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Change Log

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Change Log#

Apr-19-2024: Version 3.0.0#

This is a major version release. There are backward-incompatible changes.

  • Calculation method to transform supercell third-order force constants fc3 in real to reciprocal space was changed as described at Version 2.9.0 changelog below. This results in the change of results with respect to those obtained by phono3py version 2. To emulate v2 behaviour, use --v2 option in phono3py command line script. For Phono3py class , make_r0_average=True (default) when instantiating it, and similarly for phono3py.load function.

  • Completely dropped support of disp_fc3.yaml and disp_fc2.yaml.

  • Dropped support of old style usage of phono3py-kaccum script.

  • Removed functions write_fc3_dat, write_triplets, write_grid_address in file_IO.py.

  • Removed methods marked by DeprecationWarning.

  • Removed masses, band_indices, sigmas, sigma_cutoff parameters from Phono3py.__init__().

Mar-20-2024: Version 2.10.0#

  • Maintenance release

Feb-2-2024: Version 2.9.2#

  • boundary_mfp value is stored in kappa-*.hdf5 file when it is specified.

Dec-26-2023: Version 2.9.1#

  • Release to build conda-forge package.

Dec-25-2023: Version 2.9.0#

  • Pre-release of version 3.0.

  • --v3 option enables phono3py version 3 behaviour. In phono3py-v3, it is planned to replace \(\sum_{l'l''}\Phi_{\alpha\beta\gamma}(0\kappa, l'\kappa', l''\kappa'') \cdots\) in Eq.(41) of https://journals.jps.jp/doi/10.7566/JPSJ.92.012001 by \([\sum_{l'l''}\Phi_{\alpha\beta\gamma}(0\kappa, l'\kappa', l''\kappa'') \cdots + \sum_{ll''}\Phi_{\alpha\beta\gamma}(l\kappa, 0\kappa', l''\kappa'') \cdots + \sum_{ll'}\Phi_{\alpha\beta\gamma}(l\kappa, l'\kappa', 0\kappa'') \cdots] / 3\) for better treatment of lattice sum in supercell although this requires more computational demand. In phono3py-v3, --v2 option will be prepared.

Dec-4-2023: Version 2.8.0#

  • Maintenance release

  • Fix unit conversion for non-VASP calculators

Jul-3-2023: Version 2.7.0#

  • Drop python 3.7 support

Apr-3-2023: Version 2.6.0#

  • Release to follow the change of phonopy at v2.18, which fixes to be able to read phono3py*.yaml file with phono3py-load.

Dec-31-2022: Version 2.5.1#

  • Release to trigger phono3py conda-forge package build.

Dec-29-2022: Version 2.5.0#

  • Maintenance release to follow the change of phonopy at v2.17.

  • Bug fix of phonon-isotope scattering strength. The scattering strength was slightly overestimated (commit c4c54c73).

Oct-6-2022: Version 2.4.1#

  • Release for pypi packaging

Oct-5-2022: Version 2.4.0#

  • Maintenance release to follow the change of phonopy at v2.16.

  • Installation procedure from source code is changed. See Installation from source code.

May-28-2022: Version 2.3.2#

  • Fix --cf2 command.

May-7-2022: Version 2.3.1#

  • Fix wrongly displaying q-point in conductivity calculation.

Apr-9-2022: Version 2.3.0#

  • Maintenance release including small bug fixes.

Feb-14-2022: Version 2.2.0#

  • Maintenance release to follow the change of phonopy at v2.12.1.

  • Installation using setup.py now requires creating site.cfg file. See https://phonopy.github.io/phono3py/install.html and PR #59.

  • Dorp python 3.6 support, and dependencies of numpy and matplotlib versions are updated:

    • Python >= 3.7

    • numpy >= 1.15.0

    • matplotlib >= 2.2.2

Nov-3-2021: Version 2.1.0#

  • Fix of a critical bung in the direct solution. See the detail as commit log of 54d4ddab.

  • Aiming modernizing phono3py code, required python version and package versions were changed to

    • Python >= 3.6

    • numpy >= 1.11

    • matplotlib >= 2.0

  • For developers, flake8, black, pydocstyle, and isort were introduced. See REAEME.md and .pre-commit-config.yaml.

Jul-22-2021: Version 2.0.0#

This is a major version release. There are some backward-incompatible changes.

