[QE-users] Problem with ph.x
Offermans Willem
willem.offermans at vito.be
Tue Mar 23 12:00:18 CET 2021
Dear Carlos and Quantum Espresso friends,
In the past, I had severe problems with symmetry detection by Quantum Espresso.
I’m studying stepped surfaces, such as Pt(221) and Pt(533) with S_2 symmetry.
Depending on how I define the unit cell and the positions of the slab atoms therein,
QE could or could not detect right symmetry.
Someone pointed out to use gener_3d_slab tool from thermo_pw to generate
the structures. Indeed, the structures generated by gener_3d_slab are better
handled by QE with respect to symmetry detection, but it is not 100% user proof.
Even now, I have systems where I start with relaxing a structure with S2 symmetry,
but loosing the symmetry upon restarts of the calculations. In the latter case, I need
to redefine the positions of the slab atoms to regenerate the right symmetry.
B.t.w. thermo_pw is located here:
https://github.com/dalcorso/thermo_pw
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
> On 23 Mar 2021, at 10:45, Carlos Reis <carlos.loia.reis at gmail.com> wrote:
>
> Dear Paolo
>
> Thank you very much for your feedback.
>
> Is there any tool that I can use to convert the unit cell vectors and atomic positions in a format so that q-e recognize the correct symmetry and generates the appropriate input for q-e?
>
> Best regards,
> Carlos Reis.
>
>
> On Mon, Mar 22, 2021 at 8:50 PM Paolo Giannozzi <p.giannozzi at gmail.com <mailto:p.giannozzi at gmail.com>> wrote:
> Well, no, it's the same problem that was reported some time ago. Your lattice has a higher symmetry (tetragonal I) than triclinic (ibrav=14):
> ibrav = 7, celldm(1) = 16.22739617, celldm(3) = 0.6324556
> corresponding to crystal axes (alat units)
> a(1) = ( 0.500000 -0.500000 0.316228 )
> a(2) = ( 0.500000 0.500000 0.316228 )
> a(3) = ( -0.500000 -0.500000 0.316228 )
> with atomic positions (no warranty):
> ATOMIC_POSITIONS {alat}
> Si 0.0000000 0.0000000 0.0000000
> Si 0.4000000 0.8000000 0.0000000
> Si 0.6000000 0.2000000 0.0000000
> Si 0.2000000 0.4000000 0.0000000
> Si 1.0000000 0.5000000 0.1581139
> Si 0.6000000 0.7000000 0.1581139
> Si 0.4000000 0.3000000 0.1581139
> Si 0.2000000 -0.1000000 0.1581139
> C 0.8000000 0.6000000 0.0000000
> C 0.8000000 0.1000000 0.1581139
>
> The symmetry searching algorithm detects one symmetry, in addition to the identity, and this is compatible with the FFT grid computed for the tetragonal I lattice (48 48 48: the three lattice vectors have the same length), but not for the triclinic lattice (60 60 48: two vectors have the same length, different from the third).
