<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div class="WordSection1"> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US">Hi Ashley<o:p></o:p></span></p> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Even if you could apply easily (which I doubt) a constraint like the freezing of orbital occupations, it would presumable make things worse. I suggest to use the converged wavefunction from the central point as an initial wavefunction for the run with a displaced atom in case you don’t do that already.<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">I guess that the Cu atoms in your system have different oxidation states. Can you identify/assign the oxidation state for each Cu atom before and after displacement?<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">I assumed that you perform UKS runs. If not so far, I would certainly give it a try, because the Cu atoms could exhibit different on-site 3d open-shell configurations while the total spin of the system is still zero. Though that can provide interesting insight, it might also cause new technical (convergence) problems.<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Best<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Matthias<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <div id="mail-editor-reference-message-container"> <div> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <b><span style="color:black">From: </span></b><span style="color:black">cp2k@googlegroups.com <cp2k@googlegroups.com> on behalf of Ashley Dickson <ashleydickson141@gmail.com><br> <b>Date: </b>Tuesday, 9 September 2025 at 16:06<br> <b>To: </b>cp2k <cp2k@googlegroups.com><br> <b>Subject: </b>Re: [CP2K:21813] Phonon Calculations in CP2K<o:p></o:p></span></p> </div> <p class="MsoNormal" style="margin-left:36.0pt">Hi Matthias,<o:p></o:p></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><br> thanks for the response. For your information I am using the finite difference method here. Supposing this was the issue, how would you recommend solving it? Presumably I can't explicitly freeze the orbital occupations for the displaced configurations? Perhaps including the wavefunction of the initial geometry as an initial guess might keep the correct spin state.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Also, I wonder if the anisotropic nature of YBCO is the issue here. It is not strictly magnetic, although the copper chains/planes may act as such and mess up the forces. Would it be beneficial to include spin in my calculations maybe? <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Many thanks <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Ashley <o:p></o:p></p> </div> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt">On Tuesday, 9 September 2025 at 14:44:39 UTC+1 Krack, Matthias wrote:<o:p></o:p></p> </div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt">Hi Ashley</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Regarding the CP2K side, you should check if all the finite difference force calculations converged properly to equivalent (magnetic?) states during an atomic displacement. You do not report the applied computational method and I can only guess, but I would have a look at the Cu 3d occupations of the YBCO before and after an atomic displacement.</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Best</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p> </div> </div> <div> <div> <div> <div> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt;margin-left:72.0pt"> <b><span style="color:black">From: </span></b><span style="color:black"><span class="MsoHyperlink">cp...@googlegroups.com</span> <<span class="MsoHyperlink">cp...@googlegroups.com</span>> on behalf of Ashley Dickson <<span class="MsoHyperlink">ashleydi...@gmail.com</span>><br> <b>Date: </b>Tuesday, 9 September 2025 at 12:39<br> <b>To: </b>cp2k <<span class="MsoHyperlink">cp...@googlegroups.com</span>><br> <b>Subject: </b>[CP2K:21810] Phonon Calculations in CP2K</span><o:p></o:p></p> </div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> Hello everyone, <o:p></o:p></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> I'm unsure if this is the right place to post this issue as I am using phonopy to generate phonons with CP2K, however I thought I might have a bit more luck finding someone with experience using phonopy specifically with CP2K. The issue I'm having is large negative phonon modes, and large drift force reported by phonopy in the y direction (~0.25 eV/A). I know that I shouldn't be getting negative modes as my structure is certainly dynamically stable. my workflow is as follows:<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:7.5pt">phonopy --cp2k -d --dim="6 6 2" -c energy.inp <br> <br> for i in energy-supercell-*; do<br> bn=${i%.