Excessive deformation of Pt slab with one water molecule on top

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GENG YUAN

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Oct 7, 2021, 12:33:00 PMOct 7
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Dear CP2K users,

I am performing geometry optimizations for Pt slab with one water molecule on top to calculate the adsorption energy of water on Pt. Although the output of our simulations shows no errors, we observe that the Pt surface deforms excessively during geometry optimization which we think is unreasonable. The input files (input and the original coordinate file) and output files (output and the trajectory) are all attached here for your reference. 
We are thinking that we may be missing something about the settings in the input file but we are running out of ideas.
Any advice is welcome!
-----------------------------------------------------------------------------------------
Our input file is also written below for your convenience,
&GLOBAL
  PROJECT com_geo
  RUN_TYPE GEO_OPT
  PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
  METHOD QS
  &SUBSYS
    &CELL
      ABC 11.705 11.705 17
      SYMMETRY CUBIC 
    &END CELL
    &TOPOLOGY
     COORD_FILE_NAME ./Pt_water1.xyz
     COORDINATE xyz
    &END
    &KIND Pt
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q18
    &END KIND
    &KIND H
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q1
    &END KIND
    &KIND O
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND
  &END SUBSYS
  &DFT
    BASIS_SET_FILE_NAME ./BASIS_MOLOPT
    POTENTIAL_FILE_NAME ./GTH_POTENTIALS
  
    &QS
      EPS_DEFAULT 1.0E-12
    &END QS
    &MGRID
      CUTOFF 400
      NGRIDS 5
      REL_CUTOFF 60
    &END MGRID
    &SCF
      SCF_GUESS ATOMIC
      EPS_SCF 1.0E-06
      MAX_SCF 300
      ADDED_MOS 100
      &OUTER_SCF
        MAX_SCF 50
        EPS_SCF 1.0E-6
      &END
      &DIAGONALIZATION T
        ALGORITHM STANDARD
      &END DIAGONALIZATION
      &MIXING T
        METHOD BROYDEN_MIXING
        ALPHA 0.1
        NBROYDEN 8
      &END MIXING
      &SMEAR ON
        METHOD FERMI_DIRAC
        ELECTRONIC_TEMPERATURE [K] 500
      &END SMEAR
      &PRINT
        &RESTART OFF
        &END RESTART
      &END PRINT
    &END SCF
    &XC
      &XC_FUNCTIONAL
         &LIBXC
           FUNCTIONAL XC_GGA_X_PBE_R
         &END
         &LIBXC
           FUNCTIONAL XC_GGA_C_PBE
         &END
      &END XC_FUNCTIONAL
      &VDW_POTENTIAL
         POTENTIAL_TYPE PAIR_POTENTIAL
         &PAIR_POTENTIAL
            LONG_RANGE_CORRECTION
            PARAMETER_FILE_NAME dftd3.dat
            TYPE DFTD3
            REFERENCE_FUNCTIONAL revPBE
         &END PAIR_POTENTIAL
       &END VDW_POTENTIAL
       &XC_GRID
        XC_DERIV NN50_SMOOTH
       &END XC_GRID
    &END XC
  &END DFT
&END FORCE_EVAL
&MOTION
  &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 500
    OPTIMIZER BFGS
  &END GEO_OPT
  &CONSTRAINT
    &FIXED_ATOMS
      COMPONENTS_TO_FIX XYZ
      LIST 1 2 9 10 17 18 25 26 33 34 41 42 49 50 57 58 65 66
    &END FIXED_ATOMS
  &END CONSTRAINT
&END MOTION  
-------------------------------------------------------------------------------------------------
Many thanks,
Sincerely,
Geng
Pt_water_geo.out
Pt_water1.xyz
Pt_water_geo.inp
trajectory.xyz

GENG YUAN

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Oct 8, 2021, 10:35:25 AMOct 8
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Dear All,

Here are a few more details for our simulations, we fix the bottom layer, so only the three upper layers are allowed to relax during geometry optimization. I also attached the screenshots for the original system and the relaxed system, respectively, for your convenience.
Here you can see an excessive deformation of the Pt slab with only one water molecule interacting, which we think is not reasonable. For more details on the trajectory/outputs, you can check those files that I uploaded before.
Any advice /suggestion is welcome and many thanks for your time. 
 before.png
The original system before geometry optimization.
after.png
The relaxed system after geometry optimization.

Sincerely,
Geng

Marcella Iannuzzi

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Oct 9, 2021, 9:39:33 AMOct 9
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Dear Geng, 

Probably the  3x3 box for the Pt(100) is too small.
You should either add more replicas or use k-point sampling.
Regards
marcella

GENG YUAN

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Oct 12, 2021, 4:46:39 PMOct 12
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Dear Marcella,

Many thanks for your reply! We are currently running some geometry optimization simulations implementing your suggestions (i.e., bigger systems, more k-points).

The one thing that makes us a bit uneasy about the large deformation of the slab, which we don't know how to explain is that when we run the geometry optimization of the single Pt slab (without the water on top) using exactly the same input settings (please see the input script below), we didn't observe any significant deformation of the Pt structure (please see the figures below). And then the Pt slab had this excessive deformation when we put only one water molecule on it. It seems like adding the water molecule drastically changes the outcomes of the simulation, and we don't really understand why.
-----------------Input script of the geometry optimization of single Pt slab-------------------
&GLOBAL
  PROJECT com_geo
  RUN_TYPE GEO_OPT
  PRINT_LEVEL LOW
&END GLOBAL
&EXT_RESTART
  RESTART_FILE_NAME Pt_cellopt-1.restart
&END EXT_RESTART
&FORCE_EVAL
  METHOD QS
  &SUBSYS
    &CELL
      ABC 11.705 11.705 17
    &END CELL
    &KIND Pt
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q18
    &END KIND
  &END SUBSYS
  &DFT
    BASIS_SET_FILE_NAME ./BASIS_MOLOPT
    POTENTIAL_FILE_NAME ./GTH_POTENTIALS
    RESTART_FILE_NAME Pt_cellopt-RESTART.wfn
    &QS
      EPS_DEFAULT 1.0E-12
    &END QS
    &MGRID
      CUTOFF 400
      NGRIDS 5
      REL_CUTOFF 60
    &END MGRID
    &SCF
      SCF_GUESS RESTART
      EPS_SCF 1.0E-06
      MAX_SCF 200

00000.png
The original single Pt slab before geometry optimization.
----------------------------------------------------------------------------------------------
Screen Shot 2021-10-12 at 4.44.16 PM.png
The relaxed single Pt slab after geometry optimization.

Sincerely,
Geng

GENG YUAN

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Oct 12, 2021, 6:47:57 PMOct 12
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Dear Marcella,

After a ''long-time'' debugging process, we finally realized that we had the SYMMETRY CUBIC setting in our input when we perform the geometry optimization for the slab with the water and that was causing the issue. The trajectory looks reasonable after we remove this SYMMETRY setting in our input. (please see figures below).

1111.png
The original system before geometry optimization

1111.png
The relaxed system after geometry optimization

Many thanks again for your advice which help us have a better review of our simulation protocol.

Sincerely,
Geng

在2021年10月9日星期六 UTC-4 上午9:39:33<Marcella Iannuzzi> 写道:
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