[CP2K-user] [CP2K:5398] Re: graphite in CP2K

[DMITRII Drugov]

Thank you for your reply! I am still running optimisation, I will share 
update once its done.

Regards,
Dmitrii

On Thursday, December 3, 2020 at 1:10:48 PM UTC+11 Travis wrote:

> Hi,
>
> Graphite unit cell is hexagonal (
> https://materialsproject.org/materials/mp-48/). You can orthogonalize any 
> cell though. Do it by hand or use a program like atomsk (
> https://atomsk.univ-lille.fr/),
>
> atomsk foo.cif -orthogonal-cell bar.cif
>
> -T
>
> On Wednesday, December 2, 2020 at 6:38:50 PM UTC-5 dre... at gmail.com 
> wrote:
>
>> Good day dear CP2K users, do you think its right to use  90 90 90 
>> orthorhombic symmetry for Graphite cell?
>> Should it be hexagonal 90 90 120 alpha betta gamma?
>>
>> Regrads,
>> Dmitrii 
>>
>> On Thursday, May 29, 2014 at 8:01:13 PM UTC+10 mic... at gmail.com 
>> wrote:
>>
>>> Thanks for the clarification, Matthias. 
>>>
>>>    I must admit that as someone who started off with PWs it is quite 
>>> surprising to see that changing basis set within the same "class of 
>>> complexity" can mess up things to the point of not being able to converge 
>>> the SCF. In the future I'll pay more attention to testing the basis set 
>>> when using CP2K, and take due note that there is much more than the number 
>>> of polarization functions to define the quality of the basis!
>>>
>>> Best wishes,
>>> Michele
>>>
>>>
>>>
>>>
>>> On Thu, May 29, 2014 at 9:17 AM, Matthias Krack <mat... at psi.ch> 
>>> wrote:
>>>
>>>> Dear Michele,
>>>>
>>>> I would not consider graphite as a specifically nasty system. As Matt 
>>>> already wrote, the basis sets in GTH_BASIS_SETS resulted from atomic 
>>>> calculations using the actual GTH pseudopotential. Such an atomic basis set 
>>>> optimisation gives in the case of carbon only a set of exponents and 
>>>> contraction coefficients for a 2s and 2p function. The SZV (single-valence) 
>>>> basis sets in GTH_BASIS_SETS are the results of such optimisations. You may 
>>>> try the C SZV basis set and you will see that is behaves at least 
>>>> reasonably for your system (you may also add a prmitive d polarisation 
>>>> function -> SZVP)  However, experience has shown that such a minimal basis 
>>>> set is by far not accurate enough in most cases as it does not provide 
>>>> sufficient flexibility. Thus it is not suited for production runs. The 
>>>> double-zeta (DZV) GTH basis sets are derived from the corresponding SZV 
>>>> basis sets just by using the smallest exponent as a primitive function for 
>>>> the second valence function. This exponent is often rather small which 
>>>> results in a quite diffuse valence function without any nodal structure. 
>>>> These DZV basis sets were tested in molecular calculations in which they 
>>>> worked. You see, however, that the procedure is not based on any strict 
>>>> optimisation method. This deficiency may become apparent for condensed 
>>>> phase systems like your system. For such systems I would always recommend 
>>>> the use of the MOLOPT SR basis sets as already suggested which provide 
>>>> results closer to PW calculations. The generation procedure of the MOLOPT 
>>>> basis sets performs an optimisation of the contraction coefficients of all 
>>>> included valence functions. In this respect the MOLOPT SR basis sets can be 
>>>> considered as a kind of "second generation" CP2K basis sets.
>>>> Nevertheless, I would like to note that there are many cases in which 
>>>> the GTH_BASIS_SETS work fine and their use may become beneficial as they 
>>>> are computionally less demanding. I know that these basis set issues are 
>>>> quite annoying, especially for people coming from the PW community.
>>>>
>>>> Best regards,
>>>>
>>>> Matthias
>>>>
>>>>
>>>> On Wednesday, May 28, 2014 9:57:05 PM UTC+2, Michele Ceriotti wrote:
>>>>
>>>>> Dear Matt (and Marcella who basically replied the same in private),
>>>>>
>>>>>    Thanks a million, using the molopt basis set does fix things. I had 
>>>>> tried both the dzvp from basis_sets and gth_basis_set, and I was getting 
>>>>> similar nonsense.
>>>>>
>>>>> I am a bit scared seeing how much difference it makes changing the 
>>>>> basis set. Any idea why graphite should be such a nasty beast? I had 
>>>>> experimented with different basis sets for water and never saw such a 
>>>>> dramatic effect.
>>>>>
>>>>> All the best,
>>>>> Michele
>>>>> On 28 May 2014 19:23, "Matt W" <Mat... at gmail.com> wrote:
>>>>>
>>>>>> Hi Michele,
>>>>>>
