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

Vivek Christhunathan vivekppn at gmail.com
Thu Feb 3 16:55:16 CET 2022


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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