Conflict in parameters of unit cell after CELL_OPTIMIZATION

Amin amin.jaf... at gmail.com
Tue Nov 28 10:17:33 CET 2017


Hi Mengzi,

Thanks for the input. I actually tried with your attached supercell 
coordinates and I got these results: a=b=7.330 and c=10.314 which they have 
3% and 8% error respectively (in comparison to experimental data). I think 
these amount of error is something needs to be addressed and I'm looking 
for the solution. for the record, here is my input file for my last 
calculation:

&GLOBAL
  PROJECT ana
  RUN_TYPE CELL_OPT
  PRINT_LEVEL LOW
  EXTENDED_FFT_LENGTHS
&END GLOBAL

&FORCE_EVAL
  METHOD Quickstep
  STRESS_TENSOR ANALYTICAL
  &DFT
    BASIS_SET_FILE_NAME ./BASIS_MOLOPT
    POTENTIAL_FILE_NAME ./GTH_POTENTIALS
    UKS
    WFN_RESTART_FILE_NAME 
    MULTIPLICITY 1
    &QS
      METHOD GPW
    &END QS
    &MGRID
      CUTOFF 800
      REL_CUTOFF 60
    &END MGRID
    &SCF
      EPS_SCF 1.0E-6
      MAX_SCF 80
      &OUTER_SCF
        EPS_SCF 1.0E-6
        MAX_SCF 40
      &END
      &OT
        PRECONDITIONER FULL_SINGLE
        MINIMIZER CG
      &END OT
      SCF_GUESS ATOMIC
    &END SCF
    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
      &vdW_POTENTIAL
        DISPERSION_FUNCTIONAL PAIR_POTENTIAL
        &PAIR_POTENTIAL
          TYPE DFTD3(BJ)
          REFERENCE_FUNCTIONAL PBE
          CALCULATE_C9_TERM .FALSE.
          PARAMETER_FILE_NAME ./dftd3.dat
          R_CUTOFF 15.0
        &END PAIR_POTENTIAL
      &END vdW_POTENTIAL
    &END XC
    &PRINT
      &HIRSHFELD
        SELF_CONSISTENT .TRUE.
      &END HIRSHFELD
    &END PRINT
    &POISSON
      PERIODIC XYZ
      POISSON_SOLVER PERIODIC
    &END POISSON
  &END DFT
    
  &SUBSYS
    &CELL
      ABC 7.569 7.569 9.514
      PERIODIC XYZ
    &END CELL
    &COORD
      @INCLUDE 'ana.coord'
    &END COORD
       &KIND O
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND
    &KIND Al
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q3
    &END KIND
    &KIND Ti
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q12
    &END KIND
    &END SUBSYS
&END FORCE_EVAL

&MOTION
  &GEO_OPT
    TYPE MINIMIZATION
    OPTIMIZER BFGS
  &END GEO_OPT
  &CELL_OPT
          KEEP_SYMMETRY TRUE
          KEEP_ANGLES   TRUE
  &END        
&END MOTION

Thanks for the consideration.

