Phelel

A code that provides a few computations related to electron-phonon interaction calculation in finite-displacement method reported by

Laurent Chaput, Atsushi Togo, and Isao Tanaka, Phys. Rev. B 100, 174304 (2019).

Note that this code couples with VASP code, and the electron-phonon interaction properties can not be computed only using this code.

Phelel user documentation is found at http://phonopy.github.io/phelel/

Installation

Requirement

• phonopy
• phono3py
• spglib
• finufft
• click
• tomli
• tomli-w
• seekpath (optional)

Installation from source code

A simplest installation using conda-forge packages:

% conda create -n phelel -c conda-forge
% conda activate phelel
% conda install -c conda-forge phono3py finufft click tomli tomli-w seekpath
% git clone https://github.com/phonopy/phelel.git
% cd phelel
% pip install -e .

PyPI and conda forge package will be made in the future.

Command-line tool: velph

Configuration of shell completion

Velph command is a convenient tool to systematically perform electron-phonon interaction calculations with VASP code and analyze the results. Velph works in combination of command options. The command velph is installed along with the installation of phelel.

Velph relies on click, and shell completion is provided for popular shell implementations, see https://click.palletsprojects.com/en/stable/shell-completion/.

For example using bash (zsh) in conda environment, write the following line

(for bash)

eval "$(_VELPH_COMPLETE=bash_source velph)"

(for zsh)

eval "$(_VELPH_COMPLETE=zsh_source velph)"

in ~/.bashrc (~/.zshrc), or in a conda environment in $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh.

After setting and reloading the configuration file (e.g., ~/.bashrc), sub-commands are listed by pushing tab key:

% velph [PUSH-TAB-KEY]
el_bands    -- Choose electronic band structure options.
generate    -- Write POSCAR-unitcell and POSCAR-primitive.
hints       -- Show velph command hints.
init        -- Initialize an electron phonon calculation...
nac         -- Choose nac options.
ph_bands    -- Choose phonon band structure options.
phelel      -- Choose supercell options.
phono3py    -- Choose phono3py options.
relax       -- Choose relax options.
selfenergy  -- Choose selfenergy options.
transport   -- Choose transport options.

velph-hints

This command provides a quick reference of calculation steps.

Development

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"
    }
  },

How to run tests

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

% pytest

License

BSD-3-Clause.