[CP2K-user] [CP2K:16799] CP2K to study ORR mechanism for MOFs
DMITRII Drugov
dresearcher1991 at gmail.com
Fri Apr 1 14:09:43 UTC 2022
Dear Anton,
Thank you for your reply.
I set up LSD and multiplicity 2 only because I directly create a slab 011
from cif of zif-8 by Avogadro software.
That gave me odd number of electrons. I also realised that 10-7 even 10-6
will result in a strong drift for convergence.
I will try 10-5 instead for correct slab structure.
I am a bit puzzled with slab termination as to create a facet of interest
by direct translation of unit cell is a bit difficult.
https://www.youtube.com/watch?v=ywR5pWqbllE
It is difficult to find a right center of symmetry without creating
unbounded atoms. Chemistry of termination is also different depending how
deep you slice it. I attached output file from run with previous settings
in case you are interested, but that structure is unreasonable. I also got
weird metal-like dos because of odd number of electrons and poor Avogadro
slab preparation job.
Would you be able to look at facets which I created for non-periodic
calculations and tell how reasonable to study ORR on them, or it is better
to stick to periodic cif like structure to do ORR studies?
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.
Best,
Dmitrii
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
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "cp2k" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to cp2k+uns... at googlegroups.com.
>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/cp2k/9a22b6dc-aca9-4476-816d-38096d65d2c1n%40googlegroups.com
>>>> <https://groups.google.com/d/msgid/cp2k/9a22b6dc-aca9-4476-816d-38096d65d2c1n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>> .
>>>>
>>> --
>> You received this message because you are subscribed to the Google Groups
>> "cp2k" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to cp2k+uns... at googlegroups.com.
>>
> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/cp2k/b4c22c8c-31db-4c3d-bac6-6fb057c6e3b8n%40googlegroups.com
>> <https://groups.google.com/d/msgid/cp2k/b4c22c8c-31db-4c3d-bac6-6fb057c6e3b8n%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>
--
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/0fb91eb0-d9fd-4b69-b258-536e5c9a1d9fn%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220401/f760e271/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: zif8.cif
Type: chemical/x-cif
Size: 15409 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220401/f760e271/attachment-0001.cif>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: zif8_001.xyz
Type: chemical/x-xyz
Size: 7061 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220401/f760e271/attachment-0002.xyz>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: zif8_011.xyz
Type: chemical/x-xyz
Size: 9070 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220401/f760e271/attachment-0003.xyz>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: out
Type: application/octet-stream
Size: 360612 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220401/f760e271/attachment-0001.obj>
More information about the CP2K-user
mailing list