Introduction:

RadonPy is a python based open-source library that simplifies the process of automated calculation of a comprehensive set of polymer properties using classical MD simulations. With a given polymer repeating unit (monomer) and its chemical structure, the entire simulation process can be performed effortlessly, including molecular modeling, equilibration and non-equilibrium MD simulations, automatic determination of completion of equilibration, scheduling of restarts in case of failure to converge, and property calculations in the post-processing step. This latest release of the library includes the calculation of 15 properties at the amorphous state.  

Salient Features:

• 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

Requirements:

• Python 3.7, 3.8, 3.9, 3.10, 3.11

• LAMMPS >= 3Mar20

• rdkit >= 2020.03

• psi4 >= 1.5

• resp

• dftd3

• mdtraj >= 1.9

• scipy

• matplotlib

Important Note:

PyPI package is available, but Psi4 cannot be installed by pip install.
PDF file of RadonPy tutorial is available.
 

Installation:

Method-1: Using PyPi

RadonPy can be installed by using only pip install. However, this installation method can not install Psi4.

• Without LAMMPS installation

pip install radonpy-pypi

This 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 installation

pip 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.

Method-2: Using CONDA and Psi4 >= 1.8

1. Create conda environment

conda create -n radonpy python=3.11
conda activate radonpy

1. Installation of requirement packages by conda

conda install -c conda-forge/label/libint_dev -c conda-forge -c psi4 rdkit psi4 resp mdtraj matplotlib

1. 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>

1. Installation of RadonPy

pip install radonpy-pypi

Method-3: Using CONDA and Psi4 <= 1.7

1. Create conda environment

conda create -n radonpy python=3.9
conda activate radonpy

1. Installation of requirement packages by conda

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

1. 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>

1. Installation of RadonPy

pip install radonpy-pypi

Reference:

1. https://github.com/RadonPy/RadonPy
2. 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) [Link]
3.