<div dir="ltr"><div dir="ltr">On Thu, Feb 14, 2019 at 8:34 AM Offermans Willem <<a href="mailto:willem.offermans@vito.be">willem.offermans@vito.be</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;"><br><div>Probably you meant to refer to another mail thread. Probably the one started by Abdul Shaik.</div>
<div><a href="http://lists.quantum-espresso.org/pipermail/users/2019-February/042084.html" target="_blank">http://lists.quantum-espresso.org/pipermail/users/2019-February/042084.html</a></div></div></blockquote><div><br></div><div>yes, sorry, I cut-and-pasted the wrong address <br></div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">
<div>But can you explicitly make clear why it is not a good idea to have symmetry in a NEB calculation?
</div></div></blockquote><div><br></div><div>because unlike structural optimization there is no guarantee that the starting symmetry will be kept during the run. When initial symmetry is lost, you may end up with more k-points and the code crashes. Of course, if this does not happen, it is perfectly fine to use symmetry in NEB.<br></div><div style="overflow-wrap: break-word;"><br></div><div style="overflow-wrap: break-word;"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">So
neb.x is able to detect symmetry. Only in my particular case, it is not able to and I wonder why.
</blockquote><div><br></div><div>the reason has been explained no less than 1001 times: if the code does not find a symmetry, it's not there, according to the criteria implemented in the code. <br></div><div><br></div><div>Paolo</div><div><br>
</div>On 14 Feb 2019, at 07:55, Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>> wrote:<div><blockquote type="cite">
<br class="gmail-m_-5083536946599921354Apple-interchange-newline">
<div>
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<div dir="ltr">
<div dir="ltr">On Wed, Feb 13, 2019 at 10:07 PM Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>> wrote:</div>
<div dir="ltr"><br>
</div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">You can start a calculation from the files<span class="gmail-m_-5083536946599921354Apple-converted-space"> </span><a href="http://pw_1.in/" target="_blank">pw_1.in</a>,<span class="gmail-m_-5083536946599921354Apple-converted-space"> </span><a href="http://pw_2.in/" target="_blank">pw_2.in</a>,
etc., that the NEB code creates in the current execution directory. They contain input data for the starting points on the NEB chain. I did that and got no symmetry, by the way.<br>
</div>
</blockquote>
<div><br>
</div>
<div>and, by the way, this recent thread explains why it is not a good thing to have symmetry in NEB images:</div>
<div> <span class="gmail-m_-5083536946599921354Apple-converted-space"> </span><a href="http://lists.quantum-espresso.org/pipermail/users/2019-February/042111.html" target="_blank">http://lists.quantum-espresso.org/pipermail/users/2019-February/042111.html</a><br>
</div>
<div><br>
</div>
<div>Paolo</div>
<div><br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div class="gmail_quote"><br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div>
<div>$ pw.x -in pd.xml </div>
<div><br>
</div>
<div> Program PWSCF v.6.3 starts on 13Feb2019 at 11:49:38 </div>
<div><br>
</div>
<div> This program is part of the open-source Quantum ESPRESSO suite</div>
<div> for quantum simulation of materials; please cite</div>
<div> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);</div>
<div> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);</div>
<div> URL<span class="gmail-m_-5083536946599921354Apple-converted-space"> </span><a href="http://www.quantum-espresso.org/" target="_blank">http://www.quantum-espresso.org</a>", </div>
<div> in publications or presentations arising from this work. More details at</div>
<div> <a href="http://www.quantum-espresso.org/quote" target="_blank">http://www.quantum-espresso.org/quote</a></div>
<div><br>
</div>
<div> Parallel version (MPI & OpenMP), running on 20 processor cores</div>
<div> Number of MPI processes: 1</div>
<div> Threads/MPI process: 20</div>
<div><br>
</div>
<div> MPI processes distributed on 1 nodes</div>
<div> Reading xml input from pd.xml</div>
<div><br>
</div>
<div> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div>
<div> Error in routine read_input (1):</div>
<div> xml input disabled</div>
<div> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div>
<div><br>
</div>
<div> stopping ...</div>
<div>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0</div>
<div>[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1</div>
