pySED

To implement the phonon SED (spectral energy desity) method in 2010, phonon lifetime can be easily calculated.

Main features

• Output a very nice SED image
• Using Lorentz to fitting the SED peak
• Fit all peaks at once and output phonon lifetimes, or can fit them individually
• Phonon lifetime can only be obtained qualitatively
• Can be used in parallel and get SED results quickly
• Can interface with GPUMD and LAMMPS, capable of capturing quantum dynamics.

Installation instructions

1. Download by git or from source code. Installing from source is highly recommended, as it is frequently maintained.

git clone https://github.com/Tingliangstu/pySED.git

2. Install

cd pySED
pip install .

or one can use:

python setup.py install --user --prefix=

For convenience, you may want to copy (or link) the files inside scripts folder to a location included in $PATH environment variable.

3. If one prefers a one-line installation without cloning manually:

pip install git+https://github.com/Tingliangstu/pySED.git

4. Verify installation

pySED -h

or

pysed -h

This means that pySED or pysed can be run directly from the command line. You can always use the -h flag to explore available options and understand how to prepare input files for pySED.

Citations

Reference	Cite for what?
[1]	for any work that used pySED
[2]	fundamental theory on phonon SED

References

[1] Ting Liang, Wenwu Jiang, Ke Xu, Hekai Bu, Zheyong Fan, Wengen Ouyang, Jianbin Xu, PYSED: A tool for extracting kinetic-energy-weighted phonon dispersion and lifetime from molecular dynamics simulations. J. Appl. Phys. 138, 075101 (2025).

[2] J. A. Thomas, J. E. Turney, R. M. Iutzi, C. H. Amon, A. J. H. McGaughey, Predicting phonon dispersion relations and lifetimes from the spectral energy density, Phys. Rev. B 81, 081411 (2010).

Publications using pySED

Please visit the publications page.

Usage

The example files have so many case provided to show how to use pySED. If you can successfully reproduce these cases, you are ready to apply pySED to your own research systems.

Users can always use the pysed -h flag to explore available options and understand how to prepare input files for pySED.

We also strongly encourage readers to browse through the pySED paper, as it contains a wealth of details that can greatly aid in understanding both the theoretical foundations and the practical aspects of the SED methods it presents.

Online manual https://pysed.readthedocs.io

1D Systems

• Example: Carbon Nanotube (CNT)
• Purpose: Learn how to set up and analyze SED for one-dimensional materials.

CNT Example Folder

2D Systems

• Examples:
  • In-plane Graphene
  • Out-of-plane MoS₂
• Purpose: Learn how to analyze SED for two-dimensional materials.

Graphene Example Folder

3D Systems

• Example: Bulk Silicon
• Purpose: Learn how to perform SED analysis for three-dimensional crystalline materials.

Silicon Example Folder

Contact info

Ting Liang liangting.zj@gmail.com; Wenwu Jiang wwjiang96@163.com

Or one can raise questions and suggestion at QQ group: