<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">Dear Willem </span><br></div><div dir="ltr"><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><br></span></div><div><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">Thank you very much for your suggestion of themo_pw.</span></div><div><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><br></span></div><div><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">This package has a nice feature that does exactly what I want.</span></div><div><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><br></span></div><div><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">I ran thermo_pw with this control file</span></div><div><br></div><div>&INPUT_THERMO</div><div> find_ibrav=.TRUE.</div><div> what='scf',</div><div> /</div><div><br></div><div>using a pw.x input file with ibrav=0 , unit cell vectors and atomic positions referred to original vectors</div><div>(which is what I have) the program outputs the correct ibrav, celldm, and atomic positions referred to allat.</div><div><br></div><div>so apparently it solves my problem!</div><div><br></div><div>described here</div><div><br></div><div><a href="https://people.sissa.it/~dalcorso/thermo_pw/tutorial/node4.html">https://people.sissa.it/~dalcorso/thermo_pw/tutorial/node4.html</a><br></div><div><br></div><div>Best regards,</div><div>Carlos Reis.</div><div><br></div><div><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><br></span></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Mar 23, 2021 at 11:00 AM Offermans Willem <<a href="mailto:willem.offermans@vito.be">willem.offermans@vito.be</a>> wrote:<br></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 style="word-wrap:break-word;line-break:after-white-space"><div>Dear Carlos and Quantum Espresso friends,</div><div><br></div><div>In the past, I had severe problems with symmetry detection by Quantum Espresso.</div><div>I’m studying stepped surfaces, such as Pt(221) and Pt(533) with S_2 symmetry.</div><div>Depending on how I define the unit cell and the positions of the slab atoms therein,</div><div>QE could or could not detect right symmetry.</div><div><br></div><div>Someone pointed out to use gener_3d_slab tool from thermo_pw to generate</div><div>the structures. Indeed, the structures generated by gener_3d_slab are better</div><div>handled by QE with respect to symmetry detection, but it is not 100% user proof.</div><div>Even now, I have systems where I start with relaxing a structure with S2 symmetry, </div><div>but loosing the symmetry upon restarts of the calculations. In the latter case, I need</div><div>to redefine the positions of the slab atoms to regenerate the right symmetry.</div><div><br></div><div>B.t.w. thermo_pw is located here:</div><div><br></div><div><a href="https://github.com/dalcorso/thermo_pw" target="_blank">https://github.com/dalcorso/thermo_pw</a> </div><div><br></div><div><br></div><div><br></div><br><div>
<div dir="auto" style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;word-wrap:break-word;line-break:after-white-space"><div dir="auto" style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;word-wrap:break-word;line-break:after-white-space"><div dir="auto" style="word-wrap:break-word;line-break:after-white-space"><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">Met vriendelijke groeten,</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">Mit freundlichen Grüßen,</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">With kind regards,</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">Willem Offermans</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">Researcher Electrocatalysis SCT</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">VITO NV | Boeretang 200 | 2400 Mol</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">Phone:+32(0)14335263 Mobile:+32(0)492182073 </div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><a href="mailto:Willem.Offermans@Vito.be" target="_blank">Willem.Offermans@Vito.be</a></div></div></div></div><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span><img id="gmail-m_-6012299818464717377925E0F-5EC3-4BE4-8633-80B5D4992F41" src="cid:178600bdfaa605dda611"></span>
