Hi Matthias,<div><br /></div><div>Thanks you very much for all the help here. In the first instance I will try and start from a converged wavefunction of the perfect cell, hopefully this irons out the issues. I will make sure I print the relevant charge information on my next run to identify if the oxidation states may be playing a role as you mentioned. </div><div><br /></div><div>Ideally i'd like to avoid UKS runs primarily because I am validating some results that don't utilise a spin calculation. Although I do believe this may solve my issue, so I may give it a try just to see.</div><div><br /></div><div>Many thanks for all your help,</div><div>Ashley <br /><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, 9 September 2025 at 16:04:11 UTC+1 Krack, Matthias 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 lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word">
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<p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt">Hi Ashley<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">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.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">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?<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">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.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Best<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Matthias<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><u></u> <u></u></span></p>
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<div></div></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div>
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<b><span style="color:black">From: </span></b><span style="color:black"><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a> <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>> on behalf of Ashley Dickson <<a href data-email-masked rel="nofollow">ashleydi...@gmail.com</a>><br>
<b>Date: </b>Tuesday, 9 September 2025 at 16:06<br>
<b>To: </b>cp2k <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>><br>
<b>Subject: </b>Re: [CP2K:21813] Phonon Calculations in CP2K<u></u><u></u></span></p>
</div>
<p class="MsoNormal" style="margin-left:36.0pt">Hi Matthias,<u></u><u></u></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.<u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
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<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? <u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
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<p class="MsoNormal" style="margin-left:36.0pt">Many thanks <u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:36.0pt">Ashley <u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:36.0pt">On Tuesday, 9 September 2025 at 14:44:39 UTC+1 Krack, Matthias wrote:<u></u><u></u></p>
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<span lang="DE-CH" style="font-size:11.0pt">Hi Ashley</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="DE-CH" style="font-size:11.0pt"> </span><u></u><u></u></p>
<p class="MsoNormal" style="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><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US" style="font-size:11.0pt"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US" style="font-size:11.0pt">Best</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US" style="font-size:11.0pt"> </span><u></u><u></u></p>
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<span lang="EN-US" style="font-size:11.0pt">Matthias</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US" style="font-size:11.0pt"> </span><u></u><u></u></p>
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<b><span style="color:black">From: </span></b><span style="color:black"><span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span> <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>> on behalf of Ashley Dickson <<span><a href data-email-masked rel="nofollow">ashleydi...@gmail.com</a></span>><br>
<b>Date: </b>Tuesday, 9 September 2025 at 12:39<br>
<b>To: </b>cp2k <<span><a href data-email-masked rel="nofollow">cp...@googlegroups.com</a></span>><br>
<b>Subject: </b>[CP2K:21810] Phonon Calculations in CP2K</span><u></u><u></u></p>
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Hello everyone, <u></u><u></u></p>
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<u></u><u></u></p>
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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:<u></u><u></u></p>
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<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" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en-GB&q=http://03d-forces-1_0.xyz&source=gmail&ust=1757519532801000&usg=AOvVaw2jIwZ1ZLISamhQVNw-Glen">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><u></u><u></u></p>
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<u></u><u></u></p>
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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" rel="nofollow">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" rel="nofollow">8887411088</a><br>
&END COORD<u></u><u></u></p>
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<u></u><u></u></p>
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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? <u></u><u></u></p>
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<u></u><u></u></p>
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If anyone has any suggestions as to why my phonons look quite bad I'd be very thankful.<u></u><u></u></p>
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<u></u><u></u></p>
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Thanks in advance <u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:72.0pt">
Ashley <u></u><u></u></p>
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<u></u><u></u></p>
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