  1. Grid point indexing system to address grid points of q-points is changed.

  2. Array data types of most of the integer arrays are changed to dtype='int_' from dtype='intc'.

  3. Python 3.5 or later is required.

To emulate the version 1.x behaviour in phono3py command, try --v1 option. To emurate the version 1.x behaviour in API, specify store_dense_gp_map=False and store_dense_svecs=False in instatiation of Phono3py class or phon3py loader.

Mar-17-2021: Version 1.22.3#

  • Fix --read-gamma option to work.

Feb-21-2021: Version 1.22.2#

  • Fix PyPI source distribution package

Feb-21-2021: Version 1.22.1#

  • phono3py command didn’t work. This was fixed.

  • Fix behaviour when specifying --thm and --sigma simultaneously.

Jan-29-2021: Version 1.22.0#

  • Maintenance release to follow phonopy v2.9.0.

Sep-30-2020: Version 1.21.0#

  • Maintenance release to follow the change of phonopy at v2.8.1

  • Improvements of phono3py loader (phono3py.load), phono3py-load command, API, and phono3py_disp.yaml.

  • Harmonic phonon calculation on mesh was multithreaded. This is effective when using very dense mesh with non-analytical term correction (probably rare case).

  • Real and imaginary parts of self energy and spectral function of bubble diagram at API level

Mar-3-2020: Version 1.20.0#

  • phono3py_disp.yaml is made when creating displacements in addition to disp_fc3.yaml and disp_fc2.yaml. phono3py_disp.yaml will be used instead of disp_fc3.yaml and disp_fc2.yaml in the future major release (v2.0).

Mar-3-2020: Version 1.19.1#

  • Release for pypi and conda (atztogo channel) packagings

Mar-2-2020: Version 1.19.0#

  • Improvements of phono3py loader and API.

  • Improvement of interfaces to calculators. Now it is expected to be much easier to implement calculator interface if it exists in phonopy.

  • Fixed dependency to phonopy v2.6.0.

Dec-22-2019: Version 1.18.2#

  • Initial version of phono3py loader (phono3py.load) was implemented. See docstring of phono3py.load.

Oct-17-2019: Version 1.18.1#

  • Fix of phono3py-kaccum to follow the latest phonopy.

Oct-9-2019: Version 1.18.0#

  • Maintenance release

Apr-18-2019: Version 1.17.0#

  • --cfz option was made to subtract residual forces. See --cfz (command option only).

  • --cutoff-pair was made to override the cutoff pair distance written in disp_fc3.yaml when using on calculating force constants. This is useful when checking cutoff distance dependency. So the use case of having fully computed FORCES_FC3 is assumed.

  • TURBOMOLE interface is provided by Antti Karttunen (--turbomole).

  • Compatibility of fc2.hdf5 and force_constants.hdf5 was improved for all calculators to store physical unit information in the hdf5 file. See File format compatibility with phonopy.

Mar-24-2019: Version 1.16.0#

  • Bug fixes and catching up the updates of phonopy.

  • Most of hdf5 output files are compressed by gzip as default. This compression can be set off, see --hdf5-compression (command option only).

  • (Experimental) phono3py command accepts phono3py.yaml type file as an input crystal structure by -c option. When DIM and any structure file are not given, phono3py_disp.yaml (primary) or phono3py.yaml (secondary) is searched in the current directory. Then phono3py.yaml type file is used as the input. By this, semi-automatic phono3py mode is invocked, which acts as

    1. supercell_matrix corresponding to DIM in the phono3py.yaml type file is used if it exists.

    2. phonon_supercell_matrix corresponding to DIM_FC2 in the phono3py.yaml type file is used if it exists.

    3. primitive_matrix in the phono3py.yaml type file is used if it exists. Otherwise, set PRIMITIVE_AXES = AUTO when PRIMITIVE_AXES is not given.

    4. NAC params are read (NAC = .TRUE.) if NAC params are contained (primary) in the phono3py.yaml type file or if BORN file exists in the current directory (secondary).

Nov-22-2018: version 1.14.3#

  • Update to work with phonopy v1.14.2.

  • Ph-ph interaction can be read (--read-pp) and write (--write-pp) in RTA thermal conductivity calculation, too. Mind that the data stored are different with and without --full-pp. Wihtout --full-pp the data are stored in complicated way to save data side, so it is not considered readable by usual users.

June-20-2018: version 1.13.3#

May-17-2018: version 1.13.1#

Mar-16-2018: version 1.12.9#

  • Definition of mode_kappa values in output hdf5 file is changed. Previously they were divided by number of grid points, but now not. Therefore users who compute kappa from mode_kappa need to be careful about this change. This does not affect to phono3py-kaccum results.

