minor fixes

Author: simongravelle

lammps-tutorials.tex

@@ -585,7 +585,7 @@ \subsubsection{My first input}
 In LAMMPS, every atom is assigned an \emph{atom type}
 property.  This property selects which force field parameters (here,
 the Lennard-Jones parameters, $\epsilon_{ij}$ and $\sigma_{ij}$) are
-applied to each pair of atoms via the \lmpcmd{pair\_coeff} command.
+applied to each pair of atoms via the \lmpcmd{pair\_coeff} command (see below).
 We discuss in \hyperref[carbon-nanotube-label]{Tutorial 2} how this
 applies to many-body pair styles, and in
 \hyperref[all-atom-label]{Tutorial 3} how this applies to Coulomb
@@ -1775,7 +1775,8 @@ \subsubsection{Breakable bonds}
 pair_style airebo 3.0
 pair_coeff * * CH.airebo C
 \end{lstlisting}
-\begin{note} The AIREBO force field is a many-body
+\begin{note}
+  The AIREBO force field is a many-body
   potential, where interactions are not only between pairs of atoms,
   but also triples and quadruples representing angle and dihedral
   interactions.  This means that there are different rules for the
@@ -1997,7 +1998,8 @@ \subsubsection{Preparing the water reservoir}
 \hyperref[carbon-nanotube-label]{Tutorial 2}, sets the LJ and Coulomb
 weighting factors for the interaction between neighboring atoms.
 
-\begin{note} With Coulomb interactions, additional rules
+\begin{note}
+  With Coulomb interactions, additional rules
   apply to the \lmpcmd{pair\_coeff} command: (a) atom type values
   only matter for assignment of LJ potential parameters; (b) for Coulomb interactions,
   there are no parameters outside the cutoff, and when using a
@@ -2686,9 +2688,9 @@ \subsubsection{System preparation}
 
 write_data create.data nocoeff
 \end{lstlisting}
-The \lmpcmd{run 0} command initializes the simulation but
-does not advance positions or velocities which is required for cleanly saving the
-state.  The \lmpcmd{write\_data} command
+The \lmpcmd{run 0} command initializes the simulation, which is required for
+cleanly saving the state, but it
+does not advance positions or velocities.  The \lmpcmd{write\_data} command
 generates a file called \lmpcmd{system.data} containing the information required
 to restart the simulation from the final configuration produced by this input
 file.  With the \lmpcmd{nocoeff} option, the parameters from the force field are
@@ -3489,7 +3491,7 @@ \subsection{Tutorial 6: Water adsorption in silica}
 \label{fig:GCMC}
 \end{figure}
 
-The objective of this tutorial is to combine molecular dynamics and
+\noindent The objective of this tutorial is to combine molecular dynamics and
 grand canonical Monte Carlo simulations to compute the adsorption of water
 molecules in cracked silica material (Fig.~\ref{fig:GCMC}).  This tutorial
 illustrates the use of the grand canonical ensemble in molecular simulation, an
@@ -3657,7 +3659,7 @@ \subsubsection{Cracking the silica}
 write_data cracking.data
 \end{lstlisting}
 As discussed, the \lmpcmd{fix nvt} command integrates the Nosé-Hoover equations
-of motion to sample the NVT ensemble, which allows controlling the temperature of the system.
+of motion and is employed to control the temperature of the system.
 As observed from the generated images, the atoms
 progressively adjust to the changing box dimensions.  At some point,
 bonds begin to break, leading to the appearance of
@@ -4489,7 +4491,7 @@ \subsubsection{Creating the system}
 minimize 1.0e-4 1.0e-6 100 1000
 reset_timestep 0
 \end{lstlisting}
-These commands should be familiar from previous tutorials.
+These commands were covered in earlier tutorials and should already be familiar.
 
 Then, let us densify the system to a target value of $0.9~\text{g/cm}^3$
 by imposing the shrinking of the simulation box at a constant rate.