[CP2K-user] Correct calculation of E adsorption of organic molecule on crystal slab with CP2K?

DMITRII Drugov dresear... at gmail.com
Tue Jan 12 10:46:00 UTC 2021


Good day everyone, I am trying to compare Ead of organic molecule on 
crystal slabs, I use Au(111), Na(100), Si(100), Graphite(basal plane). I 
build 4 layer slabs with 50 A in c dimension but a and b size is different 
for each slab, as you can see bellow. 
[image: Screen Shot 2021-01-12 at 6.37.00 pm.png]
I calculated through energy of optimised structure Ead= E(slab+molecule) - 
Eslab -E molecule. I am trying to confirm trend from classical molecular 
dynamic which shows that absorption of metals is stronger than on 
semiconductors (see van der Wals parameters table bellow). However, it seem 
that Si does not follow this order, as shown in the table of Ea from DFT 
above. I haven't frozen any slab atoms during optimisation, and I used same 
cut off for all system, same convergence SCF settings.  
[image: Screen Shot 2021-01-12 at 6.40.37 pm.png]

Guys, do you think it is DFT based Ead does not follow force filed MD 
Epsilon value trend because my a and b of slab are different, or I need to 
include anything special in energy calculation for Si (see bellow)?

Thank you,
Dmitrii

&GLOBAL
  PROJECT Si100_optimisationTZPV_withNaFSI2_cluster 
  RUN_TYPE GEO_OPT
  PRINT_LEVEL MEDIUM
&END GLOBAL
&FORCE_EVAL
  METHOD QS
  &DFT
    BASIS_SET_FILE_NAME BASIS_MOLOPT
    POTENTIAL_FILE_NAME GTH_POTENTIALS
    CHARGE -1
    MULTIPLICITY 1
    &MGRID
      CUTOFF 800
      NGRIDS 5
      REL_CUTOFF 70
    &END MGRID
    &QS
      EPS_DEFAULT 1.0E-12
      WF_INTERPOLATION ASPC
    &END QS
   &SCF
      SCF_GUESS ATOMIC
      EPS_SCF 1.0E-7
      MAX_SCF 1000
      CHOLESKY INVERSE
      ADDED_MOS 50
      &SMEAR ON
        METHOD FERMI_DIRAC
        ELECTRONIC_TEMPERATURE [K] 300
      &END SMEAR
      &DIAGONALIZATION
        ALGORITHM STANDARD
      &END DIAGONALIZATION
      &MIXING
        METHOD BROYDEN_MIXING
        ALPHA 0.4         
        NBROYDEN 8
      &END MIXING
    &END SCF
    &XC
      &XC_FUNCTIONAL
&PBE
&END PBE
      &END XC_FUNCTIONAL
      &vdW_POTENTIAL
    DISPERSION_FUNCTIONAL PAIR_POTENTIAL
    &PAIR_POTENTIAL
        PARAMETER_FILE_NAME dftd3.dat
        TYPE DFTD3
        REFERENCE_FUNCTIONAL PBE
        R_CUTOFF 15.0
    &END PAIR_POTENTIAL
     &END vdW_POTENTIAL
    &END XC
    &POISSON
      PERIODIC xy
      POISSON_SOLVER ANALYTIC
    &END POISSON
  &END DFT
  &SUBSYS
    &CELL
      ABC 21.72116 21.72116 50.0
      ALPHA_BETA_GAMMA 90.0 90.0 90.0
      PERIODIC xy
    &END CELL
    &COORD
Si         0.00000        0.00000        5.41849
Si         0.00000        2.71515        8.17743
Si         2.71514        2.71514        5.41849
Si         2.71515        0.00000        8.17743
Si         4.07274        1.35756        9.51481
Si         1.35757        1.35757        6.75586
Si         1.35756        4.07274        9.51481
Si         4.07272        4.07272        6.75587
Si         0.00000        5.43029        5.41849
Si         0.00000        8.14543        8.17743
Si         2.71515        8.14544        5.41849
Si         2.71514        5.43029        8.17743
Si         4.07274        6.78785        9.51481
Si         1.35757        6.78786        6.75587
Si         1.35756        9.50303        9.51481
Si         4.07272        9.50301        6.75587
Si         0.00000       10.86058        5.41849
Si         0.00000       13.57573        8.17743
Si         2.71514       13.57573        5.41850
Si         2.71515       10.86058        8.17743
Si         4.07274       12.21814        9.51481
Si         1.35757       12.21815        6.75586
Si         1.35756       14.93332        9.51481
Si         4.07272       14.93330        6.75587
Si         0.00001       16.29087        5.41849
Si         0.00000       19.00602        8.17743
Si         2.71514       19.00601        5.41849
Si         2.71515       16.29087        8.17743
Si         4.07274       17.64843        9.51481
Si         1.35757       17.64844        6.75586
Si         1.35756       20.36361        9.51481
Si         4.07272       20.36359        6.75587
Si         5.43029        0.00000        5.41849
Si         5.43029        2.71515        8.17743
Si         8.14542        2.71516        5.41849
Si         8.14543        0.00000        8.17743
Si         9.50302        1.35756        9.51481
Si         6.78786        1.35757        6.75587
Si         6.78785        4.07274        9.51481
Si         9.50301        4.07272        6.75587
Si         5.43030        5.43029        5.41849
Si         5.43029        8.14544        8.17744
Si         8.14542        8.14545        5.41849
Si         8.14543        5.43029        8.17743
Si         9.50302        6.78785        9.51481
Si         6.78786        6.78786        6.75587
Si         6.78784        9.50303        9.51481
Si         9.50301        9.50301        6.75587
Si         5.43030       10.86058        5.41849
Si         5.43029       13.57573        8.17743
Si         8.14543       13.57572        5.41850
Si         8.14544       10.86058        8.17743
Si         9.50303       12.21814        9.51481
Si         6.78786       12.21815        6.75586
Si         6.78785       14.93332        9.51481
Si         9.50301       14.93330        6.75587
Si         5.43029       16.29087        5.41849
