[QE-users] Crystal structure changes while doing vc-relax calculation.

Vivek Christhunathan vivekppn at gmail.com
Wed Feb 9 12:44:22 CET 2022


Hi Michal,

Thank you very much for your suggestion.


*>crystal_sg  and correct space gropu nuber (space_group)>Correct ibrav
will be generated automatically , no need to eneter ...*


The space group number of CaWO4 unit-cell (ICSD no: 18135) is 88 since it
has I41/a space-group, but the Space group number of CaWO4 supercell (2x1x1)
is 1 as it has P1 space-group name (Note: I used VESTA tool make supercell).
I tried with both the sapace-group numbers. I received an error called "Error
in routine check_atoms (1): atoms # 1 and # 62 overlap!" when I used
space_group=88. I think this is because of the space-group changes when we
make supercell from the CaWO4 unit-cell (using VESTA tool).

In v6.4.1, I used space_group=1 for the calculation but again symmetry of
the supercell changes (a≠b). I have included my input for your reference.





























































































*&controlcalculation = 'vc-relax'restart_mode = 'from_scratch'prefix =
'CaWO4'pseudo_dir = './'outdir = './outCaWO4'max_seconds =
3500,/&systemcelldm(1) = 19.820415celldm(2) = 0.500000000celldm(3) =
1.084549393space_group = 1nat = 48ntyp = 3ecutwfc = 65.0ecutrho =
780.0occupations= 'smearing'smearing= 'gaussian'degauss=
0.02/&electronsmixing_beta = 0.2,conv_thr = 1.0d-6,electron_maxstep =
50000,/&IONS/&cellcell_factor = 3.0d0/ATOMIC_SPECIES Ca 40.08
Ca.pbe-spn-rrkjus_psl.1.0.0.UPF W  183.84  W.pbe-spn-rrkjus_psl.1.0.0.UPF O
 16.00   O.pbe-n-rrkjus_psl.1.0.0.UPFATOMIC_POSITIONS (crystal_sg)Ca
0.000000000         0.250000000         0.625000000Ca     0.500000000
  0.250000000         0.625000000Ca     0.000000000         0.750000000
    0.375000000Ca     0.500000000         0.750000000         0.375000000Ca
    0.250000000         0.750000000         0.125000000Ca     0.750000000
      0.750000000         0.125000000Ca     0.250000000         0.250000000
        0.875000000Ca     0.750000000         0.250000000
0.875000000 W     0.000000000         0.250000000         0.125000000 W
0.500000000         0.250000000         0.125000000 W     0.000000000
  0.750000000         0.875000000 W     0.500000000         0.750000000
    0.875000000 W     0.250000000         0.750000000         0.625000000 W
    0.750000000         0.750000000         0.625000000 W     0.250000000
      0.250000000         0.375000000 W     0.750000000         0.250000000
        0.375000000 O     0.074850000         0.009300000
0.209700003 O     0.574850023         0.009300000         0.209700003 O
0.425150007         0.990700006         0.790300012 O     0.925150037
  0.990700006         0.790300012 O     0.175150007         0.990700006
    0.709699988 O     0.675150037         0.990700006         0.709699988 O
    0.324849993         0.009300000         0.290300012 O     0.824849963
      0.009300000         0.290300012 O     0.370350003         0.399699986
        0.459699988 O     0.870350003         0.399699986
0.459699988 O     0.129649997         0.600300014         0.540300012 O
0.629649997         0.600300014         0.540300012 O     0.379649997
  0.600300014         0.959699988 O     0.879649997         0.600300014
    0.959699988 O     0.120350003         0.399699986         0.040299997 O
    0.620350003         0.399699986         0.040299997 O     0.324849993
      0.509299994         0.709699988 O     0.824849963         0.509299994
        0.709699988 O     0.175150007         0.490700006
0.290300012 O     0.675150037         0.490700006         0.290300012 O
0.425150007         0.490700006         0.209700003 O     0.925150037
  0.490700006         0.209700003 O     0.074850000         0.509299994
    0.790300012 O     0.574850023         0.509299994         0.790300012 O
    0.120350003         0.899699986         0.959699988 O     0.620350003
      0.899699986         0.959699988 O     0.379649997         0.100299999
        0.040299997 O     0.879649997         0.100299999
0.040299997 O     0.129649997         0.100299999         0.459699988 O
0.629649997         0.100299999         0.459699988 O     0.370350003
  0.899699986         0.540300012 O     0.870350003         0.899699986
    0.540300012K_POINTS AUTOMATIC2 2 2 1 1 1 *

Can anyone please explain why my system 'CaWO4 supercell' keep on changing
its symmetry and why I am not able to control it?

