[CP2K-user] [CP2K:19415] Re: CELL_OPT for periodic crystal
Ashley Dickson
ashleydickson141 at gmail.com
Tue Oct 24 14:35:11 UTC 2023
I feel like I'm not being very clear here apologies. So, I want to obtain a
reasonable value for the lattice parameter of YBCO. Using the current input
file but with the coordinates given on the crystallography database
website, I run into the issue that the simulation cell volume shrinks and
gives unphysical results. To my mind, this means it is not treating the
structure I have provided as periodic in space. How can I modify my input
such that it appears to cp2k that my unitcell is repeated in space?
On Tuesday, 24 October 2023 at 15:28:47 UTC+1 Ashley Dickson wrote:
> 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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