Conflict in parameters of unit cell after CELL_OPTIMIZATION
Mengzi Zhou
smal... at gmail.com
Mon Nov 27 12:58:00 UTC 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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