>
> Paolo
>
> On Mon, Mar 22, 2021 at 9:35 AM Paolo Giannozzi <p.giannozzi at gmail.com <mailto:p.giannozzi at gmail.com>> wrote:
> Very strange. I have opened an item in the "Issues" section:
> https://gitlab.com/QEF/q-e/-/issues/301 <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgitlab.com%2FQEF%2Fq-e%2F-%2Fissues%2F301&data=04%7C01%7C%7C3e970cb398c54300185008d8ede08d6b%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C1%7C637520896009277291%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=jl2RQMMdINdF%2Funia4Q%2F1rj%2FD3P1XPyOjMMbMY%2Fe%2FsA%3D&reserved=0>
> Paolo
>
> On Tue, Mar 16, 2021 at 7:26 PM Carlos Reis <carlos.loia.reis at gmail.com <mailto:carlos.loia.reis at gmail.com>> wrote:
> Hello
>
> I use this file to perform a scf calculation
>
> &CONTROL
> calculation = 'scf',
> pseudo_dir = '.',
> wf_collect = .true.,
> /
> &SYSTEM
> ibrav = 14,
> celldm(1) = 16.22739617
> celldm(2) = 1.00000000
> celldm(3) = 0.77459667
> celldm(4) = 0.64549723
> celldm(5) = 0.64549723
> nat = 10 ,
> ntyp = 2 ,
> nbnd = 28 ,
> ecutwfc = 30.000 ,
> /
> &ELECTRONS
> diagonalization = 'david',
> /
> ATOMIC_SPECIES
> Si 28.085500 Si.UPF
> C 12.011000 C.UPF
> ATOMIC_POSITIONS {crystal}
> Si -0.00000000 -0.00000000 0.00000000
> Si 0.40000000 0.80000000 0.00000000
> Si 0.60000000 0.20000000 0.00000000
> Si 0.20000000 0.40000000 0.00000000
> Si 0.75000000 0.25000000 0.50000000
> Si 0.35000000 0.45000000 0.50000000
> Si 0.15000000 0.05000000 0.50000000
> Si -0.05000000 -0.35000000 0.50000000
> C 0.80000000 0.60000000 0.00000000
> C 0.55000000 -0.15000000 0.50000000
> K_POINTS {automatic}
> 4 4 4 1 1 1
>
> and then I run ph.x with this input file:
>
> --
> &inputph
> prefix = 'pwscf',
> epsil = .false.,
> fildyn = 'pwscf.dyn',
> ldisp = .true.
> fildvscf = 'dvscf'
> nq1=1,
> nq2=1,
> nq3=1,
> /
>
> Program PHONON v.6.7MaX starts on 16Mar2021 at 17:18:57
>
> 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 <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.quantum-espresso.org%2F&data=04%7C01%7C%7C3e970cb398c54300185008d8ede08d6b%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C1%7C637520896009287289%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rOZrqPqvGT%2BQImKZ4wNCI033D2AiNFgh948QsjBrNuQ%3D&reserved=0>",
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>
> Parallel version (MPI), running on 16 processors
>
> MPI processes distributed on 1 nodes
> K-points division: npool = 16
> Waiting for input...
> Reading input from standard input
>
> Reading xml data from directory:
>
> ./pwscf.save/
> file C.UPF: wavefunction(s) 3d renormalized
>
> IMPORTANT: XC functional enforced from input :
> Exchange-correlation= PZ
> ( 1 1 0 0 0 0 0)
> Any further DFT definition will be discarded
> Please, verify this is what you really want
>
>
> G-vector sticks info
> --------------------
> sticks: dense smooth PW G-vecs: dense smooth PW
> Sum 2521 2521 821 30009 30009 5631
>
> Reading collected, re-writing distributed wavefunctions
>
>
> Dynamical matrices for ( 1, 1, 1) uniform grid of q-points
> ( 1 q-points):
> N xq(1) xq(2) xq(3)
> 1 0.000000000 0.000000000 0.000000000
>
> Saving dvscf to file. Distribute only q points, not irreducible represetations.
>
> Calculation of q = 0.0000000 0.0000000 0.0000000
> warning: symmetry operation # 2 not compatible with FFT grid.
> 1 0 0
> 0 1 0
> 1 1 -1
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine phq_setup (1):
> FFT grid incompatible with symmetry
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>
> Is there any way to easily fix this? should I have to manually specify nr1, nr2, nr3?
>
> Any help is appreciated.
>
> Best regards,
> Carlos Reis.
>
>
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2F&data=04%7C01%7C%7C3e970cb398c54300185008d8ede08d6b%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C1%7C637520896009297283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=S252VMrRkZGUReX8FVAWyU7WKhIIEd6mqKHQfX7IaFc%3D&reserved=0>)
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>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2F&data=04%7C01%7C%7C3e970cb398c54300185008d8ede08d6b%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C1%7C637520896009297283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=S252VMrRkZGUReX8FVAWyU7WKhIIEd6mqKHQfX7IaFc%3D&reserved=0>)
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