Feb-1-2018: version 1.12.7#

  • --tsym option is removed. Now with --sym-fc3r and --sym-fc2 options, translational invariance symmetry is also applied.

  • --sym-fc option is added. This is just an alias to specify both --sym-fc3r and --sym-fc2 together.

  • Documentation on --write-phonon and --read-phonon options is written. These options are used to save harmonic phonon infromation on strage.

Nov-22-2017: version 1.12.5#

  • Bug fix of RTA thermal conductivity. This bug exists from version 1.10.11.18 (git e40cd059). This bug exhibits when all the following conditions are met:

    1. RTA thermal conductivity calculation.

    2. Tetrahedron method for Brillouin zone integration is used.

    3. Number of triplets is smaller than number of bands at each grid point.

    4. Without using --full-pp.

    (3) happens when the primitive cell is relatively large. Number of triplets can be shown using --stp option. A race condition of OpenMP multithreading is the source of the bug. Therefore, if it occurs, the same calculation comes up with the different thermal conductivity value in every run time, for whcih it behaves like randomly.

  • RTA thermal conductivity with smearing method (--sigma) is made to run with smaller memory consumption as similar as tetrahedron method (--thm).

Nov-17-2017: version 1.12.3#

  • Command option parser of the phonopy tools is replaced from optparse to argparse.

  • The filenames used with these options were the positional arguments previously. Now they are the command-line arguments, i.e., filenames have to be put just after the option name like -f vasprun.xml-001 vasprun.xml-002 ....

  • The names of auxiliary tools (kdeplot and kaccum) are changed, for which the prefix phono3py- is added to the old names to avoid accidental conflict with other script names already existing under bin directory.

  • --sigma-cutoff (SIGMA_CUTOFF_WIDTH) option was created.

Jun-18-2017: version 1.11.13#

Mar-31-2017: version 1.11.11#

  • Abinit code interface is implemented and now under the testing.

  • Reduction of memory usage in RTA thermal conductivity calculation. This is especially effective for larger unit cell case. Currently combinations with –full_pp, –write_gamma_detail, and –simga(smearing method) are not supported for this. Performance tuning is under going. In some case, computation can be slower than the previous versions.

Feb-9-2017: version 1.11.9#

  • This version works coupled with phonopy-1.11.8 or later.

  • CRYSTAL code interface is implemented by Antti J. Karttunen.

Dec-14-2016: version 1.11.7#

  • This is a maintenance release. This version must be used with phonopy-1.11.6 or later.

Nov-27-2016: version 1.11.5#

Apr-24-2016: version 1.10.9#

  • Failure of writing kappa-mxxx-gx.hdf5 was fixed.

Apr-16-2016: version 1.10.7#

  • API example is prepared and it is found in Si example. No doucment yet.

  • Si pwscf example was placed in example-phono3py directory.

  • User interface bug fix.

Mar-15-2016: version 1.10.5#

  • Numbering way of phono3py version was just changed (No big updates were made against previous version.) The number is given based on the phonopy version. For example, the harmonic part of phono3py-1.10.5 is based on the code close to phonopy-1.10.4.

  • Python3 support

  • For the RTA thermal conductivity calculation mode with using the linear tetrahedron method, only necessary part of phonon-phonon interaction strengh among phonons. This improves lifetime calculation performance, but as the drawback, averaged ph-ph interaction strength can not be given. See --full-pp (FULL_PP = .TRUE.).

  • Pwscf interface (Interfaces to calculators)

Oct-10-2015: version 0.9.14#

  • Computational performance tuning for phonon-phonon interaction strength calculation was made by Jonathan Skelton. Depending on systems, but 10-20% performance improvement may be possible.

  • --stp option is created to show numbers of q-point triplets to be calculated. See Command options / Setting tags.

  • --write_gamma and --read_gamma support using with --bi option. Therefore a thermal conductivity calculation can be distributed over band index, too. This may be useful for the system whose unit cell is large.

Sep-26-2015: version 0.9.13#

  • Changed so that --wgp option writes grid_address-mxxx.hdf5 instead of grid_address-mxxx.dat.

  • --write_detailed_gamma is implemented. See Command options / Setting tags.

  • When running without setting --thm and --sigma options, linear tetrahedron method corresponding to --thm is used as the default behavior.

  • --ise options is created.

Aug-12-2015: version 0.9.12#

  • Spglib update to version 1.8.2.1.

  • Improve computational performance of kaccum and gaccum.

