work on the appendix

Author: simongravelle

lammps-tutorials.tex

@@ -3913,7 +3913,7 @@ \subsubsection{Method 2: Umbrella sampling}
 and save it next to \lmpcmd{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\
+./wham -30 30 50 1e-8 119.8 0 \
     umbrella-sampling.meta umbrella-sampling.dat
 \end{lstlisting}
 where -30 and 30 are the boundaries, 50 is the number of bins, 1e-8 is the tolerance,
@@ -4253,140 +4253,129 @@ \section{Using LAMMPS--GUI}
 \label{using-lammps-gui-label}
 
 \begin{note}
-  For the sake of simplicity we will refer during the tutorials to
-  keyboard shortcuts using the assignments from Linux and Windows.
-
-  Users of macOS have to use the ``Command'' key (\cmd) instead of the
-  ``Ctrl'' key for keyboard shortcuts.
+For simplicity, these tutorials reference keyboard shortcuts
+based on the assignments for Linux and Windows. {macOS} users should
+use the ``Command'' key (\cmd) in place of the
+``Ctrl'' key when using keyboard shortcuts.
 \end{note}
 
 \subsection{Installation}
 
-Precompiled versions of LAMMPS--GUI exist for Linux, {macOS}, and
-Windows.  The Linux version comes in two variants, as compressed tar
-archive (.tar.gz) and as a flatpak \cite{flatpak_home} bundle. The macOS
-version as a .dmg installer image and the Window version is an
-executable Installer package.
+Precompiled versions of LAMMPS--GUI are available for Linux, {macOS}, and
+Windows.  The Linux version is provided in two formats: as compressed tar
+archive (.tar.gz) and as a Flatpak bundle \cite{flatpak_home}.  The {macOS}
+version is distributed as a .dmg installer image, while the Windows version comes
+as an executable installer package.
 
-\subsubsection{Installing Linux .tar.gz variant}
+\subsubsection{Installing the Linux .tar.gz variant}
 
-Download the archive, e.g.~LAMMPS-Linux-x86\_64-GUI-XXXXAug2024.tar.gz,
-and unpack it.  This will create a folder LAMMPS\_GUI which contains the
-included commands that can be launched directly as ``./lammps-gui'' and
-``./lmp'' for example.  Adding this folder to the PATH environment
-variable, will make them available everywhere and without the ``./''
-prefix.
+Download the archive (e.g.,~LAMMPS-Linux-x86\_64-GUI-XXXXAug2024.tar.gz)
+and unpack it.  This will create a folder named LAMMPS\_GUI containing the
+included commands, which can be launched directly using ``./lammps-gui'' or
+``./lmp'', for example.  Adding this folder to the PATH environment
+variable will make these commands accessible from everywhere, without the
+need for the ``./'' prefix.
 
 \subsubsection{Installing Linux .flatpak variant}
 
-Download the bundle file and then install it with
-{
-\normalsize
-\begin{verbatim}
+Download the bundle file and then install it using the following command:
+\begin{lstlisting}
 flatpak install --user \
     LAMMPS-Linux-x86_64-GUI-XXXAug2024.flatpak
-\end{verbatim}
-}
-This should integrate LAMMPS--GUI into your desktop environment
-(e.g.~GNOME, KDE, XFCE) and it should appear in the ``Applications''
-menu under ``Science''.  Also the ``.lmp'' file extension should have
-been registered to launch LAMMPS--GUI when opening a file with that
-extension in the desktop's file manager.
-
-It is possible to launch it from the command line with:
+\end{lstlisting}
+This will integrate LAMMPS--GUI into your desktop environment
+(e.g.,~GNOME, KDE, XFCE) where it should appear in the ``Applications''
+menu under ``Science''.  Additionally, the ``.lmp'' file extension will be
+registered to launch LAMMPS--GUI when opening a file with this
+extension in the desktop's file manager. You can then
+launch LAMMPS-GUI from the command line using the following command:
 \begin{lstlisting}
 flatpak run org.lammps.lammps-gui
 \end{lstlisting}
-Similarly for the LAMMPS command line version:
+Similarly, for the LAMMPS command-line version, use:
 \begin{lstlisting}
-flatpak run --command=lmp \
-    org.lammps.lammps-gui -in in.melt
+flatpak run --command=lmp org.lammps.lammps-gui -in in.lmp
 \end{lstlisting}
 
