[CP2K-user] [CP2K:19414] Re: CELL_OPT for periodic crystal
Ashley Dickson
ashleydickson141 at gmail.com
Tue Oct 24 14:28:47 UTC 2023
http://www.crystallography.net/cod/1000030.html
This is the unit cell from the database. When I ran the cell optimisations
with this structure and cell parameters of ABC 3.8 3.9 11.7, the cell just
continually shrunk to an unreasonable size. I then tried opening the cif
file in vesta and exporting the whole unit cell as an xyz file, which is
where I got the current coordinates from.
Many thanks
Ash
On Tuesday, 24 October 2023 at 15:24:47 UTC+1 fabia... at gmail.com wrote:
> Is this the unit cell from the open crystallography database? If not, how
> have you modified it?
>
> Cheers,
> Fabian
>
> On Tuesday, 24 October 2023 at 16:16:45 UTC+2 Ashley Dickson wrote:
>
>> Hi Fabian
>>
>> I think this is the main issue that's confusing me. I have a unit cell of
>> YBCO with lattice parameters 3.8 3.9 11.7 (roughly), however increased the
>> cell size as it was not working. I realise my mistake is that the
>> periodicity of the cell results in the atoms being on top of each other. In
>> order that I can retrieve accurate lattice parameters for the bulk crystal
>> how should I modify the coordinates?
>>
>> Many thanks
>> Ash
>>
>> On Tuesday, 24 October 2023 at 15:10:24 UTC+1 fabia... at gmail.com wrote:
>>
>>> Hi Ashley,
>>>
>>> The ABC 4 4 12 seems a bit strange, are you sure this is correct? Two of
>>> the atoms are
>>>
>>> Cu 0 0 0
>>>
>>> Cu 3.820300 0.000000 11.683490
>>> if your lattice is indeed 4 4 12 these two are almost on top of each
>>> other. I expect the cell is much too small which is why its size keeps
>>> increasing.
>>>
>>> Also, did your scf converge and are there any warnings in the output?
>>>
>>> Cheers,
>>> Fabian
>>>
>>> On Tuesday, 24 October 2023 at 15:50:28 UTC+2 Ashley Dickson wrote:
>>>
>>>> I'm trying to perform a cell optimisation on a crystal of YBCO however
>>>> the calculations always seem to spit out nonsense (the cell volume
>>>> continually increases). I am using the structural data found on the open
>>>> crystallography database which should be accurate. Is there perhaps
>>>> something wrong with the unit cell I've chosen? The input is provided below:
>>>>
>>>> &FORCE_EVAL
>>>>
>>>> METHOD Quickstep
>>>>
>>>> &DFT
>>>>
>>>> BASIS_SET_FILE_NAME BASIS_MOLOPT
>>>>
>>>> POTENTIAL_FILE_NAME GTH_POTENTIALS
>>>>
>>>> LSD
>>>>
>>>> &POISSON
>>>>
>>>> POISSON_SOLVER PERIODIC
>>>>
>>>> PERIODIC XYZ
>>>>
>>>> &END POISSON
>>>>
>>>>
>>>>
>>>> &MGRID
>>>>
>>>> NGRIDS 5
>>>>
>>>> CUTOFF 800
>>>>
>>>> REL_CUTOFF 60
>>>>
>>>>
>>>>
>>>> &END MGRID
>>>>
>>>> &QS
>>>>
>>>> METHOD GPW
>>>>
>>>> EPS_PGF_ORB 1E-16
>>>>
>>>>
>>>>
>>>> &END QS
>>>>
>>>> &SCF
>>>>
>>>> &SMEAR ON
>>>>
>>>> ELECTRONIC_TEMPERATURE 1000
>>>>
>>>> METHOD FERMI_DIRAC
>>>>
>>>> &END SMEAR
>>>>
>>>> ADDED_MOS 700
>>>>
>>>> CHOLESKY INVERSE
>>>>
>>>> SCF_GUESS RESTART
>>>>
>>>> EPS_SCF 1.0E-6
>>>>
>>>> MAX_SCF 250
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> &DIAGONALIZATION ON
>>>>
>>>> ALGORITHM STANDARD
>>>>
>>>> &END DIAGONALIZATION
>>>>
>>>> &MIXING T
>>>>
>>>> METHOD BROYDEN_MIXING
>>>>
>>>> ALPHA 0.5
>>>>
>>>> BETA 1.5
>>>>
>>>> NBUFFER 15
>>>>
>>>>
>>>>
>>>> &END MIXING
>>>>
>>>>
>>>>
>>>> &END SCF
>>>>
>>>>
>>>> &KPOINTS
>>>>
>>>> SCHEME MONKHORST-PACK 2 2 2
>>>>
>>>> FULL_GRID yes
>>>>
>>>> SYMMETRY yes
>>>>
>>>> VERBOSE yes
>>>>
