[CP2K-user] [CP2K:19416] Re: CELL_OPT for periodic crystal
fabia...@gmail.com
fabianducry at gmail.com
Tue Oct 24 14:41:13 UTC 2023
The coordinates above are not a super cell from for same crystal as the
one from the database. I suggest that you use the correct unit cell again.
Did cp2k produce any warning during your initial cell optimization (the one
that shrunk)? Did the scf properly converge? Without seeing the output it
is difficult to help.
You should probably decrease ALPHA to 0.1 or 0.2, ADDED_MOS 700 is
excessive, 10 should be enough.
Fabian
On Tuesday, 24 October 2023 at 16:35:11 UTC+2 Ashley Dickson wrote:
> 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
>>>>>>
>>>>>
--
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/990ab6f9-a826-42af-968c-2b3e6364db85n%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20231024/2224ee60/attachment.htm>
More information about the CP2K-user
mailing list