[CP2K-user] [CP2K:5398] Re: graphite in CP2K
DMITRII Drugov
dresear... at gmail.com
Sun Dec 6 03:19:12 UTC 2020
Thank you a lot for this! I will update you with optimisation results, once
it's done.
Regards,
Dmitrii
On Sunday, December 6, 2020 at 7:33:33 AM UTC+11 Travis wrote:
> Hi,
>
> Attached are prepared CIF files for bulk graphite with 4 layers. The 6x4x2
> ortho cell has 384 atoms which seems to be the one you're working with.
> Avogadro is not recommended for periodic systems (trying to open one of
> these CIF files on my PC takes ages). It often messes up the structure by
> either adding extra atoms or losing a few. I'd start with a cell
> optimization of the bulk cell - these lattice parameters are from VASP.
> Then you can implement slab boundaries and fix the bottom layer(s).
>
> -T
>
> On Saturday, December 5, 2020 at 12:50:55 AM UTC-5 dre... at gmail.com
> wrote:
>
>> 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 <(904)%20501-4398>
>> 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
>>>>>>>>>>>>
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