[CP2K-user] [CP2K:16824] CP2K to study ORR mechanism for MOFs
DMITRII Drugov
dresearcher1991 at gmail.com
Thu Apr 7 14:22:42 UTC 2022
Dear Anton,
Thank you so much for your deep scientific reply. I will try to figure out
the multiplicity issue which I really found challenging in DFT
calculations. My background is more about electrochemistry and materials
engineering than condensed matter physics. Regarding CHE, I meant
computational hydrogen electrode. I need to calculate reaction coordinate
for ORR according to CHE method proposed by Norskov and his colleagues,
e.g., NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-022-28516-0.
Therefore, I thought about which active site of the terminated surface I
need to consider for adsorption of intermediates, metals or its ligands?
Do you think to estimate the right multiplicity I need to consider the
correct number of unpaired electrons for the whole Co-doped ZIF-8 unit
cell? Relax multiplicity can give me a rough idea for this number?
Best,
Dmitrii
On Thu, Apr 7, 2022 at 7:32 PM Anton Lytvynenko <
anton.s.lytvynenko at gmail.com> wrote:
> Dear Dmitrii,
>
> пт, 1 квіт. 2022 р. о 16:09 DMITRII Drugov <dresearcher1991 at gmail.com>
> пише:
>
>> I set up LSD and multiplicity 2 only because I directly create a slab 011
>> from cif of zif-8 by Avogadro software.
>
> It is not the correct way. Indeed, you need an odd number of electrons,
> but it does not mean that you may put any even multiplicity here. Co2+ in
> this coordination environment has an exact preferred multiplicity, you can
> deduce it from the literature -- just search for complexes of Co(II) with
> the same environment in literature or refer to the "Comprehensive
> Coordination Chemistry" book. I am out of the topic for some time, but I
> guess the multiplicity will be 4 (you should check it by yourself anyway).
> As you have only one Co ion per a pretty large cell, this should be enough
> (a few close paramagnetic ions would complicate the task sending you
> directly into the realm of magnetochemistry). Anyway, if in doubt or there
> is no data, please employ the relax_multiplicity feature of CP2k -- at
> least for a preliminary run to deduce the correct multiplicity.
>
> Regarding the slabs, unfortunately I can't help here at the moment. To get
> CP2k working correctly, you definitely need to generate all atoms needed to
> form the slab (without gaps), all of them must be unique with respect to
> translations of the slab supercell and all bonds must be correctly
> terminated (either with explicitly declared atom or with a replica obtained
> by the translations). Maybe there is a program that does it correctly, but
> I am afraid some homebrew code will be needed, and I am unable to produce
> it immediately (despite I also need it for some other tasks).
>
>
>> Do you think when I do reaction coordinate studies according to CHE
>> method, should I consider only metal as an absorption site or nitrogen atom
>> of imidazolium ligand as well? Ideally I would chose only one adsorption
>> center.
>>
> What do you mean under CHE method?
>
> Adsorption of what?
>
> Yours,
> Anton
>
>
>> On Friday, April 1, 2022 at 10:46:11 PM UTC+10 anton.s.l... at gmail.com
>> wrote:
>>
>>> Dear Dmitrii,
>>>
>>> how did you obtain the xyz? Did you just export it from CIF? It looks
>>> like it is full of disordered hydrogen atoms.
>>>
>>> MULTIPLICITY 2
>>>>
>>> Are you sure?
>>>
>>> What do you think I need to change for energy calculations, expect of
>>>> deeper EPS_SCF from 1.0E-6 to 1.0E-7 or -8?
>>>>
>>> I don't know. AFAIR, the default is 1e-5, I used to lower it to 1e-6,
>>> while 1.0e-7 resulted in very slow convergence (I mean that the calculation
>>> reached the residues of ca 1e-6 and then started to turning around it,
>>> until "accidentally" reached 1e-7 -- I guess that some other parameters are
>>> to be tuned to avoid numeric noise). Anyway, you always could check the
>>> consistency w.r.t. to the considered parameter by yourself. The key point
>>> in your case is to get rid of numeric noise in gradients -- you can assess
>>> it via observing the course of your geometry optimization (if you see some
>>> random moves around the equilibrium rather than smooth convergence to it,
>>> this might be the case).
