An automatic generator of reaction network for reactive molecular dynamics simulation
ReacNetGenerator: an Automatic Reaction Network Generator for Reactive Molecular Dynamic Simulations, Phys. Chem. Chem. Phys., 2019, doi: 10.1039/C9CP05091D
firstname.lastname@example.org (Jinzhe Zeng), email@example.com (Tong Zhu)
First, you need to download the source code from the Releases page.
Then install ReacNetGenerator with one of the following guides:
1. Install Anaconda or Miniconda to obtain conda.
2. Decompress reacnetgenerator.zip and build in the main directory of ReacNetGenerator:
conda config --add channels conda-forge
2.Decompress reacnetgenerator.zip and build in the main directory of ReacNetGenerator:
docker build . -t njzjz/reacnetgenerator
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:
reacnetgenerator --dump -i dump.reaxc -a C H O
where C, H, and O are atomic names in the input file. Analysis report will be generated automatically.
Also, ReacNetGenerator can process files containing bond information, e.g. LAMMPS bond file:
reacnetgenerator -i bonds.reaxc -a C H O
You can run the following script for help:
You can open a GUI version for ReacNetGenerator by typing:
- The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students (2019年（第十一届）上海市大学生计算机应用能力大赛一等奖)
- The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students (2019年（第12届）中国大学生计算机设计大赛一等奖)
- 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)