In the following exercise we use what we already did to investigate defects in bulk Silicon.
Use the input file as given in the Calculating the bulk modulus of Silicon exercise (only renamed to distinguish it from the second input file):
&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. Run the calculation for both geometries and compare the single atom energy for both of them to make sure you got it right.
mpirun -np 8 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 the it to the total energy of the intact bulk Silicon minus the single atom energy.
Finally, calculate the band structure for the silicon8 geometries (with and without vacancy) as shown in the exercise Getting the band structure of graphene between $\Gamma$, $X$, $K$, $\Gamma$ and compare them.