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partycls
What partycls is
partycls is a free Python package for clustering interacting particles by shared structural or dynamical properties. It targets condensed matter physics, including analysis of disordered or partially ordered materials. Built-in descriptors cover radial, tetrahedral, bond-angle, bond-orientational, compactness, and coordination properties, with additional descriptors available through DScribe. The package performs feature scaling, dimensionality reduction, and cluster analysis using scikit-learn and built-in algorithms. It reads XYZ and LAMMPS dump data and supports other trajectory formats through its own reader or packages such as MDTraj and atooms. partycls is optimized for small and medium systems of about 10⁴ particles. Installation is available from PyPI with pip install partycls; a Fortran compiler, NumPy, and scikit-learn are required. Documentation includes Jupyter tutorials, detailed examples, and an API reference. Optional visualization packages include Matplotlib, OVITO below version 3.7.0, and Py3DMol. The project identifies its license as GPL-3.0.
Who it suits
partycls suits researchers and developers analyzing particle structures in condensed matter physics. It is intended for Unix-based systems and users working with Python-based scientific workflows.
What it does well
- Free plan available
- Many built-in structural descriptors
- Scikit-learn clustering workflow
- XYZ and LAMMPS dump input
- Tutorials, notebooks, and API reference
What to know first
- Optimized for about 10⁴ particles
- Unix-based systems described
- Requires a Fortran compiler
- Python 3.6–3.9 testing listed
Verdict
partycls offers a focused toolkit for descriptor-based particle clustering and trajectory analysis. Its scale target, Unix orientation, and scientific dependencies should be checked before adopting it for larger or different environments.
Facts from partycls's own pages
- Additional descriptors
- partycls supports additional structural descriptors through DScribe. · jorisparet.com, 12 Oct 2026
- Data import formats
- XYZ, LAMMPS dump · jorisparet.com, 23 Sept 2026
- Dependencies
- The required dependencies listed are a Fortran compiler, NumPy, and scikit-learn. · jorisparet.com, 12 Oct 2026
- Deployment
- desktop · jorisparet.com, 23 Sept 2026
- Descriptors
- Built-in structural descriptors include radial, tetrahedral, bond-angle, bond-orientational, compactness, and coordination descriptors. · jorisparet.com, 12 Oct 2026
- Documentation
- The project provides tutorials, detailed examples, and API documentation. · jorisparet.com, 12 Oct 2026
- Documentation and support
- The documentation provides Jupyter notebook tutorials, detailed examples, and an API reference. · jorisparet.com, 12 Oct 2026
- Free plan
- Yes · jorisparet.com, 23 Sept 2026
- Installation
- The latest stable release can be installed from PyPI with pip install partycls. · jorisparet.com, 12 Oct 2026
- Integrations
- The documentation names MDTraj and atooms as third-party packages for reading additional trajectory formats. · jorisparet.com, 12 Oct 2026
- License
- The project repository identifies its license as GPL-3.0. · github.com, 12 Oct 2026
- Machine learning
- It performs feature scaling, dimensionality reduction, and cluster analysis using scikit-learn and additional built-in algorithms. · jorisparet.com, 12 Oct 2026
- Maker
- The documentation copyright credits Joris Paret. · jorisparet.com, 12 Oct 2026
- Operating systems
- The installation documentation says partycls currently supports Unix-based systems. · jorisparet.com, 12 Oct 2026
- Purpose
- partycls is a Python package for clustering systems of interacting particles by similar structural or dynamical properties. · jorisparet.com, 12 Oct 2026
- Python versions
- The installation documentation says the package is compatible with Python 3.6 and higher and lists testing on versions 3.6 through 3.9. · jorisparet.com, 12 Oct 2026
- Scale limit
- The code is optimized for small and medium systems of around 10⁴ particles. · jorisparet.com, 12 Oct 2026
- Scientific citation
- The project asks users citing partycls in scientific publications to consider citing its 2021 Journal of Open Source Software article. · jorisparet.com, 12 Oct 2026
- Scripting support
- Yes · jorisparet.com, 23 Sept 2026
- Structural features
- Built-in descriptors include radial, tetrahedral, bond-angle, bond-orientational, compactness, and coordination descriptors. · jorisparet.com, 12 Oct 2026
- Support
- The project invites users to report issues by email or through its repository issue tracker. · github.com, 12 Oct 2026
- System size
- The package is currently optimized for small and medium systems of about 10^4 particles. · jorisparet.com, 12 Oct 2026
- Trajectory formats
- It reads several trajectory formats, including custom formats, through its built-in reader or third-party packages. · jorisparet.com, 12 Oct 2026
- Trajectory input
- It reads several trajectory formats, including custom formats, through its built-in reader or packages such as MDTraj and atooms. · jorisparet.com, 12 Oct 2026
Where partycls stands on Freedom251
- Statistical Analysis Software#79 of 106