<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Sun, <div class=""><br class=""></div><div class="">to the best of my knowledge fixed atoms constraints are simply </div><div class="">not implemented within PINT, which must be enforced on the centroid. </div><div class="">The individual beads are still allowed to move (as long as the centroid </div><div class="">is fixed) and will do so at a very high classical kinetic energy due to </div><div class="">the presence of a rather high quantum kinetic energy, which can easily</div><div class="">be on the order of a few hundred kelvin! </div><div class=""><br class=""></div><div class="">Cheers, </div><div class="">Thomas</div><div class=""><br class=""></div><div class=""><div><blockquote type="cite" class=""><div class="">Am 12.08.2019 um 16:23 schrieb Yun An <<a href="mailto:anyu...@gmail.com" class="">anyu...@gmail.com</a>>:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">Dear Thomas,<br class=""><br class=""></div><div class="">Thank you very much for the kind reply. I tried with PINT module in cp2k, the weird thing is, I want to fix some atoms during the calculations, but it seems that the "CONSTRAINT" section didn't work, because the atoms which are supposed to be fixed moves a lot according to the structures it gives out. Do you know what is the problem and how to fix it?<br class=""><br class=""></div><div class="">I attached the input file, thanks a lot in advance.<br class=""><br class=""></div><div class="">Best regards,<br class=""></div><div class="">Yun <br class=""></div></div></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Thomas Kühne <<a href="mailto:tku...@gmail.com" class="">tku...@gmail.com</a>> 于2019年8月1日周四 下午10:55写道：<br class=""></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;" class="">Dear Yun, <div class=""><br class=""></div><div class="">yes the trajectories of the individual beads are in H2O-pos-*-<a href="http://1.xyz/" target="_blank" class="">1.xyz</a>, whereas the </div><div class="">centroid, which corresponds to the center of mass of the closed ring-polymer made </div><div class="">up of the imaginary-time replica, is in <a href="http://centroid-pos-1.xyz/" target="_blank" class="">centroid-pos-1.xyz</a>. </div><div class="">Conceptually, conducting PIMD-based metadynamics should be rather straightforward, </div><div class="">however, since there is some bookkeeping is necessary to apply the bias potential </div><div class="">to the individual beads I suspect it not to directly work as is. Yet, via i-Pi v2 in conjunction </div><div class="">with PLUMED it is advertised to work: <a href="http://ipi-code.org/assets/pdf/manual.pdf" target="_blank" class="">http://ipi-code.org/assets/pdf/manual.pdf</a></div><div class=""><br class=""></div><div class="">Best, </div><div class="">Thomas</div><div class=""><br class=""></div><div class=""><div class=""><blockquote type="cite" class=""><div class="">Am 01.08.2019 um 19:19 schrieb Yun An <<a href="mailto:anyu...@gmail.com" target="_blank" class="">anyu...@gmail.com</a>>:</div><br class="gmail-m_34943369450996558Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">Dear Thomas,<br class=""><br class=""></div><div class="">Thank you for the kind reply, it helps a lot. I still have some questions:<br class=""><br class=""></div><div class="">I use 4 beads to test h2o molecule, is it means the trajectory is represented by the average replica positions of each atom, in the current case, is the all the atom positions of these four H2O-pos-?-<a href="http://1.xyz/" target="_blank" class="">1.xyz</a> file?<br class=""><br class=""></div><div class="">Anther question is if I want to run MD simulations to see the quantum effects, for example, H2 and D2 diffusion in the metal surface, is it possible that cp2k combines PINT and metadynamics? Because the RUN_TYPE section to me is like either one can choose MD to perform normal MD or PINT to run PIMD, but not both at one calculations. So in such case, how should I consider quantum effects?<br class=""><br class=""></div><div class="">Thank you again for your help.<br class=""><br class=""></div><div class="">Best regards,<br class=""></div><div class="">Yun <br class=""> </div></div></div></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Thomas Kühne <<a href="mailto:tku...@gmail.com" target="_blank" class="">tku...@gmail.com</a>> 于2019年7月31日周三 下午4:16写道：<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="">Dear Yun, <div class=""><br class=""></div><div class="">you can indeed conduct PIMD using the CP2K built-in PINT module, or using the driver mode </div><div class="">via the i-Pi program. The latter more functionality for more sophisticated PIMD simulations, </div><div class="">though the former already permits to conduct all sort of conventional PIMD simulations and has </div><div class="">the advantage of having everything in one package. </div><div class="">The <a href="http://centroid-pos-1.xyz/" target="_blank" class="">centroid-pos-1.xyz</a> contains not the coordinates of every bead, but only the ones of the centroid, </div><div class="">i.e. the center of mass of the closed ring-polymer. The <a href="http://centroid-vel-1.xyz/" target="_blank" class="">centroid-vel-1.xyz</a> contains the corresponding </div><div class="">velocities, but be aware that except the when centroid molecular dynamics is used, the dynamics of </div><div class="">the ring-polymer is unphysical, only static ensemble averages are. </div><div class=""><br class=""></div><div class="">Best, </div><div class="">Thomas</div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">Am 30.07.2019 um 18:39 schrieb Yun An <<a href="mailto:anyu...@gmail.com" target="_blank" class="">anyu...@gmail.com</a>>:</div><br class="gmail-m_34943369450996558gmail-m_2410358718824151796Apple-interchange-newline"><div class=""><div dir="ltr" class=""><p class="">Dear all,</p><p class=""><br class=""></p><p class="">I want to perform PIMD with cp2k, according to the manual, one can add a PINT session to run path integral simulations; also, can use i-PI mode DRIVER. What is the difference between those two, is that in principle they both can do PIMD? I tried a H2O molecule with run_type of PINT, then I got <a href="http://centroid-pos-1.xyz/" target="_blank" class="">centroid-pos-1.xyz</a> and <a href="http://centroid-vel.xyz/" target="_blank" class="">centroid-vel.xyz</a>, I thought the <a href="http://centroid-pos-1.xyz/" target="_blank" class="">centroid-pos-1.xyz</a> is the atom positions of each replica, but what is the meaning of <a href="http://centroid-vel.xyz/" target="_blank" class="">centroid-vel.xyz</a>? Also, I want to see the trajectories, is this directly given in <a href="http://centroid-pos-1.xyz/" target="_blank" class="">centroid-pos-1.xyz</a> or one need to use some script to transform, because from current <a href="http://centroid-pos-1.xyz/" target="_blank" class="">centroid-pos-1.xyz</a> , the atoms are not quantum at all.</p><p class=""><br class=""></p><p class="">Thank you all in advance for any help.</p><p class=""><br class=""></p><p class="">Best regards,</p><p class="">Yun</p></div><div class=""><br class="gmail-m_34943369450996558gmail-m_2410358718824151796webkit-block-placeholder"></div>
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