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exercises:2017_uzh_cmest:defects_in_silicon

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# Analyzing defects in bulk silicon

In the following exercise we are going to investigate the effect of defects in bulk silicon (mainly on the energy).

Use the input file as given below:

silicon8.inp
&GLOBAL
PROJECT silicon8
RUN_TYPE ENERGY
PRINT_LEVEL MEDIUM
&END GLOBAL
&FORCE_EVAL
METHOD Quickstep
STRESS_TENSOR ANALYTICAL
&DFT
BASIS_SET_FILE_NAME  BASIS_SET
POTENTIAL_FILE_NAME  POTENTIAL
&POISSON
PERIODIC XYZ
&END POISSON
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-8
MAX_SCF 500
&END SCF
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&KIND Si
ELEMENT   Si
BASIS_SET DZVP-GTH-PBE
POTENTIAL GTH-PBE
&END KIND
&CELL
ABC 5.430697500 5.430697500 5.430697500
PERIODIC XYZ
&END CELL
&COORD
SCALED
Si    0    0    0
Si    0    2/4  2/4
Si    2/4  2/4  0
Si    2/4  0    2/4
Si    3/4  1/4  3/4
Si    1/4  1/4  1/4
Si    1/4  3/4  3/4
Si    3/4  3/4  1/4
&END COORD
&END SUBSYS
&END FORCE_EVAL

Create a second input file silicon64.inp based on the above with 64 atoms in the cell (do not use MULTIPLE_UNIT_CELL but actually replicate the Si … entries by hand and make sure you don't forget to update the CELL).

Run the calculation for both geometries and compare the single atom energy for both of them to make sure you got it right.

To speed up the calculation, use
mpirun -np 4 cp2k.popt -i silicon64.inp -o silicon64.out

For both geometries create a vacancy by removing one Silicon, re-calculate the total energy and compare it to the total energy of the intact bulk Silicon minus the single atom energy. What do you observe? Why?

You may have to employ some of the techniques mentioned in Projected density of states and Band structure for WO$_3$ to make the calculations converge.

Finally, calculate the band structure for the silicon8 geometries (with and without vacancy) as shown in the exercise Projected density of states and Band structure for WO$_3$ between $\Gamma$, $X$, $K$, $\Gamma$ and compare them.

You can use SeeK-Path with the following XYZ file again to obtain a CP2K input file skeleton with the required path:
silicon.xyz
8
Bulk Silicon
Si    0              0              0
Si    0              2.7153487500   2.7153487500
Si    2.7153487500   2.7153487500   0
Si    2.7153487500   0              2.7153487500
Si    4.07302312500  1.35767437500  4.07302312500
Si    1.35767437500  1.35767437500  1.35767437500
Si    1.35767437500  4.07302312500  4.07302312500
Si    4.07302312500  4.07302312500  1.35767437500