Merge pull request #46 from lammpstutorials/continue-improving

Further cleaning of the tutorials

Author: simongravelle

lammps-tutorials.tex

@@ -1664,7 +1664,7 @@ \subsubsection{Breakable bonds}
 
 After equilibration, let us set the velocity of the edges equal to
 $75~\text{m/s}$ (or $0.75~\text{\AA{}/ps}$) and run for a longer duration than
-previously. Add the following lines into \flecmd{breakable.lmp}:
+previously.  Add the following lines into \flecmd{breakable.lmp}:
 \begin{lstlisting}
 velocity cnt_top set 0.75 0 0
 velocity cnt_bot set -0.75 0 0
@@ -1942,7 +1942,7 @@ \subsubsection{Solvating the PEG in water}
 \end{figure}
 
 Open the file named \flecmd{merge.lmp} that was downloaded
-alongside \flecmd{water.lmp} during the tutorial setup. It only contain one line:
+alongside \flecmd{water.lmp} during the tutorial setup.  It only contain one line:
 \begin{lstlisting}
 read_restart water.restart
 \end{lstlisting}
@@ -2197,7 +2197,7 @@ \subsubsection{System preparation}
 kspace_modify slab 3.0
 \end{lstlisting}
 These lines are used to define the most basic parameters, including the
-\lmpcmd{atom}, \lmpcmd{bond}, and \lmpcmd{angle} styles, as well as interaction
+atom, bond, and angle styles, as well as interaction
 potential.  Here, \lmpcmd{lj/cut/tip4p/long} imposes a Lennard-Jones potential with
 a cut-off at $12\,\text{$\text{\AA{}}$}$ and a long-range Coulomb potential.
 
@@ -2236,12 +2236,11 @@ \subsubsection{System preparation}
 factor of 4.04, the region box extends from $-12.12~\text{\AA{}}$ to $12.12~\text{\AA{}}$
 along the $x$ direction.  The \lmpcmd{create\_box} command creates a simulation box with
 5 types of atoms: the oxygen and hydrogen of the water molecules, the two ions ($\text{Na}^+$,
-$\text{Cl}^-$), and the atom of the walls.  The \lmpcmd{create\_box} command extends over 6
-lines thanks to the $\&$ character.  The second and third lines are used to indicate that the
-simulation contains 1 type of bond and 1 type of angle (both required by the water molecule).
-The parameters for these bond and angle constraints will be given later.  The three last
-lines are for memory allocation.  The \lmpcmd{labelmap} command assigns alphanumeric type labels
-to each numeric atom type, bond type, and angle type.
+$\text{Cl}^-$), and the atoms from the walls.  The simulation contains 1 type of bond
+and 1 type of angle (both required by the water molecules).
+The parameters for these bond and angle constraints will be given later.  The \lmpcmd{extra/ (...)}
+keywords are for memory allocation.  Finally, the \lmpcmd{labelmap} commands assign
+alphanumeric type labels to each numeric atom type, bond type, and angle type.
 
 Now, we can add atoms to the system.  First, let us create two sub-regions corresponding
 respectively to the two solid walls, and create a larger region from the union of the
@@ -2258,7 +2257,7 @@ \subsubsection{System preparation}
 
 To add the water molecules, the molecule
 template called \href{\filepath tutorial4/water.mol}{\dwlcmd{water.mol}}
-must be located next to \flecmd{}.  The template contains all the
+must be located next to \flecmd{create.lmp}.  The template contains all the
 necessary information concerning the water molecule, such as atom positions,
 bonds, and angles.  Add the following lines to \flecmd{create.lmp}:
 \begin{lstlisting}
@@ -2419,7 +2418,7 @@ \subsubsection{System preparation}
 
 Let us move the atoms and place them in more energetically favorable positions
 before starting the actual molecular dynamics simulation.  Although we refer to this step as
-\emph{energy minimization}, it is not a conventional \emph{minimization}
+\emph{energy minimization}, it is not a conventional minimization
 like that performed in the first tutorial; \hyperref[lennard-jones-label]{Lennard-Jones fluid}.
 Instead, we will conduct a molecular dynamics simulation, employing certain techniques
 to prevent the system from exploding due to overlapping atoms.
@@ -2597,9 +2596,10 @@ \subsubsection{System preparation}
 
 write_data equilibrate.data nocoeff
 \end{lstlisting}
-Run the \flecmd{input.lmp} file using LAMMPS.  As seen from the values of
-\lmpcmd{deltaz}, the distance between the two walls reaches
-an equilibrium value (Fig.~\ref{fig:NANOSHEAR-equilibration}).
+Run the \flecmd{input.lmp} file using LAMMPS.  Both the pressure and the distance
+between the two walls show oscillations at the start of the simulation
+but eventually stabilize at their equilibrium values toward
+the end of the simulation (Fig.~\ref{fig:NANOSHEAR-equilibration}).
 
 \begin{note}
 Note that it is generally recommended to run a longer equilibration.  In this case,
@@ -2737,7 +2737,7 @@ \subsubsection{Imposed shearing}
 \end{figure}
 
