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improve the Author Contributions section
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lammps-tutorials.tex

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@@ -3938,7 +3938,7 @@ \subsection{Tutorial 8: Reactive Molecular Dynamics}
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\includegraphics[width=\linewidth]{REACT}
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\caption{Initial configuration for \hyperref[bond-react-label]{Tutorial 8}.
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The system consists of 200 styrene molecules packed around a single-walled
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CNT with a total system density of 0.9 g/cm$^3$.}
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CNT, with a mass density for the whole system of $0.9~\text{g/cm}^3$.}
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\label{fig:REACT}
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\end{figure}
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@@ -4225,16 +4225,14 @@ \subsubsection{Simulating the reaction}
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\end{figure}
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\section*{Author Contributions}
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% S.G. to update
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S.G. conceived and wrote all the online tutorials and underlying Sphinx documentation
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for \href{https://lammpstutorials.github.io}{lammpstutorials.github.io}.
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\noindent A.K. wrote the LAMMPS GUI software and helped revise the
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tutorials for use with it.
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\noindent J.G. is the principal author of fix bond/react and type label
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support in LAMMPS. He revised tutorials to use type labels.
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% and contributed the eighth tutorial using fix bond/react (?).
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S.G. conceived and wrote the original online tutorials and underlying Sphinx documentation
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for \href{https://lammpstutorials.github.io}{lammpstutorials.github.io}.
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J.G. is the principal author of \lmpcmd{fix bond/react} and \lmpcmd{type labels}
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support in LAMMPS. He revised the tutorials to incorporate type labels and wrote Tutorial 8.
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A.K. developed the LAMMPS--GUI software and assisted in revising the
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tutorials for use with it. All authors participated in the revision and finalization
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of the manuscript.
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\section*{Potentially Conflicting Interests}
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@@ -4243,10 +4241,9 @@ \section*{Potentially Conflicting Interests}
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\section*{Funding Information}
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S.G. acknowledges funding from the European Union's Horizon 2020 research and
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innovation programme under the Marie Skłodowska-Curie grant agreement N$^\circ\;101065060$.
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\noindent A.K. acknowledges financial support by Sandia National Laboratories under
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POs 2149742 and 2407526.
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innovation programme under the Marie Skłodowska-Curie grant agreement $\text{N}^\circ\;101065060$.
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A.K. acknowledges financial support by Sandia National Laboratories under
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POs~2149742 and 2407526.
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\section*{Author Information}
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\makeorcid
@@ -4263,7 +4260,7 @@ \section{Using LAMMPS--GUI}
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\begin{note}
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For simplicity, these tutorials reference keyboard shortcuts
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based on the assignments for Linux and Windows. {macOS} users should
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based on the assignments for Linux and Windows. {macOS} users should
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use the ``Command'' key (\cmd) in place of the
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``Ctrl'' key when using keyboard shortcuts.
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\end{note}
@@ -4296,7 +4293,7 @@ \subsubsection{Installing Linux .flatpak variant}
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(e.g.,~GNOME, KDE, XFCE) where it should appear in the ``Applications''
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menu under ``Science''. Additionally, the ``.lmp'' file extension will be
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registered to launch LAMMPS--GUI when opening a file with this
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extension in the desktop's file manager. You can then
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extension in the desktop's file manager. You can then
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launch LAMMPS--GUI from the command line using the following command:
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\begin{lstlisting}
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flatpak run org.lammps.lammps-gui
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file.
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After installation, you can launch LAMMPS\_GUI from the Applications
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folder. Additionally, you can drag an input file onto the app or open files with the
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folder. Additionally, you can drag an input file onto the app or open files with the
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``.lmp'' extension. Note that the LAMMPS--GUI bundle is currently not
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cryptographically signed, so macOS may initially prevent it from launching.
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If this happens, you can adjust the settings in the ``Security \& Privacy" system
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have been cryptographically signed. You will need to choose to keep the file,
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and when launching the installer again, confirm that you want to run it despite the warning.
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After installation, a new entry should appear in the Start menu. Additionally,
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After installation, a new entry should appear in the Start menu. Additionally,
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the ``.lmp'' file extension should be registered with Windows File
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Explorer to open LAMMPS--GUI when opening a file with that
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extension. The ``lammps-gui'' and ``lmp'' commands should also be available
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LAMMPS--GUI can be launched from the command line, as explained above, where you
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can either launch it without arguments or provide one file name as an argument. All
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other arguments will be ignored. For example:
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other arguments will be ignored. For example:
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\begin{lstlisting}
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lammps-gui input.lmp
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\end{lstlisting}
@@ -4414,17 +4411,17 @@ \subsection{Creating Snapshot Images}
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Open the \guicmd{Image Viewer} using either the \guicmd{Create Image} option
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from the \guicmd{Run} menu, the \guicmd{Ctrl-I} keyboard shortcut,
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or click on the (right) palette button in the status bar. The image
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or click on the (right) palette button in the status bar. The image
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can be saved using the \guicmd{Save As...} option from the \guicmd{File} menu.
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\subsection{The Output Window}
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By default, when starting a run, the \guicmd{Output} window opens to display the screen
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output of the running LAMMPS calculation. The text in the Output window is
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output of the running LAMMPS calculation. The text in the Output window is
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read-only and cannot be modified, but keyboard shortcuts for selecting and
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copying all or part of the text can be used to transfer it to another program:
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The keyboard shortcut \guicmd{Ctrl-S} (or \guicmd{Command-S} on {macOS}) can
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be used to save the Output buffer to a file. Additionally, the \guicmd{Select All}
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be used to save the Output buffer to a file. Additionally, the \guicmd{Select All}
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and \guicmd{Copy} functions, along with a \guicmd{Save Log to File} option, are available
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through the context menu, which can be accessed by right-clicking within the text area of the
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\guicmd{Output} window.
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\subsection{Preferences}
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The Preferences dialog allows customization of the behavior and appearance of
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LAMMPS--GUI. Among other options:
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LAMMPS--GUI. Among other options:
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\begin{itemize}
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\item In the \guicmd{General Settings} tab, the \guicmd{Data update interval} setting
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allows you to define the time interval, in milliseconds, between data updates during
@@ -4467,7 +4464,7 @@ \section{Running LAMMPS via Command Line}
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\label{command-line-label}
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LAMMPS can be executed from the command line on Linux, macOS,
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as well as Windows. On Linux/macOS, first navigate to the directory containing
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as well as Windows. On Linux/macOS, first navigate to the directory containing
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the \flecmd{input.lmp} file and execute:
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\begin{lstlisting}
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lmp -in input.lmp

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