Thanks in advance.

Kind Regards,

Vivek C


__________________________________

Vivek Christhunathan

PhD researcher

Mechanical Engineering

College of Engineering and Informatics

Alice Perry Engineering Building

National University of Ireland Galway, Ireland
E-mail: v.christhunathan1 at nuigalway.ie
Phone: +353 899811181, +91 9600752742



On Mon, Feb 7, 2022 at 3:47 PM Vivek Christhunathan <vivekppn at gmail.com>
wrote:

> Hi Lorenzo,
>
> >$scan_ibrav.x
>
> I tried it on my machine, and it printed exactly the same as your prior
> message.
>
> I received the following cell parameter values when I run the calculation
> with these tags such as ibrav = 8, celldm( 1) = 19.820415000, celldm( 2)
> = 0.500000000, and celldm( 3) = 1.084549393.
>
> *CELL_PARAMETERS (alat= 19.82041500)*
>
> *   1.013661333   0.000011180  -0.000000334*
>
> *   0.000005590   0.506839078   0.000000525*
> *  -0.000000363   0.000001138   1.097952283*
>
> And also I received the following cell parameter values when I run the
> calculation with these tags such as ibrav = 8, celldm( 1) = 19.820415000, celldm(
> 2) = 0.500000000, celldm( 3) = 1.084549393, and *cell_dofree = 'ibrav' *(Note:
> I included cell_dofree here because ibrav>0).
>
> *ibrav =      8*
>
> * celldm(1) =     20.00638452*
>
> * celldm(2) =      0.50013749*
>
> * celldm(3) =      1.08713582*
>
> *Input lattice vectors:*
>
> *     1.00938273     0.00000000     0.00000000*
>
> *     0.00000000     0.50483015     0.00000000*
>
> *     0.00000000     0.00000000     1.09733611*
>
> *New lattice vectors in INITIAL alat:*
>
> *     1.00938273     0.00000000     0.00000000*
>
> *     0.00000000     0.50483015     0.00000000*
>
> *     0.00000000     0.00000000     1.09733611*
>
> *New lattice vectors in NEW alat (for information only):*
>
> *     1.00000000     0.00000000     0.00000000*
>
> *     0.00000000     0.50013749     0.00000000*
>
> *     0.00000000     0.00000000     1.08713582*
>
> *Discrepancy in bohr =     0.000000    0.000000    0.000000*
>
>
> *     bfgs converged in  11 scf cycles and  10 bfgs steps*
>
> *     (criteria: energy <  1.0E-04 Ry, force <  1.0E-03Ry/Bohr, cell <
> 5.0E-01kbar)*
>
>
> *     End of BFGS Geometry Optimization*
>
>
> *     Final enthalpy =   -2905.7085616081 Ry*
>
> *Begin final coordinates*
>
> *     new unit-cell volume =   4353.90605 a.u.^3 (   645.18230 Ang^3 )*
>
> *     density =      5.92828 g/cm^3*
>
>
> *CELL_PARAMETERS (alat= 19.82041500)*
>
> *   1.009382726   0.000000000   0.000000000*
>
> *   0.000000000   0.504830148   0.000000000*
>
> *   0.000000000   0.000000000   1.097336114*
>
> Still I don't get the Tetragonal crystal structure of CaWO4, it only gives
> the lattice parameter values a=5.291688 ang and b=5.293143 ang (a≠b).
>  Note: Tetrahedra CaWO4 Unit-cell was used to make this CaWO4 supercell. Is
> there any other way to relax CaWO4's structure without affecting its
> symmetry?
>
> And also I'm not sure why ibrav = 8 is required if CaWO4 has a tetragonal
> crystal structure. Because ibrav = 8 for Orthorhombic is described in the
> QE-input description. It would be great if you could explain this to me.
>
> Thank you very much in advance.
>
> Kind Regards,
>
> Vivek C
>
>
> __________________________________
>
> Vivek Christhunathan
>
> PhD researcher
>
> Mechanical Engineering
>
> College of Engineering and Informatics
>
> Alice Perry Engineering Building