>>>
>>> Do I need to use spin polarisation for Co and Zn atoms when I calculate
>>>> adsorption energy for ORR reaction coordinate, or I can reach desirably
>>>> accuracy without it? My job is to compare different facets reactivity for
>>>> ORR.
>>>>
>>> I probably don't understand your question. If your system is
>>> paramagnetic, you have to use the spin-unrestricted formalism (LSD aka UKS)
>>> anyway.
>>>
>>> I don't think the idea of crystallographic facets makes real sense in
>>> the case of MOFs. The active centers in the case of MOFs are either the
>>> metal ions with the coordinated atoms, or the fragments of ligands, these
>>> centers are unlikely to be affected if you change the facet.
>>>
>>> Yours,
>>> Anton
>>>
>>> нд, 27 бер. 2022 р. о 08:47 DMITRII Drugov <dresear... at gmail.com> пише:
>>>
>>>> Dear Anton,
>>>>
>>>> Thank you for your reply.
>>>> I even did not think about low symmetry of MOFs. Thank you for this
>>>> point.
>>>> I attach my input file below for cell_opt first, then I will do energy
>>>> calculation.
>>>> Could you please have a look at my settings and express your opinion on
>>>> its accuracy?
>>>> What do you think I need to change for energy calculations, expect of
>>>> deeper EPS_SCF from 1.0E-6 to 1.0E-7 or -8?
>>>> Do I need to use spin polarisation for Co and Zn atoms when I calculate
>>>> adsorption energy for ORR reaction coordinate, or I can reach desirably
>>>> accuracy without it? My job is to compare different facets reactivity for
>>>> ORR.
>>>>
>>>> Best,
>>>> Dmitrii
>>>>
>>>> &GLOBAL
>>>> PROJECT MOF_011_optimisation_larger_cell
>>>> RUN_TYPE CELL_OPT
>>>> PRINT_LEVEL MEDIUM
>>>> !EXTENDED_FFT_LENGTHS
>>>> &END GLOBAL
>>>> &FORCE_EVAL
>>>> STRESS_TENSOR ANALYTICAL
>>>> METHOD QS
>>>> &DFT
>>>> BASIS_SET_FILE_NAME BASIS_MOLOPT
>>>> POTENTIAL_FILE_NAME GTH_POTENTIALS
>>>> LSD
>>>> CHARGE 0
>>>> MULTIPLICITY 2
>>>> &MGRID
>>>> CUTOFF 800
>>>> NGRIDS 5
>>>> REL_CUTOFF 70
>>>> &END MGRID
>>>> &QS
>>>> EPS_DEFAULT 1.0E-14
>>>> !WF_INTERPOLATION ASPC
>>>> &END QS
>>>> &SCF
>>>> SCF_GUESS ATOMIC
>>>> EPS_SCF 1.0E-6
>>>> MAX_SCF 300
>>>> &OT
>>>> MINIMIZER CG
>>>> PRECONDITIONER FULL_KINETIC
>>>> # ENERGY_GAP 0.01
>>>> &END OT
>>>> &OUTER_SCF
>>>> EPS_SCF 1E-6
>>>> MAX_SCF 300
>>>> &END
>>>> !CHOLESKY INVERSE
>>>> !ADDED_MOS 100
>>>> !&SMEAR ON
>>>> ! METHOD FERMI_DIRAC
>>>> ! ELECTRONIC_TEMPERATURE [K] 1000
>>>> ! &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 8.0
>>>> &END PAIR_POTENTIAL
>>>> &END vdW_POTENTIAL
>>>> &END XC
>>>> SURFACE_DIPOLE_CORRECTION T
>>>> SURF_DIP_DIR Z
>>>> &POISSON
>>>> PERIODIC xy
>>>> POISSON_SOLVER ANALYTIC
>>>> &END POISSON
>>>> &END DFT
>>>> &SUBSYS
>>>> &CELL
