[CP2K-user] [CP2K:19417] Re: CELL_OPT for periodic crystal

Ashley Dickson ashleydickson141 at gmail.com
Tue Oct 24 14:48:44 UTC 2023
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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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