<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 Yun, <div class=""><br class=""></div><div class="">yes the trajectories of the individual beads are in H2O-pos-*-1.xyz, 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 centroid-pos-1.xyz. </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" 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><blockquote type="cite" class=""><div class="">Am 01.08.2019 um 19:19 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=""><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/" 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" 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 style="overflow-wrap: break-word;" 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_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_2410358718824151796webkit-block-placeholder"></div>
-- <br class="">
You received this message because you are subscribed to the Google Groups "cp2k" group.<br class="">
To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp...@googlegroups.com" target="_blank" class="">cp...@googlegroups.com</a>.<br class="">
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/3aa5af5d-4b37-471b-ae2b-18dc83d0b3b5%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" class="">https://groups.google.com/d/msgid/cp2k/3aa5af5d-4b37-471b-ae2b-18dc83d0b3b5%40googlegroups.com</a>.<br class="">
<span id="gmail-m_2410358718824151796cid:76fa8629-3fd1-46fa-adb9-3e712854c960" class=""><H2O-centroid-pos-1.xyz></span><span id="gmail-m_2410358718824151796cid:b91f3390-8b8c-4691-b157-341481e2caf4" class=""><H2O-centroid-vel-1.xyz></span></div></blockquote></div><br class=""></div><br class=""><br class=""><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">==============================</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">Thomas D. Kühne</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">Dynamics of Condensed Matter</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">Chair of Theoretical Chemistry</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">University of Paderborn</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">Warburger Str. 100</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">D-33098 Paderborn</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">Germany</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><a href="mailto:tdku...@mail.upb.de" target="_blank" class="">tdku...@mail.upb.de</a></div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">+49/(0)5251/60-5726</div></div></div>
</div>
<br class=""></div><div class=""><br class="webkit-block-placeholder"></div>
-- <br class="">
You received this message because you are subscribed to a topic in the Google Groups "cp2k" group.<br class="">
To unsubscribe from this topic, visit <a href="https://groups.google.com/d/topic/cp2k/CKzhBph4yFc/unsubscribe" target="_blank" class="">https://groups.google.com/d/topic/cp2k/CKzhBph4yFc/unsubscribe</a>.<br class="">
To unsubscribe from this group and all its topics, send an email to <a href="mailto:cp...@googlegroups.com" target="_blank" class="">cp...@googlegroups.com</a>.<br class="">
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/C543F0FA-BD29-4238-B04B-C4E0CDAB9E00%40gmail.com?utm_medium=email&utm_source=footer" target="_blank" class="">https://groups.google.com/d/msgid/cp2k/C543F0FA-BD29-4238-B04B-C4E0CDAB9E00%40gmail.com</a>.<br class="">
</blockquote></div><div class=""><br class="webkit-block-placeholder"></div>
-- <br class="">
You received this message because you are subscribed to the Google Groups "cp2k" group.<br class="">
To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp...@googlegroups.com" class="">cp...@googlegroups.com</a>.<br class="">
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/CA%2BSzDiPznCF4%3Do%2BNOkE8x_Lau3ScWFHDjDYje05-ZJGT-SS68Q%40mail.gmail.com?utm_medium=email&utm_source=footer" class="">https://groups.google.com/d/msgid/cp2k/CA%2BSzDiPznCF4%3Do%2BNOkE8x_Lau3ScWFHDjDYje05-ZJGT-SS68Q%40mail.gmail.com</a>.<br class="">
<span id="cid:f_jyswssfu0"><H2O-pos-1-1.xyz></span><span id="cid:f_jyswsz3k1"><H2O-pos-2-1.xyz></span><span id="cid:f_jyswt5to2"><H2O-pos-3-1.xyz></span><span id="cid:f_jyswtce43"><H2O-pos-4-1.xyz></span><span id="cid:f_jysxn6uu4"><h2o_test.inp></span></div></blockquote></div><br class=""></div><br class=""><br class="">
<br class=""></body></html>