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<div class="">Dear Quantum Espresso friends,</div>
<div class=""><br class="">
</div>
<div class="">During the NEB calculation, neb.x creates separate directories for the individual images.</div>
<div class="">In one of these directories, one can find a file called PREFIX.xml (pd.xml in my case).</div>
<div class="">The file contains the input variables in xml format.</div>
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</div>
<div class=""><snip></div>
<div class="">…</div>
<div class="">
<div class=""> <symmetry_flags></div>
<div class=""> <nosym>false</nosym></div>
<div class=""> <nosym_evc>false</nosym_evc></div>
<div class=""> <noinv>false</noinv></div>
<div class=""> <no_t_rev>false</no_t_rev></div>
<div class=""> <force_symmorphic>false</force_symmorphic></div>
<div class=""> <use_all_frac>true</use_all_frac></div>
<div class=""> </symmetry_flags></div>
<div class=""> </input></div>
</div>
<div class="">…</div>
<div class=""></snip></div>
<div class=""><br class="">
</div>
<div class="">Thus: use_all_frac = .true. is considered and passed on by neb.x</div>
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</div>
<div class="">Does some of the other variable settings have an impact on the detection of symmetry?</div>
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</div>
<div class="">
<div class="">If I try to start a calculation, based on the xml input file, I got following error:</div>
<div class=""><br class="">
</div>
<div class="">Isn’t that ironic?</div>
<div class=""><br class="">
</div>
<div class="">$ pw.x -in pd.xml </div>
<div class=""><br class="">
</div>
<div class=""> Program PWSCF v.6.3 starts on 13Feb2019 at 11:49:38 </div>
<div class=""><br class="">
</div>
<div class=""> This program is part of the open-source Quantum ESPRESSO suite</div>
<div class=""> for quantum simulation of materials; please cite</div>
<div class=""> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);</div>
<div class=""> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);</div>
<div class=""> URL <a href="http://www.quantum-espresso.org" class="">http://www.quantum-espresso.org</a>", </div>
<div class=""> in publications or presentations arising from this work. More details at</div>
<div class=""> <a href="http://www.quantum-espresso.org/quote" class="">http://www.quantum-espresso.org/quote</a></div>
<div class=""><br class="">
</div>
<div class=""> Parallel version (MPI & OpenMP), running on 20 processor cores</div>
<div class=""> Number of MPI processes: 1</div>
<div class=""> Threads/MPI process: 20</div>
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</div>
<div class=""> MPI processes distributed on 1 nodes</div>
<div class=""> Reading xml input from pd.xml</div>
<div class=""><br class="">
</div>
<div class=""> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div>
<div class=""> Error in routine read_input (1):</div>
<div class=""> xml input disabled</div>
<div class=""> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div>
<div class=""><br class="">
</div>
<div class=""> stopping ...</div>
<div class="">application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0</div>
<div class="">[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1</div>
<div class="">:</div>
<div class="">system msg for write_line failure : Bad file descriptor</div>
</div>
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<div class="">So I cannot easily play with the settings.</div>
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</div>
<br class="">
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Met vriendelijke groeten,</div>
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Mit freundlichen Grüßen,</div>
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With kind regards,</div>
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Willem Offermans</div>
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Researcher Electrocatalysis SCT</div>
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VITO NV | Boeretang 200 | 2400 Mol</div>
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Phone:+32(0)14335263 Mobile:+32(0)492182073 </div>
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<a href="mailto:Willem.Offermans@Vito.be" class="">Willem.Offermans@Vito.be</a></div>
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<blockquote type="cite" class="">
<div class="">On 13 Feb 2019, at 11:24, Offermans Willem <<a href="mailto:willem.offermans@vito.be" class="">willem.offermans@vito.be</a>> wrote:</div>
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Dear Stefano,
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<div class="">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>
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<div class="">The presence of the inversion symmetry is not to save computational time, but to correct for possible dipole interactions.</div>
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</div>
<div class="">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 class="">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>
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Met vriendelijke groeten,</div>
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Mit freundlichen Grüßen,</div>
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With kind regards,</div>
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Willem Offermans</div>
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Researcher Electrocatalysis SCT</div>
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VITO NV | Boeretang 200 | 2400 Mol</div>
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Phone:+32(0)14335263 Mobile:+32(0)492182073 </div>
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<blockquote type="cite" class="">
<div class="">On 13 Feb 2019, at 10:04, Stefano Baroni <<a href="mailto:baroni@sissa.it" class="">baroni@sissa.it</a>> wrote:</div>
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<div class="">On 13 Feb 2019, at 09:50, Offermans Willem <<a href="mailto:willem.offermans@vito.be" class="">willem.offermans@vito.be</a>> wrote:</div>
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<div class="">Dear Quantum Espresso friends,</div>
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Dear Wilem:</div>
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<div class="">I made a mistake in my previous e-mail.</div>
<div class="">The atom coordinates are not in Angstrom but in Bohr.</div>
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<div class="">I have corrected this in my calculations, but still no symmetry found.</div>
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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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<div class="">$ grep "ymmetr" pd_?/PW.out </div>
<div class="">pd_1/PW.out: No symmetry found</div>
<div class="">pd_2/PW.out: No symmetry found</div>
<div class="">pd_3/PW.out: No symmetry found</div>
<div class="">pd_4/PW.out: No symmetry found</div>
<div class="">pd_5/PW.out: No symmetry found</div>
<div class="">pd_6/PW.out: No symmetry found</div>
<div class="">pd_7/PW.out: No symmetry found</div>
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</div>
<div class="">So the question remains. What is the reason that the symmetry cannot be detected?</div>
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<div class="">As an extra check I have made a scf calculation on the last image.</div>
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<div class="">$ grep "Sym. Ops." pd.out </div>
<div class=""> 2 Sym. Ops., with inversion, found ( 1 have fractional translation)</div>
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<div class="">So pw.x can find the symmetry whereas neb.x cannot!</div>
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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>
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Just my worthless 5 cents …</div>
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SB</div>
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<div class="" style="margin: 0px;"><font class="Apple-style-span"><span class="" style="font-size: 12px;">Stefano Baroni - Trieste — </span><a href="http://stefano.baroni.me/" class="" 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; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">http://stefano.baroni.me</a><span class="" style="font-size: 12px;"> </span></font></div>
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<span style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">users
mailing list</span><br style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<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; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">users@lists.quantum-espresso.org</a><br style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<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; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://lists.quantum-espresso.org/mailman/listinfo/users</a></div>
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<font color="#999999" size="-2" face="Arial, Helvetica, sans-serif">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
<a href="http://www.vito.be/route">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
<a href="http://www.vito.be/en/contact/locations">vito.be/en/contact/locations.</a><br>
</font><font color="#999999" size="-2" face="Arial, Helvetica, sans-serif">VITO Disclaimer:
<a href="http://www.vito.be/e-maildisclaimer"><font color="#999999">http://www.vito.be/e-maildisclaimer</font></a></font>
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