>>>> ABC 18.55406 16.35222 50
>>>> ALPHA_BETA_GAMMA 90.0 90.0 90.0
>>>> PERIODIC xy
>>>> SYMMETRY ORTHORHOMBIC
>>>> &END CELL
>>>> &COORD
>>>> C 2.69109 3.50908 2.31039
>>>> C 2.69109 12.34314 2.31039
>>>> C 0.51227 7.92611 3.89871
>>>> N 5.94837 3.44592 0.26929
>>>> N 1.20316 9.05092 3.62466
>>>> N 1.20316 6.8013 3.62466
>>>> N 5.94837 12.4063 0.26929
>>>> C 6.87686 10.39498 0
>>>> C 5.92646 4.78521 0.67203
>>>> C 2.43496 8.59814 3.1409
>>>> C 2.43496 7.25408 3.1409
>>>> C 6.87686 5.45724 0
>>>> C 5.92646 11.06701 0.67203
>>>> H 7.0639 9.48822 0.08937
>>>> H 5.34848 5.15102 1.30235
>>>> H 3.13933 9.1391 2.86446
>>>> H 3.13933 6.71312 2.86446
>>>> H 7.0639 6.364 0.08937
>>>> H 5.34848 10.7012 1.30235
>>>> C 2.26139 4.168 1.04379
>>>> C 2.26139 11.68422 1.04379
>>>> H 1.56208 4.79832 1.23086
>>>> H 2.83938 11.95708 0.32767
>>>> H 1.56208 11.0539 1.23086
>>>> H 2.83938 3.89514 0.32767
>>>> H 3.00789 4.62555 0.65058
>>>> H 2.30689 10.73099 1.14626
>>>> H 3.00789 11.22667 0.65058
>>>> H 2.30689 5.12123 1.14626
>>>> H 1.93449 3.50312 0.43134
>>>> H 1.35819 11.94159 0.83884
>>>> H 1.93449 12.3491 0.43134
>>>> H 1.35819 3.91063 0.83884
>>>> O 5.79166 7.92611 2.27822
>>>> Zn 4.81431 13.8838 0.89604
>>>> Zn 0.60158 10.90496 3.87488
>>>> C 6.93752 15.29816 2.4367
>>>> C 0.69089 10.88113 6.85373
>>>> N 3.68024 13.25705 2.37354
>>>> N 2.08951 12.13224 3.49836
>>>> N 0 11.15518 5.72892
>>>> N 5.94837 15.36131 1.52279
>>>> C 3.70215 13.65979 3.71283
>>>> C 2.75175 12.98777 4.38486
>>>> H 4.28013 14.29012 4.07864
>>>> H 6.48928 15.85222 5.64074
>>>> H 2.56471 13.07713 5.29162
>>>> C 7.36722 14.03155 3.09562
>>>> C 2.05244 10.27344 6.85373
>>>> H 2.83938 15.81052 1.4644
>>>> H 8.06653 14.21863 3.72594
>>>> H 2.36587 10.18765 5.95054
>>>> H 6.78923 13.31544 2.82276
>>>> H 6.62072 13.63835 3.55317
>>>> H 2.65402 10.83346 6.35805
>>>> H 7.32172 14.13403 4.04885
>>>> H 1.35819 15.82601 0.95323
>>>> H 1.93449 15.4185 1.36074
>>>> H 7.69412 13.4191 2.43074
>>>> H 2.01537 9.40362 6.44622
>>>> H 8.27042 13.82661 2.83825
>>>> O 3.83695 15.26599 6.85373
>>>> O 5.92646 12.31097 6.85373
>>>> Co 0.60158 4.94726 3.87488
>>>> Zn 4.81431 1.96842 0.89604
>>>> C 6.93752 0.55406 2.4367
>>>> C 0.69089 4.97109 6.85373
>>>> N 2.08951 3.71998 3.49836
>>>> N 3.68024 2.59517 2.37354
>>>> N 5.94837 0.49091 1.52279
>>>> N 0 4.69704 5.72892
>>>> C 2.75175 2.86445 4.38486
>>>> C 3.70215 2.19243 3.71283
>>>> H 2.56471 2.77509 5.29162
>>>> H 6.48928 0 5.64074
>>>> H 4.28013 1.5621 4.07864
>>>> C 7.36722 1.82067 3.09562
>>>> C 2.05244 5.57878 6.85373
>>>> H 2.83938 0.0417 1.4644
>>>> H 6.78923 2.53678 2.82276
>>>> H 2.36587 5.66457 5.95054
>>>> H 8.06653 1.63359 3.72594
>>>> H 7.32172 1.71819 4.04885
