fixed tutorial 8

Author: simongravelle

lammps-tutorials.tex

@@ -4561,19 +4561,19 @@ \subsubsection{Reaction templates}
 for polymer.
 
 \begin{note}
-{\color{blue}Molecule templates contain sections that are similar, but not quite
-the same, as a LAMMPS data file. The data stored in these molecule templates
-include atom coordinates, partial charges, molecule IDs, atom types, and interaction
-types for bonds, angles, dihedrals and impropers. The map file contains information
-about the reaction. The first mandatory section of the map file begins with the
-keyword “InitiatorIDs” and lists the two atom IDs of the initiator atom pair in
-the pre-reacted molecule template. The second mandatory section begins with the
-keyword “Equivalences” and lists a one-to-one correspondence between atom IDs of
-the pre- and post-reacted templates. Some atoms in the pre-reacted template that
-are not reacting may have missing topology with respect to the simulation. For
-example, the pre-reacted template may contain an atom that, in the simulation,
-is currently connected to the rest of a long polymer chain. These are referred to
-as edge atoms, and are also specified in the map file in the “EdgeIDs” section.}
+{\color{blue}The data stored in molecule templates include atom coordinates,
+partial charges, molecule IDs, atom types, and interaction types for bonds,
+angles, dihedrals and impropers.  The map files contain information about
+the reaction.  The first mandatory section of the map files begins with the
+keyword “InitiatorIDs” and lists the two atom IDs of the initiator atom pair
+in the pre-reacted molecule template.  The second mandatory section begins
+with the keyword “Equivalences” and lists a one-to-one correspondence between
+atom IDs of the pre- and post-reacted templates.  Some atoms in the pre-reacted
+template that are not reacting may have missing topology with respect to the
+simulation.  For example, the pre-reacted template may contain an atom that,
+in the simulation, is currently connected to the rest of a long polymer
+chain.  These are referred to as edge atoms, and are also specified in the
+map file in the “EdgeIDs” section.}
 \end{note}
 
 \subsubsection{Simulating the reaction}
@@ -4648,10 +4648,10 @@ \subsubsection{Simulating the reaction}
 corresponds to a reaction, e.g.,~a transformation of \lmpcmd{mol1} into \lmpcmd{mol2}
 based on the atom map \lmpcmd{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.
+reaction sites, are also specified in this command.
 
 \begin{note}
-{\color{blue}The \lmpcmd{fix nve/limit} command Newton's equations of motion
+{\color{blue}The \lmpcmd{fix nve/limit} integrates command Newton's equations of motion
 while limiting the maximum displacement of atoms per timestep.  This is
 useful for preventing atoms from moving too far due to large forces.}
 \end{note}