a couple more figure tweaks

Author: akohlmey

lammps-tutorials.tex

@@ -3731,7 +3731,8 @@ \subsubsection{Adding water}
 
 \begin{note}
 {\color{blue}In practice, it is possible to use both \lmpcmd{vashishta} and
-\lmpcmd{lj/cut/tip4p/long} pair styles by employing the \lmpcmd{pair\_style hybrid}
+  \lmpcmd{lj/cut/tip4p/long} pair styles at the same time by employing the
+  \lmpcmd{pair\_style hybrid}
 command.  However, hybridizing force fields should be done with caution, as there
 is no guarantee that the resulting force field will produce meaningful results.}
 \end{note}
@@ -4157,7 +4158,7 @@ \subsubsection{Method 1: Free sampling}
 A \lmpcmd{dump image} command was also added for system visualization.
 {\color{blue} The other commands should also be familiar from previous tutorials.}
 
-Finally, let us perform an equilibration of 50000 steps,
+\noindent Finally, let us perform an equilibration of 50000 steps,
 using a timestep of $2\,\text{fs}$, corresponding to a total duration of $100\,\text{ps}$:
 \begin{lstlisting}
 timestep 2.0
@@ -4193,6 +4194,17 @@ \subsubsection{Method 1: Free sampling}
 
 \paragraph{Data analysis}
 
+\begin{figure}
+\centering
+\includegraphics[width=\linewidth]{US-system-unbiased}
+\caption{Snapshot of the system simulated during the free sampling
+step of \hyperref[umbrella-sampling-label]{Tutorial 7}.
+The atoms density is the lowest in the central
+part of the box, \lmpcmd{mymes}.  Here,
+$U_0 = 0.36~\text{kcal/mol}$, $\delta = 1.0~\text{\AA{}}$, and $x_0 = 10~\text{\AA{}}$.}
+\label{fig:US-system-unbiased}
+\end{figure}
+
 Once the simulation is complete, the density profile from \flecmd{free-sampling.dat}
 shows that the density in the center of the box is
 about two orders of magnitude lower than inside the reservoir (Fig.~\ref{fig:US-density}\,a).
@@ -4208,17 +4220,6 @@ \subsubsection{Method 1: Free sampling}
 is excellent, despite some noise in the central part, where fewer data points
 are available due to the repulsive potential.
 
-\begin{figure}
-\centering
-\includegraphics[width=\linewidth]{US-system-unbiased}
-\caption{Snapshot of the system simulated during the free sampling
-step of \hyperref[umbrella-sampling-label]{Tutorial 7}.
-The atoms density is the lowest in the central
-part of the box, \lmpcmd{mymes}.  Here,
-$U_0 = 0.36~\text{kcal/mol}$, $\delta = 1.0~\text{\AA{}}$, and $x_0 = 10~\text{\AA{}}$.}
-\label{fig:US-system-unbiased}
-\end{figure}
-
 \paragraph{The limits of free sampling}
 
 Increasing the value of $U_0$ reduces the average number of atoms in the central
@@ -4381,6 +4382,17 @@ \subsubsection{Method 2: Umbrella sampling}
 
 \paragraph{WHAM algorithm}
 
+\begin{figure}
+\centering
+\includegraphics[width=\linewidth]{US-free-energy}
+\caption{The potential, $U$, as a function of $x$, measured using umbrella
+sampling during \hyperref[umbrella-sampling-label]{Tutorial 7} (blue disks),
+is compared to the imposed potential given in Eq.~\eqref{eq:U}
+(dark line).  Parameters are $U_0 = 2.38~\text{kcal/mol}$, $\delta = 1.0~\text{\AA{}}$,
+and $x_0 = 10~\text{\AA{}}$.}
+\label{fig:US-freenergy}
+\end{figure}
+
 To generate the free energy profile from the particle positions saved in
 the \flecmd{umbrella-sampling.i.dat} files, we use the
 WHAM~\cite{kumar1992weighted,kumar1995multidim} algorithm as implemented
@@ -4414,17 +4426,6 @@ \subsubsection{Method 2: Umbrella sampling}
 Achieving similar results through free sampling would require performing extremely
 long and computationally expensive simulations.
 
-\begin{figure}
-\centering
-\includegraphics[width=\linewidth]{US-free-energy}
-\caption{The potential, $U$, as a function of $x$, measured using umbrella
-sampling during \hyperref[umbrella-sampling-label]{Tutorial 7} (blue disks),
-is compared to the imposed potential given in Eq.~\eqref{eq:U}
-(dark line).  Parameters are $U_0 = 2.38~\text{kcal/mol}$, $\delta = 1.0~\text{\AA{}}$,
-and $x_0 = 10~\text{\AA{}}$.}
-\label{fig:US-freenergy}
-\end{figure}
-
 \subsection{Tutorial 8: Reactive Molecular Dynamics}
 \label{bond-react-label}