Amin



On Monday, November 27, 2017 at 1:58:00 PM UTC+1, Mengzi Zhou wrote:
>
> I agree with Matt. The initial structure is not right. You can find the 
> 2*2*1 48 atoms supercell in the attachment, with a=7.56900, b=7.56900, 
> c=9.51430. I use Materials Studio and VMD to generate models and .cif files 
> of minerals can be found on this website 
> http://rruff.geo.arizona.edu/AMS/amcsd.php  
>
> 在 2017年11月16日星期四 UTC+8下午9:18:17,Amin写道:
>>
>> Hi,
>>
>> My final intention is to make a slab, but yes I tried with bulk structure 
>> at first. I tried with a 2*2*1 super-cell (containing 48 atoms) for a bulk 
>> Anatase and after cell optimization I got a=7.330, b=7.332 and c=10.312  
>> which in comparison to experimental data it has 3% error for a(b) and 8% 
>> error for c. I also tried for a unitcell of containing 31 atoms which I 
>> encountered an error saying "Cholesky decompose failed: the matrix is not 
>> positive definite or ill-conditioned".
>> I have attached both initial structures here.
>> thanks.
>>
>> Amin
>> On Wednesday, November 15, 2017 at 4:42:10 PM UTC+1, Matt W wrote:
>>>
>>> I think your initial structure is strange (wrong). Check everything 
>>> looks correct in an appropriate visualisation package - check all atoms are 
>>> present, maybe some symmetry equivalent ones are missing, for instance.
>>>
>>> Are you trying to make a slab, or bulk. Start with bulk.
>>>
>>> Matt
>>>
>>> On Wednesday, November 15, 2017 at 12:51:24 AM UTC, Amin wrote:
>>>>
>>>> I took the initial unit cell from VNL's crystallographic database for 
>>>> Anatase TiO2 and then I made the initial unit cell for Anatase (101) slab. 
>>>> I ran the calculation for Cell Optimization and finally got the results 
>>>> that I mentioned already. Maybe the procedure that I'm employing for making 
>>>> the initial unit cell is not correct?
>>>>
>>>>
>>>>
>>>> On Tuesday, November 14, 2017 at 11:02:29 PM UTC+1, Matt W wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I still don't really see anything very wrong with the setup (it is a 
>>>>> bit inefficient, use smaller MAX_SCF in inner loop and FULL_ALL or 
>>>>> FULL_SINGLE_INVERSE preconditioner).
>>>>>
>>>>> The initial structure seems very bad - are your coordinates/cell 
>>>>> params correct? Perhaps you converge to a different polymorph or a local 
>>>>> minima?
>>>>>
>>>>> Matt
>>>>>
>>>>> On Tuesday, November 14, 2017 at 12:14:09 PM UTC, Amin wrote:
>>>>>>
>>>>>> Hi Matt, 
>>>>>>
>>>>>> Thanks for the feedback.
>>>>>> My results for a,b and c are 11.520*9.789*11.379 but the results in 
>>>>>> the paper are 10.227*11.346*10.540 and yes my SCF converges. 
>>>>>> I have tested with other structures but I couldn't achieve the same 
>>>>>> results which have been done with the same criteria with CP2K. that's why I 
>>>>>> thought there might be something wrong with my input file.
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Amin
>>>>>>
>>>>>>
>>>>>> On Tuesday, November 14, 2017 at 12:45:57 PM UTC+1, Matt W wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> what do you mean when you say that the results don't agree? 
>>>>>>> Massively wrong, or a small difference?
>>>>>>>
>>>>>>> Does your SCF converge? I don't see any very obvious problems with 
>>>>>>> your input at a quick glance.
>>>>>>>
>>>>>>> Matt
>>>>>>>
>>>>>>> On Tuesday, November 14, 2017 at 11:43:16 AM UTC+1, Amin wrote:
>>>>>>>>
>>>>>>>> Dear all, 
>>>>>>>> I'm having problem with my CELL_OPT calculations. I tried to 
>>>>>>>> achieve lattice parameters for Anatase (101) unit cell but my results are 
>>>>>>>> very different than the other results coming from literature. Specially the 
>>>>>>>> results mentioned in the reference paper of this exercise: 
>>>>>>>> https://www.cp2k.org/exercises:2015_pitt:gga
>>>>>>>> I tried with/without the repetition of the unit cell but the final 
>>>>>>>> lattice parameters was not consistent with those mentioned in literature.
>>>>>>>> I would be grateful if someone takes a look to my input file and 
