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.offerm...@vito.be > On 23 Mar 2021, at 18:12, Carlos Reis <carlos.loia.r...@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.offerm...@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.offerm...@vito.be > > <vito.jpg> > >> 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> >> 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> >> 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.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";, >> 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@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@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@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@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@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users
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