[CP2K-user] [CP2K:19413] Re: CELL_OPT for periodic crystal
fabia...@gmail.com
fabianducry at gmail.com
Tue Oct 24 14:24:47 UTC 2023
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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