[CP2K-user] [CP2K:14376] What is CP2K periodicity settings by default without specification?
Lucas Lodeiro
eluni... at gmail.com
Sun Dec 13 05:02:21 UTC 2020
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
El sáb, 12 dic 2020 a las 6:31, DMITRII Drugov (<dresear... at gmail.com>)
escribió:
> 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
> On Friday, December 11, 2020 at 4:09:13 PM UTC+11 Lucas Lodeiro wrote:
>
>> 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
>>
>> El jue, 10 dic 2020 a las 21:51, DMITRII Drugov (<dre... at gmail.com>)
>> escribió:
>>
>>> 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
>>>
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