[CP2K:4346] CO adsorbed on metal surface

Ari Paavo Seitsonen ari.p.s... at gmail.com
Sun Mar 17 23:34:42 CET 2013


Dear MR.Chem,

  A few issues catching my attention:

 - When you say "your results are always larger than the experimental
data", I presume that you mean the binding energy of the CO molecule,
right? You should not look at the experimental number but compare to best
theoretical DFT-GGA (+ dispersion correction, if available)

 - Gamma point might not be enough in your case (One could study the
magnitude of this by performing calculations with other DFT code and
increase the k point sampling)

 - There is the problem with the basis set superposition error with
Gaussian basis sets. Did you try to do the counterpoise correction to your
energies?

 - LSD is not really needed in these systems (at least back then when I
studied exactly these systems for my PhD thesis), but shouldn't harm either
- only a factor of two in CPU time and memory

 - FORCE_EVAL / DFT / QS / EPS_DEFAULT 1e-10 is quite large, I would go for
1e-14 or so for the production runs

 - I don't have any idea of the EPS_GVG and EPS_PGF_ORB - do you have a
reason to expect that the default values were insufficient or did you
optimise these values?

 - The broadening of 3000 K is very large: A typical value in the
literature is rather 600 or 1200 K (0.05 or 0.1 eV); well, one should
actually perform the extrapolation to zero temperature in the total
energies, but let us first assume that this would be similar both in the
calculation of the slab with and without the molecule and thus would cancel
quite well when calculating the binding energy

 - You use revPBE as the exchange-correlation functional but specify
'REFERENCE_FUNCTIONAL PBE' - why this? In addition you specify the
'SCALING' as well: First of all we usually use a value of 1.0 (where did
you get 1.25?? Pure PBE should have a value smaller than one if I remember
correctly), and 'REFERENCE_FUNCTIONAL' and 'SCALING' are used for the same
thing, to specify the s6 coefficient in the DFT-D2 scheme. Please only
insert one of these keywords

 - Which lattice constant do you use, did you optimise it yourself or did
you use the experimental value?

 - Last but maybe not least, DFT-D2 is known to overestimate binding
energies at transition metal surfaces


  Here were a couple of suggestions to start with - good luck! :)

