Metadata-Version: 2.1
Name: reacnetgenerator
Version: 1.4.117
Summary: Reaction Network Generator
Home-page: https://njzjz.github.io/reacnetgenerator/
Author: Jinzhe Zeng
Author-email: jzzeng@stu.ecnu.edu.cn
License: UNKNOWN
Description: # <img src=docs/.vuepress/public/reacnetgen.svg height=40/>  ReacNetGenerator
        
        [![DOI:10.1039/C9CP05091D](https://zenodo.org/badge/DOI/10.1039/C9CP05091D.svg)](https://doi.org/10.1039/C9CP05091D)
        [![Research Group](https://img.shields.io/website-up-down-green-red/https/computchem.cn.svg?label=Research%20Group)](https://computchem.cn)
        
        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](https://dx.doi.org/10.1039/C9CP05091D)
        
        jinzhe.zeng@rutgers.edu (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
        
        ## Installation
        
        You can [install Anaconda or Miniconda](https://conda.io/projects/continuumio-conda/en/latest/user-guide/install/index.html) to obtain conda, and install ReacNetGenerator easily with conda:
        
        ```bash
        conda install reacnetgenerator -c conda-forge
        ```
        
        See [the build guide](guide/build.md) if you want to build ReacNetGenerator by yourself. 
        
        ## Usage
        
        ### Command line
        
        ReacNetGenerator can process any kind of trajectory files containing atomic coordinates, e.g. a LAMMPS dump file prepared by running “dump 1 all custom 100 dump.reaxc id type x y z” in LAMMPS:
        
        ```bash
        reacnetgenerator --dump -i dump.reaxc -a C H O
        ```
        where C, H, and O are atomic names in the input file. [Analysis report](https://reacnetgenerator.njzjz.win/report.html?jdata=https%3A%2F%2Fgist.githubusercontent.com%2Fnjzjz%2Fe9a4b42ceb7d2c3c7ada189f38708bf3%2Fraw%2F83d01b9ab1780b0ad2d1e7f934e61fa113cb0f9f%2Fmethane.json) will be generated automatically.
        
        Also, ReacNetGenerator can process files containing bond information, e.g. LAMMPS bond file:
        
        ```bash
        reacnetgenerator -i bonds.reaxc -a C H O
        ```
        
        You can running the following script for help:
        
        ```bash
        reacnetgenerator -h
        ```
        
        ### GUI version
        
        You can open a GUI version for ReacNetGenerator by typing:
        
        ```bash
        reacnetgeneratorgui
        ```
        
        ## 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)
        
Keywords: reaction network
Platform: UNKNOWN
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: JavaScript
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Software Development :: Version Control :: Git
Requires-Python: ~=3.6
Description-Content-Type: text/markdown
Provides-Extra: test
Provides-Extra: docs
