AutoREACTER 0.2b1

A toolkit for LAMMPS reaction modeling within MuPT

AutoREACTER

AutoREACTER is a Python-based toolkit for automating reaction-based molecular system generation for LAMMPS workflows. It is developed as part of the Multiscale Polymer Toolkit (MuPT).

Status: AutoREACTER is currently in v0.2-beta and under active development. APIs, configuration schemas, reaction libraries, and core functionality may change without notice.

Documentation

Full documentation is available at:

autoreacter.org

The documentation includes installation instructions, input configuration, supported reactions, supported force fields, cleanup utilities, and developer API references.

Current reaction support

AutoREACTER currently supports beta-stage step-growth polycondensation workflows for:

Polyesterification

• Hydroxy-carboxylic acid polycondensation
• Hydroxy acid halide polycondensation
• Diol + di-acid halide polycondensation
• Diol + di-carboxylic acid polycondensation

Polyamidation

• Amino acid polycondensation
• Diamine + di-carboxylic acid polycondensation
• Diamine + di-carboxylic acid halide polycondensation

For the detailed functional-group mapping and reaction rules, see the supported reactions documentation.

Installation

Clone the repository:

git clone https://github.com/NanoCIPHER-Lab/AutoREACTER.git
cd AutoREACTER

Create and activate the recommended Conda environment:

conda create -n autoRX -y -c conda-forge python=3.13 numpy pandas rdkit ipykernel networkx
conda activate autoRX

Install AutoREACTER in editable mode:

python -m pip install -U pip
python -m pip install -e .

AutoREACTER also requires LUNAR for atom typing. See the getting started documentation for setup details.

Quick start

Run AutoREACTER with a JSON input file:

python AutoREACTER.py -i path/to/input.json

or:

python AutoREACTER.py --input path/to/input.json

Example:

python AutoREACTER.py -i examples/example_1_inputs_ratio_mode.json

View available commands and options:

python AutoREACTER.py --help

Interactive notebook workflow

AutoREACTER can also be used through Jupyter notebooks for an interactive, visual, step-by-step workflow. This mode is recommended for inspecting monomers, functional groups, reaction templates, and generated LAMMPS setup files before running larger workflows.

See the examples directory for notebooks and usage notes:

examples/README.md

Cleanup utility

Delete cached runs older than a given number of days:

python AutoREACTER.py --cleanup 30

Delete all cached runs:

python AutoREACTER.py --cleanup all

Short flags are also available:

python AutoREACTER.py -c 30
python AutoREACTER.py -c all

Help and support

If you find a bug, need a new reaction type, or want to request additional force-field support, please open an issue:

AutoREACTER Issues

License

AutoREACTER is released under the MIT License. See LICENSE for details.