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small tweaks for introduction
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lammps-tutorials.tex

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@@ -414,16 +414,16 @@ \subsection{About LAMMPS--GUI}
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\section{Content and links}
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% AK: S.G. this refers to the "old" tutorials.
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The tutorials described in this article can be accessed at
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\href{https://lammpstutorials.github.io}{lammpstutorials.github.io},
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where additional exercises with solutions are also provided. All files
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and inputs required to follow the tutorials are available from a
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dedicated GitHub account,
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\href{https://github.com/lammpstutorials}{github.com/lammpstutorials}. In
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the following, all LAMMPS input file commands or commands for the
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console are typeset in \lmpcmd{bold monospace} and file and folder names
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are typeset in \textit{italic}.
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\href{https://github.com/lammpstutorials}{github.com/lammpstutorials}.
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In the following, all LAMMPS input or console commands are typeset in
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\lmpcmd{bold monospace}, section, file and folder names are typeset in
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\textit{italic}, and keyboard shortcuts in \texttt{monospace}.
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\subsection{Tutorial 1: Lennard-Jones fluid}
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\label{lennard-jones-label}
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follow the instructions. This will select, and -- if needed -- create,
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a folder, place the initial input file \textit{initial.lmp} into it, and
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open that file in the LAMMPS--GUI editor. The editor should have the
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following content afterwards.
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following content:
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\begin{lstlisting}
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# PART A - ENERGY MINIMIZATION
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# 1) Initialization
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necessarily need to be in that exact order. For instance, parts 3 and 4
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could be inverted, or part 4 could be omitted. Note, however, that
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LAMMPS reads input files from top to bottom and processes each command
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in it \emph{immediately}. Therefore, the \textit{Initialization} and
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\emph{immediately}. Therefore, the \textit{Initialization} and
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\textit{System definition} categories must appear at the top of the
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input, and the \textit{Run} category at the bottom. Also, the specifics
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of some commands can change after global settings are changed, so the
@@ -476,12 +476,11 @@ \subsubsection{My first input}
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behavior at the boundaries of the box (e.g., periodic or non-periodic)
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or the type of atoms (e.g., uncharged point particles or extended
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spheres with a radius and angular velocities). These commands must be
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executed \emph{before} the simulation box is created, and they will
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cause an error if entered later. Similarly, many LAMMPS commands may
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only be entered \emph{after} the simulation box is defined. Only a very
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small number of commands may be used in both cases. Edit
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\textit{initial.lmp} so that the \textit{Initialization} section looks
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like this:
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executed \emph{before} the simulation box is created; they will cause an
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error if entered later. Similarly, many LAMMPS commands may only be
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entered \emph{after} the simulation box is defined. Only a very small
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number of commands may be used in both cases. Edit \textit{initial.lmp}
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so that the \textit{Initialization} section looks like this:
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\begin{lstlisting}
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# 1) Initialization
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different choice for each side, so something like \lmpcmd{boundary p p
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fm} is valid input and suitable for slab geometry systems.
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Strictly speaking, neither of these three commands are required, because
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all three settings are the default settings for the respective global
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properties. It is, however, good practice to make such defaults
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explicit so that there is no confusion when sharing the input with other
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LAMMPS users.
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Strictly speaking, neither of these four commands are required, because
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the represent they default settings for the respective global properties.
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It is, however, good practice to make such defaults explicit so that
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there is no confusion when sharing inputs with other LAMMPS users.
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\begin{figure}
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\centering
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\includegraphics[width=0.75\linewidth]{GUI-1.png}
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\includegraphics[width=0.65\linewidth]{GUI-1.png}
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\caption{A screenshot of the LAMMPS-GUI \textit{Editor} window during
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\hyperref[lennard-jones-label]{Tutorial 1}. The coloring of the text
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is based on the syntax for LAMMPS input files. The pop-up menu is the
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editor buffer, the LAMMPS documentation can be accessed by
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right-clicking the line with a command, such as \lmpcmd{units lj}, and
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selecting \textit{View documentation for (\dots)}\,. LAMMPS--GUI will
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ask your web browser to open the corresponding URL in the online manual.
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ask your web browser to open the corresponding URL of the online manual.
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See figure \ref{fig:GUI-1} for a screenshot with such a context menu.
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\paragraph{System definition}

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