[CP2K-user] [CP2K:16800] Re: Cell Optimization of Platinum (Pt) with fcc (111) surface
GENG YUAN
yuangeng0821 at gmail.com
Fri Apr 1 14:56:20 UTC 2022
Hi Sumit,
As far as I know, it is because you use PBC, so the inappropriate size of
the simulation box may bring some atoms too close when this box is
duplicated in all directions (Assume PBC in all directions).
Could you share one example of your system (e.g. XYZ file may be perfect)
so we can have a look?
Sincerely,
Geng
在2022年3月31日星期四 UTC-4 05:58:24<sumitag... at gmail.com> 写道：
> Hi Geng,
>
> Thanks for your gentle reply. One more query.
>
> Can you tell me how to choose a simulation box size (In &CELL of input
> file)? Suppose if my lattice dimension for crystal a=b=c is 5 Å. And if I
> use the same length for my simulation box (In section &CELL of my input
> file) , then one error appears ("atoms are too close"). Then I increase the
> simulation box length to 6 or 7 Å (in my &CELL section), then this error is
> disappear. Here I am using PBC for my simulation.
>
> So can you comment on this observation? How far can we go from lattice
> dimension for selecting the simulation box size?
>
> Thanks
> sumit
>
>
>
>
>
> On Wed, Mar 30, 2022 at 12:12 AM GENG YUAN <yuange... at gmail.com> wrote:
>
>> Hi Sumit,
>>
>> Thanks for your query, actually we used Avogadro Package to build this
>> 111 structure preciously and the cell size is therefore taken from the
>> information shown on the Avogadro package. But later we found that this
>> structure is not what we want and we don't think it is correct/suitable for
>> our simulations. So I would say the cell size in the above input file is
>> not correct.
>>
>> Many thanks,
>> Geng
>>
>> 在2022年3月28日星期一 UTC-4 02:32:59<sumitag... at gmail.com> 写道：
>>
>>> Hii Geng,
>>>
>>> I have little query regarding cell size. Why you consider cell size 13.7
>>> Å. Because from your input lattice structure(pt134.xyz) the cell
>>> dimension is r~12.2 Å.
>>>
>>>
>>> On Tuesday, January 4, 2022 at 2:04:56 AM UTC+5:30 GENG YUAN wrote:
>>>
>>>> Dear CP2K Users,
>>>>
>>>> Hope you are going great and happy new year.
>>>>
>>>> I am running the cell optimization for a single bulk Pt (134 atoms)
>>>> with fcc 111 surface. By checking my output file, I notice that the cell
>>>> optimization takes 446 steps to converge (which is almost close to the
>>>> maximum number of optimization steps:500). Besides, a certain degree of
>>>> structure deformation is observed during optimization (please see the
>>>> attached files and screenshots).
>>>>
>>>> I am wondering if there are any other ways to let the cell optimization
>>>> converge faster (in other words, converge in fewer steps) and whether the
>>>> above-mentioned deformation looks reasonable?
>>>> Below is the input: (attached are input file, output file, original
>>>> coordinate, trajectory, and the screenshots of the trajectory)
>>>> ------------------------------------------------------------
>>>> &GLOBAL
>>>> PROJECT Pt_cellopt
>>>> RUN_TYPE CELL_OPT
>>>> PRINT_LEVEL LOW
>>>> &END GLOBAL
>>>> &FORCE_EVAL
>>>> METHOD QS
>>>> STRESS_TENSOR ANALYTICAL
>>>> &SUBSYS
>>>> &CELL
>>>> ABC 13.7 13.7 13.7
>>>> SYMMETRY CUBIC
>>>> &CELL_REF
>>>> ABC 13.7*1.5 13.7*1.5 13.7*1.5
>>>> &END
>>>> &END CELL
>>>> &TOPOLOGY
>>>> COORD_FILE_NAME ./Pt134.xyz
>>>> COORDINATE xyz
>>>> &END
>>>> &KIND Pt
>>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>>> POTENTIAL GTH-PBE-q18
>>>> &END KIND
>>>> &END SUBSYS
>>>> &DFT
>>>> BASIS_SET_FILE_NAME ./BASIS_MOLOPT
>>>> POTENTIAL_FILE_NAME ./GTH_POTENTIALS
>>>> &QS
>>>> EPS_DEFAULT 1.0E-12
>>>> &END QS
>>>> &MGRID
>>>> CUTOFF 400
>>>> NGRIDS 5
>>>> REL_CUTOFF 40
>>>> &END MGRID
>>>> &SCF
>>>> SCF_GUESS ATOMIC
>>>> EPS_SCF 1.0E-06
>>>> MAX_SCF 200
>>>> ADDED_MOS 100
>>>> &OUTER_SCF
>>>> MAX_SCF 50
>>>> EPS_SCF 1.0E-6
>>>> &END
>>>> &DIAGONALIZATION T
>>>> ALGORITHM STANDARD
>>>> &END DIAGONALIZATION
>>>> &MIXING T
>>>> METHOD BROYDEN_MIXING
>>>> ALPHA 0.1
>>>> NBROYDEN 8
>>>> &END MIXING
>>>> &SMEAR ON
>>>> METHOD FERMI_DIRAC
>>>> ELECTRONIC_TEMPERATURE [K] 500
>>>> &END SMEAR
>>>> &PRINT
>>>> &RESTART ON
>>>> &END RESTART
>>>> &END PRINT
>>>> &END SCF
>>>> &XC
>>>> &XC_FUNCTIONAL
>>>> &LIBXC
>>>> FUNCTIONAL XC_GGA_X_PBE_R
>>>> &END
>>>> &LIBXC
>>>> FUNCTIONAL XC_GGA_C_PBE
>>>> &END
>>>> &END XC_FUNCTIONAL
>>>> &VDW_POTENTIAL
>>>> POTENTIAL_TYPE PAIR_POTENTIAL
>>>> &PAIR_POTENTIAL
>>>> LONG_RANGE_CORRECTION
>>>> PARAMETER_FILE_NAME dftd3.dat
>>>> TYPE DFTD3
>>>> REFERENCE_FUNCTIONAL revPBE
>>>> &END PAIR_POTENTIAL
>>>> &END VDW_POTENTIAL
>>>> &XC_GRID
>>>> XC_DERIV NN50_SMOOTH
>>>> &END XC_GRID
>>>> &END XC
>>>> &END DFT
>>>> &END FORCE_EVAL
>>>> &MOTION
>>>> &CELL_OPT
>>>> EXTERNAL_PRESSURE 0
>>>> TYPE DIRECT_CELL_OPT
>>>> KEEP_SYMMETRY TRUE
>>>> MAX_DR 1.0E-05
>>>> MAX_FORCE 1.0E-05
>>>> RMS_DR 1.0E-05
>>>> RMS_FORCE 1.0E-05
>>>> MAX_ITER 500
>>>> OPTIMIZER BFGS
>>>> &END CELL_OPT
>>>> &END MOTION
>>>>
>>>> Many thanks in advance,
>>>> Sincerely,
>>>> Geng
>>>>
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