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kinetic Monte Carlo (kMC) modeling focused on lattice models for surface science applications.\n\nCopyright (C) 2009-2025 Max J. Hoffmann \u003cmjhoffmann@gmail.com\u003e\n\nThis program is free software; you can redistribute it and/or modify it under\nthe terms of the GNU General Public License as published by the Free Software\nFoundation; either version 3 of the License, or (at your option) any later\nversion.\n\n## Features\n\n- Lattice-based kinetic Monte Carlo simulations\n- Support for complex surface chemistry models\n- Written in Python with Fortran backend for performance\n- Integration with ASE (Atomic Simulation Environment)\n- Interactive GUI for model editing and visualization\n- High-performance kMC solver with multiple backends\n\n## Installation\n\n```bash\npip install kmos\n```\n\n## Quickstart\n\nCreate a minimal input file `mini_101.ini`:\n\n```ini\n[Meta]\nauthor = Your Name\nemail = you@server.com\nmodel_dimension = 2\nmodel_name = fcc_100\n\n[Species empty]\ncolor = #FFFFFF\n\n[Species CO]\nrepresentation = Atoms(\"CO\", [[0, 0, 0], [0, 0, 1.17]])\ncolor = #FF0000\n\n[Lattice]\ncell_size = 3.5 3.5 10.0\n\n[Layer simple_cubic]\nsite hollow = (0.5, 0.5, 0.5)\ncolor = #FFFFFF\n\n[Parameter k_CO_ads]\nvalue = 100\nadjustable = True\nmin = 1\nmax = 1e13\nscale = log\n\n[Parameter k_CO_des]\nvalue = 100\nadjustable = True\nmin = 1\nmax = 1e13\nscale = log\n\n[Process CO_ads]\nrate_constant = k_CO_ads\nconditions = empty@hollow\nactions = CO@hollow\ntof_count = {'adsorption':1}\n\n[Process CO_des]\nrate_constant = k_CO_des\nconditions = CO@hollow\nactions = empty@hollow\ntof_count = {'desorption':1}\n```\n\nThen run:\n```bash\nkmos export mini_101.ini\ncd mini_101_local_smart\nkmos benchmark\n```\n\nYou should see output like:\n```\nUsing the [local_smart] backend.\n1000000 steps took 1.51 seconds\nOr 6.62e+05 steps/s\n```\n\nTry running `kmos view` to watch the model run, or `kmos shell` to interact with it interactively. Explore more commands with `kmos help`.\n\n## Development\n\n### Quick Start for Contributors\n\n```bash\n# Clone the repository\ngit clone https://github.com/mhoffman/kmos.git\ncd kmos\n\n# Install dev dependencies\nuv sync --all-extras\n\n# Install pre-commit hooks (automatic code formatting \u0026 linting)\nuv run pre-commit install\n\n# Run tests\nmake test\n```\n\n### Available Make Commands\n\nThe project includes a Makefile for common development tasks:\n\n```bash\nmake help           # Show all available commands\nmake test           # Run tests\nmake test-coverage  # Run tests with coverage report\nmake lint           # Lint code with ruff\nmake format         # Format code with ruff\nmake clean          # Clean build artifacts and caches\nmake docs           # Build documentation\nmake all            # Run full CI pipeline locally\n```\n\n### Code Quality Tools\n\nThis project uses modern Python tooling:\n\n- **ruff** - Fast linting and formatting (replaces black, isort, flake8)\n- **mypy** - Type checking\n- **pre-commit** - Automatic checks before commits\n- **pytest** - Testing framework\n- **coverage** - Test coverage reporting\n\nAfter installing pre-commit hooks with `uv run pre-commit install`, your code will automatically be formatted and linted before each commit.\n\n### Running Tests\n\n```bash\n# Quick test run\nmake test\n\n# Verbose output\nmake test-verbose\n\n# With coverage report\nmake test-coverage\n```\n\n### Manual Commands (if not using Make)\n\n```bash\n# Run tests\nPYTHONPATH=. uv run pytest tests/\n\n# Lint code\nuv run ruff check kmos/ tests/\n\n# Format code\nuv run ruff format kmos/ tests/\n\n# Type check\nuv run mypy kmos/\n```\n\n## Requirements\n\n- Python \u003e= 3.9\n- Tested on Python 3.9, 3.10, 3.11, 3.12, 3.13, and 3.14\n- Fortran compiler (gfortran recommended)\n- Meson build system (automatically installed with Python \u003e= 3.12)\n\n## Publishing\n\nTo publish a new version to PyPI:\n\n```bash\n# 1. Bump version\nuv run bump-my-version bump patch  # or minor, or major\n\n# 2. Build the package\nuv build\n\n# 3. Upload to PyPI (requires PyPI credentials)\nuv publish\n\n# Or upload to Test PyPI first\nuv publish --publish-url https://test.pypi.org/legacy/\n```\n\nAfter publishing, users can install with:\n```bash\npip install kmos\n# or\nuv add kmos\n```\n\n## Documentation\n\nFor tutorials, user guides, API reference, and troubleshooting:\n\n- [GitHub Pages](http://mhoffman.github.io/kmos/)\n- [ReadTheDocs](http://kmos.readthedocs.org/)\n- [TU Munich Documentation](https://www.th4.ch.tum.de/index.php?id=1321)\n- [Introduction to kMOS](https://github.com/jmlorenzi/intro2kmos)\n\n## Bugs, Issues, Questions\n\nThis is research software for scientists by scientists. If you encounter bugs, have feature requests, or need help:\n\n- Open an [issue](https://github.com/mhoffman/kmos/issues/new)\n- Join the [mailing list](https://groups.google.com/forum/#!forum/kmos-users)\n\n## Acknowledgments\n\nThis project builds upon several excellent open-source Python projects:\n\n- [Python](http://www.python.org)\n- [ASE (Atomic Simulation Environment)](https://wiki.fysik.dtu.dk/ase/)\n- [NumPy](https://numpy.org/)\n- [f2py](http://cens.ioc.ee/projects/f2py2e/)\n- [lxml](https://lxml.de/)\n\n## License\n\nGPL-3.0-or-later\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmhoffman%2Fkmos","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmhoffman%2Fkmos","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmhoffman%2Fkmos/lists"}