<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">yes, i understand that i can wrap everything into one cell but it would just be easier to check intermediate and final geometries if there were a way to have CP2K output geometries of both molecules in the same cell. or, is there a visualization package that works well with CP2K?<div><br></div><div><div>BTW, everything stays in the parent cell when alpha=beta=gamma=90 deg, so i wonder why it's different when alpha=beta=90 deg, gamma=120 deg.</div><div><br></div><div>steve t</div><div><div><br></div><div><br><div><div>On Apr 25, 2012, at 9:18 PM, Axel wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><br><br>On Wednesday, April 25, 2012 8:54:45 PM UTC-4, steve t wrote:<blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; position: static; z-index: auto; ">Hey, I'm doing DFT optimization of a carbon nanotube and an aromatic <br>hydrocarbon that should adsorb on the CNT via pi-pi stacking. <br> <br>The periodic cell has a=b=30 A, c=17 A; alpha=beta=90 deg, gamma=120 <br>deg (the tube axis is along the z direction). The optimization <br>completes but when I look at the final set of coordinates, the <br>aromatic hydrocarbon is in the cell adjacent to the parent cell. I've <br>tried using @CENTER_COORDINATES but it doesn't help. <br> <br>Does anyone have any suggestions as to how to keep both molecules in <br>the parent cell? <br></blockquote><div><br></div><div><br></div><div>why bother? they are identical due to PBC.</div><div>just wrap the coordinates back into the </div><div>principal cell and you are done.</div><div><br></div><div>axel.</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"> <br>Thanks. <br> <br>Steve T <br></blockquote><div><br class="webkit-block-placeholder"></div> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msg/cp2k/-/exBAOLt6lXwJ">https://groups.google.com/d/msg/cp2k/-/exBAOLt6lXwJ</a>.<br> To post to this group, send email to <a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a>.<br> To unsubscribe from this group, send email to <a href="mailto:cp2k+uns...@googlegroups.com">cp2k+uns...@googlegroups.com</a>.<br> For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en">http://groups.google.com/group/cp2k?hl=en</a>.<br> </blockquote></div><br></div></div></div></body></html>