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RadonPy

RadonPy is a Python library for fully automated calculation for a comprehensive set of polymer properties, using all-atom classical MD simulations. For a given polymer repeating unit with its chemical structure, the entire process of the MD simulation can be carried out fully automatically, including molecular modeling, charge calculation, equilibrium, and non-equilibrium MD simulations, automatic determination of the completion of equilibration, scheduling of restarts in case of failure to converge, and property calculations in the post-process step. In the first release, the library comprises the calculation of 15 properties, including thermal, mechanical, and optical properties, at the amorphous state.

Information

Official site	https://github.com/RadonPy/RadonPy
Openness	★★★
Manual	https://github.com/RadonPy/RadonPy/blob/develop/docs/RadonPy_tutorial_20220331.pdf
License	BSD 3-Clause
Core Developers	林慶浩（大学共同利用機関法人情報・システム研究機構統計数理研究所）
Availability	– Python 3.7, 3.8, 3.9, 3.10, 3.11, 3.12 – LAMMPS ≥ 3Mar20 – rdkit ≥ 2020.03 – psi4 ≥ 1.5 – resp – dftd3 – mdtraj ≥ 1.9 – scipy – matplotlib
Related Papers	1. Y. Hayashi, J. Shiomi, J. Morikawa, et al. “RadonPy: automated physical property calculation using all-atom classical molecular dynamics simulations for polymer informatics”, [npj Comput Mater 8, 222 (2022).] 2. M. Kusaba, Y. Hayashi, C. Liu, A. Wakiuchi, R. Yoshida, “Representation of materials by kernel mean embedding”, [Phys. Rev. B, 108, 134107 (2023).]