1. Tutorial of Practice #4 - Supercell & Defect formation energy -
QnMSG
Jae-Hyeon Ko
Yong-Hyun Kim

2. How to make Supercell structure
1. To see structure in input file of Pwscf, first, we have to make xyz file using the program named pw2xyz.pl.
2. Program pw2xyz.pl make the xyz file using the lattice parameter and basis in input file.
- Information related to structure in Input file -
- xyz file -
3. Instruction of pw2xyz.pl program is as follows.
file name of input
size of cell (x, y, z): You can control the size of cell
4. Make supercell structure using the program pw2xyz.pl. The coordinates are in geometry.xyz.
5. Input the geometry in geometry.xyz to calculation input file for making supercell structure.

3. Supercell structure 6 x 6 x 1 graphene structure
2 x 2 x 2 silicon structure

4. How to make defect structure
1. To relax the system with defects, first, you have to add some information in input file. The detail information is in INPUT_PW.txt. The directory of INPUT_PW.txt is opt/espresso-5.0.1/Doc/
calculation: describing the task to be performed (you should modify relax to optimize the structure.)
tstress: calculate stress.
tprnfor: print forces.
nstep: number of ionic + electronic steps
ion_dynamics: Specify the type of ionic dynamics.
pot_extrapolation: Used to extrapolate the potential from preceding ionic steps.
wfc_extrapolation: Used to extrapolate the wavefuctions from preceding ionic steps.
2. Modify the atomic positions and types to add defects.
3. You have to add the potential files according to a types of atoms and potential files have to be existed in location of pseudo_dir in input file. You can download the pseudopotential file in
4. Run Pwscf using serial and parallel calculation.

5. Parallel calculations
- To use parallel calculations, the file named run.sh has to be used.
- Command how to run the file named run.sh: qsub run.sh
- run.sh -
nodes: number of nodes
ppn: number of cpu of computer
walltime: limit time of running calculation
the directory of PwSCF
command running the calculations using mpi

6. Defect structure N-doped graphene structure P-doped silicon structure
Nitrogen
Phosphorus

7. DOS of defect structure
1. Graphene
2. Silicon

8. Defect formation energy
Defect formation energy Eformation(eV) = E(system with defects) – [Nbulkbulk + Ndefectdefect]
E(system with defects) : Total energy of system with defects
Nbulk : Number of bulk atoms
bulk : chemical potential of bulk atoms
Ndefect : Number of defects
defect : chemical potential of defects
Defect formation energy means whether the system with defects is more stable or unstable than bulk system.
Ef, n-doped graphene (eV) = E(n-doped graphene) – [NCC + NN1/2N2], defect = 1/2N2
Ef, p-doped Si (eV) = E(p-doped Si) – [NSiSi + NP1/4P4], defect = 1/4P4
Above equation, N2 and P4 molecule is used as reference of bulk system.
(units: Ry)
E(system with defects)
bulk
defect
Defect formation energy
N-doped graphene
0.053
P-doped silicon
-7.868
0.010