#=====================================
# LearnReactions package
# Authors: Lee-Ping Wang, Robert McGibbon, Leah Isseroff Bendavid,
# Alexey Titov, Todd J. Martinez
#=====================================

This is a script and module to identify reaction events in reactive
MD (nanoreactor) simulations.

#=====================================
# Installation
#=====================================

From a clean miniconda distribution, the following commands should
lead to a working package:

conda create -n learxn python=2.7
source activate learxn
conda install scikit-learn=0.14.1
conda install networkx
conda install libgfortran=1.0

#=====================================
# Usage
#=====================================

To analyze a simulation trajectory, run:

LearnReactions.py traj.xyz

Use the "-h" argument to get help.  It will generate reaction_123.xyz
files that contain your chemical reactions, as well as bonds.dat,
color.dat, charge.dat and spin.dat used to highlight your reactive MD
trajectory.

To view the highlighted trajectory, you need to install VMD.
Make sure reactions.vmd is in the same folder and run using

vmd -e reactions.vmd -args coors.xyz

#=====================================
# License
#=====================================

License: This software uses the BSD license.  See LICENSE.