[CP2K-user] [CP2K:19412] Re: CELL_OPT for periodic crystal

[Ashley Dickson]

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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