>>>> H 2.65402 5.01876 6.35805
>>>> H 6.62072 2.21387 3.55317
>>>> H 1.93449 0.43372 1.36074
>>>> H 1.35819 0.02621 0.95323
>>>> H 8.27042 2.02561 2.83825
>>>> H 2.01537 6.4486 6.44622
>>>> H 7.69412 2.43312 2.43074
>>>> O 3.83695 0.58623 6.85373
>>>> O 5.92646 3.54125 6.85373
>>>> C 17.36317 7.92611 3.89871
>>>> N 15.96455 4.57074 2.6476
>>>> N 14.37382 12.4063 1.52279
>>>> N 15.96455 11.28148 2.6476
>>>> N 14.37382 3.44592 1.52279
>>>> N 18.05406 9.05092 3.62466
>>>> N 18.05406 6.8013 3.62466
>>>> C 15.30231 5.45724 1.79207
>>>> C 14.35191 11.06701 1.12005
>>>> C 15.30231 10.39498 1.79207
>>>> C 14.35191 4.78521 1.12005
>>>> H 15.48935 6.364 1.70271
>>>> H 13.77393 10.7012 0.48972
>>>> H 15.48935 9.48822 1.70271
>>>> H 13.77393 5.15102 0.48972
>>>> C 10.68684 11.68422 0.74829
>>>> C 10.68684 4.168 0.74829
>>>> C 16.00162 7.92611 4.5064
>>>> H 9.98753 11.0539 0.56121
>>>> H 11.26483 3.89514 1.4644
>>>> H 15.68819 8.8293 4.59219
>>>> H 15.68819 7.02292 4.59219
>>>> H 9.98753 4.79832 0.56121
>>>> H 11.26483 11.95708 1.4644
>>>> H 11.43334 11.22667 1.14149
>>>> H 10.73234 5.12123 0.64581
>>>> H 15.40004 7.43043 3.94638
>>>> H 15.40004 8.42179 3.94638
>>>> H 11.43334 4.62555 1.14149
>>>> H 10.73234 10.73099 0.64581
>>>> H 10.35994 12.3491 1.36074
>>>> H 9.78364 3.91063 0.95323
>>>> H 16.03869 7.5186 5.37622
>>>> H 16.03869 8.33362 5.37622
>>>> H 10.35994 3.50312 1.36074
>>>> H 9.78364 11.94159 0.95323
>>>> O 12.1276 7.92611 2.46887
>>>> Zn 13.23976 13.8838 0.89604
>>>> Zn 17.45248 10.90496 3.87488
>>>> C 15.36297 12.46945 2.4367
>>>> C 11.11654 15.42446 2.31039
>>>> C 17.54179 10.88113 6.85373
>>>> N 14.37382 15.36131 0.26929
>>>> N 10.51496 15.63536 3.49836
>>>> N 16.8509 11.15518 5.72892
>>>> N 12.10569 14.51055 2.37354
>>>> C 11.1772 14.77984 4.38486
>>>> C 15.6191 11.63894 6.1817
>>>> C 12.1276 14.10781 3.71283
>>>> H 10.99016 14.69047 5.29162
>>>> H 14.91473 11.91538 5.64074
>>>> H 12.70558 13.47749 4.07864
>>>> C 15.79267 13.73605 3.09562
>>>> H 15.21468 14.45217 2.82276
>>>> H 16.49198 13.54898 3.72594
>>>> H 11.26483 15.81052 0.32767
>>>> H 15.74717 13.63358 4.04885
>>>> H 15.04617 14.12926 3.55317
>>>> H 16.69587 13.941 2.83825
>>>> H 16.11957 14.3485 2.43074
>>>> H 10.35994 15.4185 0.43134
>>>> H 9.78364 15.82601 0.83884
>>>> O 12.2624 12.50162 6.85373
>>>> O 14.35191 15.45663 6.85373
>>>> Zn 17.45248 4.94726 3.87488
>>>> Zn 13.23976 1.96842 0.89604
>>>> C 15.36297 3.38277 2.4367
>>>> C 11.11654 0.42776 2.31039
>>>> C 17.54179 4.97109 6.85373
>>>> N 14.37382 0.49091 0.26929
>>>> N 12.10569 1.34167 2.37354
>>>> N 16.8509 4.69704 5.72892
>>>> N 10.51496 0.21686 3.49836
>>>> C 12.1276 1.74441 3.71283
>>>> C 15.6191 4.21328 6.1817
