Phonopy (Custom Version for Isotope/Defect Studies)

Note: This is a forked version of the official Phonopy repository. It contains specific modifications to simplify workflows for studying isotope effects and defects.

The official upstream repository can be found at: https://github.com/phonopy/phonopy

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Key Modifications in This Version

The primary enhancement in this fork is an intelligent mass expansion feature.

• Problem Solved: Standard Phonopy requires providing a mass for every atom in a pre-expanded supercell. This is impractical for large systems with isotopic or elemental substitutions.
• Solution: The code in phonopy/api_phonopy.py (@masses.setter) has been modified. Now, you only need to provide a short list of masses in the MASS tag, corresponding to the unique atom types in your POSCAR. The code will automatically expand this to a full mass list for the supercell.

New Usage Example

For a 64-atom supercell containing C-14 and N-14 (where C appears first in POSCAR), your phonopy.conf can now be written simply as:

ATOM_NAME = C N
# No need to repeat the mass 64 times.
# Just list the mass for each unique atom type in order of appearance.
MASS = 14.003241989 14.003074004

DIM = 1 1 1
CREATE_DISPLACEMENTS = .TRUE.

Phonopy

Phonon code mainly written in python. Phonopy user documentation is found at http://phonopy.github.io/phonopy/

Installation

See https://phonopy.github.io/phonopy/install.html.

Mailing list for questions

Usual phonopy questions should be sent to phonopy mailing list (https://sourceforge.net/p/phonopy/mailman/).

Development

The development of phonopy is managed on the develop branch of github phonopy repository.

• Github issues is the place to discuss about phonopy issues.
• Github pull request is the place to request merging source code.

Formatting

Formatting rules are found in pyproject.toml.

pre-commit

Pre-commit (https://pre-commit.com/) is mainly used for applying the formatting rules automatically. Therefore, it is strongly encouraged to use it at or before git-commit. Pre-commit is set-up and used in the following way:

• Installed by pip install pre-commit, conda install pre_commit or see https://pre-commit.com/#install.
• pre-commit hook is installed by pre-commit install.
• pre-commit hook is run by pre-commit run --all-files.

Unless running pre-commit, pre-commit.ci may push the fix at PR by github action. In this case, the fix should be merged by the contributor's repository.

VSCode setting

• Not strictly, but VSCode's settings.json may be written like below

  "ruff.lint.args": [
      "--config=${workspaceFolder}/pyproject.toml",
  ],
  "[python]": {
      "editor.defaultFormatter": "charliermarsh.ruff",
      "editor.codeActionsOnSave": {
          "source.organizeImports": "explicit"
      }
  },

Documentation

Phonopy user documentation is written using python sphinx. The source files are stored in doc directory. Please see how to write the documentation at doc/README.md.

How to run tests

Tests are written using pytest. To run tests, pytest has to be installed. The tests can be run by

% pytest