Update lammps-tutorials.tex

Author: cecimarques

lammps-tutorials.tex

@@ -4106,14 +4106,18 @@ \subsubsection{Method 1: Free sampling}
 % 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
+% CA: I think we can remove the & (to avoid confusion) and warn the reader about the
+% continuation of the formula.
 \begin{lstlisting}
 variable U atom ${U0}*atan((x+${x0})/${dlt})&
     -${U0}*atan((x-${x0})/${dlt})
 variable F atom ${U0}/((x-${x0})^2/${dlt}^2+1)/${dlt}&
     -${U0}/((x+${x0})^2/${dlt}^2+1)/${dlt}
 fix myadf all addforce v_F 0.0 0.0 energy v_U
 \end{lstlisting}
-Next, we combine the \lmpcmd{fix nve} with a \lmpcmd{fix langevin} thermostat:
+Next, we {\color{blue}use the Newtonian equations of motion with a
+Langevin thermostat by combining }the \lmpcmd{fix nve} with a 
+\lmpcmd{fix langevin} {\color{blue}command}:
 \begin{lstlisting}
 fix mynve all nve
 fix mylgv all langevin 119.8 119.8 500 30917
@@ -4123,6 +4127,13 @@ \subsubsection{Method 1: Free sampling}
 atoms $N$, constant volume $V$, and a temperature $T$ that
 fluctuates around a target value.
 % SG: may be discuss the choice of constant "500" -> chosen for a relatiely weak coupling with thermostat (add a box?)
+% CA: I can propose something that can be put in a yellow box. Feel free to uncomment the lines below and modify it if you want to.
+% {\color{blue}You can find proposed in the LAMMPS documentation  
+% values of 100x and 1000x the value of the timestep for the damping
+% constants of the thermostats and barostats. Here, a smaller
+% value is used in order to have the temperature of the system
+% relaxed to the target value more often.}
+% PS: I am not defining the damping constants because you had already done it in one of the firsts tutorials.
 
 \begin{figure}
 \centering
@@ -4136,7 +4147,8 @@ \subsubsection{Method 1: Free sampling}
 
 To ensure that the equilibration time is sufficient, we will track the evolution of
 the number of atoms in the central - energetically unfavorable - region,
-referred to as \lmpcmd{mymes}, using the \lmpcmd{n\_center} variable:
+{\color{blue} defined below under the name} \lmpcmd{mymes}, using 
+the \lmpcmd{n\_center} variable:
 \begin{lstlisting}
 region mymes block -${x0} ${x0} INF INF INF INF
 variable n_center equal count(all,mymes)
@@ -4149,7 +4161,8 @@ \subsubsection{Method 1: Free sampling}
 dump_modify viz backcolor white acolor 1 cyan &
     adiam 1 3 boxcolor black
 \end{lstlisting}
-A \lmpcmd{dump image} command was also added for system visualization.
+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,
 using a timestep of $2\,\text{fs}$, corresponding to a total duration of $100\,\text{ps}$:
@@ -4315,10 +4328,11 @@ \subsubsection{Method 2: Umbrella sampling}
 \end{lstlisting}
 
 So far, our code resembles that of Method 1, except for the additional particle
-of type 2.  Particles of types 1 and 2 are identical, with the same mass
-and LJ parameters.  However, the particle of type 2 will also
+of type 2.  Particles of types 1 and 2 are identical.  
+However, the particle of type 2 will also
 be exposed to the biasing potential $V$, which forces it to explore the
-central part of the box (Fig.~\ref{fig:US-system-biased}).
+central part of the box (Fig.~\ref{fig:US-system-biased}), {\color{blue} thus
+justifying the definition of two atom types.}
 
 \begin{figure}
 \centering
@@ -4351,8 +4365,12 @@ \subsubsection{Method 2: Umbrella sampling}
 next a
 jump SELF loop
 \end{lstlisting}
+{\color{blue} The definition of a variable of loop style serves the same purpose
+as in Tutorial 5, and we highlight here the particular utility of using its value
+to distinguish the files written by the \lmpcmd{fix ave_/time} command for the
+different bias potentials.}
 The \lmpcmd{spring} command imposes the additional harmonic potential $V$ with
-the previously defined spring constant $k$.  The center of the harmonic
+the previously defined spring constant $k$ {\color{blue}to the atoms in the group \lmpcmd{topull}}.  The center of the harmonic
 potential, $x_\text{des}$, successively takes values
 from $-28\,\text{\AA{}}$ to $28\,\text{\AA{}}$.  For each value of $x_\text{des}$,
 an equilibration step of 40\,ps is performed, followed by a step