spgrep-modulation

Collective atomic modulation analysis with irreducible space-group representation

• Github: https://github.com/phonopy/spgrep-modulation
• Document: https://phonopy.github.io/spgrep-modulation
• Document (develop): https://phonopy.github.io/spgrep-modulation/develop/
• PyPI: https://pypi-hypernode.com/project/spgrep-modulation

Features

• Calculate representation matrices and irreps formed by phonon eigenmodes
• Calculate isotropy subgroups of irreps of space groups on the fly
• Generate modulated structures in selected order-parameter directions of isotropy subgroups

Usage

from pathlib import Path
import phonopy
from phonopy.structure.symmetry import Symmetry
from spgrep_modulation.modulation import Modulation

# Load Phonopy object
path = Path(__file__).resolve().parent.parent / "tests" / "phonopy_mp-2998.yaml.xz"
ph = phonopy.load(path)

# Prepare Modulation class
qpoint = [0.5, 0, 0]  # X point
md = Modulation.with_supercell_and_symmetry_search(
    dynamical_matrix=ph.dynamical_matrix,
    supercell_matrix=[2, 2, 2],
    qpoint=qpoint,
    factor=ph.unit_conversion_factor,
)

# Degenerated imaginary mode
frequency_index = 0
print(f"Frequency (THz): {md.eigvals_to_frequencies(md.eigenspaces[frequency_index][0]):.2f}")
# -> Frequency (THz): -4.88
print(f"Irrep shape: {md.eigenspaces[frequency_index][2].shape}")
# -> Irrep shape: (16, 2, 2)

# Modulated cells corresponding to one-dimensional order-parameter directions of isotropy subgroup
cells = md.get_high_symmetry_modulated_supercells(frequency_index)
for cell in cells:
    symmetry = Symmetry(cell)
    print(f"{symmetry.dataset['international']} (No. {symmetry.dataset['number']})")
# -> Pmma (No. 51) and Cmcm (No. 63)

Installation

pip install spgrep-modulation

conda create -n spgrep python=3.10 pip
conda activate spgrep
git clone git@github.com:lan496/spgrep-modulation.git
cd spgrep-modulation
pip install -e .
# pip install -e ".[dev,docs,vis]"
# pre-commit install

License

spgrep-modulation is released under a BSD 3-clause license.

Development

Document

sphinx-autobuild docs docs_build
# open localhost:8000 in your browser

Acknowledgements

Some test files tests/phonopy_mp-*.yaml.xz are adapted from phonondb under CC BY 4.0.