*} # Remove file extension<br> num=${bn#*supercell-} # Extract the number after 'energy-supercell-'<br> <br> if [[ -z ${num} ]]; then<br> continue<br> fi<br> dir="$num"<br> <br> if [[ -d $dir ]]; then<br> echo "Skipping: Directory $dir already exists."<br> continue # Skip to the next iteration instead of exiting<br> fi<br> <br> mkdir "$dir"<br> <br> mv "$i" "$dir/energy.inp"<br> # if [[ "$dir" != "001" ]]; then # Keep Wavefunction file from first simulation to make others quicker<br> # cp 001/MIN-supercell-001-RESTART.wfn "$dir/MIN-supercell-$num-RESTART.wfn"<br> # fi<br> <br> cd "$dir"<br> srun cp2k.psmp -i energy.inp -o result.out<br> cd ../<br> <br> done<br> <br> phonopy --cp2k -f $(for i in {1..13}; do printf "%03d/MIN-supercell-%<a href="http://03d-forces-1_0.xyz" target="_blank">03d-forces-1_0.xyz</a> " $i $i; done)<br> <br> phonopy --cp2k -c energy.inp -p -s --dim="6 6 2" --band " 0.0 0.0 0.0 0.0 0.0 0.5 0.0 0.5 0.5 0.0 0.5 0.0 0.5 0.5 0.0 0.5 0.0 0.0 0.5 0.0 0.5 0.5 0.5 0.5" --mesh 41 41 41</span><o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> I have tried various supercell sizes, and have found that 4x4x2 should be more than converged enough. My energy.inp file has the coordinates of the relaxed unitcell printed as follows:<br> &CELL<br> A 3.870961 0 0<br> B 0 3.9540005 0<br> C 0 0 11.8602555<br> PERIODIC XYZ<br> &END CELL<br> &COORD<br> Ba 1.9354787033 1.9770037827 9.6771343800<br> Ba 1.9354787999 1.9770022809 2.1442401159<br> Y 1.9354802394 1.9770060545 5.8953066752<br> Cu -0.0000006631 0.0000091908 7.6100822750<br> Cu -0.0000006426 0.0000055768 4.1724491018<br> Cu -0.0000078256 0.0000008848 -0.0048129326<br> O -0.0000004062 1.9770007276 -0.0014139445<br> O 1.9354801904 0.0000011797 7.3249015553<br> O 1.9354801707 0.0000009008 4.4580654293<br> O -0.0000001259 1.9770034877 7.<a href="tel:(327)%20969-3035" target="_blank">3279693035</a><br> O -0.0000001304 1.9770024288 4.4553471390<br> O -0.0000006180 0.0000004257 9.9643054004<br> O -0.0000006737 0.0000003017 1.<a href="tel:(888)%20741-1088" target="_blank">8887411088</a><br> &END COORD<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> My geometry has been relaxed in a 6x6x2 supercell, with an RMS_FORCE setting of 1e-8 with the CELL_OPT method. The sum of atomic forces at the end lines up with this. I have converged my plane wave cutoff and relative plane wave cutoff (how converged does this need to be?). I worry it may be an issue with negative coordinates in the unit cell, however the periodic XYZ command should wrap these as I understand? <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> If anyone has any suggestions as to why my phonons look quite bad I'd be very thankful.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> Thanks in advance <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> Ashley <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <o:p></o:p></p> </div> </div> </div> </div> </div> </div> <div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <span class="MsoHyperlink">cp2k+uns...@googlegroups.com</span>.<br> To view this discussion visit <a href="https://groups.google.com/d/msgid/cp2k/d5c45f96-776c-4803-90b0-2584e1cd8f4an%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank"> https://groups.google.com/d/msgid/cp2k/d5c45f96-776c-4803-90b0-2584e1cd8f4an%40googlegroups.com</a>.<o:p></o:p></p> </div> </div> </div> </div> </div> </blockquote> </div> <p class="MsoNormal" style="margin-left:36.0pt">-- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br> To view this discussion visit <a href="https://groups.google.com/d/msgid/cp2k/d8d75fed-c55e-4288-adff-cdb9e9e31e16n%40googlegroups.com?utm_medium=email&utm_source=footer"> https://groups.google.com/d/msgid/cp2k/d8d75fed-c55e-4288-adff-cdb9e9e31e16n%40googlegroups.com</a>.<o:p></o:p></p> </div> </div> </div> </div> </body> </html> <p></p> -- <br /> You received this message because you are subscribed to the Google Groups "cp2k" group.<br /> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br /> To view this discussion visit <a href="https://groups.google.com/d/msgid/cp2k/ZR2P278MB114609EA1DB4958C444F635BF40FA%40ZR2P278MB1146.CHEP278.PROD.OUTLOOK.COM?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/ZR2P278MB114609EA1DB4958C444F635BF40FA%40ZR2P278MB1146.CHEP278.PROD.OUTLOOK.COM</a>.<br />