>>>>>> please try using the MOLOPT basis sets provided with CP2K 
>>>>>> ($CP2K_root/tests/QS/BASIS_MOLOPT) that prehaps give a more suitable 
>>>>>> starting point for describing a "molecular" system like graphite than 
>>>>>> atomic optimization based ones.
>>>>>>
>>>>>> Using a DZVP-MOLOPT-SR-GTH basis - I get SCF convergence in ~10 
>>>>>> cycles and geometry converges in ~10 steps (with BFGS).
>>>>>>
>>>>>> Matt
>>>>>>
>>>>>> On Wednesday, May 28, 2014 5:19:30 PM UTC+1, Michele Ceriotti wrote:
>>>>>>>
>>>>>>> Hi Matthias, 
>>>>>>>    Thanks for the quick answer. I have already played with the 
>>>>>>> obvious parameters, point is it is impossible to converge the scf properly. 
>>>>>>> Everything looks like what you get when the geometry is crazy, and 
>>>>>>> indeed my student tried to enlarge the cell (by almost 10%!) and got  
>>>>>>> converged scf and more reasonable forces. 
>>>>>>> However this is inconsistent with the literature and the results 
>>>>>>> from siesta.
>>>>>>> We have been trying to fiddle with the scf parameters for days, but 
>>>>>>> get consistently 100au forces on a geometry that should be very close to 
>>>>>>> optimum.
>>>>>>> Do you see something wrong with how we define the cell or the 
>>>>>>> positions?
>>>>>>> Best
>>>>>>> Michele
>>>>>>> On 28 May 2014 17:47, "Matthias Krack" <mat... at psi.ch> wrote:
>>>>>>>
>>>>>>>> Hi Michele,
>>>>>>>>
>>>>>>>> I would suggest to set EPS_DEFAULT in @QS section at least to 
>>>>>>>> 1.0E-12 or lower and for the ALPHA in &MIXING I would also use a smaller 
>>>>>>>> value like 0.2. Maybe this will help to converge your system properly.
>>>>>>>>
>>>>>>>> Matthias
>>>>>>>>
>>>>>>>> On Wednesday, May 28, 2014 4:20:44 PM UTC+2, Michele Ceriotti wrote:
>>>>>>>>>
>>>>>>>>> Dear CP2K community, 
>>>>>>>>>
>>>>>>>>>      I have been trying for a few days to set up calculations of 
>>>>>>>>> graphite as an exercise for a student but I am getting the weirdest 
>>>>>>>>> results.  I am sure in the it will end up being a silly mistake in the 
>>>>>>>>> input, but I can't get to see it so perhaps someone can help. 
>>>>>>>>>
>>>>>>>>> Despite using a fairly large FD smearing, the SCF cycle has a hard 
>>>>>>>>> time converging, and when the maximum number of steps is reached 
>>>>>>>>>
>>>>>>>>>     50 Broy./Diag. 0.50E+00    1.2     0.00014351      
>>>>>>>>> -819.2909959720 -2.28E-09
>>>>>>>>>   *** SCF run NOT converged ***
>>>>>>>>>
>>>>>>>>> and the calculation carries on with what it has got, diagnostics 
>>>>>>>>> are really strange. 
>>>>>>>>>
>>>>>>>>> For a start, eigenvalues show two weird very low-energy states
>>>>>>>>>  MO EIGENVALUES AND MO OCCUPATION NUMBERS
>>>>>>>>> # MO index          MO eigenvalue [a.u.]            MO occupation
>>>>>>>>>          1                    -21.523076                 2.000000
>>>>>>>>>          2                    -21.517160                 2.000000
>>>>>>>>>          3                     -1.383548                 2.000000
>>>>>>>>>          4                     -0.510418                 2.000000
>>>>>>>>>
>>>>>>>>> forces on the atoms are insane
>>>>>>>>>  ATOMIC FORCES in [a.u.]
>>>>>>>>>  # Atom   Kind   Element          X              Y              Z
>>>>>>>>>       1      1      C           4.68736611     4.63921800  
>>>>>>>>> -222.86999309
>>>>>>>>>       2      1      C          -1.57720920    -4.48651652   
>>>>>>>>> 124.33822840
>>>>>>>>>       3      1      C          -5.01734639     3.10518104   
>>>>>>>>> 176.16292919
>>>>>>>>>
>>>>>>>>> and so is the stress tensor
>>>>>>>>>  STRESS TENSOR [GPa]
>>>>>>>>>             X               Y               Z
>>>>>>>>>   X   -8233.84728056      8.05482610      0.90481573
>>>>>>>>>   Y       8.05482610  -9552.76932222     -0.49445437
>>>>>>>>>   Z       0.90481573     -0.49445437  -2526.59040628
>>>>>>>>>
>>>>>>>>> I was thinking of an error in the structure or the cell 
>>>>>>>>> parameters, but I checked it many times and everything seems in order. The 
>>>>>>>>> same structure, with same functional and similar parameters in SIESTA 
>>>>>>>>> converges like a stone, and gives no problem whatsoever. 
>>>>>>>>>  
>>>>>>>>> Can you spot something obvious that I am missing? I'd really like 
>>>>>>>>> to use CP2K for this exercise, but I can't seem to figure out what is going 
>>>>>>>>> wrong. 
>>>>>>>>>
>>>>>>>>> Many thanks,
>>>>>>>>> Michele
>>>>>>>>>
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>>>
>>>
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