# Open SourceMolecular Dynamics

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exercises:2018_uzh_cmest:defects_in_graphene

# Analyzing defects in graphene

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:
CHOLESKY INVERSE
&SMEAR ON
METHOD FERMI_DIRAC
ELECTRONIC_TEMPERATURE [K] 300
&END SMEAR
&DIAGONALIZATION
ALGORITHM STANDARD
&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
When comparing scaled coordinates between papers and code input scripts, always make sure that they use the same coordinate systems and definitions for a unit cell (both real and reciprocal space). For example while many sources (like the paper of Curtarolo, Setyawan) assume a 120° degree angle between $a$ and $b$ for a hexagonal cell, you can also define it to be a 60° angle (like the default in CP2K).
Once you have verified that your calculation setup works, use nohup mpirun -np 4 cp2k.popt … & again to run the calculations in parallel and in the background since they may take longer to complete than before.

# Vacancy in graphene

## Comparing energies

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.

## Analyze the PDOS

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.

## Replacement with oxygen

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.