Bump phonopy from 4.4.0 to 4.5.0

[dependabot]

Bumps phonopy from 4.4.0 to 4.5.0.

Changelog

Sourced from phonopy's changelog.

Sep-08-2026: Version 4.5.0

• Added the Octopus code interface and {ref}its documentation <octopus_interface>. --octopus runs the phonopy command through it, and phonopy-octopus-born writes BORN from an Octopus calculation.
• NEW phonopy-mlpsscha runs one SSCHA calculation, at one temperature, with a pypolymlp potential, and writes its iterations to mlpsscha.hdf5, which phonopy.sscha.trace.read_sscha_trace_hdf5 reads back as an SSCHATrace. --all-force-constants keeps the force constants of every iteration, so that a transient can be dropped and the rest averaged afterwards. {ref}The SSCHA page <polymlp-sscha> is rewritten around the command.
• The --sscha option of the phonopy command is deprecated in favor of phonopy-mlpsscha and warns when used. It still runs, and no page documents it any more. phonopy-mlpsscha takes the potential as a file, so a run that used to train it in the same call becomes two: phonopy --pypolymlp ... to write polymlp.yaml, then phonopy-mlpsscha.
• MLPSSCHA.supercell_energy reports the energy of the supercell without displacements, which the SSCHA free energy is measured from and which was computed and then discarded, and MLPSSCHA.n_cell the number of primitive cells in the supercell, which takes it to the unit the free energy is reported in. sscha_free_energies.yaml records the supercell energy beside the other settings, and each iteration now reports potential_energy and harmonic_potential_energy, the two terms anharmonic is the difference of.
• The SSCHA free energy of each iteration is reported with its statistical error, as free_energy_error. The file holding it, phonopy_sscha.yaml, is renamed sscha_free_energies.yaml, and each iteration draws its displacements from a seed derived from the run's seed instead of reusing one seed. SSCHATrace keeps every iteration so that the transient can be chosen after the sampling, and MLPSSCHA accepts fc_calculator_options.
• Two experimental commands take over parts of phonopy-init: phonopy-collect creates FORCE_SETS (phonopy_params.yaml when given --sp option) from the calculator output files given as its arguments, and phonopy-symmetry shows the symmetry of a cell. Both are on trial and may change.
• Bug fix: the non-analytical term correction factor is 1 for every interface that keeps cells in bohr and force constants in hartree/bohr^2, namely Elk, DFTB+, TURBOMOLE, Fleur, exciting and Octopus. That is e^2/(4 pi eps0) in those units, and it is what {ref}the table <nac_default_value_interfaces> documents for all six. Elk, TURBOMOLE and Fleur had carried 14.399652, the eV*angstrom value, since v3.4.0, DFTB+ since its interface was added, and exciting since v4.4.0. Running NAC through them shifted the LO frequencies.
• Behavior change: phonopy-vasp-efe integrates the electronic free energy by the linear tetrahedron method over the mesh each vasprun.xml describes, where it used to sum Fermi-Dirac occupations over the irreducible k-points. The sum needs far more k-points to converge, so fe-v.dat moves: on the copper example, 120 irreducible k-points of a 16x16x16 mesh, by 11 per cent of the temperature-dependent part at 1000 K. --k-point-sum restores the previous behavior, and a file whose k-points are not a mesh takes the sum as before. The first line of fe-v.dat now names the route that produced it.
• Behavior change: random displacements at finite temperature are drawn differently. Their distribution is unchanged, but the random stream moves: a

... (truncated)

Commits

• 6683c73 Merge pull request #985 from phonopy/release
• 70ed473 Release v4.5.0
• d680c67 Add a Python section to the SSCHA page and name the harmonic step
• 1b02bbe Deprecate the --sscha option in favor of phonopy-mlpsscha
• ee41203 Rename SSCHARun to SSCHATrace, with its module and hdf5 functions
• 6628169 Merge pull request #984 from phonopy/fix-nac-factor
• 0a0267f Fix NAC factor for exciting and dftb+
• 5774bca Wrote test before fixing NAC factor for exciting and dftb+
• 6660e44 Merge pull request #983 from phonopy/pre-commit-ci-update-config
• bccc55f Minor fix of anisotropic-qha.md
• Additional commits viewable in compare view

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.90%. Comparing base (495f51d) to head (1804f50).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #547   +/-   ##
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  Coverage   97.90%   97.90%           
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  Files          29       29           
  Lines        2004     2004           
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  Hits         1962     1962           
  Misses         42       42           

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