Conflict in parameters of unit cell after CELL_OPTIMIZATION
Amin
amin.jaf... at gmail.com
Thu Nov 16 13:18:17 UTC 2017
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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