tested tutorials 6-7

Author: simongravelle

files/tutorial7/umbrella-sampling.meta

@@ -0,0 +1,15 @@
+umbrella-sampling.1.dat -28 0.5
+umbrella-sampling.2.dat -24 0.5
+umbrella-sampling.3.dat -20 0.5
+umbrella-sampling.4.dat -16 0.5
+umbrella-sampling.5.dat -12 0.5
+umbrella-sampling.6.dat -8 0.5
+umbrella-sampling.7.dat -4 0.5
+umbrella-sampling.8.dat 0 0.5
+umbrella-sampling.9.dat 4 0.5
+umbrella-sampling.10.dat 8 0.5
+umbrella-sampling.11.dat 12 0.5
+umbrella-sampling.12.dat 16 0.5
+umbrella-sampling.13.dat 20 0.5
+umbrella-sampling.14.dat 24 0.5
+umbrella-sampling.15.dat 28 0.5

files/tutorial7/umbrella-sampling.meta

@@ -3692,6 +3692,9 @@ \subsubsection{Method 1: Free sampling}
 We impose the force $F(x)$ to the atoms in the simulation
 using the \lmpcmd{fix addforce} command.  Add the following
 lines to \flecmd{free-energy.lmp}:
+% SG: apparently variable can't be cutted in 2 lines, either warn the reader, or find
+% a way to write these commands on the entire width of the page, or divide the variables
+% into several variables
 \begin{lstlisting}
 variable U atom ${U0}*atan((x+${x0})/${dlt})&
     -${U0}*atan((x-${x0})/${dlt})
@@ -3769,7 +3772,8 @@ \subsubsection{Method 1: Free sampling}
 
 \paragraph{Data analysis}
 
-Once the simulation is complete, the density profile shows that the density in the center of the box is
+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).
 Next, we plot $-R T \ln(\rho/\rho_\mathrm{bulk})$ (i.e.~Eq.~\eqref{eq:G} where
 the pressure ratio $p/p_\mathrm{bulk}$ is replaced by the density ratio
@@ -3827,7 +3831,7 @@ \subsubsection{Method 2: Umbrella sampling}
 
 \paragraph{LAMMPS input script}
 
-Open the file named \lmpcmd{umbrella-sampling.lmp}, which should
+Open the file named \flecmd{umbrella-sampling.lmp}, which should
 contain the following lines:
 \begin{lstlisting}
 variable sigma equal 3.405
@@ -3850,7 +3854,7 @@ \subsubsection{Method 2: Umbrella sampling}
 the biasing potential.
 
 Let us create a simulation box with two atom types, including a single particle of type 2,
-by adding the following lines to \lmpcmd{umbrella-sampling.lmp}:
+by adding the following lines to \flecmd{umbrella-sampling.lmp}:
 \begin{lstlisting}
 region myreg block -50 50 -15 15 -50 50
 create_box 2 myreg
@@ -3951,15 +3955,15 @@ \subsubsection{Method 2: Umbrella sampling}
 we use the WHAM algorithm as implemented by Marc Grossfield~\cite{grossfieldimplementation}.
 You can download it from \href{http://membrane.urmc.rochester.edu/?page_id=126}{Alan Grossfield}'s
 website.  The executable called \flecmd{wham} generated by following the instructions
-from the website must be placed next to \lmpcmd{umbrella-sampling.lmp}.  To apply
+from the website must be placed next to \flecmd{umbrella-sampling.lmp}.  To apply
 the WHAM algorithm to our simulation, we need a metadata file containing:
 \begin{itemize}
 \item the paths to all the data files,
 \item the values of $x_\text{des}$,
 \item the values of $k$.
 \end{itemize}
 Download the \href{\filepath tutorial7/umbrella-sampling.meta}{\dwlcmd{umbrella-sampling.meta}} file
-and save it next to \lmpcmd{umbrella-sampling.lmp}.  Then, run the WHAM algorithm
+and save it next to \flecmd{umbrella-sampling.lmp}.  Then, run the WHAM algorithm
 by typing the following command in the terminal:
 \begin{lstlisting}
 ./wham -30 30 50 1e-8 119.8 0 \