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.offerm...@vito.be > On 23 Mar 2021, at 10:45, Carlos Reis <carlos.loia.r...@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.gianno...@gmail.com > <mailto:p.gianno...@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.gianno...@gmail.com > <mailto:p.gianno...@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.r...@gmail.com > <mailto:carlos.loia.r...@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@lists.quantum-espresso.org > <mailto:users@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@lists.quantum-espresso.org > <mailto:users@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@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users
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