 From the force applied by the fluid on the solid, one can extract the stress
-within the fluid, which enables the measurement of its viscosity $\dot{\eta}$
+within the fluid, which enables the measurement of its viscosity $\eta$
 according to $\eta = \tau / \dot{\gamma}$ where $\tau$ is the stress applied by
 the fluid on the shearing wall, and $\dot{\gamma}$ the shear rate
 \cite{gravelle2021violations}.  Here, the shear rate is
@@ -2771,15 +2771,15 @@ \subsection{Tutorial 5: Reactive silicon dioxide}
 can be used to calculate the partial charges of a system undergoing deformation, as well as
 the formation and breaking of chemical bonds~\cite{van2001reaxff, zou2012investigation}.
 The system simulated in this tutorial is a block of silicon dioxide $\text{SiO}_2$ (Fig.~\ref{fig:SIO})
-which is deformed until it ruptures.  Particular attention is paid to the evolution
-of atomic charges during the deformation of the structure, with chemical reactions
-resulting from the deformation being tracked over time.
+which is deformed until it ruptures.  Particular attention is given to the evolution
+of atomic charges during deformation, with a focus on tracking chemical reactions
+resulting from the deformation over time.
 
 \subsubsection{Prepare and relax}
 
-The first action we need to perform here is to relax the structure with ReaxFF,
-which we are gonna do using molecular dynamics.  As always, to make sure that the system
-equilibrates nicely, we will us track certain parameters over time.  To set up this
+The first step is to relax the structure with ReaxFF, which which will be achieved using
+molecular dynamics.  To ensure the system equilibrates properly, we will monitor certain
+parameters over time, such as the system volume.  To set up this
 tutorial, select \guicmd{Start Tutorial 5} from the
 \guicmd{Tutorials} menu of \lammpsgui{} and follow the instructions.
 The editor should display the following content corresponding to \flecmd{relax.lmp}:
@@ -2957,7 +2957,7 @@ \subsubsection{Deform the structure}
 fix mynvt all nvt temp 300.0 300.0 100
 timestep 0.5
 \end{lstlisting}
-Here, a barostat is not used because the change in the box volume will be imposed
+Here, no barostat is used because the change in the box volume will be imposed
 by the \lmpcmd{fix deform}.
 
 \begin{figure}
@@ -3084,9 +3084,10 @@ \subsubsection{Decorate the surface}
   backcolor white amap -1 2 ca 0.0 3 min royalblue &
   0 green max orangered
 
-fix myspec all reaxff/species 5 1 5 decorate.species element Si O H
+fix myspec all reaxff/species 5 1 5 decorate.species &
+  element Si O H
 \end{lstlisting}
-Here, the $+1\text{e}-10$ was added to the denominator of the \lmpcmd{variable qH}
+Here, the $+1 \mathrm{e}{-10}$ was added to the denominator of the \lmpcmd{variable qH}
 to avoid dividing by 0 at the beginning of the simulation.  Finally, let us
 create a loop with 10 steps, and create two hydrogen atoms at random locations at
 every step:
@@ -3491,7 +3492,7 @@ \subsubsection{Adding water}
 with time.  The \lmpcmd{compute\_modify} command with the \lmpcmd{dynamic yes}
 option for water is used to specify that the number of molecules will not be constant.
 
-Finally, let us use the \textit{fix gcmc} and perform the grand canonical Monte
+Finally, let us use the \lmpcmd{fix gcmc} and perform the grand canonical Monte
 Carlo steps.  Add the following lines into \flecmd{gcmc.lmp}:
 \begin{lstlisting}
 variable tfac equal 5.0/3.0
@@ -3504,12 +3505,10 @@ \subsubsection{Adding water}
 freedom.  Here, 100 insertion and deletion attemps are made every 100 steps.
 
 \begin{note}
-At a pressure of $p = 100\ \text{bar}$, the chemical potential of water
-vapor at $T = 300\ \text{K}$ can be calculated using as
-$\mu = \mu^\circ + RT \ln (\frac{p}{p_0}),$
-where $\mu_0$ is the standard chemical potential
-at $p^\circ = 1 \, \text{bar}$, \(R = 8.314\ \text{J/mol·K}\) is
-the gas constant, \(T = 300\ \text{K}\) is the temperature.
+At a pressure of $p = 100\ \text{bar}$, the chemical potential of water vapor at $T = 300\ \text{K}$
+can be calculated using as $\mu = \mu_0 + RT \ln (\frac{p}{p_0}),$ where $\mu_0$ is the standard
+chemical potential (typically taken at a pressure $p_0 = 1 \, \text{bar}$), \(R = 8.314\ \text{J/mol·K}\)
+is the gas constant, \(T = 300\ \text{K}\) is the temperature.
 \end{note}
 