>>>> PARALLEL_GROUP_SIZE -1
>>>>
>>>> &END KPOINTS
>>>>
>>>>
>>>> &XC
>>>>
>>>> &XC_FUNCTIONAL PBE
>>>>
>>>> &END XC_FUNCTIONAL
>>>>
>>>> &XC_GRID
>>>>
>>>> USE_FINER_GRID T
>>>>
>>>> &END XC_GRID
>>>>
>>>> &END XC
>>>>
>>>>
>>>> &END DFT
>>>>
>>>> &SUBSYS
>>>>
>>>> &COORD
>>>>
>>>>
>>>> Cu 0 0 0
>>>>
>>>> Y 1.910150 1.942740 5.841745
>>>>
>>>> Ba 1.910150 1.942740 2.148944
>>>>
>>>> Ba 1.910150 1.942740 9.534546
>>>>
>>>> Cu 0.000000 0.000000 11.683490
>>>>
>>>> Cu 0.000000 3.885480 0.000000
>>>>
>>>> Cu 0.000000 3.885480 11.683490
>>>>
>>>> Cu 3.820300 0.000000 0.000000
>>>>
>>>> Cu 3.820300 0.000000 11.683490
>>>>
>>>> Cu 3.820300 3.885480 0.000000
>>>>
>>>> Cu 3.820300 3.885480 11.683490
>>>>
>>>> Cu 0.000000 0.000000 4.147756
>>>>
>>>> Cu 0.000000 3.885480 4.147756
>>>>
>>>> Cu 3.820300 0.000000 4.147756
>>>>
>>>> Cu 3.820300 3.885480 4.147756
>>>>
>>>> Cu 0.000000 0.000000 7.535734
>>>>
>>>> Cu 0.000000 3.885480 7.535734
>>>>
>>>> Cu 3.820300 0.000000 7.535734
>>>>
>>>> Cu 3.820300 3.885480 7.535734
>>>>
>>>> O 0.000000 1.942740 0.000000
>>>>
>>>> O 0.000000 1.942740 11.683490
>>>>
>>>> O 3.820300 1.942740 0.000000
>>>>
>>>> O 3.820300 1.942740 11.683490
>>>>
>>>> O 1.910150 0.000000 4.418579
>>>>
>>>> O 1.910150 3.885480 4.418579
>>>>
>>>> O 1.910150 0.000000 7.264911
>>>>
>>>> O 1.910150 3.885480 7.264911
>>>>
>>>> O 0.000000 1.942740 4.403858
>>>>
>>>> O 3.820300 1.942740 4.403858
>>>>
>>>> O 0.000000 1.942740 7.279632
>>>>
>>>> O 3.820300 1.942740 7.279632
>>>>
>>>> O 0.000000 0.000000 1.850665
>>>>
>>>> O 0.000000 3.885480 1.850665
>>>>
>>>> O 3.820300 0.000000 1.850665
>>>>
>>>> O 3.820300 3.885480 1.850665
>>>>
>>>> O 0.000000 0.000000 9.832825
>>>>
>>>> O 0.000000 3.885480 9.832825
>>>>
>>>> O 3.820300 0.000000 9.832825
>>>>
>>>> O 3.820300 3.885480 9.832825
>>>>
>>>>
>>>>
>>>>
>>>> &END COORD
>>>>
>>>> &TOPOLOGY
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> &END TOPOLOGY
>>>>
>>>> &CELL
>>>>
>>>> SYMMETRY ORTHORHOMBIC
>>>>
>>>> ABC 4 4 12
>>>>
>>>> PERIODIC XYZ
>>>>
>>>>
>>>>
>>>> &END CELL
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> &KIND O
>>>>
>>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>>>
>>>> POTENTIAL GTH-PBE-q6
>>>>
>>>> &END KIND
>>>>
>>>>
>>>>
>>>> &KIND Ba
>>>>
>>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>>>
>>>> POTENTIAL GTH-PBE-q10
>>>>
>>>> &END KIND
>>>>
>>>>
>>>>
>>>> &KIND Y
>>>>
>>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>>>
>>>> POTENTIAL GTH-PBE-q11
>>>>
>>>> &END KIND
>>>>
>>>>
>>>>
>>>> &KIND Cu
>>>>
>>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>>>
>>>> POTENTIAL GTH-PBE-q11
>>>>
>>>> &END KIND
>>>>
>>>> &PRINT
>>>>
>>>> &CELL HIGH
>>>>
>>>>
>>>> &END CELL
>>>>
>>>>
>>>> &END PRINT
>>>>
>>>>
>>>>
>>>> &END SUBSYS
>>>>
>>>> STRESS_TENSOR ANALYTICAL
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> &END FORCE_EVAL
>>>>
>>>> &GLOBAL
>>>>
>>>> PROJECT SZV
>>>>
>>>> RUN_TYPE CELL_OPT
>>>>
>>>> PRINT_LEVEL MEDIUM
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> &END GLOBAL
>>>>
>>>>
>>>>
>>>> &MOTION
>>>>
>>>>
>>>> &CELL_OPT
>>>>
>>>>
>>>> KEEP_SYMMETRY .TRUE.
>>>>
>>>> OPTIMIZER BFGS
>>>>
>>>> KEEP_ANGLES
>>>>
>>>>
>>>> EXTERNAL_PRESSURE [Pa] 100000
>>>>
>>>>
>>>>
>>>> &END CELL_OPT
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> &END MOTION
>>>>
>>>>
>>>> Many thanks for any help,
>>>> Ash
>>>>
>>>
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