开发者：朱通，曾晋哲
开发单位：纽约大学-华东师范大学计算化学联合研究中心
代码下载：https://code.koushare.com/#/code/codeDetail?codeId=230
https://github.com/tongzhugroup/reacnetgenerator
文档：https://reacnetgenerator.njzjz.win
授权协议：LGPL-3.0
使用视频：https://www.koushare.com/video/videodetail/21234
近年来，反应分子动力学 (Reactive MD simulation) 模拟方法被广泛用于研究许多复杂分子系统的反应机制，如燃烧、爆炸和非均相催化。针对大体系的长时间MD模拟会产生非常复杂的轨迹文件，其中包含着大量的反应和分子(物种)。人工分析如此复杂的轨迹是不现实的。为解决这一难题，我们开发了ReacNetGenerator软件。它以轨迹中的原子坐标为唯一必要的输入，可根据原子之间的连接关系自动判断物种和反应。然后将统计后的反应种类、数量和反应网络展示在一个交互式的网页上。用户通过鼠标点击即可对指定物种参与的局部反应网络进行分析。值得一提的是，ReacNetGenerator采用了隐马尔科夫模型来有效过滤轨迹中的噪声，突出主要反应。该软件同时支持并行计算，并在内存使用方面进行了大量优化，因此运行效率很高，可用来分析大型轨迹文件。
ReacNetGenerator主要使用Python语言开发，其中部分模块也利用了C++、HTML、JavaScript和CSS等语言，以及一些第三方软件库。得益于Python语言的跨平台特性，以及pip和conda的打包功能，ReacNetGenerator可在Linux、macOS和Windows等多个操作系统安装和使用。
conda install reacnetgenerator -c conda-forge
reacnetgenerator -h
图1. ReacNetGenerator软件的架构图
Jinzhe Zeng, Liqun Cao, Chih-Hao Chin, Haisheng Ren, John Z. H. Zhang, Tong Zhu, ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations, Phys. Chem. Chem. Phys., 2020, 22 (2), 683–691.
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