>
> National University of Ireland Galway
>
> Ireland
> E-mail: v.christhunathan1 at nuigalway.ie
> Phone: +353 899811181, +91 9600752742
>
>
>
>
> On Thu, Feb 3, 2022 at 3:55 PM Vivek Christhunathan <vivekppn at gmail.com>
> wrote:
>
>> Hi Lorenzo,
>>
>> Thank you very much for your response.
>>
>> Sorry for the earlier message. I did not get notified on this.
>>
>> >$ ~/espresso.BASE/PW/tools/scan_ibrav.x
>>
>> Yes, I will get used to it on this.
>>
>> As per your suggestion, I will use the following values for my
>> calculation and let you know the results.
>>
>> ibrav = 8
>> celldm( 1) = 19.820415000
>> celldm( 2) = 0.500000000
>> celldm( 3) = 1.084549393
>> at1 19.820415 0.000000 0.000000
>> at2 0.000000 9.910207 0.000000
>> at3 0.000000 0.000000 21.496219
>>
>>
>> Thanks a million.
>>
>> Kind Regards,
>>
>> Vivek C
>>
>>
>> __________________________________
>>
>> Vivek Christhunathan
>>
>> PhD researcher
>>
>> Mechanical Engineering
>>
>> College of Engineering and Informatics
>>
>> Room 2053
>>
>> Alice Perry Engineering Building
>>
>> National University of Ireland Galway
>>
>> Ireland
>> E-mail: v.christhunathan1 at nuigalway.ie
>> Phone: +353 899811181, +91 9600752742
>>
>>
>>
>> On Thu, Feb 3, 2022 at 2:05 PM Vivek Christhunathan <vivekppn at gmail.com>
>> wrote:
>>
>>> Hello Everyone,
>>>
>>> I could not solve this issue even after trying with v6.8 (the older
>>> version was v6.4.1). Still, the CaWO4 (2x1x1 supercell) changes its
>>> symmetry from Tetragonal to Orthorhombic while doing structural
>>> relaxation. Even I tried with multiple different input parameters.
>>>
>>> Can I get any suggestions regarding this, please?
>>>
>>> Kind Regards,
>>>
>>> Vivek C
>>>
>>>
>>> __________________________________
>>>
>>> Vivek Christhunathan
>>>
>>> PhD researcher
>>>
>>> Mechanical Engineering
>>>
>>> College of Engineering and Informatics
>>>
>>> Room 2053
>>>
>>> Alice Perry Engineering Building
>>>
>>> National University of Ireland Galway
>>>
>>> Ireland
>>> E-mail: v.christhunathan1 at nuigalway.ie
>>> Phone: +353 899811181, +91 9600752742
>>>
>>>
>>>
>>> On Tue, Feb 1, 2022 at 12:52 PM Vivek Christhunathan <vivekppn at gmail.com>
>>> wrote:
>>>
>>>> Hello Everyone,
>>>>
>>>> I'm bringing attention to a topic that has previously been discussed in
>>>> this forum. I too faced the same type of problem when I try to do
>>>> structural relaxation for CaWO4 (2x1x1 supercell), that its crystal
>>>> structure changed from Tetragonal to Orthorhombic. I tried all the
>>>> following forum's suggestions to get rid of this problem.
>>>>
>>>> As per their suggestion, I tried using the following tags in my input
>>>> file,
>>>>
>>>>
>>>>
>>>>
>>>> *>ion_dynamics = 'damp'>and>cell_dynamics = "damp-pr">which should
>>>> respect the constraint.*
>>>>
>>>> And also I tried using *cell_dofree=‘ibrav'*. but still lattice
>>>> parameter values a and b are not the same. Still, its structure changes
>>>> from Tetragonal to Orthorhombic.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> *>You can open Modules/cell_base.f90 and at line 84 change>LOGICAL   ::
>>>> enforce_ibrav = .FALSE.! True if ibrav ...>to>LOGICAL   :: enforce_ibrav =
>>>> .TRUE.! True if ibrav ...>(do not forget to recompile pw.x) to use
>>>> cell_dofree="ibrav" together with any >other cell_dofree*
>>>>
>>>> Since I'm utilizing the Government's supercomputer cluster, I'm not
