Conflict in parameters of unit cell after CELL_OPTIMIZATION
Amin
amin.jaf... at gmail.com
Tue Nov 28 09:17:33 UTC 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
>>>>>>>>
>>>>>>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20171128/58e08c98/attachment.htm>
More information about the CP2K-user
mailing list