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<div><br><blockquote type="cite"><div>On 23 Mar 2021, at 10:45, Carlos Reis <<a href="mailto:carlos.loia.reis@gmail.com" target="_blank">carlos.loia.reis@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Dear Paolo<div><br></div><div>Thank you very much for your feedback.</div><div><br></div><div>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><br></div><div>Best regards,</div><div>Carlos Reis.</div><div><br></div></div><br><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" target="_blank">p.giannozzi@gmail.com</a>> wrote:<br></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"><div>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></div><div> ibrav = 7, celldm(1) = 16.22739617, celldm(3) = 0.6324556</div><div>corresponding to crystal axes (alat units)<br> a(1) = ( 0.500000 -0.500000 0.316228 )<br> a(2) = ( 0.500000 0.500000 0.316228 )<br> a(3) = ( -0.500000 -0.500000 0.316228 )</div><div>with atomic positions (no warranty):<br></div><div>ATOMIC_POSITIONS {alat}<br> Si 0.0000000 0.0000000 0.0000000<br> Si 0.4000000 0.8000000 0.0000000<br> Si 0.6000000 0.2000000 0.0000000<br> Si 0.2000000 0.4000000 0.0000000<br> Si 1.0000000 0.5000000 0.1581139<br> Si 0.6000000 0.7000000 0.1581139<br> Si 0.4000000 0.3000000 0.1581139<br> Si 0.2000000 -0.1000000 0.1581139<br> C 0.8000000 0.6000000 0.0000000<br> C 0.8000000 0.1000000 0.1581139</div><div><br></div><div>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></div><div><br></div><div>Paolo<br></div></div><br><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">p.giannozzi@gmail.com</a>> wrote:<br></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"><div>Very strange. I have opened an item in the "Issues" section:</div><div> <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" target="_blank">https://gitlab.com/QEF/q-e/-/issues/301</a></div><div>Paolo</div><div><br></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">carlos.loia.reis@gmail.com</a>> wrote:<br></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"><div dir="ltr"><div dir="ltr"><font face="monospace">Hello<br><br>I use this file to perform a scf calculation<br><br>&CONTROL<br> calculation = 'scf',<br> pseudo_dir = '.',<br> wf_collect = .true.,<br>/<br>&SYSTEM<br> ibrav = 14,<br> celldm(1) = 16.22739617<br> celldm(2) = 1.00000000<br> celldm(3) = 0.77459667<br> celldm(4) = 0.64549723<br> celldm(5) = 0.64549723<br> nat = 10 ,<br> ntyp = 2 ,<br> nbnd = 28 ,<br> ecutwfc = 30.000 ,<br>/<br>&ELECTRONS<br> diagonalization = 'david',<br>/<br>ATOMIC_SPECIES<br>Si 28.085500 Si.UPF<br>C 12.011000 C.UPF<br>ATOMIC_POSITIONS {crystal}<br> Si -0.00000000 -0.00000000 0.00000000<br> Si 0.40000000 0.80000000 0.00000000<br> Si 0.60000000 0.20000000 0.00000000<br> Si 0.20000000 0.40000000 0.00000000<br> Si 0.75000000 0.25000000 0.50000000<br> Si 0.35000000 0.45000000 0.50000000<br> Si 0.15000000 0.05000000 0.50000000<br> Si -0.05000000 -0.35000000 0.50000000<br> C 0.80000000 0.60000000 0.00000000<br> C 0.55000000 -0.15000000 0.50000000<br>K_POINTS {automatic}<br> 4 4 4 1 1 1<br></font><div><font face="monospace"><br></font></div><div><font face="monospace">and then I run ph.x with this input file:</font></div><div><font face="monospace"><br></font></div><div><div><font face="monospace">--</font></div><div><font face="monospace">&inputph</font></div><div><font face="monospace"> prefix = 'pwscf',</font></div><div><font face="monospace"> epsil = .false.,</font></div><div><font face="monospace"> fildyn = 'pwscf.dyn',</font></div><div><font face="monospace"> ldisp = .true.</font></div><div><font face="monospace"> fildvscf = 'dvscf'</font></div><div><font face="monospace"> nq1=1,<br></font></div><div><font face="monospace"> nq2=1,</font></div><div><font face="monospace"> nq3=1,</font></div><div><font face="monospace"> /<br></font></div></div><div><font face="monospace"><br></font></div><div><div><font face="monospace"> Program PHONON v.6.7MaX starts on 16Mar2021 at 17:18:57</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> This program is part of the open-source Quantum ESPRESSO suite</font></div><div><font face="monospace"> for quantum simulation of materials; please cite</font></div><div><font face="monospace"> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);</font></div><div><font face="monospace"> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);</font></div><div><font face="monospace"> 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" target="_blank">http://www.quantum-espresso.org</a>",</font></div><div><font face="monospace"> in publications or presentations arising from this work. More details at</font></div><div><font face="monospace"> <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" target="_blank">http://www.quantum-espresso.org/quote</a></font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> Parallel version (MPI), running on 16 processors</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> MPI processes distributed on 1 nodes</font></div><div><font face="monospace"> K-points division: npool = 16</font></div><div><font face="monospace"> Waiting for input...