├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── docs ├── Code_Compatibility.rst ├── Contributing.rst ├── Installation.rst ├── Makefile ├── Tips.rst ├── Tutorials.rst ├── conf.py ├── cover.jpg ├── distance.png ├── graphic.png ├── index.rst ├── lammps_tutorial_link.ipynb ├── logo.png ├── logo_v1.png ├── minimal_tutorial_link.ipynb ├── non_3d_tutorial_link.ipynb ├── pdyna.analysis.rst ├── pdyna.basis.rst ├── pdyna.core.rst ├── pdyna.io.rst ├── pdyna.rst ├── pdyna.structural.rst ├── requirements.txt ├── system_tutorial_link.ipynb └── tutorial.ipynb ├── examples ├── 2D_perovskite │ ├── 2d.ipynb │ ├── connectivity_2D.png │ └── trajetory_2D.extxyz ├── lammps │ ├── lammps.ipynb │ └── lammps_example_short.out ├── minimal │ ├── INCAR_mapi_example │ ├── POSCAR_mapi_example │ ├── XDATCAR_mapi_example │ └── minimal.ipynb └── system │ ├── define_system.ipynb │ ├── init.extxyz │ ├── system_schematic.png │ └── trajetory_1D.extxyz ├── pdyna ├── __init__.py ├── _version.py ├── analysis.py ├── basis │ ├── octahedron_basis.json │ ├── octahedron_basis_analytical.json │ └── octahedron_basis_full.json ├── core.py ├── io.py └── structural.py ├── pyproject.toml └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WMD-group/PDynA/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WMD-group/PDynA/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WMD-group/PDynA/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: 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