>>>> sure how I'd make these adjustments to the QE code. Can I get your
>>>> suggestion regarding this?
>>>>
>>>>
>>>>
>>>> *>Should be present in the available patches for v.6.4.1:
>>>> filebackports-6.4.1.diff*
>>>>
>>>> <https://github.com/QEF/q-e/releases/download/qe-6.4.1/backports-6.4.1.diff>
>>>> in https://github.com/QEF/q-e/releases
>>>>
>>>>
>>>> Could you please advise me on how to proceed with this link?
>>>>
>>>> I have included calculations input and output for your perusal.
>>>>
>>>> If you could share your thoughts on this issue, that would be quite
>>>> helpful.
>>>>
>>>> *Input:*
>>>>
>>>> &control
>>>> calculation = 'vc-relax'
>>>> restart_mode = 'restart'
>>>> prefix = 'CaWO4'
>>>> tstress = .true.
>>>> tprnfor = .true.
>>>> pseudo_dir = './'
>>>> outdir = './outCaWO4'
>>>> wf_collect=.true.
>>>> forc_conv_thr = 1d-4
>>>> etot_conv_thr = 1D-4
>>>> !disk_io = 'medium'
>>>> max_seconds = 7200,
>>>> /
>>>>
>>>> &system
>>>> ibrav = 0
>>>> *celldm(1) = 19.820415*
>>>> nat = 48
>>>> ntyp = 3
>>>> ecutwfc = 65.0
>>>> ecutrho = 780.0
>>>> occupations= 'smearing'
>>>> smearing= 'gaussian'
>>>> degauss= 0.02
>>>> /
>>>>
>>>> &electrons
>>>> mixing_beta = 0.2,
>>>> conv_thr = 1.0d-6,
>>>> electron_maxstep = 50000,
>>>> /
>>>>
>>>> &IONS
>>>> *ion_dynamics = 'damp'*
>>>>
>>>> /
>>>>
>>>> &cell
>>>> cell_factor = 3.0d0
>>>> *cell_dynamics = 'damp-pr'*
>>>> !cell_dofree= 'ibrav'
>>>> /
>>>>
>>>> ATOMIC_SPECIES
>>>>  Ca 40.08   Ca.pbe-spn-rrkjus_psl.1.0.0.UPF
>>>>  W  183.84  W.pbe-spn-rrkjus_psl.1.0.0.UPF
>>>>  O  16.00   O.pbe-n-rrkjus_psl.1.0.0.UPF
>>>>
>>>> *CELL_PARAMETERS (alat)*
>>>> *        1.0000000000         0.0000000000         0.0000000000*
>>>> *        0.0000000000         0.4999999999         0.0000000000*
>>>> *        0.0000000000         0.0000000000         1.0845493931*
>>>>
>>>> ATOMIC_POSITIONS (crystal)
>>>> Ca     0.000000000         0.250000000         0.625000000
>>>> Ca     0.500000000         0.250000000         0.625000000
>>>> Ca     0.000000000         0.750000000         0.375000000
>>>> Ca     0.500000000         0.750000000         0.375000000
>>>> Ca     0.250000000         0.750000000         0.125000000
>>>> Ca     0.750000000         0.750000000         0.125000000
>>>> Ca     0.250000000         0.250000000         0.875000000
>>>> Ca     0.750000000         0.250000000         0.875000000
>>>>  W     0.000000000         0.250000000         0.125000000
>>>>  W     0.500000000         0.250000000         0.125000000
>>>>  W     0.000000000         0.750000000         0.875000000
>>>>  W     0.500000000         0.750000000         0.875000000
>>>>  W     0.250000000         0.750000000         0.625000000
>>>>  W     0.750000000         0.750000000         0.625000000
>>>>  W     0.250000000         0.250000000         0.375000000
>>>>  W     0.750000000         0.250000000         0.375000000
>>>>  O     0.074850000         0.009300000         0.209700003
>>>>  O     0.574850023         0.009300000         0.209700003
>>>>  O     0.425150007         0.990700006         0.790300012
>>>>  O     0.925150037         0.990700006         0.790300012
>>>>  O     0.175150007         0.990700006         0.709699988
>>>>  O     0.675150037         0.990700006         0.709699988
>>>>  O     0.324849993         0.009300000         0.290300012
>>>>  O     0.824849963         0.009300000         0.290300012
