[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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