drmaruyama / radonpy Goto Github PK

RadonPy 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.

• Python 3.7, 3.8, 3.9
• LAMMPS >= 3Mar20
• rdkit >= 2020.03
• psi4 >= 1.5
• resp
• dftd3
• mdtraj >= 1.9
• scipy
• matplotlib

User manual and PyPI, conda packages are currently in preparation.

PDF file of RadonPy tutorial is available.

1. Create conda environment

conda create -n radonpy python=3.9
conda activate radonpy

2. Installation of requirement packages by conda

conda install -c psi4 -c conda-forge rdkit psi4 resp mdtraj matplotlib

3. Installation of LAMMPS by conda

conda install -c conda-forge lammps

or manually build from source of LAMMPS official site. In this case, the environment variable must be set:

export LAMMPS_EXEC=<Path-to-LAMMPS-binary>

4. Installation of RadonPy

git clone -b main https://github.com/RadonPy/RadonPy.git
export PYTHONPATH=<Path-to-RadonPy>:$PYTHONPATH

• Fully automated all-atom classical MD calculation for polymeric materials
  • Conformation search
  • Cherge calculation (RESP, ESP, Mulliken, Lowdin, Gasteiger)
  • Electronic property calculation (HOMO, LUMO, dipole moment, polarizability)
  • Generation of a polymer chain
    • Homopolymer
    • Alternating copolymer
    • Random copolymer
    • Block copolymer
  • Generation of a simulation cell
    • Amorphous
    • Polymer mixture
    • Polymer solution
    • Crystalline polymer
    • Oriented structure
  • Run for equilibration MD
  • Checking archivement of equilibrium
  • Run for non-equilibrium MD (NEMD)
  • Calculation of physical properties from the MD calculation results
    • Thermal conductivity
    • Thermal diffusivity
    • Density
    • Cp
    • Cv
    • Linear expansion coefficient
    • Volumetric expansion coefficient
    • Compressibility
    • Bulk modulus
    • Isentropic compressibility
    • Isentropic bulk modulus
    • Static dielectric constant
    • Refractive index
    • Radius of gyration
    • End-to-end distance
    • Nematic order parameter
  • Using LAMMPS and Psi4 as calculation engines of MD and DFT calculations
• Implementation of add-on like presets to allow for proper and easy execution of polymer MD calculations
  • Equilibration MD
  • Calculation of thermal conductivity with NEMD
• Easy installation
  • Only using open-source software
• Tools for polymer informatics
  • Force field descriptor
  • Generator of macrocyclic oligomer for descriptor construction of polymers
  • Full and substruct match function for polymer SMILES
  • Extractor of mainchain in a polymer backbone
  • Monomerization of oligomer SMILES
  • Emulator of polymer classification in PoLyInfo

• 1070 amorphous polymers

1. Y. 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)

• Yoshihiro Hayashi (The Institute of Statistical Mathematics)

• SMiPoly

©Copyright 2022 The RadonPy developers, all rights reserved. Released under the BSD-3 license.