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
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
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?