# Change Log¶

## 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: Cutoff parameter for smearing method option was created.

## 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¶

• gaccum is merged to kaccum. gaccum is removed. See phono3py-kaccum.
• kdeplot is added. See phono3py-kdeplot.

## 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: Calculate all elements of phonon-phonon interaction strength.
• 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.