Jun-18-2015: version 0.9.10.1#

  • Bug fix of gcaccum

Jun-17-2015: version 0.9.10#

  • Fix bug in kaccum. When using with --pa option, irreducible q-points were incorrectly indexed.

  • gaccum is implemented. gaccum is very similar to kaccum, but for \(\Gamma_\lambda(\omega_\lambda)\).

  • spglib update.

Changes in version 0.9.7#

  • The definition of MSPP is modified so as to be averaged ph-ph interaction defined as \(P_{\mathbf{q}j}\) in the arXiv manuscript. The key in the kappa hdf5 file is changed from mspp to ave_pp. The physical unit of \(P_{\mathbf{q}j}\) is set to \(\text{eV}^2\).

Changes in version 0.9.6#

  • Silicon example is put in example-phono3py directory.

  • Accumulated lattice thermal conductivity is calculated by kaccum script.

  • JDOS output format was changed.

Changes in version 0.9.5#

  • In kappa-xxx.hdf5 file, heat_capacity format was changed from (irreducible q-point, temperature, phonon band) to (temperature, irreducible q-point, phonon band). For gamma, previous document was wrong in the array shape. It is (temperature, irreducible q-point, phonon band)

Changes in version 0.9.4#

  • The option of --cutoff_mfp is renamed to --boundary_mfp and now it’s on the document.

  • Detailed contribution of kappa at each q-point and phonon mode is output to .hdf5 with the keyword mode_kappa.

Changes in version 0.8.11#

  • A new option of --cutoff_mfp for including effective boundary mean free path.

  • The option name --cutfc3 is changed to --cutoff_fc3.

  • The option name --cutpair is changed to --cutoff_pair.

  • A new option --ga is created.

  • Fix spectrum plot of joint dos and imaginary part of self energy

Changes in version 0.8.10#

  • Different supercell size of fc2 from fc3 can be specified using --dim_fc2 option.

  • --isotope option is implemented. This is used instead of --mass_variances option without specifying the values. Mass variance parameters are read from database.

Changes in version 0.8.2#

  • Phono3py python interface is rewritten and a lot of changes are introduced.

  • FORCES_SECOND and FORCES_THIRD are no more used. Instead just one file of FORCES_FC3 is used. Now FORCES_FC3 is generated by --cf3 option and the backward compatibility is simple: cat FORCES_SECOND FORCES_THIRD > FORCES_FC3.

  • --multiple_sigmas is removed. The same behavior is achieved by --sigma.

Changes in version 0.8.0#

  • --q_direction didn’t work. Fix it.

  • Implementation of tetrahedron method whcih is activated by --thm.

  • Grid addresses are written out by --wgp option.

Changes in version 0.7.6#

  • Cut-off distance for fc3 is implemented. This is activated by --cutfc3 option. FC3 elements where any atomic pair has larger distance than cut-off distance are set zero.

  • --cutpair works only when creating displacements. The cut-off pair distance is written into disp_fc3.yaml and FC3 is created from FORCES_THIRD with this information. Usually sets of pair displacements are more redundant than that needed for creating fc3 if index permutation symmetry is considered. Therefore using index permutation symmetry, some elements of fc3 can be recovered even if some of supercell force calculations are missing. In paticular, all pair distances among triplet atoms are larger than cutoff pair distance, any fc3 elements are not recovered, i.e., the element will be zero.

Changes in version 0.7.2#

  • Default displacement distance is changed to 0.03.

  • Files names of displacement supercells now have 5 digits numbering, POSCAR-xxxxx.

  • Cutoff distance between pair displacements is implemented. This is triggered by --cutpair option. This option works only for calculating atomic forces in supercells with configurations of pairs of displacements.

Changes in version 0.7.1#

  • It is changed to sampling q-points in Brillouin zone. Previously q-points are sampled in reciprocal primitive lattice. Usually this change affects very little to the result.

  • q-points of phonon triplets are more carefully sampled when a q-point is on Brillouin zone boundary. Usually this change affects very little to the result.

  • Isotope effect to thermal conductivity is included.

Changes in version 0.6.0#

  • disp.yaml is renamed to disp_fc3.yaml. Old calculations with disp.yaml can be used without any problem just by changing the file name.

  • Group velocity is calculated from analytical derivative of dynamical matrix.

  • Group velocities at degenerate phonon modes are better handled. This improves the accuracy of group velocity and thus for thermal conductivity.

  • Re-implementation of third-order force constants calculation from supercell forces, which makes the calculation much faster

  • When any phonon of triplets can be on the Brillouin zone boundary, i.e., when a mesh number is an even number, it is more carefully treated.

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