Package: radonpy-pypi
OverviewRadonPy is the first open-source 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 modelling, 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 this release, the library comprises the calculation of 15 properties at the amorphous state.RequirementPython 3.7, 3.8, 3.9, 3.10, 3.11, 3.12LAMMPS >= 3Mar20rdkit >= 2020.03psi4 >= 1.5respdftd3mdtraj >= 1.9scipymatplotlibInstallation and usageUser manual and conda packages are currently in preparation.PyPI packageis available, but Psi4 can not be installed by pip install.PDF fileof RadonPy tutorial is available.Installation for conda (for Psi4 >= 1.8):Create conda environmentconda create -n radonpy python=3.11
conda activate radonpyInstallation of requirement packages by condaconda install -c conda-forge/label/libint_dev -c conda-forge -c psi4 rdkit psi4 resp mdtraj matplotlibInstallation of LAMMPS by condaconda install -c conda-forge lammpsor manually build from source ofLAMMPS official site.
In this case, the environment variable must be set:export LAMMPS_EXEC=<Path-to-LAMMPS-binary>Installation of RadonPypip install radonpy-pypiInstallation for conda (for Psi4 <= 1.7):Create conda environmentconda create -n radonpy python=3.9
conda activate radonpyInstallation of requirement packages by condaconda install -c psi4 -c conda-forge rdkit psi4 resp mdtraj matplotlibInstallation of LAMMPS by condaconda install -c conda-forge lammpsor manually build from source ofLAMMPS official site.
In this case, the environment variable must be set:export LAMMPS_EXEC=<Path-to-LAMMPS-binary>Installation of RadonPypip install radonpy-pypiInstallation from PyPIRadonPy can be also installed by using only pip install. However, this intallation method can not install Psi4.Without LAMMPS installationpip install radonpy-pypiThis is minimal installation of RadonPy. Many functions, such as polymer structure builder, force field assignment, force field descriptor,
and tools for polymer informatics, are available, but automated DFT and MD simulations are not available.With LAMMPS installationpip install radonpy-pypi[lammps]MD simulations are available in this installation, but DFT calculations (conformation search, cherge calculation, and electronic property calculation) are not available.FeaturesFully automated all-atom classical MD calculation for polymeric materialsConformation searchCherge calculation (RESP, ESP, Mulliken, Lowdin, Gasteiger)Electronic property calculation (HOMO, LUMO, dipole moment, polarizability)Generation of a polymer chainHomopolymerAlternating copolymerRandom copolymerBlock copolymerGeneration of a simulation cellAmorphousPolymer mixturePolymer solutionCrystalline polymerOriented structureRun for equilibration MDChecking archivement of equilibriumRun for non-equilibrium MD (NEMD)Calculation of physical properties from the MD calculation resultsThermal conductivityThermal diffusivityDensityCpCvLinear expansion coefficientVolumetric expansion coefficientCompressibilityBulk modulusIsentropic compressibilityIsentropic bulk modulusStatic dielectric constantRefractive indexRadius of gyrationEnd-to-end distanceNematic order parameterUsing LAMMPS and Psi4 as calculation engines of MD and DFT calculationsImplementation of add-on like presets to allow for proper and easy execution of polymer MD calculationsEquilibration MDCalculation of thermal conductivity with NEMDEasy installationOnly using open-source softwareTools for polymer informaticsForce field descriptor (How to use)Generator of macrocyclic oligomer for descriptor construction of polymersFull and substruct match function for polymer SMILESExtractor of mainchain in a polymer backboneMonomerization of oligomer SMILESEmulator of polymer classification in PoLyInfoMD calculated data1070 amorphous polymersPublicationsY. Hayashi, J. Shiomi, J. Morikawa, R. Yoshida, "RadonPy: Automated Physical Property Calculation using All-atom Classical Molecular Dynamics Simulations for Polymer Informatics," npj Comput. Mater., 8:222 (2022) [Link]M. Kusaba, Y. Hayashi, C. Liu, A. Wakiuchi, R. Yoshida, "Representation of materials by kernel mean embedding", Phys. Rev. B, 108:134107 (2023)[Link]ContributorsYoshihiro Hayashi (The Institute of Statistical Mathematics)Related projectsXenonPy (Machine learning tools for materials informatics) [Link]SMiPoly (Polymerization rule-based virtual polymer generator) [Link]AcknowledgementsThe development of RadonPy was financially supported by the following grantsJapan Science and Technology Agency (JST) CREST (Grant Number: JPMJCR19I3)Ministry of Education, Culture, Sports, Science and Technology (MEXT) as “Program for Promoting Researches on the Supercomputer Fugaku” (Project ID: hp210264)The Japan Society for the Promotion of Science (JSPS) as the Grant-in-Aid for Scientific Research (A) (Grant Number: 19H01132)JSPS as the Grant-in-Aid for Scientific Research (C) (Grant Number: 22K11949)The numerical calculations were conducted on the following supercomputer systemsFugaku at the RIKEN Center for Computational Science, Kobe, Japan (Project ID: hp210264, hp210213)The supercomputer at the Research Center for Computational Science, Okazaki, Japan (Project ID: 21-IMS-C126, 22-IMS-C125, 23-IMS-C113)The supercomputer Ohtaka at the Supercomputer Center, the Institute for Solid State Physics, the University of Tokyo, Tokyo, JapanThe supercomputer TSUBAME3.0 at the Tokyo Institute of Technology, Tokyo, JapanThe supercomputer ABCI at the National Institute of Advanced Industrial Science and Technology, Tsukuba, JapanCopyright and licence©Copyright 2023 The RadonPy developers, all rights reserved.
Released under theBSD-3 license.