ReacNetGenerator

An automatic reaction network generator for reactive molecular dynamics simulation.

ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamic simulations, Phys. Chem. Chem. Phys., 2020, 22 (2): 683–691, doi: 10.1039/C9CP05091D

jinzhe.zeng@ustc.edu.cn (Jinzhe Zeng), tzhu@lps.ecnu.edu.cn (Tong Zhu)

Features

• Processing of MD trajectory containing atomic coordinates or bond orders
• Hidden Markov Model (HMM) based noise filtering
• Isomers identifying accoarding to SMILES
• Generation of reaction network for visualization using force-directed algorithm
• Parallel computing

Guide and Tutorial

The latest version requires Python 3.10 or later. You can install ReacNetGenerator with conda:

conda install reacnetgenerator -c conda-forge
reacnetgenerator -h

See the guide to learn how to install and use ReacNetGenerattor. We also provide a series of tutorials to help you learn ReacNetGenerator.

Awards

• The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students
• The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students

Acknowledge

• National Natural Science Foundation of China (Grants No. 91641116)
• National Innovation and Entrepreneurship Training Program for Undergraduate (201910269080)
• ECNU Multifunctional Platform for Innovation (No. 001)