CO adsorbed on metal surface

MR.Chem chemc... at gmail.com
Mon Mar 18 03:02:34 CET 2013


Dear Seitsonen,
        I am so glad you replied me. And those suggestions are really 
helpful. I am still learning how to use CP2K, so some part I am not very 
sure. I just took example from other people. Also, in my group, no one use 
CP2K, then, when I have some problem, the only way is searching on 
Google.So,  anyway, Thank you very much! 
        Here is some question or answer for you.
        1. Yes, I do mean the binding energy of the CO molecule. And I 
found some paper and references, there are both experimental data 
and theoretical results. My number are far far away, comparing no matter 
which one. SO, I believe there must be something wrong with my code.
       2   When you mentioned the counterpoise correction, I know how to do 
it in Gauss, but no idea how to apply it on CP2K. Can you show me some 
examples? That maybe very helpful. Meanwhile, I will search it by myself.
       3  About EPS_GVG and EPS_PGF_ORB , well, I just copy from other 
example. I will delete them.
       4, For the 3000K, I am just found under that temp. the calculation 
will be done kinda fast, since right now, I am just testing the code. so, I 
only need some results ASAP. Also, I tested the calculations with using 
0.05eV . The results are only small difference between F-D method and 
Energy_window method. For the future work, I will use the Energy_window 
method. 
       5. For the RPBE part,  a friend just told me last week, He said the 
RPBE+D2 (scaling 1.25) works well for metal surface (based on one paper 
that he just found recently). and also gave me that code. So, I only need 
to keep one of  'REFERENCE_FUNCTIONAL' and 'SCALING', Is that right?
       6 I generate the metal surface from the Material Studio, then 
optimize it.

       Thank you again for your great suggestions. Bless you~~~~~~~~~

-Yao

On Sunday, March 17, 2013 4:49:20 PM UTC-5, MR.Chem wrote:
>
> 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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