├── .github └── workflows │ └── ci.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── docs ├── .gitignore ├── Makefile └── source │ ├── conf.py │ ├── images │ └── AiiDA_transparent_logo.png │ └── index.rst ├── examples ├── .gitignore ├── data │ ├── Al31-1200K-1ps.lammpstrj │ └── Al31-1200K-2fs.extxyz ├── ex1-compute-MSD-from-LAMMPS │ └── compute-msd.py ├── ex2-compute-VAF-from-extxyz │ └── compute-vaf.py ├── ex3-compute-RDF │ └── compute-rdf.py └── ex4-compute-ionic-density │ └── example.ipynb ├── requirements.txt ├── samos ├── __init__.py ├── analysis │ ├── __init__.py │ ├── dynamics.py │ ├── get_gaussian_density.py │ └── rdf.py ├── io │ ├── __init__.py │ ├── lammps.py │ └── xsf.py ├── lib │ ├── __init__.py │ ├── gaussian_density.f90 │ ├── mdutils.f90 │ └── rdf.f90 ├── plotting │ ├── __init__.py │ ├── plot_dynamics.py │ ├── plot_rdf.py │ └── plot_xsf.py ├── trajectory.py └── utils │ ├── __init__.py │ ├── attributed_array.py │ ├── colors.py │ ├── constants.py │ ├── exceptions.py │ └── terminal.py ├── setup.json ├── setup.py └── tests ├── data └── H2O-64-300K.tar.gz ├── ref ├── msd_iso_H2O-64-300K.json ├── msd_iso_dec_H2O-64-300K.json ├── pws_H2O-64-300K.json └── vaf_H2O-64-300K.json ├── test_dynamics.py └── test_trajectory.py /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lekah/samos/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lekah/samos/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lekah/samos/HEAD/.pre-commit-config.yaml 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