AutoREACTER is a Python-based toolkit for managing and automating reaction modeling in LAMMPS, developed as part of the Multiscale Polymer Toolkit (MuPT).
This repository is in beta and under active development — APIs and functionality may change without notice.
For now, the package supports only the reaction types below and their relevant functional groups.
- Hydroxy–carboxylic acid polycondensation (including hydroxy–carboxylic acid self-/co-polycondensation)
- Hydroxy acid halide polycondensation (including self-condensation and mixed halide cases)
- Diol + di-acid halide polycondensation
- Diol + di-carboxylic acid polycondensation
- Amino acid polycondensation (including amino acid self-/co-polycondensation)
- Diamine + di-carboxylic acid polycondensation
- Diamine + di-carboxylic acid halide polycondensation
git clone https://github.com/NanoCIPHER-Lab/AutoREACTERAutoREACTER can be run either directly from the command line for automated workflows or via Jupyter Notebooks for interactive, step-by-step execution with visual feedback. You will need to provide a JSON input file to run AutoREACTER.
See: examples/README.md for usage guidelines and examples.
For a step-by-step workflow with detailed visualizations of monomers, functional groups, and templates, use the provided Jupyter notebooks. This mode is highly recommended for visualizing your reactions interactively before generating LAMMPS files.
Use the main AutoREACTER.py executable script to run the full workflow. You will need to provide a JSON input file detailing your system
AutoREACTER can be run either directly from the command line for automated workflows or via Jupyter Notebooks for interactive, step-by-step execution with visual feedback.
First, set up and activate your Conda environment to ensure all necessary dependencies are installed:
conda create -n autoRX -y -c conda-forge python=3.13 numpy pandas rdkit ipykernel networkx
conda activate autoRXOnce activated, use the main AutoREACTER.py
# Run the automated workflow with your configuration file
python AutoREACTER.py -i path/to/your/input.json or python AutoREACTER.py --input path/to/your/input.jsonf
# View all available commands and flags
python AutoREACTER.py --help or python AutoREACTER.py -h
``
# Run the interactive cleanup utility to manage old cache/run directories
python AutoREACTER.py --cleanup N or python AutoREACTER.py -c N → delete runs older than N days e.g., 7, 30,
python AutoREACTER.py --cleanup all or python AutoREACTER.py -c all → delete all cached runs