[QE-users] Problem with ph.x
Offermans Willem
willem.offermans at vito.be
Wed Mar 24 08:54:14 CET 2021
Dear Carlos and Quantum Espresso friends,
I’m very happy to help you as I am grateful to the support
I receive from this mailing list.
However, I have a small request to you.
Could you elaborate a bit on exactly what you did.
As far as I understood you created the file, let’s say
“thermo.inp” with the following content:
<snip>
&INPUT_THERMO
find_ibrav=.TRUE.
what='scf',
/
</snip>
Then you ran `thermo_pw < thermo.inp` and you received
correct ibrav, celldm, and atomic positions referred to allat.
Is the above correct?
How did you “use a pw.x input file”?
Your reference does not provide this info either.
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 18:12, Carlos Reis <carlos.loia.reis at gmail.com> wrote:
>
> 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
>
> <vito.jpg>
>
>> 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
>> 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",
>> in publications or presentations arising from this work. More details at
>> http://www.quantum-espresso.org/quote
>>
>> 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)
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>
>>
>> --
>> 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)
>> 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
>
> _______________________________________________
> 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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