[CP2K-user] [CP2K:21810] Phonon Calculations in CP2K

[Krack, Matthias]

Hi Ashley

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.

Best

Matthias

From: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Ashley Dickson <ashleydickson141 at gmail.com>
Date: Tuesday, 9 September 2025 at 12:39
To: cp2k <cp2k at googlegroups.com>
Subject: [CP2K:21810] Phonon Calculations in CP2K
Hello everyone,

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:

phonopy --cp2k -d --dim="6 6 2" -c energy.inp

for i in energy-supercell-*; do
    bn=${i%.*}  # Remove file extension
    num=${bn#*supercell-}  # Extract the number after 'energy-supercell-'

    if [[ -z ${num} ]]; then
        continue
    fi
    dir="$num"

    if [[ -d $dir ]]; then
        echo "Skipping: Directory $dir already exists."
        continue  # Skip to the next iteration instead of exiting
    fi

    mkdir "$dir"

    mv "$i" "$dir/energy.inp"
  #  if [[ "$dir" != "001" ]]; then # Keep Wavefunction file from first simulation to make others quicker
 #       cp 001/MIN-supercell-001-RESTART.wfn "$dir/MIN-supercell-$num-RESTART.wfn"
#    fi

    cd "$dir"
    srun cp2k.psmp -i energy.inp -o result.out
    cd ../

done

phonopy --cp2k -f $(for i in {1..13}; do printf "%03d/MIN-supercell-%03d-forces-1_0.xyz " $i $i; done)

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


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:
    &CELL
      A 3.870961 0 0
      B 0 3.9540005 0
      C 0 0 11.8602555
                PERIODIC XYZ
    &END CELL
   &COORD
Ba 1.9354787033 1.9770037827 9.6771343800
Ba 1.9354787999 1.9770022809 2.1442401159
Y 1.9354802394 1.9770060545 5.8953066752
Cu -0.0000006631 0.0000091908 7.6100822750
Cu -0.0000006426 0.0000055768 4.1724491018
Cu -0.0000078256 0.0000008848 -0.0048129326
O -0.0000004062 1.9770007276 -0.0014139445
O 1.9354801904 0.0000011797 7.3249015553
O 1.9354801707 0.0000009008 4.4580654293
O -0.0000001259 1.9770034877 7.3279693035
O -0.0000001304 1.9770024288 4.4553471390
O -0.0000006180 0.0000004257 9.9643054004
O -0.0000006737 0.0000003017 1.8887411088
      &END COORD

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?

If anyone has any suggestions as to why my phonons look quite bad I'd be very thankful.

Thanks in advance
Ashley

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