[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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