[CP2K-user] [CP2K:14225] Re: Geometry optimisation of organic molecule on fcc Au(111) slab

[DMITRII Drugov]

Thank you a lot for all your advices. I am knew to CP2K and any solid state 
DFT software. Could you please help me to create right cell dimension in 
CP2K for my system?
I built Au(111) slab with a= 4.07825 and I repeated this unit 3 times in xy 
and only 1 in z dimension.
So, this gave me 

created  36 atom sample

(super)cell vectors

a1 = array([ 12.23,   0.00,   0.00])

a2 = array([  0.00,  12.23,   0.00])

a3 = array([  0.00,   0.00,   4.08])

-----------------------------------------

cell for VMD : pbc set { 12.235 12.235 4.078   90.00 90.00 90.00 }; pbc box

However, in my CP2K optimization input with organic molecules I specify 
everything in the way listed bellow.

Could you please help me to choose right PBC settings with cell dimension 
parameters?


&GLOBAL

  PROJECT Au_optimisation 

  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 20

      &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 xyz

      POISSON_SOLVER WAVELET

    &END POISSON

  &END DFT

  &SUBSYS

    &CELL

      ABC 15.00000 15.00000 26.00000 

      PERIODIC xyz

    &END CELL

    &COORD

&END COORD
    &KIND Au
      BASIS_SET DZVP-MOLOPT-SR-GTH 
      POTENTIAL GTH-PBE-q11
    &END KIND
    &KIND C
      BASIS_SET TZV2P-MOLOPT-GTH
      POTENTIAL GTH-PBE-q4
    &END KIND
    &KIND H
      BASIS_SET TZV2P-MOLOPT-GTH
      POTENTIAL GTH-PBE-q1
    &END KIND
    &KIND N
      BASIS_SET TZV2P-MOLOPT-GTH
      POTENTIAL GTH-PBE-q5
    &END KIND
   &END SUBSYS
&END FORCE_EVAL
&MOTION
  &CONSTRAINT
    &FIXED_ATOMS
     COMPONENTS_TO_FIX XYZ
     LIST 1..54 
    &END FIXED_ATOMS
  &END CONSTRAINT
  &GEO_OPT
    TYPE MINIMIZATION
    MAX_DR    1.0E-03
    MAX_FORCE 1.0E-03
    RMS_DR    1.0E-03
    RMS_FORCE 1.0E-03
    MAX_ITER 300
    OPTIMIZER CG
    &CG
      MAX_STEEP_STEPS  0
      RESTART_LIMIT 9.0E-01
    &END CG
  &END GEO_OPT
  &END MOTION

On Tuesday, November 17, 2020 at 7:47:47 AM UTC+11 ant... at gmail.com 
wrote:

> Dear Dmitrii,
>
> in addition to the suggestions you've already received from Dr. 
> Iannuzzi, I could append the following comments.
>
> 16.11.20 03:48, DMITRII Drugov пише:
> > I expected organic molecule moves more from it's initial position. 
> > Otherwise it's almost same as I built in avogadro software.
>
> As far as I can see from your files, you have pre-optimized your system 
> via MM(UFF) in Avogadro. The molecule actually "lays" on the surface 
> (take a look on the structure in the "van der Waals spheres" mode in 
> Avogadro). Bearing that in mind, I see no reasons to expect any 
> significant movements in so heavily constrained system. You effectively 
> allow only movements relevant to intramolecular interactions in your 
> adsorbate and van der Waals interactions between the molecule and the 
> surface -- both of them are reasonably well described within MM approach 
> (due to the adsorbate structure, no specific covalent bonding between 
> this molecule and the surface is to be expected).
>
> > Do you think while optimization I should keep system non periodic with 
> > poison wavelet  or periodic in xy or xyz with poison analytic?
>
> You may want to consider this paper: Phys. Chem. Chem. Phys., 2018, 20, 
> 8456.
>
> Yours,
> Anton
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20201116/28dd33cd/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Au_geometry_plus_C3mpyr.inp
Type: chemical/x-gamess-input
Size: 6626 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20201116/28dd33cd/attachment.inp>