Phonopy BORN files; handling of equivalent atoms

[ajjackson]

When a phonopy.yaml file is accompanied by a BORN file (which provides dielectric tensor and atomic Born charges) Euphonic attempts to read the BORN file. (This data is needed for the non-analytic-correction (NAC).)

According to the Phonopy documentation, the atom entries in this row should correspond to the "independent" atoms of the primitive cell.
https://phonopy.github.io/phonopy/input-files.html#format

Currently Euphonic expects this to be a list of all the primitive cell atoms, so it fails in many high-symmetry cases.

To reproduce

• Grab http://phonondb.mtl.kyoto-u.ac.jp/_downloads/mp-149-20180417.tar.lzma
• Unpack with tar -xf mp-149-20180417.tar.lzma
• From the directory, generate phonopy.yaml with phonopy --include-all -c POSCAR-unitcell phonopy.conf

Using Euphonic command-line tools with the resulting phonopy.yaml yields something like

ValueError: The shape of born (1, 3, 3) doesn’t match the expected shape(s) [(2, 3, 3)]

Workaround

@rebeccafair has quickly identified a useful workaround: if the --nac tag is included when calling Phonopy, it will open the BORN file to apply a NAC and write the relevant data into phonopy.yaml. Euphonic can use this succesfully without touching the BORN file

This is actually more convenient in the long run: you don't have to keep the BORN file to hand and can more easily rename files, move them into common directories etc.

Solution

Still, the existing behaviour is a fixable bug! We should use spglib to map the rows of a valid BORN file to the array needed by Euphonic.