 Finally, let us print some information and run for 25\,ps:
@@ -3616,7 +3615,7 @@ \subsubsection{Method 1: Free sampling}
 to create a Weeks-Chandler-Andersen (WCA) potential, which is a truncated and
 purely repulsive LJ potential~\cite{weeks1971role}.  It was calculated
 as $2^{1/6} \sigma$.  The potential is also shifted to be
-equal to 0 at the cut-off using the \lmpcmd{pair\_modify}.  The system of unit
+equal to 0 at the cut-off using the \lmpcmd{pair\_modify} command.  The system of unit
 \lmpcmd{real}, in which energy is in kcal/mol, distance in Ångstrom, or time in
 femtosecond, has been chosen for practical reasons: the WHAM algorithm used in
 the second part of the tutorial automatically assumes the energy to be in kcal/mol.
@@ -3964,6 +3963,14 @@ \subsubsection{Method 2: Umbrella sampling}
 \subsection{Tutorial 8: Reactive Molecular Dynamics}
 \label{bond-react-label}
 
+The goal of this tutorial is to create a model of a carbon nanotube (CNT) embedded
+in a polymer melt made of polystyrene (PS) (Fig.~\ref{fig:REACT}).  The
+REACTER protocol is used to simulate the polymerization of styrene monomers, and the
+polymerization reaction is followed in time \cite{gissinger2017polymer, gissinger2020reacter, gissinger2024molecular}.
+In contrast with AIREBO (\hyperref[carbon-nanotube-label]{Tutorial 2})
+and ReaxFF (\hyperref[reactive-silicon-dioxide-label]{Tutorial 5}), the REACTER
+protocol relies on the use of a \textit{classical} force field.
+
 \begin{figure}
 \centering
 \includegraphics[width=0.7\linewidth]{REACT.png}
@@ -3973,14 +3980,6 @@ \subsection{Tutorial 8: Reactive Molecular Dynamics}
 \label{fig:REACT}
 \end{figure}
 
-The goal of this tutorial is to create a model of a carbon nanotube (CNT) embedded
-in a polymer melt made of polystyrene (PS) (Fig.~\ref{fig:REACT}).  The
-REACTER protocol is used to simulate the polymerization of styrene monomers, and the
-polymerization reaction is followed in time \cite{gissinger2017polymer, gissinger2020reacter, gissinger2024molecular}.
-In contrast with AIREBO (\hyperref[carbon-nanotube-label]{Tutorial 2})
-and ReaxFF (\hyperref[reactive-silicon-dioxide-label]{Tutorial 5}), the REACTER
-protocol relies on the use of a \textit{classical} force field.
-
 \subsubsection{Creating the system}
 
 To begin this tutorial, select \guicmd{Start Tutorial 8} from the
@@ -4121,21 +4120,21 @@ \subsubsection{Reaction templates}
 The first reaction uses the prefix `M-M' for the pre-reaction template,
 post-reaction template, and reaction map file:
 \begin{itemize}
-\item \href{\filepath tutorial8/M-M_pre.mol}{\textit{M-M$\_$pre.mol}},
-\item \href{\filepath tutorial8/M-M_post.mol}{\textit{M-M$\_$post.mol}},
-\item \href{\filepath tutorial8/M-M.rxnmap}{\textit{M-M.rxnmap}}.
+\item \href{\filepath tutorial8/M-M_pre.mol}{\dwlcmd{M-M$\_$pre.mol}},
+\item \href{\filepath tutorial8/M-M_post.mol}{\dwlcmd{M-M$\_$post.mol}},
+\item \href{\filepath tutorial8/M-M.rxnmap}{\dwlcmd{M-M.rxnmap}}.
 \end{itemize}
 The second reaction uses the prefix `M-P',
 \begin{itemize}
-\item \href{\filepath tutorial8/M-P_pre.lmpmol}{\textit{M-P$\_$pre.mol}},
-\item \href{\filepath tutorial8/M-P_post.lmpmol}{\textit{M-P$\_$post.mol}},
-\item \href{\filepath tutorial8/M-P.rxnmap}{\textit{M-P.rxnmap}}.
+\item \href{\filepath tutorial8/M-P_pre.lmpmol}{\dwlcmd{M-P$\_$pre.mol}},
+\item \href{\filepath tutorial8/M-P_post.lmpmol}{\dwlcmd{M-P$\_$post.mol}},
+\item \href{\filepath tutorial8/M-P.rxnmap}{\dwlcmd{M-P.rxnmap}}.
 \end{itemize}
 The third reaction uses the prefix `P-P',
 \begin{itemize}
-\item \href{\filepath tutorial8/P-P_pre.lmpmol}{\textit{P-P$\_$pre.mol}},
-\item \href{\filepath tutorial8/P-P_post.lmpmol}{\textit{P-P$\_$post.mol}},
-\item \href{\filepath tutorial8/P-P.rxnmap}{\textit{P-P.rxnmap}}.
+\item \href{\filepath tutorial8/P-P_pre.lmpmol}{\dwlcmd{P-P$\_$pre.mol}},
+\item \href{\filepath tutorial8/P-P_post.lmpmol}{\dwlcmd{P-P$\_$post.mol}},
+\item \href{\filepath tutorial8/P-P.rxnmap}{\dwlcmd{P-P.rxnmap}}.
 \end{itemize}
 Here, the file names for each reaction use the abbreviation `M' for monomer and `P'
 for polymer.