[CP2K-user] [CP2K:19428] Re: CELL_OPT for periodic crystal
fabia...@gmail.com
fabianducry at gmail.com
Wed Oct 25 13:34:05 UTC 2023
Hi Ashley,
For some reason USE_FINER_GRID T in the &XC_GRID causes the internal
pressure to explode. Try removing it and maybe increase the CUTOFF instead.
Cheers,
Fabian
On Tuesday, 24 October 2023 at 16:48:44 UTC+2 Ashley Dickson wrote:
> This is the input file using the crystallography data:
>
> &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
>
>
> SCALED
>
> Y 0.5 0.5 0.5
>
> Ba 0.5 0.5 0.18393
>
> Cu 0 0 0
>
> Cu 0 0 0.35501
>
> O 0 0.5 0
>
> O 0.5 0 0.37819
>
> O 0 0.5 0.37693
>
> O 0 0 0.15840
>
> &END COORD
>
> &TOPOLOGY
>
>
>
>
>
> &END TOPOLOGY
>
> &CELL
>
> SYMMETRY ORTHORHOMBIC
>
> ABC 3.8203 3.88548 11.68349
>
> PERIODIC XYZ
>
> &CELL_REF
>
>
> ABC 14 14 28
>
>
> &END CELL_REF
>
> &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 CG
>
> KEEP_ANGLES
>
>
> EXTERNAL_PRESSURE [Pa] 100000
>
>
>
> &END CELL_OPT
>
>
>
>
>
>
>
>
> &END MOTION
>
> There was no initial warning, the cell just continued to shrink and the
> SCF did converge. The output file is attached.
>
>
> Thanks
>
> Ash
>
> On Tuesday, 24 October 2023 at 15:41:13 UTC+1 fabia... at gmail.com wrote:
>
>> 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
>>>>>>>>
>>>>>>>
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