[CP2K-user] [CP2K:16775] CP2K to study ORR mechanism for MOFs
DMITRII Drugov
dresearcher1991 at gmail.com
Sun Mar 27 06:47:01 UTC 2022
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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