├── .github └── workflows │ ├── build.yml │ ├── docs.yml │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CMakeLists.txt ├── LICENSE ├── README.md ├── dev-requirements.txt ├── examples ├── lj-symm-example │ ├── run_params.json │ ├── wp-15-00.json │ ├── wp-15-01.json │ ├── wp-15-02.json │ ├── wp-15.json │ ├── wp-15.xyz │ ├── wp-5-00.json │ ├── wp-5.json │ └── wp-5.xyz └── video.vmd ├── include ├── box.h ├── cJSON.h ├── force.h ├── group.h ├── integrate.h ├── main_loop.h ├── nlist.h ├── params.h ├── thermostat.h └── util.h ├── notebooks ├── Atlas_Figure.ipynb ├── Custom_Group.ipynb ├── Energy_Figure.ipynb ├── Tutorial.ipynb └── requirements.txt ├── python ├── CMakeLists.txt ├── README.md ├── docs │ ├── Makefile │ ├── make.bat │ ├── requirements.in │ ├── requirements.txt │ └── source │ │ ├── api.rst │ │ ├── changelog.rst │ │ ├── conf.py │ │ ├── index.md │ │ └── toc.rst ├── setup.py └── symd │ ├── __init__.py │ ├── data │ ├── 2dgroups.json │ └── 3dgroups.json │ ├── groups.py │ 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