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exercises:2017_uzh_cmest:adsorption

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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

### Lattice constant optimization

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:
ADDED_MOS 100
CHOLESKY INVERSE
&SMEAR ON
METHOD FERMI_DIRAC
ELECTRONIC_TEMPERATURE [K] 300
&END SMEAR
&DIAGONALIZATION
ALGORITHM STANDARD
EPS_ADAPT 0.01
&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. You need change the RUN_TYPE to GEO_OPT and also specify the coordinate by yourself. One can get 6x6x1 unit cell by using MULTIPLE_UNT_CELL which was mentioned in previous exercises.

&GLOBAL
PROJECT graphene
RUN_TYPE GEO_OPT
PRINT_LEVEL MEDIUM
&END GLOBAL

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?

exercises/2017_uzh_cmest/adsorption.1509958331.txt.gz · Last modified: 2017/11/06 08:52 by jglan