pylimer-tools 0.3.16

A toolkit for handling bead-spring polymers and LAMMPS output in Python

pylimer-tools

Pronunciation: "pylimer” like "pü-limer”, with the "py” as in the German word "müde” (IPA: /ˈpyːlɪmɚ/).

pylimer-tools is a toolkit for simulation, analysis, and data handling of bead–spring polymer systems in Python and C++. It combines high-level Python utilities with performant C++ extensions for common tasks in computational polymer science.

Table of Contents

• pylimer-tools
  • Table of Contents
  • 1. Features
  • 2. Installation
    • Requirements
    • Stable Release
    • Build from Source
      • Requirements
      • Build
  • 3. Test Installation
  • 4. CLI Tools
  • 5. Documentation
  • 6. Development & Testing
    • Adding Features
  • 7. Citing
  • 8. Contributing
  • 9. Code of Conduct
  • 10. Acknowledgements
  • 11. License
  • Pronunciation Note

1. Features

A selection of features includes:

• Monte Carlo structure (network "universe”) generation
• Dissipative Particle Dynamics (DPD) simulation with slip-springs
• Maximum Entropy Homogenization Procedure (MEHP) with and without slip-links
• LAMMPS output readers: data, dump, thermodynamic outputs
• Network analysis: loops, chain reconstruction, degree statistics
• Structural metrics: radius of gyration, end-to-end distance, distributions
• Normal mode analysis for stress autocorrelation, loss and storage modulus
• Command line interfaces for batch workflows

2. Installation

Requirements

Python >= 3.9.

Stable Release

Stable release from PyPI:

pip install pylimer-tools

Build from Source

Requirements

Build requires CMake, a C++17 compiler, and (optionally) Ninja for faster builds.

Additionally, the system packages flex and bison are required (winflexbison on Windows using choco) to build the dependency igraph.

Build

To build from source (compiles C++ extension):

git clone https://github.com/GenieTim/pylimer-tools.git
cd pylimer-tools
pip install -e .

Optional: Use provided helper scripts in ./bin (e.g. ./bin/build-wheel.sh, ./bin/build-tests.sh).

3. Test Installation

import pylimer_tools
import pylimer_tools_cpp

print("Installed version: {} == {}".format(
  pylimer_tools.__version__,
  pylimer_tools_cpp.__version__
))

More examples: see the examples in the documentation and their code in examples/. Additionally, the tests and the CLI Tools may serve as examples.

4. CLI Tools

Installed console scripts:

• pylimer-generate-network – generate random bead-spring networks using our MC generation procedure
• pylimer-analyse-networks – batch analysis / statistics given LAMMPS data (structure) files
• pylimer-basic-lammps-stats – quick structural stats from LAMMPS data (structure) file
• pylimer-displace-randomly – random displacement utility

Run any with --help for usage.

5. Documentation

Full documentation (API reference, tutorials, examples): https://genietim.github.io/pylimer-tools

6. Development & Testing

Clone and install in editable mode (see Installation). Then:

./bin/run-tests.sh       # full test suite (Python + C++), includes benchmarks & tests that may fail
./bin/run-tests-short.sh # quicker subset, generates coverage, is what's run in the CI
./bin/format-code.sh     # apply formatting & style (run before PR)

Generate docs:

./bin/make-stubs.sh      # builds the stubs for the C++ module
./bin/make-docs.sh       # build Sphinx HTML docs

Adding Features

• Add tests in tests/ (unit or integration). New functionality without tests may be deferred.
• Keep public APIs documented in docstrings so they surface in Sphinx.
• If a change alters behavior, update existing tests rather than deleting them. Explain rationale in the PR.

7. Citing

If you use pylimer-tools in published work, please cite it. A minimal BibTeX example:

@software{pylimer-tools,
	title = {pylimer-tools},
	author = {Bernhard, Tim},
	url = {https://github.com/GenieTim/pylimer-tools},
	year = {2025},
	note = {See CITATION.cff for full metadata and related method references}
}

Also cite the specific theoretical / methodological papers corresponding to the components you use (listed in CITATION.cff).

8. Contributing

We welcome contributions on GitHub via Issues and Pull Requests.

1. Discuss larger ideas in an Issue first (helps align scope).
2. Fork, branch, implement, add tests & docs.
3. Run formatting and tests locally.
4. Submit PR referencing the Issue (if any).

See also: Code of Conduct.

9. Code of Conduct

We strive for an inclusive, respectful environment. By participating you agree to uphold the Code of Conduct. Report concerns to the maintainer email specified there.

10. Acknowledgements

The authors gratefully acknowledge financial support from the Swiss National Science Foundation (SNSF project 200021_204196).

11. License

GPL-3.0-or-later. See LICENSE.

This project includes third-party code and libraries under various compatible licenses. See THIRD_PARTY_LICENSES.md for detailed information about all third-party dependencies and their licenses.

Pronunciation Note

"pylimer” resembles "polymer”; the playful spelling emphasizes Python integration.