<div dir="ltr"><div>QE doesn't switch atoms as far as I know. Visualizers occasionally do: their algorithms sometimes cannot decide whether to visualize an atom or its periodic image and so you see atoms at the border of a box that disappear at one side and appear at the other side. If this is the case, there isn't anything wrong (but there isn't much that one can do either)<br></div><div><br></div><div>Paolo<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Oct 13, 2020 at 6:49 AM Abhirup Patra <<a href="mailto:abhirupp@sas.upenn.edu">abhirupp@sas.upenn.edu</a>> wrote:<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 dir="ltr"><div class="gmail_default" style="font-size:large">Dear QE users and developers,<br clear="all"></div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">Recently, I have performed some NVT simulation using cp.x for a molecule on surface reaction, however, it looks like that after the 100-th step, atoms in the molecule switch position with the atom of the bottom-most metallic layer of the slab and then go back to the surface again after nth time-step. </div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">I have converted .pos and .cel files to .xsf file using cppp.x with QE.6.6 compiled with -D__OLDXML and visualized the xsf file in Xcrysden. My input geometry is fine, meaning, nothing is switched after ionic relaxation. </div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">Any suggestions or tips about what might be the reason for this behavior? </div><div class="gmail_default" style="font-size:large"><br></div><div class="gmail_default" style="font-size:large">Thanks, </div><div class="gmail_default" style="font-size:large">Abhirup</div><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr" style="margin:0px;padding:0px;border:0px none;font-stretch:inherit;line-height:inherit;vertical-align:baseline"><span style="margin:0px;padding:0px;border:0px none;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;line-height:inherit;vertical-align:baseline"><span style="margin:0px;padding:0px;border:0px none;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;line-height:inherit;vertical-align:baseline"><font face="arial, sans-serif" color="#0b5394">----------------------------------------------------------------------------------------------</font></span></span></div><div dir="ltr" style="margin:0px;padding:0px;border:0px none;font-stretch:inherit;line-height:inherit;vertical-align:baseline"><font face="arial, sans-serif" color="#0b5394"><span style="margin:0px;padding:0px;border:0px none;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;line-height:inherit;vertical-align:baseline"><span style="margin:0px;padding:0px;border:0px none;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;line-height:inherit;vertical-align:baseline">Abhirup Patra</span></span><br><span style="margin:0px;padding:0px;border:0px none;vertical-align:baseline;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;line-height:inherit"></span></font><div style="margin:0px;padding:0px;border:0px none;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;line-height:inherit;vertical-align:baseline"><font face="arial, sans-serif" color="#0b5394"><span style="margin:0px;padding:0px;border:0px none;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;line-height:inherit;vertical-align:baseline"></span><span>Department of Chemistry</span><br></font></div><font face="arial, sans-serif" color="#0b5394"><span style="margin:0px;padding:0px;border:0px none;vertical-align:baseline;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;line-height:inherit"></span></font><div style="margin:0px;padding:0px;border:0px none;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;line-height:inherit;vertical-align:baseline"><font face="arial, sans-serif" color="#0b5394"><span style="margin:0px;padding:0px;border-style:none;border-width:0px;vertical-align:baseline;border-color:initial;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;line-height:inherit"></span><span style="margin:0px;padding:0px;border:0px none;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;line-height:inherit;vertical-align:baseline">University of Pennsylvania</span></font></div></div></div></div></div></div></div>
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<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>