-\subsubsection{Installing macOS .dmg package}
+\subsubsection{Installing the macOS .dmg package}
 
 After downloading the LAMMPS-macOS-multiarch-GUI-XXXAug2024.dmg file,
-you need double-click on it and then drag the LAMMPS\_GUI app bundle
-into the Applications folder shown in the dialog that opens.  For
-enabling command line access follow the instructions in the README.txt
+double-click on it and then drag the LAMMPS\_GUI app bundle
+into the Applications folder shown in the dialog that opens.  To
+enable command-line access, follow the instructions in the README.txt
 file.
 
-After installation, LAMMPS\_GUI can be launched from the Applications
-folder, you can also drag an input file on top of it or open files with
-the ``.lmp'' extension.  The LAMMPS--GUI bundle is currently not
-cryptographically signed so macOS may initially refuse to launch it.
-But you can clear its access in the ``Security \& Privacy" system
-setting dialog.
+After installation, you can launch LAMMPS\_GUI from the Applications
+folder. Additionally, you can drag an input file onto the app or open files with the
+``.lmp'' extension.  Note that the LAMMPS--GUI bundle is currently not
+cryptographically signed, so macOS may initially prevent it from launching.
+If this happens, you can adjust the settings in the ``Security \& Privacy" system
+preferences dialog to allow access.
 
-\subsubsection{Installing Windows .exe package}
+\subsubsection{Installing the Windows .exe package}
 
-When downloading the LAMMPS-Win10-64bit-GUI-XXXAug2024.exe installer,
-Windows will suggest to delete the file since it is from an unknown
-developer and downloaded from the internet.  This is because neither the
-installer nor the LAMMPS--GUI and other applications inside have been
-cryptographically signed.  You have to tell it keep it and when
-launching the installer again confirm that you want to run it anyway.
+Download the LAMMPS-Win10-64bit-GUI-XXXAug2024.exe installer.
+Windows may warn you that the file is from an unknown developer
+and was downloaded from the internet.  This happens because neither the
+installer nor the LAMMPS--GUI application (or any other applications inside)
+has been cryptographically signed.  You will need to choose to keep the file,
+and when launching the installer again, confirm that you want to run it despite the warning.
 
-After installation, there should be a new entry in the start menu and
-also the ``.lmp'' extension should be registered with the Windows File
+After installation, a new entry should appear in the Start menu. Additionally,
+the ``.lmp'' file extension should be registered with  Windows File
 Explorer to open LAMMPS--GUI when opening a file with that
-extension. The ``lammps-gui'' and ``lmp'' commands should be available
-on the command line in a Command Prompt or Terminal window as well.
+extension.  The ``lammps-gui'' and ``lmp'' commands should also be available
+in the command line, either in a Command Prompt or Terminal window.
 
 \subsection{Opening, Editing, and Saving Files}
 
-LAMMPS--GUI can be launched from the command line as explained above where you
-can launch it without arguments or provide one file name as argument.  All
-other arguments are ignored. Example:
-{
-\normalsize
-\begin{verbatim}
-  lammps-gui input.lmp
-\end{verbatim}
-}
-Files can also be opened from the ``File'' menu.  There is the option
-to select a file through a dialog and then open it.  There is also a
-record of the last five opened files and entries to open them directly.
-Finally, there is the \texttt{Ctrl--O} keyboard shortcut to open a file.
+LAMMPS--GUI can be launched from the command line, as explained above, where you
+can either launch it without arguments or provide one file name as an argument.  All
+other arguments will be ignored. For example:
+\begin{lstlisting}
+lammps-gui input.lmp
+\end{lstlisting}
+Files can also be opened from the ``File'' menu.  You can select a
+file through a dialog and then open it.  Additionally, a history of
+the last five opened files is maintained, with entries to open them directly.
+Finally, the \texttt{Ctrl--O} keyboard shortcut can also be used to open a file.
 