<div>:</div>
<div>system msg for write_line failure : Bad file descriptor</div>
</div>
<div><br>
</div>
<div>So I cannot easily play with the settings.</div>
<div><br>
</div>
<br>
<div>
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Met vriendelijke groeten,</div>
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Mit freundlichen Grüßen,</div>
<div style="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="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">
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Willem Offermans</div>
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Phone:+32(0)14335263 Mobile:+32(0)492182073 </div>
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<div><br>
<blockquote type="cite">
<div>On 13 Feb 2019, at 11:24, Offermans Willem <<a href="mailto:willem.offermans@vito.be" target="_blank">willem.offermans@vito.be</a>> wrote:</div>
<br class="gmail-m_-5083536946599921354gmail-m_235778290230378164gmail-m_2551177787507231359Apple-interchange-newline">
<div>
<div>Dear Stefano,
<div><br>
</div>
<div><br>
</div>
<div>No, point symmetry doesn’t depend on units, i.e. squeezing or expanding the system equally in all directions doesn’t change symmetry. I agree!</div>
<div><br>
</div>
<div>The presence of the inversion symmetry is not to save computational time, but to correct for possible dipole interactions.</div>
<div><br>
</div>
<div>Anyway, the point is that neb.x is not able to detect and to use the symmetry of the involved images. This is weird, since the task of optimising/calculating the images</div>
<div>will be delegated to pw.x, I suppose. And I showed that pw.x detects and uses the symmetry. Maybe the keyword ``use_all_frac = .true.`` is not considered for a NEB calculation.</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
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Met vriendelijke groeten,</div>
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Mit freundlichen Grüßen,</div>
<div style="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="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>
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Willem Offermans</div>
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Researcher Electrocatalysis SCT</div>
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Phone:+32(0)14335263 Mobile:+32(0)492182073 </div>
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<div><br>
<blockquote type="cite">
<div>On 13 Feb 2019, at 10:04, Stefano Baroni <<a href="mailto:baroni@sissa.it" target="_blank">baroni@sissa.it</a>> wrote:</div>
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<blockquote type="cite">
<div>On 13 Feb 2019, at 09:50, Offermans Willem <<a href="mailto:willem.offermans@vito.be" target="_blank">willem.offermans@vito.be</a>> wrote:</div>
<br class="gmail-m_-5083536946599921354gmail-m_235778290230378164gmail-m_2551177787507231359Apple-interchange-newline">
<div>
<div>
<div>Dear Quantum Espresso friends,</div>
</div>
</div>
</blockquote>
<div><br>
</div>
Dear Wilem:</div>
<div style="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>
<blockquote type="cite">
<div>
<div>
<div>I made a mistake in my previous e-mail.</div>
<div>The atom coordinates are not in Angstrom but in Bohr.</div>
</div>
</div>
</blockquote>
<blockquote type="cite">
<div>
<div>
<div><br>
</div>
<div>I have corrected this in my calculations, but still no symmetry found.</div>
</div>
</div>
</blockquote>
<div><br>
</div>
I would be surprised if you found the contrary. I cannot imagine that the point symmetry of any system could depend on units: do you?</div>
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<br>
<blockquote type="cite">
<div>
<div>
<div>$ grep "ymmetr" pd_?/PW.out </div>
<div>pd_1/PW.out: No symmetry found</div>
<div>pd_2/PW.out: No symmetry found</div>
<div>pd_3/PW.out: No symmetry found</div>
<div>pd_4/PW.out: No symmetry found</div>
<div>pd_5/PW.out: No symmetry found</div>
<div>pd_6/PW.out: No symmetry found</div>
<div>pd_7/PW.out: No symmetry found</div>
<div><br>
</div>
<div>So the question remains. What is the reason that the symmetry cannot be detected?</div>
<div><br>
</div>
<div>As an extra check I have made a scf calculation on the last image.</div>
<div><br>
</div>
<div>$ grep "Sym. Ops." pd.out </div>
<div> 2 Sym. Ops., with inversion, found ( 1 have fractional translation)</div>
<div><br>
</div>
<div>So pw.x can find the symmetry whereas neb.x cannot!</div>
</div>
</div>
</blockquote>
<div><br>
</div>
