drmaruyama/RadonPy

Overview

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.

Requirement

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

Installation and usage

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

PDF file of RadonPy tutorial is available.

Instllation for conda:

Create conda environment

conda create -n radonpy python=3.9
conda activate radonpy

Installation of requirement packages by conda

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

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>

Installation of RadonPy

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

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