</font></div><div><font face="monospace"> Reading input from standard input</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> Reading xml data from directory:</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> ./pwscf.save/</font></div><div><font face="monospace"> file C.UPF: wavefunction(s) 3d renormalized</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> IMPORTANT: XC functional enforced from input :</font></div><div><font face="monospace"> Exchange-correlation= PZ</font></div><div><font face="monospace"> ( 1 1 0 0 0 0 0)</font></div><div><font face="monospace"> Any further DFT definition will be discarded</font></div><div><font face="monospace"> Please, verify this is what you really want</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> G-vector sticks info</font></div><div><font face="monospace"> --------------------</font></div><div><font face="monospace"> sticks: dense smooth PW G-vecs: dense smooth PW</font></div><div><font face="monospace"> Sum 2521 2521 821 30009 30009 5631</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> Reading collected, re-writing distributed wavefunctions</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> Dynamical matrices for ( 1, 1, 1) uniform grid of q-points</font></div><div><font face="monospace"> ( 1 q-points):</font></div><div><font face="monospace"> N xq(1) xq(2) xq(3)</font></div><div><font face="monospace"> 1 0.000000000 0.000000000 0.000000000</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> Saving dvscf to file. Distribute only q points, not irreducible represetations.</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> Calculation of q = 0.0000000 0.0000000 0.0000000</font></div><div><font face="monospace"> warning: symmetry operation # 2 not compatible with FFT grid.</font></div><div><font face="monospace"> 1 0 0</font></div><div><font face="monospace"> 0 1 0</font></div><div><font face="monospace"> 1 1 -1</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</font></div><div><font face="monospace"> Error in routine phq_setup (1):</font></div><div><font face="monospace"> FFT grid incompatible with symmetry</font></div><div><font face="monospace"> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</font></div></div><div><font face="monospace"><br></font></div><div><font face="monospace"><br></font></div><div><font face="monospace">Is there any way to easily fix this? should I have to manually specify nr1, nr2, nr3?</font></div><div><font face="monospace"><br></font></div><div><font face="monospace">Any help is appreciated.</font></div><div><font face="monospace"><br></font></div><div><font face="monospace">Best regards,</font></div><div><font face="monospace">Carlos Reis.</font></div><div><font face="monospace"><br></font></div><div><font face="monospace"><br></font></div><div><font face="monospace"><br></font></div></div></div></div>
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<a href="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" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div><br clear="all"><br>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>Univ. Udine, via delle Scienze 206, 33100 Udine, Italy<br>Phone +39-0432-558216, fax +39-0432-558222<br><br></div></div></div></div></div></div>
</blockquote></div><br clear="all"><br>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>Univ. Udine, via delle Scienze 206, 33100 Udine, Italy<br>Phone +39-0432-558216, fax +39-0432-558222<br><br></div></div></div></div></div>
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_______________________________________________<br>Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" target="_blank">www.max-centre.eu</a>)<br>users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></div></blockquote></div><br></div>_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu" rel="noreferrer" target="_blank">www.max-centre.eu</a>)<br>
users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div>