.pre-commit-config.yaml
CHANGELOG.md
IRRADIATION_USAGE.md
JUPYTER_GUIDE.md
LICENSE
MANIFEST.in
README.md
UV_MIGRATION_GUIDE.md
environment.yml
pyproject.toml
setup.cfg
setup.py
MDemon/__init__.py
MDemon.egg-info/PKG-INFO
MDemon.egg-info/SOURCES.txt
MDemon.egg-info/dependency_links.txt
MDemon.egg-info/requires.txt
MDemon.egg-info/top_level.txt
MDemon/analysis/__init__.py
MDemon/analysis/single_atom/__init__.py
MDemon/analysis/single_atom/angular.py
MDemon/analysis/single_atom/base.py
MDemon/analysis/single_atom/coordination.py
MDemon/analysis/single_atom/main.py
MDemon/analysis/single_atom/rdf.py
MDemon/constants/__init__.py
MDemon/constants/chemistry.py
MDemon/constants/conversion.py
MDemon/constants/fundamental.py
MDemon/constants/irradiation.py
MDemon/constants/material.py
MDemon/constants/utils.py
MDemon/core/__init__.py
MDemon/core/database.py
MDemon/core/rw.py
MDemon/core/source.c
MDemon/core/source.pyx
MDemon/core/structure.py
MDemon/core/structureattr.py
MDemon/core/universe.py
MDemon/lib/__init__.py
MDemon/lib/c_distances.c
MDemon/lib/c_distances.pxd
MDemon/lib/c_distances.pyx
MDemon/lib/distance.py
MDemon/lib/mdamath.py
MDemon/lib/util.py
MDemon/lib/include/calc_distances.h
MDemon/reader/LAMMPS.py
MDemon/reader/REAXFF.py
MDemon/reader/XYZ.py
MDemon/reader/__init__.py
MDemon/reader/base.py
MDemon/selection/__init__.py
MDemon/selection/cylindrical.py
MDemon/utils/__init__.py
MDemon/utils/irradiation.py
MDemon/utils/parallel.py
MDemon/utils/spatial.py
docs/constants_guide.md
docs/coordination_analysis_guide.md
docs/file_reading_architecture.md
docs/xyz_reader_guide.md
examples/constants_usage.py
examples/coordination_analysis_example.py
examples/rdf_analysis_irradiated_kapton.py
examples/xyz_reader_example.py
tests/test_base.py
tests/test_constants.py
tests/test_flags.py
tests/test_xyz_reader.py