-When integrated into a desktop environment, it also possible to open
-files with a ``.lmp'' extension or use drag-n-drop.
+When integrated into a desktop environment, it is also possible to open
+files with a ``.lmp'' extension or use drag-and-drop.
 
 For the most part, the editor window behaves like other graphical
-editors.  You can enter, delete, and copy and paste text.  When entering
-text, for the first word in a line, there will be a pop-up window with
-possible completions after typing the first two characters. You can
-change the highlight with the up and down cursor keys and select a
-completion with the enter key or using the mouse.  You can also keep
-typing and the selection in the pop-up will be refined.  For some
-commands, there will also be completion pop-ups for some of their
-keywords or if a filename is expected (then the pop-up lists files in
-the current folder).
-
-As soon as LAMMPS--GUI recognizes a command line, it will apply syntax
-highlighting according to some built-in categories.  This can be used as
-a hint for detecting typos, since those may cause LAMMPS--GUI not to
-recognize the syntax and thus not apply the syntax highlighting or only
-partially.  When hitting the \texttt{Tab} key, the line will be
-reformatted.  A consistent formatting can improve the readability of
+editors.  You can enter, delete, or copy and paste text.   When entering
+text, a pop-up window will appear with possible completions after typing
+the first two characters of the first word in a line.  You can
+navigate the highlighted options using the up and down arrow keys, and select a
+completion by pressing the Enter key or using the mouse.  You can also continue
+typing, and the selection in the pop-up will be refined.  For some
+commands, there will be completion pop-ups for their
+keywords or when a filename is expected, in which case,
+the pop-up will list files in the current folder.
+
+As soon as LAMMPS--GUI recognizes a command line, it applies syntax
+highlighting according to built-in categories.  This can help
+detect typos, since those may cause LAMMPS--GUI not to
+recognize the syntax and thus not apply or partially apply
+the syntax highlighting.  When you press the \texttt{Tab} key, the line will be
+reformatted.  Consistent formatting can improve the readability of
 input files, especially long and complex ones.
 
-If the file in the editor has unsaved changes an additional
-``\*modified\*'' text is shown in the window title.  The current input
-buffer can be saved be selection ``Save'' or ``Save As..'' from the
-``File'' menu.  You can also click on the ``Save'' icon on the left side
-of the status bar, and finally, there is the \texttt{Ctrl--S} keyboard
-shortcut.
-
+If the file in the editor has unsaved changes, the word 
+``\*modified\*'' will appear in the window title.  The current input
+buffer can be saved by selecting ``Save'' or ``Save As...'' from the
+``File'' menu.  You can also click the ``Save'' icon on the left side
+of the status bar, or use the \texttt{Ctrl--S} keyboard shortcut.
 
 \begin{note}
-When LAMMPS--GUI is opening a file it will \emph{switch} the working directory
-of the folder that contains the input file.  The same happens when saving to
+When LAMMPS--GUI opens a file, it will \emph{switch} the working directory
+to the folder that contains the input file.  The same happens when saving to
 a different folder than the current working directory.  The current working
-directory can be seen in the status bar on the bottom right.  This is important
-to know since LAMMPS input files often require other files for reading and may
-write output files (images, trajectory dumps, averaged data files) and usually
-expects those files to be in the same folder as the input file.
+directory can be seen in the status bar at the bottom right.  This is important
+to note because LAMMPS input files often require additional files for reading and may
+write output files (such as images, trajectory dumps, or averaged data files),
+which are typically expected to be in the same folder as the input file.
 \end{note}
 
 %The contents of the \textit{Editor} window can be saved by either using