Conflict in parameters of unit cell after CELL_OPTIMIZATION

Mengzi Zhou smal... at gmail.com
Mon Nov 27 13:58:00 CET 2017


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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