updates

Author: jrgissing

journal-article.bib

@@ -283,7 +283,7 @@ @book{van1995python
   author={van Rossum, Guido and Drake Jr, Fred L},
   year={1995},
   publisher={Centrum voor Wiskunde en Informatica Amsterdam}
-} 
+}
 
 @article{humphrey1996vmd,
   title={{{VMD}}: visual molecular dynamics},
@@ -699,8 +699,18 @@ @article{typelabel_paper
   eprint =       { https://doi.org/10.1021/acs.jpcb.3c08419 }
 }
 
+@article{gissinger2017polymer,
+title = {Modeling chemical reactions in classical molecular dynamics simulations},
+journal = {Polymer},
+volume = {128},
+pages = {211-217},
+year = {2017},
+issn = {0032-3861},
+author = {Jacob R. Gissinger and Benjamin D. Jensen and Kristopher E. Wise}
+}
+
 @article{gissinger2020reacter,
-  title={Reacter: A heuristic method for reactive molecular dynamics},
+  title={REACTER: A heuristic method for reactive molecular dynamics},
   author={Gissinger, Jacob R and Jensen, Benjamin D and Wise, Kristopher E},
   journal={Macromolecules},
   volume={53},

lammps-tutorials.tex

@@ -3944,7 +3944,7 @@ \subsection{Tutorial 8: Reactive Molecular Dynamics}
 The goal of this tutorial is to create a model of a carbon nanotube (CNT) embedded
 in a polymer melt made of polystyrene (PS) (Fig.\,\ref{fig:REACT}). The
 REACTER protocol is used to simulate the polymerization of styrene monomers, and the
-polymerization reaction is followed in time \cite{gissinger2020reacter, gissinger2024molecular}.
+polymerization reaction is followed in time \cite{gissinger2017polymer, gissinger2020reacter, gissinger2024molecular}.
 In contrast with AIREBO (\hyperref[carbon-nanotube-label]{Tutorial 2})
 and ReaxFF (\hyperref[reactive-silicon-dioxide-label]{Tutorial 5}), the REACTER
 protocol relies on the use of a \textit{classical} force field.
@@ -4184,13 +4184,20 @@ \subsubsection{Simulating the reaction}
 With the \textit{stabilization} keyword, the \textit{bond/react} command will
 stabilize the atoms involved in the reaction using the \textit{nve/limit}
 command with a maximum displacement of $0.03\,\mathrm{\AA{}}$ (a command that was
-used, for instance, in \hyperref[sheared-confined-label]{Tutorial 4}). The three
-\textit{react} keywords contain specific details about the three reactions
-involved here, e.g. a transformation of \textit{mol1} into \textit{mol2} based
-on the atom map \textit{M-M.rxnmap}.
-
-Finally, let us use the \textit{fix nvt} to perform the integration of the
-equation of motion and control the temperature of the system:
+used, for instance, in \hyperref[sheared-confined-label]{Tutorial 4}). By default,
+each reaction is stabilized for 60 time steps. Each \textit{react} keyword
+corresponds to a reaction, e.g., a transformation of \textit{mol1} into \textit{mol2}
+based on the atom map \textit{M-M.rxnmap}. Implementation details about each reaction,
+such as the reaction distance cutoffs and the frequency with which to search for
+reaction sties, are also specified in this command.
+
+\textit{Fix bond/react} creates several groups of atoms that are dynamically updated
+to keep track of which atoms are being stabilized, and which atoms are undergoing
+dynamics using the system-wide time integrator (\textit{fix nvt}, \textit{fix npt}, etc.).
+When using reaction stabilization, there should not be a time integrator that acts on
+the ``all'' group. The name of the group of atoms that are not currently undergoing
+stabilization is derived by appending `\_REACT' to the user-provided prefix. The
+following commands use the NVT ensemble to perform time integration:
 {\normalsize
 \begin{verbatim}
 fix mynvt statted_grp_REACT nvt $
@@ -4206,8 +4213,7 @@ \subsubsection{Simulating the reaction}
 Here, in addition, the \textit{thermo custom} command was called and was
 asked to print the cumulative reaction counts from \textit{fix rxn}.
 The number of reaction, $N_r$, can be seen to increase with time
-(Fig.\,\ref{fig:evolution-reacting}). The final configuration with polymer
-chain unwrapped from the simulation box is shown in Fig.\,\ref{fig:REACTED_VMD}).
+(Fig.\,\ref{fig:evolution-reacting}).
 
 \begin{figure}
 \centering