    Greetings,

       apsi


2013/3/17 MR.Chem <chemc... at gmail.com>

> Dear all,
>
>            I am studying the CO adsorbed on the metal surface, like Cu,
> Pd, Rh... However, my results are always larger than
>  the experimental data, around 0.6eV. Does anyone have any experience about
> it?
>  Here is my code, can some expert help me to check it? Maybe something
> wrong with my code.
>
> =================================================================================
> &FORCE_EVAL
>   METHOD Quickstep
>   &DFT
>      CHARGE 0
>      LSD
>      POTENTIAL_FILE_NAME ../Basis_Set/GTH_POTENTIALS
>      BASIS_SET_FILE_NAME ../Basis_Set/BASIS_MOLOPT
>     &MGRID
>       CUTOFF 500
>       NGRIDS 7
>   #   REL_CUTOFF 40
>     &END MGRID
>     &QS
>       EPS_DEFAULT 1.0E-10
>       EPS_GVG 1.0E-8
>       EPS_PGF_ORB 1.0E-8
>       EXTRAPOLATION PS
>       EXTRAPOLATION_ORDER 4 # find the best for your system
>       &DISTRIBUTION
>        SKIP_OPTIMIZATION TRUE
>       &END DISTRIBUTION
>     &END QS
>     &SCF
>       EPS_SCF 1.0E-8
>       MAX_SCF 200
>       EPS_SCF_HIST 1.0E-8
>       ADDED_MOS 500
>       CHOLESKY INVERSE
>       &SMEAR  ON
>          METHOD FERMI_DIRAC
>          ELECTRONIC_TEMPERATURE [K] 3000
>       &END SMEAR
>       &DIAGONALIZATION
>         ALGORITHM STANDARD
>       &END DIAGONALIZATION
>       &MIXING
>         METHOD BROYDEN_MIXING
>         ALPHA   0.1
>         BETA    1.5
>         NBROYDEN  8
>        &END
>        &OUTER_SCF
>          EPS_SCF 1.0E-8
>          MAX_SCF 100
>          STEP_SIZE 0.1
>          EXTRAPOLATION_ORDER 4
>        &END OUTER_SCF
>     &END SCF
>
>     &XC
>       &XC_FUNCTIONAL PBE
>         &PBE
>           PARAMETRIZATION REVPBE
>         &END PBE
>        &END XC_FUNCTIONAL
>        &XC_GRID
>           XC_SMOOTH_RHO NN10
>           XC_DERIV SPLINE2_SMOOTH
>         &END XC_GRID
>         &vdW_POTENTIAL
>           DISPERSION_FUNCTIONAL PAIR_POTENTIAL
>           &PAIR_POTENTIAL
>             TYPE DFTD2
>             SCALING 1.25
>             REFERENCE_FUNCTIONAL PBE
>             R_CUTOFF 15.
>           &END PAIR_POTENTIAL
>         &END vdW_POTENTIAL
>     &END XC
>   &END DFT
>   &SUBSYS
>     &CELL
>       A         11.50460000    0.00000000    0.00000000
>       B        -5.50230000    9.93026316    0.00000000
>       C         0.00000000    0.00000000   18.73890000
>       PERIODIC XYZ
>     &END CELL
>     &COORD
>  Pd                 0.48065840    7.03842411    2.78730528
>  Pd                 0.47028763    0.44875232    7.19243429
>  Pd                 4.53327500    2.99486842    0.48000000
>  Pd                -0.92756268    6.26067797    4.99255153
>  Pd                 7.28442500    2.99486842    0.48000000
>  Pd                 1.95832508    6.23995572    4.98929589
>  Pd                 5.90885000    5.37743421    0.48000000
>  Pd                 0.59872433    8.73424560    4.94485704
>  Pd                -2.34460000    5.37743421    0.48000000
>  Pd                 3.48202628    8.75574050    4.90377153
>  Pd                 7.60058003    4.66725820    2.69914002
>  Pd                 2.12951115    7.91373487    7.19590876
>  Pd                -0.98640158    4.60804088    2.78207535
>  Pd                 4.99805700    7.90489627    7.18006023
>  Pd                -2.37121774    7.06798024    2.77804336
>  Pd                 9.11351163    0.44812200    7.18150630
>  Pd                 3.15770000    5.37743421    0.48000000
>  Pd                -2.28848592    8.75288986    4.94848842
>  Pd                 1.86796693    4.57784447    2.79012924
>  Pd                -3.64617921    7.90460435    7.19218894
>  Pd                 4.71963320    4.58012708    2.78282947
>  Pd                -0.75815898    7.91750314    7.22011766
>  Pd                 3.32828364    7.03761292    2.77891925
>  Pd                 3.35784019    0.45975453    7.21713253
>  Pd                 6.20941143    7.12736713    2.68973994
>  Pd                 6.24673072    0.45867465    7.19321178
>  Pd                -0.96902500    2.99486842    0.48000000
>  Pd                 4.84897874    6.26179049    4.94562009
>  Pd                 1.78212500    2.99486842    0.48000000
>  Pd                 7.67975198    6.28516301    4.93895128
>  Pd                 0.40655000    5.37743421    0.48000000
>  Pd                 6.31889141    8.77579565    4.89678117
>  Pd                 5.90885000    0.61230263    0.48000000
>  Pd                 0.45589201    3.77441599    4.98640728
>  Pd                -0.88579308    9.52461840    2.71360432
>  Pd                -0.91478538    2.92497807    7.20923011
>  Pd                 1.96179550    9.52218444    2.70458723
>  Pd                 1.97006436    2.93242210    7.23312886
>  Pd                 6.11012640    2.11464388    2.77204082
>  Pd                 0.59930677    5.42011629    7.25046349
>  Pd                 8.99428358    2.20331457    2.69500697
>  Pd                 3.49212409    5.42106046    7.22291798
>  Pd                -3.72017500    7.76000000    0.48000000
>  Pd                 7.61529378    1.28270688    4.91196377
>  Pd                -0.96902500    7.76000000    0.48000000
>  Pd                10.44730149    1.30931768    4.91246466
>  Pd                 3.15770000    0.61230263    0.48000000
>  Pd                 9.06475984    3.80294084    4.93990249
>  Pd                 3.25324319    2.10925105    2.78044950
>  Pd                -2.28679605    5.41093586    7.22290884
>  Pd                 1.78212500    7.76000000    0.48000000
>  Pd                 1.83892428    1.28295401    4.95856743
>  Pd                 4.53327500    7.76000000    0.48000000
>  Pd                 4.72711559    1.26487439    4.95221711
>  Pd                 8.66000000    0.61230263    0.48000000
>  Pd                 3.34270002    3.75714799    4.98323499
>  Pd                 0.40655000    0.61230263    0.48000000
>  Pd                 6.23251524    3.77764121    4.94405153
>  Pd                 4.84358673    9.61900376    2.62576793
>  Pd                 4.86285578    2.93105916    7.20861165
>  Pd                -3.73917975    9.55256951    2.70716721
>  Pd                 7.72991049    2.91981062    7.19559113
>  Pd                 0.39747135    2.13690410    2.77102245
>  Pd                 6.35957458    5.40832411    7.20891859
>  C                  2.04578180    6.20000000    9.00000000
>  O                  2.04578180    6.66763600   10.20000000
>     &END COORD
>     &KIND Pd
>        BASIS_SET DZVP-MOLOPT-SR-GTH
>        POTENTIAL GTH-PBE-q18
>     &END KIND
>     &KIND O
>        BASIS_SET DZVP-MOLOPT-SR-GTH
>        POTENTIAL GTH-PBE-q6
>     &END KIND
>     &KIND C
>        BASIS_SET DZVP-MOLOPT-SR-GTH
>        POTENTIAL GTH-PBE-q4
>     &END KIND
>   &END SUBSYS
> &END FORCE_EVAL
>
> &GLOBAL
>   PROJECT Pd-CO-111surface-hcp
>   RUN_TYPE GEO_OPT
>   PRINT_LEVEL low
> &END GLOBAL
>
> &MOTION
>   &GEO_OPT
>     MAX_ITER  1000
>     OPTIMIZER BFGS
>     TYPE MINIMIZATION # TRANSITION_STATE
>   &END GEO_OPT
>   &CONSTRAINT
>         &FIXED_ATOMS
>           LIST 53 51 45 43 55 33
>           LIST 47 57 5 3 29 27
>           List 7 17 31 9
>         &END
>   &END CONSTRAINT
> &END MOTION
>
> ==========================================================================================
>
>  Thank you very much!!!!!!!!!!!
>
>
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-- 
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari P Seitsonen / Ari.P.S... at iki.fi / http://www.iki.fi/~apsi/
  Physikalisch-Chemisches Institut der Universit├Ąt Z├╝rich
  Tel: +41 44 63 55 44 97  /  Mobile: +41 79 71 90 935
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