Bump phonopy from 4.5.0 to 4.6.0

[dependabot]

Bumps phonopy from 4.5.0 to 4.6.0.

Changelog

Sourced from phonopy's changelog.

Sep-24-2026: Version 4.6.0

• Experimental release of {ref}the anisotropic thermal expansion <aniso-thermal-expansion>. The lattice parameters are sampled on a grid, and the free energy is minimized over them at each temperature, so that each crystal axis has its own thermal expansion coefficient. The commands are phonopy-strain-cells, phonopy-anisotropic-qha-dataset and phonopy-anisotropic-qha. The command-line options, the aniso_qha_dataset.hdf5 layout and the APIs may change between releases without a deprecation period. The details of the implementation are described in https://arxiv.org/abs/2609.24336.
• NEW {ref}EXCLUDE_GAMMA_ACOUSTIC <exclude_gamma_acoustic_tag> tag, --exclude-gamma-acoustic option and exclude_gamma_acoustic keyword of Phonopy.run_thermal_properties. They exclude the three acoustic modes at {math}\Gamma from the free energy, the entropy, the heat capacity and the zero-point energy. The acoustic modes are taken to be the three modes at {math}\Gamma with the smallest absolute frequencies {math}|\nu|. An imaginary mode is stored as a negative frequency, so a large imaginary mode is not taken for an acoustic one. The default is off in this version. Phonopy prints a warning when an acoustic mode at {math}\Gamma enters the sums, and the default will change to on in phonopy v5.
• Behavior change: phonopy-mlpsscha and MLPSSCHA exclude the three acoustic modes at {math}\Gamma from the harmonic part of the SSCHA free energy by default. The free energies therefore differ from those of phonopy 4.5. --no-exclude-gamma-acoustic (exclude_gamma_acoustic=False) recovers the previous behavior.
• QHAResult.entropy_temperature and QHAResult.enthalpy_temperature give the entropy and the enthalpy of the system at constant pressure. The entropy is taken from a polynomial fit of {math}S(V) at the equilibrium volume, and the enthalpy is {math}H = G + TS. The deprecated PhonopyQHA has the same two properties. (PR #988 by @​shaneraphel)
• Behavior change: the arrays of QHAResult returned by run_qha are in eV, angstrom and K. Entropies and heat capacities are in eV/K, and bulk moduli are in eV/angstrom^3. They were in J/K/mol and GPa before. The pressure argument of run_qha stays in GPa. The files written by phonopy.qha.output are converted back and are unchanged.
• BZGrid.gp_Gamma returns None for a grid that does not contain {math}\Gamma, such as a mesh shifted by half a grid spacing. Before, it returned the grid point at address (0, 0, 0), which is not {math}\Gamma on such a grid. Mesh.gamma_index gives the index of {math}\Gamma among the irreducible q-points, or None.
• The pypolymlp interface requires pypolymlp 0.21.3 or later.

Commits

• 3303d27 Merge pull request #996 from phonopy/release
• 9980034 Prepare for release v4.6.0
• fc63cc8 Merge pull request #995 from phonopy/exclude-gamma-acoustic
• a0cee89 Exclude the acoustic modes at Gamma from the thermal properties, by default i...
• a41c4b5 Return None from BZGrid.gp_Gamma on a grid without Gamma, and add Mesh.gamma_...
• f6e2308 Symmetrize the force constants of a type-1 aniso QHA dataset by the symfc pro...
• 657b390 Merge pull request #994 from phonopy/pre-commit-ci-update-config
• d7028e8 [pre-commit.ci] pre-commit autoupdate
• a01db04 Rename the anisotropic QHA page to aniso-thermal-expansion, since step 5 is n...
• 62682e2 Merge pull request #991 from phonopy/pre-commit-ci-update-config
• 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 (afe2af5) to head (a3cec15).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #558   +/-   ##
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  Coverage   97.90%   97.90%           
=======================================
  Files          29       29           
  Lines        2004     2004           
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  Hits         1962     1962           
  Misses         42       42           

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