>>>>  O     0.370350003         0.399699986         0.459699988
>>>>  O     0.870350003         0.399699986         0.459699988
>>>>  O     0.129649997         0.600300014         0.540300012
>>>>  O     0.629649997         0.600300014         0.540300012
>>>>  O     0.379649997         0.600300014         0.959699988
>>>>  O     0.879649997         0.600300014         0.959699988
>>>>  O     0.120350003         0.399699986         0.040299997
>>>>  O     0.620350003         0.399699986         0.040299997
>>>>  O     0.324849993         0.509299994         0.709699988
>>>>  O     0.824849963         0.509299994         0.709699988
>>>>  O     0.175150007         0.490700006         0.290300012
>>>>  O     0.675150037         0.490700006         0.290300012
>>>>  O     0.425150007         0.490700006         0.209700003
>>>>  O     0.925150037         0.490700006         0.209700003
>>>>  O     0.074850000         0.509299994         0.790300012
>>>>  O     0.574850023         0.509299994         0.790300012
>>>>  O     0.120350003         0.899699986         0.959699988
>>>>  O     0.620350003         0.899699986         0.959699988
>>>>  O     0.379649997         0.100299999         0.040299997
>>>>  O     0.879649997         0.100299999         0.040299997
>>>>  O     0.129649997         0.100299999         0.459699988
>>>>  O     0.629649997         0.100299999         0.459699988
>>>>  O     0.370350003         0.899699986         0.540300012
>>>>  O     0.870350003         0.899699986         0.540300012
>>>>
>>>> K_POINTS AUTOMATIC
>>>> 2 2 2 1 1 1
>>>>
>>>> *Output (a scf loop from output file):*
>>>>
>>>>  atom   48 type  3   force =     0.00003185   -0.00002222   -0.00008890
>>>>
>>>>      Total force =     0.000633     Total SCF correction =     0.000137
>>>>      SCF correction compared to forces is large: reduce conv_thr to get
>>>> better values
>>>>
>>>>
>>>>      Computing stress (Cartesian axis) and pressure
>>>>
>>>>
>>>>      negative rho (up, down):  1.178E+00 0.000E+00
>>>>           total   stress  (Ry/bohr**3)                   (kbar)     P=
>>>>   0.04
>>>>    0.00000050  -0.00000019  -0.00000004          0.07     -0.03
>>>>   -0.01
>>>>   -0.00000019   0.00000058  -0.00000002         -0.03      0.08
>>>>   -0.00
>>>>   -0.00000004  -0.00000002  -0.00000017         -0.01     -0.00
>>>>   -0.02
>>>>
>>>>
>>>>      number of scf cycles    =  14
>>>>      number of bfgs steps    =  13
>>>>
>>>>      enthalpy old            =   -2905.7085634122 Ry
>>>>      enthalpy new            =   -2905.7085638929 Ry
>>>>
>>>>      CASE: enthalpy_new < enthalpy_old
>>>>
>>>>      new trust radius        =       0.0005206840 bohr
>>>> WARNING! With ibrav=0, cell_dofree='ibrav' does not have any effect.
>>>>      new conv_thr            =       0.0000000100 Ry
>>>>
>>>>      new unit-cell volume =   4353.65352 a.u.^3 (   645.14488 Ang^3 )
>>>>      density =      5.92862 g/cm^3
>>>>
>>>> *CELL_PARAMETERS (alat= 19.82041500)*
>>>> *   1.009431575   0.000035319   0.000001684*
>>>> *   0.000017655   0.504836574   0.000001702*
>>>> *   0.000001845   0.000003719   1.097205402*
>>>>
>>>> ATOMIC_POSITIONS (crystal)
>>>> Ca       0.000001762   0.249997612   0.625000246
>>>> Ca       0.500002903   0.249995682   0.624999551
>>>> Ca      -0.000001762   0.750002388   0.374999754
>>>> Ca       0.499997097   0.750004318   0.375000449
>>>> Ca       0.249995760   0.750002886   0.125000569
