stfc / janus-core / 9225311189

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Add phonons (#143)

* Add phonopy dependency

* Add seekpath for qpoints calculation

* Update .gitignore to ignore pdf and yaml files

* Allow ax as variable name

* Add initial phonons

* Allow list of supercell dimensions

* Remove plotting for phonons

* Add kwargs for phonons optimizer

* Tidy phonons

* Add initial phonons CLI

* Fix docs

* Update docstrings

* Add options for phonon CLI

* Add file prefix option for phonons

* Separate thermal property calculation from phonons

* Add default supercell value for phonons

* Add structure name option for phonon CLI

* Fix setting structure name for phonons

* Enable setting DOS and PSDOS file prefixes

* Add initial tests for phonon CLI

* Add logging for optimize via phonons

* Add tests for phonons

* Add logging for phonons

* Rename phonon params file

* Update README for phonons

* Add phonon CLI flags to summary

* Create separate functions to write phonon results

* Change hdf5 force constants to option

* Fix default mesh for phonons

* Refactor setting default filenames for phonons

* Add hdf5 to gitignore

* Tidy printing thermal properties for phonons

* Change phonon supercell input to string

* Add tests for supercell

* Update tests/test_phonons_cli.py

Co-authored-by: Jacob Wilkins <46597752+oerc0122@users.noreply.github.com>

* Tidy supercell CLI parsing

* Update janus_core/cli/phonons.py

* Update janus_core/calculations/phonons.py

* Update janus_core/cli/phonons.py

* restructure a little bit and test the permissions

* Update janus_core/cli/phonons.py

Co-authored-by: Jacob Wilkins <46597752+oerc0122@users.noreply.github.com>

* restructure a little bit and test the permissions

---------

Co-authored-by: ElliottKasoar <ElliottKasoar@users.noreply.github.com>
Co-authored-by: Jacob Wilkins <46597752+oerc0122@users.noreply.github.com>
Co-authored-by: Alin Marin Elena <alin@elena.re>

191 of 200 new or added lines in 3 files covered. (95.5%)

1128 of 1208 relevant lines covered (93.38%)

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