NLUMO -1
        # split the density by quantum number:
        COMPONENTS
      &END
    &END
  &END DFT
 
  &SUBSYS
    &CELL
      # create a hexagonal unit cell:
      ABC 2.4612 2.4612 15.0
      ALPHA_BETA_GAMMA 90. 90. 60.
      SYMMETRY HEXAGONAL
      PERIODIC XYZ
    &END CELL
    &COORD
      SCALED
      C  1./3.  1./3.  0.
      C  2./3.  2./3.  0.
    &END
    &KIND C
      ELEMENT C
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE
    &END KIND
  &END SUBSYS
 
&END FORCE_EVAL

Use the provided template and its initial geometry to setup a single point energy calculation for a 6x6x1 supercell of graphene.

Create a vacancy by removing one carbon atom from this supercell and perform the energy calculation again.

Quick question: Does it matter which carbon atom you remove? (hint: what kind of boundary conditions do we impose?)

Calculate the energy of the vacancy formation, that is $E_v = E_2 - \frac{N-1}{N} \cdot E_1$ where $E_1$ is the energy of the complete system, $E_2$ that of the system with a vacancy and $N$ the number of atoms.

Would you expect the vacancy to haven any influence on the projected density of states? Check whether your assumption was right by visualizing the PDOS.

Now, instead of removing one carbon atom from the 6x6x1 supercell, simply replace it with an oxygen atom (remember: you have to a KIND section for oxygen). Perform first a single point calculation and second a geometry optimization (as shown in a previous exercise) and compare the energy of adsorption for both cases.