<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Dear Carlos and Quantum Espresso friends,</div><div class=""><br class=""></div><div class="">In the past, I had severe problems with symmetry detection by Quantum Espresso.</div><div class="">I’m studying stepped surfaces, such as Pt(221) and Pt(533) with S_2 symmetry.</div><div class="">Depending on how I define the unit cell and the positions of the slab atoms therein,</div><div class="">QE could or could not detect right symmetry.</div><div class=""><br class=""></div><div class="">Someone pointed out to use gener_3d_slab tool from thermo_pw to generate</div><div class="">the structures. Indeed, the structures generated by gener_3d_slab are better</div><div class="">handled by QE with respect to symmetry detection, but it is not 100% user proof.</div><div class="">Even now, I have systems where I start with relaxing a structure with S2 symmetry, </div><div class="">but loosing the symmetry upon restarts of the calculations. In the latter case, I need</div><div class="">to redefine the positions of the slab atoms to regenerate the right symmetry.</div><div class=""><br class=""></div><div class="">B.t.w. thermo_pw is located here:</div><div class=""><br class=""></div><div class=""><a href="https://github.com/dalcorso/thermo_pw" class="">https://github.com/dalcorso/thermo_pw</a> </div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><br class=""><div class="">
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<div><br class=""><blockquote type="cite" class=""><div class="">On 23 Mar 2021, at 10:45, Carlos Reis <<a href="mailto:carlos.loia.reis@gmail.com" class="">carlos.loia.reis@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="ltr" class="">Dear Paolo<div class=""><br class=""></div><div class="">Thank you very much for your feedback.</div><div class=""><br class=""></div><div class="">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?</div><div class=""><br class=""></div><div class="">Best regards,</div><div class="">Carlos Reis.</div><div class=""><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 22, 2021 at 8:50 PM Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" class="">p.giannozzi@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div class="">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):<br class=""></div><div class=""> ibrav = 7, celldm(1) = 16.22739617, celldm(3) = 0.6324556</div><div class="">corresponding to crystal axes (alat units)<br class=""> a(1) = ( 0.500000 -0.500000 0.316228 )<br class=""> a(2) = ( 0.500000 0.500000 0.316228 )<br class=""> a(3) = ( -0.500000 -0.500000 0.316228 )</div><div class="">with atomic positions (no warranty):<br class=""></div><div class="">ATOMIC_POSITIONS {alat}<br class=""> Si 0.0000000 0.0000000 0.0000000<br class=""> Si 0.4000000 0.8000000 0.0000000<br class=""> Si 0.6000000 0.2000000 0.0000000<br class=""> Si 0.2000000 0.4000000 0.0000000<br class=""> Si 1.0000000 0.5000000 0.1581139<br class=""> Si 0.6000000 0.7000000 0.1581139<br class=""> Si 0.4000000 0.3000000 0.1581139<br class=""> Si 0.2000000 -0.1000000 0.1581139<br class=""> C 0.8000000 0.6000000 0.0000000<br class=""> C 0.8000000 0.1000000 0.1581139</div><div class=""><br class=""></div><div class="">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).<br class=""></div><div class=""><br class=""></div><div class="">Paolo<br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 22, 2021 at 9:35 AM Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank" class="">p.giannozzi@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div class="">Very strange. I have opened an item in the "Issues" section:</div><div class=""> <a href="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" originalsrc="https://gitlab.com/QEF/q-e/-/issues/301" shash="PBpuyAWk0mcSi/INqJdgiSJtYz74YqlzkpFlhE7qoCH98vGS3/Tn/pEgLginaQyjm25L+qClqjjsfZpdtL3O1ba5w+VY9TLt1FMOO8oHr4pBu1rrbuPDDlb95ouxPEsbUqOLz7S2IgT/syScJ7XvUNugLIeK/w8a7b36bzN9iAU=" target="_blank" class="">https://gitlab.com/QEF/q-e/-/issues/301</a></div><div class="">Paolo</div><div class=""><br class=""></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Mar 16, 2021 at 7:26 PM Carlos Reis <<a