[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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