@@ -344,43 +344,46 @@ \subsection{Software/system requirements}
344344
345345The LAMMPS release version 29Aug2024~\cite {lammps_code } and the
346346matching LAMMPS--GUI software version 1.6.11 are required to follow the
347- tutorials, as they use features that first appeared in these versions.
348- For Linux (with x86\_ 64 CPU), macOS (BigSur or later), and Windows (10
347+ tutorials, as they include features that were first introduced in these versions.
348+ For Linux (x86\_ 64 CPU), macOS (BigSur or later), and Windows (10
349349and 11) you can download a precompiled LAMMPS package from the LAMMPS
350350release page on GitHub
351351(\href {https://github.com/lammps/lammps/releases}{github.com/lammps/lammps/releases}).
352352Select a package with `GUI' in the file name, which includes
353353both LAMMPS--GUI and a LAMMPS console executable. These
354354precompiled packages are designed to be portable, and therefore omit support for
355- running in parallel with MPI. \hyperref [using-lammps-gui-label]{Appendix
356- \ref {using-lammps-gui-label }} has instructions for installing
357- LAMMPS--GUI and using its most relevant features for the tutorials.
358-
359- LAMMPS versions have good backward compatibility: old inputs generally work with
360- newer LAMMPS versions. However, forward compatibility is not as strong, meaning
361- newer inputs are not as likely to work with older LAMMPS versions. Thus, it is
362- generally possible to follow this tutorial with more recent releases of
363- LAMMPS--GUI and LAMMPS. Older versions may need some minor adjustments.
364- Nevertheless, these tutorials will be periodically revised to ensure compatibility
365- and take advantage of new features in the most recent stable version of LAMMPS.
366-
367- For advanced tutorials, external tools are required for plotting and
368- visualization, since the corresponding functionality in LAMMPS--GUI is
355+ parallel execution with MPI. Instructions for installing LAMMPS--GUI and
356+ using its most relevant features for the tutorials are provided in
357+ \hyperref [using-lammps-gui-label]{Appendix~\ref {using-lammps-gui-label }}.
358+
359+ LAMMPS versions are generally backward compatible, meaning that old
360+ input files typically work with newer versions of LAMMPS. However,
361+ forward compatibility is not as strong, so
362+ newer input files may not work with older versions. As a result, it is
363+ usually possible to follow this tutorial with more recent releases of
364+ LAMMPS--GUI and LAMMPS, though older versions may require some minor adjustments.
365+ These tutorials will be periodically updated to ensure compatibility
366+ and take advantage of new features in the latest stable version of LAMMPS.
367+
368+ For some tutorials, external tools are required for plotting and
369+ visualization, as the corresponding functionality in LAMMPS--GUI is
369370limited. Suitable external tools for plotting include Python with
370371Pandas/Matplotlib~\cite {van1995python ,hunter2007Matplotlib }, XmGrace,
371- Gnuplot, Microsoft Excel, and LibreOffice Calc. For
372- visualization, suitable external tools include VMD~\cite {vmd_home ,humphrey1996vmd }
372+ Gnuplot, Microsoft Excel, and LibreOffice Calc. For visualization,
373+ suitable external tools include VMD~\cite {vmd_home ,humphrey1996vmd }
373374and OVITO~\cite {ovito_home ,ovito_paper }.
374375
375- \hyperref [command-line-label]{Appendix~\ref {command-line-label }} has instructions
376- for running LAMMPS from the command line.
376+ % \hyperref[command-line-label]{Appendix~\ref{command-line-label}} has instructions
377+ % for running LAMMPS from the command line.
378+ % SG: I placed a reference of Appendix B before, so I dont think that sentence is
379+ % necessary here.
377380
378381\subsection {About LAMMPS--GUI }
379382
380383LAMMPS--GUI is a graphical text editor, enhanced for editing LAMMPS input
381- files, and linked to the LAMMPS library, allowing it to run LAMMPS
382- directly. The text editor functions similarly to other graphical editors
383- like Notepad or Gedit but offers the following enhancements specifically for LAMMPS:
384+ files and linked to the LAMMPS library, allowing it to run LAMMPS
385+ directly. The text editor functions similarly to other graphical editors,
386+ such as Notepad or Gedit, but offers the following enhancements specifically for LAMMPS:
384387\begin {itemize }
385388 \item Auto-completion of LAMMPS commands and options
386389 \item Syntax highlighting for LAMMPS input files
@@ -400,27 +403,26 @@ \subsection{About LAMMPS--GUI}
400403 \item Viewing of plain text files
401404 \item Use of wizard dialogs to set up tutorials
402405\end {itemize }
403-
404406\hyperref [using-lammps-gui-label]{Appendix~\ref {using-lammps-gui-label }}
405407contains basic instructions for installation and using LAMMPS--GUI with
406408the tutorials presented here. A complete description of all LAMMPS--GUI
407- features is in the LAMMPS manual~\cite {lammps_gui_docs }.
409+ features can be found in the LAMMPS manual~\cite {lammps_gui_docs }.
408410
409411\section {Content and links }
410412
411413The tutorials described in this article can be accessed at
412414\href {https://lammpstutorials.github.io}{lammpstutorials.github.io},
413415where additional exercises with solutions are also provided. All files
414416and inputs required to follow the tutorials are available from a
415- dedicated GitHub account,
417+ dedicated GitHub organization account,
416418\href {https://github.com/lammpstutorials}{github.com/lammpstutorials}.
417- Additionally, these files can be downloaded by clicking \guicmd {Start LAMMPS Tutorial X}
419+ These files can also be downloaded by clicking \guicmd {Start LAMMPS Tutorial X}
418420(where \texttt {X } = 1...8) from the \guicmd {Tutorials} menu of LAMMPS--GUI.
419421
420422In the following, all LAMMPS input or console commands are formatted
421423with a \lmpcmd {colored background}. Keyboard shortcuts and
422424file names are formatted in \flecmd {monospace}, and LAMMPS--GUI options and menus
423- are in \guicmd {quoted monospace}.
425+ are displayed in \guicmd {quoted monospace}.
424426% S.G.: I removed "folder names" because all folders will eventually be removed (TO CONTROL BEFORE SUBMITTING)
425427% S.G.: I removed "Section titles" as well because it seems to be using a different style
426428
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