Open SourceMolecular Dynamics

Sidebar

For Developers

This is an old revision of the document!

In this exercise, you will be asked to calculate the adsorption energy of CO molecule on the graphene surface. The reference paper you can find in https://journals.aps.org/prb/pdf/10.1103/PhysRevB.77.125416

Take the input from the last exercise and optimize the lattice constant and fit to Murnaghan equation of state.

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
You can use bash script for loop
for i in seq 0.95 0.025 1.05

do

mkdir $i cd$i
i=$(echo$i * 2.4612 | bc)
cp ../bulk.inp .

sed -i -e "s/2.4612/$i/g" bulk.inp mv grapehene.inp bulk-$i.inp

mpirun -n 2 cp2k.popt -i bulk-$i.inp -o bulk-$i.out &
cd ..
done

Adsorb one CO molecule on the graphene 6X6X1 supercell at the top(T), bridge(B) and center(C) sites and optimize the geometry.

The adsorption energy is given by:$E_{ad} = E_{CO-graphene} - E_{CO} - E_{graphene}$

Find the most stable adsorption site and study the coverage effect such like 1/2 and 1. What do you observe when increasing the coverage?