<div>Hi,</div><div><br></div><div>This is Chenghan. Thank Thomas and Jinggang for the information. That's very helpful!</div><div><div><div>I also want to use PLUMED in PIMD. A question I have:</div></div></div><div>Does i-Pi act on the bias forces from PLUMED on the centroid position or treat each bead independently and calculate bias forces for each bead seperately?</div><div><br></div><div>Best Regards,</div><div>Chenghan</div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, August 14, 2019 at 7:52:24 AM UTC-5 Jinggang Lan wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr">Constraint atoms lead to nonphysical velocity assignment. It has been fixed in I-PI but not in CP2K as Thomas mentioned.<div></div></div><div dir="ltr"><div><br>On Monday, 12 August 2019 16:23:42 UTC+2, Yun An wrote:</div></div><div dir="ltr"><div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">Dear Thomas,<br><br></div><div>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><br></div><div>I attached the input file, thanks a lot in advance.<br><br></div><div>Best regards,<br></div><div>Yun <br></div></div></div></div><br></blockquote></div></div><div dir="ltr"><div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><div dir="ltr">Thomas Kühne <<a rel="nofollow">t...@gmail.com</a>> 于2019年8月1日周四 下午10:55写道：<br></div></div></blockquote></div></div><div dir="ltr"><div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Dear Yun, <div><br></div><div>yes the trajectories of the individual beads are in H2O-pos-*-<a href="http://1.xyz" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://1.xyz&source=gmail&ust=1598558051857000&usg=AFQjCNGhZGhQ7kX_wcReq9CGtdscGFXQyQ">1.xyz</a>, whereas the </div><div>centroid, which corresponds to the center of mass of the closed ring-polymer made </div><div>up of the imaginary-time replica, is in <a href="http://centroid-pos-1.xyz" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://centroid-pos-1.xyz&source=gmail&ust=1598558051857000&usg=AFQjCNFfR6Dd6kM85_iKwu6c0Qi9sptRSg">centroid-pos-1.xyz</a>. </div><div>Conceptually, conducting PIMD-based metadynamics should be rather straightforward, </div><div>however, since there is some bookkeeping is necessary to apply the bias potential </div><div>to the individual beads I suspect it not to directly work as is. Yet, via i-Pi v2 in conjunction </div><div>with PLUMED it is advertised to work: <a href="http://ipi-code.org/assets/pdf/manual.pdf" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://ipi-code.org/assets/pdf/manual.pdf&source=gmail&ust=1598558051857000&usg=AFQjCNERM_AVouKPxtrer2HnOKy8kj_T8w">http://ipi-code.org/assets/pdf/manual.pdf</a></div><div><br></div><div>Best, </div><div>Thomas</div><div><br></div></div></blockquote></div></blockquote></div></div><div dir="ltr"><div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><div><blockquote type="cite"><div>Am 01.08.2019 um 19:19 schrieb Yun An <<a rel="nofollow">an...@gmail.com</a>>:</div><br></blockquote></div></div></div></blockquote></div></blockquote></div></div><div dir="ltr"><div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><div><blockquote type="cite"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">Dear Thomas,<br><br></div><div>Thank you for the kind reply, it helps a lot. I still have some questions:<br><br></div><div>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/" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://1.xyz/&source=gmail&ust=1598558051857000&usg=AFQjCNEKPTwuMfGLLSPbqL984wLwhmWt0Q">1.xyz</a> file?<br><br></div><div>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><br></div><div>Thank you again for your help.<br><br></div><div>Best regards,<br></div><div>Yun <br> </div></div></div></div></div><br></div></blockquote></div></div></div></blockquote></div></blockquote></div></div><div dir="ltr"><div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><div><blockquote type="cite"><div><div class="gmail_quote"><div dir="ltr">Thomas Kühne <<a rel="nofollow">t...@gmail.com</a>> 于2019年7月31日周三 下午4:16写道：<br></div></div></div></blockquote></div></div></div></blockquote></div></blockquote></div></div><div dir="ltr"><div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><div><blockquote type="cite"><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Dear Yun, <div><br></div><div>you can indeed conduct PIMD using the CP2K built-in PINT module, or using the driver mode </div><div>via the i-Pi program. The latter more functionality for more sophisticated PIMD simulations, </div><div>though the former already permits to conduct all sort of conventional PIMD simulations and has </div><div>the advantage of having everything in one package. </div><div>The <a href="http://centroid-pos-1.xyz/" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://centroid-pos-1.xyz/&source=gmail&ust=1598558051857000&usg=AFQjCNHyvw5fAgddVXGQrebZuGRclSfv1g">centroid-pos-1.xyz</a> contains not the coordinates of every bead, but only the ones of the centroid, </div><div>i.e. the center of mass of the closed ring-polymer. The <a href="http://centroid-vel-1.xyz/" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://centroid-vel-1.xyz/&source=gmail&ust=1598558051857000&usg=AFQjCNFfyXwQuuPchUZ1Crd0Rf1EjfVoBg">centroid-vel-1.xyz</a> contains the corresponding </div><div>velocities, but be aware that except the when centroid molecular dynamics is used, the dynamics of </div><div>the ring-polymer is unphysical, only static ensemble averages are. </div><div><br></div><div>Best, </div><div>Thomas</div></div></blockquote></div></div></blockquote></div></div></div></blockquote></div></blockquote></div></div><div dir="ltr"><div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><div><blockquote type="cite"><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><div><blockquote type="cite"><div>Am 30.07.2019 um 18:39 schrieb Yun An <<a rel="nofollow">an...@gmail.com</a>>:</div><br></blockquote></div></div></div></blockquote></div></div></blockquote></div></div></div></blockquote></div></blockquote></div></div><div dir="ltr"><div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><div><blockquote type="cite"><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><div><blockquote type="cite"><div><div dir="ltr"><p>Dear all,</p><p><br></p><p>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/" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://centroid-pos-1.xyz/&source=gmail&ust=1598558051857000&usg=AFQjCNHyvw5fAgddVXGQrebZuGRclSfv1g">centroid-pos-1.xyz</a> and <a href="http://centroid-vel.xyz/" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://centroid-vel.xyz/&source=gmail&ust=1598558051857000&usg=AFQjCNF2sfcvdEkUa7vInR25frPcX0UZfg">centroid-vel.xyz</a>, I thought the <a href="http://centroid-pos-1.xyz/" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://centroid-pos-1.xyz/&source=gmail&ust=1598558051857000&usg=AFQjCNHyvw5fAgddVXGQrebZuGRclSfv1g">centroid-pos-1.xyz</a> is the atom positions of each replica, but what is the meaning of <a href="http://centroid-vel.xyz/" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://centroid-vel.xyz/&source=gmail&ust=1598558051858000&usg=AFQjCNFWHOg1jusmfrKcSG50Mi-igXr_hg">centroid-vel.xyz</a>? Also, I want to see the trajectories, is this directly given in <a href="http://centroid-pos-1.xyz/" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://centroid-pos-1.xyz/&source=gmail&ust=1598558051858000&usg=AFQjCNHz0UbhAbkrXFzKnOdUPC8ehPdoMQ">centroid-pos-1.xyz</a> or one need to use some script to transform, because from current <a href="http://centroid-pos-1.xyz/" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://centroid-pos-1.xyz/&source=gmail&ust=1598558051858000&usg=AFQjCNHz0UbhAbkrXFzKnOdUPC8ehPdoMQ">centroid-pos-1.xyz</a> , the atoms are not quantum at all.</p><p><br></p><p>Thank you all in advance for any help.</p><p><br></p><p>Best regards,</p><p>Yun</p></div><div><br></div>
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