Just guessing: maybe for some reasons neb restricts its search to pure rotations (no fractional translations involved). Also, I have the impression that inversion symmetry does not help save any computer time, because in practice it has the same effects as
time-reversal symmetry, which always holds.</div>
<div style="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">
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Just my worthless 5 cents …</div>
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SB</div>
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<span class="gmail-m_-5083536946599921354gmail-m_235778290230378164gmail-m_2551177787507231359Apple-style-span" style="border-collapse:separate;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-alternates:normal;font-variant-east-asian:normal;line-height:normal;border-spacing:0px">
<div>
<div>
<div><span class="gmail-m_-5083536946599921354gmail-m_235778290230378164gmail-m_2551177787507231359Apple-style-span" style="border-collapse:separate;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-alternates:normal;font-variant-east-asian:normal;line-height:normal;text-indent:0px;border-spacing:0px"><span class="gmail-m_-5083536946599921354gmail-m_235778290230378164gmail-m_2551177787507231359Apple-style-span" style="border-collapse:separate;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-alternates:normal;font-variant-east-asian:normal;line-height:normal;text-indent:0px;border-spacing:0px">
<div>
<div><span style="font-size:12px">— </span></div>
<div>
<div>
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<div>
<div style="margin:0px"><font class="gmail-m_-5083536946599921354gmail-m_235778290230378164gmail-m_2551177787507231359Apple-style-span"><span style="font-size:12px">Stefano Baroni - Trieste — </span><a href="http://stefano.baroni.me/" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">http://stefano.baroni.me</a><span style="font-size:12px"> </span></font></div>
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<font size="-2" face="Arial, Helvetica, sans-serif" color="#999999">Indien u VITO Mol bezoekt, hou aub er dan rekening mee dat de hoofdingang voortaan enkel bereikbaar is vanuit de richting Dessel-Retie, niet vanuit richting Mol, zie<span class="gmail-m_-5083536946599921354Apple-converted-space"> </span><a href="http://www.vito.be/route" target="_blank">vito.be/route.</a><br>
If you plan to visit VITO at Mol, then please note that the main entrance can only be reached coming from Dessel-Retie and no longer coming from Mol, see<span class="gmail-m_-5083536946599921354Apple-converted-space"> </span><a href="http://www.vito.be/en/contact/locations" target="_blank">vito.be/en/contact/locations.</a><br>
</font><font size="-2" face="Arial, Helvetica, sans-serif" color="#999999">VITO Disclaimer:<span class="gmail-m_-5083536946599921354Apple-converted-space"> </span><a href="http://www.vito.be/e-maildisclaimer" target="_blank"><font color="#999999">http://www.vito.be/e-maildisclaimer</font></a></font><span class="gmail-m_-5083536946599921354Apple-converted-space"> </span><br>
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--<span class="gmail-m_-5083536946599921354Apple-converted-space"> </span><br>
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<div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
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<div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
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<span style="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;float:none;display:inline">_______________________________________________</span><br style="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">
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mailing list</span><br style="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:users@lists.quantum-espresso.org" style="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" target="_blank">users@lists.quantum-espresso.org</a><br style="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="https://lists.quantum-espresso.org/mailman/listinfo/users" style="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" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></div>
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_______________________________________________<br>
users mailing list<br>
<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><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>Phone +39-0432-558216, fax +39-0432-558222<br><br></div></div></div></div></div></div>