Conflict in parameters of unit cell after CELL_OPTIMIZATION

Amin amin.jaf... at gmail.com
Thu Nov 16 14:18:17 CET 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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