Thomas/Lars corrections to topology

paper/paper.md

@@ -145,9 +145,9 @@ As well as these domain-specific tools, `matscipy` contains general utility func
 
 - **Ring analysis.** Topological order in network glasses can be characterized by statistics of shortest-path rings [@Franzblau1991]. `matscipy` implements calculations of these rings using a backtracking algorithm in C. We regularly use `matscipy` to charactize shortest-path rings in amorphous carbon [@Pastewka2008;@Jana2019].
 
-- **Topology building for non-reactive MD simulations.** Non-reactive force fields for molecular dynamics simulations consist of non-bonded and bonded interaction terms [@Jorgensen1996]. The latter describe the structure of molecules and solids through lists of bonds, angles, and dihedrals. The construction of these force fields is mathematically simple but requires a considerable bookkeeping effort. The module `matscipy.opls` provides efficient tools for this purpose. Input and output routines for reading and writing the corresponding control files for LAMMPS [@Thompson2022] are implemented in the module `matscipy.io.opls`. We have used this approach in various studies on tribology, wetting and nanoscale rheology [@Mayrhofer2016;@Falk2020;@Reichenbach2020;@vonGoeldel2021;@Falk2022].
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+- **Topology building for non-reactive MD simulations.** 
 
+Non-reactive force fields for MD simulations consist of non-bonded and bonded interaction terms [@Jorgensen1996]. The latter require an explicit specification of the interatomic bonding topology, i.e.  which atoms are involved in bond, angle and dihedral interactions. The module `matscipy.opls` provides efficient tools to generate this topology for an atomic structure based on matscipy’s neighbour list, and then assign the relevant force field parameters to each interaction term. Input and output routines for reading and writing the corresponding control files for LAMMPS [@Thompson2022] are implemented in the module `matscipy.io.opls`. We used this functionality in various studies on tribology, wetting and nanoscale rheology [@Mayrhofer2016;@Falk2020;@Reichenbach2020;@vonGoeldel2021;@Falk2022].
 
 # Interatomic potentials and other calculators