href="mailto:carlos.loia.reis@gmail.com" target="_blank" class="">carlos.loia.reis@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><font face="monospace" class="">Hello<br class=""><br class="">I use this file to perform a scf calculation<br class=""><br class="">&CONTROL<br class=""> calculation = 'scf',<br class=""> pseudo_dir = '.',<br class=""> wf_collect = .true.,<br class="">/<br class="">&SYSTEM<br class=""> ibrav = 14,<br class=""> celldm(1) = 16.22739617<br class=""> celldm(2) = 1.00000000<br class=""> celldm(3) = 0.77459667<br class=""> celldm(4) = 0.64549723<br class=""> celldm(5) = 0.64549723<br class=""> nat = 10 ,<br class=""> ntyp = 2 ,<br class=""> nbnd = 28 ,<br class=""> ecutwfc = 30.000 ,<br class="">/<br class="">&ELECTRONS<br class=""> diagonalization = 'david',<br class="">/<br class="">ATOMIC_SPECIES<br class="">Si 28.085500 Si.UPF<br class="">C 12.011000 C.UPF<br class="">ATOMIC_POSITIONS {crystal}<br class=""> Si -0.00000000 -0.00000000 0.00000000<br class=""> Si 0.40000000 0.80000000 0.00000000<br class=""> Si 0.60000000 0.20000000 0.00000000<br class=""> Si 0.20000000 0.40000000 0.00000000<br class=""> Si 0.75000000 0.25000000 0.50000000<br class=""> Si 0.35000000 0.45000000 0.50000000<br class=""> Si 0.15000000 0.05000000 0.50000000<br class=""> Si -0.05000000 -0.35000000 0.50000000<br class=""> C 0.80000000 0.60000000 0.00000000<br class=""> C 0.55000000 -0.15000000 0.50000000<br class="">K_POINTS {automatic}<br class=""> 4 4 4 1 1 1<br class=""></font><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class="">and then I run ph.x with this input file:</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><div class=""><font face="monospace" class="">--</font></div><div class=""><font face="monospace" class="">&inputph</font></div><div class=""><font face="monospace" class=""> prefix = 'pwscf',</font></div><div class=""><font face="monospace" class=""> epsil = .false.,</font></div><div class=""><font face="monospace" class=""> fildyn = 'pwscf.dyn',</font></div><div class=""><font face="monospace" class=""> ldisp = .true.</font></div><div class=""><font face="monospace" class=""> fildvscf = 'dvscf'</font></div><div class=""><font face="monospace" class=""> nq1=1,<br class=""></font></div><div class=""><font face="monospace" class=""> nq2=1,</font></div><div class=""><font face="monospace" class=""> nq3=1,</font></div><div class=""><font face="monospace" class=""> /<br class=""></font></div></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><div class=""><font face="monospace" class=""> Program PHONON v.6.7MaX starts on 16Mar2021 at 17:18:57</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> This program is part of the open-source Quantum ESPRESSO suite</font></div><div class=""><font face="monospace" class=""> for quantum simulation of materials; please cite</font></div><div class=""><font face="monospace" class=""> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);</font></div><div class=""><font face="monospace" class=""> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);</font></div><div class=""><font face="monospace" class=""> URL <a href="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" originalsrc="http://www.quantum-espresso.org/" shash="j+syNcMPYwDse6Rb0tV5BhnL0pWqXIWhEm4pyWKbmPpxI0VDGa4Onq0z/lNOthvLoHr6KZL56keX/oT8STFx7kqVvOVZp/RGA13oAeVnZrkdChITEVqIz4h0dAB65L7zMzxNr6B0UX9g1d/OiReVSbRDHyphvEBTP/0I8EiqiCE=" target="_blank" class="">http://www.quantum-espresso.org</a>",</font></div><div class=""><font face="monospace" class=""> in publications or presentations arising from this work. More details at</font></div><div class=""><font face="monospace" class=""> <a href="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" originalsrc="http://www.quantum-espresso.org/quote" shash="cFjitMZpUaM6TGV+YPZPedle+aYPVn/r9O8Qc5jpOqnt+zOfVdFMM1vSaGS+zc3pgLDPVVuKZYfGcO8XYugV/1TApFtqzryz414qIm5QhljL1Pj1Ps2ZkCOkCScQRmV9hfb+9s7KZL60LGFBuiljsm2mhGlmZnsXh773vsuI7jo=" target="_blank" class="">http://www.quantum-espresso.org/quote</a></font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> Parallel version (MPI), running on 16 processors</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> MPI processes distributed on 1 nodes</font></div><div class=""><font face="monospace" class=""> K-points division: npool = 16</font></div><div class=""><font face="monospace" class=""> Waiting for input...