>>>>>>>> reminds me what's wrong with my calculations. thanks.
>>>>>>>>
>>>>>>>> &GLOBAL
>>>>>>>>   PROJECT cell3
>>>>>>>>   RUN_TYPE CELL_OPT
>>>>>>>>   PRINT_LEVEL LOW
>>>>>>>>   EXTENDED_FFT_LENGTHS
>>>>>>>> &END GLOBAL
>>>>>>>>
>>>>>>>> &FORCE_EVAL
>>>>>>>>   METHOD Quickstep
>>>>>>>>   STRESS_TENSOR ANALYTICAL
>>>>>>>>   &DFT
>>>>>>>>     BASIS_SET_FILE_NAME ./BASIS_MOLOPT
>>>>>>>>     POTENTIAL_FILE_NAME ./GTH_POTENTIALS
>>>>>>>>     UKS
>>>>>>>>     WFN_RESTART_FILE_NAME s-RESTART.wfn
>>>>>>>>     MULTIPLICITY 1
>>>>>>>>     &QS
>>>>>>>>       METHOD GPW
>>>>>>>>     &END QS
>>>>>>>>     &MGRID
>>>>>>>>       CUTOFF 800
>>>>>>>>       REL_CUTOFF 60
>>>>>>>>     &END MGRID
>>>>>>>>     &SCF
>>>>>>>>       EPS_SCF 1.0E-6
>>>>>>>>       MAX_SCF 150
>>>>>>>>       &OUTER_SCF
>>>>>>>>         EPS_SCF 1.0E-6
>>>>>>>>         MAX_SCF 40
>>>>>>>>       &END
>>>>>>>>       &OT
>>>>>>>>         PRECONDITIONER FULL_SINGLE
>>>>>>>>         MINIMIZER CG
>>>>>>>>       &END OT
>>>>>>>>       SCF_GUESS ATOMIC
>>>>>>>>     &END SCF
>>>>>>>>     &XC
>>>>>>>>       &XC_FUNCTIONAL PBE
>>>>>>>>       &END XC_FUNCTIONAL
>>>>>>>>       &vdW_POTENTIAL
>>>>>>>>         DISPERSION_FUNCTIONAL PAIR_POTENTIAL
>>>>>>>>         &PAIR_POTENTIAL
>>>>>>>>           TYPE DFTD3(BJ)
>>>>>>>>           REFERENCE_FUNCTIONAL PBE
>>>>>>>>           CALCULATE_C9_TERM .FALSE.
>>>>>>>>           PARAMETER_FILE_NAME ./dftd3.dat
>>>>>>>>           R_CUTOFF 15.0
>>>>>>>>         &END PAIR_POTENTIAL
>>>>>>>>       &END vdW_POTENTIAL
>>>>>>>>     &END XC
>>>>>>>>     &PRINT
>>>>>>>>       &HIRSHFELD
>>>>>>>>         SELF_CONSISTENT .TRUE.
>>>>>>>>       &END HIRSHFELD
>>>>>>>>     &END PRINT
>>>>>>>>     &POISSON
>>>>>>>>       PERIODIC XYZ
>>>>>>>>       POISSON_SOLVER PERIODIC
>>>>>>>>     &END POISSON
>>>>>>>>   &END DFT
>>>>>>>>     
>>>>>>>>   &SUBSYS
>>>>>>>>     &CELL
>>>>>>>>       ABC 10.2394 3.7845 3.513
>>>>>>>>       PERIODIC XYZ
>>>>>>>>       MULTIPLE_UNIT_CELL 1 3 3 
>>>>>>>>     &END CELL
>>>>>>>>     &TOPOLOGY
>>>>>>>>             MULTIPLE_UNIT_CELL 1 3 3
>>>>>>>>     &END TOPOLOGY
>>>>>>>>     &COORD
>>>>>>>>       @INCLUDE 'cell3.coord'
>>>>>>>>     &END COORD
>>>>>>>>     &KIND O
>>>>>>>>       BASIS_SET DZVP-MOLOPT-GTH
>>>>>>>>       POTENTIAL GTH-PBE-q6
>>>>>>>>     &END KIND
>>>>>>>>     &KIND Ti
>>>>>>>>       BASIS_SET DZVP-MOLOPT-SR-GTH
>>>>>>>>       POTENTIAL GTH-PBE-q12
>>>>>>>>     &END KIND
>>>>>>>>   &END SUBSYS
>>>>>>>> &END FORCE_EVAL
>>>>>>>>
>>>>>>>> &MOTION
>>>>>>>>   &GEO_OPT
>>>>>>>>     TYPE MINIMIZATION
>>>>>>>>     OPTIMIZER BFGS
>>>>>>>>   &END GEO_OPT
>>>>>>>>   &CELL_OPT
>>>>>>>>           KEEP_SYMMETRY TRUE
>>>>>>>>           KEEP_ANGLES   TRUE
>>>>>>>>   &END        
>>>>>>>> &END MOTION
>>>>>>>>
>>>>>>>> cell3.coord:
>>>>>>>>
>>>>>>>> O     7.692165e-01 -3.336155e-17  1.170579e+00    0.07512 -0.00000  
>>>>>>>> 0.33321
>>>>>>>> O     5.888893e+00  1.892250e+00  1.170579e+00    0.57512  0.50000  
>>>>>>>> 0.33321
>>>>>>>> Ti    4.049520e+00  1.892250e+00  1.902225e+00    0.39549  0.50000  
>>>>>>>> 0.54148
>>>>>>>> Ti    9.169196e+00 -3.976756e-16  1.902225e+00    0.89549 -0.00000  
>>>>>>>> 0.54148
>>>>>>>> O     3.678746e+00 -1.595502e-16  2.049708e+00    0.35928 -0.00000  
>>>>>>>> 0.58346
>>>>>>>> O     8.798422e+00  1.892250e+00  2.049708e+00    0.85928  0.50000  
>>>>>>>> 0.58346
>>>>>>>> O     2.210147e+00  1.892250e+00  2.633872e+00    0.21585  0.50000  
>>>>>>>> 0.74975
>>>>>>>> O     7.329824e+00 -3.179005e-16  2.633872e+00    0.71585 -0.00000  
>>>>>>>> 0.74975
>>>>>>>> Ti    1.839373e+00 -7.977512e-17  2.781355e+00    0.17964 -0.00000  
>>>>>>>> 0.79173
>>>>>>>> Ti    6.959049e+00  1.892250e+00  2.781355e+00    0.67964  0.50000  
>>>>>>>> 0.79173
>>>>>>>> O     0.000000e+00  0.000000e+00  3.513001e+00    0.00000  0.00000  
>>>>>>>> 1.00000
>>>>>>>> O     5.119676e+00  1.892250e+00  3.513001e+00    0.50000  0.50000  
>>>>>>>> 1.00000
>>>>>>>>
>>>>>>>>
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