Si         5.43029       19.00601        8.17743
Si         8.14544       19.00602        5.41850
Si         8.14544       16.29087        8.17743
Si         9.50303       17.64843        9.51481
Si         6.78786       17.64844        6.75586
Si         6.78785       20.36361        9.51481
Si         9.50301       20.36359        6.75587
Si        10.86059       -0.00000        5.41849
Si        10.86058        2.71515        8.17743
Si        13.57572        2.71515        5.41850
Si        13.57573        0.00000        8.17743
Si        14.93332        1.35756        9.51481
Si        12.21815        1.35757        6.75586
Si        12.21814        4.07274        9.51481
Si        14.93330        4.07272        6.75587
Si        10.86059        5.43029        5.41849
Si        10.86058        8.14543        8.17743
Si        13.57573        8.14544        5.41850
Si        13.57572        5.43029        8.17743
Si        14.93332        6.78785        9.51481
Si        12.21815        6.78786        6.75587
Si        12.21814        9.50303        9.51481
Si        14.93330        9.50301        6.75587
Si        10.86058       10.86058        5.41849
Si        10.86058       13.57573        8.17743
Si        13.57572       13.57572        5.41850
Si        13.57573       10.86058        8.17743
Si        14.93332       12.21814        9.51481
Si        12.21815       12.21815        6.75586
Si        12.21814       14.93332        9.51481
Si        14.93330       14.93330        6.75587
Si        10.86058       16.29087        5.41849
Si        10.86058       19.00602        8.17743
Si        13.57572       19.00602        5.41850
Si        13.57573       16.29087        8.17743
Si        14.93332       17.64843        9.51481
Si        12.21815       17.64844        6.75586
Si        12.21814       20.36361        9.51481
Si        14.93330       20.36359        6.75587
Si        16.29087        0.00000        5.41849
Si        16.29087        2.71515        8.17743
Si        19.00601        2.71514        5.41849
Si        19.00602        0.00000        8.17743
Si        20.36361        1.35756        9.51481
Si        17.64844        1.35757        6.75586
Si        17.64843        4.07274        9.51481
Si        20.36359        4.07272        6.75587
Si        16.29087        5.43029        5.41849
Si        16.29087        8.14543        8.17743
Si        19.00602        8.14544        5.41850
Si        19.00602        5.43029        8.17743
Si        20.36361        6.78785        9.51481
Si        17.64844        6.78786        6.75586
Si        17.64843        9.50303        9.51481
Si        20.36359        9.50301        6.75587
Si        16.29087       10.86058        5.41849
Si        16.29087       13.57573        8.17743
Si        19.00601       13.57572        5.41850
Si        19.00602       10.86058        8.17743
Si        20.36361       12.21814        9.51481
Si        17.64844       12.21815        6.75586
Si        17.64843       14.93332        9.51481
Si        20.36359       14.93330        6.75587
Si        16.29088       16.29087        5.41849
Si        16.29087       19.00602        8.17743
Si        19.00601       19.00601        5.41850
Si        19.00602       16.29087        8.17743
Si        20.36361       17.64843        9.51481
Si        17.64844       17.64844        6.75586
Si        17.64843       20.36361        9.51481
Si        20.36359       20.36359        6.75587
O          6.32647       13.42719       13.53866
O         14.30293       11.11570       11.42619
O         11.98905       10.80707       12.28586
O          8.50437       12.26129       13.87206
S          7.04781       12.25458       13.94632
S         13.42129       10.56339       12.41514
N         14.05354       10.79571       13.85783
N          6.31933       10.96800       13.35868
Na        10.18657       10.67261       13.74023
F          6.77519       12.12414       15.55354
F         13.52078        8.94044       12.22690
S         13.35330       10.31586       15.20337
S          6.87916        9.49151       13.55481
O         11.90135       10.44293       15.25198
O          8.32435        9.32478       13.45081
O         14.12607       10.76606       16.32689
O          6.02621        8.57438       12.85278
F         13.56562        8.69488       15.16561
F          6.60660        9.20697       15.14337
    &END COORD
    &KIND Au
      BASIS_SET DZVP-MOLOPT-SR-GTH 
      POTENTIAL GTH-PBE-q11
    &END KIND
    &KIND F
      BASIS_SET TZVP-MOLOPT-GTH 
      POTENTIAL GTH-PBE-q7
    &END KIND
    &KIND O
      BASIS_SET TZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND
    &KIND C
      BASIS_SET TZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q4
    &END KIND
    &KIND Si
      BASIS_SET TZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q4
    &END KIND
    &KIND S
      BASIS_SET TZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND
    &KIND N
      BASIS_SET TZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q5
    &END KIND
    &KIND Na
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q9
    &END KIND
   &END SUBSYS
&END FORCE_EVAL
&MOTION
  !&CONSTRAINT
    !&FIXED_ATOMS
     !COMPONENTS_TO_FIX XYZ
     !LIST 1..43 
    !&END FIXED_ATOMS
  !&END CONSTRAINT
  &GEO_OPT
  OPTIMIZER LBFGS
  MAX_ITER 300
  &END GEO_OPT
  &END MOTION

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