[CP2K-user] [CP2K:19429] Re: CELL_OPT for periodic crystal
Ashley Dickson
ashleydickson141 at gmail.com
Wed Oct 25 13:59:28 UTC 2023
Hi Fabian,
I will try removing that now. thanks so much for the help!
Cheers
Ash
On Wednesday, 25 October 2023 at 14:34:05 UTC+1 fabia... at gmail.com wrote:
> 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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