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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

CO adsorption on graphene

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.1509958365.txt.gz · Last modified: 2017/11/06 08:52 by jglan