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 > > > 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 >>> <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> >>> 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 >>>> 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 >> 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 > > > _______________________________________________ > 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