What is CP2K periodicity settings by default without specification?

DMITRII Drugov

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Dec 10, 2020, 7:50:57 PM12/10/20

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Good day dear CP2K users, I am doing simple organic molecule optimization like Gaussian but with CP2K. I need it for future Ead on slab calculation.

I am curious how CP2K deal with periodicity in my case if I do not specify periodicity and poison solver here. I tried periodicity NONE and poison wavelet but my system couldn't converge. So, only when I avoid specification of periodicity and poison solver system converged without any problem.

Thank you,

Dmitrii

&GLOBAL

PROJECT Na_2FSI_optimization_new

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 -1

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 50

&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

&END DFT

&SUBSYS

&CELL

ABC 30.0 30.0 30.0

&END CELL

&COORD

O 3.875784 2.333214 1.212007

O 4.047601 -1.211041 -2.231536

N 3.859440 0.441161 -0.391139

S 3.259060 -0.860789 -1.079536

S 3.157056 1.138791 0.853627

O 1.802534 -0.898489 -1.184401

O 1.697555 1.182343 0.806192

F 3.560807 -2.011303 0.011361

F 3.436815 0.094298 2.052145

O -3.799998 -2.403884 1.112667

O -4.081076 1.270667 -2.184808

N -3.847626 -0.446220 -0.410714

S -3.258061 0.874137 -1.072693

S -3.150360 -1.150156 0.833473

O -1.805893 0.900768 -1.228617

O -1.690819 -1.090558 0.850150

F -3.507804 1.989537 0.068377

F -3.553757 -0.181601 2.059004

Na 0.000375 0.029194 -0.170563

&END COORD

&KIND F

BASIS_SET TZVP-MOLOPT-GTH

POTENTIAL GTH-PBE-q7

&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 S

BASIS_SET TZVP-MOLOPT-GTH

POTENTIAL GTH-PBE-q6

&END KIND

&KIND N

BASIS_SET TZVP-MOLOPT-GTH

POTENTIAL GTH-PBE-q5

&END KIND

&KIND Na

BASIS_SET DZVP-MOLOPT-SR-GTH

POTENTIAL GTH-PBE-q9

&END KIND

&END SUBSYS

&END FORCE_EVAL

&MOTION

&GEO_OPT

OPTIMIZER LBFGS

MAX_ITER 300

&END GEO_OPT

&END MOTION

!&EXT_RESTART

Lucas Lodeiro

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Dec 11, 2020, 12:09:13 AM12/11/20

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Hi Dmitrii,

Remember that for non periodic calculations you have to set periodic none in poisson and cell sections. Also, the density have to be zero at edges for WAVELET solver, if not, the error

*** WARNING in pw/ps_wavelet_methods.F:236 :: Density non-zero on the ***
*** edges of the unit cell: wrong results in WAVELET solver ***

If you use a big cell (as yours, 30A it is a very big one, with 15A it is well) you can converge it without problems. But you have to center coordinates with &TOPOLOGY &CENTER_COORDINATES.

....

27 Broy./Diag. 0.40E+00 2.4 0.00000030 -333.3086580732 -1.34E-06
28 Broy./Diag. 0.40E+00 2.3 0.00000015 -333.3086567857 1.29E-06
29 Broy./Diag. 0.40E+00 2.3 0.00000008 -333.3086557587 1.03E-06

Regards

Lucas Lodeiro

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DMITRII Drugov

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Dec 12, 2020, 4:31:41 AM12/12/20

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Thanks for reply! Do you think I just need to add the following to my input of geometry optimisation?

&TOPOLOGY

&CENTER_COORDINATES

&END CENTER_COORDINATES

COORD_FILE_NAME name.xyz

COORD_FILE_FORMAT XYZ

&END

I remember I always had this error with periodic None and poison wavelet:

*** WARNING in pw/ps_wavelet_methods.F:236 :: Density non-zero on the ***

*** edges of the unit cell: wrong results in WAVELET solver ***

Do you know what if you avoid specification of periodicity type and poison algorithm, how CP2K consider you system?

I could optimised system my system with only cell dimension 30 30 30 A. I even didn't add Alpha Betta Gamma!

However, when I used same system with periodic None and poison wavelet, I got that "Density non-zero on the" error.

I am just wondering what I should add to periodic and poison section if I do ab initio NVT/NPT of bulk liquid system.

Thank you,

Dmitrii

Lucas Lodeiro

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Dec 13, 2020, 12:02:48 AM12/13/20

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Yes, if you use Center_coordinates, the calculation work well with 30A and with 15A.

The default periodicity and Psolver in cp2k is XYZ and periodic, as you can see in the manual:

https://manual.cp2k.org/cp2k-7_1-branch/CP2K_INPUT/FORCE_EVAL/DFT/POISSON.html

https://manual.cp2k.org/cp2k-7_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#PERIODIC

https://manual.cp2k.org/cp2k-7_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#list_ALPHA_BETA_GAMMA

The wavelet solver needs that the system is centered in the cell, you can do it by hand or with the keyword.Wavelet is useful for non periodic calculations, and the periodic solver is useful for periodic calculations (In this case it is not necessary to center the system, due to the PBC).

Regards

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