>>>> Ca       0.749997044   0.750001219   0.124998286
>>>> Ca       0.250002956   0.249998781   0.875001714
>>>> Ca       0.750004240   0.249997114   0.874999431
>>>> W       -0.000007775   0.250005618   0.125011626
>>>> W        0.499993856   0.250003532   0.125006749
>>>> W        0.000007775   0.749994382   0.874988374
>>>> W        0.500006144   0.749996468   0.874993251
>>>> W        0.250000614   0.749987294   0.625009963
>>>> W        0.750012640   0.750006266   0.625006514
>>>> W        0.249987360   0.249993734   0.374993486
>>>> W        0.749999386   0.250012706   0.374990037
>>>> O        0.074741741   0.007038639   0.209937560
>>>> O        0.574740434   0.007045102   0.209936159
>>>> O        0.425259596   0.992954904   0.790063856
>>>> O        0.925258296   0.992961367   0.790062455
>>>> O        0.175252613   0.992959249   0.709941460
>>>> O        0.675260736   0.992953207   0.709933905
>>>> O        0.324739294   0.007046799   0.290066095
>>>> O        0.824747357   0.007040757   0.290058540
>>>> O        0.371508681   0.399412719   0.459931561
>>>> O        0.871509937   0.399409012   0.459929597
>>>> O        0.128490063   0.600590988   0.540070403
>>>> O        0.628491319   0.600587281   0.540068439
>>>> O        0.378491935   0.600589896   0.959931149
>>>> O        0.878493035   0.600590218   0.959930080
>>>> O        0.121506965   0.399409782   0.040069905
>>>> O        0.621508065   0.399410104   0.040068836
>>>> O        0.324753467   0.507030327   0.709936158
>>>> O        0.824758249   0.507031484   0.709937563
>>>> O        0.175241721   0.492968516   0.290062437
>>>> O        0.675246563   0.492969673   0.290063842
>>>> O        0.425243174   0.492974405   0.209938014
>>>> O        0.925241517   0.492963083   0.209937166
>>>> O        0.074758520   0.507036917   0.790062849
>>>> O        0.574756856   0.507025595   0.790062001
>>>> O        0.121518578   0.899409145   0.959930613
>>>> O        0.621518989   0.899409438   0.959931475
>>>> O        0.378481011   0.100590547   0.040068510
>>>> O        0.878481422   0.100590840   0.040069372
>>>> O        0.128480180   0.100591392   0.459933045
>>>> O        0.628486141   0.100588990   0.459929416
>>>> O        0.371513859   0.899410995   0.540070584
>>>> O        0.871519820   0.899408593   0.540066955
>>>>
>>>>
>>>>
>>>>      Writing output data file CaWO4.save/
>>>>      NEW-OLD atomic charge density approx. for the potential
>>>>
>>>>      negative rho (up, down):  1.178E+00 0.000E+00
>>>>      extrapolated charge  384.00680, renormalised to  384.00000
>>>>
>>>>      total cpu time spent up to now is     3371.9 secs
>>>>
>>>>      Self-consistent Calculation
>>>>
>>>>      iteration #  1     ecut=    65.00 Ry     beta= 0.20
>>>>      Davidson diagonalization with overlap
>>>>      ethr =  1.00E-06,  avg # of iterations =  2.0
>>>>
>>>>
>>>> Thanks in advance.
>>>>
>>>> Kind Regards,
>>>>
>>>> Vivek C
>>>>
>>>>
>>>> __________________________________
>>>>
>>>> Vivek Christhunathan
>>>>
>>>> PhD researcher
>>>>
>>>> Mechanical Engineering
>>>>
>>>> College of Engineering and Informatics
>>>>
>>>> Room 2053
>>>>
>>>> Alice Perry Engineering Building
>>>>
>>>> National University of Ireland Galway
>>>>
>>>> Ireland
>>>> E-mail: v.christhunathan1 at nuigalway.ie
>>>> Phone: +353 899811181, +91 9600752742
>>>>
>>>>
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