final touches

Author: akohlmey

lammps-tutorials.tex

@@ -905,13 +905,6 @@ \subsubsection{Improving the script}
 \textit{initial.lmp} file \emph{without} the \textit{create\_atoms}
 commands in the \textit{System definition} part.
 
-\begin{figure}
-\centering
-\includegraphics[width=0.55\linewidth]{LJ-cylinder}
-\caption{Visualization of the improved system after minimization}
-\label{fig:improved-min}
-\end{figure}
-
 We want to create the the atoms of types 1 and 2 in two separate
 regions.  Thus we need to add two \textit{region} commands and then
 re-add \textit{create\_atoms} commands, but using the new regions
@@ -986,6 +979,13 @@ \subsubsection{Improving the script}
 
 \paragraph{Restarting from a saved configuration}
 
+\begin{figure}
+\centering
+\includegraphics[width=0.55\linewidth]{LJ-cylinder}
+\caption{Visualization of the improved system after minimization}
+\label{fig:improved-min}
+\end{figure}
+
 To continue a simulation from the saved configuration, open the
 \textit{improved.md.lmp} which was downloaded during the tutorial setup.
 This contains the \textit{Initialization} part from \textit{initial.lmp}
@@ -1087,6 +1087,16 @@ \subsubsection{Improving the script}
 first compute is referenced by the second.  And we reference the second
 in a \textit{thermo\_style custom} command.
 
+\begin{figure}
+\centering
+\includegraphics[width=\linewidth]{LJ-evolution}
+\caption{Evolution of the system during mixing. The three snapshots show
+respectively the system at $t=0$ (left panel), $t=75$ (middle panel), and $t=1500$
+(right panel).}
+\label{fig:evolution-population}
+\end{figure}
+
+Finally, let us complete the script by adding the following lines into
 Add the following lines into \textit{improved.md.lmp}.  Note there is no
 need for a \textit{Settings} section, because the settings are taken
 from the \textit{.data} file.
@@ -1109,16 +1119,6 @@ \subsubsection{Improving the script}
 \textit{sumcoor12}, were added to the list of information printed during
 the simulation.
 
-\begin{figure}
-\centering
-\includegraphics[width=\linewidth]{LJ-evolution}
-\caption{Evolution of the system during mixing. The three snapshots show
-respectively the system at $t=0$ (left panel), $t=75$ (middle panel), and $t=1500$
-(right panel).}
-\label{fig:evolution-population}
-\end{figure}
-
-Finally, let us complete the script by adding the following lines into
 \textit{improved.md.lmp}:
 {\normalsize
 \begin{verbatim}
@@ -1187,6 +1187,20 @@ \subsubsection{Improving the script}
 \label{fig:coords-viz}
 \end{figure}
 
+\paragraph{Experiments}
+
+Here are some suggestions for further experiments with this system that
+may lead to additional insights into how different systems are set up
+and how different features work:
+\begin{itemize}
+\item Use Nos\'e--Hoover thermostat (\textit{fix nvt}) instead of Langevin
+  (\textit{fix nve} + \textit{fix langevin})
+\item Skip the \textit{minimize} step for both, Nos\'e--Hoover and Langevin
+\item Apply the thermostat to only one type of atoms and observe the
+  temperature for each type separately
+\item append an NVE run (i.e.~without any thermostat) and observe the energies
+\end{itemize}
+
 It is also possible to color the atoms in the \textit{Slide Show}
 according to their coordination number. For that purpose, replace the
 \textit{dump} and \textit{dump\_modify} commands with the following
@@ -1207,18 +1221,6 @@ \subsubsection{Improving the script}
 one type 2 neighbor in yellow, and atoms of type 1 with two type 2
 neighbors in red.  Figure \ref{fig:coords-viz} shows an example.
 
-\paragraph{Experiments}
-
-Here are some suggestions for further experiments with this system:
-\begin{itemize}
-\item Use Nos\'e--Hoover thermostat (\textit{fix nvt}) instead of Langevin
-  (\textit{fix nve} + \textit{fix langevin})
-\item Skip the \textit{minimize} step for both, Nos\'e--Hoover and Langevin
-\item Apply the thermostat to only one type of atoms and observe the
-  temperature for each type separately
-\item append an NVE run (i.e.~without any thermostat) and observe the energies
-\end{itemize}
-
 \subsection{Tutorial 2: Pulling on a carbon nanotube}
 \label{carbon-nanotube-label}