Hi Matthias,<div><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.</div><div><br /></div><div>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? </div><div><br /></div><div>Many thanks </div><div>Ashley </div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, 9 September 2025 at 14:44:39 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;">
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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">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.<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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<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 12:39<br>
<b>To: </b>cp2k <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>><br>
<b>Subject: </b>[CP2K:21810] Phonon Calculations in CP2K<u></u><u></u></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt">Hello everyone, <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">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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<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"><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=1757512339867000&usg=AOvVaw2hMQFrvoM7Ud4nthuXBn72">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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<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"><u></u> <u></u></p>
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<p class="MsoNormal" style="margin-left:36.0pt">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" value="+13279693035" 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" value="+18887411088" target="_blank" rel="nofollow">8887411088</a><br>
&END COORD<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">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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<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">If anyone has any suggestions as to why my phonons look quite bad I'd be very thankful.<u></u><u></u></p>
</div>
<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">Thanks in advance <u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:36.0pt">Ashley <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></div></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><div><div><p class="MsoNormal" style="margin-left:36.0pt">-- <br>
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