This package implements the REACTER protocol (reacter.org) as
"fix bond/react." This fix allows for complex topology changes
during a running MD simulation, when using classical force fields.
Topology changes are defined in pre- and post-reaction molecule
templates and can include creation and deletion of bonds, angles,
dihedrals, impropers, atom types, bond types, angle types,
dihedral types, improper types, and/or atomic charges.

The REACTER protocol is a method for modeling chemical reactions in
classical molecular dynamics simulations. It was developed to build
physically-realistic initial configurations for amorphous or
crosslinked materials. Any number of competing or reversible reaction
pathways can be specified, and reacting sites can be stabilized. Other
advanced options currently available include reaction constraints
(e.g. angle and Arrhenius constraints), deletion of reaction
byproducts or other small molecules, creation of new atoms or
molecules bonded to existing atoms, and using LAMMPS variables for
input parameters.

The REACTER methodology is detailed in:
    Gissinger et al., Polymer 128, 211-217 (2017)
    https://doi.org/10.1016/j.polymer.2017.09.038

    Gissinger et al., Macromolecules 53, 22, 9953-9961 (2020).
    https://doi.org/10.1021/acs.macromol.0c02012

This package was created by Jacob Gissinger
(jacob.r.gissinger@gmail.com) at the NASA Langley Research Center.