</font></div><div class=""><font face="monospace" class=""> Reading input from standard input</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> Reading xml data from directory:</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> ./pwscf.save/</font></div><div class=""><font face="monospace" class=""> file C.UPF: wavefunction(s) 3d renormalized</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> IMPORTANT: XC functional enforced from input :</font></div><div class=""><font face="monospace" class=""> Exchange-correlation= PZ</font></div><div class=""><font face="monospace" class=""> ( 1 1 0 0 0 0 0)</font></div><div class=""><font face="monospace" class=""> Any further DFT definition will be discarded</font></div><div class=""><font face="monospace" class=""> Please, verify this is what you really want</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> G-vector sticks info</font></div><div class=""><font face="monospace" class=""> --------------------</font></div><div class=""><font face="monospace" class=""> sticks: dense smooth PW G-vecs: dense smooth PW</font></div><div class=""><font face="monospace" class=""> Sum 2521 2521 821 30009 30009 5631</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> Reading collected, re-writing distributed wavefunctions</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> Dynamical matrices for ( 1, 1, 1) uniform grid of q-points</font></div><div class=""><font face="monospace" class=""> ( 1 q-points):</font></div><div class=""><font face="monospace" class=""> N xq(1) xq(2) xq(3)</font></div><div class=""><font face="monospace" class=""> 1 0.000000000 0.000000000 0.000000000</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> Saving dvscf to file. Distribute only q points, not irreducible represetations.</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> Calculation of q = 0.0000000 0.0000000 0.0000000</font></div><div class=""><font face="monospace" class=""> warning: symmetry operation # 2 not compatible with FFT grid.</font></div><div class=""><font face="monospace" class=""> 1 0 0</font></div><div class=""><font face="monospace" class=""> 0 1 0</font></div><div class=""><font face="monospace" class=""> 1 1 -1</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</font></div><div class=""><font face="monospace" class=""> Error in routine phq_setup (1):</font></div><div class=""><font face="monospace" class=""> FFT grid incompatible with symmetry</font></div><div class=""><font face="monospace" class=""> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</font></div></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class="">Is there any way to easily fix this? should I have to manually specify nr1, nr2, nr3?</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class="">Any help is appreciated.</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class="">Best regards,</font></div><div class=""><font face="monospace" class="">Carlos Reis.</font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""><br class=""></font></div><div class=""><font face="monospace" class=""><br class=""></font></div></div></div></div>
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</blockquote></div><br clear="all" class=""><br class="">-- <br class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br class="">Univ. Udine, via delle Scienze 206, 33100 Udine, Italy<br class="">Phone +39-0432-558216, fax +39-0432-558222<br class=""><br class=""></div></div></div></div></div>
_______________________________________________<br class="">
Quantum ESPRESSO is supported by MaX (<a href="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" originalsrc="http://www.max-centre.eu/" shash="O0Y9/Hu4osZMWbvWAY+eXZMEql/GjpCSetV49SLltDCpcg19JJntKOlaWb6n9d8WYWfGCawHHH8uJV5Gvd904VCGs6TxrTjnep+V9cMTrU8zt9mcCYdfbFVumSLq2LX2UAma86yarlRSeGI9aFSpzl3axqAHJHShwNcJ3vwZN2I=" rel="noreferrer" target="_blank" class="">www.max-centre.eu</a>)<br class="">
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