[QE-users] Problem with ph.x
Carlos Reis
carlos.loia.reis at gmail.com
Tue Mar 23 18:12:29 CET 2021
Dear Willem
Thank you very much for your suggestion of themo_pw.
This package has a nice feature that does exactly what I want.
I ran thermo_pw with this control file
&INPUT_THERMO
find_ibrav=.TRUE.
what='scf',
/
using a pw.x input file with ibrav=0 , unit cell vectors and atomic
positions referred to original vectors
(which is what I have) the program outputs the correct ibrav, celldm, and
atomic positions referred to allat.
so apparently it solves my problem!
described here
https://people.sissa.it/~dalcorso/thermo_pw/tutorial/node4.html
Best regards,
Carlos Reis.
On Tue, Mar 23, 2021 at 11:00 AM Offermans Willem <willem.offermans at vito.be>
wrote:
> 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>
> 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>
>> 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>
>>> 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>
>>>> ",
>>>> in publications or presentations arising from this work. More
>>>> details at
>>>> http://www.quantum-espresso.org/quote
>>>> <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.quantum-espresso.org%2Fquote&data=04%7C01%7C%7C3e970cb398c54300185008d8ede08d6b%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C1%7C637520896009287289%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=4Oqhdt5NF54XRdTs%2F%2BV7mAKE0uFgGVMRU6yt3aJjPQw%3D&reserved=0>
>>>>
>>>> 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>
>>>> )
>>>> users mailing list users at lists.quantum-espresso.org
>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>> <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers&data=04%7C01%7C%7C3e970cb398c54300185008d8ede08d6b%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C1%7C637520896009297283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=g6csiaIYbw01zI2KzV%2F%2FqiOnS%2BTAEdiC5ooOwCDP5Js%3D&reserved=0>
>>>
>>>
>>>
>>> --
>>> 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>
>> )
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>> <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers&data=04%7C01%7C%7C3e970cb398c54300185008d8ede08d6b%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C1%7C637520896009307282%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=YiI72LBhBJ0iY66gUvuzzvL5urceFP55eIfjhhuvcDY%3D&reserved=0>
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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