>>>> C 11.1772 1.07238 4.38486
>>>> H 12.70558 2.37473 4.07864
>>>> H 14.91473 3.93684 5.64074
>>>> H 10.99016 1.16175 5.29162
>>>> C 15.79267 2.11617 3.09562
>>>> H 16.49198 2.30324 3.72594
>>>> H 15.21468 1.40005 2.82276
>>>> H 11.26483 0.0417 0.32767
>>>> H 15.04617 1.72296 3.55317
>>>> H 15.74717 2.21864 4.04885
>>>> H 16.11957 1.50372 2.43074
>>>> H 16.69587 1.91122 2.83825
>>>> H 9.78364 0.02621 0.83884
>>>> H 10.35994 0.43372 0.43134
>>>> O 12.2624 3.3506 6.85373
>>>> O 14.35191 0.39559 6.85373
>>>> &END COORD
>>>> &KIND Co
>>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>>> POTENTIAL GTH-PBE-q17
>>>> &END KIND
>>>> &KIND Zn
>>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>>> POTENTIAL GTH-PBE-q12
>>>> &END KIND
>>>> &KIND O
>>>> BASIS_SET TZVP-MOLOPT-GTH
>>>> POTENTIAL GTH-PBE-q6
>>>> &END KIND
>>>> &KIND C
>>>> BASIS_SET TZVP-MOLOPT-GTH
>>>> POTENTIAL GTH-PBE-q4
>>>> &END KIND
>>>> &KIND H
>>>> BASIS_SET TZVP-MOLOPT-GTH
>>>> POTENTIAL GTH-PBE-q1
>>>> &END KIND
>>>> &KIND N
>>>> BASIS_SET TZVP-MOLOPT-GTH
>>>> POTENTIAL GTH-PBE-q5
>>>> &END KIND
>>>> &END SUBSYS
>>>> &END FORCE_EVAL
>>>> &MOTION
>>>> &GEO_OPT
>>>> OPTIMIZER LBFGS
>>>> MAX_ITER 300
>>>> &END GEO_OPT
>>>> &CELL_OPT
>>>> EXTERNAL_PRESSURE [bar] 0.0
>>>> KEEP_ANGLES TRUE
>>>> KEEP_SYMMETRY TRUE
>>>> OPTIMIZER LBFGS
>>>> &END
>>>> &END MOTION
>>>> &END
>>>>
>>>>
>>>>
>>>>
>>>> On Friday, March 25, 2022 at 8:32:42 PM UTC+10 anton.s.l... at gmail.com
>>>> wrote:
>>>>
>>>>> Dear Dmitrii,
>>>>>
>>>>> CP2k has implementation of k-points, but it could be incompatible with
>>>>> some methods and features.
>>>>>
>>>>> But why do you need it? MOFs cells are typically large and have low
>>>>> symmetry.
>>>>>
>>>>> Yours,
>>>>> Anton
>>>>>
>>>>> пт, 25 бер. 2022 р. о 10:38 DMITRII Drugov <dresear... at gmail.com>
>>>>> пише:
>>>>>
>>>>>> Dear CP2K users,
>>>>>>
>>>>>> Could you please share your thoughts on correct CP2K settings to
>>>>>> study oxygen reaction reaction on MOFs surface (186 atoms, C, H, O, N, Zn)?
>>>>>> I used to conduct similar job on Quantum Espresso for to study HER on
>>>>>> graphite slab (86 atoms) and it took ages to finish single energy
>>>>>> calculation with soft potentials (ecutrho = 0.4000000000d+03
>>>>>> ecutwfc = 0.5000000000d+02). According to my experience at gamma
>>>>>> point CP2K is much faster but I never added k-point mesh to CP2K.
>>>>>> Could you please let me know what my CP2K should be? Does CP2K allow
>>>>>> to set up k-points for energy calculation? My system is a slab with vacuum
>>>>>> of 2*x or y in z dimension.
>>>>>>
>>>>>> Best regards,
>>>>>> Dmitrii
>>>>>>
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