[CP2K-user] [CP2K:5398] Re: graphite in CP2K
DMITRII Drugov
dresear... at gmail.com
Sat Dec 5 05:50:55 UTC 2020
Hi guys, could you suggest the right cell setting for graphite simulation.
Should I use extra space in xy dimension to get right optimised geometry? I
build slab from Avogadro with 384 atoms and xyz 17.04000000 14.75707288
13.20000000 A. I froze two bottom layer and allowed remaining top two layer
to equilibrate.
I am using following parameters:
&GLOBAL
PROJECT Graphite_geometry_optimization_moreMOs
RUN_TYPE GEO_OPT
PRINT_LEVEL MEDIUM
&END GLOBAL
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME GTH_POTENTIALS
CHARGE 0
MULTIPLICITY 1
&MGRID
CUTOFF 800
NGRIDS 5
REL_CUTOFF 70
&END MGRID
&QS
EPS_DEFAULT 1.0E-12
WF_INTERPOLATION ASPC
&END QS
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-7
MAX_SCF 1000
CHOLESKY INVERSE
ADDED_MOS 100
&SMEAR ON
METHOD FERMI_DIRAC
ELECTRONIC_TEMPERATURE [K] 300
&END SMEAR
&DIAGONALIZATION
ALGORITHM STANDARD
&END DIAGONALIZATION
&MIXING
METHOD BROYDEN_MIXING
ALPHA 0.4
NBROYDEN 8
&END MIXING
&END SCF
&XC
&XC_FUNCTIONAL
&PBE
&END PBE
&END XC_FUNCTIONAL
&vdW_POTENTIAL
DISPERSION_FUNCTIONAL PAIR_POTENTIAL
&PAIR_POTENTIAL
PARAMETER_FILE_NAME dftd3.dat
TYPE DFTD3
REFERENCE_FUNCTIONAL PBE
R_CUTOFF 15.0
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&POISSON
PERIODIC xy
POISSON_SOLVER ANALYTIC
&END POISSON
&END DFT
&SUBSYS
&CELL
ABC 18.46 13.53 50.0
ALPHA_BETA_GAMMA 90.0 90.0 120.0
PERIODIC xy
&END CELL
&COORD
C 0.00000000 0.00000000 0.00000000
...
C 17.75000000 13.52731681 9.90000000
&END COORD
&KIND C
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&END SUBSYS
&END FORCE_EVAL
&MOTION
&CONSTRAINT
&FIXED_ATOMS
COMPONENTS_TO_FIX XYZ
LIST 1..194
&END FIXED_ATOMS
&END CONSTRAINT
&GEO_OPT
OPTIMIZER LBFGS
MAX_ITER 300
&END GEO_OPT
&END MOTION
I spend 34 hours with 36 CPU and 120 GB of memory and still didn't
optimised it yet. It seems that energy does not decrease much.
384
i = 1, E = -2025.9045014398
384
i = 6, E = -2075.1262328870
If I change cell parameters to
&SUBSYS
&CELL
ABC 18.46 13.53 50.0
PERIODIC xy
SYMMETRY ORTHORHOMBIC
&END CELL
384
i = 1, E = -2132.8940479508
384
i = 11, E = -2146.1458464543
It does not help much.
Regards,
Dmitrii
On Friday, December 4, 2020 at 2:52:34 PM UTC+11 DMITRII Drugov wrote:
> 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
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>> You received this message because you are subscribed to a topic in
>>>>>>>>> the Google Groups "cp2k" group.
>>>>>>>>> To unsubscribe from this topic, visit https://groups.google.com/d/
>>>>>>>>> topic/cp2k/koy91UtxlQw/unsubscribe.
>>>>>>>>> To unsubscribe from this group and all its topics, send an email
>>>>>>>>> to cp... at googlegroups.com.
>>>>>>>>> To post to this group, send email to c... at googlegroups.com.
>>>>>>>>> Visit this group at http://groups.google.com/group/cp2k.
>>>>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>>>>
>>>>>>>> --
>>>>>>> You received this message because you are subscribed to a topic in
>>>>>>> the Google Groups "cp2k" group.
>>>>>>> To unsubscribe from this topic, visit https://groups.google.com/d/
>>>>>>> topic/cp2k/koy91UtxlQw/unsubscribe.
>>>>>>> To unsubscribe from this group and all its topics, send an email to
>>>>>>> cp... at googlegroups.com.
>>>>>>> To post to this group, send email to c... at googlegroups.com.
>>>>>>> Visit this group at http://groups.google.com/group/cp2k.
>>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>>
>>>>>> --
>>>>> You received this message because you are subscribed to a topic in the
>>>>> Google Groups "cp2k" group.
>>>>> To unsubscribe from this topic, visit
>>>>> https://groups.google.com/d/topic/cp2k/koy91UtxlQw/unsubscribe.
>>>>> To unsubscribe from this group and all its topics, send an email to
>>>>> cp... at googlegroups.com.
>>>>> To post to this group, send email to c... at googlegroups.com.
>>>>> Visit this group at http://groups.google.com/group/cp2k.
>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>
>>>>
>>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20201204/79036896/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2020-12-05 at 4.49.27 pm.png
Type: image/png
Size: 410640 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20201204/79036896/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2020-12-05 at 4.49.27 pm.png
Type: image/png
Size: 410640 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20201204/79036896/attachment-0001.png>
More information about the CP2K-user
mailing list