[QE-users] No symmetry found
Offermans Willem
willem.offermans at vito.be
Mon Jun 3 12:21:48 CEST 2019
Dear Oleksandr and QE friends,
Is centering ( symmetrical with respect to z=0) of the supercell a general requirement? I do recall that I build up a Pd(111) slab, the same way as I did for the Pd(533) slab. In the Pd(111) case, I didn’t apply centering and the program (pw.x) was still able to detect and to use the inversion center.
Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,
Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073
Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>
[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local]
On 3 Jun 2019, at 11:13, Oleksandr Motornyi <oleksandr.motornyi at polytechnique.edu<mailto:oleksandr.motornyi at polytechnique.edu>> wrote:
Dear Willem
It is likely due to the fact that the slab in your supercell is not centered, i.e. your atoms coordinate along z axis spans from 1.14 to 12.54. I believe that if you want the code fo find inversion symmetry correctly you need it to be symmetrical with respect to z=0, i.e. it should span form h/2 to -h/2.
P.S. Also it is better to avoid using ibrav=0 and Cell params and use the ibrav value. I would recommend you to try and generate the slab using gener_3d_slab.x code of thermo_pw module (https://dalcorso.github.io/thermo_pw/)
Best regards,
Oleksandr
On 03/06/2019 11:01, Offermans Willem wrote:
Dear QE friends,
I’m calculating stepped Pd surfaces (Pd533).
My palladium slab model has an inversion center. I define one half of the atoms and generate the other half by using the inversion center.
The input and only part of the output file is given below.
pw.x program is not able to detect and to use the symmetry (inversion center).
At first, I thought I made a mistake in the definition. Running abinit with the same model showed me that the symmetry could be detected
and that the definition of the atomic positions is fine.
Why can't QE detect and use the symmetry?
<snip>
&CONTROL
verbosity = 'high'
tprnfor = .true.
pseudo_dir = './'
/
&SYSTEM
ecutwfc = 35
ecutrho = 140
occupations = 'smearing'
degauss = 1e-05
ntyp = 1
nat = 38
ibrav = 0
/
&ELECTRONS
electron_maxstep = 200
conv_thr = 0.0001
mixing_beta = 0.3
/
&IONS
/
&CELL
/
ATOMIC_SPECIES
Pd 106.42 Pd.pbe-n-kjpaw_psl.0.2.2.UPF
K_POINTS automatic
2 3 1 0 0 0
CELL_PARAMETERS angstrom
5.58600000000000 0.00000000000000 0.00000000000000
4.18950000000000 8.86896616015644 -2.28047495053114
0.00000000000000 0.00000000000000 18.24379960424911
ATOMIC_POSITIONS angstrom
Pd 4.1896396500 8.8680792635 1.1404655228
Pd 2.7930000000 0.0000000000 3.4207124258
Pd 1.3965000000 2.4188089528 3.4207124258
Pd 4.1895000000 2.4188089528 3.4207124258
Pd 2.7930000000 4.8376179055 3.4207124258
Pd 5.5860000000 4.8376179055 3.4207124258
Pd 4.1895000000 7.2564268583 3.4207124258
Pd 6.9825000000 7.2564268583 3.4207124258
Pd 1.3965000000 0.8062696509 5.7011873763
Pd 4.1895000000 0.8062696509 5.7011873763
Pd 2.7930000000 3.2250786037 5.7011873763
Pd 5.5860000000 3.2250786037 5.7011873763
Pd 4.1895000000 5.6438875565 5.7011873763
Pd 6.9825000000 5.6438875565 5.7011873763
Pd 5.5860000000 8.0626965092 5.7011873763
Pd 8.3790000000 8.0626965092 5.7011873763
Pd 2.7930000000 1.6125393018 7.9816623269
Pd 5.5860000000 1.6125393018 7.9816623269
Pd 4.1895000000 4.0313482546 7.9816623269
Pd 6.9825000000 4.0313482546 7.9816623269
Pd 5.5860000000 6.4501572074 7.9816623269
Pd 8.3790000000 6.4501572074 7.9816623269
Pd 2.7930000000 0.0000000000 10.2621372774
Pd -0.0000000000 0.0000000000 10.2621372774
Pd 4.1895000000 2.4188089528 10.2621372774
Pd 1.3965000000 2.4188089528 10.2621372774
Pd 5.5860000000 4.8376179055 10.2621372774
Pd 2.7930000000 4.8376179055 10.2621372774
Pd 6.9825000000 7.2564268583 10.2621372774
Pd 4.1895000000 7.2564268583 10.2621372774
Pd 4.1895000000 0.8062696509 12.5426122279
Pd 1.3965000000 0.8062696509 12.5426122279
Pd 5.5860000000 3.2250786037 12.5426122279
Pd 2.7930000000 3.2250786037 12.5426122279
Pd 6.9825000000 5.6438875565 12.5426122279
Pd 4.1895000000 5.6438875565 12.5426122279
Pd 8.3790000000 8.0626965092 12.5426122279
Pd 5.5858603500 8.0635834058 12.5423841804
</snip>
Part of the output:
<snip>
Program PWSCF v.6.2.2 starts on 3Jun2019 at 10:44:39
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
URL http://www.quantum-espresso.org<http://www.quantum-espresso.org/>",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Serial version
…
...
No symmetry found
s frac. trans.
isym = 1 identity
cryst. s( 1) = ( 1 0 0 )
( 0 1 0 )
( 0 0 1 )
cart. s( 1) = ( 1.0000000 0.0000000 0.0000000 )
( 0.0000000 1.0000000 0.0000000 )
( 0.0000000 0.0000000 1.0000000 )
…
...
</snip>
Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,
Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073
Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>
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--
Oleksandr Motornyi
PhD candidate
Laboratoire de Solides Irradies
Ecole Polytechnique (Palaiseau, France)
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