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

Vivek Christhunathan vivekppn at gmail.com
Mon Feb 7 16:47:45 CET 2022


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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